134 Adds hyper spectral imaging to qt3scan

src/qt3utils/applications/controllers/princeton_spectrometer.py

@@ -59,12 +59,12 @@ def configure(self, config_dict: dict) -> None:
         self.logger.debug("Calling configure on the Princeton Spectrometer data controller")
         self.last_config_dict.update(config_dict)
 
-        self.spectrometer.experiment_name = config_dict.get('experiment_name', self.spectrometer.experiment_name)
-        self.spectrometer.center_wavelength = float(config_dict.get('center_wavelength', self.spectrometer.center_wavelength))
+        #NOTE: If you dont type cast these then you will get serialization errors
+        self.spectrometer.experiment_name = str(config_dict.get('experiment_name', self.spectrometer.experiment_name))
         self.spectrometer.exposure_time = float(config_dict.get('exposure_time', self.spectrometer.exposure_time))
+        self.spectrometer.center_wavelength = float(config_dict.get('center_wavelength', self.spectrometer.center_wavelength))
         self.spectrometer.temperature_sensor_setpoint = float(config_dict.get('temperature_sensor_setpoint', self.spectrometer.temperature_sensor_setpoint))
-        self.spectrometer.num_frames = float(config_dict.get('num_frames', self.spectrometer.num_frames))
-        self.spectrometer.grating = config_dict.get('grating', self.spectrometer.grating)
+        self.spectrometer.grating = str(config_dict.get('grating', self.spectrometer.grating))
         self.wave_start = float(config_dict.get('wave_start', self.wave_start))
         self.wave_end = float(config_dict.get('wave_end', self.wave_end))
 
@@ -83,17 +83,17 @@ def configure_view(self, gui_root: tk.Toplevel) -> None:
 
         row += 1
         tk.Label(config_win, text="Exposure Time (ms)").grid(row=row, column=0, padx=10)
-        exposure_time_var = tk.StringVar(value=str(self.spectrometer.exposure_time))
+        exposure_time_var = tk.DoubleVar(value=self.spectrometer.exposure_time)
         tk.Entry(config_win, textvariable=exposure_time_var).grid(row=row, column=1)
 
         row += 1
         tk.Label(config_win, text="Center Wavelength (nm)").grid(row=row, column=0, padx=10)
-        center_wavelength_var = tk.StringVar(value=str(self.spectrometer.center_wavelength))
+        center_wavelength_var = tk.DoubleVar(value=self.spectrometer.center_wavelength)
         tk.Entry(config_win, textvariable=center_wavelength_var).grid(row=row, column=1)
 
         row += 1
         tk.Label(config_win, text="Temperature Sensor Setpoint (°C)").grid(row=row, column=0, padx=10)
-        temperature_sensor_setpoint_var = tk.StringVar(value=str(self.spectrometer.temperature_sensor_setpoint))
+        temperature_sensor_setpoint_var = tk.DoubleVar(value=self.spectrometer.temperature_sensor_setpoint)
         tk.Entry(config_win, textvariable=temperature_sensor_setpoint_var).grid(row=row, column=1)
 
         row += 1
@@ -103,12 +103,12 @@ def configure_view(self, gui_root: tk.Toplevel) -> None:
 
         row += 1
         tk.Label(config_win, text="Wavelength Start (nm)").grid(row=row, column=0, padx=10)
-        wave_start_var = tk.StringVar(value=str(self.wave_start))
+        wave_start_var = tk.DoubleVar(value=self.wave_start)
         tk.Entry(config_win, textvariable=wave_start_var).grid(row=row, column=1)
 
         row += 1
         tk.Label(config_win, text="Wavelength End (nm)").grid(row=row, column=0, padx=10)
-        wave_end_var = tk.StringVar(value=str(self.wave_end))
+        wave_end_var = tk.DoubleVar(value=self.wave_end)
         tk.Entry(config_win, textvariable=wave_end_var).grid(row=row, column=1)
 
         # Pack variables into a dictionary to pass to the _set_from_gui method
@@ -119,7 +119,7 @@ def configure_view(self, gui_root: tk.Toplevel) -> None:
             'temperature_sensor_setpoint': temperature_sensor_setpoint_var,
             'grating': grating_var,
             'wave_start': wave_start_var,
-            'wave_end': wave_end_var
+            'wave_end': wave_end_var, 
         }
 
         row += 1

src/qt3utils/applications/qt3scan/controller.py

@@ -218,15 +218,7 @@ class QT3ScanHyperSpectralApplicationController:
      For HyperSpectral imaging, the daq_controller object will be a spectrometer that
      acquires a spectrum at each position in the scan.
 
