class PMTControl(model.PowerSupplier):
'''
This represents the PMT control unit.
At start up the following is set:
* protection is on (=> gain is forced to 0)
* gain = 0
* power up
'''
def __init__(self,
name,
role,
port,
prot_time=1e-3,
prot_curr=30e-6,
relay_cycle=None,
powered=None,
**kwargs):
'''
port (str): port name
prot_time (float): protection trip time (in s)
prot_curr (float): protection current threshold (in Amperes)
relay_cycle (None or 0<float): if not None, will power cycle the relay
with the given delay (in s)
powered (list of str or None): set of the HwComponents controlled by the relay
Raise an exception if the device cannot be opened
'''
if powered is None:
powered = []
self.powered = powered
model.PowerSupplier.__init__(self, name, role, **kwargs)
# get protection time (s) and current (A) properties
if not 0 <= prot_time < 1e3:
raise ValueError("prot_time should be a time (in s) but got %s" %
(prot_time, ))
self._prot_time = prot_time
if not 0 <= prot_curr <= 100e-6:
raise ValueError("prot_curr (%s A) is not between 0 and 100.e-6" %
(prot_curr, ))
self._prot_curr = prot_curr
# TODO: catch errors and convert to HwError
self._ser_access = threading.Lock()
self._port = self._findDevice(port) # sets ._serial
logging.info("Found PMT Control device on port %s", self._port)
# Get identification of the PMT control device
self._idn = self._getIdentification()
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "serial driver: %s" % (driver_name, )
self._hwVersion = "%s" % (self._idn, )
# Set protection current and time
self._setProtectionCurrent(self._prot_curr)
self._setProtectionTime(self._prot_time)
# gain, powerSupply and protection VAs
self.protection = model.BooleanVA(True,
setter=self._setProtection,
getter=self._getProtection)
self._setProtection(True)
gain_rng = (MIN_VOLT, MAX_VOLT)
gain = self._getGain()
self.gain = model.FloatContinuous(gain,
gain_rng,
unit="V",
setter=self._setGain)
self.powerSupply = model.BooleanVA(True, setter=self._setPowerSupply)
self._setPowerSupply(True)
# will take care of executing supply asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
# relay initialization
if relay_cycle is not None:
logging.info("Power cycling the relay for %f s", relay_cycle)
self.setRelay(False)
time.sleep(relay_cycle)
# Reset if no powered provided
if not powered:
self.setRelay(True)
else:
self._supplied = {}
self.supplied = model.VigilantAttribute(self._supplied,
readonly=True)
self._updateSupplied()
def terminate(self):
if self._executor:
self._executor.cancel()
self._executor.shutdown()
self._executor = None
with self._ser_access:
if self._serial:
self._serial.close()
self._serial = None
@isasync
def supply(self, sup):
if not sup:
return model.InstantaneousFuture()
self._checkSupply(sup)
return self._executor.submit(self._doSupply, sup)
def _doSupply(self, sup):
"""
supply power
"""
value = list(sup.values())[0] # only care about the value
self.setRelay(value)
self._updateSupplied()
def _updateSupplied(self):
"""
update the supplied VA
"""
# update all components since they are all connected to the same switch
value = self.getRelay()
for comp in self.powered:
self._supplied[comp] = value
# it's read-only, so we change it via _value
self.supplied._value = self._supplied
self.supplied.notify(self.supplied.value)
def _getIdentification(self):
return self._sendCommand(b"*IDN?").decode('latin1')
def _setGain(self, value):
self._sendCommand(b"VOLT %f" % (value, ))
return self._getGain()
def _setProtectionCurrent(self, value):
self._sendCommand(b"PCURR %f" % (value * 1e6, )) # in µA
def _setProtectionTime(self, value):
self._sendCommand(b"PTIME %f" % (value, ))
def _getGain(self):
ans = self._sendCommand(b"VOLT?")
try:
value = float(ans)
except ValueError:
raise IOError("Gain value cannot be converted to float.")
return value
def _setPowerSupply(self, value):
if value:
self._sendCommand(b"PWR 1")
else:
self._sendCommand(b"PWR 0")
return value
def _getPowerSupply(self):
ans = self._sendCommand(b"PWR?")
return ans == b"1"
def _setProtection(self, value):
if value:
self._sendCommand(b"SWITCH 0")
else:
self._sendCommand(b"SWITCH 1")
return value
def _getProtection(self):
ans = self._sendCommand(b"SWITCH?")
return ans == b"0"
# These two methods are strictly used for the SPARC system in Monash. Use
# them to send a high/low signal via the PMT Control Unit to the relay, thus
# to pull/push the relay contact and control the power supply from the power
# board to the flippers and filter wheel.
def setRelay(self, value):
# When True, the relay contact is connected
if value:
self._sendCommand(b"RELAY 1")
else:
self._sendCommand(b"RELAY 0")
return value
def getRelay(self):
ans = self._sendCommand(b"RELAY?")
if ans == b"1":
status = True
else:
status = False
return status
def _sendCommand(self, cmd):
"""
cmd (byte str): command to be sent to PMT Control unit.
returns (byte str): answer received from the PMT Control unit
raises:
IOError: if an ERROR is returned by the PMT Control firmware.
"""
cmd = cmd + b"\n"
with self._ser_access:
logging.debug("Sending command %s", to_str_escape(cmd))
self._serial.write(cmd)
ans = b''
char = None
while char != b'\n':
char = self._serial.read()
if not char:
logging.error("Timeout after receiving %s",
to_str_escape(ans))
# TODO: See how you should handle a timeout before you raise
# an HWError
raise HwError(
"PMT Control Unit connection timeout. "
"Please turn off and on the power to the box.")
# Handle ERROR coming from PMT control unit firmware
ans += char
logging.debug("Received answer %s", to_str_escape(ans))
if ans.startswith(b"ERROR"):
raise PMTControlError(ans.split(b' ', 1)[1])
return ans.rstrip()
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a PMT control device.
port (string): the name of the serial port (e.g., /dev/ttyACM0)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
timeout=1 # s
)
# Purge
ser.flush()
ser.flushInput()
# Try to read until timeout to be extra safe that we properly flushed
while True:
char = ser.read()
if char == b'':
break
logging.debug(
"Nothing left to read, PMT Control Unit can safely initialize.")
ser.timeout = 5 # Sometimes the software-based USB can have some hiccups
return ser
def _findDevice(self, ports):
"""
Look for a compatible device
ports (str): pattern for the port name
return (str): the name of the port used
It also sets ._serial and ._idn to contain the opened serial port, and
the identification string.
raises:
IOError: if no device are found
"""
# For debugging purpose
if ports == "/dev/fake":
self._serial = PMTControlSimulator(timeout=1)
return ports
if os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
self._serial = self._openSerialPort(n)
# If the device has just been inserted, odemis-relay will block
# it for 10s while reseting the relay, so be patient
try:
fcntl.flock(self._serial.fileno(),
fcntl.LOCK_EX | fcntl.LOCK_NB)
except IOError:
logging.info("Port %s is busy, will wait and retry", n)
time.sleep(11)
fcntl.flock(self._serial.fileno(),
fcntl.LOCK_EX | fcntl.LOCK_NB)
try:
idn = self._getIdentification()
except PMTControlError:
# Can happen if the device has received some weird characters
# => try again (now that it's flushed)
logging.info("Device answered by an error, will try again")
idn = self._getIdentification()
# Check that we connect to the right device
if not idn.startswith("Delmic Analog PMT"):
logging.info("Connected to wrong device on %s, skipping.",
n)
continue
return n
except (IOError, PMTControlError):
# not possible to use this port? next one!
continue
else:
raise HwError(
"Failed to find a PMT Control device on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports, ))
@classmethod
def scan(cls):
"""
returns (list of 2-tuple): name, args (sn)
Note: it's obviously not advised to call this function if a device is already under use
"""
logging.info(
"Serial ports scanning for PMT control device in progress...")
found = [] # (list of 2-tuple): name, kwargs
if sys.platform.startswith('linux'):
# Look for each ACM device, if the IDN is the expected one
acm_paths = glob.glob('/dev/ttyACM?')
for port in acm_paths:
# open and try to communicate
try:
dev = cls(name="test", role="test", port=port)
idn = dev._getIdentification()
if idn.startswith("Delmic Analog PMT"):
found.append({"port": port})
except Exception:
pass
else:
# TODO: Windows version
raise NotImplementedError("OS not yet supported")
return found
class CoupledStage(model.Actuator):
"""
Wrapper stage that takes as children the SEM sample stage and the
ConvertStage. For each move to be performed CoupledStage moves, at the same
time, both stages.
"""
def __init__(self, name, role, children, **kwargs):
"""
children (dict str -> actuator): names to ConvertStage and SEM sample stage
"""
# SEM stage
self._master = None
# Optical stage
self._slave = None
for crole, child in children.items():
# Check if children are actuators
if not isinstance(child, model.ComponentBase):
raise ValueError("Child %s is not a component." % child)
if not hasattr(child, "axes") or not isinstance(child.axes, dict):
raise ValueError("Child %s is not an actuator." % child.name)
if "x" not in child.axes or "y" not in child.axes:
raise ValueError("Child %s doesn't have both x and y axes" % child.name)
if crole == "slave":
self._slave = child
elif crole == "master":
self._master = child
else:
raise ValueError("Child given to CoupledStage must be either 'master' or 'slave', but got %s." % crole)
if self._master is None:
raise ValueError("CoupledStage needs a master child")
if self._slave is None:
raise ValueError("CoupledStage needs a slave child")
# TODO: limit the range to the minimum of master/slave?
axes_def = {}
for an in ("x", "y"):
axes_def[an] = copy.deepcopy(self._master.axes[an])
axes_def[an].canUpdate = False
model.Actuator.__init__(self, name, role, axes=axes_def, children=children,
**kwargs)
self._metadata[model.MD_HW_NAME] = "CoupledStage"
# will take care of executing axis moves asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
self._position = {}
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
# TODO: listen to master position to update the position? => but
# then it might get updated too early, before the slave has finished
# moving.
self.referenced = model.VigilantAttribute({}, readonly=True)
# listen to changes from children
for c in self.children.value:
if model.hasVA(c, "referenced"):
logging.debug("Subscribing to reference of child %s", c.name)
c.referenced.subscribe(self._onChildReferenced)
self._updateReferenced()
self._stage_conv = None
self._createConvertStage()
def updateMetadata(self, md):
self._metadata.update(md)
# Re-initialize ConvertStage with the new transformation values
# Called after every sample holder insertion
self._createConvertStage()
def _createConvertStage(self):
"""
(Re)create the convert stage, based on the metadata
"""
self._stage_conv = ConvertStage("converter-xy", "align",
children={"aligner": self._slave},
axes=["x", "y"],
scale=self._metadata.get(MD_PIXEL_SIZE_COR, (1, 1)),
rotation=self._metadata.get(MD_ROTATION_COR, 0),
translation=self._metadata.get(MD_POS_COR, (0, 0)))
# if set(self._metadata.keys()) & {MD_PIXEL_SIZE_COR, MD_ROTATION_COR, MD_POS_COR}:
# # Schedule a null relative move, just to ensure the stages are
# # synchronised again (if some metadata is provided)
# self._executor.submit(self._doMoveRel, {})
def _updatePosition(self):
"""
update the position VA
"""
mode_pos = self._master.position.value
self._position["x"] = mode_pos['x']
self._position["y"] = mode_pos['y']
pos = self._applyInversion(self._position)
self.position._set_value(pos, force_write=True)
def _onChildReferenced(self, ref):
# ref can be from any child, so we don't use it
self._updateReferenced()
def _updateReferenced(self):
"""
update the referenced VA
"""
ref = {} # str (axes name) -> boolean (is referenced)
# consider an axis referenced iff it's referenced in every referenceable children
for c in self.children.value:
if not model.hasVA(c, "referenced"):
continue
cref = c.referenced.value
for a in (set(self.axes.keys()) & set(cref.keys())):
ref[a] = ref.get(a, True) and cref[a]
self.referenced._set_value(ref, force_write=True)
def _doMoveAbs(self, pos):
"""
move to the position
"""
f = self._master.moveAbs(pos)
try:
f.result()
finally: # synchronise slave position even if move failed
# TODO: Move simultaneously based on the expected position, and
# only if the final master position is different, move again.
mpos = self._master.position.value
# Move objective lens
f = self._stage_conv.moveAbs({"x": mpos["x"], "y": mpos["y"]})
f.result()
self._updatePosition()
def _doMoveRel(self, shift):
"""
move by the shift
"""
f = self._master.moveRel(shift)
try:
f.result()
finally:
mpos = self._master.position.value
# Move objective lens
f = self._stage_conv.moveAbs({"x": mpos["x"], "y": mpos["y"]})
f.result()
self._updatePosition()
@isasync
def moveRel(self, shift):
if not shift:
shift = {"x": 0, "y": 0}
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
return self._executor.submit(self._doMoveRel, shift)
@isasync
def moveAbs(self, pos):
if not pos:
pos = self.position.value
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
return self._executor.submit(self._doMoveAbs, pos)
def stop(self, axes=None):
# Empty the queue for the given axes
self._executor.cancel()
self._master.stop(axes)
self._stage_conv.stop(axes)
logging.warning("Stopping all axes: %s", ", ".join(axes or self.axes))
def _doReference(self, axes):
fs = []
for c in self.children.value:
# only do the referencing for the stages that support it
if not model.hasVA(c, "referenced"):
continue
ax = axes & set(c.referenced.value.keys())
fs.append(c.reference(ax))
# wait for all referencing to be over
for f in fs:
f.result()
# Re-synchronize the 2 stages by moving the slave where the master is
mpos = self._master.position.value
f = self._stage_conv.moveAbs({"x": mpos["x"], "y": mpos["y"]})
f.result()
self._updatePosition()
@isasync
def reference(self, axes):
if not axes:
return model.InstantaneousFuture()
self._checkReference(axes)
return self._executor.submit(self._doReference, axes)
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
class MFF(model.Actuator):
"""
Represents one Thorlabs Motorized Filter Flipper (ie: MFF101 or MFF102)
"""
def __init__(self, name, role, children=None, sn=None, port=None, axis="rz",
inverted=None, positions=None, **kwargs):
"""
children (dict string->model.HwComponent): they are not actually used.
This is currently in place just to enforce PMT control to be
initialized before the Fiber Flipper since we need the relay reset
to happen before the flipper is turned on.
sn (str): serial number (recommended)
port (str): port name (only if sn is not specified)
axis (str): name of the axis
inverted (set of str): names of the axes which are inverted (IOW, either
empty or the name of the axis)
positions (None, or list of 2 tuples (value, str)): positions values and
their corresponding name. If None: 0 and Pi/2 are used, without names.
"""
if (sn is None and port is None) or (sn is not None and port is not None):
raise ValueError("sn or port argument must be specified (but not both)")
if sn is not None:
if not sn.startswith(SN_PREFIX_MFF) or len(sn) != 8:
logging.warning("Serial number '%s' is unexpected for a MFF "
"device (should be 8 digits starting with %s).",
sn, SN_PREFIX_MFF)
self._port = self._getSerialPort(sn)
self._sn = sn
else:
self._port = port
# The MFF returns no serial number from GetInfo(), so find via USB
try:
self._sn = self._getSerialNumber(port)
logging.info("Found serial number %s for device %s", self._sn, name)
except LookupError:
self._sn = None
self._serial = self._openSerialPort(self._port)
self._ser_access = threading.RLock() # reentrant, so that recovery can keep sending messages
self._recover = False
self._initHw()
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
if positions is None:
positions = ((0, None), (math.radians(90), None))
else:
if len(positions) != 2 or any(len(p) != 2 for p in positions):
raise ValueError("Positions must be exactly 2 tuples of 2 values")
# TODO: have the standard inverted Actuator functions work on enumerated axis
if inverted and axis in inverted:
positions = (positions[1], positions[0])
self._pos_to_jog = {positions[0][0]: 1,
positions[1][0]: 2}
self._status_to_pos = {STA_FWD_HLS: positions[0][0],
STA_RVS_HLS: positions[1][0]}
if positions[0][1] is None:
choices = set(p[0] for p in positions)
else:
choices = dict(positions)
# TODO: add support for speed
axes = {axis: model.Axis(unit="rad", choices=choices)}
model.Actuator.__init__(self, name, role, axes=axes, **kwargs)
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "%s (serial driver: %s)" % (odemis.__version__, driver_name)
try:
snd, modl, typ, fmv, notes, hwv, state, nc = self.GetInfo()
except IOError:
# This is the first communication with the hardware, if it fails
# it can be a sign the device is in a bad state. (it is known to
# fail when turned on and plugged in before the host computer is
# turned on)
logging.exception("GetInfo() failed.")
raise HwError("USB device with S/N %s seems in bad state. "
"Check that the Thorlabs filter flipper was "
"turned on *after* the host computer." % sn)
self._hwVersion = "%s v%d (firmware %s)" % (modl, hwv, fmv)
# It has worked at least once, so if it fails, there are hopes
self._recover = True
self.position = model.VigilantAttribute({}, readonly=True)
self._updatePosition()
# It'd be nice to know when a move is over, but it the MFF10x doesn't
# report ends of move.
# self.SendMessage(MOT_RESUME_ENDOFMOVEMSGS)
# If we need constant status updates, then, we'll need to answer them
# with MOT_ACK_DCSTATUSUPDATE at least once per second.
# For now we don't track the current device status, so it's easy.
# When requesting update messages, messages are sent at ~10Hz, even if
# no change has happened.
# self.SendMessage(HW_START_UPDATEMSGS) # Causes a lot of messages
# We should make sure that the led is always off, but apparently, it's
# off by default until explicitly asking for it (cf MOD_IDENTIFY)
def terminate(self):
self._recover = False # to stop recovering if it's ongoing
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
with self._ser_access:
if self._serial:
self._serial.close()
self._serial = None
def _initHw(self):
# Ensure we don't receive anything
self.SendMessage(HW_STOP_UPDATEMSGS)
self._serial.flushInput()
# Documentation says it should be done first, though it doesn't seem
# required
self.SendMessage(HW_NO_FLASH_PROGRAMMING)
def _recoverHwError(self):
"""
Returns when the device is back online
"""
if self._serial:
self._serial.close()
self._serial = None
# keep looking for a serial port with the right serial number
while self._recover:
time.sleep(1)
try:
self._port = self._getSerialPort(self._sn)
except HwError:
logging.debug("Waiting more for the device %s to come back", self._sn)
except Exception:
raise
else:
break
else:
raise IOError("Device disappeared, and driver terminated")
# TODO: if it failed again, try again?
logging.info("Found again device %s, on port %s", self._sn, self._port)
self._serial = self._openSerialPort(self._port)
# Reinit Hw
self._initHw()
# TODO: put back to last known position? Or at least force to a known position?
self._updatePosition()
self.state._set_value(model.ST_RUNNING, force_write=True)
def SendMessage(self, msg, dest=0x50, src=1, p1=None, p2=None, data=None):
"""
Send a message to a device and possibility wait for its response
msg (APTSet or APTReq): the message definition
dest (0<int): the destination ID (always 0x50 if directly over USB)
p1 (None or 0<=int<=255): param1 (passed as byte2)
p2 (None or 0<=int<=255): param2 (passed as byte3)
data (None or bytes): data to be send further. Cannot be mixed with p1
and p2
return (None or bytes): the content of the response or None if it was
an APTSet message
raise:
IOError: if failed to send or receive message
"""
assert 0 <= dest < 0x80
# create the message
if data is None: # short message
p1 = p1 or 0
p2 = p2 or 0
com = struct.pack("<HBBBB", msg.id, p1, p2, dest, src)
else: # long message
com = struct.pack("<HHBB", msg.id, len(data), dest | 0x80, src) + data
trials = 0
with self._ser_access:
while True:
trials += 1
try:
logging.debug("Sending: '%s'", ", ".join("%02X" % ord(c) for c in com))
self._serial.write(com)
if isinstance(msg, APTReq): # read the response
# ensure everything is sent, before expecting an answer
self._serial.flush()
# Read until end of answer
while True:
rid, res = self._ReadMessage()
if rid == msg.rid:
return res
logging.debug("Skipping unexpected message %X", rid)
else:
return
except IOError as ex:
if not self._recover or trials >= 5:
raise
logging.warning("Failed to send message, trying to recover", exc_info=True)
self.state._set_value(ex, force_write=True)
self._recoverHwError()
# Note: unused
def WaitMessage(self, msg, timeout=None):
"""
Wait until a specified message is received
msg (APTMessage)
timeout (float or None): maximum amount of time to wait
return (bytes): the 2 params or the data contained in the message
raise:
IOError: if timeout happened
"""
start = time.time()
# Read until end of answer
with self._ser_access:
while True:
if timeout is not None:
left = time.time() - start + timeout
if left <= 0:
raise IOError("No message %d received in time" % msg.id)
else:
left = None
mid, res = self._ReadMessage(timeout=left)
if mid == msg.id:
return res
# TODO: instead of discarding the message, it could go into a
# queue, to be handled later
logging.debug("Skipping unexpected message %X", mid)
def _ReadMessage(self, timeout=None):
"""
Reads the next message
timeout (0 < float): maximum time to wait for the message
return:
mid (int): message ID
data (bytes): bytes 3&4 or the data of the message
raise:
IOError: if failed to send or receive message
"""
old_timeout = self._serial.timeout
if timeout is not None:
# Should be only for the first byte, but doing it for the first 6
# should rarely matter
self._serial.timeout = timeout
try:
# read the first (required) 6 bytes
msg = b""
for i in range(6):
char = self._serial.read() # empty if timeout
if not char:
raise IOError("Controller timed out, after receiving '%s'" % msg)
msg += char
finally:
self._serial.timeout = old_timeout
mid = struct.unpack("<H", msg[0:2])[0]
if not (ord(msg[4]) & 0x80): # short message
logging.debug("Received: '%s'", ", ".join("%02X" % ord(c) for c in msg))
return mid, msg[2:4]
# long message
length = struct.unpack("<H", msg[2:4])[0]
for i in range(length):
char = self._serial.read() # empty if timeout
if not char:
raise IOError("Controller timed out, after receiving '%s'" % msg)
msg += char
logging.debug("Received: '%s'", ", ".join("%02X" % ord(c) for c in msg))
return mid, msg[6:]
# Low level functions
def GetInfo(self):
"""
returns:
serial number (int)
model number (str)
type (int)
firmware version (str)
notes (str)
hardware version (int)
hardware state (int)
number of channels (int)
"""
res = self.SendMessage(HW_REQ_INFO)
# Expects 0x54 bytes
values = struct.unpack('<I8sHI48s12xHHH', res)
sn, modl, typ, fmv, notes, hwv, state, nc = values
# remove trailing 0's
modl = modl.rstrip("\x00")
notes = notes.rstrip("\x00")
# Convert firmware version to a string
fmvs = "%d.%d.%d" % ((fmv & 0xff0000) >> 16,
(fmv & 0xff00) >> 8,
fmv & 0xff)
return sn, modl, typ, fmvs, notes, hwv, state, nc
def MoveJog(self, pos):
"""
Move the position. Note: this is asynchronous.
pos (int): 1 or 2
"""
assert pos in [1, 2]
# p1 is chan ident, always 1
self.SendMessage(MOT_MOVE_JOG, p1=1, p2=pos)
def GetStatus(self):
"""
return:
pos (int): position count
status (int): status, as a flag of STA_*
"""
res = self.SendMessage(MOT_REQ_STATUSUPDATE)
# expect 14 bytes
c, pos, enccount, status = struct.unpack('<HiiI', res)
return pos, status
# high-level methods (interface)
def _updatePosition(self):
"""
update the position VA
"""
_, status = self.GetStatus()
pos = {}
for axis in self.axes: # axes contains precisely one axis
# status' flags should never be present simultaneously
for f, p in self._status_to_pos.items():
if f & status:
pos[axis] = p
break
else:
# This can happen if the mount is half-way
logging.warning("Status %X doesn't contain position information", status)
return # don't change position
# it's read-only, so we change it via _value
self.position._value = self._applyInversion(pos)
self.position.notify(self.position.value)
def _waitNoMotion(self, timeout=None):
"""
Block as long as the controller reports motion
timeout (0 < float): maximum time to wait for the end of the motion
"""
start = time.time()
# Read until end of motion
while True:
_, status = self.GetStatus()
if not (status & STA_IN_MOTION):
return
if timeout is not None and (time.time() > start + timeout):
raise IOError("Device still in motion after %g s" % (timeout,))
# Give it a small break
time.sleep(0.05) # 20Hz
@isasync
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
# TODO move to the +N next position? (and modulo number of axes)
raise NotImplementedError("Relative move on enumerated axis not supported")
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
return self._executor.submit(self._doMovePos, pos.values()[0])
def stop(self, axes=None):
self._executor.cancel()
def _doMovePos(self, pos):
jogp = self._pos_to_jog[pos]
self.MoveJog(jogp)
self._waitNoMotion(10) # by default, a move lasts ~0.5 s
self._updatePosition()
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a Thorlabs APT device.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
# For debugging purpose
if port == "/dev/fake":
return MFF102Simulator(timeout=1)
ser = serial.Serial(
port=port,
baudrate=115200,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
rtscts=True,
timeout=1 # s
)
# Purge (as recommended in the documentation)
time.sleep(0.05) # 50 ms
ser.flush()
ser.flushInput()
time.sleep(0.05) # 50 ms
# Prepare the port
ser.setRTS()
return ser
def _getSerialPort(self, sn):
"""
sn (str): serial number of the device
return (str): serial port name (eg: "/dev/ttyUSB0" on Linux)
"""
if sys.platform.startswith('linux'):
# Look for each USB device, if the serial number is good
sn_paths = glob.glob('/sys/bus/usb/devices/*/serial')
for p in sn_paths:
try:
f = open(p)
snp = f.read().strip()
except IOError:
logging.debug("Failed to read %s, skipping device", p)
if snp == sn:
break
else:
# There is a known problem with the APT devices that prevent
# them from connecting to USB if they are connected via a hub
# and powered on before the host PC.
raise HwError("No USB device with S/N %s. "
"Check that the Thorlabs filter flipper was "
"turned on *after* the host computer." % sn)
# Deduce the tty:
# .../3-1.2/serial => .../3-1.2/3-1.2:1.0/ttyUSB1
sys_path = os.path.dirname(p)
usb_num = os.path.basename(sys_path)
tty_paths = glob.glob("%s/%s/ttyUSB?*" % (sys_path, usb_num + ":1.0"))
if not tty_paths:
raise ValueError("Failed to find tty for device with S/N %s" % sn)
tty = os.path.basename(tty_paths[0])
# Convert to /dev
# Note: that works because udev rules create a dev with the same name
# otherwise, we would need to check the char numbers
return "/dev/%s" % (tty,)
else:
# TODO: Windows version
raise NotImplementedError("OS not yet supported")
def _getSerialNumber(self, port):
"""
Get the serial number of the device (via USB info)
port (str): port name of the device (eg: "/dev/ttyUSB0" on Linux)
return (str): serial number
"""
if sys.platform.startswith('linux'):
# Go reverse from getSerialPort():
# /sys/bus/usb-serial/devices/ttyUSB0
# -> read the link and remove the last two levels
try:
tty = os.path.basename(port)
sys_path = "/sys/bus/usb-serial/devices/" + tty
usb_path = os.path.join(os.path.dirname(sys_path), os.readlink(sys_path))
serial_path = usb_path + "/../../serial"
f = open(serial_path)
snp = f.read().strip()
return snp
except (IOError, OSError):
raise LookupError("Failed to find serial number of %s" % (port,))
else:
# TODO: Windows version
raise NotImplementedError("OS not yet supported")
@classmethod
def scan(cls):
"""
returns (list of 2-tuple): name, args (sn)
Note: it's obviously not advised to call this function if a device is already under use
"""
logging.info("Serial ports scanning for Thorlabs MFFxxx in progress...")
found = [] # (list of 2-tuple): name, kwargs
if sys.platform.startswith('linux'):
# Look for each USB device, if the serial number is potentially good
sn_paths = glob.glob('/sys/bus/usb/devices/*/serial')
for p in sn_paths:
try:
f = open(p)
snp = f.read().strip()
except IOError:
logging.debug("Failed to read %s, skipping device", p)
if not (snp.startswith(SN_PREFIX_MFF) and len(snp) == 8):
continue
# Deduce the tty:
# .../3-1.2/serial => .../3-1.2/3-1.2:1.0/ttyUSB1
sys_path = os.path.dirname(p)
usb_num = os.path.basename(sys_path)
logging.info("Looking at device %s with S/N=%s", usb_num, snp)
tty_paths = glob.glob("%s/%s/ttyUSB?*" % (sys_path, usb_num + ":1.0"))
if not tty_paths: # 0 or 1 paths
continue
tty = os.path.basename(tty_paths[0])
# Convert to /dev
# Note: that works because udev rules create a dev with the same name
# otherwise, we would need to check the char numbers
port = "/dev/%s" % (tty,)
# open and try to communicate
try:
dev = cls(name="test", role="test", port=port)
_, modl, typ, fmv, notes, hwv, state, nc = dev.GetInfo()
found.append((modl, {"sn": snp, "axis": "rz"}))
except Exception:
pass
else:
# TODO: Windows version
raise NotImplementedError("OS not yet supported")
return found
class Focus(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
moving the SEM focus (as it's considered an axis in Odemis)
"""
def __init__(self, name, role, parent, **kwargs):
"""
axes (set of string): names of the axes
"""
self.parent = parent
axes_def = {
# Ranges are from the documentation
"z": model.Axis(unit="m", range=(FOCUS_RANGE[0] * 1e-3, FOCUS_RANGE[1] * 1e-3)),
}
model.Actuator.__init__(self, name, role, parent=parent, axes=axes_def, **kwargs)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({},
unit="m", readonly=True)
self._updatePosition()
# Refresh regularly the position
self._pos_poll = util.RepeatingTimer(5, self._refreshPosition, "Focus position polling")
self._pos_poll.start()
def _updatePosition(self):
"""
update the position VA
"""
z = self.parent.GetFocus() * 1e-3
self.position._set_value({"z": z}, force_write=True)
def _refreshPosition(self):
"""
Called regularly to update the current position
"""
# We don't use the VA setters, to avoid sending back to the hardware a
# set request
logging.debug("Updating SEM focus position")
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating focus position")
def _doMoveRel(self, foc):
"""
move by foc
foc (float): relative change in mm
"""
try:
foc += self.parent.GetFocus() # mm
self.parent.SetFocus(foc)
finally:
# Update the position, even if the move didn't entirely succeed
self._updatePosition()
def _doMoveAbs(self, foc):
"""
move to pos
foc (float): unit mm
"""
try:
self.parent.SetFocus(foc)
finally:
# Update the position, even if the move didn't entirely succeed
self._updatePosition()
@isasync
def moveRel(self, shift):
"""
shift (dict): shift in m
"""
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
foc = shift["z"] * 1e3
f = self._executor.submit(self._doMoveRel, foc)
return f
@isasync
def moveAbs(self, pos):
"""
pos (dict): pos in m
"""
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
foc = pos["z"] * 1e3
f = self._executor.submit(self._doMoveAbs, foc)
return f
def stop(self, axes=None):
"""
Stop the last command
"""
# Empty the queue (and already stop the stage if a future is running)
self._executor.cancel()
logging.debug("Stopping all axes: %s", ", ".join(self.axes))
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
class PMD401Bus(Actuator):
"""
This represents the PMD401 motor controller bus for the PiezoMotor LEGS motors. It supports multiple controllers
(each one handling one axis), connected in a daisy chain. Only the first
controller is directly connected to the computer.
The specification for the hardware interface can be found in the document
"PiezoMotor_PMD401_Technical_Manual.pdf".
This driver works equally well with the PMD301 controller.
"""
def __init__(self,
name,
role,
port,
axes,
inverted=None,
param_file=None,
**kwargs):
"""
:param axes (dict: str -> dict): axis name --> axis parameters
Each axis is specified by a set of parameters.
After successful configuration with the pmconfig.py script, the only required parameter for a default motor
is the address which was set during the configuration process.
The spc parameter (conversion between motor steps and encoder counts) is typically saved in the flash
memory of the controller during the configuration process. The flash value is overridden by the
value in the parameter dict.
Depending on the type of motor, the encoder_resolution and range might need to be adjusted.
Axis parameters:
axis_number (0 <= int <= 127): typically 1-3 for x-z, required
closed_loop (bool): True for closed loop (with encoder), default to False
encoder_resolution (float): number of encoder counts per meter, default to 1.22e-9
motorstep_resolution (float): number of motor steps per m, default to 5e-6
range (tuple of float): in m, default to STROKE_RANGE
speed (float): speed in m/s
unit (str), default to m
:param param_file (str or None): (absolute or relative) path to a tmcm.tsv file which will be used to initialise
the axis parameters.
"""
self._axis_map = {} # axis name -> axis number used by controller
self._closed_loop = {} # axis name (str) -> bool (True if closed loop)
self._speed = {} # axis name (str) -> speed in unit/s
self._speed_steps = {
} # axis name (str) -> int, speed in steps per meter
self._counts_per_meter = {} # axis name (str) -> float
self._steps_per_meter = {} # axis name (str) -> float
self._portpattern = port
# Parse axis parameters and create axis
axes_def = {} # axis name -> Axis object
for axis_name, axis_par in axes.items():
if 'axis_number' in axis_par:
axis_num = axis_par['axis_number']
if axis_num not in range(128):
raise ValueError(
"Invalid axis number %s, needs to be 0 <= int <= 127."
% axis_num)
elif axis_num in self._axis_map.values():
axname = self._axis_map[axis_num]
raise ValueError(
"Invalid axis number %s, already assigned to axis %s."
% (axis_num, axname))
else:
self._axis_map[axis_name] = axis_par['axis_number']
else:
raise ValueError("Axis %s has no axis number." % axis_name)
if 'closed_loop' in axis_par:
closed_loop = axis_par['closed_loop']
else:
closed_loop = False
logging.info(
"Axis parameter \"closed_loop\" not specified for axis %s. Assuming open-loop.",
axis_name)
self._closed_loop[axis_name] = closed_loop
if 'motorstep_resolution' in axis_par:
self._steps_per_meter[
axis_name] = 1 / axis_par['motorstep_resolution']
else:
self._steps_per_meter[
axis_name] = 1 / DEFAULT_MOTORSTEP_RESOLUTION
logging.info(
"Axis %s has no motorstep resolution, assuming %s.",
axis_name, DEFAULT_MOTORSTEP_RESOLUTION)
if 'encoder_resolution' in axis_par:
self._counts_per_meter[
axis_name] = 1 / axis_par['encoder_resolution']
else:
self._counts_per_meter[
axis_name] = 1 / DEFAULT_ENCODER_RESOLUTION
logging.info("Axis %s has no encoder resolution, assuming %s.",
axis_name, DEFAULT_ENCODER_RESOLUTION)
if 'range' in axis_par:
axis_range = [
float(axis_par['range'][0]),
float(axis_par['range'][1])
]
else:
axis_range = STROKE_RANGE
logging.info("Axis %s has no range. Assuming %s", axis_name,
axis_range)
if 'speed' in axis_par:
self._speed[axis_name] = axis_par['speed']
else:
self._speed[axis_name] = DEFAULT_AXIS_SPEED
logging.info(
"Axis %s was not given a speed value. Assuming %s",
axis_name, self._speed[axis_name])
self._speed_steps[axis_name] = int(
round(self._speed[axis_name] *
self._steps_per_meter[axis_name]))
if 'unit' in axis_par:
axis_unit = axis_par['unit']
else:
axis_unit = "m"
logging.info("Axis %s has no unit. Assuming %s", axis_name,
axis_unit)
ad = model.Axis(canAbs=closed_loop,
unit=axis_unit,
range=axis_range)
axes_def[axis_name] = ad
Actuator.__init__(self,
name,
role,
axes=axes_def,
inverted=inverted,
**kwargs)
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
self._ser_access = threading.RLock()
# Connect to hardware
self._port = None # port number
min_axis = min(self._axis_map.values())
self._serial = self._findDevice(port, min_axis)
self._recovering = False
# Get version
hwVersions = []
for ax_name, ax_num in self._axis_map.items():
ver = self.getVersion(ax_num)
sn = self.getSerialNumber(ax_num)
hwVersions.append("Axis %s ('%s') version: %s, " %
(ax_num, ax_name, ver) +
"serial number: %s" % sn)
self._hwVersion = ", ".join(hwVersions)
logging.debug("Hardware versions: %s", hwVersions)
# Configuration
for axis in self._axis_map.values():
self.setWaveform(axis, WAVEFORM_DELTA)
driver_name = getSerialDriver(self._port)
self._swVersion = "Serial driver: %s" % (driver_name, )
# Position and referenced VAs
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self.referenced = model.VigilantAttribute({}, readonly=True)
self._updatePosition()
for axname in self._axis_map.keys():
self.referenced.value[
axname] = False # just assume they haven't been referenced
self.speed = model.VigilantAttribute(self._speed,
unit="m/s",
readonly=True)
# Write parameters from parameter file
if param_file:
if not os.path.isabs(param_file):
param_file = os.path.join(os.path.dirname(__file__),
param_file)
try:
f = open(param_file)
except Exception as ex:
raise ValueError("Failed to open file %s: %s" %
(param_file, ex))
try:
axis_params = self.parse_tsv_config(f)
except Exception as ex:
raise ValueError("Failed to parse file %s: %s" %
(param_file, ex))
f.close()
logging.debug("Extracted param file config: %s", axis_params)
self.apply_params(axis_params)
def terminate(self):
# terminate can be called several times, do nothing if ._serial is already None
if self._serial is None:
return
self._serial.close()
self._serial = None
for axis in self._axis_map.values():
self.setWaveform(axis, WAVEFORM_PARK) # power off
super(PMD401Bus, self).terminate()
def stop(self, axes=None):
self._executor.cancel()
axes = axes or self._axis_map.keys()
for ax in axes:
self.stopAxis(self._axis_map[ax])
@isasync
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
@isasync
def moveAbs(self, pos):
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
@isasync
def reference(self, axes):
self._checkReference(axes)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doReference, f, axes)
return f
def _doReference(self, f, axes):
self._check_hw_error()
# Request referencing on all axes
# Referencing procedure: index signal is in the middle of the rod (when using encoder)
# * move to the limit switch in the negative direction (fixed end of the rod)
# * once we reach the limit switch, PMD error 6 will be raised
# * move back in the opposite direction until indexing signal is registered
# In case there is no encoder, it is still possible to reference. The motor has an internal indexing
# signal 8.9 µm from fixed end of the rod (the end of the rod should be the most negative position if
# the axis is not inverted). By referencing, this position can be set to 0 and absolute moves are possible
# (although with less accuracy). However, we do not currently support this type of referencing without
# encoder. With our hardware attached to the motor, it is impossible to reach the 8.9 µm indexing position.
for axname in axes:
if f._must_stop.is_set():
self.stopAxis(self._axis_map[axname])
raise CancelledError()
axis = self._axis_map[axname]
self.referenced._value[axname] = False
# First, search for the index in negative direction.
idx_found = self._search_index(f, axname, direction=-1)
# If it wasn't found, try again in positive direction.
if not idx_found:
logging.debug("Referencing axis %s in the positive direction",
axis)
idx_found = self._search_index(f, axname, direction=1)
# If it's still not found, something went wrong.
if not idx_found:
raise ValueError(
"Couldn't find index on axis %s (%s), referencing failed."
% (axis, axname))
# Referencing complete
logging.debug("Finished referencing axis %s." % axname)
self.stopAxis(
axis
) # the axis should already be stopped, make sure for safety
self.referenced._value[axname] = True
# read-only so manually notify
self.referenced.notify(self.referenced.value)
self._updatePosition()
def _search_index(self, f, axname, direction):
"""
:param f (Future)
:param axname (str): axis name (as seen by the user)
:param direction (-1 or 1): -1 for negative direction (beginning of the rod), 1 for positive direction
returns (bool): True if index was found, false if limit was reached
raises PMDError for all other errors except limit exceeded error
IOError in case of timeout
"""
axis = self._axis_map[axname]
maxdist = self._axes[axname].range[1] - self._axes[axname].range[
0] # complete rodlength
steps = int(maxdist * self._steps_per_meter[axname])
maxdur = maxdist / self._speed[axname] + 1
end_time = time.time() + 2 * maxdur
logging.debug("Searching for index in direction %s.", direction)
self.startIndexMode(axis)
self.moveToIndex(axis, steps * direction)
index_found = False
while not index_found:
if f._must_stop.is_set():
self.stopAxis(axis)
raise CancelledError()
# Check for timeout
if time.time() > end_time:
self.stopAxis(axis) # exit index mode
raise IOError(
"Timeout while waiting for end of motion on axis %s" %
axis)
# Check if limit is reached
try:
self._check_hw_error()
except PMDError as ex:
if ex.errno == 6: # external limit reached
logging.debug("Axis %d limit reached during referencing",
axis)
self.stopAxis(
axis
) # that seems to be necessary after reaching the limit
break
else:
raise
# Get index status
index_found = self.getIndexStatus(self._axis_map[axname])[-1]
time.sleep(0.05)
return index_found
def _doMoveAbs(self, f, pos):
self._check_hw_error()
self._updatePosition()
current_pos = self._applyInversion(self.position.value)
shifts = {}
if f._must_stop.is_set():
raise CancelledError()
for axname, val in pos.items():
if self._closed_loop[axname]:
shifts[axname] = val - current_pos[axname]
encoder_cnts = round(val * self._counts_per_meter[axname])
self.runAbsTargetMove(self._axis_map[axname], encoder_cnts,
self._speed_steps[axname])
else:
# No absolute move for open-loop => convert to relative move
shifts[axname] = val - current_pos[axname]
steps_float = shifts[axname] * self._steps_per_meter[axname]
steps = int(steps_float)
usteps = int((steps_float - steps) * USTEPS_PER_STEP)
self.runMotorJog(self._axis_map[axname], steps, usteps,
self._speed_steps[axname])
try:
self._waitEndMotion(f, shifts)
finally:
# Leave target mode in case of closed-loop move
for ax in pos:
self.stopAxis(self._axis_map[ax])
self._updatePosition()
def _doMoveRel(self, f, shift):
self._check_hw_error()
shifts = {}
if f._must_stop.is_set():
raise CancelledError()
for axname, val in shift.items():
if self._closed_loop[axname]:
shifts[axname] = val
encoder_cnts = val * self._counts_per_meter[axname]
self.runRelTargetMove(self._axis_map[axname], encoder_cnts,
self._speed_steps[axname])
else:
shifts[axname] = val
steps_float = val * self._steps_per_meter[axname]
steps = int(steps_float)
usteps = int((steps_float - steps) * USTEPS_PER_STEP)
self.runMotorJog(self._axis_map[axname], steps, usteps,
self._speed_steps[axname])
try:
self._waitEndMotion(f, shifts)
finally:
# Leave target mode in case of closed-loop move
for ax in shift:
self.stopAxis(self._axis_map[ax])
self._updatePosition()
def _waitEndMotion(self, f, shifts):
"""
Wait until move is done.
:param f: (CancellableFuture) move future
:param shifts: (dict: str --> floats) relative move (in m) between current position and previous position
"""
dur = 0
for ax, shift in shifts.items():
dur = max(abs(shift / self._speed[ax]), dur)
max_dur = dur * 2 + 1
logging.debug("Expecting a move of %g s, will wait up to %g s", dur,
max_dur)
end_time = time.time() + max_dur
moving_axes = set(shifts.keys()) # All axes (still) moving
logging.debug(f"Axes {moving_axes} are moving.")
while moving_axes:
if f._must_stop.is_set():
for axname in moving_axes:
self.stopAxis(self._axis_map[axname])
raise CancelledError()
if time.time() > end_time:
raise TimeoutError(
"Timeout while waiting for end of motion on axes %s for %g s"
% (moving_axes, max_dur))
for axname in moving_axes.copy(
): # Copy as the set can change during the iteration
axis = self._axis_map[axname]
if self._closed_loop[axname]:
moving = self.isMovingClosedLoop(axis)
logging.debug(f"Axis {axis} is moving closed loop."
) if moving else None
else:
moving = self.isMovingOpenLoop(axis)
logging.debug(f"Axis {axis} is moving open loop."
) if moving else None
if not moving:
logging.debug(f"Axis {axis} finished moving.")
moving_axes.discard(axname)
self._check_hw_error()
time.sleep(0.05)
logging.debug("All axis finished moving")
def _check_hw_error(self):
"""
Read hardware status and raise exception if error is detected.
"""
for ax, axnum in self._axis_map.items():
status = self.getStatus(axnum)
# Always log the status
logging.debug("Device status: %s", status)
if status[0] & 8:
raise PMDError(
1,
"Communication Error on axis %s (wrong baudrate, data collision, "
"or buffer overflow)" % ax)
elif status[0] & 4:
raise PMDError(
2,
"Encoder error on axis %s (serial communication or reported error from "
"serial encoder)" % ax)
elif status[0] & 2:
raise PMDError(
3,
"Supply voltage or motor fault was detected on axis %s." %
ax)
elif status[0] & 1:
raise PMDError(
4,
"Command timeout occurred or a syntax error was detected on axis %s when "
"response was not allowed." % ax)
elif status[1] & 8:
# That's really not a big deal since everything is working fine after power-on, so don't raise an error.
logging.debug(
"Power-on/reset has occurred and detected on axis %s." %
ax)
elif status[1] & 4:
raise PMDError(
6, "External limit reached, detected on axis %s." % ax)
def _updatePosition(self):
"""
Update the position VA.
"""
pos = {}
for axname, axis in self._axis_map.items():
# TODO: if not in closed-loop, it's probably because there is no encoder, so we need a different way
pos[axname] = self.getEncoderPosition(axis)
logging.debug("Reporting new position at %s", pos)
pos = self._applyInversion(pos)
self.position._set_value(pos, force_write=True)
def stopAxis(self, axis):
self._sendCommand(b'X%dS' % axis)
def getVersion(self, axis):
"""
:param axis: (int) axis number
:returns (str): controller type and firmware version, e.g. 'PMD401 V13'
"""
return self._sendCommand(b'X%d?' % axis)
def getSerialNumber(self, axis):
"""
:param axis: (int) axis number
:returns (str): serial number
"""
return self._sendCommand(b'X%dY42' % axis)
def initFromFlash(self, axis):
"""
Initialize settings from values stored in flash.
