def stateRequest(self, request, timeout=TIMEOUT):
"""
Helper method used to get or set camera state.
Parameters
----------
request : `string`
Command to be passed to the camera
timeout : `float`
Time to wait for camera answer
Returns
-------
`int`
"""
self.socket.send(request)
timer = Timer(timeout)
r = b''
while b'\n' not in r and timer.wait(self.socket):
r += self.socket.recv(1)
if timer.expired():
raise RuntimeError('Camera is not answering')
r = r.strip(b'\x00\n')
return int(r, 0)
def waitForIdle(self):
"""
Blocks until the camera server is completely idle. This is required because
the camera and the server are slow and certain operations, in particular,
multiple sequential acquisitions would fail without waiting for some
time. Acquiring two images and dezingering them only works with
this method being called between the acquisitions.
"""
# Minimum reliable wait time between two acquisitions was empirically found
# to be 1.3 seconds. For wait times smaller than this, the camera server may
# return it's ready even though it's not.
timer = Timer(1.3)
self.waitWhile(self.STATE_MASK_ACQUIRING | self.STATE_MASK_READING
| self.STATE_MASK_CORRECTING | self.STATE_MASK_WRITING
| self.STATE_MASK_DEZINGERING | self.STATE_MASK_BUSY)
timer.wait()
def stateRequest(self, request, timeout=TIMEOUT):
"""
Helper method used to get or set camera state.
Parameters
----------
request : `string`
Command to be passed to the camera
timeout : `float`
Time to wait for camera answer
Returns
-------
`int`
"""
self.socket.send(request)
timer = Timer(timeout)
r = b''
while b'\n' not in r and timer.wait(self.socket):
r += self.socket.recv(1)
if timer.expired():
raise RuntimeError('Camera is not answering')
r = r.strip(b'\x00\n')
return int(r, 0)
class MarCCD(StandardDevice, ICountable):
"""
Class to control MarCCD cameras via TCP sockets.
Examples
--------
>>> from shutil import move
>>> from py4syn.epics.MarCCDClass import MarCCD
>>>
>>> def getImage(host='localhost', port=2222, fileName='image.tif', shutter=''):
... camera = MarCCD(name, (host, port), shutterType='simple', shutter=shutter)
... camera.setCountTime(10)
... camera.startCount()
... camera.wait()
... camera.stopCount()
... camera.writeImage('/remote/' + fileName)
... move('/remote/' + fileName, '/home/user/' + fileName)
... camera.close()
...
>>> def cameraWithoutShutter(name='', host='localhost', port=2222):
... return MarCCD(name, (host, port), shutterType='null')
...
>>> def acquireSetWithCorrection(camera, exposure=10, count=10, prefix='data'):
... try:
... camera.darkNoise()
... camera.setCountTime(exposure)
... camera.setSubScan(count=2)
...
... for i in range(count):
... remote = '/remote/%s-%02d.tif' % (prefix, i)
... local = '/home/user/%s-%02d.tif' % (prefix, i)
... camera.startCount()
... camera.wait()
... camera.stopCount()
... camera.startCount()
... camera.wait()
... camera.stopCount()
... camera.dezinger()
... camera.correct()
... camera.writeImage(remote)
... move(remote, local)
... finally:
... camera.close()
...
"""
STATE_MASK_BUSY = 0x8
STATE_MASK_ACQUIRING = 0x30
STATE_MASK_READING = 0x300
STATE_MASK_CORRECTING = 0x3000
STATE_MASK_WRITING = 0x30000
STATE_MASK_DEZINGERING = 0x300000
STATE_MASK_SAVING = 0x33300
STATE_MASK_ERROR = 0x44444
TIMEOUT = 60
URGENT_TIMEOUT = 0.5
def __init__(self,
mnemonic,
address,
shutterType,
shutter=None,
shutterReadBack=None):
"""
**Constructor**
See :class:`py4syn.epics.StandardDevice`
Parameters
----------
mnemonic : `string`
Camera mnemonic
address : `tuple`
Camera host server Internet address
shutterType : `string`
The type of software controlled shutter. The type can be "simple", "toggle"
or "null". The null shutter completely disables software controlled shutter.
The simple shutter is an EPICS PV that must be set to 0 to open the shutter
and 1 to close the shutter. The toggle shutter uses two PVs, one that
changes the shutter state whenever written to and another to read back the
current shutter state.
shutter : `string`
The shutter PV name. Only meaningful if the shutter type is not null.
shutterReadBack : `string`
The toggle shutter read back PV.
