Merge pull request #930 from TheDeanLab/926

926

Author: AdvancedImagingUTSW

README.md

@@ -11,7 +11,8 @@ navigate
 [![Tests](https://github.com/TheDeanLab/navigate/actions/workflows/push_checks.yaml/badge.svg)](https://github.com/TheDeanLab/navigate/actions/workflows/push_checks.yaml)
 [![codecov](https://codecov.io/gh/TheDeanLab/navigate/branch/develop/graph/badge.svg?token=270RFSZGG5)](https://codecov.io/gh/TheDeanLab/navigate)
 
-Navigate is an open source Python package for control of light-sheet microscopes. It allows for easily reconfigurable hardware setups and automated acquisition rotuines.
+**navigate** is an open source Python package for control of light-sheet microscopes.
+It allows for easily reconfigurable hardware setups and automated acquisition rotuines.
 
 ### Quick install
 
@@ -31,23 +32,27 @@ Please refer to and contribute to the documentation, which can be found on GitHu
 
 ### Command Line Arguments
 
-* optional arguments:
-	*  -h, --help            show this help message and exit
-
-* Input Arguments:
-  	* -sh, --synthetic_hardware
-  	* --config_file CONFIG_FILE
-  	* --experiment_file EXPERIMENT_FILE
-  	* --etl_const_file ETL_CONST_FILE
-	*  --rest_api_file REST_API_FILE
-  	* --logging_config LOGGING_CONFIG
-
-### Authors
-* Kevin Dean
-* Zach Marin
-* Xiaoding 'Annie' Wang
-* Dax Collison
-* Sampath Rapuri
-* Samir Mamtani
-* Renil Gupta
-* Andrew Jamieson
+Below are the optional arguments that can be passed to the navigate software:
+
+- `-h, --help`
+  Provides information on the optional arguments that can be passed to **navigate**.
+- `-sh, --synthetic_hardware`
+  Open the software without any hardware attached for testing
+  and setting up a new system.
+- `-c, --configurator`
+  Open the **navigate** configuration wizard, which provides a
+  graphical interface for setting up the hardware configuration.
+- `-d`
+  Enables the debugging menu in the software.
+- `--config-file`
+  Pass a non-default `configuration.yaml` file to **navigate**.
+- `--experiment_file`
+  Pass a non-default `experiment.yaml` file to **navigate**.
+- `--gui-config-file`
+  Pass a non-default `gui_config.yaml` file to **navigate**.
+- `--waveform-constants-file`
+  Pass a non-default waveform constants file to **navigate**.
+- `--rest_api_file`
+  Pass a non-default REST API file to **navigate**.
+- `--logging_config`
+  Pass a non-default logging configuration file to **navigate**.

src/navigate/config/config.py

@@ -1,4 +1,4 @@
-# Copyright (c) 2021-2022  The University of Texas Southwestern Medical Center.
+# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.
 # All rights reserved.
 
 # Redistribution and use in source and binary forms, with or without
@@ -89,65 +89,38 @@ def get_configuration_paths():
         Path to file containing REST API configuration
     waveform_templates_path : str
         Path to file containing waveform templates
+    gui_configuration_path : str
+        Path to file containing GUI configuration
     """
+    # Create the navigate home directory if it doesn't exist
     navigate_directory = get_navigate_path()
     if not os.path.exists(navigate_directory):
         os.mkdir(navigate_directory)
+
+    # Create the configuration directory if it doesn't exist
     configuration_directory = Path(os.path.join(navigate_directory, "config"))
     if not os.path.exists(configuration_directory):
         os.mkdir(configuration_directory)
 
-    # Configuration files should be stored in this directory
-    configuration_path = Path.joinpath(configuration_directory, "configuration.yaml")
-    experiment_path = Path.joinpath(configuration_directory, "experiment.yml")
-    waveform_constants_path = Path.joinpath(
-        configuration_directory, "waveform_constants.yml"
-    )
-    rest_api_path = Path.joinpath(configuration_directory, "rest_api_config.yml")
-    waveform_templates_path = Path.joinpath(
-        configuration_directory, "waveform_templates.yml"
-    )
-
-    # If they are not already,
-    # copy the default ones that ship with the software to this folder
-    if not os.path.exists(configuration_path):
-        copy_base_directory = Path(__file__).resolve().parent
-        copy_configuration_path = Path.joinpath(
-            copy_base_directory, "configuration.yaml"
-        )
-        shutil.copyfile(copy_configuration_path, configuration_path)
+    configuration_files = [
+        "configuration.yaml",
+        "experiment.yml",
+        "waveform_constants.yml",
+        "rest_api_config.yml",
+        "waveform_templates.yml",
+        "gui_configuration.yml",
+    ]
 
-    if not os.path.exists(experiment_path):
-        copy_base_directory = Path(__file__).resolve().parent
-        copy_experiment_path = Path.joinpath(copy_base_directory, "experiment.yml")
-        shutil.copyfile(copy_experiment_path, experiment_path)
+    base_directory = Path(__file__).resolve().parent
+    paths = []
+    for file in configuration_files:
+        copy_file_path = Path.joinpath(base_directory, file)
+        file_path = Path.joinpath(configuration_directory, file)
+        paths.append(file_path)
+        if not os.path.exists(file_path):
+            shutil.copyfile(copy_file_path, file_path)
 
