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behaviour-analysis-pipeline.py
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behaviour-analysis-pipeline.py
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import cv2
import glob
import os
import shutil
from tierpsy.processing.processMultipleFilesFun import processMultipleFilesFun
from tierpsy.summary.collect import calculate_summaries
path = './data/jpeg-30s/'
img_extension = "*.jpg"
fps = 10
masked_video_dir = path + 'MaskedVideos'
results_dir = path + 'Results'
parameters_file = path + 'parameters.json'
try:
shutil.rmtree(masked_video_dir)
shutil.rmtree(results_dir)
except OSError as e:
print("error couldnt delete files")
def file_name_str_to_int(f_path):
f_name = os.path.basename(f_path)
str_key, _ = os.path.splitext(f_name)
return int(str_key)
img_files = glob.glob(path + img_extension)
img_files.sort(key=file_name_str_to_int)
images = [cv2.imread(file) for file in img_files]
width, height, layers = images[0].shape
video = cv2.VideoWriter(path + "test.avi", cv2.VideoWriter_fourcc(*'XVID'), fps, (height, width))
for img in images:
video.write(img)
video.release()
# code to call tierpsy batch processing
processMultipleFilesFun(path, masked_video_dir, results_dir,
'', parameters_file, '', '*.avi', '', 3, 10.0, False,
'COMPRESS', 'FEAT_TIERPSY', False,
['COMPRESS', 'TRAJ_CREATE', 'TRAJ_JOIN', 'SKE_INIT', 'BLOB_FEATS', 'SKE_CREATE', 'SKE_FILT', 'SKE_ORIENT', 'INT_PROFILE', 'INT_SKE_ORIENT', 'FEAT_INIT', 'FEAT_TIERPSY'],
False, False, True
)
# code to generate results csv
fold_args = dict(n_folds = 5, frac_worms_to_keep = 0.8, time_sample_seconds = 600.0)
calculate_summaries(
path,
'tierpsy',
'plate',
False,
True,
**fold_args
)