Merge pull request #172 from spacetelescope/feature/ocean_optics_usb4000

Add services for Ocean Optics spectrometers

catkit2/services/oceanoptics_spectrometer/oceanoptics_spectrometer.py

@@ -0,0 +1,193 @@
+'''
+This module contains a service for Ocean Optics Spectrometers.
+'''
+import numpy as np
+
+from seabreeze.spectrometers import Spectrometer
+from seabreeze.spectrometers import SeaBreezeError
+
+from catkit2.testbed.service import Service
+
+
+class OceanOpticsSpectrometer(Service):
+    '''
+    Service for Ocean Optics Spectrometer.
+
+    This service is a wrapper around the python seabreeze package.
+    It provides a simple interface to control the spectrometer and acquire spectra.
+
+    Attributes
+    ----------
+    spectrometer : Spectrometer
+        The spectrometer to control.
+    serial_number : str
+        The serial number of the spectrometer.
+    model : str
+        The model of the spectrometer.
+    pixels_number : int
+        number of pixels in the spectrum.
+    interval : float
+        The interval between spectrum acquisitions in seconds.
+    spectra : DataStream
+        A data stream to submit spectra from the spectrometer.
+    is_saturating : DataStream
+        A data stream to submit whether the spectrometer is currently saturating.
+    NUM_FRAMES : int
+        The number of frames to allocate for the data streams.
+
+    Methods
+    -------
+    open()
+        Open the service.
+    main()
+        The main function of the service.
+    close()
+        Close the service.
+    take_one_spectrum()
+        Get a spectrum from the spectrometer.
+    '''
+    NUM_FRAMES = 20
+
+    def __init__(self):
+        '''
+        Create a new OceanOpticsSpectrometer service.
+        '''
+        super().__init__('oceanoptics_spectrometer')
+
+        self.serial_number = str(self.config['serial_number'])
+        self.interval = self.config.get('interval', 1)
+        self._exposure_time = self.config.get('exposure_time', 1000)
+
+        self.spectrometer = None
+        self.model = None
+        self.pixels_number = None
+
+    def open(self):
+        '''
+        Open the service.
+
+        This function is called when the service is opened.
+        It initializes the spectrometer and creates the data streams and properties.
+
+        Raises
+        ------
+        ImportError
+            If the spectrometer cannot be found.
+        '''
+
+        # Find the spectrometer
+        try:
+            self.spectrometer = Spectrometer.from_serial_number(self.serial_number)
+        except SeaBreezeError:
+            raise ImportError(f'OceanOptics: Could not find spectrometer with serial number {self.serial_number}')
+
+        # exctract attributes
+        self.model = self.spectrometer.model
+        self.pixels_number = self.spectrometer.pixels
+
+        # Define and set default exposure time.
+        self.exposure_time = self._exposure_time
+
+        # Create datastreams
+        self.spectra = self.make_data_stream('spectra', 'float32', [self.pixels_number], self.NUM_FRAMES)
+
+        self.is_saturating = self.make_data_stream('is_saturating', 'int8', [1], self.NUM_FRAMES)
+        self.is_saturating.submit_data(np.array([0], dtype='int8'))
+
+        # Create properties
+        def make_property_helper(name, read_only=False):
+            if read_only:
+                self.make_property(name, lambda: getattr(self, name))
+            else:
+                self.make_property(name, lambda: getattr(self, name), lambda val: setattr(self, name, val))
+
+        make_property_helper('exposure_time')
+        make_property_helper('wavelengths', read_only=True)
+
+    def main(self):
+        '''
+        The main function of the service.
+
+        This function is called when the service is started.
+        '''
+        while not self.should_shut_down:
+            intensities = self.take_one_spectrum()
+            self.spectra.submit_data(np.array(intensities, dtype='float32'))
+
+            if np.max(intensities) == self.spectrometer.max_intensity:
+                self.is_saturating.submit_data(np.array([1], dtype='int8'))
+            else:
+                self.is_saturating.submit_data(np.array([0], dtype='int8'))
+
+            self.sleep(self.interval)
+
+    def take_one_spectrum(self):
+        '''
+        Measure and return one spectrum.
+        '''
+        return self.spectrometer.intensities()
+
+    @property
+    def wavelengths(self):
+        '''
+        The wavelengths of the spectrometer in nm.
+
+        Returns:
+        --------
+        ndarray of float:
+            wavelengths of the spectrometer.
+        '''
+        return self.spectrometer.wavelengths()
+
+    @property
+    def exposure_time(self):
+        '''
+        The exposure time in microseconds.
+
+        Returns:
+        --------
+        int:
+            The exposure time in microseconds.
+        '''
+        return self._exposure_time
+
+    @exposure_time.setter
+    def exposure_time(self, exposure_time: int):
+        '''
+        Set the exposure time in microseconds.
+
+        This property can be used to set the exposure time of the spectrometer.
+
+        If the `exposure_time` parameter is inferior to the minimum allowed exposure time for this
+        spectrometer (set by Ocean Optics), it is set to the minimum allowed exposure time.
+        If the `exposure_time` is larger than the maximum allowed exposure time, it is set to the
+        maximum allowed exposure time.
+
+        Parameters
+        ----------
+        exposure_time : int
+            The exposure time in microseconds.
+        '''
+        int_time_range = self.spectrometer.integration_time_micros_limits
+        if exposure_time < int_time_range[0]:
+            exposure_time = int_time_range[0]
+        if exposure_time > int_time_range[1]:
+            exposure_time = int_time_range[1]
+
+        self._exposure_time = exposure_time
+        self.spectrometer.integration_time_micros(exposure_time)
+
+    def close(self):
+        '''
+        Close the service.
+
+        This function is called when the service is closed.
+        It closes the spectrometer.
+        '''
+        self.spectrometer.close()
+        self.spectrometer = None
+
+
+if __name__ == '__main__':
+    service = OceanOpticsSpectrometer()
+    service.run()

