sam_annotate.py

Controls

• c: Go to next image
• q: Close the entire program
• r: Delete current (red) segmentation and start over
• spacebar: Accept current (red) segmentation (turns it green)
• left and right arrow keys: Alternate between SAM proposed masks
• left mouse click: Add clicked point to set of positive points for SAM
• right mouse click: Add clicked point to set of negative points for SAM (makes it so that the clicked area will not be segmented hopefully)

Notes

• Adding many points to SAM doesn't always give good results, if a log is troublesome, it might be better to press 'r' and start over
• All necessary config should be on lines 28 to 32
• Only way to delete accepted (green) segmentations is to manually delete the corresponding bitmaps from segmentations/ folder
• Before running you need to create the src/segmentations folder
• To install just run install.sh from the folder that it is in. Append ' 2>&1 | tee err_log.txt' to get script log to fi.e.
• NB! sam_annotate.py needs to be run from inside src folder, because if the folder that sam_annotate.py is in also has the sam2 folder, then it complains that the local folder might conflict with installed version of sam2

merge.py

The python script merge.py merges a series of image masks located in a specified folder into a single mask image and then deletes the original mask files.

Example

python src/merge.py segmentations/20250228_204152 0 12

This command will merge the images named 00000.png through 00012.png (inclusive) located in the segmentations/20250228_204152 folder. The merged image will be saved as 00000_mask.png in the same folder, and the original files will be deleted.