Typo & Naming

The laser ni class had a typo from the recent import.

Also found that the photometrics class was riddled with things that don't adhere to our naming styles. Updated and will test. Also added another note to the documentation about the most recent version of the PVCAM library.

Author: AdvancedImagingUTSW

docs/source/user_guide/hardware/pvcam.rst

@@ -19,3 +19,11 @@ Photometrics Drivers
     in in srcs/model/devices/APIs/photo_metrics/PyVCAM-master. To install this API, go to this
     folder in the command line and from within your **navigate** environment, run
     ``python setup.py install``.
+
+.. Note::
+
+    The most up-to-date version of PVCAM can be found on `GitHub <https://github.com/Photometrics/PyVCAM>`_.
+
+
+
+

src/navigate/model/devices/camera/photometrics.py

@@ -50,7 +50,7 @@
 
 
 def build_photometrics_connection(camera_connection):
-    """Build Sutter Stage Serial Port connection
+    """Build Photometrics connection
 
     Import Photometrics API and Initialize Camera Controller.
 
@@ -66,7 +66,6 @@ def build_photometrics_connection(camera_connection):
     """
     try:
         pvc.init_pvcam()
-        # camera_names = Camera.get_available_camera_names()
         camera_to_open = Camera.select_camera(camera_connection)
         camera_to_open.open()
         return camera_to_open
@@ -97,8 +96,8 @@ def __init__(
         microscope_name: str,
         device_connection: Any,
         configuration: Dict[str, Any],
-        *args: Optional[Any],
-        **args: Optional[Any],
+        *_: Optional[Any],
+        **__: Optional[Any],
     ) -> None:
         """Initialize the Photometrics class.
 
@@ -113,6 +112,15 @@ def __init__(
         """
         super().__init__(microscope_name, device_connection, configuration)
 
+        #: int: Binning in x direction
+        self.x_binning = None
+
+        #: int: Binning in y direction
+        self.y_binning = None
+
+        #: obj: Data Buffer
+        self._data_buffer = None
+
         self.camera_parameters["supported_readout_directions"] = [
             "Top-to-Bottom",
             "Bottom-to-Top",
@@ -128,19 +136,19 @@ def __init__(
         self.configuration = configuration
 
         #: int: Exposure Time in milliseconds
-        self._exposuretime = 20
+        self._exposure_time = 20
 
         #: int: Scan Mode (0 = Normal, 1 = ASLM)
-        self._scanmode = 0
+        self._scan_mode = 0
 
         #: int: Scan Delay
-        self._scandelay = 1
+        self._scan_delay = 1
 
         #: int: Number of frames
-        self._numberofframes = 100
+        self._number_of_frames = 100
 
         #: obj: Data Buffer
-        self._databuffer = None
+        self._data_buffer = None
 
         #: int: Number of frames received
         self._frames_received = 0
@@ -182,7 +190,7 @@ def __del__(self):
 
     @classmethod
     def connect(cls, camera_connection):
-        """Build Sutter Stage Serial Port connection
+        """Build Photometrics Stage Serial Port connection
 
         Import Photometrics API and Initialize Camera Controller.
 
@@ -232,7 +240,7 @@ def report_settings(self):
         print("internal_line_interval")
         print("sensor size" + str(self.camera_controller.sensor_size))
         print("image_height and width" + str(self.x_pixels) + ", " + str(self.y_pixels))
-        print("exposure_time" + str(self._exposuretime))
+        print("exposure_time" + str(self._exposure_time))
 
     def close_camera(self):
         """Close Photometrics Camera"""
@@ -251,7 +259,7 @@ def set_sensor_mode(self, mode):
         modes_dict = {"Normal": 0, "Light-Sheet": 1}
         if mode in modes_dict:
             self.camera_controller.prog_scan_mode = modes_dict[mode]
-            self._scanmode = modes_dict[mode]
+            self._scan_mode = modes_dict[mode]
         else:
             print("Camera mode not supported" + str(modes_dict[mode]))
             logger.debug("Camera mode not supported" + str(modes_dict[mode]))
@@ -278,7 +286,7 @@ def set_readout_direction(self, mode):
             logger.debug("Camera readout direction not supported")
 
     def calculate_readout_time(self):
-        """Calculate duration of time needed to readout an image.
+        """Calculate duration of time needed to read out an image.
 
         Calculates the readout time and maximum frame rate according to the camera
         configuration settings.
@@ -290,7 +298,7 @@ def calculate_readout_time(self):
         Returns
         -------
         readout_time : float
-            Duration of time needed to readout an image in seconds.
+            Duration of time needed to read out an image in seconds.
         """
 
