Merge pull request #3 from acquire-project/dgmccart-patch-2

Create getting_started.md

getting_started.md

@@ -0,0 +1,244 @@
+# Getting Started with Acquire
+
+Acquire (`acquire-imaging` [on PyPI](https://pypi.org/project/acquire-imaging/)) is a Python package providing a multi-camera video streaming library focused on performant microscopy, with support for up to two simultaneous, independent, video streams.
+
+This tutorial covers Acquire installation and shows an example of using Acquire with its provided simulated cameras to demonstrate the acquisition process. 
+
+## Installation
+
+To install Acquire on Windows, macOS, or Ubuntu, simply run the following command:
+
+```
+python -m pip install acquire-imaging
+```
+
+You will probably want to have a fresh conda environment or virtualenv.
+For example, with conda:
+
+```
+conda create -n acquire python=3.10 # follow the prompts and proceed with the defaults
+conda activate acquire
+python -m pip install acquire-imaging
+```
+
+or with virtualenv:
+
+```shell
+$ python -m venv venv
+$ . ./venv/bin/activate # or on Windows: .\venv\Scripts\Activate.bat or .\venv\Scripts\Activate.ps1
+(venv) $ python -m pip install acquire-imaging
+```
+
+Once you have Acquire installed, simply call `import acquire` in your script, notebook, or module to start utilizing the package.
+
+```python
+import acquire
+```
+
+## Supported Cameras and File Formats
+
+Acquire supports the following cameras (currently only on Windows):
+
+- [Hamamatsu Orca Fusion BT (C15440-20UP)](https://www.hamamatsu.com/eu/en/product/cameras/cmos-cameras/C15440-20UP.html)
+- [Vieworks VC-151MX-M6H00](https://www.visionsystech.com/products/cameras/vieworks-vc-151mx-sony-imx411-sensor-ultra-high-resolution-cmos-camera-151-mp)
+- [FLIR Blackfly USB3 (BFLY-U3-23S6M-C)](https://www.flir.com/products/blackfly-usb3/?model=BFLY-U3-23S6M-C&vertical=machine+vision&segment=iis)
+- [FLIR Oryx 10GigE (ORX-10GS-51S5M-C)](https://www.flir.com/products/oryx-10gige/?model=ORX-10GS-51S5M-C&vertical=machine+vision&segment=iis)
+
+Acquire also supports the following output file formats:
+
+- [Tiff](https://en.wikipedia.org/wiki/TIFF)
+- [Zarr](https://zarr.dev/)
+
+For testing and demonstration purposes, Acquire provides a few simulated cameras, as well as raw and trash output devices.
+To see all the devices that Acquire supports, you can run the following script:
+
+```python
+import acquire
+
+for device in acquire.Runtime().device_manager().devices():
+    print(device)
+```
+
+## Tutorial Prerequisites
+
+We will be writing to and reading from the [Zarr format](https://zarr.readthedocs.io/en/stable/), using the [Dask library](https://www.dask.org/) to load and inspect the data, and visualizing the data using [napari](https://napari.org/stable/).
+
+You can install these prerequisites with:
+
+```
+python -m pip install dask "napari[all]" zarr
+```
+
+## Setup for Acquisition
+
+We will use one of Acquire's simulated cameras to generate data for us and use Zarr for our output file format.
+
+Let's set up our runtime and device manager, then list the currently supported devices.
+
+```python
+import acquire
+
+runtime = acquire.Runtime()
+dm = runtime.device_manager()
+
+for device in dm.devices():
+    print(device)
+```
+The **runtime** is the main entry point in Acquire.
+Through the runtime, you configure your devices, start acquisition, check acquisition status, inspect data as it streams from your cameras, and terminate acquisition.
+
+Let's configure our devices now.
+To do this, we'll get a copy of the current runtime configuration.
+We can update the configuration with identifiers from the the runtime's **device manager**, but we won't actually instantiate these devices until we start acquiring.
+
+Acquire supports up to two video streams.
+These streams consist of a **source** (i.e., a camera), optionally a **filter**, and a **sink** (an output, like a Zarr dataset or a Tiff file).
+Before configuring the streams, grab the current configuration of the `Runtime` object with:
+
+```python
+config = runtime.get_configuration()
+```
+
+Video streams are configured independently. Configure the first video stream by setting properties on `config.video[0]` and the second video stream with `config.video[1]`. We'll be using simulated cameras, one generating a radial sine pattern and one generating a random pattern.
+
+```python
+config.video[0].camera.identifier = dm.select(acquire.DeviceKind.Camera, "simulated: radial sin")