:param axis: (int) axis number
"""
# 2 for init from flash, 3 for factory values
self._sendCommand(b'X%dY1,2' % axis)
def setLimitType(self, axis, limit_type):
"""
:param axis: (int) axis number
:param limit_type: (0 <= int <= 3) 0 no limit, 1 active high, 2 active low
"""
self._sendCommand(b'X%dY2,%d' % (axis, limit_type))
def getEncoderPosition(self, axis):
"""
:param axis: (int) axis number
:returns (float): current position of the axis as reported by encoders (in m)
"""
axname = [name for name, num in self._axis_map.items()
if num == axis][0] # get axis name from number
return int(self._sendCommand(
b'X%dE' % axis)) / self._counts_per_meter[axname]
def runRelTargetMove(self, axis, encoder_cnts, speed):
"""
Closed-loop relative move.
:param axis: (int) axis number
:param encoder_cnts: (int)
:param speed: (int) speed in motor steps per s
"""
# There are two possibilities: move relative to current position (XC) and move relative to
# target position (XR). We are moving relative to the current position (might be more intuitive
# if something goes wrong and we're stuck in the wrong position).
self._sendCommand(b'X%dC%d,%d' % (axis, encoder_cnts, speed))
def runMotorJog(self, axis, motor_steps, usteps, speed):
"""
Open loop stepping.
:param axis: (int) axis number
:param motor_steps: (int) number of motor steps to move
:param usteps: (int) number of microsteps (1 motor step = 8192 microsteps)
:param speed: (int) speed in steps / m
"""
self._sendCommand(b'X%dJ%d,%d,%d' % (axis, motor_steps, usteps, speed))
def runAbsTargetMove(self, axis, encoder_cnts, speed):
"""
Closed loop move.
:param axis: (int) axis number
:param encoder_cnts: (int)
:param speed: speed in motor steps per s
"""
self._sendCommand(b'X%dT%d,%d' % (axis, encoder_cnts, speed))
def setWaveform(self, axis, wf):
"""
:param axis: (int) axis number
:param wf: (WAVEFORM_RHOMB, WAVEFORM_DELTA, WAVEFORM_PARK) waveform to set
"""
if wf not in (WAVEFORM_DELTA, WAVEFORM_RHOMB, WAVEFORM_PARK):
raise ValueError("wf %s not a valid waveform" % wf)
self._sendCommand(b'X%dM%d' % (axis, wf))
def getStatus(self, axis):
"""
:returns (list of 4 int): 4-bit status code
The most important values are the following
First bit:
8: communication error (wrong baudrate, data collision, or buffer overflow)
4: encoder error (serial communication or reported error from serial encoder)
2: voltage error (supply voltage or motor fault was detected)
1: command error (command timeout occurred or a syntax error was detected when response was not allowed)
Second bit:
8: reset (power on/ reset occurred)
4: set if the last motor movement was stopped by external limit switch
1: index (index signal was detected since last report)
For all codes, please refer to the PMD-401 manual.
"""
return [int(i) for i in self._sendCommand(b'X%dU0' % axis)]
def isMovingClosedLoop(self, axis):
"""
:param axis: (int) axis number
:returns: (bool) True if moving, False otherwise
"""
_, d2, d3, _ = self.getStatus(axis)
# Check d2 (second status value) bit 2 (external limit)
if d2 & 0b100:
logging.debug(
f"External limit reached on axis {axis}, current position is {self.position.value}"
)
raise PMDError(6, f"External limit reached on axis {axis}.")
# Check d3 (third status value) bit 2 (targetLimit: position limit reached) and bit 0 (targetReached)
if not d3 & 0b010: # closed loop not active, thus it is not moving in closed loop
logging.debug(
f"Closed loop not active, therefore not moving in closed loop on axis {axis}."
)
return False
elif d3 & 0b101:
logging.debug(
f"Target reached or position limit reached on axis {axis}.")
return False
else:
return True
def isMovingOpenLoop(self, axis):
"""
:param axis: (int) axis number
:returns: (bool) True if moving, False otherwise
"""
resp = self._sendCommand(
b'X%dJ' % axis
) # will be 0 if finished, otherwise +/-222 (contrary to manual!)
return int(resp) != 0
def startIndexMode(self, axis):
"""
Enters index mode.
"""
self._sendCommand(b'X%dN4' % axis)
def moveToIndex(self, axis, dist):
"""
Move towards the index until it's found.
"""
axname = [name for name, num in self._axis_map.items()
if num == axis][0] # get axis name from number
self._sendCommand(b'X%dI%d,0,%d' %
(axis, dist, self._speed_steps[axname]))
def getIndexStatus(self, axis):
"""
Returns a description of the index status.
:returns (tuple of 4):
mode (0 or 1): index mode (1 if position has been reset at index)
position (float):
logged (bool): position was logged since last report
indexed (bool): position has been reset at index
"""
# Check if referencing was successful
# Response looks like this: "1,132.,indexed"
ret = self._sendCommand(b'X%dN?' % axis).split(',')
try:
mode = ret[0]
if mode == '1':
mode = 1
else: # empty string means mode 0
mode = 0
if ret[1][-1] == '.':
# . means position was logged since last report
logged = True
position = ret[1][:-1]
else:
logged = False
position = ret[1]
if len(ret) > 2 and 'indexed' in ret[2]:
indexed = True
else:
indexed = False
return mode, position, logged, indexed
except Exception as ex:
logging.exception("Failed to parse index status %s, ex: %s", ret,
ex)
raise
def setAxisAddress(self, current_address, new_address):
"""
Set the address of the axis. The factory default is 0 for all boards. Don't use this
command if multiple axes with the same number are connected.
:param current_address: (int) current axis number
:param new_address: (int) new axis number
"""
self._sendCommand(b"X%dY40,%d" % (current_address, new_address))
def runAutoConf(self, axis):
"""
Runs automatic configuration for the encoder parameters.
:param axis: (int) axis number
"""
self._sendCommand(b"X%dY25,1" % axis)
def writeParamsToFlash(self, axis):
self._sendCommand(b"X%dY32" % axis)
def setParam(self, axis, param, value):
self._sendCommand(b"X%dY%d,%d" % (axis, param, value))
def readParam(self, axis, param):
"""
:returns (str): parameter value from device
"""
return self._sendCommand(b"X%dY%d" % (axis, param))
def _createMoveFuture(self):
"""
:returns: (CancellableFuture) a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event(
) # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set(
) # tell the thread taking care of the move it's over
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
def _sendCommand(self, cmd):
"""
:param cmd: (bytes) command to be sent to the hardware
:returns: (str) response
"""
cmd += EOL
with self._ser_access:
logging.debug("Sending command %s", to_str_escape(cmd))
try:
self._serial.write(cmd)
# TODO: what kind of exception is raised? Needs to be more specific.
except:
logging.warning("Failed to read from PMT Control firmware, "
"trying to reconnect.")
if self._recovering:
raise
else:
self._tryRecover()
# don't send command again
raise IOError("Failed to read from PMT Control firmware, "
"restarted serial connection.")
resp = b""
while resp[-len(EOL):] != EOL:
try:
char = self._serial.read()
# TODO: what kind of exception is raised? Needs to be more specific.
except:
logging.warning(
"Failed to read from PMT Control firmware, "
"trying to reconnect.")
if self._recovering:
raise
else:
self._tryRecover()
# don't send command again
raise IOError(
"Failed to read from PMT Control firmware, "
"restarted serial connection.")
if not char:
raise IOError("Timeout after receiving %s" %
to_str_escape(resp))
else:
resp += char
logging.debug("Received response %s", to_str_escape(resp))
# Check response (command should be echoed back)
if not resp.startswith(cmd[:-len(EOL) - 1]):
raise IOError("Response starts with %s != %s" %
(to_str_escape(resp[:len(cmd)]), cmd))
if b"_??_" in resp:
raise ValueError(
"Received response %s, command %s not understood." %
(to_str_escape(resp), cmd))
if b"!" in resp:
raise PMDError(0, to_str_escape(resp))
# Format:
# * for query with response: <cmd>:<ret><EOL> (will return <ret>)
# * for set command without response: <cmd><EOL> (will return "")
return resp[len(cmd) + 1 - len(EOL):-len(EOL)].decode("latin1")
def _tryRecover(self):
self._recovering = True
self.state._set_value(HwError("Connection lost, reconnecting..."),
force_write=True)
# Retry to open the serial port (in case it was unplugged)
# _ser_access should already be acquired, but since it's an RLock it can be acquired
# again in the same thread
try:
with self._ser_access:
while True:
if self._serial:
self._serial.close()
self._serial = None
try:
logging.debug("Searching for the device on port %s",
self._portpattern)
min_axis = min(self._axis_map.values())
self._port = self._findDevice(self._portpattern,
min_axis)
except IOError:
time.sleep(2)
except Exception:
logging.exception(
"Unexpected error while trying to recover device")
raise
else:
# We found it back!
break
# it now should be accessible again
self.state._set_value(model.ST_RUNNING, force_write=True)
logging.info("Recovered device on port %s", self._port)
finally:
self._recovering = False
def _findDevice(self, port, address=0):
"""
Look for a compatible device
port (str): pattern for the port name
address (None or int): the address of the stage controller
return (serial, int): the (opened) serial port used, and the actual address
raises:
IOError: if no device are found
"""
if port.startswith("/dev/fake"):
names = [port]
elif os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(port)
for n in names:
try:
ser = self._openSerialPort(n)
except IOError as ex:
# not possible to use this port? next one!
logging.info("Skipping port %s, which is not available (%s)",
n, ex)
continue
# check whether it answers with the right address
try:
# If any garbage was previously received, make it discarded.
self._serial = ser
self._serial.flush()
v = self.getVersion(address)
# The driver was writte for PMD401, but PMD301 has the same API and is more compatible with our hardware
if 'PMD401 ' in v or 'PMD301 ' in v:
self._port = n
return ser # found it!
except Exception as ex:
logging.debug(
"Port %s doesn't seem to have a PMD device connected: %s",
n, ex)
ser.close() # make sure to close/unlock that port
else:
raise IOError(
"Failed to find a PMD controller with adress %s on ports '%s'. "
"Check that the device is turned on and "
"connected to the computer." % (
address,
port,
))
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a PiezoMotor PMD device.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
raise HwError: if the serial port cannot be opened (doesn't exist, or
already opened)
"""
# For debugging purpose
if port == "/dev/fake":
return PMDSimulator(timeout=0.1)
try:
ser = serial.Serial(
port=port,
baudrate=BAUDRATE,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=0.3, # s
)
except IOError:
raise HwError("Failed to find a PMD controller on port '%s'. "
"Check that the device is turned on and "
"connected to the computer." % (port, ))
return ser
@classmethod
def scan(cls):
"""
returns (list of 2-tuple): name, kwargs
Note: it's obviously not advised to call this function if a device is already under use
"""
ports = [p.device for p in serial.tools.list_ports.comports()]
logging.info("Scanning for Piezomotor controllers in progress...")
found = [] # (list of 2-tuple): name, kwargs
for p in ports:
axes = {}
for axis in range(5): # most of the time, it's a small axis number
try:
logging.debug("Trying port %s, axis %s", p, axis)
dev = cls(None, None, p, axes={"x": {"axis_number": axis}})
except IOError:
# not possible to use this port? next one!
continue
except Exception:
logging.exception("Error while communicating with port %s",
p)
continue
axes["a%s" % axis] = {"axis_number": axis}
try:
ver = dev.getVersion(axis)
except Exception as ex:
ver = "Unknown"
logging.error(
"Could not get version number for device on axis %s, ex: %s",
axis, ex)
if axes:
found.append(("%s" % ver, {"port": p, "axes": axes}))
return found
@staticmethod
def parse_tsv_config(f):
"""
Parse a tab-separated value (TSV) file in the following format:
axis param value # comment
axis 0->127 (axis: number)
param is the parameter number (int)
value is a number (int))
f (File): opened file
return:
axis_params (dict (int, int) -> int): axis number/param number -> value
"""
axis_params = {} # (axis/add) -> val (int)
# read the parameters "database" the file
for l in f:
# comment or empty line?
mc = re.match(r"\s*(#|$)", l)
if mc:
logging.debug("Comment line skipped: '%s'", l.rstrip("\n\r"))
continue
m = re.match(
r"(?P<num>[0-9]+)\t(?P<param>[0-9]+)\t(?P<value>[-+]?[0-9]+)\s*(#.*)?$",
l)
if not m:
raise ValueError("Failed to parse line '%s'" %
l.rstrip("\n\r"))
num, add, val = int(m.group("num")), int(m.group("param")), int(
m.group("value"))
axis_params[(num, add)] = val
return axis_params
def apply_params(self, params):
for (axis, param), val in params.items():
self.setParam(axis, param, val)
class Stage(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
moving the Zeiss stage and updating the position.
"""
def __init__(self, name, role, parent, rng=None, **kwargs):
"""
inverted (set of str): names of the axes which are inverted
rng (dict str -> (float,float)): axis name -> min/max of the position on
this axis. Note: if the axis is inverted, the range passed will be
inverted. Also, if the hardware reports position outside of the range,
move might fail, as it is considered outside of the range.
"""
if rng is None:
rng = {}
if "x" not in rng:
rng["x"] = (5e-3, 152e-3)
if "y" not in rng:
rng["y"] = (5e-3, 152e-3)
if "z" not in rng:
rng["z"] = (5e-3, 40e-3)
axes_def = {
# Ranges are from the documentation
"x": model.Axis(unit="m", range=(rng["x"][0], rng["x"][1])),
"y": model.Axis(unit="m", range=(rng["y"][0], rng["y"][1])),
"z": model.Axis(unit="m", range=(rng["z"][0], rng["z"][1])),
}
model.Actuator.__init__(self, name, role, parent=parent, axes=axes_def, **kwargs)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
# Refresh regularly the position
self._pos_poll = util.RepeatingTimer(5, self._refreshPosition, "Position polling")
self._pos_poll.start()
def _updatePosition(self, raw_pos=None):
"""
update the position VA
raw_pos (dict str -> float): the position in mm (as received from the SEM)
"""
if raw_pos is None:
x, y, z, _ = self.parent.GetStagePosition()
else:
x, y, z = raw_pos["x"], raw_pos["y"], raw_pos["z"]
pos = {"x": x * 1e-3,
"y": y * 1e-3,
"z": z * 1e-3,
}
self.position._set_value(self._applyInversion(pos), force_write=True)
def _refreshPosition(self):
"""
Called regularly to update the current position
"""
# We don't use the VA setters, to avoid sending back to the hardware a
# set request
logging.debug("Updating SEM stage position")
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
def _doMoveRel(self, future, shift):
"""
move by the shift
shift (float): unit m
"""
x, y, z, _ = self.parent.GetStagePosition()
if "x" in shift:
x += shift["x"] * 1e3
if "y" in shift:
y += shift["y"] * 1e3
if "z" in shift:
z += shift["z"] * 1e3
target_pos = self._applyInversion({"x": x * 1e-3, "y": y * 1e-3, "z": z * 1e-3})
# Check range (for the axes we are moving)
for an in shift.keys():
rng = self.axes[an].range
p = target_pos[an]
if not rng[0] <= p <= rng[1]:
raise ValueError("Relative move would cause axis %s out of bound (%g m)" % (an, p))
self._moveTo(future, x, y, z)
def _doMoveAbs(self, future, pos):
"""
move to position pos
pos (float): unit m
"""
# Don't change position for unspecified coordinates
x, y, z, _ = self.parent.GetStagePosition()
# Convert to mm
if "x" in pos:
x = pos["x"] * 1e3
if "y" in pos:
y = pos["y"] * 1e3
if "z" in pos:
z = pos["z"] * 1e3
self._moveTo(future, x, y, z)
def _moveTo(self, future, x, y, z, timeout=60):
with future._moving_lock:
try:
if future._must_stop.is_set():
raise CancelledError()
logging.debug("Moving to position (%s, %s, %s)", x, y, z)
self.parent.MoveStage(x, y, z)
# documentation suggests to wait 1s before calling
# GetStagePosition() after MoveStage()
time.sleep(1)
# Wait until the move is over
# Don't check for future._must_stop because anyway the stage will
# stop moving, and so it's nice to wait until we know the stage is
# not moving.
moving = True
tstart = time.time()
while moving:
x, y, z, moving = self.parent.GetStagePosition()
# Take the opportunity to update .position
self._updatePosition({"x": x, "y": y, "z": z})
if time.time() > tstart + timeout:
self.parent.Abort()
logging.error("Timeout after submitting stage move. Aborting move.")
break
# 50 ms is about the time it takes to read the stage status
time.sleep(50e-3)
# If it was cancelled, Abort() has stopped the stage before, and
# we still have waited until the stage stopped moving. Now let
# know the user that the move is not complete.
if future._must_stop.is_set():
raise CancelledError()
except RemconError:
if future._must_stop.is_set():
raise CancelledError()
raise
finally:
future._was_stopped = True
# Update the position, even if the move didn't entirely succeed
self._updatePosition()
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set() # tell the thread taking care of the move it's over
self.parent.Abort()
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
def _createFuture(self):
"""
Return (CancellableFuture): a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event() # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
@isasync
def moveRel(self, shift):
"""
shift (dict): shift in m
"""
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
@isasync
def moveAbs(self, pos):
"""
pos (dict): position in m
"""
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
def stop(self, axes=None):
# Empty the queue (and already stop the stage if a future is running)
self._executor.cancel()
# Try to stop the stage, even if no future is running, for safety
logging.warning("Stopping all axes: %s", ", ".join(self.axes))
self.parent.Abort()
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
class SpectraPro(model.Actuator):
def __init__(self,
name,
role,
port,
turret=None,
calib=None,
_noinit=False,
dependencies=None,
**kwargs):
"""
port (string): name of the serial port to connect to.
turret (None or 1<=int<=3): turret number set-up. If None, consider that
the current turret known by the device is correct.
calib (None or list of (int, int and 5 x (float or str))):
calibration data, as saved by Winspec. Data can be either in float
or as an hexadecimal value "hex:9a,99,99,99,99,79,40,40"
blaze in nm, groove gl/mm, center adjust, slope adjust,
focal length, inclusion angle, detector angle
inverted (None): it is not allowed to invert the axes
dependencies (dict str -> Component): "ccd" should be the CCD used to acquire
the spectrum.
_noinit (boolean): for internal use only, don't try to initialise the device
"""
if kwargs.get("inverted", None):
raise ValueError("Axis of spectrograph cannot be inverted")
# start with this opening the port: if it fails, we are done
try:
self._serial = self.openSerialPort(port)
except serial.SerialException:
raise HwError(
"Failed to find spectrograph %s (on port '%s'). "
"Check the device is turned on and connected to the "
"computer. You might need to turn it off and on again." %
(name, port))
self._port = port
# to acquire before sending anything on the serial port
self._ser_access = threading.Lock()
self._try_recover = False
if _noinit:
return
self._initDevice()
self._try_recover = True
try:
self._ccd = dependencies["ccd"]
except (TypeError, KeyError):
# TODO: only needed if there is calibration info (for the pixel size)
# otherwise it's fine without CCD.
raise ValueError("Spectrograph needs a dependency 'ccd'")
# according to the model determine how many gratings per turret
model_name = self.GetModel()
self.max_gratings = MAX_GRATINGS_NUM.get(model_name, 3)
if turret is not None:
if turret < 1 or turret > self.max_gratings:
raise ValueError(
"Turret number given is %s, while expected a value between 1 and %d"
% (turret, self.max_gratings))
self.SetTurret(turret)
self._turret = turret
else:
self._turret = self.GetTurret()
# for now, it's fixed (and it's unlikely to be useful to allow less than the max)
max_speed = 1000e-9 / 10 # about 1000 nm takes 10s => max speed in m/s
self.speed = model.MultiSpeedVA(max_speed,
range=[max_speed, max_speed],
unit="m/s",
readonly=True)
gchoices = self.GetGratingChoices()
# remove the choices which are not valid for the current turret
for c in gchoices:
t = 1 + (c - 1) // self.max_gratings
if t != self._turret:
del gchoices[c]
# TODO: report the grating with its wavelength range (possible to compute from groove density + blaze wl?)
# range also depends on the max grating angle (40°, CCD pixel size, CCD horizontal size, focal length,+ efficienty curve?)
# cf http://www.roperscientific.de/gratingcalcmaster.html
# TODO: a more precise way to find the maximum wavelength (looking at the available gratings?)
# TODO: what's the min? 200nm seems the actual min working, although wavelength is set to 0 by default !?
axes = {
"wavelength":
model.Axis(unit="m",
range=(0, 2400e-9),
speed=(max_speed, max_speed)),
"grating":
model.Axis(choices=gchoices)
}
# provides a ._axes
model.Actuator.__init__(self,
name,
role,
axes=axes,
dependencies=dependencies,
**kwargs)
# First step of parsing calib parmeter: convert to (int, int) -> ...
calib = calib or ()
if not isinstance(calib, collections.Iterable):
raise ValueError("calib parameter must be in the format "
"[blz, gl, ca, sa, fl, ia, da], "
"but got %s" % (calib, ))
dcalib = {}
for c in calib:
if not isinstance(c, collections.Iterable) or len(c) != 7:
raise ValueError("calib parameter must be in the format "
"[blz, gl, ca, sa, fl, ia, da], "
"but got %s" % (c, ))
gt = (c[0], c[1])
if gt in dcalib:
raise ValueError(
"calib parameter contains twice calibration for "
"grating (%d nm, %d gl/mm)" % gt)
dcalib[gt] = c[2:]
# store calibration for pixel -> wavelength conversion and wavelength offset
# int (grating number 1 -> 9) -> center adjust, slope adjust,
# focal length, inclusion angle/2, detector angle
self._calib = {}
# TODO: read the info from MONO-EESTATUS (but it's so
# huge that it's not fun to parse). There is also detector angle.
dfl = FOCAL_LENGTH_OFFICIAL[model_name] # m
dia = math.radians(INCLUSION_ANGLE_OFFICIAL[model_name]) # rad
for i in gchoices:
# put default values
self._calib[i] = (0, 0, dfl, dia, 0)
try:
blz = self._getBlaze(i) # m
gl = self._getGrooveDensity(i) # gl/m
except ValueError:
logging.warning("Failed to parse info of grating %d" % i,
exc_info=True)
continue
# parse calib info
gt = (int(blz * 1e9), int(gl * 1e-3))
if gt in dcalib:
calgt = dcalib[gt]
ca = self._readCalibVal(calgt[0]) # ratio
sa = self._readCalibVal(calgt[1]) # ratio
fl = self._readCalibVal(calgt[2]) * 1e-3 # mm -> m
ia = math.radians(self._readCalibVal(calgt[3])) # ° -> rad
da = math.radians(self._readCalibVal(calgt[4])) # ° -> rad
self._calib[i] = ca, sa, fl, ia, da
logging.info(
"Calibration data for grating %d (%d nm, %d gl/mm) "
"-> %s" % (i, gt[0], gt[1], self._calib[i]))
else:
logging.warning("No calibration data for grating %d "
"(%d nm, %d gl/mm)" % (i, gt[0], gt[1]))
# set HW and SW version
self._swVersion = "%s (serial driver: %s)" % (
odemis.__version__, driver.getSerialDriver(port))
self._hwVersion = "%s (s/n: %s)" % (model_name,
(self.GetSerialNumber()
or "Unknown"))
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
# for storing the latest calibrated wavelength value
self._wl = (None, None, None
) # grating id, raw center wl, calibrated center wl
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
def _readCalibVal(self, rawv):
"""
rawv (str or number)
return (float)
"""
if isinstance(rawv, basestring):
if rawv.startswith("hex:"):
rawv = rawv[4:]
return hextof(rawv)
elif isinstance(rawv, numbers.Real):
return rawv
else:
raise ValueError("Cannot convert %s to a number" % (rawv, ))
# Low-level methods: to access the hardware (should be called with the lock acquired)
def _sendOrder(self, *args, **kwargs):
"""
Send a command which does not expect any report back (just OK)
com (str): command to send (non including the \r)
raise
SPError: if the command doesn't answer the expected OK.
IOError: in case of timeout
"""
# same as a query but nothing to do with the response
self._sendQuery(*args, **kwargs)
def _sendQuery(self, com, timeout=1):
"""
Send a command which expects a report back (in addition to the OK)
com (str): command to send (non including the \r)
timeout (0<float): maximum read timeout for the response
return (str): the response received (without the ok)
raises:
SPError: if the command doesn't answer the expected OK.
IOError: in case of timeout
"""
# All commands or strings of commands must be terminated with a carriage
# return (0D hex). The monochromator responds to a command when the
# command has been completed by returning the characters " ok" followed by
# carriage return and line feed (hex ASCII sequence 20 6F 6B 0D 0A).
# Examples of error answers:
# MODEL\r
# \x00X\xf0~\x00X\xf0~MODEL ? \r\n
# ?\r
# \r\nAddress Error \r\nA=3F4F4445 PC=81444
assert (1 < len(com) <= 100) # commands cannot be long
com += "\r"
logging.debug("Sending: %s", com.encode('string_escape'))
# send command until it succeeds
while True:
try:
self._serial.write(com)
break
except IOError:
if self._try_recover:
self._tryRecover()
else:
raise
# read response until timeout or known end of response
response = ""
timeend = time.time() + timeout
while ((time.time() <= timeend)
and not (response.endswith(" ok\r\n")
or response.endswith("? \r\n"))):
self._serial.timeout = max(0.1, timeend - time.time())
char = self._serial.read()
if not char: # timeout
break
response += char
logging.debug("Received: %s", response.encode('string_escape'))
if response.endswith(" ok\r\n"):
return response[:-5]
else:
# if the device hasn't answered anything, it might have been disconnected
if len(response) == 0:
if self._try_recover:
self._tryRecover()
else:
raise IOError("Device timeout after receiving '%s'." %
response.encode('string_escape'))
else: # just non understood command
# empty the serial port
self._serial.timeout = 0.1
garbage = self._serial.read(100)
if len(garbage) == 100:
raise IOError("Device keeps sending data")
response += garbage
raise SPError("Sent '%s' and received error: '%s'" %
(com.encode('string_escape'),
response.encode('string_escape')))
def _tryRecover(self):
# no other access to the serial port should be done
# so _ser_access should already be acquired
# Retry to open the serial port (in case it was unplugged)
while True:
try:
self._serial.close()
self._serial = None
except:
pass
try:
logging.debug("retrying to open port %s", self._port)
self._serial = self.openSerialPort(self._port)
except IOError:
time.sleep(2)
except Exception:
logging.exception(
"Unexpected error while trying to recover device")
raise
else:
break
self._try_recover = False # to avoid recursion
self._initDevice()
self._try_recover = True
def _initDevice(self):
# If no echo is desired, the command NO-ECHO will suppress the echo. The
# command ECHO will return the SP-2150i to the default echo state.
#
# If is connected via the real serial port (not USB), it is in echo
# mode, so we first need to disable it, while allowing echo of the
# command we've just sent.
try:
self._sendOrder("no-echo")
except SPError:
logging.info(
"Failed to disable echo, hopping the device has not echo anyway"
)
# empty the serial port
self._serial.timeout = 0.1
garbage = self._serial.read(100)
if len(garbage) == 100:
raise IOError("Device keeps sending data")
def GetTurret(self):
"""
returns (1 <= int <= 3): the current turret number
"""
# ?TURRET Returns the correctly installed turret numbered 1 - 3
res = self._sendQuery("?turret")
val = int(res)
if val < 1 or val > 3:
raise SPError("Unexpected turret number '%s'" % res)
return val
def SetTurret(self, t):
"""
Set the number of the current turret (for correct settings by the hardware)
t (1 <= int <= 3): the turret number
Raise:
ValueError if the turret has no grating configured
"""
# TURRET Specifies the presently installed turret or the turret to be installed.
# Doesn't change the hardware, just which gratings are available
assert (1 <= t <= 3)
# TODO check that there is grating configured for this turret (using GetGratingChoices)
self._sendOrder("%d turret" % t)
# regex to read the gratings
RE_NOTINSTALLED = re.compile("\D*(\d+)\s+Not Installed")
RE_INSTALLED = re.compile(
"\D*(\d+)\s+(\d+)\s*g/mm BLZ=\s*([0-9][.0-9]*)\s*(nm|NM|um|UM)")
RE_GRATING = re.compile("\D*(\d+)\s+(.+\S)\s*\r")
def GetGratingChoices(self):
"""
return (dict int -> string): grating number to description
"""
# ?GRATINGS Returns the list of installed gratings with position groove density and blaze. The
# present grating is specified with an arrow.
# Example output:
# \r\n 1 300 g/mm BLZ= 500NM \r\n\x1a2 300 g/mm BLZ= 750NM \r\n 3 Not Installed \r\n 4 Not Installed \r\n 5 Not Installed \r\n 6 Not Installed \r\n 7 Not Installed \r\n 8 Not Installed \r\n ok\r\n
# \r\n\x1a1 600 g/mm BLZ= 1.6UM \r\n 2 150 g/mm BLZ= 2UM \r\n 3 Not Installed \r\n 4 Not Installed \r\n 5 Not Installed \r\n 6 Not Installed \r\n 7 Not Installed \r\n 8 Not Installed \r\n 9 Not Installed \r\n ok\r\n
# From the spectrapro_300i_ll.c of fsc2, it seems the format is:
# non-digit*,digits=grating number,spaces,"Not Installed"\r\n
# non-digit*,digits=grating number,space+,digit+:g/mm,space*,"g/mm BLZ=", space*,digit+:blaze wl in nm,space*,"nm"\r\n
res = self._sendQuery("?gratings")
gratings = {}
for line in res[:-1].split(
"\n"): # avoid the last \n to not make an empty last line
m = self.RE_NOTINSTALLED.search(line)
if m:
logging.debug("Decoded grating %s as not installed, skipping.",
m.group(1))
continue
m = self.RE_GRATING.search(line)
if not m:
logging.debug("Failed to decode grating description '%s'",
line)
continue
num = int(m.group(1))
desc = m.group(2)
# TODO: provide a nicer description, using RE_INSTALLED?
gratings[num] = desc
return gratings
RE_GDENSITY = re.compile("(\d+)\s*g/mm")
def _getGrooveDensity(self, gid):
"""
Returns the groove density of the given grating
gid (int): index of the grating
returns (float): groove density in lines/meter
raise
LookupError if the grating is not installed
ValueError: if the groove density cannot be found out
"""
gstring = self.axes["grating"].choices[gid]
m = self.RE_GDENSITY.search(gstring)
if not m:
raise ValueError("Failed to find groove density in '%s'" % gstring)
density = float(m.group(1)) * 1e3 # l/m
return density
RE_BLZ = re.compile("BLZ=\s+(?P<blz>[0-9.]+)\s*(?P<unit>[NU]M)")
def _getBlaze(self, gid):
"""
Returns the blaze (=optimal center wavelength) of the given grating
gid (int): index of the grating
returns (float): blaze (in m)
raise
LookupError if the grating is not installed
ValueError: if the groove density cannot be found out
"""
gstring = self.axes["grating"].choices[gid]
m = self.RE_BLZ.search(gstring)
if not m:
raise ValueError("Failed to find blaze in '%s'" % gstring)
blaze, unit = float(m.group("blz")), m.group("unit").upper()
blaze *= {"UM": 1e-6, "NM": 1e-9}[unit] # m
return blaze
def GetGrating(self):
"""
Retuns the current grating in use
returns (1<=int<=9) the grating in use
"""
# ?GRATING Returns the number of gratings presently being used numbered 1 - 9.
# On the SP-2150i, it's only up to 6
res = self._sendQuery("?grating")
val = int(res)
if not 1 <= val <= 9:
raise SPError("Unexpected grating number '%s'" % res)
return val
def SetGrating(self, g):
"""
Change the current grating (the turret turns).
g (1<=int<=9): the grating number to change to
The method is synchronous, it returns once the grating is selected. It
might take up to 20 s.
Note: the grating is dependent on turret number (and the self.max_gratting)!
Note: after changing the grating, the wavelength, might have changed
"""
# GRATING Places specified grating in position to the [current] wavelength
# Note: it always reports ok, and doesn't change the grating if not
# installed or wrong value
assert (1 <= g <= (3 * self.max_gratings))
# TODO check that the grating is configured
self._sendOrder("%d grating" % g, timeout=20)
def GetWavelength(self):
"""
Return (0<=float): the current wavelength at the center (in m)
"""
# ?NM Returns present wavelength in nm to 0.01nm resolution with units
# nm appended.
# Note: For the SP-2150i, it seems there is no unit appended
# ?NM 300.00 nm
res = self._sendQuery("?nm")
m = re.search("\s*(\d+.\d+)( nm)?", res)
wl = float(m.group(1)) * 1e-9
if wl > 1e-3:
raise SPError("Unexpected wavelength of '%s'" % res)
return wl
def SetWavelength(self, wl):
"""
Change the wavelength at the center
wl (0<=float<=10e-6): wavelength in meter
returns when the move is complete
The method is synchronous, it returns once the grating is selected. It
might take up to 20 s.
"""
# GOTO: Goes to a destination wavelength at maximum motor speed. Accepts
# destination wavelength in nm as a floating point number with up to 3
# digits after the decimal point or whole number wavelength with no
# decimal point.
# 345.65 GOTO
# Note: NM goes to the wavelength slowly (in order to perform a scan).
# It shouldn't be needed for spectrometer
# Out of bound values are silently ignored by going to the min or max.
assert (0 <= wl <= 10e-6)
# TODO: check that the value fit the grating configuration?
self._sendOrder("%.3f goto" % (wl * 1e9), timeout=20)
def GetModel(self):
"""
Return (str): the model name
"""
# MODEL Returns model number of the Acton SP series monochromator.
# returns something like ' SP-2-150i '
res = self._sendQuery("model")
return res.strip()
def GetSerialNumber(self):
"""
Return the serial number or None if it cannot be determined
"""
try:
res = self._sendQuery("serial")
except SPError:
logging.exception("Device doesn't support serial number query")
return None
return res.strip()
# TODO diverter (mirror) functions: no diverter on SP-2??0i anyway.
def _getCalibratedWavelength(self):
"""
Read the center wavelength, and adapt it based on the calibration (if
it is available for the current grating)
return (float): wavelength in m
"""
gid = self.GetGrating()
rawwl = self.GetWavelength()
# Do we already now the answer?
if (gid, rawwl) == self._wl[0:2]:
return self._wl[2]
ca, sa, fl, ia, da = self._calib[gid]
# It's pretty hard to reverse the formula, so we approximate a8 using
# rawwl (instead of wl), which usually doesn't bring error > 0.01 nm
gl = self._getGrooveDensity(gid)
psz = self._ccd.pixelSize.value[0] # m/px
a8 = (rawwl * gl / 2) / math.cos(ia / 2)
ga = math.asin(a8) # rad
dispersion = math.cos(ia / 2 + ga) / (gl * fl) # m/m
pixbw = psz * dispersion
wl = (rawwl - ca * pixbw) / (sa + 1)
wl = max(0, wl)
return wl
def _setCalibratedWavelength(self, wl):
"""
wl (float): center wavelength in m
"""
gid = self.GetGrating()
ca, sa, fl, ia, da = self._calib[gid]
# This is approximately what Winspec does, but it seems not exactly,
# because the values differ ± 0.1nm
gl = self._getGrooveDensity(gid)
psz = self._ccd.pixelSize.value[0] # m/px
a8 = (wl * gl / 2) / math.cos(ia / 2)
ga = math.asin(a8) # rad
dispersion = math.cos(ia / 2 + ga) / (gl * fl) # m/m
pixbw = psz * dispersion
offset = ca * pixbw + sa * wl
if abs(offset) > 50e-9:
# we normally don't expect offset more than 10 nm
logging.warning("Center wavelength offset computed of %g nm",
offset * 1e9)
else:
logging.debug("Center wavelength offset computed of %g nm",
offset * 1e9)
rawwl = max(0, wl + offset)
self.SetWavelength(rawwl)
# store the corresponding official wl value as it's hard to inverse the
# conversion (for displaying in .position)
self._wl = (gid, self.GetWavelength(), wl)
# high-level methods (interface)
def _updatePosition(self):
"""
update the position VA
Note: it should not be called while holding _ser_access
"""
with self._ser_access:
pos = {
"wavelength": self._getCalibratedWavelength(),
"grating": self.GetGrating()
}
# it's read-only, so we change it via _value
self.position._value = pos
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
"""
Move the stage the defined values in m for each axis given.
shift dict(string-> float): name of the axis and shift in m
returns (Future): future that control the asynchronous move
"""
self._checkMoveRel(shift)
for axis in shift:
if axis == "wavelength":
# cannot convert it directly to an absolute move, because
# several in a row must mean they accumulate. So we queue a
# special task. That also means the range check is delayed until
# the actual position is known.
return self._executor.submit(self._doSetWavelengthRel,
shift[axis])
@isasync
def moveAbs(self, pos):
"""
Move the stage the defined values in m for each axis given.
pos dict(string-> float): name of the axis and new position in m
returns (Future): future that control the asynchronous move
"""
self._checkMoveAbs(pos)
# If grating needs to be changed, change it first, then the wavelength
if "grating" in pos:
g = pos["grating"]
wl = pos.get("wavelength")
return self._executor.submit(self._doSetGrating, g, wl)
elif "wavelength" in pos:
wl = pos["wavelength"]
return self._executor.submit(self._doSetWavelengthAbs, wl)
else: # nothing to do
return model.InstantaneousFuture()
def _doSetWavelengthRel(self, shift):
"""
Change the wavelength by a value
"""
with self._ser_access:
pos = self.position.value["wavelength"] + shift
# it's only now that we can check the absolute position is wrong
minp, maxp = self.axes["wavelength"].range
if not minp <= pos <= maxp:
raise ValueError(
"Position %f of axis '%s' not within range %f→%f" %
(pos, "wavelength", minp, maxp))
self._setCalibratedWavelength(pos)
self._updatePosition()
def _doSetWavelengthAbs(self, pos):
"""
Change the wavelength to a value
"""
with self._ser_access:
self._setCalibratedWavelength(pos)
self._updatePosition()
def _doSetGrating(self, g, wl=None):
"""
Setter for the grating VA.
g (1<=int<=3): the new grating
wl (None or float): wavelength to set afterwards. If None, will put the
same wavelength as before the change of grating.
returns the actual new grating
Warning: synchronous until the grating is finished (up to 20s)
"""
try:
with self._ser_access:
if wl is None:
wl = self.position.value["wavelength"]
self.SetGrating(g)
self._setCalibratedWavelength(wl)
except Exception:
logging.exception("Failed to change grating to %d", g)
raise
self._updatePosition()
def stop(self, axes=None):
"""
stops the motion
Warning: Only not yet-executed moves can be cancelled, this hardware
doesn't support stopping while a move is going on.
"""
self._executor.cancel()
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
if self._serial:
self._serial.close()
self._serial = None
def getPixelToWavelength(self, npixels, pxs):
"""
Return the lookup table pixel number of the CCD -> wavelength observed.
npixels (1 <= int): number of pixels on the CCD (horizontally), after
binning.
pxs (0 < float): pixel size in m (after binning)
return (list of floats): pixel number -> wavelength in m
"""
centerpixel = (npixels - 1) / 2
cw = self.position.value["wavelength"] # m
gid = self.position.value["grating"]
gl = self._getGrooveDensity(gid)
ca, sa, fl, ia, da = self._calib[gid]
# Formula based on the Winspec documentation:
# "Equations used in WinSpec Wavelength Calibration", p. 257 of the manual
# ftp://ftp.piacton.com/Public/Manuals/Princeton%20Instruments/WinSpec%202.6%20Spectroscopy%20Software%20User%20Manual.pdf
# Converted to code by Benjamin Brenny (from AMOLF)
G = math.asin(cw / (math.cos(ia / 2) * 2 / gl))
wllist = []
for i in range(npixels):
pxd = pxs * (i - centerpixel) # distance of pixel to sensor centre
E = math.atan((pxd * math.cos(da)) / (fl + pxd * math.sin(da)))
wl = (math.sin(G - ia / 2) + math.sin(G + ia / 2 + E)) / gl
wllist.append(wl)
return wllist
# def getPolyToWavelength(self):
# """
# Compute the right polynomial to convert from a position on the sensor to the
# wavelength detected. It depends on the current grating, center
# wavelength (and focal length of the spectrometer).
# Note: It will always return some not-too-stupid values, but the only way
# to get precise values is to have provided a calibration data file.
# Without it, it will just base the calculations on the theoretical
# perfect spectrometer.
# returns (list of float): polynomial coefficients to apply to get the current
# wavelength corresponding to a given distance from the center:
# w = p[0] + p[1] * x + p[2] * x²...
# where w is the wavelength (in m), x is the position from the center
# (in m, negative are to the left), and p is the polynomial (in m, m^0, m^-1...).
# """
# # FIXME: shall we report the error on the polynomial? At least say if it's
# # using calibration or not.
# # TODO: have a calibration procedure, a file format, and load it at init
# # See fsc2, their calibration is like this for each grating:
# # INCLUSION_ANGLE_1 = 30.3
# # FOCAL_LENGTH_1 = 301.2 mm
# # DETECTOR_ANGLE_1 = 0.324871
# # TODO: use detector angle
# fl = self._focal_length # m
# ia = self._inclusion_angle # rad
# cw = self.position.value["wavelength"] # m
# if not fl:
# # "very very bad" calibration
# return [cw]
#
# # When no calibration available, fallback to theoretical computation
# # based on http://www.roperscientific.de/gratingcalcmaster.html
# gl = self._getGrooveDensity(self.position.value["grating"]) # g/m
# # fL = focal length (mm)
# # wE = inclusion angle (°) = the angle between the incident and the reflected beam for the center wavelength of the grating
# # gL = grating lines (l/mm)
# # cW = center wavelength (nm)
# # Grating angle
# # A8 = (cW/1000*gL/2000)/Math.cos(wE* Math.PI/180);
# # E8 = Math.asin(A8)*180/Math.PI;
# try:
# a8 = (cw * gl/2) / math.cos(ia)
# ga = math.asin(a8) # radians
# except (ValueError, ZeroDivisionError):
# logging.exception("Failed to compute polynomial for wavelength conversion")
# return [cw]
# # if (document.forms[0].E8.value == "NaN deg." || E8 > 40){document.forms[0].E8.value = "> 40 deg."; document.forms[0].E8.style.colour="red";
# if 0.5 > math.degrees(ga) or math.degrees(ga) > 40:
# logging.warning("Failed to compute polynomial for wavelength "
# "conversion, got grating angle = %g°", math.degrees(ga))
# return [cw]
#
# # dispersion: wavelength(m)/distance(m)
# # F8a = Math.cos(Math.PI/180*(wE*1 + E8))*(1000000)/(gL*fL); // nm/mm
# # to convert from nm/mm -> m/m : *1e-6
# dispersion = math.cos(ia + ga) / (gl*fl) # m/m
# if 0 > dispersion or dispersion > 0.5e-3: # < 500 nm/mm
# logging.warning("Computed dispersion is not within expected bounds: %f nm/mm",
# dispersion * 1e6)
# return [cw]
#
# # polynomial is cw + dispersion * x
# return [cw, dispersion]
def selfTest(self):
"""
check as much as possible that it works without actually moving the motor
return (boolean): False if it detects any problem
"""
try:
with self._ser_access:
modl = self.GetModel()
if not modl.startswith("SP-"):
# accept it anyway
logging.warning("Device reports unexpected model '%s'",
modl)
turret = self.GetTurret()
if turret not in (1, 2, 3):
return False
return True
except Exception:
logging.exception("Selftest failed")
return False
@staticmethod
def scan(port=None):
"""
port (string): name of the serial port. If None, all the serial ports are tried
returns (list of 2-tuple): name, args (port)
Note: it's obviously not advised to call this function if a device is already under use
"""
if port:
ports = [port]
else:
if os.name == "nt":
ports = ["COM" + str(n) for n in range(8)]
else:
ports = glob.glob('/dev/ttyS?*') + glob.glob('/dev/ttyUSB?*')
logging.info(
"Serial ports scanning for Acton SpectraPro spectrograph in progress..."
)
found = [] # (list of 2-tuple): name, kwargs
for p in ports:
try:
logging.debug("Trying port %s", p)
dev = SpectraPro(None, None, p, _noinit=True)
except (serial.SerialException, HwError):
# not possible to use this port? next one!
continue
# Try to connect and get back some answer.
try:
model = dev.GetModel()
if model.startswith("SP-"):
found.append((model, {"port": p}))
else:
logging.info(
"Device on port '%s' responded correctly, but with unexpected model name '%s'.",
p, model)
except:
continue
return found
@staticmethod
def openSerialPort(port):
"""
Opens the given serial port the right way for the SpectraPro.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
# according to doc:
# "port set-up is 9600 baud, 8 data bits, 1 stop bit and no parity"
ser = serial.Serial(
port=port,
baudrate=9600,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=2 # s
)
return ser
class Chamber(model.Actuator):
"""
Simulated chamber component. Just pretends to be able to change pressure
"""
def __init__(self, name, role, positions, has_pressure=True, **kwargs):
"""
Initialises the component
positions (list of str): each pressure positions supported by the
component (among the allowed ones)
has_pressure (boolean): if True, has a pressure VA with the current
pressure.