"""
super().__init__(mnemonic)
self.socket = socket(AF_INET, SOCK_STREAM)
self.socket.connect(address)
self.counting = False
self.timer = Timer(1)
self.subScan = False
self.subScanStep = 0
shutterName = mnemonic + '_shutter'
if shutterType == 'toggle':
self.shutter = ToggleShutter(shutterName, shutter, shutterReadback)
elif shutterType == 'simple':
self.shutter = SimpleShutter(shutterName, shutter)
else:
self.shutter = NullShutter(shutterName)
self.shutter.close(wait=True)
# Force clearing busy and error flags. Both busy and error flags
# May get stuck after exceptional conditions.
try:
state = self.waitWhile(self.STATE_MASK_BUSY, self.URGENT_TIMEOUT)
except RuntimeError:
self.socket.send(b'abort\n')
try:
self.setState(0, self.URGENT_TIMEOUT)
except RuntimeError as e:
self.socket.close()
raise e from None
def close(self):
"""
Cleans up and closes camera remote connection. This method must be called when
finishing operation with the camera.
"""
self.stopCount()
self.shutter.close()
# If we caused an error, send an abort to try to fix things
try:
if self.getState(self.URGENT_TIMEOUT) & self.STATE_MASK_ERROR:
self.socket.send(b'abort\n')
except:
pass
self.socket.close()
def __str__(self):
return '%s %s' % (self.getMnemonic(), str(self.socket.getpeername()))
def darkNoise(self, delay=0, moveShutter=True):
"""
Prepares a dark noise image to be used as a correction image by the server.
One of the steps after acquiring an image is to correct it by subtracting the
dark noise image from it. This method is used to generate the dark noise image
to be used later in the acquisitions. The method must be called with the camera
covered. A dark noise image must be generated at least once after starting the
MarCCD server.
.. note::
The following guideline is available on the MarCCD user guide: "The
background doesn't have to be retaken for every data image taken, but
generally should be retaken at the start of every new data set, or once every
half hour, whichever is sooner (depending on the thermal stability of the
hutch). For the MarCCD detector, if a mismatch in the level of the 4 quadrants
of data frames is noticed, the bias is probably drifting and should be
recollected (and maybe should be set to be collected more often)."
Parameters
----------
delay : `float`
The time for each background acquisition. The MarCCD camera can either
be calibrated with a zero delay between the acquisitions (this is called
a bias frame acquisition in MarCCD manual), or with a non-zero (a standard
dark frame acquisition). Note that 2 background acquisitions are done.
They are then passed through the dezinger algorithm, which averages and
removes outlier spots in the image.
moveShutter : 'bool'
Set to True to close and restore the shutter while acquiring the dark image.
"""
closed = not self.shutter.isOpen()
if not closed and moveShutter:
self.shutter.close()
self.socket.send(b'start\n')
sleep(delay)
self.socket.send(b'readout,2\n')
self.socket.send(b'start\n')
sleep(delay)
self.socket.send(b'readout,1\n')
self.socket.send(b'dezinger,1\n')
if not closed and moveShutter:
self.shutter.open()
def getValue(self, **kwargs):
"""
This is a dummy getValue method that always returns zero, which is part
of the :class:`py4syn.epics.ICountable` interface. The MarCCD does not return
a value while scanning. Instead, it stores a file with the resulting image.
"""
return 0
def setCountTime(self, t):
"""
Sets the image acquisition time.
Parameters
----------
t : `float`
Acquisition time
"""
self.timer = Timer(t)
def setPresetValue(self, channel, val):
pass
def setSubScan(self, count=2):
"""
Configure the MarCCD object to know that each acquisition will be done in
multiple steps. This effectivelly means that a series of acquisitions will
be done in sequence, which will be processed together, resulting in a single
final image. This method is mainly required for the :meth:`dezinger` method
to work.
Parameters
----------
count : `int`
Number of sub scans that will compose a single final image. Can be either
1, to disable sub scan logic, or 2, which will make :meth:`stopCount` store
images alternatedly in "scratch" (auxiliary) memory and "raw" (main) memory.
"""
if count < 1 or count > 2:
raise ValueError('Invalid count value')
self.subScan = count == 2
self.subScanStep = 0
def startCount(self):
"""
Starts acquiring an image. This will acquire image data until asked to stop
with :meth:`stopCount`. This method automatically opens the shutter.
.. note::
Due to way the camera protocol is currently implemented, this method
ignores the configured acquisition count time. Because of that, the proper
way to do a timed acquisition is to follow this method call with :meth:`wait`,
then immediatelly call :meth:`stopCount`. The :func:`py4syn.utils.scan.scan`
function in Py4Syn executes this method sequence.
See: :meth:`setCountTime`, :meth:`stopCount`, :meth:`wait`
Examples
--------
>>> def acquire(marccd, time):
... marccd.setCountTime(time)
... marccd.startCount()
... marccd.wait()
... marccd.stopCount()
...
