예제 #1
0
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
예제 #2
0
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
예제 #3
0
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
예제 #4
0
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
예제 #5
0
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
예제 #6
0
class PMDSimulator(object):
    """
    Simulates beamshift controller with three axes on axes 1, 2 and 3.
    """
    def __init__(self, timeout=0.3):
        self.timeout = timeout
        self._input_buf = ""  # use str internally instead of bytes, makes indexing easier
        self._output_buf = ""

        self.waveform = {1: WAVEFORM_PARK, 2: WAVEFORM_PARK, 3: WAVEFORM_PARK}
        self.target_pos = {1: 0, 2: 0, 3: 0}
        self.current_pos = {1: 0, 2: 0, 3: 0}
        self.speed = 0
        self.is_moving = False
        self.status = "0000"
        self.indexing = True
        self.closed_loop = {1: False, 2: False, 3: False}

        self.executor = CancellableThreadPoolExecutor(1)

    def write(self, data):
        self._input_buf += data.decode('ascii')
        msg = ""
        while self._input_buf[:len(EOL)] != sEOL:
            msg += self._input_buf[0]
            self._input_buf = self._input_buf[1:]
        self._input_buf = self._input_buf[len(EOL):]  # remove EOL

        self._parseMessage(msg)

    def read(self, size=1):
        ret = self._output_buf[:size]
        self._output_buf = self._output_buf[len(ret):]

        if len(ret) < size:
            # simulate timeout
            time.sleep(self.timeout)
        return ret.encode('ascii')

    def flush(self):
        self._input_buf = ""

    def flushInput(self):
        self._output_buf = ""

    def close(self):
        # using read or write will fail after that
        del self._output_buf
        del self._input_buf

    def _parseMessage(self, msg):
        """
        :param msg (str): the message to parse
        :returns (None): self._output_buf is updated if necessary
        """
        # Message structure:
        # X<axis><cmd><EOL> or
        # X<cmd><EOL> or
        # X<axis><cmd><arg0>,...,<argN><EOL>
        # Axis can in principle have multiple digits, but we only care about 1-3, so let's keep
        # it simple
        logging.debug("Received message %s" % msg)

        if msg[0] != "X":
            self._output_buf += "_??_%s" % msg[1:]
            logging.error("Command %s doesn't start with 'X'.", msg)
            return
        try:  # first symbol is axis number
            axis = int(msg[1])
            cmd = msg[2]
            args = msg[3:].split(',')
        except ValueError:
            # msg[1] is not an int --> axis number 0 assumed
            axis = 0
            cmd = msg[1]
            args = msg[2:].split(',')
        args = [] if args == [''] else args

