def walk_current_folder(root_path, mars_opts):
trials_to_run = []
fullpaths = []
for path, subdirs, filenames in os.walk(root_path):
for numv, fname in enumerate(filenames):
# start by looping over all movie files that have "Top" in their name
cond1 = all(x not in fname
for x in ['.seq', '.avi', '.mpg', '.mp4'])
cond2 = 'skipped' in path
cond3 = 'Top' not in fname and '_t.seq' not in fname
if cond1 | cond2 | cond3:
continue
if 'Top' in fname or '_t.seq' in fname:
front_fname, top_fname, mouse_name = mof.get_names(fname)
print(front_fname + ' ' + top_fname + ' ' + mouse_name)
if top_fname != fname: continue
fullpath_to_front = os.path.join(path, front_fname)
fullpath_to_top = os.path.join(path, top_fname)
cond1 = not (os.path.exists(fullpath_to_front))
cond2 = mars_opts['doFront']
cond3 = not mars_opts['doTop']
cond4 = not mars_opts['doToppcf']
# If the front video doesn't exist and we need it, continue.
if (cond1 and cond2): # |(cond3 and cond4):
continue
elif 'Front' in fname:
front_fname = fname
front_fname, top_fname, mouse_name = mof.get_names(front_fname)
# if front_fname != fname: continue
fullpath_to_top = os.path.join(path, top_fname)
fullpath_to_front = os.path.join(path, front_fname)
cond1 = not (os.path.exists(fullpath_to_top))
cond2 = mars_opts['doTop']
cond3 = not mars_opts['doFront']
cond4 = not mars_opts['doToppcf']
if (cond1 and cond2 and cond4) | cond3:
continue
else:
# This is a movie file, but doesnt have "Top" or "Front" in it. Let's skip it.
continue
# Save the paths we want to use.
mouse_trial = dict()
mouse_trial['top'] = fullpath_to_top
mouse_trial['front'] = fullpath_to_front
trials_to_run.append(mouse_trial)
fullpaths.append(fullpath_to_top)
return trials_to_run, fullpaths
def dump_bento_across_dir(root_path):
''' This function makes a bento file for a specific directory.'''
wb = xlwt.Workbook(encoding='utf-8')
ws1 = wb.add_sheet('Sheet1', cell_overwrite_ok=True)
ws1.write(0, 0, os.path.abspath(root_path)) # A1
ws1.write(0, 1, 'Ca framerate:') # B1
ws1.write(0, 2, 0) # C1
ws1.write(0, 3, 'Annot framerate:') # D1
ws1.write(0, 4, 30) # E1
ws1.write(0, 5, 'Multiple trials/Ca file:') # F1
ws1.write(0, 6, 0) # G1
ws1.write(0, 7, 'Multiple trails/annot file') # H1
ws1.write(0, 8, 0) # I1
ws1.write(0, 9, 'Includes behavior movies:') # J1
ws1.write(0, 10, 1) # K1
ws1.write(
0, 11,
'Offset (in seconds; positive values = annot starts before Ca):') # L1
ws1.write(0, 12, 0) # M1
ws1.write(0, 13, 'Includes tracking data:')
ws1.write(0, 14, 0)
ws1.write(0, 15, 'Includes audio files:')
ws1.write(0, 16, 0)
ws1.write(1, 0, 'Mouse') # A2
mouse_col_num = 0
session_col_num = 1
trial_col_num = 2
ws1.write(1, 1, 'Sessn') # B2
ws1.write(1, 2, 'Trial') # C2
ws1.write(1, 3, 'Stim') # D2
ws1.write(1, 4, 'Calcium imaging file') # E2
ws1.write(1, 5, 'Start Ca') # F2
ws1.write(1, 6, 'Stop Ca') # G2
ws1.write(1, 7, 'FR Ca') # H2
ws1.write(1, 8, 'Alignments') # I2
ws1.write(1, 9, 'Annotation file') # J2
annot_file_col_num = 9
ws1.write(1, 10, 'Start Anno') # K2
ws1.write(1, 11, 'Stop Anno') # L2
ws1.write(1, 12, 'FR Anno') # M2
ws1.write(1, 13, 'Offset') # N2
ws1.write(1, 14, 'Behavior movie') # O2
behavior_movie_col_num = 14
ws1.write(1, 15, 'Tracking') # P2
tracking_file_col_num = 15
ws1.write(1, 16, 'Audio file')
audio_file_col_num = 16
ws1.write(1, 17, 'tSNE')