+
+# how many adjacent pixels in each direction to combine by averaging; here, 1 means not to combine
+config.video[0].camera.settings.binning = 1
+
+# how long (in microseconds) your camera should collect light from the sample; for simulated cameras,
+# this is just a waiting period before generating the next frame
+config.video[0].camera.settings.exposure_time_us = 5e4  # 50 ms
+
+# the data type representing each pixel; here we choose unsigned 8-bit integer
+config.video[0].camera.settings.pixel_type = acquire.SampleType.U8
+
+# the shape, in pixels, of the image; width first, then height
+config.video[0].camera.settings.shape = (1024, 768)
+```
+
+
+```python
+config.video[1].camera.identifier = dm.select(acquire.DeviceKind.Camera, "simulated: uniform random")
+
+# how many adjacent pixels in each direction to combine by averaging; here, 1 means not to combine
+config.video[1].camera.settings.binning = 1
+
+# how long (in microseconds) your camera should collect light from the sample; for simulated cameras,
+# this is just a waiting period before generating the next frame
+config.video[1].camera.settings.exposure_time_us = 1e4  # 10 ms
+
+# the data type representing each pixel; here we choose unsigned 8-bit integer
+config.video[1].camera.settings.pixel_type = acquire.SampleType.U8
+
+# the shape, in pixels, of the image; width first, then height
+config.video[1].camera.settings.shape = (1280, 720)
+```
+
+Now we'll configure each output, or sink device.
+For both simulated cameras, we'll be writing to Zarr, a format which supports chunked arrays.
+
+
+```python
+config.video[0].storage.identifier = dm.select(acquire.DeviceKind.Storage, "Zarr")
+
+# what file or directory to write the data to
+config.video[0].storage.settings.filename = "output1.zarr"
+
+# where applicable, how large should a chunk file get before opening the next chunk file
+config.video[0].storage.settings.chunking.max_bytes_per_chunk = 32 * 2**20  # 32 MiB chunk sizes
+```
+
+
+```python
+config.video[1].storage.identifier = dm.select(acquire.DeviceKind.Storage, "Zarr")
+
+# what file or directory to write the data to
+config.video[1].storage.settings.filename = "output2.zarr"
+
+# where applicable, how large should a chunk file get before opening the next chunk file
+config.video[1].storage.settings.chunking.max_bytes_per_chunk = 64 * 2**20  # 64 MiB chunk sizes
+```
+
+Finally, let's specify how many frames to generate for each camera before stopping our simulated acquisition.
+We also need to register our configuration with the runtime.
+
+If you want to let the runtime just keep acquiring effectively forever, you can set `max_frame_count` to `2**64 - 1`.
+
+```python
+config.video[0].max_frame_count = 100 # collect 100 frames
+config.video[1].max_frame_count = 150 # collect 150 frames
+
+config = runtime.set_configuration(config)
+```
+
+---
+**NOTE**
+
+If you run this tutorial multiple times, you can clear output from previous runs with:
+
+```python
+import os
+import shutil
+
+if config.video[0].storage.settings.filename in os.listdir("."):
+    shutil.rmtree(config.video[0].storage.settings.filename)
+
+if config.video[1].storage.settings.filename in os.listdir("."):
+    shutil.rmtree(config.video[1].storage.settings.filename)
+```
+---
+## Acquire Data
+
+To start aquiring data:
+
+```python
+runtime.start()
+```
+
+Acquisition happens in a separate thread, so at any point we can check on the status by calling `runtime.get_state()`.
+
+
+```python
+runtime.get_state()
+```
+
+Finally, once we're done acquiring, we call `runtime.stop()`.
+This method will wait until you've reached the number of frames specified in `config.video[0].max_frame_count` or `config.video[1].max_frame_count`, whichever is larger.
+
+```python
+runtime.stop()
+```
+
+## Visualizing the Data with napari
+
+Let's take a look at what we've written.
+We'll load each Zarr dataset as a Dask array and inspect its dimensions, then we'll use napari to view it.
+
+```python
+import dask.array as da
+import napari
+```
+
+```python
+data1 = da.from_zarr(config.video[0].storage.settings.filename, component="0")
+data1
+```
+
+```python
+data2 = da.from_zarr(config.video[1].storage.settings.filename, component="0")
+data2
+```
+
+```python
+viewer1 = napari.view_image(data1)
+```
+
+```python
+viewer2 = napari.view_image(data2)
+```
+
+## Conclusion
+
+For more examples of using Acquire, check out our [tutorials page](). #ADD LINK