"""
if self.counting == True:
raise RuntimeError('Already counting')
# Best effort wait for idle state
try:
self.waitWhile(self.STATE_MASK_ACQUIRING, self.URGENT_TIMEOUT)
except RuntimeError as e:
pass
# Wait for reading done when doing fast exposures
if self.timer.timeout < 1:
try:
self.waitWhile(self.STATE_MASK_READING, self.URGENT_TIMEOUT)
except RuntimeError as e:
pass
self.socket.send(b'start\n')
self.shutter.open()
self.timer.mark()
self.counting = True
def stopCount(self):
"""
Stops acquiring the image and stores it into server memory. The acquired image
will be available to apply corrections and to be written to an output file.
This method closes the shutter.
If no call to :meth:`startCount` was done before calling this method, then
nothing is done.
"""
if not self.counting:
return
self.shutter.close()
if self.subScan and self.subScanStep == 0:
cmd = b'readout,2\n'
self.subScanStep = 1
else:
cmd = b'readout,0\n'
self.subScanStep = 0
self.socket.send(cmd)
self.counting = False
def correct(self):
"""
Queues image correction on the MarCCD server. After the image is corrected,
it can be saved to a file.
There are three corrections applied: dark noise image subtraction, flat field
correction and geometric correction. The dark noise correction uses a dark image
to fix the reference (zero) intensity levels for each pixel. The flat field
correction uses a bright image to correct the gain for each pixel.
The geometric correction fixes distortion from the fiber optic taper.
.. note::
The dark noise image should be frequently generated. Use the method
:meth:`darkNoise` for that.
See: :meth:`darkNoise`
"""
self.waitWhile(
self.STATE_MASK_DEZINGERING | self.STATE_MASK_CORRECTING
| self.STATE_MASK_BUSY, self.TIMEOUT)
self.socket.send(b'correct\n')
def dezinger(self):
"""
Apply the dezinger correction algorithm in 2 images and store the resulting
image in the MarCCD server. The dezinger algorithm averages corresponding pixels
from each image, but if they deviate too much, it discards the brighter one and
keeps the lower value. This removes the "zingers", bright spots in the image,
which are not caused by the input light.
To be able to use the dezinger method, 2 images must be present in server
memory. This can be accomplished by calling :meth:`setSubScan` before the
acquisition.
.. note::
The following guildeline is present in MarCCD manual: "Dezingering does
require special care that the two images are truly identical (same X-ray
dose, same movement of the sample, etc.); otherwise the statistical test
will yield unpredictable results. In particular, if the X-ray beam is not
constant intensity, or the sample is decaying, then the exposure times and
diffractometer motions must compensate for that. If there are significant
differences between the frames, then the artifacts created by dezingering
may yield worse results than simply using normal, single-read images with
zingers in them. Though they are not aethetically pleasing, some kinds of
data analysis can tolerate many zingers.
Examples
--------
>>> def acquireTwiceAndDezinger(marccd, time):
... marccd.setCountTime(time)
... marccd.setSubScan(count=2)
... marccd.startCount()
... marccd.wait()
... marccd.stopCount()
... marccd.startCount()
... marccd.wait()
... marccd.stopCount()
... marccd.dezinger()
...
"""
# It's not clear if dezinger can be correctly queued while reading and
# correction is being done, so just wait until everything is finished
# to make sure that dezinger will apply to the right images. There
# have been cases where dezinger finished before the read command finished.
self.waitWhile(
self.STATE_MASK_READING | self.STATE_MASK_CORRECTING
| self.STATE_MASK_DEZINGERING | self.STATE_MASK_BUSY, self.TIMEOUT)
self.socket.send(b'dezinger,0\n')
def writeImage(self, fileName, wait=True):
"""
Write the image stored in MarCCD server memory in a file. This method does not
store the resulting image in the local machine. Since current MarCCD server
protocol does not allow locally downloading the resulting image, this method only
asks for the MarCCD camera server to store the image in a remote location. To
make the file accessible locally, other means must be used, for example, by
instructing the server to save the image in shared storage.