        # Message is always echoed back
        self._output_buf += msg

        try:
            if cmd == "M":
                if not args:
                    self._output_buf += ":%d" % self.waveform[axis]
                elif len(args) == 1:
                    self.waveform[axis] = int(args[0])
                else:
                    raise ValueError()
            elif cmd == "?":
                if not args:
                    self._output_buf += ":PMD401 V1"
                else:
                    raise ValueError()
            elif cmd == "T":
                # Absolute move
                self.closed_loop[axis] = True
                if not args:
                    self._output_buf += ":%d" % self.target_pos[axis]
                elif len(args) == 1:
                    steps = int(args[0]) - self.target_pos[axis]
                    self.target_pos[axis] = int(args[0])
                    steps = int(steps * DEFAULT_ENCODER_RESOLUTION /
                                DEFAULT_MOTORSTEP_RESOLUTION)
                    self.move(steps)
                elif len(args) == 2:
                    steps = int(args[0]) - self.target_pos[axis]
                    self.target_pos[axis] = int(args[0])
                    self.speed = int(args[1])
                    steps = int(steps * DEFAULT_ENCODER_RESOLUTION /
                                DEFAULT_MOTORSTEP_RESOLUTION)
                    self.move(steps)
                else:
                    raise ValueError()
            elif cmd == "S":  # stop axis
                self.is_moving = False
                self.closed_loop[axis] = False
            elif cmd == "C":
                # Relative move
                self.closed_loop[axis] = True
                if not args:
                    self._output_buf += ":%d" % self.target_pos[axis]
                elif len(args) == 1:
                    self.target_pos[axis] += int(args[0])
                    steps = int(
                        int(args[0]) * DEFAULT_ENCODER_RESOLUTION /
                        DEFAULT_MOTORSTEP_RESOLUTION)
                    self.move(steps)
                elif len(args) == 2:
                    self.target_pos[axis] += int(args[0])
                    self.speed = int(args[1])
                    steps = int(
                        int(args[0]) * DEFAULT_ENCODER_RESOLUTION /
                        DEFAULT_MOTORSTEP_RESOLUTION)
                    self.move(steps)
                else:
                    raise ValueError()
            elif cmd == "E":
                if not args:
                    self._output_buf += ":%d" % self.current_pos[axis]
                elif len(args) == 1:
                    self.target_pos[axis] += int(args[0])
                else:
                    raise ValueError()
            elif cmd == "J":
                if not args:
                    if self.is_moving:
                        self._output_buf += ":222"
                    else:
                        self._output_buf += ":0"
                elif len(args) == 1:
                    pass  # simulate move
                elif len(args) == 2:
                    pass  # simulate move
                elif len(args) == 3:
                    # simulate move
                    self.speed = int(args[1])
                else:
                    raise ValueError()
            elif cmd == "I":
                self.find_index()
            elif cmd == "N":
                if self.indexing:
                    self._output_buf += "1,132.,indexed"
                else:
                    self._output_buf += "1,132"
            elif cmd == "Y":
                if len(args) == 1:
                    if int(args[0]) == 42:  # serial number
                        self._output_buf += ":12345678"
                    elif int(args[0]) == 11:  # spc parameter
                        self._output_buf += ":70000"
            elif cmd == "U":
                if self.is_moving:
                    # "0020" means targetMode (closed loop mode) active
                    self.status = "0020" if self.closed_loop[axis] else "0000"
                else:
                    # "0030" means targetMode (closed loop mode) active and targetReached, "0010" means targetReached
                    self.status = "0030" if self.closed_loop[axis] else "0010"
                self._output_buf += ":%s" % self.status
            else:
                # Syntax error is indicated by inserting _??_ in the response
                self._output_buf = self._output_buf[:-len(msg)]
                self._output_buf += "X%s_??_%s" % (
                    axis, ''.join(args))  # args can be str or list of str
                logging.error("Unknown command %s" % cmd)
        except ValueError as ex:
            # Assume something is wrong with the arguments
            self._output_buf = self._output_buf[:-len(msg)]
            self._output_buf += "X%s%s_??_" % (axis, cmd)
            logging.error("Parsing %s failed with exception %s" % (msg, ex))

        self._output_buf += sEOL

    def move(self, steps):
        # simple move, same duration for every length, don't care about speed
        self.executor.submit(self._do_move, steps)

    def find_index(self):
        t = Thread(target=self._do_indexing)
        t.start()

    def _do_indexing(self):
        self.indexing = True
        time.sleep(1)
        self.indexing = False

    def _do_move(self, steps):
        self.is_moving = True
        startt = time.time()
        dur = abs(steps / self.speed)
        # be a bit faster than the real hardware because the real hardware can move multiple axes at the same time
        dur /= 2
        while time.time() < startt + dur:
            if not self.is_moving:  # stopped
                return
            else:
                time.sleep(0.1)
        self.current_pos = copy.deepcopy(self.target_pos)
        self.is_moving = False
예제 #7
0
파일: pmtctrl.py 프로젝트: delmic/odemis
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
예제 #8
0
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
예제 #9
0
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
예제 #10
0
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, ))
예제 #11
0
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
예제 #12
0
파일: zeiss.py 프로젝트: delmic/odemis
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")
예제 #13
0
파일: actuator.py 프로젝트: arijitxx/odemis
class AntiBacklashActuator(model.Actuator):
    """
    This is a stage wrapper that takes a stage and ensures that every move 
    always finishes in the same direction.
    """
    def __init__(self, name, role, children, backlash, **kwargs):
        """
        children (dict str -> Stage): dict containing one component, the stage 
        to wrap
        backlash (dict str -> float): for each axis of the stage, the additional 
        distance to move (and the direction). If an axis of the stage is not 
        present, then it’s the same as having 0 as backlash (=> no antibacklash 
        motion is performed for this axis)

