110 lines
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3.5 KiB
ReStructuredText
110 lines
No EOL
3.5 KiB
ReStructuredText
Microscope configuration
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========================
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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.. _MicroscopeRC:
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Microscope RC file
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------------------
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Microscope configuration is made persistent via a microscope runtime-config (RC) file. By default, this
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file exists at ``~/.openflexure/microscope_settings.yaml``, and contains basic parameters to set up the microscope.
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Additionally, by default, configurations for specific pieces of hardware (i.e. the Pi camera) are located
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in separate "auxillary" config files, and are linked together by adding the config file's path to your main
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microscope RC file. This is set up by default, as shown below:
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Default microscope_settings.yaml
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++++++++++++++++++++++++++++++++
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.. code-block:: yaml
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# Resolutions for streaming and capture
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stream_resolution: [832, 624]
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image_resolution: [2592, 1944]
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numpy_resolution: [1312, 976]
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# Field of view, in stage steps
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fov: [4100, 3146]
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# Capture quality
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jpeg_quality: 75
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# Parameters specific to PiCamera objects
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picamera_settings: ~/.openflexure/picamera_settings.yaml
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# Default plugins
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plugins:
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- openflexure_microscope.plugins.default.autofocus:AutofocusPlugin
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- openflexure_microscope.plugins.default.camera_calibration:Plugin
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Example picamera_settings.yaml
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++++++++++++++++++++++++++++++
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.. code-block:: yaml
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analog_gain: !!python/object/apply:fractions.Fraction ['1']
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awb_gains: !!python/tuple
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- !!python/object/apply:fractions.Fraction [221/256]
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- !!python/object/apply:fractions.Fraction [709/256]
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awb_mode: auto
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digital_gain: !!python/object/apply:fractions.Fraction [585/256]
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exposure_mode: auto
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framerate: !!python/object/apply:picamera.mmalobj.PiCameraFraction ['30']
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lens_shading_table: ...
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saturation: 0
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shutter_speed: 0
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Loading the runtime-config
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++++++++++++++++++++++++++
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By default, a microscope object will load the a runtime-config from the default location.
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This RC can then be passed to any hardware attached to the microscope. This can be particularly
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useful when creating a dummy microscope object before attaching hardware. For example:
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.. code-block:: python
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from openflexure_microscope import Microscope
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from openflexure_microscope.camera.pi import StreamingCamera
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from openflexure_stage import OpenFlexureStage
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# Create an empty microscope
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api_microscope = Microscope(None, None)
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# Create a picamera StreamingCamera, using our config
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camera_obj = StreamingCamera(config=api_microscope.rc.read())
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# Create an OpenFlexure Stage attached to /dev/ttyUSB0
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stage_obj = OpenFlexureStage("/dev/ttyUSB0")
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# Attach devices to the Microscope object
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api_microscope.attach(camera_obj, stage_obj)
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Alternatively, a config can be loaded prior to creating a microscope, allowing the microscope
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hardware to be created and attached in a single line. For example:
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.. code-block:: python
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from openflexure_microscope.config import OpenflexureConfig
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from openflexure_microscope import Microscope
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from openflexure_microscope.camera.pi import StreamingCamera
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from openflexure_stage import OpenFlexureStage
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# Create a runtime-config from the default location
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rc = OpenflexureConfig(expand=True)
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# Create a populated microscope
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api_microscope = Microscope(
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StreamingCamera(config=rc),
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OpenFlexureStage("/dev/ttyUSB0"),
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config=rc
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)
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Config module and OpenflexureConfig class
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-----------------------------------------
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.. automodule:: openflexure_microscope.config
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:members: |