-    if not os.path.exists(waveform_constants_path):
-        copy_base_directory = Path(__file__).resolve().parent
-        copy_waveform_constants_path = Path.joinpath(
-            copy_base_directory, "waveform_constants.yml"
-        )
-        shutil.copyfile(copy_waveform_constants_path, waveform_constants_path)
-
-    if not os.path.exists(rest_api_path):
-        copy_base_directory = Path(__file__).resolve().parent
-        copy_rest_api_path = Path.joinpath(copy_base_directory, "rest_api_config.yml")
-        shutil.copyfile(copy_rest_api_path, rest_api_path)
-
-    if not os.path.exists(waveform_templates_path):
-        copy_base_directory = Path(__file__).resolve().parent
-        copy_waveform_templates_path = Path.joinpath(
-            copy_base_directory, "waveform_templates.yml"
-        )
-        shutil.copyfile(copy_waveform_templates_path, waveform_templates_path)
-
-    return (
-        configuration_path,
-        experiment_path,
-        waveform_constants_path,
-        rest_api_path,
-        waveform_templates_path,
-    )
+    return [path for path in paths]
 
 
 def load_configs(manager, **kwargs):
@@ -942,19 +915,21 @@ def verify_configuration(manager, configuration):
                 microscope_name_seq.append(microscope_name.strip())
             continue
 
-        if ")" not in microscope_name[parenthesis_l+1:]:
+        if ")" not in microscope_name[parenthesis_l + 1 :]:
             microscope_name_seq.append(microscope_name.strip())
             continue
 
-        parenthesis_r = microscope_name[parenthesis_l+1:].index(")")
-        parent_microscope_name = microscope_name[parenthesis_l+1: parenthesis_l+parenthesis_r+1].strip()
+        parenthesis_r = microscope_name[parenthesis_l + 1 :].index(")")
+        parent_microscope_name = microscope_name[
+            parenthesis_l + 1 : parenthesis_l + parenthesis_r + 1
+        ].strip()
 
         if parent_microscope_name not in microscope_name_seq:
             microscope_name_seq.append(parent_microscope_name)
-        
+
         idx = microscope_name_seq.index(parent_microscope_name)
         child_microscope_name = microscope_name[:parenthesis_l].strip()
-        microscope_name_seq.insert(idx+1, child_microscope_name)
+        microscope_name_seq.insert(idx + 1, child_microscope_name)
         inherited_microscope_dict[child_microscope_name] = parent_microscope_name
         device_config[child_microscope_name] = device_config.pop(microscope_name)
 
@@ -964,11 +939,16 @@ def verify_configuration(manager, configuration):
             continue
         parent_microscope_name = inherited_microscope_dict[microscope_name]
         if parent_microscope_name not in device_config.keys():
-            raise Exception(f"Microscope {parent_microscope_name} is not defined in configuration.yaml")
-        
+            raise Exception(
+                f"Microscope {parent_microscope_name} is not "
+                f"defined in configuration.yaml"
+            )
+
         for device_name in device_config[parent_microscope_name].keys():
             if device_name not in device_config[microscope_name].keys():
-                device_config[microscope_name][device_name] = device_config[parent_microscope_name][device_name]
+                device_config[microscope_name][device_name] = device_config[
+                    parent_microscope_name
+                ][device_name]
 
     channel_count = 5
     # generate hardware header section
@@ -980,16 +960,26 @@ def verify_configuration(manager, configuration):
         "zoom": None,
         "mirror": None,
     }
-    required_devices = ["camera", "daq", "filter_wheel", "shutter", "remote_focus_device", "galvo", "stage", "lasers"]
+    required_devices = [
+        "camera",
+        "daq",
+        "filter_wheel",
+        "shutter",
+        "remote_focus_device",
+        "galvo",
+        "stage",
+        "lasers",
+    ]
     for microscope_name in device_config.keys():
         # camera
         # delay_percent -> delay
         for device_name in required_devices:
             if device_name not in device_config[microscope_name]:
-                print("**************************************************************************")
-                print(f"*** Please make sure you have {device_name} in the configuration for microscope {microscope_name}.")
-                print(f"*** Or please makesure {microscope_name} is inherited from another valid microscope!")
-                print("**************************************************************************")
+                print(
+                    f"*** Please make sure you have {device_name} "
+                    f"in the configuration for microscope {microscope_name}, or "
+                    f"{microscope_name} is inherited from another valid microscope!"
+                )
                 raise Exception()
         camera_config = device_config[microscope_name]["camera"]
         if "delay" not in camera_config.keys():
@@ -1029,7 +1019,8 @@ def verify_configuration(manager, configuration):
         # zoom (one zoom)
         if "zoom" not in hardware_dict:
             zoom_config = device_config[microscope_name]["zoom"]["hardware"]
-            # zoom_idx = build_ref_name("-", zoom_config["type"], zoom_config["servo_id"])
+            # zoom_idx = build_ref_name("-", zoom_config["type"],
+            # zoom_config["servo_id"])
             hardware_dict["zoom"] = zoom_config
 