        """
        if len(children) != 1:
            raise ValueError("AntiBacklashActuator needs 1 child")

        self._child = children.values()[0]
        self._backlash = backlash
        axes_def = self._child.axes

        # look for axes in backlash not existing in the child
        missing = set(backlash.keys()) - set(axes_def.keys())
        if missing:
            raise ValueError("Child actuator doesn't have the axes %s", missing)

        model.Actuator.__init__(self, name, role, axes=axes_def,
                                children=children, **kwargs)

        # will take care of executing axis moves asynchronously
        self._executor = CancellableThreadPoolExecutor(max_workers=1)  # one task at a time

        # Duplicate VAs which are just identical
        # TODO: shall we "hide" the antibacklash move by not updating position
        # while doing this move?
        self.position = self._child.position

        if (hasattr(self._child, "referenced") and
            isinstance(self._child.referenced, model.VigilantAttributeBase)):
            self.referenced = self._child.referenced
        if (hasattr(self._child, "speed") and
            isinstance(self._child.speed, model.VigilantAttributeBase)):
            self.speed = self._child.speed


    def terminate(self):
        if self._executor:
            self.stop()
            self._executor.shutdown()
            self._executor = None

    def _doMoveRel(self, shift):
        # move with the backlash subtracted
        sub_shift = {}
        sub_backlash = {} # same as backlash but only contains the axes moved
        for a, v in shift.items():
            if a not in self._backlash:
                sub_shift[a] = v
            else:
                # optimisation: if move goes in the same direction as backlash
                # correction, then no need to do the correction
                # TODO: only do this if backlash correction has already been applied once?
                if v * self._backlash[a] >= 0:
                    sub_shift[a] = v
                else:
                    sub_shift[a] = v - self._backlash[a]
                    sub_backlash[a] = self._backlash[a]
        f = self._child.moveRel(sub_shift)
        f.result()

        # backlash move
        f = self._child.moveRel(sub_backlash)
        f.result()

    def _doMoveAbs(self, pos):
        sub_pos = {}
        fpos = {} # same as pos but only contains the axes moved due to backlash
        for a, v in pos.items():
            if a not in self._backlash:
                sub_pos[a] = v
            else:
                shift = v - self.position.value[a]
                if shift * self._backlash[a] >= 0:
                    sub_pos[a] = v
                else:
                    sub_pos[a] = v - self._backlash[a]
                    fpos[a] = pos[a]
        f = self._child.moveAbs(sub_pos)
        f.result()

        # backlash move
        f = self._child.moveAbs(fpos)
        return f

    @isasync
    def moveRel(self, shift):
        if not shift:
            return model.InstantaneousFuture()
        self._checkMoveRel(shift)

        return self._executor.submit(self._doMoveRel, shift)

    @isasync
    def moveAbs(self, pos):
        if not pos:
            return model.InstantaneousFuture()
        self._checkMoveAbs(pos)

        return self._executor.submit(self._doMoveAbs, pos)

    def stop(self, axes=None):
        self._child.stop()

    @isasync
    def reference(self, axes):
        f = self._child.reference(axes)
        return f
예제 #14
0
class AntiBacklashActuator(model.Actuator):
    """
    This is a stage wrapper that takes a stage and ensures that every move 
    always finishes in the same direction.
    """
    def __init__(self, name, role, children, backlash, **kwargs):
        """
        children (dict str -> Stage): dict containing one component, the stage 
        to wrap
        backlash (dict str -> float): for each axis of the stage, the additional 
        distance to move (and the direction). If an axis of the stage is not 
        present, then it’s the same as having 0 as backlash (=> no antibacklash 
        motion is performed for this axis)

        """
        if len(children) != 1:
            raise ValueError("AntiBacklashActuator needs 1 child")

        self._child = children.values()[0]
        self._backlash = backlash
        axes_def = self._child.axes

        # look for axes in backlash not existing in the child
        missing = set(backlash.keys()) - set(axes_def.keys())
        if missing:
            raise ValueError("Child actuator doesn't have the axes %s",
                             missing)

        model.Actuator.__init__(self,
                                name,
                                role,
                                axes=axes_def,
                                children=children,
                                **kwargs)