"""
# TODO: or just provide .targetPressure (like .targetTemperature) ?
# Or maybe provide .targetPosition: position that would be reached if
# all the requested move were instantly applied?
chp = {}
for p in positions:
try:
chp[PRESSURES[p]] = p
except KeyError:
raise ValueError("Pressure position %s is unknown" % (p,))
axes = {"pressure": model.Axis(unit="Pa", choices=chp)}
model.Actuator.__init__(self, name, role, axes=axes, **kwargs)
# For simulating moves
self._position = PRESSURE_VENTED # last official position
self._goal = PRESSURE_VENTED
self._time_goal = 0 # time the goal was/will be reached
self._time_start = 0 # time the move started
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute(
{"pressure": self._position},
unit="Pa", readonly=True)
if has_pressure:
# Almost the same as position, but gives the current position
self.pressure = model.VigilantAttribute(self._position,
unit="Pa", readonly=True)
self._press_timer = util.RepeatingTimer(1, self._updatePressure,
"Simulated pressure update")
self._press_timer.start()
else:
self._press_timer = None
# Indicates whether the chamber is opened or not
# Just pretend it's always closed, and allow the user to change that
# for instance via CLI.
self.opened = model.BooleanVA(False)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
def terminate(self):
if self._press_timer:
self._press_timer.cancel()
self._press_timer = None
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
def _updatePressure(self):
"""
update the pressure VA (called regularly from a thread)
"""
# Compute the current pressure
now = time.time()
if self._time_goal < now: # done
# goal ±5%
pos = self._goal * random.uniform(0.95, 1.05)
else:
# TODO make it logarithmic
ratio = (now - self._time_start) / (self._time_goal - self._time_start)
pos = self._position + (self._goal - self._position) * ratio
# it's read-only, so we change it via _value
self.pressure._value = pos
self.pressure.notify(pos)
def _updatePosition(self):
"""
update the position VA
"""
# .position contains the last known/valid position
# it's read-only, so we change it via _value
self.position._value = {"pressure": self._position}
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
# convert into an absolute move
pos = {}
for a, v in shift.items:
pos[a] = self.position.value[a] + v
return self.moveAbs(pos)
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
new_pres = pos["pressure"]
est_start = time.time() + 0.1
f = model.ProgressiveFuture(start=est_start,
end=est_start + self._getDuration(new_pres))
return self._executor.submitf(f, self._changePressure, f, new_pres)
def _getDuration(self, pos):
return abs(self._position - pos) / SPEED_PUMP
def _changePressure(self, f, p):
"""
Synchronous change of the pressure
p (float): target pressure
"""
# TODO: allow to cancel during the change
now = time.time()
duration = self._getDuration(p) # s
self._time_start = now
self._time_goal = now + duration # s
self._goal = p
time.sleep(duration / 2)
# DEBUG: for testing wrong time estimation
# f.set_progress(start=self._time_start, end=self._time_goal + 10)
time.sleep(duration / 2)
self._position = p
self._updatePosition()
def stop(self, axes=None):
self._executor.cancel()
logging.warning("Stopped pressure change")
class CoupledStage(model.Actuator):
"""
Wrapper stage that takes as children the SEM sample stage and the
ConvertStage. For each move to be performed CoupledStage moves, at the same
time, both stages.
"""
def __init__(self, name, role, children, **kwargs):
"""
children (dict str -> actuator): names to ConvertStage and SEM sample stage
"""
# SEM stage
self._master = None
# Optical stage
self._slave = None
for crole, child in children.items():
# Check if children are actuators
if not isinstance(child, model.ComponentBase):
raise ValueError("Child %s is not a component." % child)
if not hasattr(child, "axes") or not isinstance(child.axes, dict):
raise ValueError("Child %s is not an actuator." % child.name)
if "x" not in child.axes or "y" not in child.axes:
raise ValueError("Child %s doesn't have both x and y axes" % child.name)
if crole == "slave":
self._slave = child
elif crole == "master":
self._master = child
else:
raise ValueError("Child given to CoupledStage must be either 'master' or 'slave', but got %s." % crole)
if self._master is None:
raise ValueError("CoupledStage needs a master child")
if self._slave is None:
raise ValueError("CoupledStage needs a slave child")
# TODO: limit the range to the minimum of master/slave?
axes_def = {}
for an in ("x", "y"):
axes_def[an] = copy.deepcopy(self._master.axes[an])
axes_def[an].canUpdate = False
model.Actuator.__init__(self, name, role, axes=axes_def, children=children,
**kwargs)
self._metadata[model.MD_HW_NAME] = "CoupledStage"
# will take care of executing axis moves asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
self._position = {}
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
# TODO: listen to master position to update the position? => but
# then it might get updated too early, before the slave has finished
# moving.
self.referenced = model.VigilantAttribute({}, readonly=True)
# listen to changes from children
for c in self.children.value:
if model.hasVA(c, "referenced"):
logging.debug("Subscribing to reference of child %s", c.name)
c.referenced.subscribe(self._onChildReferenced)
self._updateReferenced()
self._stage_conv = None
self._createConvertStage()
def updateMetadata(self, md):
self._metadata.update(md)
# Re-initialize ConvertStage with the new transformation values
# Called after every sample holder insertion
self._createConvertStage()
def _createConvertStage(self):
"""
(Re)create the convert stage, based on the metadata
"""
self._stage_conv = ConvertStage("converter-xy", "align",
children={"aligner": self._slave},
axes=["x", "y"],
scale=self._metadata.get(MD_PIXEL_SIZE_COR, (1, 1)),
rotation=self._metadata.get(MD_ROTATION_COR, 0),
translation=self._metadata.get(MD_POS_COR, (0, 0)))
# if set(self._metadata.keys()) & {MD_PIXEL_SIZE_COR, MD_ROTATION_COR, MD_POS_COR}:
# # Schedule a null relative move, just to ensure the stages are
# # synchronised again (if some metadata is provided)
# self._executor.submit(self._doMoveRel, {})
def _updatePosition(self):
"""
update the position VA
"""
mode_pos = self._master.position.value
self._position["x"] = mode_pos['x']
self._position["y"] = mode_pos['y']
pos = self._applyInversion(self._position)
self.position._set_value(pos, force_write=True)
def _onChildReferenced(self, ref):
# ref can be from any child, so we don't use it
self._updateReferenced()
def _updateReferenced(self):
"""
update the referenced VA
"""
ref = {} # str (axes name) -> boolean (is referenced)
# consider an axis referenced iff it's referenced in every referenceable children
for c in self.children.value:
if not model.hasVA(c, "referenced"):
continue
cref = c.referenced.value
for a in (set(self.axes.keys()) & set(cref.keys())):
ref[a] = ref.get(a, True) and cref[a]
self.referenced._set_value(ref, force_write=True)
def _doMoveAbs(self, pos):
"""
move to the position
"""
f = self._master.moveAbs(pos)
try:
f.result()
finally: # synchronise slave position even if move failed
# TODO: Move simultaneously based on the expected position, and
# only if the final master position is different, move again.
mpos = self._master.position.value
# Move objective lens
f = self._stage_conv.moveAbs({"x": mpos["x"], "y": mpos["y"]})
f.result()
self._updatePosition()
def _doMoveRel(self, shift):
"""
move by the shift
"""
f = self._master.moveRel(shift)
try:
f.result()
finally:
mpos = self._master.position.value
# Move objective lens
f = self._stage_conv.moveAbs({"x": mpos["x"], "y": mpos["y"]})
f.result()
self._updatePosition()
@isasync
def moveRel(self, shift):
if not shift:
shift = {"x": 0, "y": 0}
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
return self._executor.submit(self._doMoveRel, shift)
@isasync
def moveAbs(self, pos):
if not pos:
pos = self.position.value
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
return self._executor.submit(self._doMoveAbs, pos)
def stop(self, axes=None):
# Empty the queue for the given axes
self._executor.cancel()
self._master.stop(axes)
self._stage_conv.stop(axes)
logging.warning("Stopping all axes: %s", ", ".join(axes or self.axes))
def _doReference(self, axes):
fs = []
for c in self.children.value:
# only do the referencing for the stages that support it
if not model.hasVA(c, "referenced"):
continue
ax = axes & set(c.referenced.value.keys())
fs.append(c.reference(ax))
# wait for all referencing to be over
for f in fs:
f.result()
# Re-synchronize the 2 stages by moving the slave where the master is
mpos = self._master.position.value
f = self._stage_conv.moveAbs({"x": mpos["x"], "y": mpos["y"]})
f.result()
self._updatePosition()
@isasync
def reference(self, axes):
if not axes:
return model.InstantaneousFuture()
self._checkReference(axes)
return self._executor.submit(self._doReference, axes)
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
class DPSS(model.PowerSupplier):
'''
Implements the PowerSupplier class to regulate the power supply of the
Cobolt DPSS laser, connected via USB.
'''
def __init__(self, name, role, port, light_name, max_power, **kwargs):
'''
port (str): port name. Can be a pattern, in which case it will pick the
first one which responds well
ligth_name (str): the name of the component that is controlled by this
power supplier
max_power (float): maximum power, in W. Will be set at initialisation.
'''
# TODO: allow to pass the serial number, to select the right device
model.PowerSupplier.__init__(self, name, role, **kwargs)
self._light_name = light_name
self._ser_access = threading.Lock()
self._port = self._findDevice(port) # sets ._serial
logging.info("Found Cobolt DPSS device on port %s", self._port)
self._sn = self.GetSerialNumber()
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "serial driver: %s" % (driver_name, )
self._hwVersion = "Cobolt DPSS (s/n: %s)" % (self._sn, )
# Reset sequence
# TODO: do a proper one. For now it's just everything we can throw, so
# that it's a bit easier to debug
self._sendCommand("ilk?")
self._sendCommand("leds?")
self._sendCommand("@cobasky?")
self._sendCommand("cf") # Clear fault
# self._sendCommand("@cob1") # used to force the laser on after interlock opened error
# will take care of executing switch asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
# Dict str -> bool: component name -> turn on/off
self.supplied = model.VigilantAttribute({light_name: False},
readonly=True)
self._updateSupplied()
self.SetOutputPower(max_power)
# Wrapper for the actual firmware functions
def GetSerialNumber(self):
return self._sendCommand("sn?")
def SetOutputPower(self, p):
"""
p (0 < float): power in W
"""
assert 1e-6 < p < 1e6
self._sendCommand("p %.5f" % p)
def SetLaser(self, state):
"""
state (bool): True to turn on
"""
v = 1 if state else 0
self._sendCommand("l%d" %
v) # No space, as they are different commands
@isasync
def supply(self, sup):
"""
Change the power supply to the defined state for each component given.
This is an asynchronous method.
sup dict(string-> boolean): name of the component and new state
returns (Future): object to control the supply request
"""
if not sup:
return model.InstantaneousFuture()
self._checkSupply(sup)
return self._executor.submit(self._doSupply, sup)
def _doSupply(self, sup):
"""
supply power
"""
for comp, val in sup.items():
self.SetLaser(val)
self._updateSupplied()
def _updateSupplied(self):
"""
update the supplied VA
"""
res = self._sendCommand("l?")
pwrd = (res == "1")
# it's read-only, so we change it via _value
self.supplied._set_value({self._light_name: pwrd}, force_write=True)
def terminate(self):
if self._executor:
self._executor.cancel()
self._executor.shutdown()
self._executor = None
if self._serial:
self.SetLaser(
False) # TODO: allow to configure with argument to DPSS
with self._ser_access:
self._serial.close()
self._serial = None
self._file.close()
def _sendCommand(self, cmd):
"""
cmd (str): command to be sent to device (without the CR)
returns (str): answer received from the device (without \n or \r)
raises:
DPSSError: if an ERROR is returned by the device.
"""
cmd = cmd + "\r"
with self._ser_access:
logging.debug("Sending command %s", cmd.encode('string_escape'))
self._serial.write(cmd)
ans = ''
while ans[-2:] != '\r\n':
char = self._serial.read()
if not char:
raise IOError("Timeout after receiving %s" %
ans.encode('string_escape'))
ans += char
logging.debug("Received answer %s", ans.encode('string_escape'))
# TODO: check for other error answer?
# Normally the device either answers OK, or a value, for commands finishing with a "?"
if ans.startswith("Syntax error"):
raise DPSSError(ans)
return ans.rstrip()
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a Power control device.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
baudrate=115200,
timeout=1 # s
)
# Purge
ser.flush()
ser.flushInput()
# Try to read until timeout to be extra safe that we properly flushed
while True:
char = ser.read()
if char == '':
break
return ser
def _findDevice(self, ports):
"""
Look for a compatible device
ports (str): pattern for the port name
return (str): the name of the port used
It also sets ._serial and ._idn to contain the opened serial port, and
the identification string.
raises:
IOError: if no device are found
"""
# TODO: For debugging purpose
# if ports == "/dev/fake":
# self._serial = DPSSSimulator(timeout=1)
# return ports
if os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
# Ensure no one will talk to it simultaneously, and we don't talk to devices already in use
self._file = open(n) # Open in RO, just to check for lock
try:
fcntl.flock(
self._file.fileno(), fcntl.LOCK_EX
| fcntl.LOCK_NB) # Raises IOError if cannot lock
except IOError:
logging.info("Port %s is busy, will not use", n)
continue
self._serial = self._openSerialPort(n)
try:
sn = self.GetSerialNumber()
except DPSSError:
# Can happen if the device has received some weird characters
# => try again (now that it's flushed)
logging.info("Device answered by an error, will try again")
sn = self.GetSerialNumber()
return n
except (IOError, DPSSError):
logging.info(
"Skipping device on port %s, which didn't seem to be a Cobolt",
n)
# not possible to use this port? next one!
continue
else:
raise HwError(
"Failed to find a Cobolt device on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports, ))
class PMTControl(model.PowerSupplier):
'''
This represents the PMT control unit.
At start up the following is set:
* protection is on (=> gain is forced to 0)
* gain = 0
* power up
'''
def __init__(self, name, role, port, prot_time=1e-3, prot_curr=30e-6,
relay_cycle=None, powered=None, **kwargs):
'''
port (str): port name
prot_time (float): protection trip time (in s)
prot_curr (float): protection current threshold (in Amperes)
relay_cycle (None or 0<float): if not None, will power cycle the relay
with the given delay (in s)
powered (list of str or None): set of the HwComponents controlled by the relay
Raise an exception if the device cannot be opened
'''
if powered is None:
powered = []
self.powered = powered
model.PowerSupplier.__init__(self, name, role, **kwargs)
# get protection time (s) and current (A) properties
if not 0 <= prot_time < 1e3:
raise ValueError("prot_time should be a time (in s) but got %s" % (prot_time,))
self._prot_time = prot_time
if not 0 <= prot_curr <= 100e-6:
raise ValueError("prot_curr (%s A) is not between 0 and 100.e-6" % (prot_curr,))
self._prot_curr = prot_curr
# TODO: catch errors and convert to HwError
self._ser_access = threading.Lock()
self._port = self._findDevice(port) # sets ._serial
logging.info("Found PMT Control device on port %s", self._port)
# Get identification of the PMT control device
self._idn = self._getIdentification()
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "serial driver: %s" % (driver_name,)
self._hwVersion = "%s" % (self._idn,)
# Set protection current and time
self._setProtectionCurrent(self._prot_curr)
self._setProtectionTime(self._prot_time)
# gain, powerSupply and protection VAs
self.protection = model.BooleanVA(True, setter=self._setProtection,
getter=self._getProtection)
self._setProtection(True)
gain_rng = (MIN_VOLT, MAX_VOLT)
gain = self._getGain()
self.gain = model.FloatContinuous(gain, gain_rng, unit="V",
setter=self._setGain)
self.powerSupply = model.BooleanVA(True, setter=self._setPowerSupply)
self._setPowerSupply(True)
# will take care of executing supply asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# relay initialization
if relay_cycle is not None:
logging.info("Power cycling the relay for %f s", relay_cycle)
self.setRelay(False)
time.sleep(relay_cycle)
# Reset if no powered provided
if not powered:
self.setRelay(True)
else:
self._supplied = {}
self.supplied = model.VigilantAttribute(self._supplied, readonly=True)
self._updateSupplied()
def terminate(self):
if self._executor:
self._executor.cancel()
self._executor.shutdown()
self._executor = None
with self._ser_access:
if self._serial:
self._serial.close()
self._serial = None
@isasync
def supply(self, sup):
if not sup:
return model.InstantaneousFuture()
self._checkSupply(sup)
return self._executor.submit(self._doSupply, sup)
def _doSupply(self, sup):
"""
supply power
"""
value = sup.values()[0] # only care about the value
self.setRelay(value)
self._updateSupplied()
def _updateSupplied(self):
"""
update the supplied VA
"""
# update all components since they are all connected to the same switch
value = self.getRelay()
for comp in self.powered:
self._supplied[comp] = value
# it's read-only, so we change it via _value
self.supplied._value = self._supplied
self.supplied.notify(self.supplied.value)
def _getIdentification(self):
return self._sendCommand("*IDN?")
def _setGain(self, value):
self._sendCommand("VOLT %f" % (value,))
return self._getGain()
def _setProtectionCurrent(self, value):
self._sendCommand("PCURR %f" % (value * 1e6,)) # in µA
def _setProtectionTime(self, value):
self._sendCommand("PTIME %f" % (value,))
def _getGain(self):
ans = self._sendCommand("VOLT?")
try:
value = float(ans)
except ValueError:
raise IOError("Gain value cannot be converted to float.")
return value
def _setPowerSupply(self, value):
if value:
self._sendCommand("PWR 1")
else:
self._sendCommand("PWR 0")
return value
def _getPowerSupply(self):
ans = self._sendCommand("PWR?")
return ans == "1"
def _setProtection(self, value):
if value:
self._sendCommand("SWITCH 0")
else:
self._sendCommand("SWITCH 1")
return value
def _getProtection(self):
ans = self._sendCommand("SWITCH?")
return ans == "0"
# These two methods are strictly used for the SPARC system in Monash. Use
# them to send a high/low signal via the PMT Control Unit to the relay, thus
# to pull/push the relay contact and control the power supply from the power
# board to the flippers and filter wheel.
def setRelay(self, value):
# When True, the relay contact is connected
if value:
self._sendCommand("RELAY 1")
else:
self._sendCommand("RELAY 0")
return value
def getRelay(self):
ans = self._sendCommand("RELAY?")
if ans == "1":
status = True
else:
status = False
return status
def _sendCommand(self, cmd):
"""
cmd (str): command to be sent to PMT Control unit.
returns (str): answer received from the PMT Control unit
raises:
IOError: if an ERROR is returned by the PMT Control firmware.
"""
cmd = cmd + "\n"
with self._ser_access:
logging.debug("Sending command %s", cmd.encode('string_escape'))
self._serial.write(cmd)
ans = ''
char = None
while char != '\n':
char = self._serial.read()
if not char:
logging.error("Timeout after receiving %s", ans.encode('string_escape'))
# TODO: See how you should handle a timeout before you raise
# an HWError
raise HwError("PMT Control Unit connection timeout. "
"Please turn off and on the power to the box.")
# Handle ERROR coming from PMT control unit firmware
ans += char
logging.debug("Received answer %s", ans.encode('string_escape'))
if ans.startswith("ERROR"):
raise PMTControlError(ans.split(' ', 1)[1])
return ans.rstrip()
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a PMT control device.
port (string): the name of the serial port (e.g., /dev/ttyACM0)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
timeout=1 # s
)
# Purge
ser.flush()
ser.flushInput()
# Try to read until timeout to be extra safe that we properly flushed
while True:
char = ser.read()
if char == '':
break
logging.debug("Nothing left to read, PMT Control Unit can safely initialize.")
ser.timeout = 5 # Sometimes the software-based USB can have some hiccups
return ser
def _findDevice(self, ports):
"""
Look for a compatible device
ports (str): pattern for the port name
return (str): the name of the port used
It also sets ._serial and ._idn to contain the opened serial port, and
the identification string.
raises:
IOError: if no device are found
"""
# For debugging purpose
if ports == "/dev/fake":
self._serial = PMTControlSimulator(timeout=1)
return ports
if os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
self._serial = self._openSerialPort(n)
# If the device has just been inserted, odemis-relay will block
# it for 10s while reseting the relay, so be patient
try:
fcntl.flock(self._serial.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB)
except IOError:
logging.info("Port %s is busy, will wait and retry", n)
time.sleep(11)
fcntl.flock(self._serial.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB)
try:
idn = self._getIdentification()
except PMTControlError:
# Can happen if the device has received some weird characters
# => try again (now that it's flushed)
logging.info("Device answered by an error, will try again")
idn = self._getIdentification()
# Check that we connect to the right device
if not idn.startswith("Delmic Analog PMT"):
logging.info("Connected to wrong device on %s, skipping.", n)
continue
return n
except (IOError, PMTControlError):
# not possible to use this port? next one!
continue
else:
raise HwError("Failed to find a PMT Control device on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports,))
@classmethod
def scan(cls):
"""
returns (list of 2-tuple): name, args (sn)
Note: it's obviously not advised to call this function if a device is already under use
"""
logging.info("Serial ports scanning for PMT control device in progress...")
found = [] # (list of 2-tuple): name, kwargs
if sys.platform.startswith('linux'):
# Look for each ACM device, if the IDN is the expected one
acm_paths = glob.glob('/dev/ttyACM?')
for port in acm_paths:
# open and try to communicate
try:
dev = cls(name="test", role="test", port=port)
idn = dev._getIdentification()
if idn.startswith("Delmic Analog PMT"):
found.append({"port": port})
except Exception:
pass
else:
# TODO: Windows version
raise NotImplementedError("OS not yet supported")
return found
class TMCM3110(model.Actuator):
"""
Represents one Trinamic TMCM-3110 controller.
Note: it must be set to binary communication mode (that's the default).
"""
def __init__(self, name, role, port, axes, ustepsize, refproc=None, temp=False, **kwargs):
"""
port (str): port name (use /dev/fake for a simulator)
axes (list of str): names of the axes, from the 1st to the 3rd.
ustepsize (list of float): size of a microstep in m (the smaller, the
bigger will be a move for a given distance in m)
refproc (str or None): referencing (aka homing) procedure type. Use
None to indicate it's not possible (no reference/limit switch) or the
name of the procedure. For now only "2xFinalForward" is accepted.
temp (bool): if True, will read the temperature from the analogue input
(10 mV <-> 1 °C)
inverted (set of str): names of the axes which are inverted (IOW, either
empty or the name of the axis)
"""
if len(axes) != 3:
raise ValueError("Axes must be a list of 3 axis names (got %s)" % (axes,))
self._axes_names = axes # axes names in order
if len(axes) != len(ustepsize):
raise ValueError("Expecting %d ustepsize (got %s)" %
(len(axes), ustepsize))
if refproc not in {REFPROC_2XFF, REFPROC_FAKE, None}:
raise ValueError("Reference procedure %s unknown" % (refproc, ))
self._refproc = refproc
for sz in ustepsize:
if sz > 10e-3: # sz is typically ~1µm, so > 1 cm is very fishy
raise ValueError("ustepsize should be in meter, but got %g" % (sz,))
self._ustepsize = ustepsize
try:
self._serial = self._openSerialPort(port)
except serial.SerialException:
raise HwError("Failed to find device %s on port %s. Ensure it is "
"connected to the computer." % (name, port))
self._port = port
self._ser_access = threading.Lock()
self._target = 1 # Always one, when directly connected via USB
self._resynchonise()
modl, vmaj, vmin = self.GetVersion()
if modl != 3110:
logging.warning("Controller TMCM-%d is not supported, will try anyway",
modl)
if name is None and role is None: # For scan only
return
if port != "/dev/fake": # TODO: support programs in simulator
# Detect if it is "USB bus powered" by using the fact that programs
# don't run when USB bus powered
addr = 80 # big enough to not overlap with REFPROC_2XFF programs
prog = [(9, 50, 2, 1), # Set global param 50 to 1
(28,), # STOP
]
self.UploadProgram(prog, addr)
if not self._isFullyPowered():
# Only a warning, at the power can be connected afterwards
logging.warning("Device %s has no power, the motor will not move", name)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
axes_def = {}
for n, sz in zip(self._axes_names, self._ustepsize):
# Mov abs supports ±2³¹ but the actual position is only within ±2²³
rng = [(-2 ** 23) * sz, (2 ** 23 - 1) * sz]
# Probably not that much, but there is no info unless the axis has
# limit switches and we run a referencing
axes_def[n] = model.Axis(range=rng, unit="m")
model.Actuator.__init__(self, name, role, axes=axes_def, **kwargs)
for i, a in enumerate(self._axes_names):
self._init_axis(i)
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "%s (serial driver: %s)" % (odemis.__version__, driver_name)
self._hwVersion = "TMCM-%d (firmware %d.%02d)" % (modl, vmaj, vmin)
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
# TODO: add support for changing speed. cf p.68: axis param 4 + p.81 + TMC 429 p.6
self.speed = model.VigilantAttribute({}, unit="m/s", readonly=True)
self._updateSpeed()
if refproc is not None:
# str -> boolean. Indicates whether an axis has already been referenced
axes_ref = dict([(a, False) for a in axes])
self.referenced = model.VigilantAttribute(axes_ref, readonly=True)
if temp:
# One sensor is at the top, one at the bottom of the sample holder.
# The most interesting is the temperature difference, so just
# report both.
self.temperature = model.FloatVA(0, unit=u"°C", readonly=True)
self.temperature1 = model.FloatVA(0, unit=u"°C", readonly=True)
self._temp_timer = util.RepeatingTimer(10, self._updateTemperatureVA,
"TMCM temperature update")
self._updateTemperatureVA() # make sure the temperature is correct
self._temp_timer.start()
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown(wait=True)
self._executor = None
if hasattr(self, "_temp_timer"):
self._temp_timer.cancel()
del self._temp_timer
with self._ser_access:
if self._serial:
self._serial.close()
self._serial = None
def _init_axis(self, axis):
"""
Initialise the given axis with "good" values for our needs (Delphi)
axis (int): axis number
"""
self.SetAxisParam(axis, 4, 1398) # maximum velocity to 1398 == 2 mm/s
self.SetAxisParam(axis, 5, 7) # maximum acc to 7 == 20 mm/s2
self.SetAxisParam(axis, 140, 8) # number of usteps ==2^8 =256 per fullstep
self.SetAxisParam(axis, 6, 15) # maximum RMS-current to 15 == 15/255 x 2.8 = 165mA
self.SetAxisParam(axis, 7, 0) # standby current to 0
self.SetAxisParam(axis, 204, 100) # power off after 100 ms standstill
self.SetAxisParam(axis, 154, 0) # step divider to 0 ==2^0 ==1
self.SetAxisParam(axis, 153, 0) # acc divider to 0 ==2^0 ==1
self.SetAxisParam(axis, 163, 0) # chopper mode
self.SetAxisParam(axis, 162, 2) # Chopper blank time (1 = for low current applications)
self.SetAxisParam(axis, 167, 3) # Chopper off time (2 = minimum)
self.MoveRelPos(axis, 0) # activate parameter with dummy move
if self._refproc == REFPROC_2XFF:
# set up the programs needed for the referencing
# Interrupt: stop the referencing
# The original idea was to mark the current position as 0 ASAP, and then
# later on move back to there. Now, we just stop ASAP, and hope it
# takes always the same time to stop. This allows to read how far from
# a previous referencing position we were during the testing.
prog = [# (6, 1, axis), # GAP 1, Motid # read pos
# (35, 60 + axis, 2), # AGP 60, 2 # save pos to 2/60
# (32, 10 + axis, axis), # CCO 10, Motid // Save the current position # doesn't work??
# TODO: see if it's needed to do like in original procedure: set 0 ASAP
# (5, 1, axis, 0), # SAP 1, MotId, 0 // Set actual pos 0
(13, 1, axis), # RFS STOP, MotId // Stop the reference search
(38,), # RETI
]
addr = 50 + 10 * axis # at addr 50/60/70
self.UploadProgram(prog, addr)
# Program: start and wait for referencing
# It's independent enough that even if the controlling computer
# stops during the referencing the motor will always eventually stop.
timeout = 20 # s (it can take up to 20 s to reach the home as fast speed)
timeout_ticks = int(round(timeout * 100)) # 1 tick = 10 ms
gparam = 50 + axis
addr = 0 + 15 * axis # Max with 3 axes: ~40
prog = [(9, gparam, 2, 0), # Set global param to 0 (=running)
(13, 0, axis), # RFS START, MotId
(27, 4, axis, timeout_ticks), # WAIT RFS until timeout
(21, 8, 0, addr + 6), # JC ETO, to TIMEOUT (= +6)
(9, gparam, 2, 1), # Set global param to 1 (=all went fine)
(28,), # STOP
(13, 1, axis), # TIMEOUT: RFS STOP, Motid
(9, gparam, 2, 2), # Set global param to 2 (=RFS timed-out)
(28,), # STOP
]
self.UploadProgram(prog, addr)
# Communication functions
@staticmethod
def _instr_to_str(instr):
"""
instr (buffer of 9 bytes)
"""
target, n, typ, mot, val, chk = struct.unpack('>BBBBiB', instr)
s = "%d, %d, %d, %d, %d (%d)" % (target, n, typ, mot, val, chk)
return s
@staticmethod
def _reply_to_str(rep):
"""
rep (buffer of 9 bytes)
"""
ra, rt, status, rn, rval, chk = struct.unpack('>BBBBiB', rep)
s = "%d, %d, %d, %d, %d (%d)" % (ra, rt, status, rn, rval, chk)
return s
def _resynchonise(self):
"""
Ensures the device communication is "synchronised"
"""
with self._ser_access:
self._serial.flushInput()
garbage = self._serial.read(1000)
if garbage:
logging.debug("Received unexpected bytes '%s'", garbage)
if len(garbage) == 1000:
# Probably a sign that it's not the device we are expecting
logging.warning("Lots of garbage sent from device")
# In case the device has received some data before, resynchronise by
# sending one byte at a time until we receive a reply.
# On Ubuntu, when plugging the device, udev automatically checks
# whether this is a real modem, which messes up everything immediately.
# As there is no command 0, either we will receive a "wrong command" or
# a "wrong checksum", but it's unlikely to ever do anything more.
for i in range(9): # a message is 9 bytes
self._serial.write(b"\x00")
self._serial.flush()
res = self._serial.read(9)
if len(res) == 9:
break # just got synchronised
elif len(res) == 0:
continue
else:
logging.error("Device not answering with a 9 bytes reply: %s", res)
else:
logging.error("Device not answering to a 9 bytes message")
# TODO: finish this method and use where possible
def SendInstructionRecoverable(self, n, typ=0, mot=0, val=0):
try:
self.SendInstruction(n, typ, mot, val)
except IOError:
# TODO: could serial.outWaiting() give a clue on what is going on?
# One possible reason is that the device disappeared because the
# cable was pulled out, or the power got cut (unlikely, as it's
# powered via 2 sources).
# TODO: detect that the connection was lost if the port we have
# leads to nowhere. => It seems os.path.exists should fail ?
# or /proc/pid/fd/n link to a *(deleted)
# How to handle the fact it will then probably get a different name
# on replug? Use a pattern for the file name?
self._resynchonise()
def SendInstruction(self, n, typ=0, mot=0, val=0):
"""
Sends one instruction, and return the reply.
n (0<=int<=255): instruction ID
typ (0<=int<=255): instruction type
mot (0<=int<=255): motor/bank number
val (0<=int<2**32): value to send
return (0<=int<2**32): value of the reply (if status is good)
raises:
IOError: if problem with sending/receiving data over the serial port
TMCLError: if status if bad
"""
msg = numpy.empty(9, dtype=numpy.uint8)
struct.pack_into('>BBBBiB', msg, 0, self._target, n, typ, mot, val, 0)
# compute the checksum (just the sum of all the bytes)
msg[-1] = numpy.sum(msg[:-1], dtype=numpy.uint8)
with self._ser_access:
logging.debug("Sending %s", self._instr_to_str(msg))
self._serial.write(msg)
self._serial.flush()
while True:
res = self._serial.read(9)
if len(res) < 9: # TODO: TimeoutError?
raise IOError("Received only %d bytes after %s" %
(len(res), self._instr_to_str(msg)))
logging.debug("Received %s", self._reply_to_str(res))
ra, rt, status, rn, rval, chk = struct.unpack('>BBBBiB', res)
# Check it's a valid message
npres = numpy.frombuffer(res, dtype=numpy.uint8)
good_chk = numpy.sum(npres[:-1], dtype=numpy.uint8)
if chk == good_chk:
if rt != self._target:
logging.warning("Received a message from %d while expected %d",
rt, self._target)
if rn != n:
logging.info("Skipping a message about instruction %d (waiting for %d)",
rn, n)
continue
if not status in TMCL_OK_STATUS:
raise TMCLError(status, rval, self._instr_to_str(msg))
else:
# TODO: investigate more why once in a while (~1/1000 msg)
# the message is garbled
logging.warning("Message checksum incorrect (%d), will assume it's all fine", chk)
return rval
# Low level functions
def GetVersion(self):
"""
return (int, int, int):
Controller ID: 3110 for the TMCM-3110
Firmware major version number
Firmware minor version number
"""
val = self.SendInstruction(136, 1) # Ask for binary reply
cont = val >> 16
vmaj, vmin = (val & 0xff00) >> 8, (val & 0xff)
return cont, vmaj, vmin
def GetAxisParam(self, axis, param):
"""
Read the axis/parameter setting from the RAM
axis (0<=int<=2): axis number
param (0<=int<=255): parameter number
return (0<=int): the value stored for the given axis/parameter
"""
val = self.SendInstruction(6, param, axis)
return val
def SetAxisParam(self, axis, param, val):
"""
Write the axis/parameter setting from the RAM
axis (0<=int<=2): axis number
param (0<=int<=255): parameter number
val (int): the value to store
"""
self.SendInstruction(5, param, axis, val)
def GetGlobalParam(self, bank, param):
"""
Read the parameter setting from the RAM
bank (0<=int<=2): bank number
param (0<=int<=255): parameter number
return (0<=int): the value stored for the given bank/parameter
"""
val = self.SendInstruction(10, param, bank)
return val
def SetGlobalParam(self, bank, param, val):
"""
Write the parameter setting from the RAM
bank (0<=int<=2): bank number
param (0<=int<=255): parameter number
val (int): the value to store
"""
self.SendInstruction(9, param, bank, val)
def GetIO(self, bank, port):
"""
Read the input/output value
bank (0<=int<=2): bank number
port (0<=int<=255): port number
return (0<=int): the value read from the given bank/port
"""
val = self.SendInstruction(15, port, bank)
return val
def GetCoordinate(self, axis, num):
"""
Read the axis/parameter setting from the RAM
axis (0<=int<=2): axis number
num (0<=int<=20): coordinate number
return (0<=int): the coordinate stored
"""
val = self.SendInstruction(30, num, axis)
return val
def MoveAbsPos(self, axis, pos):
"""
Requests a move to an absolute position. This is non-blocking.
axis (0<=int<=2): axis number
pos (-2**31 <= int 2*31-1): position
"""
self.SendInstruction(4, 0, axis, pos) # 0 = absolute
def MoveRelPos(self, axis, offset):
"""
Requests a move to a relative position. This is non-blocking.
axis (0<=int<=2): axis number
offset (-2**31 <= int 2*31-1): relative position
"""
self.SendInstruction(4, 1, axis, offset) # 1 = relative
# it returns the expected final absolute position
def MotorStop(self, axis):
self.SendInstruction(3, mot=axis)
def StartRefSearch(self, axis):
self.SendInstruction(13, 0, axis) # 0 = start
def StopRefSearch(self, axis):
self.SendInstruction(13, 1, axis) # 1 = stop
def GetStatusRefSearch(self, axis):
"""
return (bool): False if reference is not active, True if reference is active.
"""
val = self.SendInstruction(13, 2, axis) # 2 = status
return (val != 0)
def _isOnTarget(self, axis):
"""
return (bool): True if the target position is reached
"""
reached = self.GetAxisParam(axis, 8)
return (reached != 0)
def UploadProgram(self, prog, addr):
"""
Upload a program in memory
prog (sequence of tuples of 4 ints): list of the arguments for SendInstruction
addr (int): starting address of the program
"""
# cf TMCL reference p. 50
# http://pandrv.com/ttdg/phpBB3/viewtopic.php?f=13&t=992
# To download a TMCL program into a module, the following steps have to be performed:
# - Send the "enter download mode command" to the module (command 132 with value as address of the program)
# - Send your commands to the module as usual (status byte return 101)
# - Send the "exit download mode" command (command 133 with all 0)
# Each instruction is numbered +1, starting from 0
self.SendInstruction(132, val=addr)
for inst in prog:
# TODO: the controller sometimes fails to return the correct response
# when uploading a program... not sure why, but for now we hope it
# worked anyway.
try:
self.SendInstruction(*inst)
except IOError:
logging.warning("Controller returned wrong answer, but will assume it's fine")
self.SendInstruction(133)
def RunProgram(self, addr):
"""
Run the progam at the given address
addr (int): starting address of the program
"""
self.SendInstruction(129, typ=1, val=addr) # type 1 = use specified address
# To check the program runs (ie, it's not USB bus powered), you can
# check the program counter increases:
# assert self.GetGlobalParam(0, 130) > addr
def StopProgram(self):
"""
Stop a progam if any is running
"""
self.SendInstruction(128)
def SetInterrupt(self, id, addr):
"""
Associate an interrupt to run a program at the given address
id (int): interrupt number
addr (int): starting address of the program
"""
# Note: interrupts seem to only be executed when a program is running
self.SendInstruction(37, typ=id, val=addr)
def EnableInterrupt(self, id):
"""
Enable an interrupt
See global parameters to configure the interrupts
id (int): interrupt number
"""
self.SendInstruction(25, typ=id)
def DisableInterrupt(self, id):
"""
Disable an interrupt
See global parameters to configure the interrupts
id (int): interrupt number
"""
self.SendInstruction(26, typ=id)
def _setInputInterrupt(self, axis):
"""
Setup the input interrupt handler for stopping the reference search
axis (int): axis number
"""
addr = 50 + 10 * axis # at addr 50/60/70
intid = 40 + axis # axis 0 = IN1 = 40
self.SetInterrupt(intid, addr)
self.SetGlobalParam(3, intid, 3) # configure the interrupt: look at both edges
self.EnableInterrupt(intid)
self.EnableInterrupt(255) # globally switch on interrupt processing
def _isFullyPowered(self):
"""
return (boolean): True if the device is "self-powered" (meaning the
motors will be able to move) or False if the device is "USB bus powered"
(meaning it does answer to the computer, but nothing more).
"""
# We use a strange fact that programs will not run if the device is not
# self-powered.
gparam = 50
self.SetGlobalParam(2, gparam, 0)
self.RunProgram(80) # our stupid program address
time.sleep(0.01) # 10 ms should be more than enough to run one instruction
status = self.GetGlobalParam(2, gparam)
return (status == 1)
def _doInputReference(self, axis, speed):
"""
Run synchronously one reference search
axis (int): axis number
speed (int): speed in (funky) hw units for the move
return (bool): True if the search was done in the positive direction,
otherwise False
raise:
TimeoutError: if the search failed within a timeout (20s)
"""
timeout = 20 # s
# Set speed
self.SetAxisParam(axis, 194, speed) # maximum home velocity
self.SetAxisParam(axis, 195, speed) # maximum switching point velocity (useless for us)
# Set direction
edge = self.GetIO(0, 1 + axis) # IN1 = bank 0, port 1->3
logging.debug("Going to do reference search in dir %d", edge)
if edge == 1: # Edge is high, so we need to go positive dir
self.SetAxisParam(axis, 193, 7 + 128) # RFS with positive dir
else: # Edge is low => go negative dir
self.SetAxisParam(axis, 193, 8) # RFS with negative dir
gparam = 50 + axis
self.SetGlobalParam(2, gparam, 0)
# Run the basic program (we need one, otherwise interrupt handlers are
# not processed)
addr = 0 + 15 * axis
endt = time.time() + timeout + 2 # +2 s to let the program first timeout
self.RunProgram(addr)
# Wait until referenced
status = self.GetGlobalParam(2, gparam)
while status == 0:
time.sleep(0.01)
status = self.GetGlobalParam(2, gparam)
if time.time() > endt:
self.StopRefSearch(axis)
self.StopProgram()
self.MotorStop(axis)
raise IOError("Timeout during reference search from device")
if status == 2:
# if timed out raise
raise IOError("Timeout during reference search dir %d" % edge)
return (edge == 1)
# Special methods for referencing
def _startReferencing(self, axis):
"""
Do the referencing (this is synchronous). The current implementation
only supports one axis referencing at a time.
raise:
IOError: if timeout happen
"""
logging.info("Starting referencing of axis %d", axis)
if self._refproc == REFPROC_2XFF:
if not self._isFullyPowered():
raise IOError("Device is not powered, so motors cannot move")
# Procedure devised by NTS:
# It requires the ref signal to be active for half the length. Like:
# ___________________ 1
# |
# 0 ___________________|
# ----------------------------------------> forward
# It first checks on which side of the length the actuator is, and
# then goes towards the edge. If the movement was backward, then
# it does the search a second time forward, to increase the
# repeatability.
# All this is done twice, once a fast speed finishing with negative
# direction, then at slow speed to increase precision, finishing
# in positive direction. Note that as the fast speed finishes with
# negative direction, normally only one run (in positive direction)
# is required on slow speed.
# Note also that the reference signal is IN1-3, instead of the
# official "left/home switches". It seems the reason is that it was
# because when connecting a left switch, a right switch must also
# be connected, but that's very probably false. Because of that,
# we need to set an interrupt to stop the RFS command when the edge
# changes. As interrupts only work when a program is running, we
# have a small program that waits for the RFS and report the status.
# In conclusion, RFS is used pretty much just to move at a constant
# speed.
# Note also that it seem "negative/positive" direction of the RFS
# are opposite to the move relative negative/positive direction.
try:
self._setInputInterrupt(axis)
# TODO: be able to cancel (=> set a flag + call RFS STOP)
pos_dir = self._doInputReference(axis, 350) # fast (~0.5 mm/s)
if pos_dir: # always finish first by negative direction
self._doInputReference(axis, 350) # fast (~0.5 mm/s)
# Go back far enough that the slow referencing always need quite
# a bit of move. This is not part of the official NTS procedure
# but without that, the final reference position is affected by
# the original position.
self.MoveRelPos(axis, -20000) # ~ 100µm
for i in range(100):
time.sleep(0.01)
if self._isOnTarget(axis):
break
else:
logging.warning("Relative move failed to finish in time")
pos_dir = self._doInputReference(axis, 50) # slow (~0.07 mm/s)
if not pos_dir: # if it was done in negative direction (unlikely), redo
logging.debug("Doing one last reference move, in positive dir")
# As it always wait for the edge to change, the second time
# should be positive
pos_dir = self._doInputReference(axis, 50)
if not pos_dir:
logging.warning("Second reference search was again in negative direction")
finally:
# Disable interrupt
intid = 40 + axis # axis 0 = IN1 = 40
self.DisableInterrupt(intid)
# TODO: to support multiple axes referencing simultaneously,
# only this global interrupt would need to be handle globally
# (= only disable iff noone needs interrupt).
self.DisableInterrupt(255)
# For safety, but also necessary to make sure SetAxisParam() works
self.MotorStop(axis)
# Reset the absolute 0 (by setting current pos to 0)
logging.debug("Changing referencing position by %d", self.GetAxisParam(axis, 1))
self.SetAxisParam(axis, 1, 0)
elif self._refproc == REFPROC_FAKE:
logging.debug("Simulating referencing")
self.MotorStop(axis)
self.SetAxisParam(axis, 1, 0)
else:
raise NotImplementedError("Unknown referencing procedure %s" % self._refproc)
# high-level methods (interface)
def _updatePosition(self, axes=None):
"""
update the position VA
axes (set of str): names of the axes to update or None if all should be
updated
"""
if axes is None:
axes = self._axes_names
pos = self.position.value
for i, n in enumerate(self._axes_names):
if n in axes:
# param 1 = current position
pos[n] = self.GetAxisParam(i, 1) * self._ustepsize[i]
# it's read-only, so we change it via _value
self.position._value = pos
self.position.notify(self.position.value)
def _updateSpeed(self):
"""
Update the speed VA from the controller settings
"""
speed = {}
# As described in section 3.4.1:
# fCLK * velocity
# usf = ------------------------
# 2**pulse_div * 2048 * 32
for i, n in enumerate(self._axes_names):
velocity = self.GetAxisParam(i, 4)
pulse_div = self.GetAxisParam(i, 154)
# fCLK = 16 MHz
usf = (16e6 * velocity) / (2 ** pulse_div * 2048 * 32)
speed[n] = usf * self._ustepsize[i] # m/s
# it's read-only, so we change it via _value
self.speed._value = speed
self.speed.notify(self.speed.value)
def _updateTemperatureVA(self):
"""
Update the temperature VAs, assuming that the 2 analogue inputs are
connected to a temperature sensor with mapping 10 mV <-> 1 °C. That's
conveniently what is in the Delphi.