Parameters
----------
fileName : `string`
Target file name in remote MarCCD server
wait : `bool`
Set to True if the method should block until the image is written to disk
"""
self.waitWhile(
self.STATE_MASK_ACQUIRING | self.STATE_MASK_READING
| self.STATE_MASK_CORRECTING | self.STATE_MASK_WRITING
| self.STATE_MASK_BUSY, self.TIMEOUT)
cmd = 'writefile,%s,1\n' % fileName
self.socket.send(cmd.encode())
if wait:
# Wait some time for the camera to say it started writing. This
# is necessary because the server may return finished state (0)
# before it started writing.
try:
self.waitUntil(self.STATE_MASK_WRITING, self.URGENT_TIMEOUT)
except RuntimeError:
pass
self.waitWhile(
self.STATE_MASK_ACQUIRING | self.STATE_MASK_READING
| self.STATE_MASK_CORRECTING | self.STATE_MASK_WRITING
| self.STATE_MASK_BUSY, self.TIMEOUT)
def canMonitor(self):
return False
def canStopCount(self):
return True
def isCounting(self):
return self.counting
def wait(self):
"""
Blocks until the configured count time passes since the call to
:meth:`startCount`. The time amount is configured with :meth:`setCountTime`, or
1 second by default.
If an acquisition has not been started, this method returns immediatelly.
See: :meth:`setCountTime`, :meth:`startCount`
"""
if not self.isCounting():
return
ca.flush_io()
self.timer.wait()
def stateRequest(self, request, timeout=TIMEOUT):
"""
Helper method used to get or set camera state.
Parameters
----------
request : `string`
Command to be passed to the camera
timeout : `float`
Time to wait for camera answer
Returns
-------
`int`
"""
self.socket.send(request)
timer = Timer(timeout)
r = b''
while b'\n' not in r and timer.wait(self.socket):
r += self.socket.recv(1)
if timer.expired():
raise RuntimeError('Camera is not answering')
r = r.strip(b'\x00\n')
return int(r, 0)
def getState(self, timeout=TIMEOUT):
"""
Returns the camera state. The state can be used to check for errors, to find out
which operations are queued or being executed and if the server is busy
interpreting a command.
The camera state is an integer with a 4-bit value, plus five 4-bit fields:
acquire, read, correct, write and (highest) dezinger. The low 4-bit state value
can be 0, for idle, 7 for bad request and 8 for busy. Each 4-bit field has
4 flags: queued (0x1), executing (0x2), error (0x4) and reserved (0x8).
For example, the state 0x011200 means that a read is executing, a correction is
queued and a write is queued. The state mask 0x444444 can be used to look for an
error on any operation. The lowest field (state) uses the value 8 to indicate
it's busy processing a command, so state 0x8 means "interpreting command".
Parameters
----------
timeout : `float`
Time to wait for camera answer
Returns
-------
`int`
"""
return self.stateRequest(b'get_state\n', timeout)
def setState(self, state, timeout=TIMEOUT):
"""
Changes the camera state bit field. This method does not change the operating
state, just the reported integer value. It is a helper method to deal with a
quirk in the MarCCD server that makes the error and busy bits to get stuck and
never reset. Usually the only value that makes sense for the state is zero,
to clear all the bits.
See: :meth:`getState`
Parameters
----------
state : `int`
Time to wait for camera answer
timeout : `float`
Time to wait for camera answer
"""
cmd = 'set_state,%d\n' % state
self.stateRequest(cmd.encode(), timeout)
def waitWhileOrUntil(self, condition, timeout=TIMEOUT, until=False):
"""
Helper method that implements :meth:`waitWhile` and :meth:`waitUntil`
"""
state = self.getState(timeout)
timer = Timer(timeout)
while until ^ bool(state & condition) and timer.check():
state = self.getState(timeout)
if state & self.STATE_MASK_ERROR:
raise RuntimeError('Camera returned error: %x' % state)
if timer.expired():
raise RuntimeError('Camera got stuck condition: %x, state: %x' %
(condition, state))
def waitWhile(self, condition, timeout=TIMEOUT):
"""
Blocks while the camera state asserts a certain condition. This method can
be used to confirm that an operation has finished, or if the camera is reporting
an error. The condition is a bit mask with the same meanings as described in
:meth:`getState`. For example, calling this method with condition set to
0x30 blocks while an aquisition is either queued or executing. Similarly,
it's possible to block while the camera server is either processing or writing
the image with condition set to 0x333308.
This method detects errors automatically by raising an exception if any error
bit is set.
See: :meth:`getState`
Parameters
----------
condition : `int`
State condition mask. If any of the condition bits is set, the condition
is considered to be true.
timeout : `float`
Time to wait for the condition to be deasserted
"""
self.waitWhileOrUntil(condition, timeout, until=False)
def waitUntil(self, condition, timeout=TIMEOUT):
"""
Blocks until the camera state asserts a certain condition. This method can
be used to confirm that an operation has started, or if the camera is reporting
an error. The condition is a bit mask with the same meanings as described in
:meth:`getState`. For example, calling this method with condition set to
0x20 blocks until an aquisition is executing.
This method detects errors automatically by raising an exception if any error
bit is set.