        # will take care of executing axis moves asynchronously
        self._executor = CancellableThreadPoolExecutor(
            max_workers=1)  # one task at a time

        # Duplicate VAs which are just identical
        # TODO: shall we "hide" the antibacklash move by not updating position
        # while doing this move?
        self.position = self._child.position

        if (hasattr(self._child, "referenced") and isinstance(
                self._child.referenced, model.VigilantAttributeBase)):
            self.referenced = self._child.referenced
        if (hasattr(self._child, "speed") and isinstance(
                self._child.speed, model.VigilantAttributeBase)):
            self.speed = self._child.speed

    def terminate(self):
        if self._executor:
            self.stop()
            self._executor.shutdown()
            self._executor = None

    def _doMoveRel(self, shift):
        # move with the backlash subtracted
        sub_shift = {}
        sub_backlash = {}  # same as backlash but only contains the axes moved
        for a, v in shift.items():
            if a not in self._backlash:
                sub_shift[a] = v
            else:
                # optimisation: if move goes in the same direction as backlash
                # correction, then no need to do the correction
                # TODO: only do this if backlash correction has already been applied once?
                if v * self._backlash[a] >= 0:
                    sub_shift[a] = v
                else:
                    sub_shift[a] = v - self._backlash[a]
                    sub_backlash[a] = self._backlash[a]
        f = self._child.moveRel(sub_shift)
        f.result()

        # backlash move
        f = self._child.moveRel(sub_backlash)
        f.result()

    def _doMoveAbs(self, pos):
        sub_pos = {}
        fpos = {
        }  # same as pos but only contains the axes moved due to backlash
        for a, v in pos.items():
            if a not in self._backlash:
                sub_pos[a] = v
            else:
                shift = v - self.position.value[a]
                if shift * self._backlash[a] >= 0:
                    sub_pos[a] = v
                else:
                    sub_pos[a] = v - self._backlash[a]
                    fpos[a] = pos[a]
        f = self._child.moveAbs(sub_pos)
        f.result()

        # backlash move
        f = self._child.moveAbs(fpos)
        return f

    @isasync
    def moveRel(self, shift):
        if not shift:
            return model.InstantaneousFuture()
        self._checkMoveRel(shift)

        return self._executor.submit(self._doMoveRel, shift)

    @isasync
    def moveAbs(self, pos):
        if not pos:
            return model.InstantaneousFuture()
        self._checkMoveAbs(pos)

        return self._executor.submit(self._doMoveAbs, pos)

    def stop(self, axes=None):
        self._child.stop()

    @isasync
    def reference(self, axes):
        f = self._child.reference(axes)
        return f
예제 #15
0
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
예제 #16
0
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")
예제 #17
0
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
예제 #18
0
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
예제 #19
0
class FixedPositionsActuator(model.Actuator):
    """
    A generic actuator component which only allows moving to fixed positions
    defined by the user upon initialization. It is actually a wrapper to just
    one axis/actuator and it can also apply cyclic move e.g. in case the
    actuator moves a filter wheel.
    """

    def __init__(self, name, role, children, axis_name, positions, cycle=None, **kwargs):
        """
        name (string)
        role (string)
        children (dict str -> actuator): axis name (in this actuator) -> actuator to be used for this axis
        axis_name (str): axis name in the child actuator
        positions (set or dict value -> str): positions where the actuator is allowed to move
        cycle (float): if not None, it means the actuator does a cyclic move and this value represents a full cycle
        """
        # TODO: forbid inverted
        if len(children) != 1:
            raise ValueError("FixedPositionsActuator needs precisely one child")

        self._cycle = cycle
        self._move_sum = 0
        self._position = {}
        self._referenced = {}
        axis, child = children.items()[0]
        self._axis = axis
        self._child = child
        self._caxis = axis_name
        self._positions = positions
        # Executor used to reference and move to nearest position
        self._executor = CancellableThreadPoolExecutor(max_workers=1)  # one task at a time

        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 cycle is not None:
            # just an offset to reference switch position
            self._offset = self._cycle / len(self._positions)
            if not all(0 <= p < cycle for p in positions.keys()):
                raise ValueError("Positions must be between 0 and %s (non inclusive)" % (cycle,))

        ac = child.axes[axis_name]
        axes = {axis: model.Axis(choices=positions, unit=ac.unit)}  # TODO: allow the user to override the unit?