"""
try:
# The analogue port return 0..4095 -> 0..10 V
val = self.GetIO(1, 0) # 0 = first (analogue) port
v = val * 10 / 4095 # V
t0 = v / 10e-3 # °C
val = self.GetIO(1, 4) # 4 = second (analogue) port
v = val * 10 / 4095 # V
t1 = v / 10e-3 # °C
except Exception:
logging.exception("Failed to read the temperature")
return
logging.info("Temperature 0 = %g °C, temperature 1 = %g °C", t0, t1)
self.temperature._value = t0
self.temperature.notify(t0)
self.temperature1._value = t1
self.temperature1.notify(t1)
def _createFuture(self):
"""
Return (CancellableFuture): a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event() # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
shift = self._applyInversionRel(shift)
# Check if the distance is big enough to make sense
for an, v in shift.items():
aid = self._axes_names.index(an)
if abs(v) < self._ustepsize[aid]:
# TODO: store and accumulate all the small moves instead of dropping them?
del shift[an]
logging.info("Dropped too small move of %f m", abs(v))
if not shift:
return model.InstantaneousFuture()
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversionRel(pos)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
moveAbs.__doc__ = model.Actuator.moveAbs.__doc__
@isasync
def reference(self, axes):
if not axes:
return model.InstantaneousFuture()
self._checkReference(axes)
f = self._executor.submit(self._doReference, axes)
return f
reference.__doc__ = model.Actuator.reference.__doc__
def stop(self, axes=None):
self._executor.cancel()
def _doMoveRel(self, future, pos):
"""
Blocking and cancellable relative move
future (Future): the future it handles
pos (dict str -> float): axis name -> relative target position
"""
with future._moving_lock:
end = 0 # expected end
moving_axes = set()
for an, v in pos.items():
aid = self._axes_names.index(an)
moving_axes.add(aid)
usteps = int(round(v / self._ustepsize[aid]))
self.MoveRelPos(aid, usteps)
# compute expected end
dur = abs(usteps) * self._ustepsize[aid] / self.speed.value[an]
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
logging.debug("move successfully completed")
def _doMoveAbs(self, future, pos):
"""
Blocking and cancellable absolute move
future (Future): the future it handles
pos (dict str -> float): axis name -> absolute target position
"""
with future._moving_lock:
end = 0 # expected end
old_pos = self.position.value
moving_axes = set()
for an, v in pos.items():
aid = self._axes_names.index(an)
moving_axes.add(aid)
usteps = int(round(v / self._ustepsize[aid]))
self.MoveAbsPos(aid, usteps)
# compute expected end
dur = abs(v - old_pos[an]) / self.speed.value[an]
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
logging.debug("move successfully completed")
def _waitEndMove(self, future, axes, end=0):
"""
Wait until all the given axes are finished moving, or a request to
stop has been received.
future (Future): the future it handles
axes (set of int): the axes IDs to check
end (float): expected end time
raise:
CancelledError: if cancelled before the end of the move
"""
moving_axes = set(axes)
last_upd = time.time()
last_axes = moving_axes.copy()
try:
while not future._must_stop.is_set():
for aid in moving_axes.copy(): # need copy to remove during iteration
if self._isOnTarget(aid):
moving_axes.discard(aid)
if not moving_axes:
# no more axes to wait for
return
# Update the position from time to time (10 Hz)
if time.time() - last_upd > 0.1 or last_axes != moving_axes:
last_names = set(self._axes_names[i] for i in last_axes)
self._updatePosition(last_names)
last_upd = time.time()
last_axes = moving_axes.copy()
# Wait half of the time left (maximum 0.1 s)
left = end - time.time()
sleept = max(0, min(left / 2, 0.1))
future._must_stop.wait(sleept)
logging.debug("Move of axes %s cancelled before the end", axes)
# stop all axes still moving them
for i in moving_axes:
self.MotorStop(i)
future._was_stopped = True
raise CancelledError()
finally:
self._updatePosition() # update (all axes) with final position
def _doReference(self, axes):
"""
Actually runs the referencing code
axes (set of str)
"""
# do the referencing for each axis
for a in axes:
aid = self._axes_names.index(a)
self._startReferencing(aid)
# TODO: handle cancellation
# If not cancelled and successful, update .referenced
# We only notify after updating the position so that when a listener
# receives updates both values are already updated.
for a in axes:
self.referenced._value[a] = True
self._updatePosition(axes) # all the referenced axes should be back to 0
# read-only so manually notify
self.referenced.notify(self.referenced.value)
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set() # tell the thread taking care of the move it's over
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a Thorlabs APT device.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
# For debugging purpose
if port == "/dev/fake":
return TMCM3110Simulator(timeout=0.1)
ser = serial.Serial(
port=port,
baudrate=9600, # TODO: can be changed by RS485 setting p.85?
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=0.1 # s
)
return ser
@classmethod
def scan(cls):
"""
returns (list of 2-tuple): name, args (sn)
Note: it's obviously not advised to call this function if a device is already under use
"""
# TODO: use serial.tools.list_ports.comports() (but only availabe in pySerial 2.6)
if os.name == "nt":
ports = ["COM" + str(n) for n in range (0, 8)]
else:
ports = glob.glob('/dev/ttyACM?*')
logging.info("Scanning for TMCM controllers in progress...")
found = [] # (list of 2-tuple): name, args (port, axes(channel -> CL?)
for p in ports:
try:
logging.debug("Trying port %s", p)
dev = cls(None, None, p, axes=["x", "y", "z"],
ustepsize=[10e-9, 10e-9, 10e-9])
modl, vmaj, vmin = dev.GetVersion()
# TODO: based on the model name (ie, the first number) deduce
# the number of axes
except (serial.SerialException, IOError):
# not possible to use this port? next one!
continue
except Exception:
logging.exception("Error while communicating with port %s", p)
continue
found.append(("TMCM-%s" % modl,
{"port": p,
"axes": ["x", "y", "z"],
"ustepsize": [10e-9, 10e-9, 10e-9]})
)
return found
class SpectraPro(model.Actuator):
def __init__(self, name, role, port, turret=None, _noinit=False, **kwargs):
"""
port (string): name of the serial port to connect to.
turret (None or 1<=int<=3): turret number set-up. If None, consider that
the current turret known by the device is correct.
inverted (None): it is not allowed to invert the axes
_noinit (boolean): for internal use only, don't try to initialise the device
"""
if kwargs.get("inverted", None):
raise ValueError("Axis of spectrograph cannot be inverted")
# start with this opening the port: if it fails, we are done
try:
self._serial = self.openSerialPort(port)
except serial.SerialException:
raise HwError("Failed to find spectrograph %s (on port '%s'). "
"Check the device is turned on and connected to the "
"computer. You might need to turn it off and on again."
% (name, port))
self._port = port
# to acquire before sending anything on the serial port
self._ser_access = threading.Lock()
self._try_recover = False
if _noinit:
return
self._initDevice()
self._try_recover = True
# according to the model determine how many gratings per turret
model_name = self.GetModel()
self.max_gratings = MAX_GRATINGS_NUM.get(model_name, 3)
if turret is not None:
if turret < 1 or turret > self.max_gratings:
raise ValueError("Turret number given is %s, while expected a value between 1 and %d" %
(turret, self.max_gratings))
self.SetTurret(turret)
self._turret = turret
else:
self._turret = self.GetTurret()
# for now, it's fixed (and it's unlikely to be useful to allow less than the max)
max_speed = 1000e-9 / 10 # about 1000 nm takes 10s => max speed in m/s
self.speed = model.MultiSpeedVA(max_speed, range=[max_speed, max_speed], unit="m/s",
readonly=True)
gchoices = self.GetGratingChoices()
# remove the choices which are not valid for the current turret
for c in gchoices:
t = 1 + (c - 1) // self.max_gratings
if t != self._turret:
del gchoices[c]
# TODO: report the grating with its wavelength range (possible to compute from groove density + blaze wl?)
# range also depends on the max grating angle (40°, CCD pixel size, CCD horizontal size, focal length,+ efficienty curve?)
# cf http://www.roperscientific.de/gratingcalcmaster.html
# TODO: a more precise way to find the maximum wavelength (looking at the available gratings?)
# TODO: what's the min? 200nm seems the actual min working, although wavelength is set to 0 by default !?
axes = {"wavelength": model.Axis(unit="m", range=(0, 2400e-9),
speed=(max_speed, max_speed)),
"grating": model.Axis(choices=gchoices)
}
# provides a ._axes
model.Actuator.__init__(self, name, role, axes=axes, **kwargs)
# set HW and SW version
self._swVersion = "%s (serial driver: %s)" % (odemis.__version__, driver.getSerialDriver(port))
self._hwVersion = "%s (s/n: %s)" % (model_name, (self.GetSerialNumber() or "Unknown"))
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
pos = {"wavelength": self.GetWavelength(),
"grating": self.GetGrating()}
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute(pos, unit="m", readonly=True)
# store focal length and inclusion angle for the polynomial computation
try:
self._focal_length = FOCAL_LENGTH_OFFICIAL[model_name]
self._inclusion_angle = math.radians(INCLUSION_ANGLE_OFFICIAL[model_name])
except KeyError:
self._focal_length = None
self._inclusion_angle = None
# Low-level methods: to access the hardware (should be called with the lock acquired)
def _sendOrder(self, *args, **kwargs):
"""
Send a command which does not expect any report back (just OK)
com (str): command to send (non including the \r)
raise
SPError: if the command doesn't answer the expected OK.
IOError: in case of timeout
"""
# same as a query but nothing to do with the response
self._sendQuery(*args, **kwargs)
def _sendQuery(self, com, timeout=1):
"""
Send a command which expects a report back (in addition to the OK)
com (str): command to send (non including the \r)
timeout (0<float): maximum read timeout for the response
return (str): the response received (without the ok)
raises:
SPError: if the command doesn't answer the expected OK.
IOError: in case of timeout
"""
# All commands or strings of commands must be terminated with a carriage
# return (0D hex). The monochromator responds to a command when the
# command has been completed by returning the characters " ok" followed by
# carriage return and line feed (hex ASCII sequence 20 6F 6B 0D 0A).
# Examples of error answers:
#MODEL\r
# \x00X\xf0~\x00X\xf0~MODEL ? \r\n
#?\r
# \r\nAddress Error \r\nA=3F4F4445 PC=81444
assert(len(com) > 1 and len(com) <= 100) # commands cannot be long
com += "\r"
logging.debug("Sending: %s", com.encode('string_escape'))
# send command until it succeeds
while True:
try:
self._serial.write(com)
break
except IOError:
if self._try_recover:
self._tryRecover()
else:
raise
# read response until timeout or known end of response
response = ""
timeend = time.time() + timeout
while ((time.time() <= timeend) and
not (response.endswith(" ok\r\n") or response.endswith("? \r\n"))):
self._serial.timeout = max(0.1, timeend - time.time())
char = self._serial.read()
if not char: # timeout
break
response += char
logging.debug("Received: %s", response.encode('string_escape'))
if response.endswith(" ok\r\n"):
return response[:-5]
else:
# if the device hasn't answered anything, it might have been disconnected
if len(response) == 0:
if self._try_recover:
self._tryRecover()
else:
raise IOError("Device timeout after receiving '%s'." % response.encode('string_escape'))
else: # just non understood command
# empty the serial port
self._serial.timeout = 0.1
garbage = self._serial.read(100)
if len(garbage) == 100:
raise IOError("Device keeps sending data")
response += garbage
raise SPError("Sent '%s' and received error: '%s'" %
(com.encode('string_escape'), response.encode('string_escape')))
def _tryRecover(self):
# no other access to the serial port should be done
# so _ser_access should already be acquired
# Retry to open the serial port (in case it was unplugged)
while True:
try:
self._serial.close()
self._serial = None
except:
pass
try:
logging.debug("retrying to open port %s", self._port)
self._serial = self.openSerialPort(self._port)
except IOError:
time.sleep(2)
except Exception:
logging.exception("Unexpected error while trying to recover device")
raise
else:
break
self._try_recover = False # to avoid recursion
self._initDevice()
self._try_recover = True
def _initDevice(self):
# If no echo is desired, the command NO-ECHO will suppress the echo. The
# command ECHO will return the SP-2150i to the default echo state.
#
# If is connected via the real serial port (not USB), it is in echo
# mode, so we first need to disable it, while allowing echo of the
# command we've just sent.
try:
r = self._sendOrder("no-echo")
except SPError:
logging.info("Failed to disable echo, hopping the device has not echo anyway")
# empty the serial port
self._serial.timeout = 0.1
garbage = self._serial.read(100)
if len(garbage) == 100:
raise IOError("Device keeps sending data")
def GetTurret(self):
"""
returns (1 <= int <= 3): the current turret number
"""
# ?TURRET Returns the correctly installed turret numbered 1 - 3
res = self._sendQuery("?turret")
val = int(res)
if val < 1 or val > 3:
raise SPError("Unexpected turret number '%s'" % res)
return val
def SetTurret(self, t):
"""
Set the number of the current turret (for correct settings by the hardware)
t (1 <= int <= 3): the turret number
Raise:
ValueError if the turret has no grating configured
"""
# TURRET Specifies the presently installed turret or the turret to be installed.
# Doesn't change the hardware, just which gratings are available
assert(1 <= t and t <= 3)
# TODO check that there is grating configured for this turret (using GetGratingChoices)
self._sendOrder("%d turret" % t)
# regex to read the gratings
RE_NOTINSTALLED = re.compile("\D*(\d+)\s+Not Installed")
RE_INSTALLED = re.compile("\D*(\d+)\s+(\d+)\s*g/mm BLZ=\s*([0-9][.0-9]*)\s*(nm|NM|um|UM)")
RE_GRATING = re.compile("\D*(\d+)\s+(.+\S)\s*\r")
def GetGratingChoices(self):
"""
return (dict int -> string): grating number to description
"""
# ?GRATINGS Returns the list of installed gratings with position groove density and blaze. The
# present grating is specified with an arrow.
# Example output:
# \r\n 1 300 g/mm BLZ= 500NM \r\n\x1a2 300 g/mm BLZ= 750NM \r\n 3 Not Installed \r\n 4 Not Installed \r\n 5 Not Installed \r\n 6 Not Installed \r\n 7 Not Installed \r\n 8 Not Installed \r\n ok\r\n
# \r\n\x1a1 600 g/mm BLZ= 1.6UM \r\n 2 150 g/mm BLZ= 2UM \r\n 3 Not Installed \r\n 4 Not Installed \r\n 5 Not Installed \r\n 6 Not Installed \r\n 7 Not Installed \r\n 8 Not Installed \r\n 9 Not Installed \r\n ok\r\n
# From the spectrapro_300i_ll.c of fsc2, it seems the format is:
# non-digit*,digits=grating number,spaces,"Not Installed"\r\n
# non-digit*,digits=grating number,space+,digit+:g/mm,space*,"g/mm BLZ=", space*,digit+:blaze wl in nm,space*,"nm"\r\n
res = self._sendQuery("?gratings")
gratings = {}
for line in res[:-1].split("\n"): # avoid the last \n to not make an empty last line
m = self.RE_NOTINSTALLED.search(line)
if m:
logging.debug("Decoded grating %s as not installed, skipping.", m.group(1))
continue
m = self.RE_GRATING.search(line)
if not m:
logging.debug("Failed to decode grating description '%s'", line)
continue
num = int(m.group(1))
desc = m.group(2)
# TODO: provide a nicer description, using RE_INSTALLED?
gratings[num] = desc
return gratings
RE_GDENSITY = re.compile("(\d+)\s*g/mm")
def _getGrooveDensity(self, gid):
"""
Returns the groove density of the given grating
gid (int): index of the grating
returns (float): groove density in lines/meter
raise
LookupError if the grating is not installed
ValueError: if the groove density cannot be found out
"""
gstring = self.axes["grating"].choices[gid]
m = self.RE_GDENSITY.search(gstring)
if not m:
raise ValueError("Failed to find groove density in '%s'" % gstring)
density = float(m.group(1)) * 1e3 # l/m
return density
def GetGrating(self):
"""
Retuns the current grating in use
returns (1<=int<=9) the grating in use
"""
# ?GRATING Returns the number of gratings presently being used numbered 1 - 9.
# On the SP-2150i, it's only up to 6
res = self._sendQuery("?grating")
val = int(res)
if val < 1 or val > 9:
raise SPError("Unexpected grating number '%s'" % res)
return val
def SetGrating(self, g):
"""
Change the current grating (the turret turns).
g (1<=int<=9): the grating number to change to
The method is synchronous, it returns once the grating is selected. It
might take up to 20 s.
Note: the grating is dependent on turret number (and the self.max_gratting)!
Note: after changing the grating, the wavelength, might have changed
"""
#GRATING Places specified grating in position to the [current] wavelength
# Note: it always reports ok, and doesn't change the grating if not
# installed or wrong value
assert(1 <= g and g <= (3 * self.max_gratings))
# TODO check that the grating is configured
self._sendOrder("%d grating" % g, timeout=20)
def GetWavelength(self):
"""
Return (0<=float): the current wavelength at the center (in m)
"""
# ?NM Returns present wavelength in nm to 0.01nm resolution with units
# nm appended.
# Note: For the SP-2150i, it seems there is no unit appended
# ?NM 300.00 nm
res = self._sendQuery("?nm")
m = re.search("\s*(\d+.\d+)( nm)?", res)
wl = float(m.group(1)) * 1e-9
if wl > 1e-3:
raise SPError("Unexpected wavelength of '%s'" % res)
return wl
def SetWavelength(self, wl):
"""
Change the wavelength at the center
wl (0<=float<=10e-6): wavelength in meter
returns when the move is complete
The method is synchronous, it returns once the grating is selected. It
might take up to 20 s.
"""
# GOTO: Goes to a destination wavelength at maximum motor speed. Accepts
# destination wavelength in nm as a floating point number with up to 3
# digits after the decimal point or whole number wavelength with no
# decimal point.
# 345.65 GOTO
# Note: NM goes to the wavelength slowly (in order to perform a scan).
# It shouldn't be needed for spectrometer
# Out of bound values are silently ignored by going to the min or max.
assert(0 <= wl and wl <= 10e-6)
# TODO: check that the value fit the grating configuration?
self._sendOrder("%.3f goto" % (wl * 1e9), timeout=20)
def GetModel(self):
"""
Return (str): the model name
"""
# MODEL Returns model number of the Acton SP series monochromator.
# returns something like ' SP-2-150i '
res = self._sendQuery("model")
return res.strip()
def GetSerialNumber(self):
"""
Return the serial number or None if it cannot be determined
"""
try:
res = self._sendQuery("serial")
except SPError:
logging.exception("Device doesn't support serial number query")
return None
return res.strip()
# TODO diverter (mirror) functions: no diverter on SP-2??0i anyway.
# high-level methods (interface)
def _updatePosition(self):
"""
update the position VA
Note: it should not be called while holding _ser_access
"""
with self._ser_access:
pos = {"wavelength": self.GetWavelength(),
"grating": self.GetGrating()
}
# it's read-only, so we change it via _value
self.position._value = pos
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
"""
Move the stage the defined values in m for each axis given.
shift dict(string-> float): name of the axis and shift in m
returns (Future): future that control the asynchronous move
"""
self._checkMoveRel(shift)
for axis in shift:
if axis == "wavelength":
# cannot convert it directly to an absolute move, because
# several in a row must mean they accumulate. So we queue a
# special task. That also means the range check is delayed until
# the actual position is known.
return self._executor.submit(self._doSetWavelengthRel, shift[axis])
@isasync
def moveAbs(self, pos):
"""
Move the stage the defined values in m for each axis given.
pos dict(string-> float): name of the axis and new position in m
returns (Future): future that control the asynchronous move
"""
self._checkMoveAbs(pos)
# If grating needs to be changed, change it first, then the wavelength
if "grating" in pos:
g = pos["grating"]
wl = pos.get("wavelength")
return self._executor.submit(self._doSetGrating, g, wl)
elif "wavelength" in pos:
wl = pos["wavelength"]
return self._executor.submit(self._doSetWavelengthAbs, wl)
else: # nothing to do
return model.InstantaneousFuture()
def _doSetWavelengthRel(self, shift):
"""
Change the wavelength by a value
"""
with self._ser_access:
pos = self.GetWavelength() + shift
# it's only now that we can check the absolute position is wrong
minp, maxp = self.axes["wavelength"].range
if not minp <= pos <= maxp:
raise ValueError("Position %f of axis '%s' not within range %f→%f" %
(pos, "wavelength", minp, maxp))
self.SetWavelength(pos)
self._updatePosition()
def _doSetWavelengthAbs(self, pos):
"""
Change the wavelength to a value
"""
with self._ser_access:
self.SetWavelength(pos)
self._updatePosition()
def _doSetGrating(self, g, wl=None):
"""
Setter for the grating VA.
g (1<=int<=3): the new grating
wl (None or float): wavelength to set afterwards. If None, will put the
same wavelength as before the change of grating.
returns the actual new grating
Warning: synchronous until the grating is finished (up to 20s)
"""
try:
with self._ser_access:
if wl is None:
wl = self.position.value["wavelength"]
self.SetGrating(g)
self.SetWavelength(wl)
except Exception:
logging.exception("Failed to change grating to %d", g)
raise
self._updatePosition()
def stop(self, axes=None):
"""
stops the motion
Warning: Only not yet-executed moves can be cancelled, this hardware
doesn't support stopping while a move is going on.
"""
self._executor.cancel()
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
if self._serial:
self._serial.close()
self._serial = None
def getPolyToWavelength(self):
"""
Compute the right polynomial to convert from a position on the sensor to the
wavelength detected. It depends on the current grating, center
wavelength (and focal length of the spectrometer).
Note: It will always return some not-too-stupid values, but the only way
to get precise values is to have provided a calibration data file.
Without it, it will just base the calculations on the theoretical
perfect spectrometer.
returns (list of float): polynomial coefficients to apply to get the current
wavelength corresponding to a given distance from the center:
w = p[0] + p[1] * x + p[2] * x²...
where w is the wavelength (in m), x is the position from the center
(in m, negative are to the left), and p is the polynomial (in m, m^0, m^-1...).
"""
# FIXME: shall we report the error on the polynomial? At least say if it's
# using calibration or not.
# TODO: have a calibration procedure, a file format, and load it at init
# See fsc2, their calibration is like this for each grating:
# INCLUSION_ANGLE_1 = 30.3
# FOCAL_LENGTH_1 = 301.2 mm
# DETECTOR_ANGLE_1 = 0.324871
fl = self._focal_length # m
ia = self._inclusion_angle # rad
cw = self.position.value["wavelength"] # m
if not fl:
# "very very bad" calibration
return [cw]
# When no calibration available, fallback to theoretical computation
# based on http://www.roperscientific.de/gratingcalcmaster.html
gl = self._getGrooveDensity(self.position.value["grating"]) # g/m
# fL = focal length (mm)
# wE = inclusion angle (°) = the angle between the incident and the reflected beam for the center wavelength of the grating
# gL = grating lines (l/mm)
# cW = center wavelength (nm)
# Grating angle
#A8 = (cW/1000*gL/2000)/Math.cos(wE* Math.PI/180);
# E8 = Math.asin(A8)*180/Math.PI;
try:
a8 = (cw * gl/2) / math.cos(ia)
ga = math.asin(a8) # radians
except (ValueError, ZeroDivisionError):
logging.exception("Failed to compute polynomial for wavelength conversion")
return [cw]
# if (document.forms[0].E8.value == "NaN deg." || E8 > 40){document.forms[0].E8.value = "> 40 deg."; document.forms[0].E8.style.colour="red";
if 0.5 > math.degrees(ga) or math.degrees(ga) > 40:
logging.warning("Failed to compute polynomial for wavelength "
"conversion, got grating angle = %g°", math.degrees(ga))
return [cw]
# dispersion: wavelength(m)/distance(m)
# F8a = Math.cos(Math.PI/180*(wE*1 + E8))*(1000000)/(gL*fL); // nm/mm
# to convert from nm/mm -> m/m : *1e-6
dispersion = math.cos(ia + ga) / (gl*fl) # m/m
if 0 > dispersion or dispersion > 0.5e-3: # < 500 nm/mm
logging.warning("Computed dispersion is not within expected bounds: %f nm/mm",
dispersion * 1e6)
return [cw]
# polynomial is cw + dispersion * x
return [cw, dispersion]
def selfTest(self):
"""
check as much as possible that it works without actually moving the motor
return (boolean): False if it detects any problem
"""
try:
with self._ser_access:
model = self.GetModel()
if not model.startswith("SP-"):
# accept it anyway
logging.warning("Device reports unexpected model '%s'", model)
turret = self.GetTurret()
if not turret in (1,2,3):
return False
return True
except:
logging.exception("Selftest failed")
return False
@staticmethod
def scan(port=None):
"""
port (string): name of the serial port. If None, all the serial ports are tried
returns (list of 2-tuple): name, args (port)
Note: it's obviously not advised to call this function if a device is already under use
"""
if port:
ports = [port]
else:
if os.name == "nt":
ports = ["COM" + str(n) for n in range (0,8)]
else:
ports = glob.glob('/dev/ttyS?*') + glob.glob('/dev/ttyUSB?*')
logging.info("Serial ports scanning for Acton SpectraPro spectrograph in progress...")
found = [] # (list of 2-tuple): name, kwargs
for p in ports:
try:
logging.debug("Trying port %s", p)
dev = SpectraPro(None, None, p, _noinit=True)
except serial.SerialException:
# not possible to use this port? next one!
continue
# Try to connect and get back some answer.
try:
model = dev.GetModel()
if model.startswith("SP-"):
found.append((model, {"port": p}))
else:
logging.info("Device on port '%s' responded correctly, but with unexpected model name '%s'.", p, model)
except:
continue
return found
@staticmethod
def openSerialPort(port):
"""
Opens the given serial port the right way for the SpectraPro.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
# according to doc:
# "port set-up is 9600 baud, 8 data bits, 1 stop bit and no parity"
ser = serial.Serial(
port = port,
baudrate = 9600,
bytesize = serial.EIGHTBITS,
parity = serial.PARITY_NONE,
stopbits = serial.STOPBITS_ONE,
timeout = 2 #s
)
return ser
class Focus(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
moving the SEM focus (as it's considered an axis in Odemis)
"""
def __init__(self, name, role, parent, **kwargs):
"""
axes (set of string): names of the axes
"""
self.parent = parent
axes_def = {
# Ranges are from the documentation
"z": model.Axis(unit="m", range=(FOCUS_RANGE[0] * 1e-3, FOCUS_RANGE[1] * 1e-3)),
}
model.Actuator.__init__(self, name, role, parent=parent, axes=axes_def, **kwargs)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({},
unit="m", readonly=True)
self._updatePosition()
# Refresh regularly the position
self._pos_poll = util.RepeatingTimer(5, self._refreshPosition, "Position polling")
self._pos_poll.start()
def _updatePosition(self):
"""
update the position VA
"""
z = self.parent.GetFocus() * 1e-3
self.position._set_value({"z": z}, force_write=True)
def _refreshPosition(self):
"""
Called regularly to update the current position
"""
# We don't use the VA setters, to avoid sending back to the hardware a
# set request
logging.debug("Updating SEM stage position")
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
def _doMoveRel(self, foc):
"""
move by foc
foc (float): relative change in mm
"""
try:
foc += self.parent.GetFocus() # mm
self.parent.SetFocus(foc)
finally:
# Update the position, even if the move didn't entirely succeed
self._updatePosition()
def _doMoveAbs(self, foc):
"""
move to pos
foc (float): unit mm
"""
try:
self.parent.SetFocus(foc)
finally:
# Update the position, even if the move didn't entirely succeed
self._updatePosition()
@isasync
def moveRel(self, shift):
"""
shift (dict): shift in m
"""
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
foc = shift["z"] * 1e3
f = self._executor.submit(self._doMoveRel, foc)
return f
@isasync
def moveAbs(self, pos):
"""
pos (dict): pos in m
"""
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
foc = pos["z"] * 1e3
f = self._executor.submit(self._doMoveAbs, foc)
return f
def stop(self, axes=None):
"""
Stop the last command
"""
# Empty the queue (and already stop the stage if a future is running)
self._executor.cancel()
logging.debug("Stopping all axes: %s", ", ".join(self.axes))
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
class PowerControlUnit(model.PowerSupplier):
'''
Implements the PowerSupplier class to regulate the power supply of the
components connected to the Power Control Unit board. It also takes care of
communication with the PCU firmware.
'''
def __init__(self,
name,
role,
port,
pin_map=None,
delay=None,
init=None,
ids=None,
termination=None,
**kwargs):
'''
port (str): port name
pin_map (dict of str -> int): names of the components
and the pin where the component is connected.
delay (dict str -> float): time to wait for each component after it is
turned on.
init (dict str -> boolean): turn on/off the corresponding component upon
initialization.
ids (list str): EEPROM ids expected to be detected during initialization.
termination (dict str -> bool/None): indicate for every component
if it should be turned off on termination (False), turned on (True)
or left as-is (None).
Raise an exception if the device cannot be opened
'''
if pin_map:
self.powered = list(pin_map.keys())
else:
self.powered = []
model.PowerSupplier.__init__(self, name, role, **kwargs)
# TODO: catch errors and convert to HwError
self._ser_access = threading.Lock()
self._file = None
self._port = self._findDevice(port) # sets ._serial and ._file
logging.info("Found Power Control device on port %s", self._port)
# Get identification of the Power control device
self._idn = self._getIdentification()
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "serial driver: %s" % (driver_name, )
self._hwVersion = "%s" % (self._idn, )
pin_map = pin_map or {}
self._pin_map = pin_map
delay = delay or {}
# fill the missing pairs with 0 values
self._delay = dict.fromkeys(pin_map, 0)
self._delay.update(delay)
self._last_start = dict.fromkeys(self._delay, time.time())
# only keep components that should be changed on termination
termination = termination or {}
self._termination = {
k: v
for k, v in termination.items() if v is not None
}
for comp in self._termination:
if comp not in pin_map:
raise ValueError(
"Component %s in termination not found in pin_map." % comp)
# will take care of executing switch asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
self._supplied = {}
self.supplied = model.VigilantAttribute(self._supplied, readonly=True)
self._updateSupplied()
init = init or {}
# Remove all None's from the dict, so it can be passed as-is to _doSupply()
init = {k: v for k, v in init.items() if v is not None}
for comp in init:
if comp not in pin_map:
raise ValueError("Component %s in init not found in pin_map." %
comp)
try:
self._doSupply(init, apply_delay=False)
except IOError as ex:
# This is in particular to handle some cases where the device resets
# when turning on the power. One or more trials and the
logging.exception("Failure during turning on initial power.")
raise HwError(
"Device error when initialising power: %s. "
"Try again or contact support if the problem persists." %
(ex, ))
self.memoryIDs = model.VigilantAttribute(None,
readonly=True,
getter=self._getIdentities)
if ids:
mem_ids = self.memoryIDs.value
for eid in ids:
if eid not in mem_ids:
raise HwError("EEPROM id %s was not detected. Make sure "
"all EEPROM components are connected." %
(eid, ))
@isasync
def supply(self, sup):
"""
Change the power supply to the defined state for each component given.
This is an asynchronous method.
sup dict(string-> boolean): name of the component and new state
returns (Future): object to control the supply request
"""
if not sup:
return model.InstantaneousFuture()
self._checkSupply(sup)
return self._executor.submit(self._doSupply, sup)
def _doSupply(self, sup, apply_delay=True):
"""
supply power
apply_delay (bool): If true, wait the amount of time requested in delay
after turning on the power
"""
for comp, val in sup.items():
# find pin and values corresponding to component
pin = self._pin_map[comp]
# should always be able to get the value, default values just to be
# on the safe side
if apply_delay:
delay = self._delay.get(comp, 0)
else:
# We still wait a little, to avoid starting all components
# _exactly_ at the same time, which could cause a power peak.
delay = 1
if val:
self._sendCommand("PWR " + str(pin) + " 1")
state = self.supplied.value[comp]
if state:
# Already on, wait the time remaining
remaining = (self._last_start[comp] + delay) - time.time()
time.sleep(max(0, remaining))
else:
# wait full time
self._last_start[comp] = time.time()
time.sleep(delay)
# Check it really worked
ans = self._sendCommand("PWR? " + str(pin))
if ans != "1":
logging.warning("Failed to turn on component %s", comp)
else:
self._sendCommand("PWR " + str(pin) + " 0")
self._updateSupplied()
def _updateSupplied(self):
"""
update the supplied VA
"""
pins_updated = set(self._pin_map.values()
) # to avoid asking for the same pin multiple times
for pin in pins_updated:
ans = self._sendCommand("PWR? " + str(pin))
# Update all components that are connected to the same pin
to_update = [c for c in self.powered if pin == self._pin_map[c]]
for c_update in to_update:
self._supplied[c_update] = (ans == "1")
# it's read-only, so we change it via _value
self.supplied._value = self._supplied
self.supplied.notify(self.supplied.value)
def terminate(self):
if self._executor:
self._executor.cancel()
self._executor.shutdown()
self._executor = None
# Power components on/off according to ._termination
# If nothing is specified, leave it as-is.
logging.debug("Changing power supply on termination: %s" %
self._termination)
self._doSupply(self._termination)
if self._serial:
with self._ser_access:
self._serial.close()
self._serial = None
if self._file:
self._file.close()
self._file = None
def _getIdentification(self):
return self._sendCommand("*IDN?")
def writeMemory(self, id, address, data):
"""
Write data to EEPROM.
id (str): EEPROM registration number #hex (little-endian format)
address (str): starting address #hex
data (str): data to be written #hex (little-endian format)
"""
self._sendCommand("WMEM %s %s %s" % (id, address, data))
def readMemory(self, id, address, length):
"""
Read data from EEPROM.
id (str): EEPROM registration number #hex (little-endian format)
address (str): starting address #hex
length (int): number of bytes to be read
returns (str): data read back #hex (little-endian format)
"""
ans = self._sendCommand("RMEM %s %s %s" % (id, address, length))
return ans
def readEEPROM(self, id):
"""
We use this method to get a dict that contains all the data written in
the EEPROM with the given id.
id (str): EEPROM registration number #hex (little-endian format)
"""
if id not in self.memoryIDs.value:
raise KeyError("There was no EEPROM with the given id found")
mem_cont = self.readMemory(id, "00", EEPROM_CAPACITY)
mem_yaml = ""
while mem_cont != "":
if mem_cont[:2] != "00":
mem_yaml += chr(int(mem_cont[:2], 16))
mem_cont = mem_cont[2:]
dct = yaml.load(mem_yaml)
return dct
def _getIdentities(self):
"""
Return the ids of connected EEPROMs
"""
try:
ans = self._sendCommand("SID")
except PowerControlError as e:
# means there is no power provided
raise HwError(
"There is no power provided to the Power Control Unit. "
"Please make sure the board is turned on.")
return [x for x in ans.split(',') if x != '']
def _sendCommand(self, cmd):
"""
cmd (str): command to be sent to Power Control unit.
returns (str): answer received from the Power Control unit
raises:
IOError: if an ERROR is returned by the Power Control firmware.
"""
cmd = (cmd + "\n").encode('latin1')
with self._ser_access:
logging.debug("Sending command %s" % to_str_escape(cmd))
self._serial.write(cmd)
ans = b''
char = None
while char != b'\n':
char = self._serial.read()
if not char:
logging.error("Timeout after receiving %s",
to_str_escape(ans))
# TODO: See how you should handle a timeout before you raise
# an HWError
raise HwError(
"Power Control Unit connection timeout. "
"Please turn off and on the power to the box.")
# Handle ERROR coming from Power control unit firmware
ans += char
logging.debug("Received answer %s", to_str_escape(ans))
ans = ans.decode('latin1')
if ans.startswith("ERROR"):
raise PowerControlError(ans.split(' ', 1)[1])
return ans.rstrip()
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a Power control device.
port (string): the name of the serial port (e.g., /dev/ttyACM0)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
timeout=1 # s
)
# Purge
ser.flush()
ser.flushInput()
# Try to read until timeout to be extra safe that we properly flushed
while True:
char = ser.read()
if char == b'':
break
logging.debug(
"Nothing left to read, Power Control Unit can safely initialize.")
ser.timeout = 5 # Sometimes the software-based USB can have some hiccups
return ser
def _findDevice(self, ports):
"""
Look for a compatible device
ports (str): pattern for the port name
return (str): the name of the port used
It also sets ._serial and ._idn to contain the opened serial port, and
the identification string.
raises:
IOError: if no device are found
"""
# For debugging purpose
if ports == "/dev/fake":
self._serial = PowerControlSimulator(timeout=1)
return ports
if os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
self._file = open(n) # Open in RO, just to check for lock
try:
fcntl.flock(self._file.fileno(),
fcntl.LOCK_EX | fcntl.LOCK_NB)
except IOError:
logging.info("Port %s is busy, will wait and retry", n)
time.sleep(11)
fcntl.flock(self._file.fileno(),
fcntl.LOCK_EX | fcntl.LOCK_NB)
self._serial = self._openSerialPort(n)
try:
idn = self._getIdentification()
except PowerControlError:
# Can happen if the device has received some weird characters
# => try again (now that it's flushed)
logging.info("Device answered by an error, will try again")
idn = self._getIdentification()
# Check that we connect to the right device
if not idn.startswith("Delmic Analog Power"):
logging.info("Connected to wrong device on %s, skipping.",
n)
continue
return n
except (IOError, PowerControlError):
# not possible to use this port? next one!
logging.debug(
"Skipping port %s which doesn't seem the right device", n)
continue
else:
raise HwError(
"Failed to find a Power Control device on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports, ))
@classmethod
def scan(cls):
"""
returns (list of 2-tuple): name, args (sn)
Note: it's obviously not advised to call this function if a device is already under use
"""
logging.info(
"Serial ports scanning for Power control device in progress...")
found = [] # (list of 2-tuple): name, kwargs
if sys.platform.startswith('linux'):
# Look for each ACM device, if the IDN is the expected one
acm_paths = glob.glob('/dev/ttyACM?')
for port in acm_paths:
# open and try to communicate
try:
dev = cls(name="test", role="test", port=port)
idn = dev._getIdentification()
if idn.startswith("Delmic Analog Power"):
found.append({"port": port})
except Exception:
pass
else:
# TODO: Windows version
raise NotImplementedError("OS not yet supported")
return found
class MultiplexActuator(model.Actuator):
"""
An object representing an actuator made of several (real actuators)
= a set of axes that can be moved and optionally report their position.
"""
def __init__(self, name, role, children, axes_map, ref_on_init=None, **kwargs):
"""
name (string)
role (string)
children (dict str -> actuator): axis name (in this actuator) -> actuator to be used for this axis
axes_map (dict str -> str): axis name in this actuator -> axis name in the child actuator
ref_on_init (None, list or dict (str -> float or None)): axes to be referenced during
initialization. If it's a dict, it will go the indicated position
after referencing, otherwise, it'll stay where it is.
"""
if not children:
raise ValueError("MultiplexActuator needs children")
if set(children.keys()) != set(axes_map.keys()):
raise ValueError("MultiplexActuator needs the same keys in children and axes_map")
# Convert ref_on_init list to dict with no explicit move after
if isinstance(ref_on_init, list):
ref_on_init = {a: None for a in ref_on_init}
self._ref_on_init = ref_on_init or {}
self._axis_to_child = {} # axis name => (Actuator, axis name)
self._position = {}
self._speed = {}
self._referenced = {}
axes = {}
for axis, child in children.items():
caxis = axes_map[axis]
self._axis_to_child[axis] = (child, caxis)
# Ducktyping (useful to support also testing with MockComponent)
# At least, it has .axes
if not isinstance(child, model.ComponentBase):
raise ValueError("Child %s is not a component." % (child,))
if not hasattr(child, "axes") or not isinstance(child.axes, dict):
raise ValueError("Child %s is not an actuator." % child.name)
axes[axis] = copy.deepcopy(child.axes[caxis])
self._position[axis] = child.position.value[axes_map[axis]]
if model.hasVA(child, "speed") and caxis in child.speed.value:
self._speed[axis] = child.speed.value[caxis]
if model.hasVA(child, "referenced") and caxis in child.referenced.value:
self._referenced[axis] = child.referenced.value[caxis]
# this set ._axes and ._children
model.Actuator.__init__(self, name, role, axes=axes,
children=children, **kwargs)
if len(self.children.value) > 1:
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# TODO: make use of the 'Cancellable' part (for now cancelling a running future doesn't work)
else: # Only one child => optimize by passing all requests directly
self._executor = None
# keep a reference to the subscribers so that they are not
# automatically garbage collected
self._subfun = []
children_axes = {} # dict actuator -> set of string (our axes)
for axis, (child, ca) in self._axis_to_child.items():
logging.debug("adding axis %s to child %s", axis, child.name)
if child in children_axes:
children_axes[child].add(axis)
else:
children_axes[child] = {axis}
# position & speed: special VAs combining multiple VAs
self.position = model.VigilantAttribute(self._position, readonly=True)
for c, ax in children_axes.items():
def update_position_per_child(value, ax=ax, c=c):
logging.debug("updating position of child %s", c.name)
for a in ax:
try:
self._position[a] = value[axes_map[a]]
except KeyError:
logging.error("Child %s is not reporting position of axis %s", c.name, a)
self._updatePosition()
c.position.subscribe(update_position_per_child)
self._subfun.append(update_position_per_child)
# TODO: change the speed range to a dict of speed ranges
self.speed = model.MultiSpeedVA(self._speed, [0., 10.], setter=self._setSpeed)
for axis in self._speed.keys():
c, ca = self._axis_to_child[axis]
def update_speed_per_child(value, a=axis, ca=ca, cname=c.name):
try:
self._speed[a] = value[ca]
except KeyError:
logging.error("Child %s is not reporting speed of axis %s (%s): %s", cname, a, ca, value)
self._updateSpeed()
c.speed.subscribe(update_speed_per_child)
self._subfun.append(update_speed_per_child)
# whether the axes are referenced
self.referenced = model.VigilantAttribute(self._referenced.copy(), readonly=True)
for axis in self._referenced.keys():
c, ca = self._axis_to_child[axis]
def update_ref_per_child(value, a=axis, ca=ca, cname=c.name):
try:
self._referenced[a] = value[ca]
except KeyError:
logging.error("Child %s is not reporting reference of axis %s (%s)", cname, a, ca)
self._updateReferenced()
c.referenced.subscribe(update_ref_per_child)
self._subfun.append(update_ref_per_child)
for axis, pos in self._ref_on_init.items():
# If the axis can be referenced => do it now (and move to a known position)
if axis not in self._referenced:
raise ValueError("Axis '%s' cannot be referenced, while should be referenced at init" % (axis,))
if not self._referenced[axis]:
# The initialisation will not fail if the referencing fails, but
# the state of the component will be updated
def _on_referenced(future, axis=axis):
try:
future.result()
except Exception as e:
c, ca = self._axis_to_child[axis]
c.stop({ca}) # prevent any move queued
self.state._set_value(e, force_write=True)
logging.exception(e)
f = self.reference({axis})
f.add_done_callback(_on_referenced)
# If already referenced => directly move
# otherwise => put move on the queue, so that any move by client will
# be _after_ the init position.
if pos is not None:
self.moveAbs({axis: pos})
def _updatePosition(self):
"""
update the position VA
"""
# it's read-only, so we change it via _value
pos = self._applyInversion(self._position)
logging.debug("reporting position %s", pos)
self.position._set_value(pos, force_write=True)
def _updateSpeed(self):
"""
update the speed VA
"""
# we must not call the setter, so write directly the raw value
self.speed._value = self._speed
self.speed.notify(self._speed)
def _updateReferenced(self):
"""
update the referenced VA
"""
# .referenced is copied to detect changes to it on next update
self.referenced._set_value(self._referenced.copy(), force_write=True)
def _setSpeed(self, value):
"""
value (dict string-> float): speed for each axis
returns (dict string-> float): the new value
"""
# FIXME the problem with this implementation is that the subscribers
# will receive multiple notifications for each set:
# * one for each axis (via _updateSpeed from each child)
# * the actual one (but it's probably dropped as it's the same value)
final_value = value.copy() # copy
for axis, v in value.items():
child, ma = self._axis_to_child[axis]
new_speed = child.speed.value.copy() # copy
new_speed[ma] = v
child.speed.value = new_speed
final_value[axis] = child.speed.value[ma]
return final_value
def _moveToChildMove(self, mv):
child_to_move = collections.defaultdict(dict) # child -> moveRel argument
for axis, distance in mv.items():
child, child_axis = self._axis_to_child[axis]
child_to_move[child].update({child_axis: distance})
logging.debug("Moving axis %s (-> %s) by %g", axis, child_axis, distance)
return child_to_move
def _axesToChildAxes(self, axes):
child_to_axes = collections.defaultdict(set) # child -> set(str): axes
for axis in axes:
child, child_axis = self._axis_to_child[axis]
child_to_axes[child].add(child_axis)
logging.debug("Interpreting axis %s (-> %s)", axis, child_to_axes)
return child_to_axes
@isasync
def moveRel(self, shift, **kwargs):
"""
Move the stage the defined values in m for each axis given.
shift dict(string-> float): name of the axis and shift in m
**kwargs: Mostly there to support "update" argument (but currently works
only if there is only one child)
"""
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
if self._executor:
f = self._executor.submit(self._doMoveRel, shift, **kwargs)
else:
cmv = self._moveToChildMove(shift)
child, move = cmv.popitem()
assert not cmv
f = child.moveRel(move, **kwargs)
return f
def _doMoveRel(self, shift, **kwargs):
# TODO: updates don't work because we still wait for the end of the
# move before we get to the next one => multi-threaded queue? Still need
# to ensure the order (ie, X>AB>X can be executed as X/AB>X or X>AB/X but
# XA>AB>X must be in the order XA>AB/X
futures = []
for child, move in self._moveToChildMove(shift).items():
f = child.moveRel(move, **kwargs)
futures.append(f)
# just wait for all futures to finish
for f in futures:
f.result()
@isasync
def moveAbs(self, pos, **kwargs):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
if self._executor:
f = self._executor.submit(self._doMoveAbs, pos, **kwargs)
else:
cmv = self._moveToChildMove(pos)
child, move = cmv.popitem()
assert not cmv
f = child.moveAbs(move, **kwargs)
return f
def _doMoveAbs(self, pos, **kwargs):
futures = []
for child, move in self._moveToChildMove(pos).items():
f = child.moveAbs(move, **kwargs)
futures.append(f)
# just wait for all futures to finish
for f in futures:
f.result()
@isasync
def reference(self, axes):
if not axes:
return model.InstantaneousFuture()
self._checkReference(axes)
if self._executor:
f = self._executor.submit(self._doReference, axes)
else:
cmv = self._axesToChildAxes(axes)
child, a = cmv.popitem()
assert not cmv
f = child.reference(a)
return f
reference.__doc__ = model.Actuator.reference.__doc__
def _doReference(self, axes):
child_to_axes = self._axesToChildAxes(axes)
futures = []
for child, a in child_to_axes.items():
f = child.reference(a)
futures.append(f)
# just wait for all futures to finish
for f in futures:
f.result()
def stop(self, axes=None):
"""
stops the motion
axes (iterable or None): list of axes to stop, or None if all should be stopped
"""
# Empty the queue for the given axes
if self._executor:
self._executor.cancel()
all_axes = set(self.axes.keys())
axes = axes or all_axes
unknown_axes = axes - all_axes
if unknown_axes:
logging.error("Attempting to stop unknown axes: %s", ", ".join(unknown_axes))
axes &= all_axes
threads = []
for child, a in self._axesToChildAxes(axes).items():
# it's synchronous, but we want to stop all of them as soon as possible
thread = threading.Thread(name="Stopping axis", target=child.stop, args=(a,))
thread.start()
threads.append(thread)
# wait for completion
for thread in threads:
thread.join(1)
if thread.is_alive():
logging.warning("Stopping child actuator of '%s' is taking more than 1s", self.name)
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
class ESP(model.Actuator):
def __init__(self, name, role, port, axes=None, **kwargs):
"""
A driver for a Newport ESP 301 Stage Actuator.
