Fix Configuration File Reading, Add Simulated Camera with Adjustable Parameters #2

cccoolll · 2024-07-26T09:01:09Z

Changes

Configuration File Reading

Bug Fixes:
- Resolved issues with configuration file reading.

Simulated Camera Implementation

Features Added:
- Implemented functionality to read images from different illumination channels captured previously, and to return a random image if no specific channel image is available.
- Introduced the simulated camera with capabilities for movement, focus, illumination, and exposure time adjustment.

Docker Configurations

New Additions:
- Added Dockerfile and docker-compose.yaml to simplify deployment and setup for development and testing environments.

oeway · 2024-07-26T09:41:34Z

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 · 2024-08-06T10:20:49Z

@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?

oeway · 2024-08-07T06:48:15Z

scripts/main_hcs.py

 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"


Why change to nosimulation? The default mode should not be simulation IMO

oeway · 2024-08-07T06:49:36Z

scripts/tools/convert_limit_mm_to_usteps.py

+STEPS_PER_REVOLUTION = 200 * 8  # Full steps per revolution times microstepping factor
+
+# Edge positions in mm
+edge_positions_mm = [


These should not be hardcoded, can we put them in a file which generated during a calibration process?

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.

oeway · 2024-08-07T06:51:36Z

squid_control/control/config.py

-    # Ensure the .squid-control directory exists
-    config_dir.mkdir(exist_ok=True)
+    config_dir = os.path.abspath(__file__)
+    config_dir = Path(config_dir)


I would merge the two lines into one, and why removing config_dir.mkdir(exist_ok=True)?

oeway · 2024-08-20T15:30:24Z

.gitignore

 #.idea/

+cache_config_file_path.txt
+configuration_HCS_v2.ini


Why this is added?

oeway · 2024-08-20T15:31:04Z

Dockerfile

+FROM python:3.9-slim
+
+# Set the working directory in the container
+WORKDIR /home/tao/workspace/reef-imaging/reef_imaging/control/squid_microscope/squid-control


Why add tao in the path?

oeway · 2024-08-20T15:43:17Z

scripts/main_hcs.py

 import squid_control.control.gui_hcs as gui

-from configparser import ConfigParser
+from configparser import ConfigParsers


This should be ConfigParsers

Suggested change

from configparser import ConfigParsers

from configparser import ConfigParser

oeway · 2024-08-20T15:44:55Z

scripts/tools/hypha_storage.py

I would remove this file

oeway · 2024-08-20T15:45:57Z

squid_control/.gitignore

This should be removed

oeway · 2024-08-20T15:46:44Z

squid_control/control/camera/camera_default.py

-                self.current_frame[901:1100, 901:1100] = 200 * 256
+        blur_intensity = 6
+
+


Remove empty lines, keep 1 empty line

Update main_hcs.py

…creation, listing, removal, and setting active filesets

…ding creation, listing, activation, and removal of filesets.

…ve organization and clarity in Hypha service.

…ntroller.py`

…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

cccoolll changed the title ~~Fix Configuration File Reading, Add Docker Integration~~ Fix Configuration File Reading, add simulated camera with movement, focus, illumination and exposure time adjustment. Aug 6, 2024

cccoolll changed the title ~~Fix Configuration File Reading, add simulated camera with movement, focus, illumination and exposure time adjustment.~~ Fix Configuration File Reading, Add Simulated Camera with Adjustable Parameters Aug 6, 2024

oeway reviewed Aug 7, 2024

View reviewed changes

oeway reviewed Aug 20, 2024

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.gitignore

#.idea/

cache_config_file_path.txt

configuration_HCS_v2.ini

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Why this is added?

oeway reviewed Aug 20, 2024

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scripts/tools/hypha_storage.py Outdated

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I would remove this file

oeway reviewed Aug 20, 2024

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squid_control/.gitignore

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This should be removed

oeway reviewed Aug 20, 2024

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cccoolll referenced this pull request in aicell-lab/squid-control Dec 7, 2024

Merge pull request #2 from cccoolll/chatbot-control

b3a6e4d

Update main_hcs.py

cccoolll force-pushed the main branch from a9634d0 to 47e414a Compare March 17, 2025 10:27

cccoolll and others added 15 commits July 9, 2025 14:34

Add Zarr fileset management functions to Microscope class, including …

3f201e8

…creation, listing, removal, and setting active filesets

Implement Zarr fileset management functions in SquidController, inclu…

52406e1

…ding creation, listing, activation, and removal of filesets.