-     Note that the DAQ controller here must implement QT3ScanCounterDAQControllerInterface
-
-
-     The following methods are required for a daq_controller object that
-     are not currently in the QT3ScanDAQControllerInterface.
-     We should find a way to declare these methods for any spectrometer
-     that is used for hyperspectral imaging. This could be another interface,
-     or perhaps using the concept of Python MixIns. To be discussed....
-
+     Note that the DAQ controller here must implement QT3ScanSpectrometerDAQControllerInterface
     """
     def __init__(self,
                  position_controller: QT3ScanPositionControllerInterface,
@@ -390,9 +382,7 @@ def scan_axis(self, axis, min, max, step_size) -> Tuple[np.ndarray, np.ndarray]:
         time.sleep(self.raster_line_pause)
         for val in np.arange(min, max, step_size):
             self.position_controller.go_to_position(**{axis: val})
-
             measured_spectrum, measured_wavelengths = self.daq_controller.sample_spectrum()
-            spectrums_in_scan.append(measured_spectrum)
 
             if initial_spectrum_size is None:
                 initial_spectrum_size = len(measured_spectrum)
@@ -407,6 +397,8 @@ def scan_axis(self, axis, min, max, step_size) -> Tuple[np.ndarray, np.ndarray]:
                 raise QT3Error("Inconsistent wavelength array and spectrum size obtained during scan! Check your hardware.")
             if np.array_equal(wavelength_array, measured_wavelengths) is False:
                 raise QT3Error("Inconsistent wavelength array obtained during scan! Check your hardware.")
+
+            spectrums_in_scan.append(measured_spectrum)
 
         return np.array(spectrums_in_scan), wavelength_array
 
@@ -442,9 +434,9 @@ def set_scan_range(self, xmin: float, xmax: float, ymin: float, ymax: float) ->
     def get_completed_scan_range(self) -> Tuple[float, float, float, float]:
         """
         Returns a tuple of the scan range that has been completed
-        :return: _xmin, _xmax, _ymin, current_y
+        :return: xmin, xmax, ymin, current_y
         """
-        return self._xmin, self._xmax, self._ymin, self.current_y
+        return self.xmin, self.xmax, self.ymin, self.current_y
 
     def save_scan(self, afile_name) -> None:
         file_type = afile_name.split('.')[-1]

src/qt3utils/applications/qt3scan/main.py

@@ -445,10 +445,8 @@ def _load_controller_from_dict(self, config: dict, a_protocol: Protocol) -> Any:
         controller = cls(logger.level)
 
         logger.debug(f"asserting {config['class_name']} of proper type {a_protocol}")
-        if isinstance(controller, a_protocol) is False:
-            logger.warning(f"\n\n{config['class_name']} does not pass isinstance check of {a_protocol}!")
-            logger.warning(f"Proceed with caution. It's likely that qt3scan will fail when trying to call methods of {a_protocol}\n")
-
+        assert isinstance(controller, a_protocol)
+
         # configure the controller
         # all controllers *should* have a configure method
         logger.debug(f"calling {a_protocol} configure method")

src/qt3utils/datagenerators/princeton.py

@@ -2,21 +2,22 @@
 import logging
 import numpy as np
 from time import sleep
+from pathlib import Path
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 try:
     import clr
 
-    lf_root = os.environ['LIGHTFIELD_ROOT']
-    automation_path = lf_root + '\PrincetonInstruments.LightField.AutomationV4.dll'
-    addin_path = lf_root + '\AddInViews\PrincetonInstruments.LightFieldViewV4.dll'
-    support_path = lf_root + '\PrincetonInstruments.LightFieldAddInSupportServices.dll'
+    lf_root = Path(os.environ['LIGHTFIELD_ROOT'])
+    automation_path = lf_root / 'PrincetonInstruments.LightField.AutomationV4.dll'
+    addin_path = lf_root / 'AddInViews' / 'PrincetonInstruments.LightFieldViewV4.dll'
+    support_path = lf_root / 'PrincetonInstruments.LightFieldAddInSupportServices.dll'
 
-    addin_class = clr.AddReference(addin_path)
-    automation_class = clr.AddReference(automation_path)
-    support_class = clr.AddReference(support_path)
+    addin_class = clr.AddReference(str(addin_path))
+    automation_class = clr.AddReference(str(automation_path))
+    support_class = clr.AddReference(str(support_path))
 
     import PrincetonInstruments.LightField as lf
 
@@ -32,7 +33,6 @@
 
 class LightfieldApp:
     def __init__(self, visible):
-
         self._addinbase = lf.AddIns.AddInBase()
         self._automation = lf.Automation.Automation(visible, List[String]())
         self._application = self._automation.LightFieldApplication
@@ -108,7 +108,7 @@ def acquire(self):
         """
 
         acquisition_time = self.get(lf.AddIns.CameraSettings.ShutterTimingExposureTime) #to allow the camera to capture the desired amount of data during the specified exposure time.
-        num_frames = self.get(lf.AddIns.ExperimentSettings.FrameSettingsFramesToStore)
+        num_frames = self.get(lf.AddIns.ExperimentSettings.AcquisitionFramesToStore)
         self.experiment.Acquire()
 
         sleep(0.001 * acquisition_time * num_frames)  #sleep delay that waits for the exposure duration of the camera
@@ -229,14 +229,14 @@ def num_frames(self):
         """
         Returns the number of frames taken during the acquisition.
         """
-        return self.light.get(lf.AddIns.ExperimentSettings.FrameSettingsFramesToStore)
+        return self.light.get(lf.AddIns.ExperimentSettings.AcquisitionFramesToStore)
 
     @num_frames.setter
     def num_frames(self, num_frames):
         """
         Sets the number of frames to be taken during acquisition to number.
         """
-        return self.light.set(lf.AddIns.ExperimentSettings.FrameSettingsFramesToStore, num_frames)
+        return self.light.set(lf.AddIns.ExperimentSettings.AcquisitionFramesToStore, num_frames)
 
     @property
     def exposure_time(self):