         # filter wheel
@@ -1094,7 +1085,9 @@ def verify_configuration(manager, configuration):
                     filter_wheel_config["hardware"]["type"],
                     filter_wheel_config["hardware"]["wheel_number"],
                 )
-                filter_wheel_ids.remove(ref_list["filter_wheel"].index(filter_wheel_idx))
+                filter_wheel_ids.remove(
+                    ref_list["filter_wheel"].index(filter_wheel_idx)
+                )
             for i in filter_wheel_ids:
                 temp_config.insert(i, filter_wheel_seq[i])
 

src/navigate/config/gui_configuration.yml

@@ -0,0 +1,48 @@
+channel_settings:
+  count: 5
+  laser_power:
+    step: 1
+    min: 0
+    max: 100
+  exposure_time:
+    step: 1
+    min: 1
+    max: 1000
+  interval:
+    step: 1
+    min: 1
+    max: 10
+  defocus:
+    step: 1
+    min: 0
+    max: 100
+stack_acquisition:
+  step_size:
+    step: 0.01
+    min: 0.01
+    max: 1000
+  z_start_pos:
+    step: 1.0
+    min: -10000
+    max: 10000
+  z_end_pos:
+    step: 1.0
+    min: -10000
+    max: 10000
+  f_start_pos:
+    step: 0.01
+    min: -200
+    max: 2000
+  f_end_pos:
+    step: 0.01
+    min: -200
+    max: 200
+time:
+  stack_pause:
+    step: 0.1
+    min: 0
+    max: 1000
+  timepoints:
+    step: 1
+    min: 1
+    max: 5000

src/navigate/controller/configuration_controller.py

@@ -251,9 +251,9 @@ def get_stage_position_limits(self, suffix):
 
         """
         axis = ["x", "y", "z", "theta", "f"]
+        position_limits = {}
         if self.microscope_config is not None:
             stage_dict = self.microscope_config["stage"]
-            position_limits = {}
             for a in axis:
                 position_limits[a] = stage_dict[a + suffix]
         else:
@@ -379,9 +379,7 @@ def number_of_channels(self):
             Number of channels.
         """
         if self.microscope_config is not None:
-            return self.configuration["configuration"]["gui"]["channels"].get(
-                "count", 5
-            )
+            return self.configuration["gui"]["channel_settings"].get("count", 5)
         return 5
 
     @property

src/navigate/controller/controller.py

@@ -105,6 +105,7 @@ def __init__(
         waveform_constants_path,
         rest_api_path,
         waveform_templates_path,
+        gui_configuration_path,
         args,
     ):
         """Initialize the Navigate Controller.
@@ -130,6 +131,9 @@ def __init__(
         waveform_templates_path : string
             Path to the waveform templates yaml file.
             Provides waveform templates for each channel.
+        gui_configuration_path : string
+            Path to the GUI configuration yaml file.
+            Provides GUI configuration parameters.
         *args :
             Command line input arguments for non-default
             file paths or using synthetic hardware modes.
@@ -152,6 +156,7 @@ def __init__(
             waveform_constants=waveform_constants_path,
             rest_api_config=rest_api_path,
             waveform_templates=waveform_templates_path,
+            gui=gui_configuration_path,
         )
 
         verify_configuration(self.manager, self.configuration)
@@ -192,33 +197,40 @@ def __init__(
         # Sub Gui Controllers
         #: AcquireBarController: Acquire Bar Sub-Controller.
         self.acquire_bar_controller = AcquireBarController(self.view.acqbar, self)
+
         #: ChannelsTabController: Channels Tab Sub-Controller.
         self.channels_tab_controller = ChannelsTabController(
             self.view.settings.channels_tab, self
         )
+
         #: MultiPositionController: Multi-Position Tab Sub-Controller.
         self.multiposition_tab_controller = MultiPositionController(
             self.view.settings.multiposition_tab.multipoint_list, self
         )
+
         #: CameraViewController: Camera View Tab Sub-Controller.
         self.camera_view_controller = CameraViewController(
             self.view.camera_waveform.camera_tab, self
         )
+
         #: CameraSettingController: Camera Settings Tab Sub-Controller.
         self.camera_setting_controller = CameraSettingController(
             self.view.settings.camera_settings_tab, self
         )
+
         #: StageController: Stage Sub-Controller.
         self.stage_controller = StageController(
             self.view.settings.stage_control_tab,
             self.view,
             self.camera_view_controller.canvas,
             self,
         )
+
         #: WaveformTabController: Waveform Display Sub-Controller.
         self.waveform_tab_controller = WaveformTabController(
             self.view.camera_waveform.waveform_tab, self
         )
+
         #: KeystrokeController: Keystroke Sub-Controller.
         self.keystroke_controller = KeystrokeController(self.view, self)