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Author: henrypinkard

micro-manager_setup.md

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+ # 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()
+```