See: :meth:`getState`
Parameters
----------
condition : `int`
State condition mask. If any of the condition bits is set, the condition
is considered to be true.
timeout : `float`
Time to wait for the condition to be deasserted
"""
self.waitWhileOrUntil(condition, timeout, until=True)
def waitForImage(self):
"""
Blocks until the acquired image has been corrected and written to disk. This
can be used any time after calling :meth:`stopCount` to make sure file
operations can be performed on the resulting image (copied, post-processed, etc.)
"""
# Wait some time for the camera to say it started writing. This
# is necessary because the server may return finished state (0)
# before it started writing.
try:
self.waitUntil(self.STATE_MASK_WRITING, self.URGENT_TIMEOUT)
except RuntimeError:
pass
try:
self.waitWhile(self.STATE_MASK_SAVING | self.STATE_MASK_BUSY)
except RuntimeError:
raise RuntimeError('Camera took too long to write image file')
class MarCCD(StandardDevice, ICountable):
"""
Class to control MarCCD cameras via TCP sockets.
Examples
--------
>>> from shutil import move
>>> from py4syn.epics.MarCCDClass import MarCCD
>>>
>>> def getImage(host='localhost', port=2222, fileName='image.tif', shutter=''):
... camera = MarCCD(name, (host, port), shutterType='simple', shutter=shutter)
... camera.setCountTime(10)
... camera.startCount()
... camera.wait()
... camera.stopCount()
... camera.writeImage('/remote/' + fileName)
... move('/remote/' + fileName, '/home/user/' + fileName)
... camera.close()
...
>>> def cameraWithoutShutter(name='', host='localhost', port=2222):
... return MarCCD(name, (host, port), shutterType='null')
...
>>> def acquireSetWithCorrection(camera, exposure=10, count=10, prefix='data'):
... try:
... camera.darkNoise()
... camera.setCountTime(exposure)
... camera.setSubScan(count=2)
...
... for i in range(count):
... remote = '/remote/%s-%02d.tif' % (prefix, i)
... local = '/home/user/%s-%02d.tif' % (prefix, i)
... camera.startCount()
... camera.wait()
... camera.stopCount()
... camera.startCount()
... camera.wait()
... camera.stopCount()
... camera.dezinger()
... camera.correct()
... camera.writeImage(remote)
... move(remote, local)
... finally:
... camera.close()
...
"""
STATE_MASK_BUSY = 0x8
STATE_MASK_ACQUIRING = 0x30
STATE_MASK_READING = 0x300
STATE_MASK_CORRECTING = 0x3000
STATE_MASK_WRITING = 0x30000
STATE_MASK_DEZINGERING = 0x300000
STATE_MASK_SAVING = 0x33300
STATE_MASK_ERROR = 0x44444
TIMEOUT = 60
URGENT_TIMEOUT = 0.5
def __init__(self, mnemonic, address, shutterType, shutter=None,
shutterReadBack=None):
"""
**Constructor**
See :class:`py4syn.epics.StandardDevice`
Parameters
----------
mnemonic : `string`
Camera mnemonic
address : `tuple`
Camera host server Internet address
shutterType : `string`
The type of software controlled shutter. The type can be "simple", "toggle"
or "null". The null shutter completely disables software controlled shutter.
The simple shutter is an EPICS PV that must be set to 0 to open the shutter
and 1 to close the shutter. The toggle shutter uses two PVs, one that
changes the shutter state whenever written to and another to read back the
current shutter state.
shutter : `string`
The shutter PV name. Only meaningful if the shutter type is not null.
shutterReadBack : `string`
The toggle shutter read back PV.
"""
super().__init__(mnemonic)
self.socket = socket(AF_INET, SOCK_STREAM)
self.socket.connect(address)
self.counting = False
self.timer = Timer(1)
self.subScan = False
self.subScanStep = 0
shutterName = mnemonic + '_shutter'
if shutterType == 'toggle':
self.shutter = ToggleShutter(shutterName, shutter, shutterReadback)
elif shutterType == 'simple':
self.shutter = SimpleShutter(shutterName, shutter)
else:
self.shutter = NullShutter(shutterName)
self.shutter.close(wait=True)
# Force clearing busy and error flags. Both busy and error flags
# May get stuck after exceptional conditions.
try:
state = self.waitWhile(self.STATE_MASK_BUSY, self.URGENT_TIMEOUT)
except RuntimeError:
self.socket.send(b'abort\n')
try:
self.setState(0, self.URGENT_TIMEOUT)
except RuntimeError as e:
self.socket.close()
raise e from None
def close(self):
"""
Cleans up and closes camera remote connection. This method must be called when
finishing operation with the camera.