# ws1.write(2, 0, 1) # A2
# ws1.write(2, 1, 1) # B2
# ws1.write(2, 2, 1) # C2
# ws1.write(2, 3, '') # D2
# ws1.write(2, 4, '') # E2
# ws1.write(2, 5, '') # F2
# ws1.write(2, 6, '') # G2
# ws1.write(2, 7, '') # H2
# ws1.write(2, 8, '') # I2
mouse_number = 0
row_num = 2
# Going through everything in this directory.
audio_filenames = []
add_audio_count = 0
nonaudio_filenames = []
for path, subdirs, filenames in os.walk(root_path):
for fname in sorted(filenames):
fname = os.path.join(path, fname)
if fname.endswith('.wav'):
audio_filenames.append(fname)
else:
nonaudio_filenames.append(fname)
audio_filenames = sorted(audio_filenames)
nonaudio_filenames = sorted(nonaudio_filenames)
for fname in nonaudio_filenames:
try:
cond1 = '.seq' not in fname
cond2 = 'skipped' in path
if (cond1) | cond2:
continue
if 'Top' in fname:
front_fname, top_fname, mouse_name = mof.get_names(fname)
fullpath_to_front = os.path.join(path, front_fname)
fullpath_to_top = os.path.join(path, top_fname)
else:
# This is a seq file, but doesnt have "Top" or "Front" in it. Let's skip it.
continue
# Add their info to the bento file at the appropriate level.
video_fullpath = fullpath_to_top
output_suffix = ''
video_path = os.path.dirname(video_fullpath)
video_name = os.path.basename(video_fullpath)
# Get the output folder for this specific mouse.
output_folder = mof.get_mouse_output_dir(
dir_output_should_be_in=video_path,
video_name=video_name,
output_suffix=output_suffix)
_, _, mouse_name = mof.get_names(video_name=video_name)
pose_basename = mof.get_pose_no_ext(video_fullpath=video_fullpath,
output_folder=output_folder,
view='top',
output_suffix=output_suffix)
top_pose_fullpath = pose_basename + '.json'
same_path_ann = [
os.path.join(root_path, f) for f in os.listdir(root_path)
if is_annotation_file(f, mouse_name)
]
ann = [
os.path.join(output_folder, f)
for f in os.listdir(output_folder)
if is_annotation_file(f, mouse_name)
]
ann = sorted(ann)
ann = [get_normrel_path(f, root_path) for f in ann]
pose_cond = os.path.exists(top_pose_fullpath)
video_cond = os.path.exists(video_fullpath)
should_write = (pose_cond and video_cond)
if should_write:
old_mouse_number = mouse_number
mouse_number = get_mouse_number(video_fullpath)
mouse_cond = (old_mouse_number == mouse_number)
# TODO: Session condition
sess_cond = (True)
if mouse_cond and sess_cond:
trial_count += 1
else:
trial_count = 1
ws1.write(row_num, mouse_col_num, mouse_number) # A2
ws1.write(row_num, session_col_num, 1) # B2
ws1.write(row_num, trial_col_num, trial_count) # C2
ws1.write(row_num, annot_file_col_num, ';'.join(ann)) # J2
ws1.write(row_num, 10, '') # K2
ws1.write(row_num, 11, '') # L2
ws1.write(row_num, 12, '') # M2
ws1.write(row_num, 13, '') # N2
track_file = get_normrel_path(top_pose_fullpath, root_path)
ws1.write(row_num, behavior_movie_col_num,
get_normrel_path(fullpath_to_top, root_path)) # O2
ws1.write(row_num, tracking_file_col_num, track_file) # P2
row_num += 1
except Exception as e:
print(e)
error_msg = 'ERROR: ' + fname + ' has failed. ' + str(e)
continue
# End of try-except block
# End of particular fname
# End of the particular root_path
last_row = row_num
row_num = 2
for audio_file_count, audio_file in enumerate(audio_filenames):
# Write the files in order.
ws1.write(row_num + audio_file_count, audio_file_col_num + 2,
get_normrel_path(audio_file, root_path))
bento_name = 'bento_' + mof.get_version_suffix() + '.xls'
wb.save(os.path.join(root_path, bento_name))
return