Merge pull request #950 from TheDeanLab/637-dichroic-control-1

637 dichroic control 1

Author: AdvancedImagingUTSW

docs/source/user_guide/hardware/dichroic.rst

@@ -0,0 +1,66 @@
+================
+Dichroic Turrets
+================
+
+Dichroics can be used to reflect the excitation light towards the camera, while
+permitting the emission light that is captured by the objective to be transmitted
+to the camera. Alternatively, they can be placed in the detection path to separate
+different emission wavelengths and to direct it to the appropriate camera.
+
+Currently, **navigate** incorporates a dichroic turret as a filter wheel, which enables
+you to add as many different dichroic turrets as you would like.
+
+.. note::
+
+    The `name` parameter under `hardware` is optional. If not provided, the name of the
+    device will be default to Filter 0, Filter 1, ... Filter N in the GUI. However, if
+    is is provided, then the GUI will automatically use the name provided as a label.
+
+ASI
+---
+
+C60-CUBE-SLDR
+~~~~~~~~~~~~~
+
+The `C60-CUBE-SLDR <https://www.asiimaging.com/illumination-control/c60-cube-sldr/>`_
+is a motorized dichroic slider that can be controlled by the ASI Tiger Controller.
+The example below shows the configuration file with one dichroic turret, and one
+filter wheel. The same communication instance is used for both the stage and filter
+wheel. It holds a maximum of 4 dichroics.
+
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+          -
+            filter_wheel:
+              hardware:
+                type: ASI
+                name: Filter Wheel 1
+                wheel_number: 1
+                port: COM1
+                baudrate: 115200
+              filter_wheel_delay: 0.03
+              available_filters:
+                Empty-Alignment: 0
+                GFP: 1
+                RFP: 2
+                Far-Red: 3
+          -
+            filter_wheel:
+              hardware:
+                type: ASICubeSlider
+                name: Dichroic Turret 1
+                wheel_number: 2
+                port: COM1
+                baudrate: 115200
+              filter_wheel_delay: 0.25
+              available_filters:
+                510LP: 0
+                560LP: 1
+                600LP: 2
+                660LP: 3
+|

docs/source/user_guide/hardware/filter_wheel.rst

@@ -17,6 +17,7 @@ file as follows:
           -
             filter_wheel:
               hardware:
+                name: Lower Filter Wheel
                 type: SutterFilterWheel
                 wheel_number: 1
                 port: COM1
@@ -30,6 +31,7 @@ file as follows:
           -
             filter_wheel:
               hardware:
+                name: Upper Filter Wheel
                 type: SutterFilterWheel
                 wheel_number: 2
                 port: COM1
@@ -42,6 +44,12 @@ file as follows:
                 Far-Red: 3
 |
 
+.. note::
+
+    The `name` parameter under `hardware` is optional. If not provided, the name of the
+    device will be default to Filter 0, Filter 1, ... Filter N in the GUI. However, if
+    is is provided, then the GUI will automatically use the name provided as a label.
+
 -----------
 
 Sutter Instruments
@@ -107,7 +115,7 @@ for the stage. A single communication instance is used for both the stage and fi
                 type: ASI
                 wheel_number: 1
                 port: COM1
-                baudrate: 9600
+                baudrate: 115200
               filter_wheel_delay: 0.03
               available_filters:
                 Empty-Alignment: 0

docs/source/user_guide/hardware/hardware_home.rst

@@ -21,6 +21,7 @@ Additional devices are available by installing the
    remote_focus.rst
    stage.rst
    filter_wheel.rst
+   dichroic.rst
    galvo.rst
    laser.rst
    shutter.rst

docs/source/user_guide/hardware/stage.rst

@@ -72,7 +72,7 @@ first establish communication with the device using `ASI provided software <http
                   stages:
                   refmode:
                   port: COM12
-                  baudrate: 9600
+                  baudrate: 115200
                   timeout: 0.25
               joystick_axes: [x, y, z]
               x_min: -10000.0
@@ -233,7 +233,7 @@ the software is restarted, it should work.
                   serial_number: 001
                   axes: [x, y, z]
                   axes_mapping: [x, y, z]
-                  feedback_alignment: 
+                  feedback_alignment:
                   volts_per_micron: 0.0
                   min: 0.0
                   max: 25000
@@ -314,16 +314,16 @@ C-884
                   serial_number: 119060508
                   axes: [x, y, z, theta, f]
                   axes_mapping: [1, 2, 3, 4, 5]
-                  feedback_alignment: 
+                  feedback_alignment:
                   volts_per_micron: 0.0
-                  min: 
-                  max: 
+                  min:
+                  max:
                   controllername: C-884
                   stages: L-509.20DG10 L-509.40DG10 L-509.20DG10 M-060.DG M-406.4PD NOSTAGE
                   refmode: FRF FRF FRF FRF FRF FRF
-                  port: 
-                  baudrate: 
-                  timeout: 
+                  port:
+                  baudrate:
+                  timeout:
               joystick_axes: [x, y, z]
               x_min: -10000.0
               x_max: 10000.0
@@ -365,16 +365,16 @@ E-709
                   serial_number: 119060508
                   axes: [x, y, z, theta, f]
                   axes_mapping: [1, 2, 3, 4, 5]
-                  feedback_alignment: 
+                  feedback_alignment:
                   volts_per_micron: 0.0
-                  min: 
-                  max: 
+                  min:
+                  max:
                   controllername: E-709
                   stages: L-509.20DG10 L-509.40DG10 L-509.20DG10 M-060.DG M-406.4PD NOSTAGE
                   refmode: FRF FRF FRF FRF FRF FRF
-                  port: 
-                  baudrate: 
-                  timeout: 
+                  port:
+                  baudrate:
+                  timeout:
               joystick_axes: [x, y, z]
               x_min: -10000.0
               x_max: 10000.0
@@ -424,16 +424,16 @@ positioning.
                   serial_number: 74000375
                   axes: [f]
                   axes_mapping: [1]
-                  feedback_alignment: 
+                  feedback_alignment:
                   volts_per_micron: 0.0
-                  min: 
-                  max: 
+                  min:
+                  max:
                   controllername:
-                  stages: 
-                  refmode: 
-                  port: 
-                  baudrate: 
-                  timeout: 
+                  stages:
+                  refmode:
+                  port:
+                  baudrate:
+                  timeout:
               joystick_axes: [f]
               x_min: -10000.0
               x_max: 10000.0
@@ -481,11 +481,11 @@ KST101
                   min: 0
                   max: 25
                   controllername:
-                  stages: 
-                  refmode: 
-                  port: 
-                  baudrate: 
-                  timeout: 
+                  stages:
+                  refmode:
+                  port:
+                  baudrate:
+                  timeout:
               joystick_axes: [f]
               x_min: -10000.0
               x_max: 10000.0