"""
self.stopCount()
self.shutter.close()
# If we caused an error, send an abort to try to fix things
try:
if self.getState(self.URGENT_TIMEOUT) & self.STATE_MASK_ERROR:
self.socket.send(b'abort\n')
except:
pass
self.socket.close()
def __str__(self):
return '%s %s' % (self.getMnemonic(), str(self.socket.getpeername()))
def darkNoise(self, delay=0, moveShutter=True):
"""
Prepares a dark noise image to be used as a correction image by the server.
One of the steps after acquiring an image is to correct it by subtracting the
dark noise image from it. This method is used to generate the dark noise image
to be used later in the acquisitions. The method must be called with the camera
covered. A dark noise image must be generated at least once after starting the
MarCCD server.
.. note::
The following guideline is available on the MarCCD user guide: "The
background doesn't have to be retaken for every data image taken, but
generally should be retaken at the start of every new data set, or once every
half hour, whichever is sooner (depending on the thermal stability of the
hutch). For the MarCCD detector, if a mismatch in the level of the 4 quadrants
of data frames is noticed, the bias is probably drifting and should be
recollected (and maybe should be set to be collected more often)."
Parameters
----------
delay : `float`
The time for each background acquisition. The MarCCD camera can either
be calibrated with a zero delay between the acquisitions (this is called
a bias frame acquisition in MarCCD manual), or with a non-zero (a standard
dark frame acquisition). Note that 2 background acquisitions are done.
They are then passed through the dezinger algorithm, which averages and
removes outlier spots in the image.
moveShutter : 'bool'
Set to True to close and restore the shutter while acquiring the dark image.
"""
closed = not self.shutter.isOpen()
if not closed and moveShutter:
self.shutter.close()
self.socket.send(b'start\n')
sleep(delay)
self.socket.send(b'readout,2\n')
self.socket.send(b'start\n')
sleep(delay)
self.socket.send(b'readout,1\n')
self.socket.send(b'dezinger,1\n')
if not closed and moveShutter:
self.shutter.open()
def getValue(self, **kwargs):
"""
This is a dummy getValue method that always returns zero, which is part
of the :class:`py4syn.epics.ICountable` interface. The MarCCD does not return
a value while scanning. Instead, it stores a file with the resulting image.
"""
return 0
def setCountTime(self, t):
"""
Sets the image acquisition time.
Parameters
----------
t : `float`
Acquisition time
"""
self.timer = Timer(t)
def setPresetValue(self, channel, val):
pass
def setSubScan(self, count=2):
"""
Configure the MarCCD object to know that each acquisition will be done in
multiple steps. This effectivelly means that a series of acquisitions will
be done in sequence, which will be processed together, resulting in a single
final image. This method is mainly required for the :meth:`dezinger` method
to work.
Parameters
----------
count : `int`
Number of sub scans that will compose a single final image. Can be either
1, to disable sub scan logic, or 2, which will make :meth:`stopCount` store
images alternatedly in "scratch" (auxiliary) memory and "raw" (main) memory.
"""
if count < 1 or count > 2:
raise ValueError('Invalid count value')
self.subScan = count == 2
self.subScanStep = 0
def startCount(self):
"""
Starts acquiring an image. This will acquire image data until asked to stop
with :meth:`stopCount`. This method automatically opens the shutter.
.. note::
Due to way the camera protocol is currently implemented, this method
ignores the configured acquisition count time. Because of that, the proper
way to do a timed acquisition is to follow this method call with :meth:`wait`,
then immediatelly call :meth:`stopCount`. The :func:`py4syn.utils.scan.scan`
function in Py4Syn executes this method sequence.
See: :meth:`setCountTime`, :meth:`stopCount`, :meth:`wait`
Examples
--------
>>> def acquire(marccd, time):
... marccd.setCountTime(time)
... marccd.startCount()
... marccd.wait()
... marccd.stopCount()
...
"""
if self.counting == True:
raise RuntimeError('Already counting')
# Best effort wait for idle state
try:
self.waitWhile(self.STATE_MASK_ACQUIRING, self.URGENT_TIMEOUT)
except RuntimeError as e:
pass
# Wait for reading done when doing fast exposures
if self.timer.timeout < 1:
try:
self.waitWhile(self.STATE_MASK_READING, self.URGENT_TIMEOUT)
except RuntimeError as e:
pass
self.socket.send(b'start\n')
self.shutter.open()
self.timer.mark()
self.counting = True
def stopCount(self):
"""
Stops acquiring the image and stores it into server memory. The acquired image
will be available to apply corrections and to be written to an output file.
This method closes the shutter.
If no call to :meth:`startCount` was done before calling this method, then
nothing is done.