This driver supports a serial connection. Note that as of the Linux
kernel 4.13, the USB connection is known to _not_ work, as the TI 3410
chipset apparently behind is not handled properly. Use a of the
RS-232 port is required (via a USB adapter if necessary).
name: (str)
role: (str)
port: (str) port name. Can be a pattern, in which case all the ports
fitting the pattern will be tried.
Use /dev/fake for a simulator
axes: dict str (axis name) -> dict (axis parameters)
axis parameters: {
number (1 <= int <= 3): axis number on the hardware
range: [float, float], default is -1 -> 1
unit (str): the external unit of the axis (internal is mm),
default is "m".
conv_factor (float): a conversion factor that converts to the
device internal unit (mm), default is 1000.
}
inverted: (bool) defines if the axes are inverted
The offset can be specified by setting MD_POS_COR as a coordinate dictionary
"""
if len(axes) == 0:
raise ValueError("Needs at least 1 axis.")
# Connect to serial port
self._ser_access = threading.Lock()
self._serial = None
self._file = None
self._port, self._version = self._findDevice(
port) # sets ._serial and ._file
logging.info("Found Newport ESP301 device on port %s, Ver: %s",
self._port, self._version)
self.LockKeypad(
KEYPAD_LOCK_EXCEPT_STOP) # lock user input for the controller
# Clear errors at start
try:
self.checkError()
except ESPError:
pass
self._offset = {}
self._axis_conv_factor = {}
# Not to be mistaken with axes which is a simple public view
self._axis_map = {} # axis name -> axis number used by controller
axes_def = {} # axis name -> Axis object
speed = {}
accel = {}
decel = {}
self._id = {}
for axis_name, axis_par in axes.items():
# Unpack axis parameters from the definitions in the YAML
try:
axis_num = axis_par['number']
except KeyError:
raise ValueError(
"Axis %s must have a number to identify it. " %
(axis_name, ))
try:
axis_range = axis_par['range']
except KeyError:
logging.info("Axis %s has no range. Assuming (-1, 1)",
axis_name)
axis_range = (-1, 1)
try:
axis_unit = axis_par['unit']
except KeyError:
logging.info("Axis %s has no unit. Assuming m", axis_name)
axis_unit = "m"
try:
conv_factor = float(axis_par['conv_factor'])
except KeyError:
logging.info(
"Axis %s has no conversion factor. Assuming 1000 (m to mm)",
axis_name)
conv_factor = 1000.0
self._axis_map[axis_name] = axis_num
self._axis_conv_factor[axis_num] = conv_factor
self._id[axis_num] = self.GetIdentification(axis_num)
speed[axis_name] = self.GetSpeed(axis_num)
accel[axis_name] = self.GetAcceleration(axis_num)
decel[axis_name] = self.GetDeceleration(axis_num)
# Force millimetres for consistency as the internal unit.
self.SetAxisUnit(axis_num, "mm")
# initialize each motor
self.MotorOn(axis_num)
ad = model.Axis(canAbs=True, unit=axis_unit, range=axis_range)
axes_def[axis_name] = ad
model.Actuator.__init__(self, name, role, axes=axes_def, **kwargs)
# whether the axes are referenced
self.referenced = model.VigilantAttribute({a: False
for a in axes},
readonly=True)
self._hwVersion = str(self._id)
self._swVersion = self._version
# Get the position in object coord with the offset applied.
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({}, readonly=True)
self._updatePosition()
self._speed = speed
self._accel = accel
self._decel = decel
# set offset due to mounting of components (float)
self._metadata[model.MD_POS_COR] = {}
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(1) # one task at a time
# Check the error state
self.checkError()
def terminate(self):
if self._serial.isOpen():
self.LockKeypad(
KEYPAD_UNLOCK) # unlock user input for the controller
with self._ser_access:
self._serial.close()
model.Actuator.terminate(self)
def updateMetadata(self, md):
super(ESP, self).updateMetadata(md)
try:
value = md[model.MD_POS_COR]
except KeyError:
# there is no offset set.
return
if not isinstance(value, dict):
raise ValueError(
"Invalid metadata, should be a coordinate dictionary but got %s."
% (value, ))
# update all axes
for n in self._axis_map.keys():
if n in value:
self._offset[n] = value[n]
logging.debug("Updating offset to %s.", value)
self._updatePosition()
# Connection methods
@staticmethod
def _openSerialPort(port, baudrate):
"""
Opens the given serial port the right way for a Power control device.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
baudrate (int)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
baudrate=baudrate,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
rtscts=True,
timeout=1 # s
)
# Purge
ser.flush()
ser.flushInput()
# Try to read until timeout to be extra safe that we properly flushed
ser.timeout = 0
while True:
char = ser.read()
if char == b'':
break
ser.timeout = 1
return ser
def _findDevice(self, ports, baudrate=19200):
"""
Look for a compatible device
ports (str): pattern for the port name
baudrate (0<int)
return:
(str): the name of the port used
(str): the hardware version string
Note: will also update ._file and ._serial
raises:
IOError: if no devices are found
"""
# For debugging purpose
if ports == "/dev/fake":
self._serial = ESPSimulator(timeout=1)
self._file = None
ve = self.GetVersion()
return ports, ve
if os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
# Ensure no one will talk to it simultaneously, and we don't talk to devices already in use
self._file = open(n) # Open in RO, just to check for lock
try:
fcntl.flock(
self._file.fileno(), fcntl.LOCK_EX
| fcntl.LOCK_NB) # Raises IOError if cannot lock
except IOError:
logging.info("Port %s is busy, will not use", n)
continue
self._serial = self._openSerialPort(n, baudrate)
try:
ve = self.GetVersion()
if not "ESP301" in ve.upper():
raise IOError(
"Device at %s is not an ESP301 controller. Reported version string: %s"
% (ports, ve))
except ESPError as e:
# Can happen if the device has received some weird characters
# => try again (now that it's flushed)
logging.info(
"Device answered by an error %s, will try again", e)
ve = self.GetVersion()
return n, ve
except (IOError, ESPError) as e:
logging.debug(e)
logging.info(
"Skipping device on port %s, which didn't seem to be compatible",
n)
# not possible to use this port? next one!
continue
else:
raise HwError(
"Failed to find a device on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports, ))
def _sendOrder(self, cmd):
"""
cmd (byte str): command to be sent to device (without the CR)
"""
cmd = cmd + b"\r"
with self._ser_access:
logging.debug("Sending command %s", to_str_escape(cmd))
self._serial.write(cmd)
def _sendQuery(self, cmd):
"""
cmd (byte str): command to be sent to device (without the CR, but with the ?)
returns (str): answer received from the device (without \n or \r)
raise:
IOError if no answer is returned in time
"""
cmd = cmd + b"\r"
with self._ser_access:
logging.debug("Sending command %s", to_str_escape(cmd))
self._serial.write(cmd)
self._serial.timeout = 1
ans = b''
while ans[-1:] != b'\r':
char = self._serial.read()
if not char:
raise IOError("Timeout after receiving %s" %
to_str_escape(ans))
ans += char
logging.debug("Received answer %s", to_str_escape(ans))
return ans.strip().decode("latin1")
# Low level serial commands.
# Note: These all convert to internal units of the controller
def GetErrorCode(self):
# Checks the device error register
return int(self._sendQuery(b"TE?"))
def checkError(self):
# Checks if an error occurred and raises an exception accordingly.
err_q = []
# Get all of the errors in the error FIFO stack
while True:
errcode = self.GetErrorCode()
if errcode == 0: # No error
break
else:
err_q.append(errcode)
# After errors are collected
if len(err_q) > 0:
for err in err_q[:-1]:
logging.warning("Discarding error %d", err)
raise ESPError("Error code %d" % (err_q[-1], ), err_q[-1])
def SetAxisUnit(self, axis_num, unit):
# Set the internal unit used by the controller
if not unit in UNIT_DEF:
raise ValueError("Unknown unit name %s" % (unit, ))
self._sendOrder(b"%d SN %d" % (axis_num, UNIT_DEF[unit]))
def MoveLimit(self, aid, limit):
"""
Requests a move to the positive or negative limit.
limit (str): either '+' or '-', defining positive or negative limit
"""
if not limit in ("+", "-"):
raise ValueError(
"Asked to move %d to %s limit. Only + or - allowed." % (
aid,
limit,
))
self._sendOrder(b"%d MV %s" % (aid, limit))
def LockKeypad(self, lock_type):
"""
Lock keypad on device from preventing bad user input
lock_type (KEYPAD_*)
"""
self._sendOrder(b"LC %d" % (lock_type, ))
def HomeSearch(self, aid, search_type):
"""
Searches for home using a search type (int 0,1,2,3,4,5,6) as per manual
"""
self._sendOrder(b"%d OR %d" % (aid, search_type))
def SetHome(self, aid, value):
"""
Set the position value to use at the origin (home)
"""
self._sendOrder(b"%d SH %f" % (aid, value))
def SaveMemory(self):
"""
Save configuration to non - volatile memory
"""
self._sendOrder(b"SM")
def MoveAbsPos(self, axis_num, pos):
"""
Requests a move to an absolute position. This is non-blocking.
Converts to internal unit of the controller
"""
self._sendOrder(b"%d PA %f" % (axis_num, pos))
def MoveRelPos(self, axis_num, rel):
"""
Requests a move to a relative position. This is non-blocking.
"""
self._sendOrder(b"%d PR %f" % (axis_num, rel)) # 0 = absolute
def GetDesiredPos(self, axis_num):
# Get the target position programmed into the controller
return float(self._sendQuery(b"%d DP?" % (axis_num, )))
def StopMotion(self, axis):
# Stop the motion on the specified axis
self._sendOrder(b"%d ST" % (axis, ))
def MotorOn(self, axis):
# Start the motor
self._sendOrder(b"%d MO" % (axis, ))
def MotorOff(self, axis):
# Stop the motor
self._sendOrder(b"%d MF" % (axis, ))
def GetMotionDone(self, axis_n):
# Return true or false based on if the axis is still moving.
done = int(self._sendQuery(b"%d MD?" % axis_n))
logging.debug("Motion done: %d", done)
return bool(done)
def GetPosition(self, axis_n):
# Get the position of the axis
return float(self._sendQuery(b"%d TP?" % axis_n))
def GetSpeed(self, axis_n):
# Get the speed of the axis
return float(self._sendQuery(b"%d VA?" % axis_n))
def SetSpeed(self, axis_n, speed):
# Set the axis speed
self._sendOrder(b"%d VA %f" % (
axis_n,
speed,
))
def GetAcceleration(self, axis_n):
# Get axis accel
return float(self._sendQuery(b"%d AC?" % axis_n))
def SetAcceleration(self, axis_n, ac):
# Set axis accel
self._sendOrder(b"%d AC %f" % (
axis_n,
ac,
))
def GetDeceleration(self, axis_n):
return float(self._sendQuery(b"%d AG?" % axis_n))
def SetDeceleration(self, axis_n, dc):
self._sendOrder(b"%d AG %f" % (
axis_n,
dc,
))
def GetIdentification(self, axis):
"""
return (str): the identification string as-is for the first axis
"""
return self._sendQuery(b"%d ID?" % (axis, ))
def GetVersion(self):
"""
return (str): the version string as-is
"""
return self._sendQuery(b"VE?")
def SaveMem(self):
"""
Instruct the controller to save the current settings to non-volatile memory
"""
self._sendOrder(b"SM")
"""
High level commands (ie, Odemis Actuator API)
"""
def _applyOffset(self, pos):
"""
Apply the offset to the position and return it
"""
ret = dict(pos)
for axis in self._offset:
if axis in ret:
ret[axis] -= self._offset[axis]
return ret
def _removeOffset(self, pos):
"""
Remove the offset from the position and return it
"""
ret = dict(pos)
for axis in self._offset:
if axis in ret:
ret[axis] += self._offset[axis]
return ret
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
pos = self._removeOffset(pos) # Get the position in controller coord.
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
def _doMoveRel(self, future, pos):
"""
Blocking and cancellable relative move
future (Future): the future it handles
_pos (dict str -> float): axis name -> relative target position
raise:
ValueError: if the target position is
TMCLError: if the controller reported an error
CancelledError: if cancelled before the end of the move
"""
with future._moving_lock:
end = 0 # expected end
moving_axes = set()
for an, v in pos.items():
aid = self._axis_map[an]
moving_axes.add(aid)
self.MoveRelPos(aid, v * self._axis_conv_factor[aid])
# compute expected end
# convert to mm units
dur = driver.estimateMoveDuration(
abs(v) * self._axis_conv_factor[aid], self._speed[an],
self._accel[an])
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
self.checkError()
logging.debug("move successfully completed")
def _doMoveAbs(self, future, pos):
"""
Blocking and cancellable absolute move
future (Future): the future it handles
_pos (dict str -> float): axis name -> absolute target position
raise:
TMCLError: if the controller reported an error
CancelledError: if cancelled before the end of the move
"""
with future._moving_lock:
end = 0 # expected end
old_pos = self._applyInversion(self.position.value)
moving_axes = set()
for an, v in pos.items():
aid = self._axis_map[an]
moving_axes.add(aid)
self.MoveAbsPos(aid, v * self._axis_conv_factor[aid])
d = abs(v - old_pos[an])
# convert displacement unit to mm
dur = driver.estimateMoveDuration(
d * self._axis_conv_factor[aid], self._speed[an],
self._accel[an])
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
self.checkError()
logging.debug("move successfully completed")
def _waitEndMove(self, future, axes, end=0):
"""
Wait until all the given axes are finished moving, or a request to
stop has been received.
future (Future): the future it handles
axes (set of int): the axes IDs to check
end (float): expected end time
raise:
TimeoutError: if took too long to finish the move
CancelledError: if cancelled before the end of the move
"""
moving_axes = set(axes)
last_upd = time.time()
dur = max(0.01, min(end - last_upd, 60))
max_dur = dur * 2 + 1
logging.debug("Expecting a move of %g s, will wait up to %g s", dur,
max_dur)
timeout = last_upd + max_dur
last_axes = moving_axes.copy()
try:
while not future._must_stop.is_set():
for aid in moving_axes.copy(
): # need copy to remove during iteration
if self.GetMotionDone(aid):
moving_axes.discard(aid)
if not moving_axes:
# no more axes to wait for
break
now = time.time()
if now > timeout:
logging.warning("Stopping move due to timeout after %g s.",
max_dur)
for i in moving_axes:
self.StopMotion(i)
raise TimeoutError("Move is not over after %g s, while "
"expected it takes only %g s" %
(max_dur, dur))
# Update the position from time to time (10 Hz)
if now - last_upd > 0.1 or last_axes != moving_axes:
last_names = set(n for n, i in self._axis_map.items()
if i in last_axes)
self._updatePosition(last_names)
last_upd = time.time()
last_axes = moving_axes.copy()
# Wait half of the time left (maximum 0.1 s)
left = end - time.time()
sleept = max(0.001, min(left / 2, 0.1))
future._must_stop.wait(sleept)
else:
logging.debug("Move of axes %s cancelled before the end", axes)
# stop all axes still moving them
for i in moving_axes:
self.StopMotion(i)
future._was_stopped = True
raise CancelledError()
finally:
# TODO: check if the move succeded ? (= Not failed due to stallguard/limit switch)
self._updatePosition() # update (all axes) with final position
# high-level methods (interface)
def _updatePosition(self, axes=None):
"""
update the position VA
axes (set of str): names of the axes to update or None if all should be
updated
"""
# uses the current values (converted to internal representation)
pos = self._applyInversion(self.position.value)
for n, i in self._axis_map.items():
if axes is None or n in axes:
pos[n] = self.GetPosition(i) / self._axis_conv_factor[i]
pos = self._applyInversion(pos)
pos = self._applyOffset(pos) # Appy the offset back for display
logging.debug("Updated position to %s", pos)
self.position._set_value(pos, force_write=True)
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set(
) # tell the thread taking care of the move it's over
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
def stop(self, axes=None):
self._executor.cancel()
# For safety, just force stop every axis
for an, aid in self._axis_map.items():
if axes is None or an in axes:
self.StopMotion(aid)
try:
self.checkError()
except ESPError as e:
logging.warning("Cancellation error %d", e.code)
# Should now turn the motor back on
self.MotorOn(aid)
def _createMoveFuture(self):
"""
Return (CancellableFuture): a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event(
) # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
@isasync
def reference(self, axes):
if not axes:
return model.InstantaneousFuture()
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doReference, f, axes)
return f
def _doReference(self, future, axes):
"""
Actually runs the referencing code
axes (set of str)
raise:
IOError: if referencing failed due to hardware
CancelledError if was cancelled
"""
# Reset reference so that if it fails, it states the axes are not
# referenced (anymore)
with future._moving_lock:
try:
# do the referencing for each axis sequentially
# (because each referencing is synchronous)
for a in axes:
if future._must_stop.is_set():
raise CancelledError()
aid = self._axis_map[a]
self.referenced._value[a] = False
self.HomeSearch(
aid, REF_NEGATIVE_LIMIT
) # search for the negative limit signal to set an origin
self._waitEndMove(future, (aid, ),
time.time() +
100) # block until it's over
self.SetHome(aid, 0.0) # set negative limit as origin
self.referenced._value[a] = True
except CancelledError:
# FIXME: if the referencing is stopped, the device refuses to
# move until referencing is run (and successful).
# => Need to put back the device into a mode where at least
# relative moves work.
logging.warning(
"Referencing cancelled, device will not move until another referencing"
)
future._was_stopped = True
raise
except Exception:
logging.exception("Referencing failure")
raise
finally:
# We only notify after updating the position so that when a listener
# receives updates both values are already updated.
self._updatePosition(
axes) # all the referenced axes should be back to 0
# read-only so manually notify
self.referenced.notify(self.referenced.value)
class PowerControlUnit(model.PowerSupplier):
'''
Implements the PowerSupplier class to regulate the power supply of the
components connected to the Power Control Unit board. It also takes care of
communication with the PCU firmware.
'''
def __init__(self, name, role, port, pin_map=None, delay=None, init=None, ids=None, **kwargs):
'''
port (str): port name
pin_map (dict of str -> int): names of the components
and the pin where the component is connected.
delay (dict str -> float): time to wait for each component after it is
turned on.
init (dict str -> boolean): turn on/off the corresponding component upon
initialization.
ids (list str): EEPROM ids expected to be detected during initialization.
Raise an exception if the device cannot be opened
'''
if pin_map:
self.powered = pin_map.keys()
else:
self.powered = []
model.PowerSupplier.__init__(self, name, role, **kwargs)
# TODO: catch errors and convert to HwError
self._ser_access = threading.Lock()
self._file = None
self._port = self._findDevice(port) # sets ._serial and ._file
logging.info("Found Power Control device on port %s", self._port)
# Get identification of the Power control device
self._idn = self._getIdentification()
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "serial driver: %s" % (driver_name,)
self._hwVersion = "%s" % (self._idn,)
pin_map = pin_map or {}
self._pin_map = pin_map
delay = delay or {}
# fill the missing pairs with 0 values
self._delay = dict.fromkeys(pin_map, 0)
self._delay.update(delay)
self._last_start = dict.fromkeys(self._delay, time.time())
# will take care of executing switch asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
self._supplied = {}
self.supplied = model.VigilantAttribute(self._supplied, readonly=True)
self._updateSupplied()
init = init or {}
# Remove all None's from the dict, so it can be passed as-is to _doSupply()
for k, v in init.items():
if v is None:
del init[k]
try:
self._doSupply(init, apply_delay=False)
except IOError as ex:
# This is in particular to handle some cases where the device resets
# when turning on the power. One or more trials and the
logging.exception("Failure during turning on initial power.")
raise HwError("Device error when initialising power: %s. "
"Try again or contact support if the problem persists." %
(ex,))
self.memoryIDs = model.VigilantAttribute(None, readonly=True, getter=self._getIdentities)
if ids:
mem_ids = self.memoryIDs.value
for eid in ids:
if eid not in mem_ids:
raise HwError("EEPROM id %s was not detected. Make sure "
"all EEPROM components are connected." % (eid,))
@isasync
def supply(self, sup):
"""
Change the power supply to the defined state for each component given.
This is an asynchronous method.
sup dict(string-> boolean): name of the component and new state
returns (Future): object to control the supply request
"""
if not sup:
return model.InstantaneousFuture()
self._checkSupply(sup)
return self._executor.submit(self._doSupply, sup)
def _doSupply(self, sup, apply_delay=True):
"""
supply power
apply_delay (bool): If true, wait the amount of time requested in delay
after turning on the power
"""
for comp, val in sup.items():
# find pin and values corresponding to component
pin = self._pin_map[comp]
# should always be able to get the value, default values just to be
# on the safe side
if apply_delay:
delay = self._delay.get(comp, 0)
else:
# We still wait a little, to avoid starting all components
# _exactly_ at the same time, which could cause a power peak.
delay = 1
if val:
self._sendCommand("PWR " + str(pin) + " 1")
state = self.supplied.value[comp]
if state:
# Already on, wait the time remaining
remaining = (self._last_start[comp] + delay) - time.time()
time.sleep(max(0, remaining))
else:
# wait full time
self._last_start[comp] = time.time()
time.sleep(delay)
# Check it really worked
ans = self._sendCommand("PWR? " + str(pin))
if ans != "1":
logging.warning("Failed to turn on component %s", comp)
else:
self._sendCommand("PWR " + str(pin) + " 0")
self._updateSupplied()
def _updateSupplied(self):
"""
update the supplied VA
"""
pins_updated = set(self._pin_map.values()) # to avoid asking for the same pin multiple times
for pin in pins_updated:
ans = self._sendCommand("PWR? " + str(pin))
# Update all components that are connected to the same pin
to_update = [c for c in self.powered if pin == self._pin_map[c]]
for c_update in to_update:
self._supplied[c_update] = (ans == "1")
# it's read-only, so we change it via _value
self.supplied._value = self._supplied
self.supplied.notify(self.supplied.value)
def terminate(self):
if self._executor:
self._executor.cancel()
self._executor.shutdown()
self._executor = None
if self._serial:
with self._ser_access:
self._serial.close()
self._serial = None
if self._file:
self._file.close()
self._file = None
def _getIdentification(self):
return self._sendCommand("*IDN?")
def writeMemory(self, id, address, data):
"""
Write data to EEPROM.
id (str): EEPROM registration number #hex (little-endian format)
address (str): starting address #hex
data (str): data to be written #hex (little-endian format)
"""
self._sendCommand("WMEM %s %s %s" % (id, address, data))
def readMemory(self, id, address, length):
"""
Read data from EEPROM.
id (str): EEPROM registration number #hex (little-endian format)
address (str): starting address #hex
length (int): number of bytes to be read
returns (str): data read back #hex (little-endian format)
"""
ans = self._sendCommand("RMEM %s %s %s" % (id, address, length))
return ans
def readEEPROM(self, id):
"""
We use this method to get a dict that contains all the data written in
the EEPROM with the given id.
id (str): EEPROM registration number #hex (little-endian format)
"""
if id not in self.memoryIDs.value:
raise KeyError("There was no EEPROM with the given id found")
mem_cont = self.readMemory(id, "00", EEPROM_CAPACITY)
mem_yaml = ""
while mem_cont != "":
if mem_cont[:2] != "00":
mem_yaml += chr(int(mem_cont[:2], 16))
mem_cont = mem_cont[2:]
dct = yaml.load(mem_yaml)
return dct
def _getIdentities(self):
"""
Return the ids of connected EEPROMs
"""
try:
ans = self._sendCommand("SID")
except PowerControlError as e:
# means there is no power provided
raise HwError("There is no power provided to the Power Control Unit. "
"Please make sure the board is turned on.")
x = ans.split(',')
return filter(lambda a: a != '', x)
def _sendCommand(self, cmd):
"""
cmd (str): command to be sent to Power Control unit.
returns (str): answer received from the Power Control unit
raises:
IOError: if an ERROR is returned by the Power Control firmware.
"""
cmd = cmd + "\n"
with self._ser_access:
logging.debug("Sending command %s", cmd.encode('string_escape'))
self._serial.write(cmd)
ans = ''
char = None
while char != '\n':
char = self._serial.read()
if not char:
logging.error("Timeout after receiving %s", ans.encode('string_escape'))
# TODO: See how you should handle a timeout before you raise
# an HWError
raise HwError("Power Control Unit connection timeout. "
"Please turn off and on the power to the box.")
# Handle ERROR coming from Power control unit firmware
ans += char
logging.debug("Received answer %s", ans.encode('string_escape'))
if ans.startswith("ERROR"):
raise PowerControlError(ans.split(' ', 1)[1])
return ans.rstrip()
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a Power control device.
port (string): the name of the serial port (e.g., /dev/ttyACM0)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
timeout=1 # s
)
# Purge
ser.flush()
ser.flushInput()
# Try to read until timeout to be extra safe that we properly flushed
while True:
char = ser.read()
if char == '':
break
logging.debug("Nothing left to read, Power Control Unit can safely initialize.")
ser.timeout = 5 # Sometimes the software-based USB can have some hiccups
return ser
def _findDevice(self, ports):
"""
Look for a compatible device
ports (str): pattern for the port name
return (str): the name of the port used
It also sets ._serial and ._idn to contain the opened serial port, and
the identification string.
raises:
IOError: if no device are found
"""
# For debugging purpose
if ports == "/dev/fake":
self._serial = PowerControlSimulator(timeout=1)
return ports
if os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
self._file = open(n) # Open in RO, just to check for lock
try:
fcntl.flock(self._file.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB)
except IOError:
logging.info("Port %s is busy, will wait and retry", n)
time.sleep(11)
fcntl.flock(self._file.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB)
self._serial = self._openSerialPort(n)
try:
idn = self._getIdentification()
except PowerControlError:
# Can happen if the device has received some weird characters
# => try again (now that it's flushed)
logging.info("Device answered by an error, will try again")
idn = self._getIdentification()
# Check that we connect to the right device
if not idn.startswith("Delmic Analog Power"):
logging.info("Connected to wrong device on %s, skipping.", n)
continue
return n
except (IOError, PowerControlError):
# not possible to use this port? next one!
logging.debug("Skipping port %s which doesn't seem the right device", n)
continue
else:
raise HwError("Failed to find a Power Control device on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports,))
@classmethod
def scan(cls):
"""
returns (list of 2-tuple): name, args (sn)
Note: it's obviously not advised to call this function if a device is already under use
"""
logging.info("Serial ports scanning for Power control device in progress...")
found = [] # (list of 2-tuple): name, kwargs
if sys.platform.startswith('linux'):
# Look for each ACM device, if the IDN is the expected one
acm_paths = glob.glob('/dev/ttyACM?')
for port in acm_paths:
# open and try to communicate
try:
dev = cls(name="test", role="test", port=port)
idn = dev._getIdentification()
if idn.startswith("Delmic Analog Power"):
found.append({"port": port})
except Exception:
pass
else:
# TODO: Windows version
raise NotImplementedError("OS not yet supported")
return found
class PMD401Bus(Actuator):
"""
This represents the PMD401 motor controller bus for the PiezoMotor LEGS motors. It supports multiple controllers
(each one handling one axis), connected in a daisy chain. Only the first
controller is directly connected to the computer.
The specification for the hardware interface can be found in the document
"PiezoMotor_PMD401_Technical_Manual.pdf".
"""
def __init__(self, name, role, port, axes, inverted=None, **kwargs):
"""
:param axes (dict: {"x", "y", "z"} --> dict): axis name --> axis parameters
Each axis is specified by a set of parameters.
After successful configuration with the pmconfig.py script, the only required parameter for a default motor
is the address which was set during the configuration process.
The spc parameter (conversion between motor steps and encoder counts) is typically saved in the flash
memory of the controller during the configuration process. The flash value is overridden by the
value in the parameter dict.
Depending on the type of motor, the encoder_resolution and range might need to be adjusted.
Axis parameters:
axis_number (0 <= int <= 127): typically 1-3 for x-z, required
closed_loop (bool): True for closed loop (with encoder), default to True
encoder_resolution (float): encoder resolution in m/step
spc (float): motor steps per encoder count, default to value in non-volatile memory
limit_type (0 <= int <= 2): type of limit switch, 0: no limit, 1: active high, 2: active low, default 0
range (tuple of float): in m, default to (0, STROKE_RANGE)
speed (float): speed in m/s
unit (str), default to m
"""
self._axis_map = {} # axis name -> axis number used by controller
self._closed_loop = {} # axis name (str) -> bool (True if closed loop)
self._speed_steps = {
} # axis name (str) -> int, speed in steps per meter
self._portpattern = port
# Conversion factors
# Count refers to encoder counts, step refers to motor steps. The encoder counts are fixed and given
# as a parameter to the axis, the motor counts are determined during configuration and are usually
# stored in flash memory.
# ._steps_per_meter is redundant, but convenient
self._steps_per_count = {} # axis name (str) -> float
self._steps_per_meter = {} # axis name (str) -> float
self._counts_per_meter = {} # axis name (str) -> float
# Parse axis parameters and create axis
axes_def = {} # axis name -> Axis object
for axis_name, axis_par in axes.items():
if 'axis_number' in axis_par:
axis_num = axis_par['axis_number']
if axis_num not in range(128):
raise ValueError(
"Invalid axis number %s, needs to be 0 <= int <= 127."
% axis_num)
elif axis_num in self._axis_map.values():
axname = self._axis_map[axis_num]
raise ValueError(
"Invalid axis number %s, already assigned to axis %s."
% (axis_num, axname))
else:
self._axis_map[axis_name] = axis_par['axis_number']
else:
raise ValueError("Axis %s has no axis number." % axis_name)
if 'closed_loop' in axis_par:
closed_loop = axis_par['closed_loop']
else:
closed_loop = False
logging.info(
"Axis mode (closed/open loop) not specified for axis %s. Assuming closed loop.",
axis_name)
self._closed_loop[axis_name] = closed_loop
if 'encoder_resolution' in axis_par:
self._counts_per_meter[axis_name] = 1 / axis_par[
'encoder_resolution'] # approximately 5e-6 m / step
else:
self._counts_per_meter[axis_name] = DEFAULT_COUNTS_PER_METER
logging.info(
"Axis %s has no encoder resolution, assuming %s." %
(axis_name, 1 / DEFAULT_COUNTS_PER_METER))
if 'limit_type' in axis_par:
limit_type = axis_par['limit_type']
else:
logging.info("Axis %s has not limit switch." % axis_name)
limit_type = 0
if 'range' in axis_par:
axis_range = axis_par['range']
else:
axis_range = (0, STROKE_RANGE)
logging.info("Axis %s has no range. Assuming %s", axis_name,
axis_range)
if 'spc' in axis_par:
self._steps_per_count[axis_name] = axis_par[
'spc'] # approximately 5e-6 m / step
else:
logging.info(
"Axis %s has no spc parameter, will use value from flash."
% axis_name)
# None for now, will read value from flash later.
self._steps_per_count[axis_name] = None
if 'speed' in axis_par:
self._speed = axis_par['speed']
else:
self._speed = DEFAULT_AXIS_SPEED
logging.info(
"Axis %s was not given a speed value. Assuming %s",
axis_name, self._speed)
if 'unit' in axis_par:
axis_unit = axis_par['unit']
else:
axis_unit = "m"
logging.info("Axis %s has no unit. Assuming %s", axis_name,
axis_unit)
ad = model.Axis(canAbs=closed_loop,
unit=axis_unit,
range=axis_range)
axes_def[axis_name] = ad
Actuator.__init__(self,
name,
role,
axes=axes_def,
inverted=inverted,
**kwargs)
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
self._ser_access = threading.RLock()
# Connect to hardware
self._port = None # port number
min_axis = min(self._axis_map.values())
self._serial = self._findDevice(port, min_axis)
self._recovering = False
# Get version
hwVersions = []
for ax_name, ax_num in self._axis_map.items():
ver = self.getVersion(ax_num)
sn = self.getSerialNumber(ax_num)
hwVersions.append("Axis %s ('%s') version: %s, " %
(ax_num, ax_name, ver) +
"serial number: %s" % sn)
self._hwVersion = ", ".join(hwVersions)
# Configuration
for axis in self._axis_map.values():
self.setWaveform(axis, WAVEFORM_DELTA)
driver_name = getSerialDriver(self._port)
self._swVersion = "Serial driver: %s" % (driver_name, )
# Position and referenced VAs
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self.referenced = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
for axname in self._axis_map.keys():
self.referenced.value[
axname] = False # just assume they haven't been referenced
# Load values from flash, write spc if provided, otherwise read spc
for axname, axis in self._axis_map.items():
# Load values from flash (most importantly spc parameter)
self.initFromFlash(axis)
if self._steps_per_count[axname]:
# Write SPC if provided
# Value that's written to register needs to be multiplied by (65536 * 4) (see manual)
self.writeParam(axis, 11,
self._steps_per_count[axname] * (65536 * 4))
else:
# Read spc from flash. If value is not reasonable, use default
val = int(self.readParam(axis, 11))
if not 20000 <= val <= 150000:
# that's not a reasonable value, the flash was probably not configured
logging.warning(
"Axis %s spc value not configured properly, current value: %s"
% (axis, val))
logging.info("Axis %s using spc value %s" %
(axis, DEFAULT_SPC))
val = DEFAULT_SPC
else:
val = val / (65536 * 4)
logging.info("Axis %s is using spc value from flash: %s" %
(axis, val))
self._steps_per_count[axname] = val
self._steps_per_meter[axname] = self._steps_per_count[
axname] * self._counts_per_meter[axname]
self._speed_steps[axis_name] = round(
self._speed * self._steps_per_meter[axis_name])
# Limit switch
for axis in self._axis_map.values():
self.setLimitType(axis, limit_type)
def terminate(self):
# terminate can be called several times, do nothing if ._serial is already None
if self._serial is None:
return
self._serial.close()
self._serial = None
for axis in self._axis_map.values():
self.setWaveform(axis, WAVEFORM_PARK) # power off
super(PMD401Bus, self).terminate()
def stop(self, axes=None):
self._executor.cancel()
axes = axes or self._axis_map.keys()
for ax in axes:
self.stopAxis(self._axis_map[ax])
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
def moveAbs(self, pos):
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
def reference(self, axes):
self._checkReference(axes)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doReference, f, axes)
return f
def _doReference(self, f, axes):
self._check_hw_error()
# Request referencing on all axes
for axname in axes:
# If we're already at the index position or behind (index is at 8.9 µm from limit),
# referencing doesn't work.
# To avoid this, we first make a small move in the opposite direction (10 µm).
fmove = self._createMoveFuture()
self._doMoveRel(fmove, {axname: 1e-5})
self.startIndexMode(self._axis_map[axname])
self.moveToIndex(self._axis_map[axname])
# Wait until referencing is done
timeout = 2 * (abs(self.axes[axname].range[1] -
self.axes[axname].range[0]) / self._speed)
startt = time.time()
for axname in axes:
self.referenced._value[axname] = False
while not self.getIndexStatus(self._axis_map[axname])[-1]:
if f._must_stop.is_set():
return
if time.time() - startt > timeout:
self.stop() # exit index mode
raise ValueError("Referencing axis %s failed." %
self._axis_map[axname])
time.sleep(0.1)
logging.debug("Finished referencing axis %s." % axname)
self.stopAxis(self._axis_map[axname])
self.referenced._value[axname] = True
# read-only so manually notify
self.referenced.notify(self.referenced.value)
self._updatePosition()
def _doMoveAbs(self, f, pos):
self._check_hw_error()
targets = {}
for axname, val in pos.items():
if self._closed_loop[axname]:
encoder_cnts = round(val * self._counts_per_meter[axname])
self.runAbsTargetMove(self._axis_map[axname], encoder_cnts,
self._speed_steps[axname])
targets[axname] = val
else:
target = val - self.position.value[axname]
steps_float = target * self._steps_per_meter[axname]
steps = int(steps_float)
usteps = int((steps_float - steps) * USTEPS_PER_STEP)
self.runMotorJog(self._axis_map[axname], steps, usteps,
self._speed_steps[axname])
targets[axname] = None
self._waitEndMotion(f, targets)
# Leave target mode in case of closed-loop move
for ax in pos:
self.stopAxis(self._axis_map[ax])
self._updatePosition()
def _doMoveRel(self, f, shift):
self._check_hw_error()
targets = {}
self._updatePosition()
for axname, val in shift.items():
if self._closed_loop[axname]:
targets[axname] = self.position.value[axname] + val
encoder_cnts = val * self._counts_per_meter[axname]
self.runRelTargetMove(self._axis_map[axname], encoder_cnts)
else:
steps_float = val * self._steps_per_meter[axname]
steps = int(steps_float)
usteps = int((steps_float - steps) * USTEPS_PER_STEP)
self.runMotorJog(self._axis_map[axname], steps, usteps,
self._speed_steps[axname])
targets[axname] = None
self._waitEndMotion(f, targets)
# Leave target mode in case of closed-loop move
for ax in shift:
self.stopAxis(self._axis_map[ax])
self._updatePosition()
def _waitEndMotion(self, f, targets):
"""
Wait until move is done.
:param f: (CancellableFuture) move future
:param targets: (dict: str --> int) target (for closed-loop), None for open loop
"""
move_length = 0
self._updatePosition()
for ax, target in targets.items():
if target is not None:
move_length = max(abs(self.position.value[ax] - target),
move_length)
if move_length == 0: # open loop
move_length = STROKE_RANGE
dur = move_length / self._speed
max_dur = max(dur * 2, 0.1) # wait at least 0.1 s
logging.debug("Expecting a move of %g s, will wait up to %g s", dur,
max_dur)
for axname, target in targets.items():
axis = self._axis_map[axname]
moving = True
end_time = time.time() + max_dur
while moving:
if f._must_stop.is_set():
return
if time.time() > end_time:
raise IOError(
"Timeout while waiting for end of motion on axis %s" %
axis)
if self._closed_loop[axname]:
if target is None:
raise ValueError(
"No target provided for closed-loop move on axis %s."
% axis)
moving = self.isMovingClosedLoop(axis)
else:
moving = self.isMovingOpenLoop(axis)
self._check_hw_error()
time.sleep(0.05)
def _check_hw_error(self):
"""
Read hardware status and raise exception if error is detected.
"""
for ax, axnum in self._axis_map.items():
status = self.getStatus(axnum)
if status[0] & 8:
raise PMDError(
1,
"Communication Error (wrong baudrate, data collision, or buffer overflow)"
)
elif status[0] & 4:
raise PMDError(
2,
"Encoder error(serial communication or reported error from serial encoder)"
)
elif status[0] & 2:
raise PMDError(3,
"Supply voltage or motor fault was detected.")
elif status[0] & 1:
raise PMDError(
4,
"Command timeout occurred or a syntax error was detected when response was not "
"allowed.")
elif status[1] & 8:
raise PMDError(5, "Power-on/reset has occurred.")
def _updatePosition(self):
"""
Update the position VA.
"""
pos = {}
for axname, axis in self._axis_map.items():
pos[axname] = self.getEncoderPosition(axis)
logging.debug("Reporting new position at %s", pos)
pos = self._applyInversion(pos)
self.position._set_value(pos, force_write=True)
def stopAxis(self, axis):
self._sendCommand(b'X%dS' % axis)
def getVersion(self, axis):
"""
:param axis: (int) axis number
:returns (str): controller type and firmware version, e.g. 'PMD401 V13'
"""
return self._sendCommand(b'X%d?' % axis)
def getSerialNumber(self, axis):
"""
:param axis: (int) axis number
:returns (str): serial number
"""
return self._sendCommand(b'X%dY42' % axis)
def initFromFlash(self, axis):
"""
Initialize settings from values stored in flash.
:param axis: (int) axis number
"""
# 2 for init from flash, 3 for factory values
self._sendCommand(b'X%dY1,2' % axis)
def setLimitType(self, axis, limit_type):
"""
:param axis: (int) axis number
:param limit_type: (0 <= int <= 3) 0 no limit, 1 active high, 2 active low
"""
self._sendCommand(b'X%dY2,%d' % (axis, limit_type))
def getEncoderPosition(self, axis):
"""
:param axis: (int) axis number
:returns (float): current position of the axis as reported by encoders (in m)
"""
axname = [name for name, num in self._axis_map.items()
if num == axis][0] # get axis name from number
return int(self._sendCommand(
b'X%dE' % axis)) / self._counts_per_meter[axname]
def runRelTargetMove(self, axis, encoder_cnts):
"""
Closed-loop relative move.
:param axis: (int) axis number
:param encoder_cnts: (int)
"""
# There are two possibilities: move relative to current position (XC) and move relative to
# target position (XR). We are moving relative to the current position (might be more intuitive
# if something goes wrong and we're stuck in the wrong position).
self._sendCommand(b'X%dC%d,%d' %
(axis, encoder_cnts, self._speed_steps['x']))
def runMotorJog(self, axis, motor_steps, usteps, speed):
"""
Open loop stepping.
:param axis: (int) axis number
:param motor_steps: (int) number of motor steps to move
:param usteps: (int) number of microsteps (1 motor step = 8192 microsteps)
:param speed: (int) speed in steps / m
"""
self._sendCommand(b'X%dJ%d,%d,%d' % (axis, motor_steps, usteps, speed))
def runAbsTargetMove(self, axis, encoder_cnts, speed):
"""
Closed loop move.
:param axis: (int) axis number
:param encoder_cnts: (int)
:param speed: speed in motor steps per s
"""
self._sendCommand(b'X%dT%d,%d' % (axis, encoder_cnts, speed))
def setWaveform(self, axis, wf):
"""
:param wf: (WAVEFORM_RHOMB, WAVEFORM_DELTA, WAVEFORM_PARK) waveform to set
"""
if wf not in (WAVEFORM_DELTA, WAVEFORM_RHOMB, WAVEFORM_PARK):
raise ValueError("wf %s not a valid waveform" % wf)
self._sendCommand(b'X%dM%d' % (axis, wf))
def getStatus(self, axis):
"""
:returns (list of 4 int): 4-bit status code
The most important values are the following
First bit:
8: communication error (wrong baudrate, data collision, or buffer overflow)
4: encoder error (serial communication or reported error from serial encoder)
2: voltage error (supply voltage or motor fault was detected)
1: command error (command timeout occurred or a syntax error was detected when response was not allowed)
Second bit:
8: reset (power on/ reset occurred)
1: index (index signal was detected since last report)
For all codes, please refer to the PMD-401 manual.
"""
return [int(i) for i in self._sendCommand(b'X%dU0' % axis)]
def isMovingClosedLoop(self, axis):
"""
:param axis: (int) axis number
:param target: (float) target position for axes
:returns: (bool) True if moving, False otherwise
"""
# Check d3 (third status value) bit 2 (targetLimit) and bit 0 (targetReached)
_, _, d3, _ = self.getStatus(axis)
if d3 & 0b0101:
# target or limit reached
return False
else:
return True
def isMovingOpenLoop(self, axis):
"""
:param axis: (int) axis number
:returns: (bool) True if moving, False otherwise
"""
resp = self._sendCommand(
b'X%dJ' % axis
) # will be 0 if finished, otherwise +/-222 (contrary to manual!)
return int(resp) != 0
def startIndexMode(self, axis):
"""
Enters index mode.
"""
self._sendCommand(b'X%dN4' % axis)
def moveToIndex(self, axis):
"""
Move towards the index until it's found.
"""
axname = [name for name, num in self._axis_map.items()
if num == axis][0] # get axis name from number
# Move towards fixed end (negative direction)
maxdist = int(-self._axes[axname].range[1] *
self._counts_per_meter[axname] *
DEFAULT_SPC) # complete rodlength
self._sendCommand(b'X%dI%d,0,%d' %
(axis, maxdist, self._speed_steps[axname]))
def getIndexStatus(self, axis):
"""
Returns a description of the index status.
:returns (tuple of 4):
mode (0 or 1): index mode (1 if position has been reset at index)
position (float):
logged (bool): position was logged since last report
indexed (bool): position has been reset at index
"""
# Check if referencing was successful
# Response looks like this: "1,132.,indexed"
ret = self._sendCommand(b'X%dN?' % axis).split(',')
try:
mode = ret[0]
if mode == '1':
mode = 1
else: # empty string means mode 0
mode = 0
if ret[1][-1] == '.':
# . means position was logged since last report
logged = True
position = ret[1][:-1]
else:
logged = False
position = ret[1]
if len(ret) > 2 and 'indexed' in ret[2]:
indexed = True
else:
indexed = False
return mode, position, logged, indexed
except Exception as ex:
logging.exception("Failed to parse index status %s", ret)
raise
def setAxisAddress(self, current_address, new_address):
"""
Set the address of the axis. The factory default is 0 for all boards. Don't use this
command if multiple axes with the same number are connected.
:param current_address: (int) current axis number
:param new_address: (int) new axis number
"""
self._sendCommand(b"X%dY40,%d" % (current_address, new_address))
def runAutoConf(self, axis):
"""
Runs automatic configuration for the encoder parameters.