src/navigate/config/configuration_database.py

@@ -57,7 +57,8 @@
 
 filter_wheel_device_types = {
     "Sutter Instruments": "SutterFilterWheel",
-    "Applied Scientific Instrumentation": "ASI",
+    "ASI Filter Wheel": "ASI",
+    "ASI Dichroic Slider": "ASICubeSlider",
     "Ludl Electronic Products": "LUDLFilterWheel",
     "Analog/Digital Device": "NI",
     "Virtual Device": "synthetic",
@@ -85,6 +86,7 @@
     "hardware/wheel_number": ["Number of Wheels", "Spinbox", "int", None, "Example: 1"],
     "hardware/port": ["Serial Port", "Input", "string", None, "Example: COM1"],
     "hardware/baudrate": ["Baudrate", "Input", "int", None, "Example: 9600"],
+    "hardware/name": ["GUI Label", "Input", "string", None, "Example: Filter Wheel 1"],
     "filter_wheel_delay": [
         "Filter Wheel Delay (s)",
         "Input",

src/navigate/controller/configuration_controller.py

@@ -396,6 +396,24 @@ def number_of_filter_wheels(self):
             return len(self.microscope_config["filter_wheel"])
         return 1
 
+    @property
+    def filter_wheel_names(self):
+        """Return a list of filter wheel names
+
+        Returns
+        -------
+        filter_wheel_names : list
+            List of filter wheel names.
+        """
+        filter_wheel_names = []
+        if self.microscope_config is not None:
+            for i in range(self.number_of_filter_wheels):
+                name = self.microscope_config["filter_wheel"][i]["hardware"].get(
+                    "name", f"Filter Wheel {i}"
+                )
+                filter_wheel_names.append(name)
+        return filter_wheel_names
+
     @property
     def microscope_list(self):
         """Return a list of microscope names

src/navigate/controller/sub_controllers/channels_settings.py

@@ -70,7 +70,9 @@ def __init__(self, view, parent_controller=None, configuration_controller=None):
             self.configuration_controller.number_of_filter_wheels
         )
         self.view.populate_frame(
-            channels=self.num, filter_wheels=self.number_of_filter_wheels
+            channels=self.num,
+            filter_wheels=self.number_of_filter_wheels,
+            filter_wheel_names=self.configuration_controller.filter_wheel_names,
         )
 
         #: str: The mode of the channel setting controller. Either 'live' or 'stop'.

src/navigate/model/device_startup_functions.py

@@ -189,8 +189,6 @@ def load_camera_connection(configuration, camera_id=0, is_synthetic=False):
         camera_connection = configuration["configuration"]["hardware"]["camera"][
             camera_id
         ]["camera_connection"]
-
-        # return camera object in the auto_redial function.
         return auto_redial(
             build_photometrics_connection, (camera_connection,), exception=Exception
         )
@@ -875,7 +873,7 @@ def load_filter_wheel_connection(device_info, is_synthetic=False, plugin_devices
             exception=Exception,
         )
 
-    elif device_type == "ASI":
+    elif device_type == "ASI" or device_type == "ASICubeSlider":
         from navigate.model.devices.filter_wheel.asi import (
             build_filter_wheel_connection,
         )
@@ -969,6 +967,11 @@ def start_filter_wheel(
 
         return ASIFilterWheel(device_connection, device_config)
 
+    elif device_type == "ASICubeSlider":
+        from navigate.model.devices.filter_wheel.asi import ASICubeSlider
+
+        return ASICubeSlider(device_connection, device_config)
+
     elif device_type == "NI":
         from navigate.model.devices.filter_wheel.ni import DAQFilterWheel
 
@@ -1058,7 +1061,7 @@ def start_shutter(
         Name of microscope in configuration
     device_connection : object
         Hardware device to connect to
-    configuration : multiprocesing.managers.DictProxy
+    configuration : multiprocessing.managers.DictProxy
         Global configuration of the microscope
     is_synthetic : bool
         Run synthetic version of hardware?