issue to get coordinates of all bodyparts of dlc prediction

[josefinemeyer]

imutils code in get_absolute_bodyparts_coords.sh of epifluorescence_calcium_imaging pipeline is limited to one body part. see line:

https://github.com/ulisesrey/imutils/blob/9258cdc911ceec0b68a54e61c76d2ae7f3e8281e/imutils/src/bodyparts_coordinates.py#L47

thank you

[ulisesrey]

should be fixed, now. Can you check @josefinemeyer ? make sure that you have the latest version of the file epifluorescence_calcium_imaging/bash_scripts/get_absolute_bodyparts_coords.sh

[josefinemeyer]

I added the config.yaml and got this error

could you please check that out, @ulisesrey ?

All jobs in this array have:

• SLURM_ARRAY_JOB_ID=7622447
• SLURM_ARRAY_TASK_COUNT=5
• SLURM_ARRAY_TASK_MIN=1
• SLURM_ARRAY_TASK_MAX=5 This job in the array has:
• SLURM_JOB_ID=7622450
• SLURM_ARRAY_TASK_ID=1 My PROJECT iS /scratch/neurobiology/zimmer/active_sensing/zim06/zim2391/recordings_zim2391_RIA/20230516/data/worm3 My config.yaml filepath is /scratch/neurobiology/zimmer/active_sensing/zim06/zim2391/recordings_zim2391_RIA/20230516/data/worm3/config.yaml Environment loaded? Entering Python code.. The recording has 440 520 as center of coordiantes usage: bodyparts_coordinates.py [-h] -p PROJECT_PATH -img_center_coords IMAGE_CENTER_COORDINATES [IMAGE_CENTER_COORDINATES ...] -px_dim PIXEL_DIMENSIONS bodyparts_coordinates.py: error: argument -img_center_coords/--image_center_coordinates: invalid float value: '{BEH_CENTER_X}' usage: bodyparts_coordinates.py [-h] -p PROJECT_PATH -img_center_coords IMAGE_CENTER_COORDINATES [IMAGE_CENTER_COORDINATES ...] -px_dim PIXEL_DIMENSIONS bodypartscoordinates.py: error: argument -img_center_coords/--image_center_coordinates: invalid float value: '{BEH_CENTER_X}'_ usage: bodyparts_coordinates.py [-h] -p PROJECT_PATH -img_center_coords IMAGE_CENTER_COORDINATES [IMAGE_CENTER_COORDINATES ...] -px_dim PIXEL_DIMENSIONS bodyparts_coordinates.py: error: argument -img_center_coords/--image_center_coordinates: invalid float value: '{BEH_CENTER_X}' FINISHED find: missing argument to `-exec'

[ulisesrey]

It works now after changing this: https://github.com/ulisesrey/epifluorescence_calcium_imaging/commit/34c24be6e30bcc8a431ba9435175cb5280540f7f

Important, the nose is annotated in DLC as head, so the file is named head_coords_mm.csv now.