        model.Actuator.__init__(self, name, role, axes=axes, children=children, **kwargs)

        self._position = {}
        self.position = model.VigilantAttribute({}, readonly=True)

        logging.debug("Subscribing to position of child %s", child.name)
        child.position.subscribe(self._update_child_position, init=True)

        if model.hasVA(child, "referenced") and axis_name in child.referenced.value:
            self._referenced[axis] = child.referenced.value[axis_name]
            self.referenced = model.VigilantAttribute(self._referenced.copy(), readonly=True)
            child.referenced.subscribe(self._update_child_ref)

        # If the axis can be referenced => do it now (and move to a known position)
        # In case of cyclic move always reference
        if not self._referenced.get(axis, True) or (self._cycle and axis in self._referenced):
            # The initialisation will not fail if the referencing fails
            f = self.reference({axis})
            f.add_done_callback(self._on_referenced)
        else:
            # If not at a known position => move to the closest known position
            nearest = util.find_closest(self._child.position.value[self._caxis], self._positions.keys())
            self.moveAbs({self._axis: nearest}).result()

    def _on_referenced(self, future):
        try:
            future.result()
        except Exception as e:
            self._child.stop({self._caxis})  # prevent any move queued
            self.state._set_value(e, force_write=True)
            logging.exception(e)

    def _update_child_position(self, value):
        p = value[self._caxis]
        if self._cycle is not None:
            p %= self._cycle
        self._position[self._axis] = p
        self._updatePosition()

    def _update_child_ref(self, value):
        self._referenced[self._axis] = value[self._caxis]
        self._updateReferenced()

    def _updatePosition(self):
        """
        update the position VA
        """
        # if it is an unsupported position report the nearest supported one
        real_pos = self._position[self._axis]
        nearest = util.find_closest(real_pos, self._positions.keys())
        if not util.almost_equal(real_pos, nearest):
            logging.warning("Reporting axis %s @ %s (known position), while physical axis %s @ %s",
                            self._axis, nearest, self._caxis, real_pos)
        pos = {self._axis: nearest}
        logging.debug("reporting position %s", pos)
        self.position._set_value(pos, force_write=True)

    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)

    @isasync
    def moveRel(self, shift):
        if not shift:
            return model.InstantaneousFuture()
        self._checkMoveRel(shift)
        raise NotImplementedError("Relative move on fixed positions axis not supported")

    @isasync
    def moveAbs(self, pos):
        """
        Move the actuator to the defined position in m for each axis given.
        pos dict(string-> float): name of the axis and position in m
        """
        if not pos:
            return model.InstantaneousFuture()
        self._checkMoveAbs(pos)
        pos = self._applyInversion(pos)
        f = self._executor.submit(self._doMoveAbs, pos)

        return f

    def _doMoveAbs(self, pos):
        axis, distance = pos.items()[0]
        logging.debug("Moving axis %s (-> %s) to %g", self._axis, self._caxis, distance)

        if self._cycle is None:
            move = {self._caxis: distance}
            self._child.moveAbs(move).result()
        else:
            # Optimize by moving through the closest way
            cur_pos = self._child.position.value[self._caxis]
            vector1 = distance - cur_pos
            mod1 = vector1 % self._cycle
            vector2 = cur_pos - distance
            mod2 = vector2 % self._cycle
            if abs(mod1) < abs(mod2):
                self._move_sum += mod1
                if self._move_sum >= self._cycle:
                    # Once we are about to complete a full cycle, reference again
                    # to get rid of accumulated error
                    self._move_sum = 0
                    # move to the reference switch
                    move_to_ref = (self._cycle - cur_pos) % self._cycle + self._offset
                    self._child.moveRel({self._caxis: move_to_ref}).result()
                    self._child.reference({self._caxis}).result()
                    move = {self._caxis: distance}
                else:
                    move = {self._caxis: mod1}
            else:
                move = {self._caxis:-mod2}
                self._move_sum -= mod2

            self._child.moveRel(move).result()

    def _doReference(self, axes):
        logging.debug("Referencing axis %s (-> %s)", self._axis, self._caxis)
        f = self._child.reference({self._caxis})
        f.result()