Refactor server attribute initialization in Microscope class to impro…

bc1b0b8

…ve organization and clarity in Hypha service.

Add comprehensive tests for Zarr fileset management in `test_squid_co…

af9c8e3

…ntroller.py`

Add setup completion tracking in Microscope class to ensure service h…

ecbdacb

…ealth checks only proceed after initialization.

Merge pull request aicell-lab#51 from cccoolll/feature/video-stream-i…

f51507b

…n-GoogleMap-style Feature/video stream in google map style

Revert "Feature/video stream in google map style"

644edd9

Merge pull request aicell-lab#52 from aicell-lab/revert-51-feature/vi…

d31933d

…deo-stream-in-GoogleMap-style Revert "Feature/video stream in google map style"

Remove setup completion tracking from Microscope class to simplify se…

45d70d0

…rvice health checks and initialization process.

Refactor chatbot service connection logic in Microscope class to impr…

93ecbe6

…ove error handling and streamline initialization process.

Update hypha-rpc dependency version in requirements.txt from 0.20.55 …

7b7fce9

…to 0.20.65 for improved functionality and compatibility.

Refactor Zarr directory cleanup in SquidController to only remove .za…

e39175d

…rr folders on startup

Enhance Zarr export functionality by implementing background processi…

cf9ccf6

…ng and improving ZIP path handling.

Update documentation for ZIP path manipulation and compliance standar…

27219e0

…ds. Disable Zarr directory cleanup on startup for backward compatibility.

Enhance Zarr canvas initialization and loading logic in SquidControll…

b4ac192

…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.

cccoolll and others added 30 commits September 8, 2025 15:21

fix logging setup

a45579f

reduce memory usage

148fa89

fix memeory management

1ea1897

fix docker command

9c27a60

service public in simulation mode

c2c3755

Merge pull request aicell-lab#65 from aicell-lab/main

5c189f9

update branch

Add functionality to skip processing if a .done file is found and cre…

a56c47b

…ate a .done file after processing

Merge branch 'offline-stitching-uploading' of github.com:aicell-lab/s…

d7e7c21

…quid-control into offline-stitching-uploading

add cleanup functionality

7f0ff2e

remove unused script

9de1090

rename file

ebd6636

update test for offline processing

29e741d

New virtual sample source

32b7512

fix chunk loading

a869036

fix drift correction logic

423f46d

timestamp extraction and dataset naming in OfflineProcessor

0d53dde

Time stamp format: YYYYMMDD-HHMMSS

12606f0

Merge pull request aicell-lab#64 from aicell-lab/offline-stitching-up…

67040fc

…loading Offline stitching uploading

Merge pull request aicell-lab#66 from aicell-lab/update-simulated-sample

5df0140

Update simulated sample

fix zattrs file write

fa64419

fix channel activate for zattrs file

ec79c5e

cleanup .done file after upload

8199fa7

Implement cleanup of partial Zarr files in OfflineProcessor before ex…

d45791d

…port and during error handling

set ping interval

b46438f

update simulated sample id

f193eb0

add logging for image stitching

3ff9d32

add OME-Zarr metadata when calling info Hyhpa tools

afb21e7

clean up directories for pytest

3df19aa

Merge pull request aicell-lab#67 from aicell-lab/update-simulated-sample

793e7e5

Update simulated sample

Update well canvas stitching

17122be

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Fix Configuration File Reading, Add Simulated Camera with Adjustable Parameters #2

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	from configparser import ConfigParsers
	from configparser import ConfigParser

		self.current_frame[901:1100, 901:1100] = 200 * 256
		blur_intensity = 6

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Changes

Configuration File Reading

Simulated Camera Implementation

Docker Configurations

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oeway commented Jul 26, 2024

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cccoolll commented Jul 26, 2024 •

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