Merge pull request #1 from Gronemeyer: pymmcore-device-objects

Hardware.yaml, refined ExperimentConfig, refactored imports, click->argparse CLI, flattened file structure, arducam support, streamlined file_path generation for saving data

dev.yaml

@@ -0,0 +1,31 @@
+memory_buffer_size: 10000
+viewer_type: "static"
+
+encoder:
+  type: "wheel"
+  port: "COM4"
+  baudrate: 57600
+  cpr: 2400
+  diameter_mm: 80
+  sample_interval_ms: 20
+  development_mode: False
+
+cameras:
+  - id: "dev"
+    name: "devcam1"
+    backend: "micromanager"
+    micromanager_path: "C:/Program Files/Micro-Manager-2.0"
+
+
+  - id: "dev"
+    name: "devcam2"
+    backend: "micromanager"
+    micromanager_path: "C:/Program Files/Micro-Manager-thor"
+
+
+
+  # - id: "arducam"
+  #   name: "arducam"
+  #   backend: "opencv"
+  #   properties:
+  #     fps: 30

hardware.yaml

@@ -0,0 +1,47 @@
+memory_buffer_size: 10000
+viewer_type: "static"
+
+encoder:
+  type: "wheel"
+  port: "COM4"
+  baudrate: 57600
+  cpr: 2400
+  diameter_mm: 80
+  sample_interval_ms: 20
+  development_mode: False
+
+cameras:
+  - id: "Dhyana"
+    name: "mesoscope"
+    backend: "micromanager"
+    micromanager_path: "C:/Program Files/Micro-Manager-2.0"
+    configuration_path: "C:/Program Files/Micro-Manager-2.0/mm-sipefield.cfg"
+    properties:
+      Dhyana:
+        Output Trigger Port: 2
+        Gain: "HDR"
+        fps: 49 # IMPORTANT: This is validated externally and is a value used merely to calculate experiment duration and frames to capture
+      Arduino-Shutter: 
+        OnOff: "1"
+      Arduino-Switch: 
+        Sequence: "On"
+      Core:
+        Shutter: "Arduino-Shutter"
+
+  - id: "ThorCam"
+    name: "pupil"
+    backend: "micromanager"
+    micromanager_path: "C:/Program Files/Micro-Manager-thor"
+    configuration_path: "C:/Program Files/Micro-Manager-2.0/ThorCam.cfg"
+    properties:
+      ThorCam:
+        Exposure: 20
+        fps: 30 # IMPORTANT: This is validated externally and is a value used merely to calculate experiment duration and frames to capture
+        ROI: [440, 305, 509, 509]
+
+
+  # - id: "arducam"
+  #   name: "arducam"
+  #   backend: "opencv"
+  #   properties:
+  #     fps: 30

mesofield/__main__.py

@@ -1,84 +1,83 @@
-"""Entry point for mesofield."""
+"""CLI Interface entry point for mesofield python package"""
 
 import os
-# os.environ['NUMEXPR_MAX_THREADS'] = '4'
-# os.environ['NUMEXPR_NUM_THREADS'] = '2'
-# import numexpr as ne 
+import logging
+import argparse
 
-import click
 from PyQt6.QtWidgets import QApplication
+
 from mesofield.gui.maingui import MainWindow
 from mesofield.config import ExperimentConfig
-from mesofield.startup import Startup
-'''
-This is the client terminal command line interface
-
-The client terminal commands are:
-
-    launch: Launch the mesofield acquisition interface
-        - dev: Set to True to launch in development mode with simulated MMCores
-    test_mda: Test the mesofield acquisition interface
-
-'''
-
-
-@click.group()
-def cli():
-    """mesofields Command Line Interface"""
-    pass
-
-@cli.command()
-@click.option('--dev', default=False, help='launch in development mode with simulated MMCores.')
-@click.option('--params', default='params.json', help='Path to the config JSON file.')
-def launch(dev, params):
-    """ Launch mesofield acquisition interface.
-    
-    This function initializes and launches the mesofield acquisition application. 
-    
-    It sets up the necessary hardware and configuration based on
-    the provided parameters.
-    
-    Parameters:
-    `dev (str)`: The device identifier to be used for the acquisition.
-    `params (str)`: The path to the configuration file. Default is the params.json file in the current directory.
-    
-    """
-
+
+# Disable pymmcore-plus logger
+package_logger = logging.getLogger('pymmcore-plus')
+
+# Set the logging level to CRITICAL to suppress lower-level logs
+package_logger.setLevel(logging.CRITICAL)
+
+# Disable debugger warning about the use of frozen modules
+os.environ["PYDEVD_DISABLE_FILE_VALIDATION"] = "1"
+
+
+
+def launch(params):
+    """Launch the mesofield acquisition interface."""
     print('Launching mesofield acquisition interface...')
     app = QApplication([])
-    config_path = params
-    config = ExperimentConfig(config_path, dev)
-    config.hardware.initialize_cores(config)
+    config = ExperimentConfig(params)
+    config.hardware.configure_engines(config)
+    print(config.hardware.cameras[0])
     mesofield = MainWindow(config)
     mesofield.show()
-    app.exec_()
+    app.exec()
 
-@cli.command()
 def controller():
     """Launch the mesofield controller."""
-    from mesofield.controller import Controller
+    from mesofield.gui.controller import Controller
     app = QApplication([])
-    controller = Controller()
-    controller.show()
-    app.exec_()
+    c = Controller()
+    c.show()
+    app.exec()
 
-@cli.command()
-@click.option('--frames', default=100, help='Number of frames for the MDA test.')
 def test_mda(frames):
-    """
-    Run a test of the mesofield Multi-Dimensional Acquisition (MDA) 
-    """
+    """Run a test of the mesofield Multi-Dimensional Acquisition (MDA)."""
     from mesofield.startup import test_mda
 
-@cli.command()
-def run_mda():
+def run_mda_command():
     """Run the Multi-Dimensional Acquisition (MDA) without the GUI."""
-    run_mda()
-
-
-if __name__ == "__main__":  # pragma: no cover
-    cli()
-
-
-
 
+def main():
+    parser = argparse.ArgumentParser(description="mesofields Command Line Interface")
+    subparsers = parser.add_subparsers(dest='command', help='Available subcommands')
+
+    # Subcommand: launch
+    parser_launch = subparsers.add_parser('launch', help='Launch the mesofield acquisition interface')
+    parser_launch.add_argument('--params', default='dev.yaml',
+                               help='Path to the config file')
+
+    # Subcommand: controller
+    parser_controller = subparsers.add_parser('controller', help='Launch the mesofield controller')
+
+    # Subcommand: test_mda
+    parser_test_mda = subparsers.add_parser('test_mda', help='Run a test MDA')
+    parser_test_mda.add_argument('--frames', type=int, default=100,
+                                 help='Number of frames for the MDA test')
+
+    # Subcommand: run_mda
+    subparsers.add_parser('run_mda', help='Run MDA without the GUI')
+
+    args = parser.parse_args()
+
+    if args.command == 'launch':
+        launch(args.params)
+    elif args.command == 'controller':
+        controller()
+    elif args.command == 'test_mda':
+        test_mda(args.frames)
+    elif args.command == 'run_mda':
+        run_mda_command()
+    else:
+        parser.print_help()
+
+if __name__ == "__main__":
+    main()