        # If we just did homing and ended up to an unsupported position, move to
        # the nearest supported position
        cp = self._child.position.value[self._caxis]
        if (cp not in self._positions):
            nearest = util.find_closest(cp, self._positions.keys())
            self._doMoveAbs({self._axis: nearest})

    @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):
        """
        stops the motion
        axes (iterable or None): list of axes to stop, or None if all should be stopped
        """
        if axes is not None:
            axes = set()
            if self._axis in axes:
                axes.add(self._caxis)

        self._child.stop(axes=axes)

    def terminate(self):
        if self._executor:
            self.stop()
            self._executor.shutdown(wait=True)
            self._executor = None

        self._child.position.unsubscribe(self._update_child_position)
예제 #20
0
파일: zeiss.py 프로젝트: Mahmood-B/odemis
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")
예제 #21
0
파일: powerctrl.py 프로젝트: delmic/odemis
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
예제 #22
0
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
예제 #23
0
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
예제 #24
0
class FixedPositionsActuator(model.Actuator):
    """
    A generic actuator component which only allows moving to fixed positions
    defined by the user upon initialization. It is actually a wrapper to just
    one axis/actuator and it can also apply cyclic move e.g. in case the
    actuator moves a filter wheel.
    """

    def __init__(self, name, role, children, axis_name, positions, cycle=None, **kwargs):
        """
        name (string)
        role (string)
        children (dict str -> actuator): axis name (in this actuator) -> actuator to be used for this axis
        axis_name (str): axis name in the child actuator
        positions (set or dict value -> str): positions where the actuator is allowed to move
        cycle (float): if not None, it means the actuator does a cyclic move and this value represents a full cycle
        """
        # TODO: forbid inverted
        if len(children) != 1:
            raise ValueError("FixedPositionsActuator needs precisely one child")

        self._cycle = cycle
        self._move_sum = 0
        self._position = {}
        self._referenced = {}
        axis, child = children.items()[0]
        self._axis = axis
        self._child = child
        self._caxis = axis_name
        self._positions = positions
        # Executor used to reference and move to nearest position
        self._executor = CancellableThreadPoolExecutor(max_workers=1)  # one task at a time

        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 cycle is not None:
            # just an offset to reference switch position
            self._offset = self._cycle / len(self._positions)
            if not all(0 <= p < cycle for p in positions.keys()):
                raise ValueError("Positions must be between 0 and %s (non inclusive)" % (cycle,))

        ac = child.axes[axis_name]
        axes = {axis: model.Axis(choices=positions, unit=ac.unit)}  # TODO: allow the user to override the unit?

        model.Actuator.__init__(self, name, role, axes=axes, children=children, **kwargs)

        self._position = {}
        self.position = model.VigilantAttribute({}, readonly=True)

        logging.debug("Subscribing to position of child %s", child.name)
        child.position.subscribe(self._update_child_position, init=True)

        if model.hasVA(child, "referenced") and axis_name in child.referenced.value:
            self._referenced[axis] = child.referenced.value[axis_name]
            self.referenced = model.VigilantAttribute(self._referenced.copy(), readonly=True)
            child.referenced.subscribe(self._update_child_ref)

        # If the axis can be referenced => do it now (and move to a known position)
        # In case of cyclic move always reference
        if not self._referenced.get(axis, True) or (self._cycle and axis in self._referenced):
            # The initialisation will not fail if the referencing fails
            f = self.reference({axis})
            f.add_done_callback(self._on_referenced)
        else:
            # If not at a known position => move to the closest known position
            nearest = util.find_closest(self._child.position.value[self._caxis], self._positions.keys())
            self.moveAbs({self._axis: nearest}).result()

    def _on_referenced(self, future):
        try:
            future.result()
        except Exception as e:
            self._child.stop({self._caxis})  # prevent any move queued
            self.state._set_value(e, force_write=True)
            logging.exception(e)

    def _update_child_position(self, value):
        p = value[self._caxis]
        if self._cycle is not None:
            p %= self._cycle
        self._position[self._axis] = p
        self._updatePosition()

