Remove redundant naming

Currently we import model.device.camera.CameraHamamatsu...  The second name of Camera is unnecessary, and just makes our imports long...

Converted to model.device.camera.hamamatsu

Author: AdvancedImagingUTSW

src/navigate/model/device_startup_functions.py

@@ -8,7 +8,7 @@
 import serial
 from time import sleep
 
-from navigate.model.devices.lasers.laser_base import LaserBase
+from navigate.model.devices.lasers.base import LaserBase
 
 # Logger Setup
 p = __name__.split(".")[1]

src/navigate/model/devices/APIs/coherent/ObisLaser.py

@@ -5,7 +5,7 @@
 
 # from time import time
 
-from navigate.model.devices.lasers.laser_base import LaserBase
+from navigate.model.devices.lasers.base import LaserBase
 
 # Logger Setup
 p = __name__.split(".")[1]

src/navigate/model/devices/APIs/omicron/LuxxLaser.py

@@ -1,12 +1,12 @@
 """ Hardware devices. """
 
-from .daq.daq_synthetic import SyntheticDAQ  # noqa
-from .camera.camera_synthetic import SyntheticCamera  # noqa
-from .filter_wheel.filter_wheel_synthetic import SyntheticFilterWheel  # noqa
-from .galvo.galvo_synthetic import SyntheticGalvo  # noqa
-from .remote_focus.remote_focus_synthetic import SyntheticRemoteFocus  # noqa
-from .shutter.laser_shutter_synthetic import SyntheticShutter  # noqa
-from .stages.stage_synthetic import SyntheticStage  # noqa
-from .zoom.zoom_synthetic import SyntheticZoom  # noqa
-from .lasers.laser_synthetic import SyntheticLaser  # noqa
-from .mirrors.mirror_synthetic import SyntheticMirror  # noqa
+from .daq.synthetic import SyntheticDAQ  # noqa
+from .camera.synthetic import SyntheticCamera  # noqa
+from .filter_wheel.synthetic import SyntheticFilterWheel  # noqa
+from .galvo.synthetic import SyntheticGalvo  # noqa
+from .remote_focus.synthetic import SyntheticRemoteFocus  # noqa
+from .shutter.synthetic import SyntheticShutter  # noqa
+from .stages.synthetic import SyntheticStage  # noqa
+from .zoom.synthetic import SyntheticZoom  # noqa
+from .lasers.synthetic import SyntheticLaser  # noqa
+from .mirrors.synthetic import SyntheticMirror  # noqa

src/navigate/model/devices/__init__.py

@@ -99,8 +99,10 @@ def __init__(self, microscope_name, device_connection, configuration):
         self.minimum_exposure_time = 0.001
         self.camera_parameters["x_pixels"] = 2048
         self.camera_parameters["y_pixels"] = 2048
-        # TODO: trigger_source, readout_speed, trigger_active, trigger_mode and trigger_polarity
-        # can be removed after updating how we get the readout time in model and controller
+        # TODO: trigger_source, readout_speed,
+        #  trigger_active, trigger_mode and trigger_polarity
+        # can be removed after updating how we get the
+        # readout time in model and controller
         self.camera_parameters["trigger_source"] = 2.0
         self.camera_parameters["readout_speed"] = 1.0
         self.camera_parameters["pixel_size_in_microns"] = 6.5
@@ -111,7 +113,7 @@ def __init__(self, microscope_name, device_connection, configuration):
             "Top-to-Bottom",
             "Bottom-to-Top",
             "Bidirectional",
-            "Rev. Bidirectional"
+            "Rev. Bidirectional",
         ]
 
         # Initialize offset and variance maps, if present

src/navigate/model/devices/camera/camera_base.py renamed to src/navigate/model/devices/camera/base.py

@@ -36,7 +36,7 @@
 # Third Party Imports
 
 # Local Imports
-from navigate.model.devices.camera.camera_base import CameraBase
+from navigate.model.devices.camera.base import CameraBase
 
 # Logger Setup
 p = __name__.split(".")[1]
@@ -385,7 +385,8 @@ def initialize_image_series(self, data_buffer=None, number_of_frames=100):
         Parameters
         ----------
         data_buffer :
-            List of SharedNDArrays of shape=(self.img_height, self.img_width) and dtype="uint16" # noqa
+            List of SharedNDArrays of shape=(self.img_height,
+            self.img_width) and dtype="uint16"
             Default is None.
         number_of_frames : int
             Number of frames.  Default is 100.

src/navigate/model/devices/camera/camera_hamamatsu.py renamed to src/navigate/model/devices/camera/hamamatsu.py

@@ -40,7 +40,7 @@
 from pyvcam.camera import Camera
 
 # Local Imports
-from navigate.model.devices.camera.camera_base import CameraBase
+from navigate.model.devices.camera.base import CameraBase
 
 # Logger Setup
 p = __name__.split(".")[1]

src/navigate/model/devices/camera/camera_photometrics.py renamed to src/navigate/model/devices/camera/photometrics.py

@@ -41,7 +41,7 @@
 
 # Local Imports
 from navigate.model.analysis import camera
-from navigate.model.devices.camera.camera_base import CameraBase
+from navigate.model.devices.camera.base import CameraBase
 
 # Logger Setup
 p = __name__.split(".")[1]
@@ -231,7 +231,7 @@ def load_images(self, filenames=None, ds=None):
                     tif = TiffFile(image_file)
                     if len(tif.pages) == 1:
                         self.tif_images.append([tif.asarray()])
-                    else: 
+                    else:
                         self.tif_images.append(tif.asarray())
                     idx += len(tif.pages)
                     if idx >= self.num_of_frame:
@@ -317,6 +317,5 @@ def calculate_readout_time(self):
             Duration of time needed to readout an image.
 
         """
-        exposure_time = self.camera_controller.get_property_value("exposure_time")
         readout_time = 0.01  # 10 milliseconds.
         return readout_time

src/navigate/model/devices/camera/camera_synthetic.py renamed to src/navigate/model/devices/camera/synthetic.py

@@ -83,9 +83,12 @@ def __init__(self, configuration):
 
         # Camera Parameters
         #: float: Camera delay percentage
-        self.camera_delay = self.configuration["configuration"]["microscopes"][
-            self.microscope_name
-        ]["camera"]["delay"] / 1000
+        self.camera_delay = (
+            self.configuration["configuration"]["microscopes"][self.microscope_name][
+                "camera"
+            ]["delay"]
+            / 1000
+        )
 
         #: dict: Dictionary of waveforms.
         self.waveform_dict = {}
@@ -153,9 +156,12 @@ def enable_microscope(self, microscope_name):
         if microscope_name != self.microscope_name:
             self.microscope_name = microscope_name
 
-        self.camera_delay = self.configuration["configuration"]["microscopes"][
-            microscope_name
-        ]["camera"]["delay"] / 1000
+        self.camera_delay = (
+            self.configuration["configuration"]["microscopes"][microscope_name][
+                "camera"
+            ]["delay"]
+            / 1000
+        )
         self.sample_rate = self.configuration["configuration"]["microscopes"][
             microscope_name
         ]["daq"]["sample_rate"]

src/navigate/model/devices/daq/daq_base.py renamed to src/navigate/model/devices/daq/base.py

@@ -42,7 +42,7 @@
 import numpy as np
 
 # Local Imports
-from navigate.model.devices.daq.daq_base import DAQBase
+from navigate.model.devices.daq.base import DAQBase
 from navigate.tools.waveform_template_funcs import get_waveform_template_parameters
 
 # Logger Setup