         # get the readout time from the Photometrics camera in us
@@ -313,9 +321,9 @@ def set_exposure_time(self, exposure_time):
         exposure_time : float
             Exposure time in milliseconds.
         """
-        self._exposuretime = int(exposure_time * 1000)
-        self.camera_controller.exp_time = self._exposuretime
-        self.camera_controller.start_live(self._exposuretime)
+        self._exposure_time = int(exposure_time * 1000)
+        self.camera_controller.exp_time = self._exposure_time
+        self.camera_controller.start_live(self._exposure_time)
         return exposure_time
 
     def set_line_interval(self, line_interval_time):
@@ -326,8 +334,8 @@ def set_line_interval(self, line_interval_time):
         line_interval_time : float
             Line interval duration.
         """
-        # todo calculate line delay from scandelay
-        self._scandelay = line_interval_time
+        # todo calculate line delay from scan delay
+        self._scan_delay = line_interval_time
         self.camera_controller.prog_scan_line_delay = line_interval_time
 
     def calculate_light_sheet_exposure_time(
@@ -354,36 +362,36 @@ def calculate_light_sheet_exposure_time(
         """
 
         # size of ROI
-        nbrows = self.y_pixels
+        number_rows = self.y_pixels
 
         # transform exposure time to milliseconds for Photometrics API.
         full_chip_exposure_time = full_chip_exposure_time * 1000
 
         # equations to calculate ASLM parameters
-        linedelay = self.camera_parameters.get("unitforlinedelay", 1) / 1000
-        ASLM_lineExposure = int(
-            np.ceil(full_chip_exposure_time / (1 + (1 + nbrows) / shutter_width))
+        line_delay = self.camera_parameters.get("unitforlinedelay", 1) / 1000
+        aslm_line_exposure = int(
+            np.ceil(full_chip_exposure_time / (1 + (1 + number_rows) / shutter_width))
         )
-        ASLM_line_delay = (
+        aslm_line_delay = (
             int(
                 np.ceil(
-                    (full_chip_exposure_time - ASLM_lineExposure)
-                    / ((nbrows + 1) * linedelay)
+                    (full_chip_exposure_time - aslm_line_exposure)
+                    / ((number_rows + 1) * line_delay)
                 )
             )
             - 1
         )
 
-        ASLM_acquisition_time = (
-            (ASLM_line_delay + 1) * nbrows * linedelay
-            + ASLM_lineExposure
-            + (ASLM_line_delay + 1) * linedelay
+        aslm_acquisition_time = (
+            (aslm_line_delay + 1) * number_rows * line_delay
+            + aslm_line_exposure
+            + (aslm_line_delay + 1) * line_delay
         )
 
-        self.camera_parameters["line_interval"] = ASLM_lineExposure
-        self._exposuretime = ASLM_lineExposure
-        self._scandelay = ASLM_line_delay
-        return ASLM_lineExposure / 1000, ASLM_line_delay, ASLM_acquisition_time / 1000
+        self.camera_parameters["line_interval"] = aslm_line_exposure
+        self._exposure_time = aslm_line_exposure
+        self._scan_delay = aslm_line_delay
+        return aslm_line_exposure / 1000, aslm_line_delay, aslm_acquisition_time / 1000
 
     def set_binning(self, binning_string):
         """Set Photometrics binning mode.
@@ -488,11 +496,11 @@ def initialize_image_series(self, data_buffer=None, number_of_frames=100):
         """
 
         # set camera parameters depending on acquisition mode
-        self._scanmode = self.camera_controller.prog_scan_mode
-        if self._scanmode == 1:
+        self._scan_mode = self.camera_controller.prog_scan_mode
+        if self._scan_mode == 1:
             # Programmable scan mode (ASLM)
             self.camera_controller.exp_mode = "Edge Trigger"
-            self.camera_controller.prog_scan_line_delay = self._scandelay
+            self.camera_controller.prog_scan_line_delay = self._scan_delay
             self.camera_controller.exp_out_mode = 4
 
         else:
@@ -502,7 +510,7 @@ def initialize_image_series(self, data_buffer=None, number_of_frames=100):
 
         # Prepare for buffered acquisition
         #: int: Number of frames
-        self._numberofframes = number_of_frames
+        self._number_of_frames = number_of_frames
 
         #: obj: Data Buffer
         self._data_buffer = data_buffer
@@ -542,13 +550,12 @@ def _receive_images(self):
                 frame["pixel_data"][:]
             )
             # Delete copied frame for memory management
-            frame = None
             del frame
 
             frame_to_return = [self._frames_received]
             self._frames_received += 1
             # check to make sure the next frame exist in buffer
-            if self._frames_received >= self._numberofframes:
+            if self._frames_received >= self._number_of_frames:
                 self._frames_received = 0
             return frame_to_return
 

src/navigate/model/devices/laser/ni.py

@@ -86,13 +86,14 @@ def __init__(
             "laser"
         ][device_id]["onoff"]["hardware"].get("type", None)
 
-
         if analog == "NI" and digital == "NI":
             modulation_type = "mixed"
         elif analog == "NI":
-            odulation_type = "analog"
+            modulation_type = "analog"
         elif digital == "NI":
             modulation_type = "digital"
+        else:
+            raise ValueError("Laser modulation type not recognized.")
 
         #: str: The modulation type of the laser - Analog, Digital, or Mixed.
         self.modulation_type = modulation_type
@@ -261,4 +262,4 @@ def __del__(self):
             try:
                 self.laser_do_task.close()
             except Exception as e:
-                logger.exception(f"Error stopping task: {traceback.format_exc()}")
+                logger.exception(f"Error stopping task: {traceback.format_exc()}")