    def _update_child_ref(self, value):
        self._referenced[self._axis] = value[self._caxis]
        self._updateReferenced()

    def _updatePosition(self):
        """
        update the position VA
        """
        # if it is an unsupported position report the nearest supported one
        real_pos = self._position[self._axis]
        nearest = util.find_closest(real_pos, self._positions.keys())
        if not util.almost_equal(real_pos, nearest):
            logging.warning("Reporting axis %s @ %s (known position), while physical axis %s @ %s",
                            self._axis, nearest, self._caxis, real_pos)
        pos = {self._axis: nearest}
        logging.debug("reporting position %s", pos)
        self.position._set_value(pos, force_write=True)

    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)

    @isasync
    def moveRel(self, shift):
        if not shift:
            return model.InstantaneousFuture()
        self._checkMoveRel(shift)
        raise NotImplementedError("Relative move on fixed positions axis not supported")

    @isasync
    def moveAbs(self, pos):
        """
        Move the actuator to the defined position in m for each axis given.
        pos dict(string-> float): name of the axis and position in m
        """
        if not pos:
            return model.InstantaneousFuture()
        self._checkMoveAbs(pos)
        pos = self._applyInversion(pos)
        f = self._executor.submit(self._doMoveAbs, pos)

        return f

    def _doMoveAbs(self, pos):
        axis, distance = pos.items()[0]
        logging.debug("Moving axis %s (-> %s) to %g", self._axis, self._caxis, distance)

        if self._cycle is None:
            move = {self._caxis: distance}
            self._child.moveAbs(move).result()
        else:
            # Optimize by moving through the closest way
            cur_pos = self._child.position.value[self._caxis]
            vector1 = distance - cur_pos
            mod1 = vector1 % self._cycle
            vector2 = cur_pos - distance
            mod2 = vector2 % self._cycle
            if abs(mod1) < abs(mod2):
                self._move_sum += mod1
                if self._move_sum >= self._cycle:
                    # Once we are about to complete a full cycle, reference again
                    # to get rid of accumulated error
                    self._move_sum = 0
                    # move to the reference switch
                    move_to_ref = (self._cycle - cur_pos) % self._cycle + self._offset
                    self._child.moveRel({self._caxis: move_to_ref}).result()
                    self._child.reference({self._caxis}).result()
                    move = {self._caxis: distance}
                else:
                    move = {self._caxis: mod1}
            else:
                move = {self._caxis:-mod2}
                self._move_sum -= mod2

            self._child.moveRel(move).result()

    def _doReference(self, axes):
        logging.debug("Referencing axis %s (-> %s)", self._axis, self._caxis)
        f = self._child.reference({self._caxis})
        f.result()

        # If we just did homing and ended up to an unsupported position, move to
        # the nearest supported position
        cp = self._child.position.value[self._caxis]
        if (cp not in self._positions):
            nearest = util.find_closest(cp, self._positions.keys())
            self._doMoveAbs({self._axis: nearest})

    @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):
        """
        stops the motion
        axes (iterable or None): list of axes to stop, or None if all should be stopped
        """
        if axes is not None:
            axes = set()
            if self._axis in axes:
                axes.add(self._caxis)

        self._child.stop(axes=axes)

    def terminate(self):
        if self._executor:
            self.stop()
            self._executor.shutdown(wait=True)
            self._executor = None

        self._child.position.unsubscribe(self._update_child_position)
예제 #25
0
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
예제 #26
0
파일: cobolt.py 프로젝트: delmic/odemis
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,))
예제 #27
0
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")
예제 #28
0
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
예제 #29
0
파일: tlfw.py 프로젝트: lanery/odemis
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
예제 #30
0
파일: tlfw.py 프로젝트: delmic/odemis
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
예제 #31
0
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

        # 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 isinstance(pos, dict):
            raise ValueError("Dictionary required")

        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
        """
        # TODO: allow to cancel during the change
        now = time.time()
        duration = abs(self._position - p) / SPEED_PUMP  # s
        self._time_start = now
        self._time_goal = now + duration  # s
        self._goal = p

        time.sleep(duration)

        self._position = p
        self._updatePosition()

    def stop(self, axes=None):
        self._executor.cancel()
        logging.warning("Stopped pressure change")