:param axis: (int) axis number
"""
self._sendCommand(b"X%dY25,1" % axis)
def writeParamsToFlash(self, axis):
self._sendCommand(b"X%dY32" % axis)
def setParam(self, axis, param, value):
self._sendCommand(b"X%dY%d,%d" % (axis, param, value))
def readParam(self, axis, param):
"""
:returns (str): parameter value from device
"""
return self._sendCommand(b"X%dY%d" % (axis, param))
def _createMoveFuture(self):
"""
:returns: (CancellableFuture) a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event(
) # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set(
) # tell the thread taking care of the move it's over
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
def _sendCommand(self, cmd):
"""
:param cmd: (bytes) command to be sent to the hardware
:returns: (str) response
"""
cmd += EOL
with self._ser_access:
logging.debug("Sending command %s", to_str_escape(cmd))
self._serial.write(cmd)
resp = b""
while resp[-len(EOL):] != EOL:
try:
char = self._serial.read()
except IOError:
logging.warning(
"Failed to read from PMT Control firmware, "
"trying to reconnect.")
if self._recovering:
raise
else:
self._tryRecover()
# don't send command again
raise IOError(
"Failed to read from PMT Control firmware, "
"restarted serial connection.")
if not char:
raise IOError("Timeout after receiving %s" %
to_str_escape(resp))
else:
resp += char
logging.debug("Received response %s", to_str_escape(resp))
# Check response (command should be echoed back)
if not resp.startswith(cmd[:-len(EOL) - 1]):
raise IOError("Response starts with %s != %s" %
(resp[:len(cmd)], cmd))
if b"_??_" in resp:
raise ValueError(
"Received response %s, command %s not understood." %
(resp, cmd))
if b"!" in resp:
raise PMDError(0, resp)
# Format:
# * for query with response: <cmd>:<ret><EOL> (will return <ret>)
# * for set command without response: <cmd><EOL> (will return "")
return resp[len(cmd) + 1 - len(EOL):-len(EOL)].decode("latin1")
def _tryRecover(self):
self._recovering = True
self.state._set_value(HwError("Connection lost, reconnecting..."),
force_write=True)
# Retry to open the serial port (in case it was unplugged)
# _ser_access should already be acquired, but since it's an RLock it can be acquired
# again in the same thread
try:
with self._ser_access:
while True:
try:
if self._serial:
self._serial.close()
self._serial = None
except Exception:
pass
try:
logging.debug("Searching for the device on port %s",
self._portpattern)
min_axis = min(self._axis_map.values())
self._port = self._findDevice(self._portpattern,
min_axis)
except IOError:
time.sleep(2)
except Exception:
logging.exception(
"Unexpected error while trying to recover device")
raise
else:
# We found it back!
break
# it now should be accessible again
self.state._set_value(model.ST_RUNNING, force_write=True)
logging.info("Recovered device on port %s", self._port)
finally:
self._recovering = False
def _findDevice(self, port, address=0):
"""
Look for a compatible device
port (str): pattern for the port name
address (None or int): the address of the stage controller
return (serial, int): the (opened) serial port used, and the actual address
raises:
IOError: if no device are found
"""
if port.startswith("/dev/fake"):
names = [port]
elif os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(port)
for n in names:
try:
serial = self._openSerialPort(n)
except IOError as ex:
# not possible to use this port? next one!
logging.info("Skipping port %s, which is not available (%s)",
n, ex)
continue
# check whether it answers with the right address
try:
# If any garbage was previously received, make it discarded.
self._serial = serial
self._serial.flush()
if 'PMD401 ' in self.getVersion(address):
self._port = n
return serial # found it!
except Exception as ex:
logging.debug(
"Port %s doesn't seem to have a PMD device connected: %s",
n, ex)
serial.close() # make sure to close/unlock that port
else:
raise IOError(
"Failed to find a PMD controller with adress %s on ports '%s'. "
"Check that the device is turned on and "
"connected to the computer." % (
address,
port,
))
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a PiezoMotor PMD device.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
raise HwError: if the serial port cannot be opened (doesn't exist, or
already opened)
"""
# For debugging purpose
if port == "/dev/fake":
return PMDSimulator(timeout=0.1)
try:
ser = serial.Serial(
port=port,
baudrate=BAUDRATE,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=0.3, # s
)
except IOError:
raise HwError("Failed to find a PMD controller on port '%s'. "
"Check that the device is turned on and "
"connected to the computer." % (port, ))
return ser
class Stage(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
moving the Tescan stage and updating the position.
"""
def __init__(self, name, role, parent, **kwargs):
"""
axes (set of string): names of the axes
"""
axes_def = {}
self._position = {}
rng = [-0.5, 0.5]
axes_def["x"] = model.Axis(unit="m", range=rng)
axes_def["y"] = model.Axis(unit="m", range=rng)
axes_def["z"] = model.Axis(unit="m", range=rng)
# Demand calibrated stage
if parent._device.StgIsCalibrated() !=1:
logging.warning("Stage was not calibrated. We are performing calibration now.")
parent._device.StgCalibrate()
#Wait for stage to be stable after calibration
while parent._device.StgIsBusy() != 0:
# If the stage is busy (movement is in progress), current position is
# updated approximately every 500 ms
time.sleep(0.5)
x, y, z, rot, tilt = parent._device.StgGetPosition()
self._position["x"] = -x * 1e-3
self._position["y"] = -y * 1e-3
self._position["z"] = -z * 1e-3
model.Actuator.__init__(self, name, role, parent=parent, axes=axes_def, **kwargs)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute(
self._applyInversionAbs(self._position),
unit="m", readonly=True)
def _updatePosition(self):
"""
update the position VA
"""
# it's read-only, so we change it via _value
self.position._value = self._applyInversionAbs(self._position)
self.position.notify(self.position.value)
def _doMove(self, pos):
"""
move to the position
"""
# Perform move through Tescan API
# Position from m to mm and inverted
self.parent._device.StgMoveTo(-pos["x"] * 1e3,
- pos["y"] * 1e3,
- pos["z"] * 1e3)
# Obtain the finally reached position after move is performed.
# This is mainly in order to keep the correct position in case the
# move we tried to perform was greater than the maximum possible
# one.
with self.parent._acquisition_init_lock:
x, y, z, rot, tilt = self.parent._device.StgGetPosition()
self._position["x"] = -x * 1e-3
self._position["y"] = -y * 1e-3
self._position["z"] = -z * 1e-3
self._updatePosition()
@isasync
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversionRel(shift)
for axis, change in shift.items():
self._position[axis] += change
pos = self._position
return self._executor.submit(self._doMove, pos)
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversionAbs(pos)
for axis, new_pos in pos.items():
self._position[axis] = new_pos
pos = self._position
return self._executor.submit(self._doMove, pos)
def stop(self, axes=None):
# Empty the queue for the given axes
self._executor.cancel()
logging.warning("Stopping all axes: %s", ", ".join(self.axes))
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
class Stage(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
moving the Zeiss stage and updating the position.
"""
def __init__(self, name, role, parent, rng=None, **kwargs):
"""
inverted (set of str): names of the axes which are inverted
rng (dict str -> (float,float)): axis name -> min/max of the position on
this axis. Note: if the axis is inverted, the range passed will be
inverted. Also, if the hardware reports position outside of the range,
move might fail, as it is considered outside of the range.
"""
if rng is None:
rng = {}
if "x" not in rng:
rng["x"] = (5e-3, 152e-3)
if "y" not in rng:
rng["y"] = (5e-3, 152e-3)
if "z" not in rng:
rng["z"] = (5e-3, 40e-3)
axes_def = {
# Ranges are from the documentation
"x": model.Axis(unit="m", range=(rng["x"][0], rng["x"][1])),
"y": model.Axis(unit="m", range=(rng["y"][0], rng["y"][1])),
"z": model.Axis(unit="m", range=(rng["z"][0], rng["z"][1])),
}
model.Actuator.__init__(self, name, role, parent=parent, axes=axes_def, **kwargs)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
# Refresh regularly the position
self._pos_poll = util.RepeatingTimer(5, self._refreshPosition, "Position polling")
self._pos_poll.start()
def _updatePosition(self, raw_pos=None):
"""
update the position VA
raw_pos (dict str -> float): the position in mm (as received from the SEM)
"""
if raw_pos is None:
x, y, z, _ = self.parent.GetStagePosition()
else:
x, y, z = raw_pos["x"], raw_pos["y"], raw_pos["z"]
pos = {"x": x * 1e-3,
"y": y * 1e-3,
"z": z * 1e-3,
}
self.position._set_value(self._applyInversion(pos), force_write=True)
def _refreshPosition(self):
"""
Called regularly to update the current position
"""
# We don't use the VA setters, to avoid sending back to the hardware a
# set request
logging.debug("Updating SEM stage position")
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
def _doMoveRel(self, future, shift):
"""
move by the shift
shift (float): unit m
"""
x, y, z, _ = self.parent.GetStagePosition()
if "x" in shift:
x += shift["x"] * 1e3
if "y" in shift:
y += shift["y"] * 1e3
if "z" in shift:
z += shift["z"] * 1e3
target_pos = self._applyInversion({"x": x * 1e-3, "y": y * 1e-3, "z": z * 1e-3})
# Check range (for the axes we are moving)
for an in shift.keys():
rng = self.axes[an].range
p = target_pos[an]
if not rng[0] <= p <= rng[1]:
raise ValueError("Relative move would cause axis %s out of bound (%g m)" % (an, p))
self._moveTo(future, x, y, z)
def _doMoveAbs(self, future, pos):
"""
move to position pos
pos (float): unit m
"""
# Don't change position for unspecified coordinates
x, y, z, _ = self.parent.GetStagePosition()
# Convert to mm
if "x" in pos:
x = pos["x"] * 1e3
if "y" in pos:
y = pos["y"] * 1e3
if "z" in pos:
z = pos["z"] * 1e3
self._moveTo(future, x, y, z)
def _moveTo(self, future, x, y, z, timeout=60):
with future._moving_lock:
try:
if future._must_stop.is_set():
raise CancelledError()
logging.debug("Moving to position (%s, %s, %s)", x, y, z)
self.parent.MoveStage(x, y, z)
# documentation suggests to wait 1s before calling
# GetStagePosition() after MoveStage()
time.sleep(1)
# Wait until the move is over
# Don't check for future._must_stop because anyway the stage will
# stop moving, and so it's nice to wait until we know the stage is
# not moving.
moving = True
tstart = time.time()
while moving:
x, y, z, moving = self.parent.GetStagePosition()
# Take the opportunity to update .position
self._updatePosition({"x": x, "y": y, "z": z})
if time.time() > tstart + timeout:
self.parent.Abort()
logging.error("Timeout after submitting stage move. Aborting move.")
break
# 50 ms is about the time it takes to read the stage status
time.sleep(50e-3)
# If it was cancelled, Abort() has stopped the stage before, and
# we still have waited until the stage stopped moving. Now let
# know the user that the move is not complete.
if future._must_stop.is_set():
raise CancelledError()
except RemconError:
if future._must_stop.is_set():
raise CancelledError()
raise
finally:
future._was_stopped = True
# Update the position, even if the move didn't entirely succeed
self._updatePosition()
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set() # tell the thread taking care of the move it's over
self.parent.Abort()
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
def _createFuture(self):
"""
Return (CancellableFuture): a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event() # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
@isasync
def moveRel(self, shift):
"""
shift (dict): shift in m
"""
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
@isasync
def moveAbs(self, pos):
"""
pos (dict): position in m
"""
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
def stop(self, axes=None):
# Empty the queue (and already stop the stage if a future is running)
self._executor.cancel()
# Try to stop the stage, even if no future is running, for safety
logging.warning("Stopping all axes: %s", ", ".join(self.axes))
self.parent.Abort()
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
class EbeamFocus(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
adjusting the ebeam focus by changing the working distance i.e. the distance
between the end of the objective and the surface of the observed specimen
"""
def __init__(self, name, role, parent, axes, ranges=None, **kwargs):
assert len(axes) > 0
if ranges is None:
ranges = {}
axes_def = {}
self._position = {}
# Just z axis
a = axes[0]
# The maximum, obviously, is not 1 meter. We do not actually care
# about the range since Tescan API will adjust the value set if the
# required one is out of limits.
rng = [0, 1]
axes_def[a] = model.Axis(unit="m", range=rng)
# start at the centre
self._position[a] = parent._device.GetWD() * 1e-3
model.Actuator.__init__(self, name, role, parent=parent, axes=axes_def, **kwargs)
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute(
self._applyInversionAbs(self._position),
unit="m", readonly=True)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
def _updatePosition(self):
"""
update the position VA
"""
# it's read-only, so we change it via _value
self.position._value = self._applyInversionAbs(self._position)
self.position.notify(self.position.value)
def _doMove(self, pos):
"""
move to the position
"""
# Perform move through Tescan API
# Position from m to mm and inverted
self.parent._device.SetWD(self._position["z"] * 1e03)
# Obtain the finally reached position after move is performed.
with self.parent._acquisition_init_lock:
wd = self.parent._device.GetWD()
self._position["z"] = wd * 1e-3
# Changing WD results to change in fov
self.parent._scanner.updateHorizontalFOV()
self._updatePosition()
@isasync
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversionRel(shift)
for axis, change in shift.items():
self._position[axis] += change
pos = self._position
return self._executor.submit(self._doMove, pos)
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversionAbs(pos)
for axis, new_pos in pos.items():
self._position[axis] = new_pos
pos = self._position
return self._executor.submit(self._doMove, pos)
def stop(self, axes=None):
# Empty the queue for the given axes
self._executor.cancel()
logging.warning("Stopping all axes: %s", ", ".join(self.axes))
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
class PM8742(model.Actuator):
"""
Represents one New Focus picomotor controller 8742.
"""
def __init__(self, name, role, address, axes, stepsize, sn=None, **kwargs):
"""
address (str): ip address (use "autoip" to automatically scan and find the
controller, "fake" for a simulator)
axes (list of str): names of the axes, from the 1st to the 4th, if present.
if an axis is not connected, put a "".
stepsize (list of float): size of a step in m (the smaller, the
bigger will be a move for a given distance in m)
sn (str or None): serial number of the device (eg, "11500"). If None, the
driver will use whichever controller is first found.
inverted (set of str): names of the axes which are inverted (IOW, either
empty or the name of the axis)
"""
if not 1 <= len(axes) <= 4:
raise ValueError("Axes must be a list of 1 to 4 axis names (got %s)" % (axes,))
if len(axes) != len(stepsize):
raise ValueError("Expecting %d stepsize (got %s)" %
(len(axes), stepsize))
self._name_to_axis = {} # str -> int: name -> axis number
for i, n in enumerate(axes):
if n == "": # skip this non-connected axis
continue
self._name_to_axis[n] = i + 1
for sz in stepsize:
if sz > 10e-3: # sz is typically ~1µm, so > 1 cm is very fishy
raise ValueError("stepsize should be in meter, but got %g" % (sz,))
self._stepsize = stepsize
self._address = address
self._sn = sn
self._accesser = self._openConnection(address, sn)
self._recover = False
self._resynchonise()
if name is None and role is None: # For scan only
return
# Seems to really be the device, so handle connection errors fully
self._recover = True
modl, fw, sn = self.GetIdentification()
if modl != "8742":
logging.warning("Controller %s is not supported, will try anyway", modl)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# Let the controller check the actuators are connected
self.MotorCheck()
axes_def = {}
speed = {}
for n, i in self._name_to_axis.items():
sz = self._stepsize[i - 1]
# TODO: allow to pass the range in m in the arguments
# Position supports ±2³¹, probably not that much in reality, but
# there is no info.
rng = [(-2 ** 31) * sz, (2 ** 31 - 1) * sz]
# Check the actuator is connected
mt = self.GetMotorType(i)
if mt in {MT_NONE, MT_UNKNOWN}:
raise HwError("Controller failed to detect motor %d, check the "
"actuator is connected to the controller" %
(i,))
max_stp_s = {MT_STANDARD: 2000, MT_TINY: 1750}[mt]
srng = (0, self._speedToMS(i, max_stp_s))
speed[n] = self._speedToMS(i, self.GetVelocity(i))
axes_def[n] = model.Axis(range=rng, speed=srng, unit="m")
model.Actuator.__init__(self, name, role, axes=axes_def, **kwargs)
self._swVersion = "%s (IP connection)" % (odemis.__version__,)
self._hwVersion = "New Focus %s (firmware %s, S/N %s)" % (modl, fw, sn)
# Note that the "0" position is just the position at which the
# controller turned on
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
max_speed = max(a.speed[1] for a in axes_def.values())
self.speed = model.MultiSpeedVA(speed, range=(0, max_speed),
unit="m/s", setter=self._setSpeed)
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown(wait=True)
self._executor = None
if self._accesser:
self._accesser.terminate()
self._accesser = None
def _sendOrderCommand(self, cmd, val="", axis=None):
return self._accesser.sendOrderCommand(cmd, val, axis)
def _sendQueryCommand(self, cmd, val="", axis=None):
"""
Same as accesser's sendQueryCommand, but with error recovery
"""
trials = 0
while True:
try:
return self._accesser.sendQueryCommand(cmd, val, axis)
except IOError: # Typically due to timeout
trials += 1
if not self._recover and trials < 5:
raise
self._recover = False
try:
# can also happen just due to error
# => first read error and see if that explains anything
self._checkError()
except IOError:
# Sometimes the hardware seems to lose connection
# => try to reconnect
logging.warning("Device seems disconnected, will try to reconnect")
# Sometimes the device gets confused and answers are shifted.
# Reset helps, but it also reset the current position, which
# is not handy.
# self._accesser.sendOrderCommand("RS")
self._accesser.terminate()
time.sleep(0.5)
self._accesser = self._openConnection(self._address, self._sn)
self._checkError()
logging.info("Recovered lost connection to device %s", self.name)
finally:
self._recover = True
# Low level functions
def GetIdentification(self):
"""
return (str, str, str):
Model name
Firmware version (and date)
serial number
"""
resp = self._sendQueryCommand("*IDN")
# expects something like this:
# New_Focus 8742 v2.2 08/01/13 11511
try:
m = re.match("\w+ (?P<model>\w+) (?P<fw>v\S+ \S+) (?P<sn>\d+)", resp)
modl, fw, sn = m.groups()
except Exception:
raise IOError("Failed to decode firmware answer '%s'" %
resp.encode('string_escape'))
return modl, fw, sn
def GetMotorType(self, axis):
"""
Read the motor type.
The motor check action must have been performed before to get correct
values.
axis (1<=int<=4): axis number
return (0<=int<=3): the motor type
"""
resp = self._sendQueryCommand("QM", axis=axis)
return int(resp)
def GetVelocity(self, axis):
"""
Read the max speed
axis (1<=int<=4): axis number
return (0<=int<=2000): the speed in step/s
"""
resp = self._sendQueryCommand("VA", axis=axis)
return int(resp)
def SetVelocity(self, axis, val):
"""
Write the max speed
axis (1<=int<=4): axis number
val (1<=int<=2000): the speed in step/s
"""
if not 1 <= val <= 2000:
raise ValueError("Velocity outside of the range 0->2000")
self._sendOrderCommand("VA", "%d" % (val,), axis)
def GetAccel(self, axis):
"""
Read the acceleration
axis (1<=int<=4): axis number
return (0<=int): the acceleration in step/s²
"""
resp = self._sendQueryCommand("AC", axis=axis)
return int(resp)
def SetAccel(self, axis, val):
"""
Write the acceleration
axis (1<=int<=4): axis number
val (1<=int<=200000): the acceleration in step/s²
"""
if not 1 <= val <= 200000:
raise ValueError("Acceleration outside of the range 0->200000")
self._sendOrderCommand("AC", "%d" % (val,), axis)
def MotorCheck(self):
"""
Run the motor check command, that automatically configure the right
values based on the type of motors connected.
"""
self._sendOrderCommand("MC")
def MoveAbs(self, axis, pos):
"""
Requests a move to an absolute position. This is non-blocking.
axis (1<=int<=4): axis number
pos (-2**31 <= int 2*31-1): position in step
"""
self._sendOrderCommand("PA", "%d" % (pos,), axis)
def GetTarget(self, axis):
"""
Read the target position for the given axis
axis (1<=int<=4): axis number
return (int): the position in steps
"""
# Note, it's not clear what's the difference with PR?
resp = self._sendQueryCommand("PA", axis=axis)
return int(resp)
def MoveRel(self, axis, offset):
"""
Requests a move to a relative position. This is non-blocking.
axis (1<=int<=4): axis number
offset (-2**31 <= int 2*31-1): offset in step
"""
self._sendOrderCommand("PR", "%d" % (offset,), axis)
def GetPosition(self, axis):
"""
Read the actual position for the given axis
axis (1<=int<=4): axis number
return (int): the position in steps
"""
resp = self._sendQueryCommand("TP", axis=axis)
return int(resp)
def IsMotionDone(self, axis):
"""
Check whether the axis is in motion
axis (1<=int<=4): axis number
return (bool): False if in motion, True if motion is finished
"""
resp = self._sendQueryCommand("MD", axis=axis)
if resp == "0": # motion in progress
return False
elif resp == "1": # no motion
return True
else:
raise IOError("Failed to decode answer about motion '%s'" %
resp.encode('string_escape'))
def AbortMotion(self):
"""
Stop immediately the motion on all the axes
"""
self._sendOrderCommand("AB")
def StopMotion(self, axis):
"""
Stop nicely the motion (using accel/decel values)
axis (1<=int<=4): axis number
"""
self._sendOrderCommand("ST", axis=axis)
def GetError(self):
"""
Read the oldest error in memory.
The error buffer is FIFO with 10 elements, so it might not be the
latest error if multiple errors have happened since the last time this
function was called.
return (None or (int, str)): the error number and message
"""
# Note: there is another one "TE" which only returns the number, and so
# is faster, but then there is no way to get the message
resp = self._sendQueryCommand("TB")
# returns something like "108, MOTOR NOT CONNECTED"
try:
m = re.match("(?P<no>\d+), (?P<msg>.+)", resp)
no, msg = int(m.group("no")), m.group("msg")
except Exception:
raise IOError("Failed to decode error info '%s'" %
resp.encode('string_escape'))
if no == 0:
return None
else:
return no, msg
def _checkError(self):
"""
Check if an error happened and convert to a python exception
return None
raise NewFocusError if an error happened
"""
err = self.GetError()
if err:
errno, msg = err
raise NewFocusError(errno, msg)
def _resynchonise(self):
"""
Ensures the device communication is "synchronised"
"""
self._accesser.flushInput()
# drop all the errors
while self.GetError():
pass
# high-level methods (interface)
def _updatePosition(self, axes=None):
"""
update the position VA
axes (set of str): names of the axes to update or None if all should be
updated
"""
# uses the current values (converted to internal representation)
pos = self._applyInversion(self.position.value)
for n, i in self._name_to_axis.items():
if axes is None or n in axes:
pos[n] = self.GetPosition(i) * self._stepsize[i - 1]
pos = self._applyInversion(pos)
# it's read-only, so we change it via _value
self.position._value = pos
self.position.notify(self.position.value)
def _speedToMS(self, axis, sps):
"""
Convert speed in step/s to m/s
axis (1<=int<=4): axis number
sps (int): steps/s
return (float): m/s
"""
return sps * self._stepsize[axis - 1]
def _setSpeed(self, value):
"""
value (dict string-> float): speed for each axis
returns (dict string-> float): the new value
"""
if set(value.keys()) != set(self._axes.keys()):
raise ValueError("Requested speed %s doesn't specify all axes %s" %
(value, self._axes.keys()))
for axis, v in value.items():
rng = self._axes[axis].speed
if not rng[0] < v <= rng[1]:
raise ValueError("Requested speed of %f for axis %s not within %f->%f" %
(v, axis, rng[0], rng[1]))
i = self._name_to_axis[axis]
sps = max(1, int(round(v / self._stepsize[i - 1])))
self.SetVelocity(i, sps)
return value
def _createFuture(self):
"""
Return (CancellableFuture): a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event() # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
# Check if the distance is big enough to make sense
for an, v in shift.items():
aid = self._name_to_axis[an]
if abs(v) < self._stepsize[aid - 1]:
# TODO: store and accumulate all the small moves instead of dropping them?
del shift[an]
logging.info("Dropped too small move of %g m < %g m",
abs(v), self._stepsize[aid - 1])
if not shift:
return model.InstantaneousFuture()
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
moveAbs.__doc__ = model.Actuator.moveAbs.__doc__
def stop(self, axes=None):
self._executor.cancel()
def _doMoveRel(self, future, pos):
"""
Blocking and cancellable relative move
future (Future): the future it handles
pos (dict str -> float): axis name -> relative target position
"""
with future._moving_lock:
end = 0 # expected end
moving_axes = set()
for an, v in pos.items():
aid = self._name_to_axis[an]
moving_axes.add(aid)
steps = int(round(v / self._stepsize[aid - 1]))
self.MoveRel(aid, steps)
# compute expected end
dur = abs(steps) * self._stepsize[aid - 1] / self.speed.value[an]
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
logging.debug("move successfully completed")
def _doMoveAbs(self, future, pos):
"""
Blocking and cancellable absolute move
future (Future): the future it handles
pos (dict str -> float): axis name -> absolute target position
"""
with future._moving_lock:
end = 0 # expected end
old_pos = self._applyInversion(self.position.value)
moving_axes = set()
for an, v in pos.items():
aid = self._name_to_axis[an]
moving_axes.add(aid)
steps = int(round(v / self._stepsize[aid - 1]))
self.MoveAbs(aid, steps)
# compute expected end
dur = abs(v - old_pos[an]) / self.speed.value[an]
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
logging.debug("move successfully completed")
def _waitEndMove(self, future, axes, end=0):
"""
Wait until all the given axes are finished moving, or a request to
stop has been received.
future (Future): the future it handles
axes (set of int): the axes IDs to check
end (float): expected end time
raise:
CancelledError: if cancelled before the end of the move
"""
moving_axes = set(axes)
last_upd = time.time()
last_axes = moving_axes.copy()
try:
while not future._must_stop.is_set():
for aid in moving_axes.copy(): # need copy to remove during iteration
if self.IsMotionDone(aid):
moving_axes.discard(aid)
if not moving_axes:
# no more axes to wait for
break
# Update the position from time to time (10 Hz)
if time.time() - last_upd > 0.1 or last_axes != moving_axes:
last_names = set(n for n, i in self._name_to_axis.items() if i in last_axes)
self._updatePosition(last_names)
last_upd = time.time()
last_axes = moving_axes.copy()
# Wait half of the time left (maximum 0.1 s)
left = end - time.time()
sleept = max(0.001, min(left / 2, 0.1))
future._must_stop.wait(sleept)
# TODO: timeout if really too long
else:
logging.debug("Move of axes %s cancelled before the end", axes)
# stop all axes still moving them
for i in moving_axes:
self.StopMotion(i)
future._was_stopped = True
raise CancelledError()
except Exception:
raise
else:
# Did everything really finished fine?
self._checkError()
finally:
self._updatePosition() # update (all axes) with final position
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set() # tell the thread taking care of the move it's over
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
@classmethod
def scan(cls):
"""
returns (list of (str, dict)): name, kwargs
Note: it's obviously not advised to call this function if a device is already under use
"""
logging.info("Scanning for New Focus controllers in progress...")
found = [] # (list of 2-tuple): name, kwargs
try:
conts = cls._scanOverIP()
except IOError as exp:
logging.exception("Failed to scan for New Focus controllers: %s", exp)
for hn, host, port in conts:
try:
logging.debug("Trying controller at %s", host)
dev = cls(None, None, address=host, axes=["a"], stepsize=[1e-6])
modl, fw, sn = dev.GetIdentification()
# find out about the axes
dev.MotorCheck()
axes = []
stepsize = []
for i in range(1, 5):
mt = dev.GetMotorType(i)
n = chr(ord('a') + i - 1)
# No idea about the stepsize, but make it different to allow
# distinguishing between motor types
if mt == MT_STANDARD:
ss = 1e-6
elif mt == MT_TINY:
ss = 0.1e-6
else:
n = ""
ss = 0
axes.append(n)
stepsize.append(ss)
except IOError:
# not possible to use this port? next one!
continue
except Exception:
logging.exception("Error while communicating with controller %s @ %s:%s",
hn, host, port)
continue
found.append(("NF-%s-%s" % (modl, sn),
{"address": host,
"axes": axes,
"stepsize": stepsize,
"sn": sn})
)
return found
@classmethod
def _openConnection(cls, address, sn=None):
"""
return (Accesser)
"""
if address == "fake":
host, port = "fake", 23
elif address == "autoip":
conts = cls._scanOverIP()
if sn is not None:
for hn, host, port in conts:
# Open connection to each controller and ask for their SN
dev = cls(None, None, address=host, axes=["a"], stepsize=[1e-6])
_, _, devsn = dev.GetIdentification()
if sn == devsn:
break
else:
raise HwError("Failed to find New Focus controller %s over the "
"network. Ensure it is turned on and connected to "
"the network." % (sn))
else:
# just pick the first one
# TODO: only pick the ones of model 8742
try:
hn, host, port = conts[0]
logging.info("Connecting to New Focus %s", hn)
except IndexError:
raise HwError("Failed to find New Focus controller over the "
"network. Ensure it is turned on and connected to "
"the network.")
else:
# split the (IP) port, separated by a :
if ":" in address:
host, ipport_str = port.split(":")
port = int(ipport_str)
else:
host = address
port = 23 # default
return IPAccesser(host, port)
@staticmethod
def _scanOverIP():
"""
Scan the network for all the responding new focus controllers
Note: it actually calls a separate executable because it relies on opening
a network port which needs special privileges.
return (list of (str, str, int)): hostname, ip address, and port number
"""
# Run the separate program via authbind
try:
exc = os.path.join(os.path.dirname(__file__), "nfpm_netscan.py")
out = subprocess.check_output(["authbind", "python", exc])
except CalledProcessError as exp:
# and handle all the possible errors:
# - no authbind (127)
# - cannot find the separate program (2)
# - no authorisation (13)
ret = exp.returncode
if ret == 127:
raise IOError("Failed to find authbind")
elif ret == 2:
raise IOError("Failed to find %s" % exc)
elif ret == 13:
raise IOError("No permission to open network port 23")
# or decode the output
# hostname \t host \t port
ret = []
for l in out.split("\n"):
if not l:
continue
try:
hn, host, port = l.split("\t")
except Exception:
logging.exception("Failed to decode scanner line '%s'", l)
ret.append((hn, host, port))
return ret
class ChamberPressure(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
adjusting the chamber pressure. It actually allows the user to evacuate or
vent the chamber and get the current pressure of it.
"""
def __init__(self, name, role, parent, ranges=None, **kwargs):
axes = {"pressure": model.Axis(unit="Pa",
choices={PRESSURE_VENTED: "vented",
PRESSURE_PUMPED: "vacuum"})}
model.Actuator.__init__(self, name, role, parent=parent, axes=axes, **kwargs)
# last official position
if self.GetStatus() == 0:
self._position = PRESSURE_PUMPED
else:
self._position = PRESSURE_VENTED
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute(
{"pressure": self._position},
unit="Pa", readonly=True)
# Almost the same as position, but gives the current position
self.pressure = model.VigilantAttribute(self._position,
unit="Pa", readonly=True)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
def GetStatus(self):
"""
return int: vacuum status,
-1 error
0 ready for operation
1 pumping in progress
2 venting in progress
3 vacuum off (pumps are switched off, valves are closed)
4 chamber open
"""
with self.parent._acquisition_init_lock:
status = self.parent._device.VacGetStatus() # channel 0, reserved
return status
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
def _updatePosition(self):
"""
update the position VA and .pressure VA
"""
# it's read-only, so we change it via _value
pos = self.parent._device.VacGetPressure(0)
self.pressure._value = pos
self.pressure.notify(pos)
# .position contains the last known/valid position
# it's read-only, so we change it via _value
self.position._value = {"pressure": self._position}
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
# convert into an absolute move
pos = {}
for a, v in shift.items:
pos[a] = self.position.value[a] + v
return self.moveAbs(pos)
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
return self._executor.submit(self._changePressure, pos["pressure"])
def _changePressure(self, p):
"""
Synchronous change of the pressure
p (float): target pressure
"""
if p["pressure"] == PRESSURE_VENTED:
self.parent._device.VacVent()
else:
self.parent._device.VacPump()
start = time.time()
while not self.GetStatus() == 0:
if (time.time() - start) >= VACUUM_TIMEOUT:
raise TimeoutError("Vacuum action timed out")
# Update chamber pressure until pumping/venting process is done
self._updatePosition()
self._position = p
self._updatePosition()
def stop(self, axes=None):
self._executor.cancel()
logging.warning("Stopped pressure change")
class Chamber(model.Actuator):
"""
Simulated chamber component. Just pretends to be able to change pressure
"""
def __init__(self, name, role, positions, has_pressure=True, **kwargs):
"""
Initialises the component
positions (list of str): each pressure positions supported by the
component (among the allowed ones)
has_pressure (boolean): if True, has a pressure VA with the current
pressure.
"""
# TODO: or just provide .targetPressure (like .targetTemperature) ?
# Or maybe provide .targetPosition: position that would be reached if
# all the requested move were instantly applied?
chp = {}
for p in positions:
try:
chp[PRESSURES[p]] = p
except KeyError:
raise ValueError("Pressure position %s is unknown" % (p,))
axes = {"pressure": model.Axis(unit="Pa", choices=chp)}
model.Actuator.__init__(self, name, role, axes=axes, **kwargs)
# For simulating moves
self._position = PRESSURE_VENTED # last official position
self._goal = PRESSURE_VENTED
self._time_goal = 0 # time the goal was/will be reached
self._time_start = 0 # time the move started
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute(
{"pressure": self._position},
unit="Pa", readonly=True)
if has_pressure:
# Almost the same as position, but gives the current position
self.pressure = model.VigilantAttribute(self._position,
unit="Pa", readonly=True)
self._press_timer = util.RepeatingTimer(1, self._updatePressure,
"Simulated pressure update")
self._press_timer.start()
else:
self._press_timer = None
# Indicates whether the chamber is opened or not
# Just pretend it's always closed, and allow the user to change that
# for instance via CLI.
self.opened = model.BooleanVA(False)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
def terminate(self):
if self._press_timer:
self._press_timer.cancel()
self._press_timer = None
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
def _updatePressure(self):
"""
update the pressure VA (called regularly from a thread)
"""
# Compute the current pressure
now = time.time()
if self._time_goal < now: # done
# goal ±5%
pos = self._goal * random.uniform(0.95, 1.05)
else:
# TODO make it logarithmic
ratio = (now - self._time_start) / (self._time_goal - self._time_start)
pos = self._position + (self._goal - self._position) * ratio
# it's read-only, so we change it via _value
self.pressure._value = pos
self.pressure.notify(pos)
def _updatePosition(self):
"""
update the position VA
"""
# .position contains the last known/valid position
# it's read-only, so we change it via _value
self.position._value = {"pressure": self._position}
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
# convert into an absolute move
pos = {}
for a, v in shift.items:
pos[a] = self.position.value[a] + v
return self.moveAbs(pos)
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
new_pres = pos["pressure"]
est_start = time.time() + 0.1
f = model.ProgressiveFuture(start=est_start,
end=est_start + self._getDuration(new_pres))
return self._executor.submitf(f, self._changePressure, f, new_pres)
def _getDuration(self, pos):
return abs(self._position - pos) / SPEED_PUMP
def _changePressure(self, f, p):
"""
Synchronous change of the pressure
p (float): target pressure
"""
# TODO: allow to cancel during the change
now = time.time()
duration = self._getDuration(p) # s
self._time_start = now
self._time_goal = now + duration # s
self._goal = p
time.sleep(duration / 2)
# DEBUG: for testing wrong time estimation
# f.set_progress(start=self._time_start, end=self._time_goal + 10)
time.sleep(duration / 2)
self._position = p
self._updatePosition()
def stop(self, axes=None):
self._executor.cancel()
logging.warning("Stopped pressure change")
class FW102c(model.Actuator):
"""
Represents a Thorlabs filter wheel FW102C as an actuator.
It provides one enumerated axis, whose actual band values are provided by
the user at init.
"""
# Regex matching the compatible identification strings
re_idn = "THORLABS.*FW102C.*"
def __init__(self, name, role, port, bands, _scan=False, **kwargs):
"""
port (string): name of the serial port to connect to. Can be a pattern,
in which case, all the ports fitting the pattern will be tried, and the
first one which looks like an FW102C will be used.
bands (dict 1<=int<=12 -> 2-tuple of floats > 0 or str):
filter position -> lower and higher bound of the wavelength (m) of the
light which goes _through_. If it's a list, it implies that the filter
is multi-band.
_scan (bool): only for internal usage
raise IOError if no device answering or not a compatible device
"""
self._ser_access = threading.Lock()
self._port = self._findDevice(port)
logging.info("Found FW102C device on port %s", self._port)
if _scan:
return
# check bands contains correct data
self._maxpos = self.GetMaxPosition()
if not bands:
raise ValueError("Argument bands must contain at least one band")
try:
for pos, band in bands.items():
if not 1 <= pos <= self._maxpos:
raise ValueError("Filter position should be between 1 and "
"%d, but got %d." % (self._maxpos, pos))
# To support "weird" filter, we accept strings
if isinstance(band, basestring):
if not band.strip():
raise ValueError("Name of filter %d is empty" % pos)
else:
driver.checkLightBand(band)
except Exception:
logging.exception("Failed to parse bands %s", bands)
raise
curpos = self.GetPosition()
if curpos not in bands:
logging.info("Current position %d is not configured, will add it", curpos)
bands[curpos] = "unknown"
axes = {"band": model.Axis(choices=bands)}
model.Actuator.__init__(self, name, role, axes=axes, **kwargs)
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "%s (serial driver: %s)" % (odemis.__version__, driver_name)
self._hwVersion = self._idn
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
self._speed = self.GetSpeed()
self.position = model.VigilantAttribute({"band": curpos}, readonly=True)
def getMetadata(self):
return self._metadata
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
with self._ser_access:
if self._serial:
self._serial.close()
self._serial = None
super(FW102c, self).terminate()
def _findDevice(self, ports):
"""
Look for a compatible device
ports (str): pattern for the port name
return (str): the name of the port used
It also sets ._serial and ._idn to contain the opened serial port, and
the identification string.
raises:
IOError: if no device are found
"""
if os.name == "nt":
# TODO
# ports = ["COM" + str(n) for n in range(15)]
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
self._serial = self._openSerialPort(n)
except serial.SerialException:
# not possible to use this port? next one!
continue
# check whether it looks like a FW102C
try:
# If any garbage was previously received, make it discarded.
self._serial.write(b"\r")
# can have some \x00 bytes at the beginning + "CMD_NOT_DEFINED"
self._flushInput()
idn = self.GetIdentification()
if re.match(self.re_idn, idn):
self._idn = idn
return n # found it!
except Exception as ex:
logging.debug("Port %s doesn't seem to have a FW102C device connected. " +
"Identification failed with exception: %s", n, ex)
else:
raise HwError("Failed to find a filter wheel FW102C on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports,))
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for the FW102C.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
baudrate=115200, # only correct if setting was not changed
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=10 # s (can take time when filter changes)
)
return ser
def _flushInput(self):
"""
Ensure there is no more data queued to be read on the bus (=serial port)
"""
with self._ser_access:
self._serial.flush()
self._serial.flushInput()
# Shouldn't be necessary, but just in case
skipped = self._serial.read(1000) # More than 1000 chars => give up
logging.debug("Skipping input %s", to_str_escape(skipped))
re_err = br"Command error (.*)"
def _sendQuery(self, com):
"""
Send a command which expects an answer
com (byte string): command to send (not including the ? and the \r)
return (byte string): the answer without newline and suffix ("> ")
raises
IOError: if there is a timeout
TLFWError: if the hardware reports an error
"""
# TODO: handle IOError and automatically try to reconnect (cf LLE)
assert isinstance(com, bytes), 'com argument needs to be a byte string'
assert(len(com) <= 50) # commands cannot be long
full_com = com + b"\r"
with self._ser_access:
logging.debug("Sending: '%s'", to_str_escape(full_com))
self._serial.write(full_com)
# ensure everything is received, before expecting an answer
self._serial.flush()
# Read until end of answer
line = b""
while True:
char = self._serial.read() # empty if timeout
if not char: # should always finish by a "> "
raise IOError("Controller timeout, after receiving '%s'" % to_str_escape(line))
# normal char
line += char
if line[-2:] == b"> ":
break
logging.debug("Received: '%s'", to_str_escape(line))
# remove echo + suffix + new line
line = line[len(full_com):-2].rstrip(b"\r")
# if it's an error message => raise an error
m = re.match(self.re_err, line)
if m:
err = m.group(1)
raise TLFWError("Device rejected command '%s': %s" % (com, err))
return line
def _sendCommand(self, com):
"""
Send a command which does not expect any answer
com (byte string): command to send (not including the ? and the \r)
return when the command is finished processed
raises
IOError: if there is a timeout
TLFWError: if the hardware reports an error
"""
self._sendQuery(com)
# don't return anything
def GetIdentification(self):
"""
return (str): model name as reported by the device
"""
# answer is like "THORLABS FW102C/FW212C Filter Wheel version 1.04"
return self._sendQuery(b"*idn?").decode("latin1")
def GetMaxPosition(self):
"""
return (1<int): maximum number of positions available (eg, 6, 12)
"""
ans = self._sendQuery(b"pcount?")
return int(ans)
def GetPosition(self):
"""
return (1<=int<=maxpos): current position
Note: might be different from the last position set if the user has
manually changed it.
"""
ans = self._sendQuery(b"pos?")
return int(ans)
def GetSpeed(self):
"""
return (0 or 1): current "speed" of the wheel, the bigger the faster
"""
ans = self._sendQuery(b"speed?")
return int(ans)
def SetPosition(self, pos):
"""
pos (1<=int<=maxpos): current position
returns when the new position is set
raise Exception in case of error
"""
assert(1 <= pos <= self._maxpos)
# Estimate how long it'll take
cur_pos = self.position.value["band"]
p1, p2 = sorted([pos, cur_pos])
dist = min(p2 - p1, (6 + p1) - p2)
if self._speed == 0:
dur_one = 2 # s
else:
dur_one = 1 # s
maxdur = 1 + dist * dur_one * 2 # x 2 as a safe bet
prev_timeout = self._serial.timeout
try:
self._serial.timeout = maxdur
self._sendCommand(b"pos=%d" % pos)
finally:
self._serial.timeout = prev_timeout
logging.debug("Move to pos %d finished", pos)
# What we don't need:
# speed?\r1\r>
# trig?\r0\r>
# sensors?\r0\r>
def _doMoveBand(self, pos):
"""
move to the position and updates the metadata and position once it's over
"""
self.SetPosition(pos)
self._updatePosition()
# high-level methods (interface)
def _updatePosition(self):
"""
update the position VA
Note: it should not be called while holding _ser_access
"""
pos = {"band": self.GetPosition()}
# it's read-only, so we change it via _value
self.position._value = pos
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
# TODO move to the +N next position? (and modulo number of axes)
raise NotImplementedError("Relative move on enumerated axis not supported")
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
return self._executor.submit(self._doMoveBand, pos["band"])
def stop(self, axes=None):
self._executor.cancel()
def selfTest(self):
"""
check as much as possible that it works without actually moving the motor
return (boolean): False if it detects any problem
"""
try:
pos = self.GetPosition()
maxpos = self.GetMaxPosition()
if 1 <= pos <= maxpos:
return True
except Exception:
logging.exception("Selftest failed")
return False
@classmethod
def scan(cls, port=None):
"""
port (string): name of the serial port. If None, all the serial ports are tried
returns (list of 2-tuple): name, args (port)
Note: it's obviously not advised to call this function if a device is already under use
"""
if port:
ports = [port]
else:
if os.name == "nt":
ports = ["COM" + str(n) for n in range(15)]
else:
ports = glob.glob('/dev/ttyS?*') + glob.glob('/dev/ttyUSB?*')
logging.info("Serial ports scanning for Thorlabs filter wheel in progress...")
found = [] # (list of 2-tuple): name, kwargs
for p in ports:
try:
logging.debug("Trying port %s", p)
dev = cls(None, None, p, bands=None, _scan=True)
except (serial.SerialException, IOError):
# not possible to use this port? next one!
continue
# Get some more info
try:
maxpos = dev.GetMaxPosition()
except Exception:
continue
else:
# create fake band argument
bands = {}
for i in range(1, maxpos + 1):
bands[i] = (i * 100e-9, (i + 1) * 100e-9)
found.append((dev._idn, {"port": p, "bands": bands}))
return found
class MultiplexActuator(model.Actuator):
"""
An object representing an actuator made of several (real actuators)
= a set of axes that can be moved and optionally report their position.