catkit2/services/oceanoptics_spectrometer_sim/oceanoptics_spectrometer_sim.py

@@ -0,0 +1,150 @@
+'''
+This module contains a service for simulation Ocean Optics Spectrometers.
+'''
+import numpy as np
+from catkit2.testbed.service import Service
+
+
+class OceanOpticsSpectrometerSim(Service):
+    '''
+    Service for simulated Ocean Optics Spectrometer.
+
+    Attributes
+    ----------
+    spectrometer : Spectrometer
+        The spectrometer to control.
+    serial_number : str
+        The serial number of the spectrometer.
+    pixels_number : int
+        Number of pixels in the spectrum.
+    interval : float
+        The interval between spectrum acquisitions in seconds.
+    spectra : DataStream
+        A data stream to submit spectra from the spectrometer.
+    is_saturating : DataStream
+        A data stream to submit whether the spectrometer is currently saturating.
+    NUM_FRAMES : int
+        The number of frames to allocate for the data streams.
+
+    Methods
+    -------
+    open()
+        Open the service.
+    main()
+        The main function of the service.
+    close()
+        Close the service.
+    take_one_spectrum()
+        Get a spectrum from the spectrometer.
+    '''
+    NUM_FRAMES = 20
+
+    def __init__(self):
+        '''
+        Create a new OceanOpticsSpectrometer service.
+        '''
+        super().__init__('oceanoptics_spectrometer_sim')
+
+        self.serial_number = str(self.config['serial_number'])
+        self.interval = self.config.get('interval', 1)
+        self._exposure_time = self.config.get('exposure_time', 1000)
+
+
+        self.pixels_number = 3000
+
+        self.spectra = None
+        self.is_saturating = None
+
+    def open(self):
+        '''
+        Open the service.
+
+        This function is called when the service is opened.
+        It initializes the spectrometer and creates the data streams and properties.
+
+        Raises
+        ------
+        RuntimeError
+            If the spectrometer cannot be found.
+        '''
+
+        # Define and set defaut exposure time
+        self.exposure_time = self._exposure_time
+
+        # Create datastreams
+        self.spectra = self.make_data_stream('spectra', 'float32', [self.pixels_number], self.NUM_FRAMES)
+
+        self.is_saturating = self.make_data_stream('is_saturating', 'int8', [1], self.NUM_FRAMES)
+        self.is_saturating.submit_data(np.array([0], dtype='int8'))
+
+        # Create properties
+        def make_property_helper(name, read_only=False):
+            if read_only:
+                self.make_property(name, lambda: getattr(self, name))
+            else:
+                self.make_property(name, lambda: getattr(self, name), lambda val: setattr(self, name, val))
+
+        make_property_helper('exposure_time')
+        make_property_helper('wavelengths', read_only=True)
+
+    def main(self):
+        '''
+        The main function of the service.
+
+        This function is called when the service is started.
+        '''
+        while not self.should_shut_down:
+            intensities = self.take_one_spectrum(self.pixels_number)
+            self.spectra.submit_data(np.array(intensities, dtype='float32'))
+            self.is_saturating.submit_data(np.array([0], dtype='int8'))
+
+            self.sleep(self.interval)
+
+    def take_one_spectrum(self):
+        '''
+        Measure and return one spectrum.
+        Simulated service: random numpy array.
+        '''
+        return np.random.random(self.pixels_number) + 1000
+
+    @property
+    def wavelengths(self):
+        '''
+        The wavelengths of the spectrometer in nm.
+        Simulated service: linear vector evenly spaced bewtween 350 and 1000 nm.
+
+        Returns:
+        --------
+        ndarray of float:
+            wavelengths of the spectrometer.
+        '''
+        return np.linspace(350, 1000, num=self.pixels_number)
+
+    @property
+    def exposure_time(self):
+        '''
+        The exposure time in microseconds.
+
+        Returns:
+        --------
+        int:
+            The exposure time in microseconds.
+        '''
+        return self._exposure_time
+
+    @exposure_time.setter
+    def exposure_time(self, exposure_time: int):
+        '''
+        Set the exposure time in microseconds.
+
+        Parameters
+        ----------
+        exposure_time : int
+            The exposure time in microseconds.
+        '''
+        self._exposure_time = exposure_time
+
+
+if __name__ == '__main__':
+    service = OceanOpticsSpectrometerSim()
+    service.run()

catkit2/testbed/proxies/__init__.py

@@ -7,7 +7,8 @@
     'NiDaqProxy',
     'NktSuperkProxy',
     'ThorlabsCubeMotorKinesisProxy',
-    'WebPowerSwitchProxy'
+    'WebPowerSwitchProxy',
+    'OceanopticsSpectroProxy'
 ]
 
 from .bmc_dm import *
@@ -17,5 +18,6 @@
 from .newport_picomotor import *
 from .ni_daq import *
 from .nkt_superk import *
+from .oceanoptics_spectrometer import *
 from .thorlabs_cube_motor_kinesis import *
 from .web_power_switch import *

catkit2/testbed/proxies/oceanoptics_spectrometer.py

@@ -0,0 +1,22 @@
+from ..service_proxy import ServiceProxy
+
+@ServiceProxy.register_service_interface('oceanoptics_spectrometer')
+class OceanopticsSpectroProxy(ServiceProxy):
+
+    def take_raw_exposures(self, num_exposures):
+        first_frame_id = self.spectra.newest_available_frame_id
+
+        i = 0
+        num_exposures_remaining = num_exposures
+
+        while num_exposures_remaining >= 1:
+            try:
+                frame = self.spectra.get_frame(first_frame_id + i, 1000)
+            except RuntimeError:
+                # The frame wasn't available anymore because we were waiting too long.
+                continue
+            finally:
+                i += 1
+
+            yield frame.data.copy()
+            num_exposures_remaining -= 1

docs/index.rst

@@ -30,6 +30,7 @@ Catkit2
    services/newport_xps_q8
    services/ni_daq
    services/nkt_superk
+   services/oceanoptics_spectrometer
    services/omega_ithx_w3
    services/safety_monitor
    services/snmp_ups