Author - Liam McKay (adapted from scripts from Justin Biel)
For local use with hitsDB web application.
Stand-alone drop-image overlay and analysis tool for Formulatrix RockImager 1000 machine plate well images.
Uses OpenCV, Numpy, Pandas
- Make a virtual environment
pip3 install -r requirements.txt
When using -convex or -circle do not expect every image to be overlayed with a convex or circle drop image.
If it is not possible/reasonable to overlay a circle or convex shape, it will overlay a rectangular image.
Example command: python3 echo_pregui_run.py -ids 10818 -temp 20 -convex -dir echo_pregui_example
Use -h flag for help on command-line arguments
[-h] help
-ids PLATEID [PLATEID ...] Rockimager plate ID (looks like 10930 or 9580)
-dir OUTPUT_PLATE_FOLDER Output location of analysis and images from this script
-temp PLATE_TEMP Temperature plate is stored at (must be '4' or "20" - not 4c or 20c)
[-box] (default) Overlay full rectangular drop image onto overview image
[-convex] Overlay a convex shaped cutout of the drop image onto the overview image
[-circle] Overlay a circular cutout of the drop image onto the overview image
[-debug] Show images during finding the drop location bounding box
▶ python3 echo_pregui_run.py -ids 10818 -temp 20 -convex -dir images/march30_readme_outout
rsync -nmav --include */ --exclude *_th.jpg --include *.jpg -e ssh xray@169.230.29.134:/volume1/RockMakerStorage/WellImages/818/plateID_10818/ images/march30_readme_outout/10818/
xray@169.230.29.134's password:
batch IDs selected: droplocation, dropimg: 103969 106812
drop image: 96 images
overview ef: 96 images
overview drop location: 96 images
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 288/288 [00:00<00:00, 396702.64it/s]
rsync -mav -P --files-from=images/march30_readme_outout/10818/files_to_transfer.txt -e ssh xray@169.230.29.134:/volume1/RockMakerStorage/WellImages/818/plateID_10818 images/march30_readme_outout/10818/
xray@169.230.29.134's password:
Downloaded Files = 288 (should be 288 = 96*3)
organizing images.
overlaying images.
75%|███████████████████████████████████████████████████████████████████████████████████████████████████▊ | 72/96 [00:10<00:03, 6.09it/s]not overlaying an image, drop location is the entire well (not accurate)
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 96/96 [00:12<00:00, 7.75it/s]
Completed images (should be 96 for 96 well): 96
overviewimgs = 96
Finding pixel location of wells.
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 96/96 [00:05<00:00, 18.82it/s]
created: /Users/liam_msg/Documents/echo_pregui_scripts/echo_pregui_scripts/images/march30_readme_outout/10818/imagesmarch30_readme_outout10818.json
wrote to json