Repository for all the needed for the preprocessing of the obtained animal AOSLO data.
To operate, run the animal_processing_pipeline.py script which performs the following operations:
- Asks for the directory where the data to be preprocessed is located
- Asks for the number of frames that are in all video
- Asks for the imaging session date
- Aks if the data contains iORG data
- Aks for the location of the video locations csv file
- For each file name:
- The modality is determined and modified compatibility with the BMC registration software
- The binary file is convered to an array in the row, col, number frames orintation
- The video data array is desinusoided using the grid matrix file generated
- Using the rename information, the video is writen to a BMC compatiple format
- After renameing the split detector and dark field videos are generated
- If the dataset contains iORG data, the stimulus presentation will be aligned throughout the dataset
- All visible modality videos are found to find when the stimulus was presented
- The frames that comprise the pre, post, and during stimulus presentation and the video condition (control/stim) are found for all videos and writen to a csv
- All modalities undergo stimulus alignment and cropping using the minimum of the pre stimulus presentation to align the frame in which the stimulus is presented throughout the dataset
- All video are saved into a folder called "Stim_Aligned"