"""
if not self.counting:
return
self.shutter.close()
if self.subScan and self.subScanStep == 0:
cmd = b'readout,2\n'
self.subScanStep = 1
else:
cmd = b'readout,0\n'
self.subScanStep = 0
self.socket.send(cmd)
self.counting = False
def correct(self):
"""
Queues image correction on the MarCCD server. After the image is corrected,
it can be saved to a file.
There are three corrections applied: dark noise image subtraction, flat field
correction and geometric correction. The dark noise correction uses a dark image
to fix the reference (zero) intensity levels for each pixel. The flat field
correction uses a bright image to correct the gain for each pixel.
The geometric correction fixes distortion from the fiber optic taper.
.. note::
The dark noise image should be frequently generated. Use the method
:meth:`darkNoise` for that.
See: :meth:`darkNoise`
"""
self.waitWhile(self.STATE_MASK_DEZINGERING | self.STATE_MASK_CORRECTING |
self.STATE_MASK_BUSY, self.TIMEOUT)
self.socket.send(b'correct\n')
def dezinger(self):
"""
Apply the dezinger correction algorithm in 2 images and store the resulting
image in the MarCCD server. The dezinger algorithm averages corresponding pixels
from each image, but if they deviate too much, it discards the brighter one and
keeps the lower value. This removes the "zingers", bright spots in the image,
which are not caused by the input light.
To be able to use the dezinger method, 2 images must be present in server
memory. This can be accomplished by calling :meth:`setSubScan` before the
acquisition.
.. note::
The following guildeline is present in MarCCD manual: "Dezingering does
require special care that the two images are truly identical (same X-ray
dose, same movement of the sample, etc.); otherwise the statistical test
will yield unpredictable results. In particular, if the X-ray beam is not
constant intensity, or the sample is decaying, then the exposure times and
diffractometer motions must compensate for that. If there are significant
differences between the frames, then the artifacts created by dezingering
may yield worse results than simply using normal, single-read images with
zingers in them. Though they are not aethetically pleasing, some kinds of
data analysis can tolerate many zingers.
Examples
--------
>>> def acquireTwiceAndDezinger(marccd, time):
... marccd.setCountTime(time)
... marccd.setSubScan(count=2)
... marccd.startCount()
... marccd.wait()
... marccd.stopCount()
... marccd.startCount()
... marccd.wait()
... marccd.stopCount()
... marccd.dezinger()
...
"""
# It's not clear if dezinger can be correctly queued while reading and
# correction is being done, so just wait until everything is finished
# to make sure that dezinger will apply to the right images. There
# have been cases where dezinger finished before the read command finished.
self.waitWhile(self.STATE_MASK_READING | self.STATE_MASK_CORRECTING |
self.STATE_MASK_DEZINGERING | self.STATE_MASK_BUSY, self.TIMEOUT)
self.socket.send(b'dezinger,0\n')
def writeImage(self, fileName, wait=True):
"""
Write the image stored in MarCCD server memory in a file. This method does not
store the resulting image in the local machine. Since current MarCCD server
protocol does not allow locally downloading the resulting image, this method only
asks for the MarCCD camera server to store the image in a remote location. To
make the file accessible locally, other means must be used, for example, by
instructing the server to save the image in shared storage.
Parameters
----------
fileName : `string`
Target file name in remote MarCCD server
wait : `bool`
Set to True if the method should block until the image is written to disk
"""
self.waitWhile(self.STATE_MASK_ACQUIRING | self.STATE_MASK_READING |
self.STATE_MASK_CORRECTING |self.STATE_MASK_WRITING |
self.STATE_MASK_BUSY, self.TIMEOUT)
cmd = 'writefile,%s,1\n' % fileName
self.socket.send(cmd.encode())
if wait:
# Wait some time for the camera to say it started writing. This
# is necessary because the server may return finished state (0)
# before it started writing.
try:
self.waitUntil(self.STATE_MASK_WRITING, self.URGENT_TIMEOUT)
except RuntimeError:
pass
self.waitWhile(self.STATE_MASK_ACQUIRING | self.STATE_MASK_READING |
self.STATE_MASK_CORRECTING |self.STATE_MASK_WRITING |
self.STATE_MASK_BUSY, self.TIMEOUT)
def canMonitor(self):
return False
def canStopCount(self):
return True
def isCounting(self):
return self.counting
def wait(self):
"""
Blocks until the configured count time passes since the call to
:meth:`startCount`. The time amount is configured with :meth:`setCountTime`, or
1 second by default.
If an acquisition has not been started, this method returns immediatelly.