"""
def __init__(self, name, role, children, axes_map, ref_on_init=None, **kwargs):
"""
name (string)
role (string)
children (dict str -> actuator): axis name (in this actuator) -> actuator to be used for this axis
axes_map (dict str -> str): axis name in this actuator -> axis name in the child actuator
ref_on_init (list): axes to be referenced during initialization
"""
if not children:
raise ValueError("MultiplexActuator needs children")
if set(children.keys()) != set(axes_map.keys()):
raise ValueError("MultiplexActuator needs the same keys in children and axes_map")
ref_on_init = ref_on_init or []
self._axis_to_child = {} # axis name => (Actuator, axis name)
self._position = {}
self._speed = {}
self._referenced = {}
axes = {}
for axis, child in children.items():
caxis = axes_map[axis]
self._axis_to_child[axis] = (child, caxis)
# Ducktyping (useful to support also testing with MockComponent)
# At least, it has .axes
if not isinstance(child, model.ComponentBase):
raise ValueError("Child %s is not a component." % (child,))
if not hasattr(child, "axes") or not isinstance(child.axes, dict):
raise ValueError("Child %s is not an actuator." % child.name)
axes[axis] = copy.deepcopy(child.axes[caxis])
self._position[axis] = child.position.value[axes_map[axis]]
if model.hasVA(child, "speed") and caxis in child.speed.value:
self._speed[axis] = child.speed.value[caxis]
if model.hasVA(child, "referenced") and caxis in child.referenced.value:
self._referenced[axis] = child.referenced.value[caxis]
# this set ._axes and ._children
model.Actuator.__init__(self, name, role, axes=axes,
children=children, **kwargs)
if len(self.children.value) > 1:
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# TODO: make use of the 'Cancellable' part (for now cancelling a running future doesn't work)
else: # Only one child => optimize by passing all requests directly
self._executor = None
# keep a reference to the subscribers so that they are not
# automatically garbage collected
self._subfun = []
children_axes = {} # dict actuator -> set of string (our axes)
for axis, (child, ca) in self._axis_to_child.items():
logging.debug("adding axis %s to child %s", axis, child.name)
if child in children_axes:
children_axes[child].add(axis)
else:
children_axes[child] = set([axis])
# position & speed: special VAs combining multiple VAs
self.position = model.VigilantAttribute(self._position, readonly=True)
for c, ax in children_axes.items():
def update_position_per_child(value, ax=ax, c=c):
logging.debug("updating position of child %s", c.name)
for a in ax:
try:
self._position[a] = value[axes_map[a]]
except KeyError:
logging.error("Child %s is not reporting position of axis %s", c.name, a)
self._updatePosition()
c.position.subscribe(update_position_per_child)
self._subfun.append(update_position_per_child)
# TODO: change the speed range to a dict of speed ranges
self.speed = model.MultiSpeedVA(self._speed, [0., 10.], setter=self._setSpeed)
for axis in self._speed.keys():
c, ca = self._axis_to_child[axis]
def update_speed_per_child(value, a=axis, ca=ca, cname=c.name):
try:
self._speed[a] = value[ca]
except KeyError:
logging.error("Child %s is not reporting speed of axis %s (%s): %s", cname, a, ca, value)
self._updateSpeed()
c.speed.subscribe(update_speed_per_child)
self._subfun.append(update_speed_per_child)
# whether the axes are referenced
self.referenced = model.VigilantAttribute(self._referenced.copy(), readonly=True)
for axis in self._referenced.keys():
c, ca = self._axis_to_child[axis]
def update_ref_per_child(value, a=axis, ca=ca, cname=c.name):
try:
self._referenced[a] = value[ca]
except KeyError:
logging.error("Child %s is not reporting reference of axis %s (%s)", cname, a, ca)
self._updateReferenced()
c.referenced.subscribe(update_ref_per_child)
self._subfun.append(update_ref_per_child)
self._axes_referencing = []
for axis in ref_on_init:
# If the axis can be referenced => do it now (and move to a known position)
if not self._referenced.get(axis, True):
# The initialisation will not fail if the referencing fails
f = self.reference({axis})
self._axes_referencing.append(axis)
f.add_done_callback(self._on_referenced)
def _on_referenced(self, future):
try:
future.result()
except Exception as e:
for ax in self._axes_referencing:
c, ca = self._axis_to_child[ax]
c.stop({ca}) # prevent any move queued
self.state._set_value(e, force_write=True)
logging.exception(e)
def _updatePosition(self):
"""
update the position VA
"""
# it's read-only, so we change it via _value
pos = self._applyInversion(self._position)
logging.debug("reporting position %s", pos)
self.position._set_value(pos, force_write=True)
def _updateSpeed(self):
"""
update the speed VA
"""
# we must not call the setter, so write directly the raw value
self.speed._value = self._speed
self.speed.notify(self._speed)
def _updateReferenced(self):
"""
update the referenced VA
"""
# .referenced is copied to detect changes to it on next update
self.referenced._set_value(self._referenced.copy(), force_write=True)
def _setSpeed(self, value):
"""
value (dict string-> float): speed for each axis
returns (dict string-> float): the new value
"""
# FIXME the problem with this implementation is that the subscribers
# will receive multiple notifications for each set:
# * one for each axis (via _updateSpeed from each child)
# * the actual one (but it's probably dropped as it's the same value)
final_value = value.copy() # copy
for axis, v in value.items():
child, ma = self._axis_to_child[axis]
new_speed = child.speed.value.copy() # copy
new_speed[ma] = v
child.speed.value = new_speed
final_value[axis] = child.speed.value[ma]
return final_value
def _moveToChildMove(self, mv):
child_to_move = collections.defaultdict(dict) # child -> moveRel argument
for axis, distance in mv.items():
child, child_axis = self._axis_to_child[axis]
child_to_move[child].update({child_axis: distance})
logging.debug("Moving axis %s (-> %s) by %g", axis, child_axis, distance)
return child_to_move
def _axesToChildAxes(self, axes):
child_to_axes = collections.defaultdict(set) # child -> set(str): axes
for axis in axes:
child, child_axis = self._axis_to_child[axis]
child_to_axes[child].add(child_axis)
logging.debug("Interpreting axis %s (-> %s)", axis, child_to_axes)
return child_to_axes
@isasync
def moveRel(self, shift, **kwargs):
"""
Move the stage the defined values in m for each axis given.
shift dict(string-> float): name of the axis and shift in m
**kwargs: Mostly there to support "update" argument (but currently works
only if there is only one child)
"""
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
if self._executor:
f = self._executor.submit(self._doMoveRel, shift, **kwargs)
else:
cmv = self._moveToChildMove(shift)
child, move = cmv.popitem()
assert not cmv
f = child.moveRel(move, **kwargs)
return f
def _doMoveRel(self, shift, **kwargs):
# TODO: updates don't work because we still wait for the end of the
# move before we get to the next one => multi-threaded queue? Still need
# to ensure the order (ie, X>AB>X can be executed as X/AB>X or X>AB/X but
# XA>AB>X must be in the order XA>AB/X
futures = []
for child, move in self._moveToChildMove(shift).items():
f = child.moveRel(move, **kwargs)
futures.append(f)
# just wait for all futures to finish
for f in futures:
f.result()
@isasync
def moveAbs(self, pos, **kwargs):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
if self._executor:
f = self._executor.submit(self._doMoveAbs, pos, **kwargs)
else:
cmv = self._moveToChildMove(pos)
child, move = cmv.popitem()
assert not cmv
f = child.moveAbs(move, **kwargs)
return f
def _doMoveAbs(self, pos, **kwargs):
futures = []
for child, move in self._moveToChildMove(pos).items():
f = child.moveAbs(move, **kwargs)
futures.append(f)
# just wait for all futures to finish
for f in futures:
f.result()
@isasync
def reference(self, axes):
if not axes:
return model.InstantaneousFuture()
self._checkReference(axes)
if self._executor:
f = self._executor.submit(self._doReference, axes)
else:
cmv = self._axesToChildAxes(axes)
child, a = cmv.popitem()
assert not cmv
f = child.reference(a)
return f
reference.__doc__ = model.Actuator.reference.__doc__
def _doReference(self, axes):
child_to_axes = self._axesToChildAxes(axes)
futures = []
for child, a in child_to_axes.items():
f = child.reference(a)
futures.append(f)
# just wait for all futures to finish
for f in futures:
f.result()
def stop(self, axes=None):
"""
stops the motion
axes (iterable or None): list of axes to stop, or None if all should be stopped
"""
# Empty the queue for the given axes
if self._executor:
self._executor.cancel()
all_axes = set(self.axes.keys())
axes = axes or all_axes
unknown_axes = axes - all_axes
if unknown_axes:
logging.error("Attempting to stop unknown axes: %s", ", ".join(unknown_axes))
axes &= all_axes
threads = []
for child, a in self._axesToChildAxes(axes).items():
# it's synchronous, but we want to stop all of them as soon as possible
thread = threading.Thread(name="Stopping axis", target=child.stop, args=(a,))
thread.start()
threads.append(thread)
# wait for completion
for thread in threads:
thread.join(1)
if thread.is_alive():
logging.warning("Stopping child actuator of '%s' is taking more than 1s", self.name)
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
class ChamberPressure(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
adjusting the chamber pressure. It actually allows the user to evacuate or
vent the chamber and get the current pressure of it.
"""
def __init__(self, name, role, parent, ranges=None, **kwargs):
axes = {
"pressure":
model.Axis(unit="Pa",
choices={
PRESSURE_VENTED: "vented",
PRESSURE_PUMPED: "vacuum"
})
}
model.Actuator.__init__(self,
name,
role,
parent=parent,
axes=axes,
**kwargs)
# last official position
if self.GetStatus() == 0:
self._position = PRESSURE_PUMPED
else:
self._position = PRESSURE_VENTED
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({"pressure": self._position},
unit="Pa",
readonly=True)
# Almost the same as position, but gives the current position
self.pressure = model.VigilantAttribute(self._position,
unit="Pa",
readonly=True)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
def GetStatus(self):
"""
return int: vacuum status,
-1 error
0 ready for operation
1 pumping in progress
2 venting in progress
3 vacuum off (pumps are switched off, valves are closed)
4 chamber open
"""
with self.parent._acquisition_init_lock:
status = self.parent._device.VacGetStatus() # channel 0, reserved
return status
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
def _updatePosition(self):
"""
update the position VA and .pressure VA
"""
# it's read-only, so we change it via _value
pos = self.parent._device.VacGetPressure(0)
self.pressure._value = pos
self.pressure.notify(pos)
# .position contains the last known/valid position
# it's read-only, so we change it via _value
self.position._value = {"pressure": self._position}
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
# convert into an absolute move
pos = {}
for a, v in shift.items:
pos[a] = self.position.value[a] + v
return self.moveAbs(pos)
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
return self._executor.submit(self._changePressure, pos["pressure"])
def _changePressure(self, p):
"""
Synchronous change of the pressure
p (float): target pressure
"""
if p["pressure"] == PRESSURE_VENTED:
self.parent._device.VacVent()
else:
self.parent._device.VacPump()
start = time.time()
while not self.GetStatus() == 0:
if (time.time() - start) >= VACUUM_TIMEOUT:
raise TimeoutError("Vacuum action timed out")
# Update chamber pressure until pumping/venting process is done
self._updatePosition()
self._position = p
self._updatePosition()
def stop(self, axes=None):
self._executor.cancel()
logging.warning("Stopped pressure change")
class DPSS(model.PowerSupplier):
'''
Implements the PowerSupplier class to regulate the power supply of the
Cobolt DPSS laser, connected via USB.
'''
def __init__(self, name, role, port, light_name, max_power, **kwargs):
'''
port (str): port name. Can be a pattern, in which case it will pick the
first one which responds well
ligth_name (str): the name of the component that is controlled by this
power supplier
max_power (float): maximum power, in W. Will be set at initialisation.
'''
# TODO: allow to pass the serial number, to select the right device
model.PowerSupplier.__init__(self, name, role, **kwargs)
self._light_name = light_name
self._ser_access = threading.Lock()
self._port = self._findDevice(port) # sets ._serial
logging.info("Found Cobolt DPSS device on port %s", self._port)
self._sn = self.GetSerialNumber()
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "serial driver: %s" % (driver_name,)
self._hwVersion = "Cobolt DPSS (s/n: %s)" % (self._sn,)
# Reset sequence
# TODO: do a proper one. For now it's just everything we can throw, so
# that it's a bit easier to debug
self._sendCommand("ilk?")
self._sendCommand("leds?")
self._sendCommand("@cobasky?")
self._sendCommand("cf") # Clear fault
# self._sendCommand("@cob1") # used to force the laser on after interlock opened error
# will take care of executing switch asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# Dict str -> bool: component name -> turn on/off
self.supplied = model.VigilantAttribute({light_name: False}, readonly=True)
self._updateSupplied()
self.SetOutputPower(max_power)
# Wrapper for the actual firmware functions
def GetSerialNumber(self):
return self._sendCommand("sn?")
def SetOutputPower(self, p):
"""
p (0 < float): power in W
"""
assert 1e-6 < p < 1e6
self._sendCommand("p %.5f" % p)
def SetLaser(self, state):
"""
state (bool): True to turn on
"""
v = 1 if state else 0
self._sendCommand("l%d" % v) # No space, as they are different commands
@isasync
def supply(self, sup):
"""
Change the power supply to the defined state for each component given.
This is an asynchronous method.
sup dict(string-> boolean): name of the component and new state
returns (Future): object to control the supply request
"""
if not sup:
return model.InstantaneousFuture()
self._checkSupply(sup)
return self._executor.submit(self._doSupply, sup)
def _doSupply(self, sup):
"""
supply power
"""
for comp, val in sup.items():
self.SetLaser(val)
self._updateSupplied()
def _updateSupplied(self):
"""
update the supplied VA
"""
res = self._sendCommand("l?")
pwrd = (res == "1")
# it's read-only, so we change it via _value
self.supplied._set_value({self._light_name: pwrd}, force_write=True)
def terminate(self):
if self._executor:
self._executor.cancel()
self._executor.shutdown()
self._executor = None
if self._serial:
self.SetLaser(False) # TODO: allow to configure with argument to DPSS
with self._ser_access:
self._serial.close()
self._serial = None
self._file.close()
def _sendCommand(self, cmd):
"""
cmd (str): command to be sent to device (without the CR)
returns (str): answer received from the device (without \n or \r)
raises:
DPSSError: if an ERROR is returned by the device.
"""
cmd = cmd + "\r"
with self._ser_access:
logging.debug("Sending command %s", cmd.encode('string_escape'))
self._serial.write(cmd)
ans = ''
while ans[-2:] != '\r\n':
char = self._serial.read()
if not char:
raise IOError("Timeout after receiving %s" % ans.encode('string_escape'))
ans += char
logging.debug("Received answer %s", ans.encode('string_escape'))
# TODO: check for other error answer?
# Normally the device either answers OK, or a value, for commands finishing with a "?"
if ans.startswith("Syntax error"):
raise DPSSError(ans)
return ans.rstrip()
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for a Power control device.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
baudrate=115200,
timeout=1 # s
)
# Purge
ser.flush()
ser.flushInput()
# Try to read until timeout to be extra safe that we properly flushed
while True:
char = ser.read()
if char == '':
break
return ser
def _findDevice(self, ports):
"""
Look for a compatible device
ports (str): pattern for the port name
return (str): the name of the port used
It also sets ._serial and ._idn to contain the opened serial port, and
the identification string.
raises:
IOError: if no device are found
"""
# TODO: For debugging purpose
# if ports == "/dev/fake":
# self._serial = DPSSSimulator(timeout=1)
# return ports
if os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
# Ensure no one will talk to it simultaneously, and we don't talk to devices already in use
self._file = open(n) # Open in RO, just to check for lock
try:
fcntl.flock(self._file.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB) # Raises IOError if cannot lock
except IOError:
logging.info("Port %s is busy, will not use", n)
continue
self._serial = self._openSerialPort(n)
try:
sn = self.GetSerialNumber()
except DPSSError:
# Can happen if the device has received some weird characters
# => try again (now that it's flushed)
logging.info("Device answered by an error, will try again")
sn = self.GetSerialNumber()
return n
except (IOError, DPSSError):
logging.info("Skipping device on port %s, which didn't seem to be a Cobolt", n)
# not possible to use this port? next one!
continue
else:
raise HwError("Failed to find a Cobolt device on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports,))
class Stage(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
moving the Tescan stage and updating the position.
"""
def __init__(self, name, role, parent, **kwargs):
"""
axes (set of string): names of the axes
"""
axes_def = {}
self._position = {}
rng = [-0.5, 0.5]
axes_def["x"] = model.Axis(unit="m", range=rng)
axes_def["y"] = model.Axis(unit="m", range=rng)
axes_def["z"] = model.Axis(unit="m", range=rng)
# Demand calibrated stage
if parent._device.StgIsCalibrated() != 1:
logging.warning(
"Stage was not calibrated. We are performing calibration now.")
parent._device.StgCalibrate()
#Wait for stage to be stable after calibration
while parent._device.StgIsBusy() != 0:
# If the stage is busy (movement is in progress), current position is
# updated approximately every 500 ms
time.sleep(0.5)
x, y, z, rot, tilt = parent._device.StgGetPosition()
self._position["x"] = -x * 1e-3
self._position["y"] = -y * 1e-3
self._position["z"] = -z * 1e-3
model.Actuator.__init__(self,
name,
role,
parent=parent,
axes=axes_def,
**kwargs)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute(self._applyInversionAbs(
self._position),
unit="m",
readonly=True)
def _updatePosition(self):
"""
update the position VA
"""
# it's read-only, so we change it via _value
self.position._value = self._applyInversionAbs(self._position)
self.position.notify(self.position.value)
def _doMove(self, pos):
"""
move to the position
"""
# Perform move through Tescan API
# Position from m to mm and inverted
self.parent._device.StgMoveTo(-pos["x"] * 1e3, -pos["y"] * 1e3,
-pos["z"] * 1e3)
# Obtain the finally reached position after move is performed.
# This is mainly in order to keep the correct position in case the
# move we tried to perform was greater than the maximum possible
# one.
with self.parent._acquisition_init_lock:
x, y, z, rot, tilt = self.parent._device.StgGetPosition()
self._position["x"] = -x * 1e-3
self._position["y"] = -y * 1e-3
self._position["z"] = -z * 1e-3
self._updatePosition()
@isasync
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversionRel(shift)
for axis, change in shift.items():
self._position[axis] += change
pos = self._position
return self._executor.submit(self._doMove, pos)
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversionAbs(pos)
for axis, new_pos in pos.items():
self._position[axis] = new_pos
pos = self._position
return self._executor.submit(self._doMove, pos)
def stop(self, axes=None):
# Empty the queue for the given axes
self._executor.cancel()
logging.warning("Stopping all axes: %s", ", ".join(self.axes))
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
class SpectraPro(model.Actuator):
def __init__(self, name, role, port, turret=None, calib=None,
_noinit=False, children=None, **kwargs):
"""
port (string): name of the serial port to connect to.
turret (None or 1<=int<=3): turret number set-up. If None, consider that
the current turret known by the device is correct.
calib (None or list of (int, int and 5 x (float or str))):
calibration data, as saved by Winspec. Data can be either in float
or as an hexadecimal value "hex:9a,99,99,99,99,79,40,40"
blaze in nm, groove gl/mm, center adjust, slope adjust,
focal length, inclusion angle, detector angle
inverted (None): it is not allowed to invert the axes
children (dict str -> Component): "ccd" should be the CCD used to acquire
the spectrum.
_noinit (boolean): for internal use only, don't try to initialise the device
"""
if kwargs.get("inverted", None):
raise ValueError("Axis of spectrograph cannot be inverted")
# start with this opening the port: if it fails, we are done
try:
self._serial = self.openSerialPort(port)
except serial.SerialException:
raise HwError("Failed to find spectrograph %s (on port '%s'). "
"Check the device is turned on and connected to the "
"computer. You might need to turn it off and on again."
% (name, port))
self._port = port
# to acquire before sending anything on the serial port
self._ser_access = threading.Lock()
self._try_recover = False
if _noinit:
return
self._initDevice()
self._try_recover = True
try:
self._ccd = children["ccd"]
except (TypeError, KeyError):
# TODO: only needed if there is calibration info (for the pixel size)
# otherwise it's fine without CCD.
raise ValueError("Spectrograph needs a child 'ccd'")
# according to the model determine how many gratings per turret
model_name = self.GetModel()
self.max_gratings = MAX_GRATINGS_NUM.get(model_name, 3)
if turret is not None:
if turret < 1 or turret > self.max_gratings:
raise ValueError("Turret number given is %s, while expected a value between 1 and %d" %
(turret, self.max_gratings))
self.SetTurret(turret)
self._turret = turret
else:
self._turret = self.GetTurret()
# for now, it's fixed (and it's unlikely to be useful to allow less than the max)
max_speed = 1000e-9 / 10 # about 1000 nm takes 10s => max speed in m/s
self.speed = model.MultiSpeedVA(max_speed, range=[max_speed, max_speed], unit="m/s",
readonly=True)
gchoices = self.GetGratingChoices()
# remove the choices which are not valid for the current turret
for c in gchoices:
t = 1 + (c - 1) // self.max_gratings
if t != self._turret:
del gchoices[c]
# TODO: report the grating with its wavelength range (possible to compute from groove density + blaze wl?)
# range also depends on the max grating angle (40°, CCD pixel size, CCD horizontal size, focal length,+ efficienty curve?)
# cf http://www.roperscientific.de/gratingcalcmaster.html
# TODO: a more precise way to find the maximum wavelength (looking at the available gratings?)
# TODO: what's the min? 200nm seems the actual min working, although wavelength is set to 0 by default !?
axes = {"wavelength": model.Axis(unit="m", range=(0, 2400e-9),
speed=(max_speed, max_speed)),
"grating": model.Axis(choices=gchoices)
}
# provides a ._axes
model.Actuator.__init__(self, name, role, axes=axes, **kwargs)
# First step of parsing calib parmeter: convert to (int, int) -> ...
calib = calib or ()
if not isinstance(calib, collections.Iterable):
raise ValueError("calib parameter must be in the format "
"[blz, gl, ca, sa, fl, ia, da], "
"but got %s" % (calib))
dcalib = {}
for c in calib:
if not isinstance(c, collections.Iterable) or len(c) != 7:
raise ValueError("calib parameter must be in the format "
"[blz, gl, ca, sa, fl, ia, da], "
"but got %s" % (c,))
gt = (c[0], c[1])
if gt in dcalib:
raise ValueError("calib parameter contains twice calibration for "
"grating (%d nm, %d gl/mm)" % gt)
dcalib[gt] = c[2:]
# store calibration for pixel -> wavelength conversion and wavelength offset
# int (grating number 1 -> 9) -> center adjust, slope adjust,
# focal length, inclusion angle/2, detector angle
self._calib = {}
# TODO: read the info from MONO-EESTATUS (but it's so
# huge that it's not fun to parse). There is also detector angle.
dfl = FOCAL_LENGTH_OFFICIAL[model_name] # m
dia = math.radians(INCLUSION_ANGLE_OFFICIAL[model_name]) # rad
for i in gchoices:
# put default values
self._calib[i] = (0, 0, dfl, dia, 0)
try:
blz = self._getBlaze(i) # m
gl = self._getGrooveDensity(i) # gl/m
except ValueError:
logging.warning("Failed to parse info of grating %d" % i, exc_info=True)
continue
# parse calib info
gt = (int(blz * 1e9), int(gl * 1e-3))
if gt in dcalib:
calgt = dcalib[gt]
ca = self._readCalibVal(calgt[0]) # ratio
sa = self._readCalibVal(calgt[1]) # ratio
fl = self._readCalibVal(calgt[2]) * 1e-3 # mm -> m
ia = math.radians(self._readCalibVal(calgt[3])) # ° -> rad
da = math.radians(self._readCalibVal(calgt[4])) # ° -> rad
self._calib[i] = ca, sa, fl, ia, da
logging.info("Calibration data for grating %d (%d nm, %d gl/mm) "
"-> %s" % (i, gt[0], gt[1], self._calib[i]))
else:
logging.warning("No calibration data for grating %d "
"(%d nm, %d gl/mm)" % (i, gt[0], gt[1]))
# set HW and SW version
self._swVersion = "%s (serial driver: %s)" % (odemis.__version__, driver.getSerialDriver(port))
self._hwVersion = "%s (s/n: %s)" % (model_name, (self.GetSerialNumber() or "Unknown"))
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
# for storing the latest calibrated wavelength value
self._wl = (None, None, None) # grating id, raw center wl, calibrated center wl
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
def _readCalibVal(self, rawv):
"""
rawv (str or number)
return (float)
"""
if isinstance(rawv, basestring):
if rawv.startswith("hex:"):
rawv = rawv[4:]
return hextof(rawv)
elif isinstance(rawv, numbers.Real):
return rawv
else:
raise ValueError("Cannot convert %s to a number" % (rawv,))
# Low-level methods: to access the hardware (should be called with the lock acquired)
def _sendOrder(self, *args, **kwargs):
"""
Send a command which does not expect any report back (just OK)
com (str): command to send (non including the \r)
raise
SPError: if the command doesn't answer the expected OK.
IOError: in case of timeout
"""
# same as a query but nothing to do with the response
self._sendQuery(*args, **kwargs)
def _sendQuery(self, com, timeout=1):
"""
Send a command which expects a report back (in addition to the OK)
com (str): command to send (non including the \r)
timeout (0<float): maximum read timeout for the response
return (str): the response received (without the ok)
raises:
SPError: if the command doesn't answer the expected OK.
IOError: in case of timeout
"""
# All commands or strings of commands must be terminated with a carriage
# return (0D hex). The monochromator responds to a command when the
# command has been completed by returning the characters " ok" followed by
# carriage return and line feed (hex ASCII sequence 20 6F 6B 0D 0A).
# Examples of error answers:
# MODEL\r
# \x00X\xf0~\x00X\xf0~MODEL ? \r\n
# ?\r
# \r\nAddress Error \r\nA=3F4F4445 PC=81444
assert(len(com) > 1 and len(com) <= 100) # commands cannot be long
com += "\r"
logging.debug("Sending: %s", com.encode('string_escape'))
# send command until it succeeds
while True:
try:
self._serial.write(com)
break
except IOError:
if self._try_recover:
self._tryRecover()
else:
raise
# read response until timeout or known end of response
response = ""
timeend = time.time() + timeout
while ((time.time() <= timeend) and
not (response.endswith(" ok\r\n") or response.endswith("? \r\n"))):
self._serial.timeout = max(0.1, timeend - time.time())
char = self._serial.read()
if not char: # timeout
break
response += char
logging.debug("Received: %s", response.encode('string_escape'))
if response.endswith(" ok\r\n"):
return response[:-5]
else:
# if the device hasn't answered anything, it might have been disconnected
if len(response) == 0:
if self._try_recover:
self._tryRecover()
else:
raise IOError("Device timeout after receiving '%s'." % response.encode('string_escape'))
else: # just non understood command
# empty the serial port
self._serial.timeout = 0.1
garbage = self._serial.read(100)
if len(garbage) == 100:
raise IOError("Device keeps sending data")
response += garbage
raise SPError("Sent '%s' and received error: '%s'" %
(com.encode('string_escape'), response.encode('string_escape')))
def _tryRecover(self):
# no other access to the serial port should be done
# so _ser_access should already be acquired
# Retry to open the serial port (in case it was unplugged)
while True:
try:
self._serial.close()
self._serial = None
except:
pass
try:
logging.debug("retrying to open port %s", self._port)
self._serial = self.openSerialPort(self._port)
except IOError:
time.sleep(2)
except Exception:
logging.exception("Unexpected error while trying to recover device")
raise
else:
break
self._try_recover = False # to avoid recursion
self._initDevice()
self._try_recover = True
def _initDevice(self):
# If no echo is desired, the command NO-ECHO will suppress the echo. The
# command ECHO will return the SP-2150i to the default echo state.
#
# If is connected via the real serial port (not USB), it is in echo
# mode, so we first need to disable it, while allowing echo of the
# command we've just sent.
try:
r = self._sendOrder("no-echo")
except SPError:
logging.info("Failed to disable echo, hopping the device has not echo anyway")
# empty the serial port
self._serial.timeout = 0.1
garbage = self._serial.read(100)
if len(garbage) == 100:
raise IOError("Device keeps sending data")
def GetTurret(self):
"""
returns (1 <= int <= 3): the current turret number
"""
# ?TURRET Returns the correctly installed turret numbered 1 - 3
res = self._sendQuery("?turret")
val = int(res)
if val < 1 or val > 3:
raise SPError("Unexpected turret number '%s'" % res)
return val
def SetTurret(self, t):
"""
Set the number of the current turret (for correct settings by the hardware)
t (1 <= int <= 3): the turret number
Raise:
ValueError if the turret has no grating configured
"""
# TURRET Specifies the presently installed turret or the turret to be installed.
# Doesn't change the hardware, just which gratings are available
assert(1 <= t and t <= 3)
# TODO check that there is grating configured for this turret (using GetGratingChoices)
self._sendOrder("%d turret" % t)
# regex to read the gratings
RE_NOTINSTALLED = re.compile("\D*(\d+)\s+Not Installed")
RE_INSTALLED = re.compile("\D*(\d+)\s+(\d+)\s*g/mm BLZ=\s*([0-9][.0-9]*)\s*(nm|NM|um|UM)")
RE_GRATING = re.compile("\D*(\d+)\s+(.+\S)\s*\r")
def GetGratingChoices(self):
"""
return (dict int -> string): grating number to description
"""
# ?GRATINGS Returns the list of installed gratings with position groove density and blaze. The
# present grating is specified with an arrow.
# Example output:
# \r\n 1 300 g/mm BLZ= 500NM \r\n\x1a2 300 g/mm BLZ= 750NM \r\n 3 Not Installed \r\n 4 Not Installed \r\n 5 Not Installed \r\n 6 Not Installed \r\n 7 Not Installed \r\n 8 Not Installed \r\n ok\r\n
# \r\n\x1a1 600 g/mm BLZ= 1.6UM \r\n 2 150 g/mm BLZ= 2UM \r\n 3 Not Installed \r\n 4 Not Installed \r\n 5 Not Installed \r\n 6 Not Installed \r\n 7 Not Installed \r\n 8 Not Installed \r\n 9 Not Installed \r\n ok\r\n
# From the spectrapro_300i_ll.c of fsc2, it seems the format is:
# non-digit*,digits=grating number,spaces,"Not Installed"\r\n
# non-digit*,digits=grating number,space+,digit+:g/mm,space*,"g/mm BLZ=", space*,digit+:blaze wl in nm,space*,"nm"\r\n
res = self._sendQuery("?gratings")
gratings = {}
for line in res[:-1].split("\n"): # avoid the last \n to not make an empty last line
m = self.RE_NOTINSTALLED.search(line)
if m:
logging.debug("Decoded grating %s as not installed, skipping.", m.group(1))
continue
m = self.RE_GRATING.search(line)
if not m:
logging.debug("Failed to decode grating description '%s'", line)
continue
num = int(m.group(1))
desc = m.group(2)
# TODO: provide a nicer description, using RE_INSTALLED?
gratings[num] = desc
return gratings
RE_GDENSITY = re.compile("(\d+)\s*g/mm")
def _getGrooveDensity(self, gid):
"""
Returns the groove density of the given grating
gid (int): index of the grating
returns (float): groove density in lines/meter
raise
LookupError if the grating is not installed
ValueError: if the groove density cannot be found out
"""
gstring = self.axes["grating"].choices[gid]
m = self.RE_GDENSITY.search(gstring)
if not m:
raise ValueError("Failed to find groove density in '%s'" % gstring)
density = float(m.group(1)) * 1e3 # l/m
return density
RE_BLZ = re.compile("BLZ=\s+(?P<blz>[0-9.]+)\s*(?P<unit>[NU]M)")
def _getBlaze(self, gid):
"""
Returns the blaze (=optimal center wavelength) of the given grating
gid (int): index of the grating
returns (float): blaze (in m)
raise
LookupError if the grating is not installed
ValueError: if the groove density cannot be found out
"""
gstring = self.axes["grating"].choices[gid]
m = self.RE_BLZ.search(gstring)
if not m:
raise ValueError("Failed to find blaze in '%s'" % gstring)
blaze, unit = float(m.group("blz")), m.group("unit").upper()
blaze *= {"UM": 1e-6, "NM": 1e-9}[unit] # m
return blaze
def GetGrating(self):
"""
Retuns the current grating in use
returns (1<=int<=9) the grating in use
"""
# ?GRATING Returns the number of gratings presently being used numbered 1 - 9.
# On the SP-2150i, it's only up to 6
res = self._sendQuery("?grating")
val = int(res)
if not 1 <= val <= 9:
raise SPError("Unexpected grating number '%s'" % res)
return val
def SetGrating(self, g):
"""
Change the current grating (the turret turns).
g (1<=int<=9): the grating number to change to
The method is synchronous, it returns once the grating is selected. It
might take up to 20 s.
Note: the grating is dependent on turret number (and the self.max_gratting)!
Note: after changing the grating, the wavelength, might have changed
"""
# GRATING Places specified grating in position to the [current] wavelength
# Note: it always reports ok, and doesn't change the grating if not
# installed or wrong value
assert(1 <= g <= (3 * self.max_gratings))
# TODO check that the grating is configured
self._sendOrder("%d grating" % g, timeout=20)
def GetWavelength(self):
"""
Return (0<=float): the current wavelength at the center (in m)
"""
# ?NM Returns present wavelength in nm to 0.01nm resolution with units
# nm appended.
# Note: For the SP-2150i, it seems there is no unit appended
# ?NM 300.00 nm
res = self._sendQuery("?nm")
m = re.search("\s*(\d+.\d+)( nm)?", res)
wl = float(m.group(1)) * 1e-9
if wl > 1e-3:
raise SPError("Unexpected wavelength of '%s'" % res)
return wl
def SetWavelength(self, wl):
"""
Change the wavelength at the center
wl (0<=float<=10e-6): wavelength in meter
returns when the move is complete
The method is synchronous, it returns once the grating is selected. It
might take up to 20 s.
"""
# GOTO: Goes to a destination wavelength at maximum motor speed. Accepts
# destination wavelength in nm as a floating point number with up to 3
# digits after the decimal point or whole number wavelength with no
# decimal point.
# 345.65 GOTO
# Note: NM goes to the wavelength slowly (in order to perform a scan).
# It shouldn't be needed for spectrometer
# Out of bound values are silently ignored by going to the min or max.
assert(0 <= wl <= 10e-6)
# TODO: check that the value fit the grating configuration?
self._sendOrder("%.3f goto" % (wl * 1e9), timeout=20)
def GetModel(self):
"""
Return (str): the model name
"""
# MODEL Returns model number of the Acton SP series monochromator.
# returns something like ' SP-2-150i '
res = self._sendQuery("model")
return res.strip()
def GetSerialNumber(self):
"""
Return the serial number or None if it cannot be determined
"""
try:
res = self._sendQuery("serial")
except SPError:
logging.exception("Device doesn't support serial number query")
return None
return res.strip()
# TODO diverter (mirror) functions: no diverter on SP-2??0i anyway.
def _getCalibratedWavelength(self):
"""
Read the center wavelength, and adapt it based on the calibration (if
it is available for the current grating)
return (float): wavelength in m
"""
gid = self.GetGrating()
rawwl = self.GetWavelength()
# Do we already now the answer?
if (gid, rawwl) == self._wl[0:2]:
return self._wl[2]
ca, sa, fl, ia, da = self._calib[gid]
# It's pretty hard to reverse the formula, so we approximate a8 using
# rawwl (instead of wl), which usually doesn't bring error > 0.01 nm
gl = self._getGrooveDensity(gid)
psz = self._ccd.pixelSize.value[0] # m/px
a8 = (rawwl * gl / 2) / math.cos(ia / 2)
ga = math.asin(a8) # rad
dispersion = math.cos(ia / 2 + ga) / (gl * fl) # m/m
pixbw = psz * dispersion
wl = (rawwl - ca * pixbw) / (sa + 1)
wl = max(0, wl)
return wl
def _setCalibratedWavelength(self, wl):
"""
wl (float): center wavelength in m
"""
gid = self.GetGrating()
ca, sa, fl, ia, da = self._calib[gid]
# This is approximately what Winspec does, but it seems not exactly,
# because the values differ ± 0.1nm
gl = self._getGrooveDensity(gid)
psz = self._ccd.pixelSize.value[0] # m/px
a8 = (wl * gl / 2) / math.cos(ia / 2)
ga = math.asin(a8) # rad
dispersion = math.cos(ia / 2 + ga) / (gl * fl) # m/m
pixbw = psz * dispersion
offset = ca * pixbw + sa * wl
if abs(offset) > 50e-9:
# we normally don't expect offset more than 10 nm
logging.warning("Center wavelength offset computed of %g nm", offset * 1e9)
else:
logging.debug("Center wavelength offset computed of %g nm", offset * 1e9)
rawwl = max(0, wl + offset)
self.SetWavelength(rawwl)
# store the corresponding official wl value as it's hard to inverse the
# conversion (for displaying in .position)
self._wl = (gid, self.GetWavelength(), wl)
# high-level methods (interface)
def _updatePosition(self):
"""
update the position VA
Note: it should not be called while holding _ser_access
"""
with self._ser_access:
pos = {"wavelength": self._getCalibratedWavelength(),
"grating": self.GetGrating()
}
# it's read-only, so we change it via _value
self.position._value = pos
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
"""
Move the stage the defined values in m for each axis given.
shift dict(string-> float): name of the axis and shift in m
returns (Future): future that control the asynchronous move
"""
self._checkMoveRel(shift)
for axis in shift:
if axis == "wavelength":
# cannot convert it directly to an absolute move, because
# several in a row must mean they accumulate. So we queue a
# special task. That also means the range check is delayed until
# the actual position is known.
return self._executor.submit(self._doSetWavelengthRel, shift[axis])
@isasync
def moveAbs(self, pos):
"""
Move the stage the defined values in m for each axis given.
pos dict(string-> float): name of the axis and new position in m
returns (Future): future that control the asynchronous move
"""
self._checkMoveAbs(pos)
# If grating needs to be changed, change it first, then the wavelength
if "grating" in pos:
g = pos["grating"]
wl = pos.get("wavelength")
return self._executor.submit(self._doSetGrating, g, wl)
elif "wavelength" in pos:
wl = pos["wavelength"]
return self._executor.submit(self._doSetWavelengthAbs, wl)
else: # nothing to do
return model.InstantaneousFuture()
def _doSetWavelengthRel(self, shift):
"""
Change the wavelength by a value
"""
with self._ser_access:
pos = self.position.value["wavelength"] + shift
# it's only now that we can check the absolute position is wrong
minp, maxp = self.axes["wavelength"].range
if not minp <= pos <= maxp:
raise ValueError("Position %f of axis '%s' not within range %f→%f" %
(pos, "wavelength", minp, maxp))
self._setCalibratedWavelength(pos)
self._updatePosition()
def _doSetWavelengthAbs(self, pos):
"""
Change the wavelength to a value
"""
with self._ser_access:
self._setCalibratedWavelength(pos)
self._updatePosition()
def _doSetGrating(self, g, wl=None):
"""
Setter for the grating VA.
g (1<=int<=3): the new grating
wl (None or float): wavelength to set afterwards. If None, will put the
same wavelength as before the change of grating.
returns the actual new grating
Warning: synchronous until the grating is finished (up to 20s)
"""
try:
with self._ser_access:
if wl is None:
wl = self.position.value["wavelength"]
self.SetGrating(g)
self._setCalibratedWavelength(wl)
except Exception:
logging.exception("Failed to change grating to %d", g)
raise
self._updatePosition()
def stop(self, axes=None):
"""
stops the motion
Warning: Only not yet-executed moves can be cancelled, this hardware
doesn't support stopping while a move is going on.
"""
self._executor.cancel()
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
if self._serial:
self._serial.close()
self._serial = None
def getPixelToWavelength(self, npixels, pxs):
"""
Return the lookup table pixel number of the CCD -> wavelength observed.
npixels (1 <= int): number of pixels on the CCD (horizontally), after
binning.
pxs (0 < float): pixel size in m (after binning)
return (list of floats): pixel number -> wavelength in m
"""
centerpixel = (npixels - 1) / 2
cw = self.position.value["wavelength"] # m
gid = self.position.value["grating"]
gl = self._getGrooveDensity(gid)
ca, sa, fl, ia, da = self._calib[gid]
# Formula based on the Winspec documentation:
# "Equations used in WinSpec Wavelength Calibration", p. 257 of the manual
# ftp://ftp.piacton.com/Public/Manuals/Princeton%20Instruments/WinSpec%202.6%20Spectroscopy%20Software%20User%20Manual.pdf
# Converted to code by Benjamin Brenny (from AMOLF)
G = math.asin(cw / (math.cos(ia / 2) * 2 / gl))
wllist = []
for i in range(npixels):
pxd = pxs * (i - centerpixel) # distance of pixel to sensor centre
E = math.atan((pxd * math.cos(da)) / (fl + pxd * math.sin(da)))
wl = (math.sin(G - ia / 2) + math.sin(G + ia / 2 + E)) / gl
wllist.append(wl)
return wllist
# def getPolyToWavelength(self):
# """
# Compute the right polynomial to convert from a position on the sensor to the
# wavelength detected. It depends on the current grating, center
# wavelength (and focal length of the spectrometer).
# Note: It will always return some not-too-stupid values, but the only way
# to get precise values is to have provided a calibration data file.
# Without it, it will just base the calculations on the theoretical
# perfect spectrometer.
# returns (list of float): polynomial coefficients to apply to get the current
# wavelength corresponding to a given distance from the center:
# w = p[0] + p[1] * x + p[2] * x²...
# where w is the wavelength (in m), x is the position from the center
# (in m, negative are to the left), and p is the polynomial (in m, m^0, m^-1...).
# """
# # FIXME: shall we report the error on the polynomial? At least say if it's
# # using calibration or not.
# # TODO: have a calibration procedure, a file format, and load it at init
# # See fsc2, their calibration is like this for each grating:
# # INCLUSION_ANGLE_1 = 30.3
# # FOCAL_LENGTH_1 = 301.2 mm
# # DETECTOR_ANGLE_1 = 0.324871
# # TODO: use detector angle
# fl = self._focal_length # m
# ia = self._inclusion_angle # rad
# cw = self.position.value["wavelength"] # m
# if not fl:
# # "very very bad" calibration
# return [cw]
#
# # When no calibration available, fallback to theoretical computation
# # based on http://www.roperscientific.de/gratingcalcmaster.html
# gl = self._getGrooveDensity(self.position.value["grating"]) # g/m
# # fL = focal length (mm)
# # wE = inclusion angle (°) = the angle between the incident and the reflected beam for the center wavelength of the grating
# # gL = grating lines (l/mm)
# # cW = center wavelength (nm)
# # Grating angle
# # A8 = (cW/1000*gL/2000)/Math.cos(wE* Math.PI/180);
# # E8 = Math.asin(A8)*180/Math.PI;
# try:
# a8 = (cw * gl/2) / math.cos(ia)
# ga = math.asin(a8) # radians
# except (ValueError, ZeroDivisionError):
# logging.exception("Failed to compute polynomial for wavelength conversion")
# return [cw]
# # if (document.forms[0].E8.value == "NaN deg." || E8 > 40){document.forms[0].E8.value = "> 40 deg."; document.forms[0].E8.style.colour="red";
# if 0.5 > math.degrees(ga) or math.degrees(ga) > 40:
# logging.warning("Failed to compute polynomial for wavelength "
# "conversion, got grating angle = %g°", math.degrees(ga))
# return [cw]
#
# # dispersion: wavelength(m)/distance(m)
# # F8a = Math.cos(Math.PI/180*(wE*1 + E8))*(1000000)/(gL*fL); // nm/mm
# # to convert from nm/mm -> m/m : *1e-6
# dispersion = math.cos(ia + ga) / (gl*fl) # m/m
# if 0 > dispersion or dispersion > 0.5e-3: # < 500 nm/mm
# logging.warning("Computed dispersion is not within expected bounds: %f nm/mm",
# dispersion * 1e6)
# return [cw]
#
# # polynomial is cw + dispersion * x
# return [cw, dispersion]
def selfTest(self):
"""
check as much as possible that it works without actually moving the motor
return (boolean): False if it detects any problem
"""
try:
with self._ser_access:
modl = self.GetModel()
if not modl.startswith("SP-"):
# accept it anyway
logging.warning("Device reports unexpected model '%s'", modl)
turret = self.GetTurret()
if turret not in (1, 2, 3):
return False
return True
except Exception:
logging.exception("Selftest failed")
return False
@staticmethod
def scan(port=None):
"""
port (string): name of the serial port. If None, all the serial ports are tried
returns (list of 2-tuple): name, args (port)
Note: it's obviously not advised to call this function if a device is already under use
"""
if port:
ports = [port]
else:
if os.name == "nt":
ports = ["COM" + str(n) for n in range(8)]
else:
ports = glob.glob('/dev/ttyS?*') + glob.glob('/dev/ttyUSB?*')
logging.info("Serial ports scanning for Acton SpectraPro spectrograph in progress...")
found = [] # (list of 2-tuple): name, kwargs
for p in ports:
try:
logging.debug("Trying port %s", p)
dev = SpectraPro(None, None, p, _noinit=True)
except (serial.SerialException, HwError):
# not possible to use this port? next one!
continue
# Try to connect and get back some answer.
try:
model = dev.GetModel()
if model.startswith("SP-"):
found.append((model, {"port": p}))
else:
logging.info("Device on port '%s' responded correctly, but with unexpected model name '%s'.", p, model)
except:
continue
return found
@staticmethod
def openSerialPort(port):
"""
Opens the given serial port the right way for the SpectraPro.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
# according to doc:
# "port set-up is 9600 baud, 8 data bits, 1 stop bit and no parity"
ser = serial.Serial(
port=port,
baudrate=9600,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=2 # s
)
return ser
class EbeamFocus(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
adjusting the ebeam focus by changing the working distance i.e. the distance
between the end of the objective and the surface of the observed specimen
"""
def __init__(self, name, role, parent, axes, ranges=None, **kwargs):
assert len(axes) > 0
if ranges is None:
ranges = {}
axes_def = {}
self._position = {}
# Just z axis
a = axes[0]
# The maximum, obviously, is not 1 meter. We do not actually care
# about the range since Tescan API will adjust the value set if the
# required one is out of limits.
rng = [0, 1]
axes_def[a] = model.Axis(unit="m", range=rng)
# start at the centre
self._position[a] = parent._device.GetWD() * 1e-3
model.Actuator.__init__(self,
name,
role,
parent=parent,
axes=axes_def,
**kwargs)
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute(self._applyInversionAbs(
self._position),
unit="m",
readonly=True)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
def _updatePosition(self):
"""
update the position VA
"""
# it's read-only, so we change it via _value
self.position._value = self._applyInversionAbs(self._position)
self.position.notify(self.position.value)
def _doMove(self, pos):
"""
move to the position
"""
# Perform move through Tescan API
# Position from m to mm and inverted
self.parent._device.SetWD(self._position["z"] * 1e03)
# Obtain the finally reached position after move is performed.
with self.parent._acquisition_init_lock:
wd = self.parent._device.GetWD()
self._position["z"] = wd * 1e-3
# Changing WD results to change in fov
self.parent._scanner.updateHorizontalFOV()
self._updatePosition()
@isasync
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversionRel(shift)
for axis, change in shift.items():
self._position[axis] += change
pos = self._position
return self._executor.submit(self._doMove, pos)
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversionAbs(pos)
for axis, new_pos in pos.items():
self._position[axis] = new_pos
pos = self._position
return self._executor.submit(self._doMove, pos)
def stop(self, axes=None):
# Empty the queue for the given axes
self._executor.cancel()
logging.warning("Stopping all axes: %s", ", ".join(self.axes))
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
class PM8742(model.Actuator):
"""
Represents one New Focus picomotor controller 8742.
