Merge pull request micro-manager#9 from henrypinkard/main

Add MM example and improve packaging

.github/workflows/run-tests.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -e .[test]
+        pip install -e ".[test, all]"
 
     - name: Test with pytest
       run: |

micro-manager_setup.md

@@ -0,0 +1,83 @@
+ # Setup and examples for using the ExEngine with a micro-manager backend
+
+ - clone the repository
+ - install it, specifying which device and data storage backends
+ 	`pip install -e ".[micromanager, ndstorage]"`
+ - install Micro-Manager
+
+```python
+from mmpycorex import download_and_install_mm 
+download_and_install_mm()
+```
+
+
+## Running the ExEngine
+
+```python
+from mmpycorex import create_core_instance, download_and_install_mm, terminate_core_instances
+from exengine.kernel.executor import ExecutionEngine
+from exengine.kernel.data_coords import DataCoordinates
+from exengine.kernel.ex_event_base import DataHandler
+from exengine.backends.micromanager.mm_device_implementations import MicroManagerCamera, MicroManagerSingleAxisStage
+from exengine.storage_backends.NDTiffandRAM import NDRAMStorage
+from exengine.events.detector_events import StartCapture, ReadoutData
+
+
+# Start Micro-Manager core instance with Demo config
+create_core_instance()
+
+executor = ExecutionEngine()
+
+
+# get access to the micro-manager devices
+camera = MicroManagerCamera()
+z_stage = MicroManagerSingleAxisStage()
+
+```
+
+
+### Example 1: Use the exengine to acquire a timelapse
+
+```python
+# Capture 100 images on the camera
+num_images = 100
+data_handler = DataHandler(storage=NDRAMStorage())
+
+start_capture_event = StartCapture(num_images=num_images, detector=camera)
+readout_images_event = ReadoutData(num_images=num_images, detector=camera,
+                                   data_coordinates_iterator=[DataCoordinates(time=t) for t in range(num_images)],
+                                   data_handler=data_handler)
+
+_ = executor.submit(start_capture_event)
+future = executor.submit(readout_images_event)
+
+# block until all images have been read out
+future.await_execution()
+
+# Tell the data handler no more images are expected
+data_handler.finish()
+
+```
+
+### Example 2: create series of events with multi-d function
+```python
+from exengine.events.multi_d_events import multi_d_acquisition_events
+
+data_handler = DataHandler(storage=NDRAMStorage())
+events = multi_d_acquisition_events(z_start=0, z_end=10, z_step=2)
+
+futures = executor.submit(events)
+# wait until the final event finished
+futures[-1].await_execution()
+
+# Tell the data handler no more images are expected
+data_handler.finish()
+```
+
+
+```python
+# shutdown the engine
+executor.shutdown()
+# shutdown micro-manager
+terminate_core_instances()
+```

pyproject.toml

@@ -11,16 +11,27 @@ classifiers = [
     "Operating System :: OS Independent"
     ]
 dependencies = [
-"mmpycorex",
-"ndstorage",
 "pydantic"
 ]
+
 dynamic = ["version"]
 description = "Microscopy execution engine with support for multiple hardware backends"
 readme = "README.md"
 
 [project.optional-dependencies]
-test = ["pytest"]  # New test dependencies group
+test = ["pytest"]  
+
+# all backends
+all = [
+    "mmpycorex",
+    "ndstorage"
+    ]
+
+# device backends
+micromanager = ["mmpycorex"]
+
+# storage backends
+ndstorage = ["ndstorage"]
 
 
 [project.urls]

src/exengine/examples/micromanager_example.py

@@ -23,9 +23,9 @@
 num_images = 100
 data_handler = DataHandler(storage=NDRAMStorage())
 
-start_capture_event = StartCapture(num_images=num_images, camera=camera)
-readout_images_event = ReadoutData(num_images=num_images, camera=camera,
-                                   data_coordinate_iterator=[DataCoordinates(time=t) for t in range(num_images)],
+start_capture_event = StartCapture(num_images=num_images, detector=camera)
+readout_images_event = ReadoutData(num_images=num_images, detector=camera,
+                                   data_coordinates_iterator=[DataCoordinates(time=t) for t in range(num_images)],
                                    data_handler=data_handler)
 executor.submit(start_capture_event)
 future = executor.submit(readout_images_event)
@@ -35,6 +35,8 @@
 
 data_handler.finish()
 
+
+
 executor.shutdown()
 terminate_core_instances()