See: :meth:`setCountTime`, :meth:`startCount`
"""
if not self.isCounting():
return
ca.flush_io()
self.timer.wait()
def stateRequest(self, request, timeout=TIMEOUT):
"""
Helper method used to get or set camera state.
Parameters
----------
request : `string`
Command to be passed to the camera
timeout : `float`
Time to wait for camera answer
Returns
-------
`int`
"""
self.socket.send(request)
timer = Timer(timeout)
r = b''
while b'\n' not in r and timer.wait(self.socket):
r += self.socket.recv(1)
if timer.expired():
raise RuntimeError('Camera is not answering')
r = r.strip(b'\x00\n')
return int(r, 0)
def getState(self, timeout=TIMEOUT):
"""
Returns the camera state. The state can be used to check for errors, to find out
which operations are queued or being executed and if the server is busy
interpreting a command.
The camera state is an integer with a 4-bit value, plus five 4-bit fields:
acquire, read, correct, write and (highest) dezinger. The low 4-bit state value
can be 0, for idle, 7 for bad request and 8 for busy. Each 4-bit field has
4 flags: queued (0x1), executing (0x2), error (0x4) and reserved (0x8).
For example, the state 0x011200 means that a read is executing, a correction is
queued and a write is queued. The state mask 0x444444 can be used to look for an
error on any operation. The lowest field (state) uses the value 8 to indicate
it's busy processing a command, so state 0x8 means "interpreting command".
Parameters
----------
timeout : `float`
Time to wait for camera answer
Returns
-------
`int`
"""
return self.stateRequest(b'get_state\n', timeout)
def setState(self, state, timeout=TIMEOUT):
"""
Changes the camera state bit field. This method does not change the operating
state, just the reported integer value. It is a helper method to deal with a
quirk in the MarCCD server that makes the error and busy bits to get stuck and
never reset. Usually the only value that makes sense for the state is zero,
to clear all the bits.
See: :meth:`getState`
Parameters
----------
state : `int`
Time to wait for camera answer
timeout : `float`
Time to wait for camera answer
"""
cmd = 'set_state,%d\n' % state
self.stateRequest(cmd.encode(), timeout)
def waitWhileOrUntil(self, condition, timeout=TIMEOUT, until=False):
"""
Helper method that implements :meth:`waitWhile` and :meth:`waitUntil`
"""
state = self.getState(timeout)
timer = Timer(timeout)
while until ^ bool(state & condition) and timer.check():
state = self.getState(timeout)
if state & self.STATE_MASK_ERROR:
raise RuntimeError('Camera returned error: %x' % state)
if timer.expired():
raise RuntimeError('Camera got stuck condition: %x, state: %x' %
(condition, state))
def waitWhile(self, condition, timeout=TIMEOUT):
"""
Blocks while the camera state asserts a certain condition. This method can
be used to confirm that an operation has finished, or if the camera is reporting
an error. The condition is a bit mask with the same meanings as described in
:meth:`getState`. For example, calling this method with condition set to
0x30 blocks while an aquisition is either queued or executing. Similarly,
it's possible to block while the camera server is either processing or writing
the image with condition set to 0x333308.
This method detects errors automatically by raising an exception if any error
bit is set.
See: :meth:`getState`
Parameters
----------
condition : `int`
State condition mask. If any of the condition bits is set, the condition
is considered to be true.
timeout : `float`
Time to wait for the condition to be deasserted
"""
self.waitWhileOrUntil(condition, timeout, until=False)
def waitUntil(self, condition, timeout=TIMEOUT):
"""
Blocks until the camera state asserts a certain condition. This method can
be used to confirm that an operation has started, or if the camera is reporting
an error. The condition is a bit mask with the same meanings as described in
:meth:`getState`. For example, calling this method with condition set to
0x20 blocks until an aquisition is executing.
This method detects errors automatically by raising an exception if any error
bit is set.
See: :meth:`getState`
Parameters
----------
condition : `int`
State condition mask. If any of the condition bits is set, the condition
is considered to be true.
timeout : `float`
Time to wait for the condition to be deasserted
"""
self.waitWhileOrUntil(condition, timeout, until=True)
def waitForImage(self):
"""
Blocks until the acquired image has been corrected and written to disk. This
can be used any time after calling :meth:`stopCount` to make sure file
operations can be performed on the resulting image (copied, post-processed, etc.)
"""
# Wait some time for the camera to say it started writing. This
# is necessary because the server may return finished state (0)
# before it started writing.
try:
self.waitUntil(self.STATE_MASK_WRITING, self.URGENT_TIMEOUT)
except RuntimeError:
pass
try:
self.waitWhile(self.STATE_MASK_SAVING | self.STATE_MASK_BUSY)
except RuntimeError:
raise RuntimeError('Camera took too long to write image file')
