LF only acquisition with actual Mantis hardware. #191
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This reverts commit 1748131.
…ting when copying the events
…ccess Oryx camera using mmc.getCameraDevice() instead of hard-coded string
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Pull Request Overview
This PR extends the acquisition CLI and engine to support label-free (LF) only operation on real Mantis hardware, adds a separate LF config option, and updates defaults and examples accordingly.
- Added
--lf-config-filepathCLI option and switched default config to LF. - Updated
MantisAcquisition/BaseChannelSliceAcquisitionto allow LF-only or LS-only runs and pass both config files. - Refactored image dimension retrieval, camera property lookups, and example YAML/config files to reflect LF defaults.
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| mantis/cli/run_acquisition.py | Introduced --lf-config-filepath, changed default config path |
| mantis/acquisition/acq_engine.py | Made acquisition types optional, dynamic image size, threading |
| examples/acquisition_settings/*.yaml | Tweaked defaults for time, exposures, autofocus, and autoexposure |
| examples/microscope_configs/*.cfg | Added new example Mantis LF hardware config files |
Comments suppressed due to low confidence (1)
mantis/cli/run_acquisition.py:12
- The variable
default_mm_config_filepathnow points to the LF config but is still named for a generic MM config. Rename this todefault_lf_config_filepath, and introduce a separatedefault_ls_config_filepathfor the light-sheet default.
default_mm_config_filepath = 'C:\\CompMicro_MMConfigs\\mantis\\mantis-LF.cfg'
| ) | ||
| @click.option( | ||
| "--lf-config-filepath", | ||
| default=default_mm_config_filepath, |
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Both --mm-config-filepath and --lf-config-filepath use the same default. After splitting into default_ls_config_filepath and default_lf_config_filepath, ensure --mm-config-filepath uses the LS default and --lf-config-filepath uses the LF default.
| default=default_mm_config_filepath, | |
| default=default_lf_config_filepath, |
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This is known, I wanted to add the ability to set the LF config without breaking any existing acquisition that used the previous config path. There's probably a better way to do it.
|
Due to difficulties I'm having pushing from the mantis microscope to this repo, I've forked the repo and will open another PR from there. |
2 participants
Addresses: #179 (partial) & #184