Fix Configuration File Reading, Add Simulated Camera with Adjustable Parameters#2
Fix Configuration File Reading, Add Simulated Camera with Adjustable Parameters#2cccoolll wants to merge 866 commits intocephlainc:mainfrom
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Hi @cccoolll Thanks! A general comment, I would remove any thing related to the web and hypha for now (you can move it to other repo, e.g. the reef imaging repo). For now it would be good to keep this repo clean, only contain code about the basic microscope control. |
cccoolll
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cccoolll
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@oeway I've updated the pull request to include a new feature for the simulated camera. The current PR now covers configuration file reading, bug fixes, simulated camera implementation, and Docker configurations. I created a new branch for the simulated camera and then merged it into my fork's main branch. Is that OK? Is that OK, or should I have kept my main branch only for stable changes? |
| parser = argparse.ArgumentParser() | ||
| parser.add_argument( | ||
| "--simulation", help="Run the GUI with simulated hardware.", action="store_true" | ||
| "--nosimulation", help="Run the GUI with simulated hardware.", action="store_true" |
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Why change to nosimulation? The default mode should not be simulation IMO
| STEPS_PER_REVOLUTION = 200 * 8 # Full steps per revolution times microstepping factor | ||
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| # Edge positions in mm | ||
| edge_positions_mm = [ |
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These should not be hardcoded, can we put them in a file which generated during a calibration process?
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This is a very old file. The current version of 'mm_to_usteps' is here: https://github.com/cccoolll/squid-control/blob/156f9e188df9007d5fd3d7ea42004a3bfdffbf4b/squid_control/control/utils/generate_software_limit.py#L19
So we should remove this file.
| # Ensure the .squid-control directory exists | ||
| config_dir.mkdir(exist_ok=True) | ||
| config_dir = os.path.abspath(__file__) | ||
| config_dir = Path(config_dir) |
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I would merge the two lines into one, and why removing config_dir.mkdir(exist_ok=True)?
| #.idea/ | ||
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| cache_config_file_path.txt | ||
| configuration_HCS_v2.ini |
| FROM python:3.9-slim | ||
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| # Set the working directory in the container | ||
| WORKDIR /home/tao/workspace/reef-imaging/reef_imaging/control/squid_microscope/squid-control |
| import squid_control.control.gui_hcs as gui | ||
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| from configparser import ConfigParser | ||
| from configparser import ConfigParsers |
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This should be ConfigParsers
| from configparser import ConfigParsers | |
| from configparser import ConfigParser |
| self.current_frame[901:1100, 901:1100] = 200 * 256 | ||
| blur_intensity = 6 | ||
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Remove empty lines, keep 1 empty line
…creation, listing, removal, and setting active filesets
…ding creation, listing, activation, and removal of filesets.
…ve organization and clarity in Hypha service.
…ealth checks only proceed after initialization.
…n-GoogleMap-style Feature/video stream in google map style
…deo-stream-in-GoogleMap-style Revert "Feature/video stream in google map style"
…rvice health checks and initialization process.
…ove error handling and streamline initialization process.
…to 0.20.65 for improved functionality and compatibility.
…rr folders on startup
…ng and improving ZIP path handling.
…ds. Disable Zarr directory cleanup on startup for backward compatibility.
…er. Implement ZIP file validation and integrity checks in artifact management to ensure reliable uploads. Introduce ZIP64 support for large archives in ZarrCanvas export functionality.
update branch
…ate a .done file after processing
…quid-control into offline-stitching-uploading
…loading Offline stitching uploading
Update simulated sample
…port and during error handling
Update simulated sample
2 participants
Changes
Configuration File Reading
Simulated Camera Implementation
Docker Configurations
Dockerfileanddocker-compose.yamlto simplify deployment and setup for development and testing environments.