img_back = np.uint8(img_back)
logging.debug('Writing shape: %s', str(img_back.shape))
logging.debug('Writing min: %s', np.min(img_back))
logging.debug('Writing max: %s', np.max(img_back))
vid_writer.write(img_back)
vid_writer.release()
if replace_vid:
os.remove(vid_fpath)
os.rename(os.path.join(denoised_dir, filename), vid_fpath)
if replace_vid:
os.rmdir(denoised_dir)
if __name__ == '__main__':
import miniscope_file
from load_args import *
session_fpaths = miniscope_file.list_session_dirs(local_miniscope_path,
experiment_date,
animal_name)
for session_fpath in session_fpaths:
logging.info('Removing noise in session dir %s', session_fpath)
vid_fpaths = miniscope_file.list_vidfiles(session_fpath, vid_prefix)
maskFFT = create_FFT_Mask(vid_fpaths)
meanFrame = calc_mean_frame_vals(vid_fpaths)
meanFrameFiltered = lowpass_filter_vals(meanFrame)
denoise_vids(vid_fpaths, maskFFT, meanFrameFiltered, replace_vid=True)
if len(animal_roi) == 0:
raise Exception('Roi definition not found for animal: ' + animal_name)
x1 = animal_roi['x1'].values[0]
x2 = animal_roi['x2'].values[0]
y1 = animal_roi['y1'].values[0]
y2 = animal_roi['y2'].values[0]
rotation = 0
if 'rotation' in animal_roi.columns:
rotation = animal_roi['rotation'].values[0]
return (x1, x2, y1, y2), rotation
if __name__ == '__main__':
from load_args import *
import miniscope_file
local_rois_fpath = os.path.join(local_miniscope_path, 'rois.csv')
logging.info('local miniscope path: ' + local_miniscope_path)
crop_roi, rotation = get_roi_xy(local_rois_fpath, animal_name)
session_fpaths = miniscope_file.list_session_dirs(local_miniscope_path,
experiment_date,
animal_name)
for s_fpath in session_fpaths:
vids_fpath = miniscope_file.list_vidfiles(s_fpath, vid_prefix)
for video in vids_fpath:
output_vid_path = crop_and_downsample(video, crop_roi, rotation,
spatial_downsampling)
if output_vid_path is None:
logging.info('Video file unchanged: ' + video)