"""
def __init__(self, name, role, address, axes, stepsize, sn=None, **kwargs):
"""
address (str): ip address (use "autoip" to automatically scan and find the
controller, "fake" for a simulator)
axes (list of str): names of the axes, from the 1st to the 4th, if present.
if an axis is not connected, put a "".
stepsize (list of float): size of a step in m (the smaller, the
bigger will be a move for a given distance in m)
sn (str or None): serial number of the device (eg, "11500"). If None, the
driver will use whichever controller is first found.
inverted (set of str): names of the axes which are inverted (IOW, either
empty or the name of the axis)
"""
if not 1 <= len(axes) <= 4:
raise ValueError(
"Axes must be a list of 1 to 4 axis names (got %s)" % (axes, ))
if len(axes) != len(stepsize):
raise ValueError("Expecting %d stepsize (got %s)" %
(len(axes), stepsize))
self._name_to_axis = {} # str -> int: name -> axis number
for i, n in enumerate(axes):
if n == "": # skip this non-connected axis
continue
self._name_to_axis[n] = i + 1
for sz in stepsize:
if sz > 10e-3: # sz is typically ~1µm, so > 1 cm is very fishy
raise ValueError("stepsize should be in meter, but got %g" %
(sz, ))
self._stepsize = stepsize
self._address = address
self._sn = sn
self._accesser = self._openConnection(address, sn)
self._recover = False
self._resynchonise()
if name is None and role is None: # For scan only
return
# Seems to really be the device, so handle connection errors fully
self._recover = True
modl, fw, sn = self.GetIdentification()
if modl != "8742":
logging.warning("Controller %s is not supported, will try anyway",
modl)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
# Let the controller check the actuators are connected
self.MotorCheck()
axes_def = {}
speed = {}
for n, i in self._name_to_axis.items():
sz = self._stepsize[i - 1]
# TODO: allow to pass the range in m in the arguments
# Position supports ±2³¹, probably not that much in reality, but
# there is no info.
rng = [(-2**31) * sz, (2**31 - 1) * sz]
# Check the actuator is connected
mt = self.GetMotorType(i)
if mt in {MT_NONE, MT_UNKNOWN}:
raise HwError(
"Controller failed to detect motor %d, check the "
"actuator is connected to the controller" % (i, ))
max_stp_s = {MT_STANDARD: 2000, MT_TINY: 1750}[mt]
srng = (0, self._speedToMS(i, max_stp_s))
speed[n] = self._speedToMS(i, self.GetVelocity(i))
axes_def[n] = model.Axis(range=rng, speed=srng, unit="m")
model.Actuator.__init__(self, name, role, axes=axes_def, **kwargs)
self._swVersion = "%s (IP connection)" % (odemis.__version__, )
self._hwVersion = "New Focus %s (firmware %s, S/N %s)" % (modl, fw, sn)
# Note that the "0" position is just the position at which the
# controller turned on
self.position = model.VigilantAttribute({}, unit="m", readonly=True)
self._updatePosition()
max_speed = max(a.speed[1] for a in axes_def.values())
self.speed = model.MultiSpeedVA(speed,
range=(0, max_speed),
unit="m/s",
setter=self._setSpeed)
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown(wait=True)
self._executor = None
if self._accesser:
self._accesser.terminate()
self._accesser = None
def _sendOrderCommand(self, cmd, val="", axis=None):
return self._accesser.sendOrderCommand(cmd, val, axis)
def _sendQueryCommand(self, cmd, val="", axis=None):
"""
Same as accesser's sendQueryCommand, but with error recovery
"""
trials = 0
while True:
try:
return self._accesser.sendQueryCommand(cmd, val, axis)
except IOError: # Typically due to timeout
trials += 1
if not self._recover and trials < 5:
raise
self._recover = False
try:
# can also happen just due to error
# => first read error and see if that explains anything
self._checkError()
except IOError:
# Sometimes the hardware seems to lose connection
# => try to reconnect
logging.warning(
"Device seems disconnected, will try to reconnect")
# Sometimes the device gets confused and answers are shifted.
# Reset helps, but it also reset the current position, which
# is not handy.
# self._accesser.sendOrderCommand("RS")
self._accesser.terminate()
time.sleep(0.5)
self._accesser = self._openConnection(
self._address, self._sn)
self._checkError()
logging.info("Recovered lost connection to device %s",
self.name)
finally:
self._recover = True
# Low level functions
def GetIdentification(self):
"""
return (str, str, str):
Model name
Firmware version (and date)
serial number
"""
resp = self._sendQueryCommand("*IDN")
# expects something like this:
# New_Focus 8742 v2.2 08/01/13 11511
try:
m = re.match("\w+ (?P<model>\w+) (?P<fw>v\S+ \S+) (?P<sn>\d+)",
resp)
modl, fw, sn = m.groups()
except Exception:
raise IOError("Failed to decode firmware answer '%s'" %
resp.encode('string_escape'))
return modl, fw, sn
def GetMotorType(self, axis):
"""
Read the motor type.
The motor check action must have been performed before to get correct
values.
axis (1<=int<=4): axis number
return (0<=int<=3): the motor type
"""
resp = self._sendQueryCommand("QM", axis=axis)
return int(resp)
def GetVelocity(self, axis):
"""
Read the max speed
axis (1<=int<=4): axis number
return (0<=int<=2000): the speed in step/s
"""
resp = self._sendQueryCommand("VA", axis=axis)
return int(resp)
def SetVelocity(self, axis, val):
"""
Write the max speed
axis (1<=int<=4): axis number
val (1<=int<=2000): the speed in step/s
"""
if not 1 <= val <= 2000:
raise ValueError("Velocity outside of the range 0->2000")
self._sendOrderCommand("VA", "%d" % (val, ), axis)
def GetAccel(self, axis):
"""
Read the acceleration
axis (1<=int<=4): axis number
return (0<=int): the acceleration in step/s²
"""
resp = self._sendQueryCommand("AC", axis=axis)
return int(resp)
def SetAccel(self, axis, val):
"""
Write the acceleration
axis (1<=int<=4): axis number
val (1<=int<=200000): the acceleration in step/s²
"""
if not 1 <= val <= 200000:
raise ValueError("Acceleration outside of the range 0->200000")
self._sendOrderCommand("AC", "%d" % (val, ), axis)
def MotorCheck(self):
"""
Run the motor check command, that automatically configure the right
values based on the type of motors connected.
"""
self._sendOrderCommand("MC")
def MoveAbs(self, axis, pos):
"""
Requests a move to an absolute position. This is non-blocking.
axis (1<=int<=4): axis number
pos (-2**31 <= int 2*31-1): position in step
"""
self._sendOrderCommand("PA", "%d" % (pos, ), axis)
def GetTarget(self, axis):
"""
Read the target position for the given axis
axis (1<=int<=4): axis number
return (int): the position in steps
"""
# Note, it's not clear what's the difference with PR?
resp = self._sendQueryCommand("PA", axis=axis)
return int(resp)
def MoveRel(self, axis, offset):
"""
Requests a move to a relative position. This is non-blocking.
axis (1<=int<=4): axis number
offset (-2**31 <= int 2*31-1): offset in step
"""
self._sendOrderCommand("PR", "%d" % (offset, ), axis)
def GetPosition(self, axis):
"""
Read the actual position for the given axis
axis (1<=int<=4): axis number
return (int): the position in steps
"""
resp = self._sendQueryCommand("TP", axis=axis)
return int(resp)
def IsMotionDone(self, axis):
"""
Check whether the axis is in motion
axis (1<=int<=4): axis number
return (bool): False if in motion, True if motion is finished
"""
resp = self._sendQueryCommand("MD", axis=axis)
if resp == "0": # motion in progress
return False
elif resp == "1": # no motion
return True
else:
raise IOError("Failed to decode answer about motion '%s'" %
resp.encode('string_escape'))
def AbortMotion(self):
"""
Stop immediately the motion on all the axes
"""
self._sendOrderCommand("AB")
def StopMotion(self, axis):
"""
Stop nicely the motion (using accel/decel values)
axis (1<=int<=4): axis number
"""
self._sendOrderCommand("ST", axis=axis)
def GetError(self):
"""
Read the oldest error in memory.
The error buffer is FIFO with 10 elements, so it might not be the
latest error if multiple errors have happened since the last time this
function was called.
return (None or (int, str)): the error number and message
"""
# Note: there is another one "TE" which only returns the number, and so
# is faster, but then there is no way to get the message
resp = self._sendQueryCommand("TB")
# returns something like "108, MOTOR NOT CONNECTED"
try:
m = re.match("(?P<no>\d+), (?P<msg>.+)", resp)
no, msg = int(m.group("no")), m.group("msg")
except Exception:
raise IOError("Failed to decode error info '%s'" %
resp.encode('string_escape'))
if no == 0:
return None
else:
return no, msg
def _checkError(self):
"""
Check if an error happened and convert to a python exception
return None
raise NewFocusError if an error happened
"""
err = self.GetError()
if err:
errno, msg = err
raise NewFocusError(errno, msg)
def _resynchonise(self):
"""
Ensures the device communication is "synchronised"
"""
self._accesser.flushInput()
# drop all the errors
while self.GetError():
pass
# high-level methods (interface)
def _updatePosition(self, axes=None):
"""
update the position VA
axes (set of str): names of the axes to update or None if all should be
updated
"""
# uses the current values (converted to internal representation)
pos = self._applyInversion(self.position.value)
for n, i in self._name_to_axis.items():
if axes is None or n in axes:
pos[n] = self.GetPosition(i) * self._stepsize[i - 1]
pos = self._applyInversion(pos)
# it's read-only, so we change it via _value
self.position._value = pos
self.position.notify(self.position.value)
def _speedToMS(self, axis, sps):
"""
Convert speed in step/s to m/s
axis (1<=int<=4): axis number
sps (int): steps/s
return (float): m/s
"""
return sps * self._stepsize[axis - 1]
def _setSpeed(self, value):
"""
value (dict string-> float): speed for each axis
returns (dict string-> float): the new value
"""
if set(value.keys()) != set(self._axes.keys()):
raise ValueError("Requested speed %s doesn't specify all axes %s" %
(value, self._axes.keys()))
for axis, v in value.items():
rng = self._axes[axis].speed
if not rng[0] < v <= rng[1]:
raise ValueError(
"Requested speed of %f for axis %s not within %f->%f" %
(v, axis, rng[0], rng[1]))
i = self._name_to_axis[axis]
sps = max(1, int(round(v / self._stepsize[i - 1])))
self.SetVelocity(i, sps)
return value
def _createFuture(self):
"""
Return (CancellableFuture): a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event(
) # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
# Check if the distance is big enough to make sense
for an, v in shift.items():
aid = self._name_to_axis[an]
if abs(v) < self._stepsize[aid - 1]:
# TODO: store and accumulate all the small moves instead of dropping them?
del shift[an]
logging.info("Dropped too small move of %g m < %g m", abs(v),
self._stepsize[aid - 1])
if not shift:
return model.InstantaneousFuture()
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
moveRel.__doc__ = model.Actuator.moveRel.__doc__
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
moveAbs.__doc__ = model.Actuator.moveAbs.__doc__
def stop(self, axes=None):
self._executor.cancel()
def _doMoveRel(self, future, pos):
"""
Blocking and cancellable relative move
future (Future): the future it handles
pos (dict str -> float): axis name -> relative target position
"""
with future._moving_lock:
end = 0 # expected end
moving_axes = set()
for an, v in pos.items():
aid = self._name_to_axis[an]
moving_axes.add(aid)
steps = int(round(v / self._stepsize[aid - 1]))
self.MoveRel(aid, steps)
# compute expected end
dur = abs(steps) * self._stepsize[aid -
1] / self.speed.value[an]
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
logging.debug("move successfully completed")
def _doMoveAbs(self, future, pos):
"""
Blocking and cancellable absolute move
future (Future): the future it handles
pos (dict str -> float): axis name -> absolute target position
"""
with future._moving_lock:
end = 0 # expected end
old_pos = self._applyInversion(self.position.value)
moving_axes = set()
for an, v in pos.items():
aid = self._name_to_axis[an]
moving_axes.add(aid)
steps = int(round(v / self._stepsize[aid - 1]))
self.MoveAbs(aid, steps)
# compute expected end
dur = abs(v - old_pos[an]) / self.speed.value[an]
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
logging.debug("move successfully completed")
def _waitEndMove(self, future, axes, end=0):
"""
Wait until all the given axes are finished moving, or a request to
stop has been received.
future (Future): the future it handles
axes (set of int): the axes IDs to check
end (float): expected end time
raise:
CancelledError: if cancelled before the end of the move
"""
moving_axes = set(axes)
last_upd = time.time()
last_axes = moving_axes.copy()
try:
while not future._must_stop.is_set():
for aid in moving_axes.copy(
): # need copy to remove during iteration
if self.IsMotionDone(aid):
moving_axes.discard(aid)
if not moving_axes:
# no more axes to wait for
break
# Update the position from time to time (10 Hz)
if time.time() - last_upd > 0.1 or last_axes != moving_axes:
last_names = set(n for n, i in self._name_to_axis.items()
if i in last_axes)
self._updatePosition(last_names)
last_upd = time.time()
last_axes = moving_axes.copy()
# Wait half of the time left (maximum 0.1 s)
left = end - time.time()
sleept = max(0.001, min(left / 2, 0.1))
future._must_stop.wait(sleept)
# TODO: timeout if really too long
else:
logging.debug("Move of axes %s cancelled before the end", axes)
# stop all axes still moving them
for i in moving_axes:
self.StopMotion(i)
future._was_stopped = True
raise CancelledError()
except Exception:
raise
else:
# Did everything really finished fine?
self._checkError()
finally:
self._updatePosition() # update (all axes) with final position
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set(
) # tell the thread taking care of the move it's over
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
@classmethod
def scan(cls):
"""
returns (list of (str, dict)): name, kwargs
Note: it's obviously not advised to call this function if a device is already under use
"""
logging.info("Scanning for New Focus controllers in progress...")
found = [] # (list of 2-tuple): name, kwargs
try:
conts = cls._scanOverIP()
except IOError as exp:
logging.exception("Failed to scan for New Focus controllers: %s",
exp)
for hn, host, port in conts:
try:
logging.debug("Trying controller at %s", host)
dev = cls(None,
None,
address=host,
axes=["a"],
stepsize=[1e-6])
modl, fw, sn = dev.GetIdentification()
# find out about the axes
dev.MotorCheck()
axes = []
stepsize = []
for i in range(1, 5):
mt = dev.GetMotorType(i)
n = chr(ord('a') + i - 1)
# No idea about the stepsize, but make it different to allow
# distinguishing between motor types
if mt == MT_STANDARD:
ss = 1e-6
elif mt == MT_TINY:
ss = 0.1e-6
else:
n = ""
ss = 0
axes.append(n)
stepsize.append(ss)
except IOError:
# not possible to use this port? next one!
continue
except Exception:
logging.exception(
"Error while communicating with controller %s @ %s:%s", hn,
host, port)
continue
found.append(("NF-%s-%s" % (modl, sn), {
"address": host,
"axes": axes,
"stepsize": stepsize,
"sn": sn
}))
return found
@classmethod
def _openConnection(cls, address, sn=None):
"""
return (Accesser)
"""
if address == "fake":
host, port = "fake", 23
elif address == "autoip":
conts = cls._scanOverIP()
if sn is not None:
for hn, host, port in conts:
# Open connection to each controller and ask for their SN
dev = cls(None,
None,
address=host,
axes=["a"],
stepsize=[1e-6])
_, _, devsn = dev.GetIdentification()
if sn == devsn:
break
else:
raise HwError(
"Failed to find New Focus controller %s over the "
"network. Ensure it is turned on and connected to "
"the network." % (sn, ))
else:
# just pick the first one
# TODO: only pick the ones of model 8742
try:
hn, host, port = conts[0]
logging.info("Connecting to New Focus %s", hn)
except IndexError:
raise HwError(
"Failed to find New Focus controller over the "
"network. Ensure it is turned on and connected to "
"the network.")
else:
# split the (IP) port, separated by a :
if ":" in address:
host, ipport_str = address.split(":")
port = int(ipport_str)
else:
host = address
port = 23 # default
return IPAccesser(host, port)
@staticmethod
def _scanOverIP():
"""
Scan the network for all the responding new focus controllers
Note: it actually calls a separate executable because it relies on opening
a network port which needs special privileges.
return (list of (str, str, int)): hostname, ip address, and port number
"""
# Run the separate program via authbind
try:
exc = os.path.join(os.path.dirname(__file__), "nfpm_netscan.py")
out = subprocess.check_output(["authbind", "python", exc])
except CalledProcessError as exp:
# and handle all the possible errors:
# - no authbind (127)
# - cannot find the separate program (2)
# - no authorisation (13)
ret = exp.returncode
if ret == 127:
raise IOError("Failed to find authbind")
elif ret == 2:
raise IOError("Failed to find %s" % exc)
elif ret == 13:
raise IOError("No permission to open network port 23")
# or decode the output
# hostname \t host \t port
ret = []
for l in out.split("\n"):
if not l:
continue
try:
hn, host, port = l.split("\t")
except Exception:
logging.exception("Failed to decode scanner line '%s'", l)
ret.append((hn, host, port))
return ret
class Stage(model.Actuator):
"""
This is an extension of the model.Actuator class. It provides functions for
moving the TFS stage and updating the position.
"""
def __init__(self, name, role, parent, rng=None, **kwargs):
if rng is None:
rng = {}
stage_info = parent.stage_info()
if "x" not in rng:
rng["x"] = stage_info["range"]["x"]
if "y" not in rng:
rng["y"] = stage_info["range"]["y"]
if "z" not in rng:
rng["z"] = stage_info["range"]["z"]
axes_def = {
# Ranges are from the documentation
"x": model.Axis(unit="m", range=rng["x"]),
"y": model.Axis(unit="m", range=rng["y"]),
"z": model.Axis(unit="m", range=rng["z"]),
}
model.Actuator.__init__(self,
name,
role,
parent=parent,
axes=axes_def,
**kwargs)
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(
max_workers=1) # one task at a time
self.position = model.VigilantAttribute({},
unit=stage_info["unit"],
readonly=True)
self._updatePosition()
# Refresh regularly the position
self._pos_poll = util.RepeatingTimer(5, self._refreshPosition,
"Position polling")
self._pos_poll.start()
def _updatePosition(self, raw_pos=None):
"""
update the position VA
raw_pos (dict str -> float): the position in mm (as received from the SEM)
"""
if raw_pos is None:
position = self.parent.get_stage_position()
x, y, z = position["x"], position["y"], position["z"]
else:
x, y, z = raw_pos["x"], raw_pos["y"], raw_pos["z"]
pos = {
"x": x,
"y": y,
"z": z,
}
self.position._set_value(self._applyInversion(pos), force_write=True)
def _refreshPosition(self):
"""
Called regularly to update the current position
"""
# We don't use the VA setters, to avoid sending back to the hardware a
# set request
logging.debug("Updating SEM stage position")
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
def _moveTo(self, future, pos, timeout=60):
with future._moving_lock:
try:
if future._must_stop.is_set():
raise CancelledError()
logging.debug("Moving to position {}".format(pos))
self.parent.move_stage(pos, rel=False)
time.sleep(0.5)
# Wait until the move is over.
# Don't check for future._must_stop because anyway the stage will
# stop moving, and so it's nice to wait until we know the stage is
# not moving.
moving = True
tstart = time.time()
while moving:
pos = self.parent.get_stage_position()
moving = self.parent.stage_is_moving()
# Take the opportunity to update .position
self._updatePosition(pos)
if time.time() > tstart + timeout:
self.parent.stop_stage_movement()
logging.error(
"Timeout after submitting stage move. Aborting move."
)
break
# Wait for 50ms so that we do not keep using the CPU all the time.
time.sleep(50e-3)
# If it was cancelled, Abort() has stopped the stage before, and
# we still have waited until the stage stopped moving. Now let
# know the user that the move is not complete.
if future._must_stop.is_set():
raise CancelledError()
except Exception:
if future._must_stop.is_set():
raise CancelledError()
raise
finally:
future._was_stopped = True
# Update the position, even if the move didn't entirely succeed
self._updatePosition()
def _doMoveRel(self, future, shift):
pos = self.parent.get_stage_position()
for k, v in shift.items():
pos[k] += v
target_pos = self._applyInversion(pos)
# Check range (for the axes we are moving)
for an in shift.keys():
rng = self.axes[an].range
p = target_pos[an]
if not rng[0] <= p <= rng[1]:
raise ValueError(
"Relative move would cause axis %s out of bound (%g m)" %
(an, p))
self._moveTo(future, pos)
@isasync
def moveRel(self, shift):
"""
Shift the stage the given position in meters. This is non-blocking.
Throws an error when the requested position is out of range.
Parameters
----------
shift: dict(string->float)
Relative shift to move the stage to per axes in m. Axes are 'x' and 'y'.
"""
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
def _doMoveAbs(self, future, pos):
self._moveTo(future, pos)
@isasync
def moveAbs(self, pos):
"""
Move the stage the given position in meters. This is non-blocking.
Throws an error when the requested position is out of range.
Parameters
----------
pos: dict(string->float)
Absolute position to move the stage to per axes in m. Axes are 'x' and 'y'.
"""
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
def stop(self, axes=None):
"""Stop the movement of the stage."""
self._executor.cancel()
self.parent.stop_stage_movement()
try:
self._updatePosition()
except Exception:
logging.exception("Unexpected failure when updating position")
def _createFuture(self):
"""
Return (CancellableFuture): a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event(
) # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set(
) # tell the thread taking care of the move it's over
self.parent.stop_stage_movement()
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
class FW102c(model.Actuator):
"""
Represents a Thorlabs filter wheel FW102C as an actuator.
It provides one enumerated axis, whose actual band values are provided by
the user at init.
"""
# Regex matching the compatible identification strings
re_idn = "THORLABS.*FW102C.*"
def __init__(self, name, role, port, bands, _scan=False, **kwargs):
"""
port (string): name of the serial port to connect to. Can be a pattern,
in which case, all the ports fitting the pattern will be tried, and the
first one which looks like an FW102C will be used.
bands (dict 1<=int<=12 -> 2-tuple of floats > 0 or str):
filter position -> lower and higher bound of the wavelength (m) of the
light which goes _through_. If it's a list, it implies that the filter
is multi-band.
_scan (bool): only for internal usage
raise IOError if no device answering or not a compatible device
"""
self._ser_access = threading.Lock()
self._port = self._findDevice(port)
logging.info("Found FW102C device on port %s", self._port)
if _scan:
return
# check bands contains correct data
self._maxpos = self.GetMaxPosition()
if not bands:
raise ValueError("Argument bands must contain at least one band")
try:
for pos, band in bands.items():
if not 1 <= pos <= self._maxpos:
raise ValueError("Filter position should be between 1 and "
"%d, but got %d." % (self._maxpos, pos))
# To support "weird" filter, we accept strings
if isinstance(band, basestring):
if not band.strip():
raise ValueError("Name of filter %d is empty" % pos)
else:
driver.checkLightBand(band)
except Exception:
logging.exception("Failed to parse bands %s", bands)
raise
curpos = self.GetPosition()
if curpos not in bands:
logging.info("Current position %d is not configured, will add it", curpos)
bands[curpos] = "unknown"
axes = {"band": model.Axis(choices=bands)}
model.Actuator.__init__(self, name, role, axes=axes, **kwargs)
driver_name = driver.getSerialDriver(self._port)
self._swVersion = "%s (serial driver: %s)" % (odemis.__version__, driver_name)
self._hwVersion = self._idn
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(max_workers=1) # one task at a time
self._speed = self.GetSpeed()
self.position = model.VigilantAttribute({"band": curpos}, readonly=True)
def getMetadata(self):
return self._metadata
def terminate(self):
if self._executor:
self.stop()
self._executor.shutdown()
self._executor = None
with self._ser_access:
if self._serial:
self._serial.close()
self._serial = None
def _findDevice(self, ports):
"""
Look for a compatible device
ports (str): pattern for the port name
return (str): the name of the port used
It also sets ._serial and ._idn to contain the opened serial port, and
the identification string.
raises:
IOError: if no device are found
"""
if os.name == "nt":
# TODO
# ports = ["COM" + str(n) for n in range(15)]
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
self._serial = self._openSerialPort(n)
except serial.SerialException:
# not possible to use this port? next one!
continue
# check whether it looks like a FW102C
try:
# If any garbage was previously received, make it discarded.
self._serial.write("\r")
# can have some \x00 bytes at the beginning + "CMD_NOT_DEFINED"
self._flushInput()
idn = self.GetIdentification()
if re.match(self.re_idn, idn):
self._idn = idn
return n # found it!
except Exception:
logging.debug("Port %s doesn't seem to have a FW102C device connected", n)
else:
raise HwError("Failed to find a filter wheel FW102C on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports,))
@staticmethod
def _openSerialPort(port):
"""
Opens the given serial port the right way for the FW102C.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
baudrate=115200, # only correct if setting was not changed
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
timeout=10 # s (can take time when filter changes)
)
return ser
def _flushInput(self):
"""
Ensure there is no more data queued to be read on the bus (=serial port)
"""
with self._ser_access:
self._serial.flush()
self._serial.flushInput()
# Shouldn't be necessary, but just in case
skipped = self._serial.read(1000) # More than 1000 chars => give up
logging.debug("Skipping input %s", skipped.encode('string_escape'))
re_err = r"Command error (.*)"
def _sendQuery(self, com):
"""
Send a command which expects an answer
com (string): command to send (not including the ? and the \r)
return (string): the answer without newline and suffix ("> ")
raises
IOError: if there is a timeout
TLFWError: if the hardware reports an error
"""
# TODO: handle IOError and automatically try to reconnect (cf LLE)
assert(len(com) <= 50) # commands cannot be long
full_com = com + "\r"
with self._ser_access:
logging.debug("Sending: '%s'", full_com.encode('string_escape'))
self._serial.write(full_com)
# ensure everything is received, before expecting an answer
self._serial.flush()
# Read until end of answer
line = b""
while True:
char = self._serial.read() # empty if timeout
if not char: # should always finish by a "> "
raise IOError("Controller timeout, after receiving '%s'" % line.encode('string_escape'))
# normal char
line += char
if line[-2:] == "> ":
break
logging.debug("Received: '%s'", line.encode('string_escape'))
# remove echo + suffix + new line
line = line[len(full_com):-2].rstrip("\r")
# if it's an error message => raise an error
m = re.match(self.re_err, line)
if m:
err = m.group(1)
raise TLFWError("Device rejected command '%s': %s" % (com, err))
return line
def _sendCommand(self, com):
"""
Send a command which does not expect any answer
com (string): command to send (not including the ? and the \r)
return when the command is finished processed
raises
IOError: if there is a timeout
TLFWError: if the hardware reports an error
"""
self._sendQuery(com)
# don't return anything
def GetIdentification(self):
"""
return (str): model name as reported by the device
"""
# answer is like "THORLABS FW102C/FW212C Filter Wheel version 1.04"
return self._sendQuery("*idn?")
def GetMaxPosition(self):
"""
return (1<int): maximum number of positions available (eg, 6, 12)
"""
ans = self._sendQuery("pcount?")
return int(ans)
def GetPosition(self):
"""
return (1<=int<=maxpos): current position
Note: might be different from the last position set if the user has
manually changed it.
"""
ans = self._sendQuery("pos?")
return int(ans)
def GetSpeed(self):
"""
return (0 or 1): current "speed" of the wheel, the bigger the faster
"""
ans = self._sendQuery("speed?")
return int(ans)
def SetPosition(self, pos):
"""
pos (1<=int<=maxpos): current position
returns when the new position is set
raise Exception in case of error
"""
assert(1 <= pos <= self._maxpos)
# Estimate how long it'll take
cur_pos = self.position.value["band"]
p1, p2 = sorted([pos, cur_pos])
dist = min(p2 - p1, (6 + p1) - p2)
if self._speed == 0:
dur_one = 2 # s
else:
dur_one = 1 # s
maxdur = 1 + dist * dur_one * 2 # x 2 as a safe bet
prev_timeout = self._serial.timeout
try:
self._serial.timeout = maxdur
self._sendCommand("pos=%d" % pos)
finally:
self._serial.timeout = prev_timeout
logging.debug("Move to pos %d finished", pos)
# What we don't need:
# speed?\r1\r>
# trig?\r0\r>
# sensors?\r0\r>
def _doMoveBand(self, pos):
"""
move to the position and updates the metadata and position once it's over
"""
self.SetPosition(pos)
self._updatePosition()
# high-level methods (interface)
def _updatePosition(self):
"""
update the position VA
Note: it should not be called while holding _ser_access
"""
pos = {"band": self.GetPosition()}
# it's read-only, so we change it via _value
self.position._value = pos
self.position.notify(self.position.value)
@isasync
def moveRel(self, shift):
if not shift:
return model.InstantaneousFuture()
self._checkMoveRel(shift)
# TODO move to the +N next position? (and modulo number of axes)
raise NotImplementedError("Relative move on enumerated axis not supported")
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
self._checkMoveAbs(pos)
return self._executor.submit(self._doMoveBand, pos["band"])
def stop(self, axes=None):
self._executor.cancel()
def selfTest(self):
"""
check as much as possible that it works without actually moving the motor
return (boolean): False if it detects any problem
"""
try:
pos = self.GetPosition()
maxpos = self.GetMaxPosition()
if 1 <= pos <= maxpos:
return True
except Exception:
logging.exception("Selftest failed")
return False
@classmethod
def scan(cls, port=None):
"""
port (string): name of the serial port. If None, all the serial ports are tried
returns (list of 2-tuple): name, args (port)
Note: it's obviously not advised to call this function if a device is already under use
"""
if port:
ports = [port]
else:
if os.name == "nt":
ports = ["COM" + str(n) for n in range(15)]
else:
ports = glob.glob('/dev/ttyS?*') + glob.glob('/dev/ttyUSB?*')
logging.info("Serial ports scanning for Thorlabs filter wheel in progress...")
found = [] # (list of 2-tuple): name, kwargs
for p in ports:
try:
logging.debug("Trying port %s", p)
dev = cls(None, None, p, bands=None, _scan=True)
except (serial.SerialException, IOError):
# not possible to use this port? next one!
continue
# Get some more info
try:
maxpos = dev.GetMaxPosition()
except Exception:
continue
else:
# create fake band argument
bands = {}
for i in range(1, maxpos + 1):
bands[i] = (i * 100e-9, (i + 1) * 100e-9)
found.append((dev._idn, {"port": p, "bands": bands}))
return found
class ESP(model.Actuator):
def __init__(self, name, role, port, axes=None, **kwargs):
"""
A driver for a Newport ESP 301 Stage Actuator.
This driver supports a serial connection. Note that as of the Linux
kernel 4.13, the USB connection is known to _not_ work, as the TI 3410
chipset apparently behind is not handled properly. Use a of the
RS-232 port is required (via a USB adapter if necessary).
name: (str)
role: (str)
port: (str) port name. Can be a pattern, in which case all the ports
fitting the pattern will be tried.
Use /dev/fake for a simulator
axes: dict str (axis name) -> dict (axis parameters)
axis parameters: {
number (1 <= int <= 3): axis number on the hardware
range: [float, float], default is -1 -> 1
unit (str): the external unit of the axis (internal is mm),
default is "m".
conv_factor (float): a conversion factor that converts to the
device internal unit (mm), default is 1000.
}
inverted: (bool) defines if the axes are inverted
The offset can be specified by setting MD_POS_COR as a coordinate dictionary
"""
if len(axes) == 0:
raise ValueError("Needs at least 1 axis.")
# Connect to serial port
self._ser_access = threading.Lock()
self._serial = None
self._file = None
self._port, self._version = self._findDevice(port) # sets ._serial and ._file
logging.info("Found Newport ESP301 device on port %s, Ver: %s",
self._port, self._version)
self._offset = {}
self._axis_conv_factor = {}
# Not to be mistaken with axes which is a simple public view
self._axis_map = {} # axis name -> axis number used by controller
axes_def = {} # axis name -> Axis object
speed = {}
accel = {}
decel = {}
self._id = {}
for axis_name, axis_par in axes.items():
# Unpack axis parameters from the definitions in the YAML
try:
axis_num = axis_par['number']
except KeyError:
raise ValueError("Axis %s must have a number to identify it. " % (axis_name,))
try:
axis_range = axis_par['range']
except KeyError:
logging.info("Axis %s has no range. Assuming (-1, 1)", axis_name)
axis_range = (-1, 1)
try:
axis_unit = axis_par['unit']
except KeyError:
logging.info("Axis %s has no unit. Assuming m", axis_name)
axis_unit = "m"
try:
conv_factor = float(axis_par['conv_factor'])
except KeyError:
logging.info("Axis %s has no conversion factor. Assuming 1000 (m to mm)", axis_name)
conv_factor = 1000.0
self._axis_map[axis_name] = axis_num
self._axis_conv_factor[axis_num] = conv_factor
self._id[axis_num] = self.GetIdentification(axis_num)
speed[axis_name] = self.GetSpeed(axis_num)
accel[axis_name] = self.GetAcceleration(axis_num)
decel[axis_name] = self.GetDeceleration(axis_num)
# Force millimetres for consistency as the internal unit.
self.SetAxisUnit(axis_num, "mm")
# initialize each motor
self.MotorOn(axis_num)
ad = model.Axis(canAbs=True, unit=axis_unit, range=axis_range)
axes_def[axis_name] = ad
model.Actuator.__init__(self, name, role, axes=axes_def, **kwargs)
self._hwVersion = str(self._id)
self._swversion = self._version
# Get the position in object coord with the offset applied.
# RO, as to modify it the client must use .moveRel() or .moveAbs()
self.position = model.VigilantAttribute({}, readonly=True)
self._updatePosition()
self._speed = speed
self._accel = accel
self._decel = decel
# set offset due to mounting of components (float)
self._metadata[model.MD_POS_COR] = {}
# will take care of executing axis move asynchronously
self._executor = CancellableThreadPoolExecutor(1) # one task at a time
# Check the error state
self.checkError()
def terminate(self):
with self._ser_access:
self._serial.close()
model.Actuator.terminate(self)
def updateMetadata(self, md):
super(ESP, self).updateMetadata(md)
try:
value = md[model.MD_POS_COR]
except KeyError:
# there is no offset set.
return
if not isinstance(value, dict):
raise ValueError("Invalid metadata, should be a coordinate dictionary but got %s." % (value,))
# update all axes
for n in self._axis_map.keys():
if n in value:
self._offset[n] = value[n]
logging.debug("Updating offset to %s.", value)
self._updatePosition()
# Connection methods
@staticmethod
def _openSerialPort(port, baudrate):
"""
Opens the given serial port the right way for a Power control device.
port (string): the name of the serial port (e.g., /dev/ttyUSB0)
baudrate (int)
return (serial): the opened serial port
"""
ser = serial.Serial(
port=port,
baudrate=baudrate,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE,
rtscts=True,
timeout=1 # s
)
# Purge
ser.flush()
ser.flushInput()
# Try to read until timeout to be extra safe that we properly flushed
ser.timeout = 0
while True:
char = ser.read()
if char == '':
break
ser.timeout = 1
return ser
def _findDevice(self, ports, baudrate=19200):
"""
Look for a compatible device
ports (str): pattern for the port name
baudrate (0<int)
return:
(str): the name of the port used
(str): the hardware version string
Note: will also update ._file and ._serial
raises:
IOError: if no devices are found
"""
# For debugging purpose
if ports == "/dev/fake":
self._serial = ESPSimulator(timeout=1)
self._file = None
ve = self.GetVersion()
return ports, ve
if os.name == "nt":
raise NotImplementedError("Windows not supported")
else:
names = glob.glob(ports)
for n in names:
try:
# Ensure no one will talk to it simultaneously, and we don't talk to devices already in use
self._file = open(n) # Open in RO, just to check for lock
try:
fcntl.flock(self._file.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB) # Raises IOError if cannot lock
except IOError:
logging.info("Port %s is busy, will not use", n)
continue
self._serial = self._openSerialPort(n, baudrate)
try:
ve = self.GetVersion()
except ESPError as e:
# Can happen if the device has received some weird characters
# => try again (now that it's flushed)
logging.info("Device answered by an error %s, will try again", e)
ve = self.GetVersion()
return n, ve
except (IOError, ESPError) as e:
logging.debug(e)
logging.info("Skipping device on port %s, which didn't seem to be compatible", n)
# not possible to use this port? next one!
continue
else:
raise HwError("Failed to find a device on ports '%s'. "
"Check that the device is turned on and connected to "
"the computer." % (ports,))
def _sendOrder(self, cmd):
"""
cmd (str): command to be sent to device (without the CR)
"""
cmd = cmd + "\r"
with self._ser_access:
logging.debug("Sending command %s", cmd.encode('string_escape'))
self._serial.write(cmd.encode('ascii'))
def _sendQuery(self, cmd):
"""
cmd (str): command to be sent to device (without the CR, but with the ?)
returns (str): answer received from the device (without \n or \r)
raise:
IOError if no answer is returned in time
"""
cmd = cmd + "\r"
with self._ser_access:
logging.debug("Sending command %s", cmd.encode('string_escape'))
self._serial.write(cmd.encode('ascii'))
self._serial.timeout = 1
ans = ''
while ans[-1:] != '\r':
char = self._serial.read()
if not char:
raise IOError("Timeout after receiving %s" % ans.encode('string_escape'))
ans += char
logging.debug("Received answer %s", ans.encode('string_escape'))
return ans.strip()
# Low level serial commands.
# Note: These all convert to internal units of the controller
def GetErrorCode(self):
# Checks the device error register
return int(self._sendQuery("TE?"))
def checkError(self):
# Checks if an error occurred and raises an exception accordingly.
err_q = []
# Get all of the errors in the error FIFO stack
while True:
errcode = self.GetErrorCode()
if errcode == 0: # No error
break
else:
err_q.append(errcode)
# After errors are collected
if len(err_q) > 0:
raise ESPError("Error code(s) %s" % (err_q))
def SetAxisUnit(self, axis_num, unit):
# Set the internal unit used by the controller
if not unit in UNIT_DEF:
raise ValueError("Unknown unit name %s" % (unit,))
self._sendOrder("%d SN %d" % (axis_num, UNIT_DEF[unit]))
def MoveAbsPos(self, axis_num, pos):
"""
Requests a move to an absolute position. This is non-blocking.
Converts to internal unit of the controller
"""
self._sendOrder("%d PA %f" % (axis_num, pos))
def MoveRelPos(self, axis_num, rel):
"""
Requests a move to a relative position. This is non-blocking.
"""
self._sendOrder("%d PR %f" % (axis_num, rel)) # 0 = absolute
def GetDesiredPos(self, axis_num):
# Get the target position programmed into the controller
return float(self._sendQuery("%d DP?" % (axis_num,)))
def StopMotion(self, axis):
# Stop the motion on the specified axis
self._sendOrder("%d ST" % (axis,))
def MotorOn(self, axis):
# Start the motor
self._sendOrder("%d MO" % (axis,))
def MotorOff(self, axis):
# Stop the motor
self._sendOrder("%d MF" % (axis,))
def GetMotionDone(self, axis_n):
# Return true or false based on if the axis is still moving.
done = int(self._sendQuery("%d MD?" % axis_n))
logging.debug("Motion done: %d", done)
return bool(done)
def GetPosition(self, axis_n):
# Get the position of the axis
return float(self._sendQuery("%d TP?" % axis_n))
def GetSpeed(self, axis_n):
# Get the speed of the axis
return float(self._sendQuery("%d VA?" % axis_n))
def SetSpeed(self, axis_n, speed):
# Set the axis speed
self._sendOrder("%d VA %f" % (axis_n, speed,))
def GetAcceleration(self, axis_n):
# Get axis accel
return float(self._sendQuery("%d AC?" % axis_n))
def SetAcceleration(self, axis_n, ac):
# Set axis accel
self._sendOrder("%d AC %f" % (axis_n, ac,))
def GetDeceleration(self, axis_n):
return float(self._sendQuery("%d AG?" % axis_n))
def SetDeceleration(self, axis_n, dc):
self._sendOrder("%d AG %f" % (axis_n, dc,))
def GetIdentification(self, axis):
"""
return (str): the identification string as-is for the first axis
"""
return self._sendQuery("%d ID?" % (axis,))
def GetVersion(self):
"""
return (str): the version string as-is
"""
return self._sendQuery("VE?")
def SaveMem(self):
"""
Instruct the controller to save the current settings to non-volatile memory
"""
self._sendOrder("SM")
"""
High level commands (ie, Odemis Actuator API)
"""
def _applyOffset(self, pos):
"""
Apply the offset to the position and return it
"""
ret = dict(pos)
for axis in self._offset:
if axis in ret:
ret[axis] -= self._offset[axis]
return ret
def _removeOffset(self, pos):
"""
Remove the offset from the position and return it
"""
ret = dict(pos)
for axis in self._offset:
if axis in ret:
ret[axis] += self._offset[axis]
return ret
@isasync
def moveAbs(self, pos):
if not pos:
return model.InstantaneousFuture()
pos = self._removeOffset(pos) # Get the position in controller coord.
self._checkMoveAbs(pos)
pos = self._applyInversion(pos)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doMoveAbs, f, pos)
return f
@isasync
def moveRel(self, shift):
self._checkMoveRel(shift)
shift = self._applyInversion(shift)
f = self._createMoveFuture()
f = self._executor.submitf(f, self._doMoveRel, f, shift)
return f
def _doMoveRel(self, future, pos):
"""
Blocking and cancellable relative move
future (Future): the future it handles
_pos (dict str -> float): axis name -> relative target position
raise:
ValueError: if the target position is
TMCLError: if the controller reported an error
CancelledError: if cancelled before the end of the move
"""
with future._moving_lock:
end = 0 # expected end
moving_axes = set()
for an, v in pos.items():
aid = self._axis_map[an]
moving_axes.add(aid)
self.MoveRelPos(aid, v * self._axis_conv_factor[aid])
# compute expected end
# convert to mm units
dur = driver.estimateMoveDuration(abs(v) * self._axis_conv_factor[aid],
self._speed[an],
self._accel[an])
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
self.checkError()
logging.debug("move successfully completed")
def _doMoveAbs(self, future, pos):
"""
Blocking and cancellable absolute move
future (Future): the future it handles
_pos (dict str -> float): axis name -> absolute target position
raise:
TMCLError: if the controller reported an error
CancelledError: if cancelled before the end of the move
"""
with future._moving_lock:
end = 0 # expected end
old_pos = self._applyInversion(self.position.value)
moving_axes = set()
for an, v in pos.items():
aid = self._axis_map[an]
moving_axes.add(aid)
self.MoveAbsPos(aid, v * self._axis_conv_factor[aid])
d = abs(v - old_pos[an])
# convert displacement unit to mm
dur = driver.estimateMoveDuration(d * self._axis_conv_factor[aid],
self._speed[an],
self._accel[an])
end = max(time.time() + dur, end)
self._waitEndMove(future, moving_axes, end)
self.checkError()
logging.debug("move successfully completed")
def _waitEndMove(self, future, axes, end=0):
"""
Wait until all the given axes are finished moving, or a request to
stop has been received.
future (Future): the future it handles
axes (set of int): the axes IDs to check
end (float): expected end time
raise:
TimeoutError: if took too long to finish the move
CancelledError: if cancelled before the end of the move
"""
moving_axes = set(axes)
last_upd = time.time()
dur = max(0.01, min(end - last_upd, 60))
max_dur = dur * 2 + 1
logging.debug("Expecting a move of %g s, will wait up to %g s", dur, max_dur)
timeout = last_upd + max_dur
last_axes = moving_axes.copy()
try:
while not future._must_stop.is_set():
for aid in moving_axes.copy(): # need copy to remove during iteration
if self.GetMotionDone(aid):
moving_axes.discard(aid)
if not moving_axes:
# no more axes to wait for
break
now = time.time()
if now > timeout:
logging.warning("Stopping move due to timeout after %g s.", max_dur)
for i in moving_axes:
self.StopMotion(i)
raise TimeoutError("Move is not over after %g s, while "
"expected it takes only %g s" %
(max_dur, dur))
# Update the position from time to time (10 Hz)
if now - last_upd > 0.1 or last_axes != moving_axes:
last_names = set(n for n, i in self._axis_map.items() if i in last_axes)
self._updatePosition(last_names)
last_upd = time.time()
last_axes = moving_axes.copy()
# Wait half of the time left (maximum 0.1 s)
left = end - time.time()
sleept = max(0.001, min(left / 2, 0.1))
future._must_stop.wait(sleept)
else:
logging.debug("Move of axes %s cancelled before the end", axes)
# stop all axes still moving them
for i in moving_axes:
self.StopMotion(i)
future._was_stopped = True
raise CancelledError()
finally:
# TODO: check if the move succeded ? (= Not failed due to stallguard/limit switch)
self._updatePosition() # update (all axes) with final position
# high-level methods (interface)
def _updatePosition(self, axes=None):
"""
update the position VA
axes (set of str): names of the axes to update or None if all should be
updated
"""
# uses the current values (converted to internal representation)
pos = self._applyInversion(self.position.value)
for n, i in self._axis_map.items():
if axes is None or n in axes:
pos[n] = self.GetPosition(i) / self._axis_conv_factor[i]
pos = self._applyInversion(pos)
pos = self._applyOffset(pos) # Appy the offset back for display
logging.debug("Updated position to %s", pos)
self.position._set_value(pos, force_write=True)
def _cancelCurrentMove(self, future):
"""
Cancels the current move (both absolute or relative). Non-blocking.
future (Future): the future to stop. Unused, only one future must be
running at a time.
return (bool): True if it successfully cancelled (stopped) the move.
"""
# The difficulty is to synchronise correctly when:
# * the task is just starting (not finished requesting axes to move)
# * the task is finishing (about to say that it finished successfully)
logging.debug("Cancelling current move")
future._must_stop.set() # tell the thread taking care of the move it's over
with future._moving_lock:
if not future._was_stopped:
logging.debug("Cancelling failed")
return future._was_stopped
def stop(self, axes=None):
self._executor.cancel()
# For safety, just force stop every axis
for an, aid in self._axis_map.items():
if axes is None or an in axes:
self.StopMotion(aid)
def _createMoveFuture(self):
"""
Return (CancellableFuture): a future that can be used to manage a move
"""
f = CancellableFuture()
f._moving_lock = threading.Lock() # taken while moving
f._must_stop = threading.Event() # cancel of the current future requested
f._was_stopped = False # if cancel was successful
f.task_canceller = self._cancelCurrentMove
return f
