def scan_folder_for_NWBfiles(folder, Nmax=1000000, verbose=True):
if verbose:
print('inspecting the folder "%s" [...]' % folder)
t0 = time.time()
FILES = get_files_with_extension(folder, extension='.nwb', recursive=True)
DATES = np.array([f.split(os.path.sep)[-1].split('-')[0] for f in FILES])
SUBJECTS = []
for f in FILES[:Nmax]:
try:
data = Data(f, metadata_only=True)
SUBJECTS.append(data.metadata['subject_ID'])
except BaseException as be:
SUBJECTS.append('N/A')
if verbose:
print(be)
print('\n /!\ Pb with "%s" \n' % f)
if verbose:
print(' -> found n=%i datafiles (in %.1fs) ' % (len(FILES),
(time.time() - t0)))
return np.array(FILES), np.array(DATES), np.array(SUBJECTS)
def build_Ca_filelist(folder):
CA_FILES = {'Bruker_folder':[], 'Bruker_file':[],
'date':[], 'protocol':[],'StartTimeString':[],
'StartTime':[], 'EndTime':[], 'absoluteTime':[]}
for bdf in get_TSeries_folders(folder):
fn = get_files_with_extension(bdf, extension='.xml')[0]
try:
xml = bruker_xml_parser(fn)
if len(xml['Ch1']['relativeTime'])>0:
CA_FILES['date'].append(stringdatetime_to_date(xml['date']))
CA_FILES['Bruker_folder'].append(bdf)
CA_FILES['Bruker_file'].append(fn)
CA_FILES['StartTimeString'].append(xml['StartTime'])
start = StartTime_to_day_seconds(xml['StartTime'])
CA_FILES['StartTime'].append(start+xml['Ch1']['absoluteTime'][0])
CA_FILES['EndTime'].append(start+xml['Ch1']['absoluteTime'][-1])
CA_FILES['protocol'].append('')
except BaseException as e:
print(e)
print(100*'-')
print('Problem with file: "%s"' % fn)
print(100*'-')
return CA_FILES
def compute_subjects(self):
FILES = get_files_with_extension(FOLDERS[self.fbox.currentText()],
extension='.nwb',
recursive=True)
SUBJECTS, DISPLAY_NAMES = [], []
for fn in FILES:
infos = self.preload_datafolder(fn)
SUBJECTS.append(infos['subject'])
DISPLAY_NAMES.append(infos['display_name'])
self.SUBJECTS = {}
for s in np.unique(SUBJECTS):
cond = (np.array(SUBJECTS) == s)
self.SUBJECTS[s] = {
'display_names': np.array(DISPLAY_NAMES)[cond],
'datafiles': np.array(FILES)[cond]
}
print(' -> found n=%i subjects ' % len(self.SUBJECTS.keys()))
self.sbox.clear()
self.sbox.addItems([self.subject_default_key]+\
list(self.SUBJECTS.keys()))
self.sbox.setCurrentIndex(0)
def scan_folder(self):
print('inspecting the folder "%s" [...]' %
FOLDERS[self.fbox.currentText()])
FILES = get_files_with_extension(FOLDERS[self.fbox.currentText()],
extension='.nwb',
recursive=True)
DATES = np.array(
[f.split(os.path.sep)[-1].split('-')[0] for f in FILES])
self.FILES_PER_DAY = {}
for d in np.unique(DATES):
try:
self.cal.setDateTextFormat(
QtCore.QDate(
datetime.date(*[int(dd) for dd in d.split('_')])),
self.highlight_format)
self.FILES_PER_DAY[d] = [os.path.join(FOLDERS[self.fbox.currentText()], f)\
for f in np.array(FILES)[DATES==d]]
except BaseException as be:
print(be)
# except ValueError:
# pass
print(' -> found n=%i datafiles ' % len(FILES))
def scan_folder(self):
print('inspecting the folder "%s" [...]' %
FOLDERS[self.fbox.currentText()])
FILES0 = get_files_with_extension(FOLDERS[self.fbox.currentText()],
extension='.nwb',
recursive=True)
TIMES, DATES, FILES = [], [], []
for f in FILES0:
Time = f.split(os.path.sep)[-1].replace('.nwb', '').split('-')
if len(Time) >= 4:
TIMES.append(3600 * int(Time[0]) + 60 * int(Time[1]) +
int(Time[2]))
DATES.append(f.split(os.path.sep)[-1].split('-')[0])
FILES.append(f)
TIMES, DATES, FILES = np.array(TIMES), np.array(DATES), np.array(FILES)
NDATES = np.array([
datetime.date(*[int(dd) for dd in date.split('_')]).toordinal()
for date in DATES
])
self.FILES_PER_DAY = {}
guiparts.reinit_calendar(
self,
min_date=tuple(
int(dd) for dd in DATES[np.argmin(NDATES)].split('_')),
max_date=tuple(
int(dd) for dd in DATES[np.argmax(NDATES)].split('_')))
for d in np.unique(DATES):
try:
self.cal.setDateTextFormat(
QtCore.QDate(
datetime.date(*[int(dd) for dd in d.split('_')])),
self.highlight_format)
day_cond = (DATES == d)
time_sorted = np.argsort(TIMES[day_cond])
self.FILES_PER_DAY[d] = [os.path.join(FOLDERS[self.fbox.currentText()], f)\
for f in np.array(FILES)[day_cond][time_sorted]]
except BaseException as be:
print(be)
print('error for date %s' % d)
print(' -> found n=%i datafiles ' % len(FILES))
def load_data(self, folder):
if folder != '':
self.folder = folder
xml_file = os.path.join(
folder,
get_files_with_extension(self.folder, extension='.xml')[0])
self.bruker_data = bruker_xml_parser(xml_file)
self.cframe = 0
self.nframes = len(
self.bruker_data[self.channelB.currentText()]['tifFile'])
self.display_frames()
self.ROIS = []
if os.path.isfile(os.path.join(self.folder, 'cells.npy')):
cells = np.load(os.path.join(self.folder, 'cells.npy'),
allow_pickle=True).item()
for x, y, z in zip(cells['x'], cells['y'], cells['z']):
self.ROIS.append(cellROI(depth=z, pos=(x, y), parent=self))
else:
print('"%s" is not a valid folder' % folder)
def compute_subjects(self):
FILES = get_files_with_extension(FOLDERS[self.fbox.currentText()],
extension='.nwb',
recursive=True)
print(
' looping over n=%i datafiles to fetch "subjects" metadata [...]' %
len(FILES))
DATES = np.array(
[f.split(os.path.sep)[-1].split('-')[0] for f in FILES])
SUBJECTS, DISPLAY_NAMES, SDATES, NDATES = [], [], [], []
for fn, date in zip(FILES, DATES):
infos = self.preload_datafolder(fn)
SDATES.append(date)
SUBJECTS.append(infos['subject'])
DISPLAY_NAMES.append(infos['display_name'])
NDATES.append(
datetime.date(*[int(dd)
for dd in date.split('_')]).toordinal())
self.SUBJECTS = {}
for s in np.unique(SUBJECTS):
cond = (np.array(SUBJECTS) == s)
self.SUBJECTS[s] = {
'display_names': np.array(DISPLAY_NAMES)[cond],
'datafiles': np.array(FILES)[cond],
'dates': np.array(SDATES)[cond],
'dates_num': np.array(NDATES)[cond]
}
print(' -> found n=%i subjects ' % len(self.SUBJECTS.keys()))
self.sbox.clear()
self.sbox.addItems([self.subject_default_key]+\
list(self.SUBJECTS.keys()))
self.sbox.setCurrentIndex(0)
# compression_metadata = {'tool':tool,
# 'subsampling':subsampling,
# 'smoothing':smoothing,
# 'extension':extension,
# 'Nframe_per_file':Nframe_per_file,
# 'max_file':max_file}
# np.save(os.path.join(directory, 'compression-metadata.npy'), compression_metadata)
if __name__ == '__main__':
# fn = '/home/yann/DATA/2020_11_03/TSeries-28102020-231-00-031/'
folder = '/home/yann/DATA/2020_11_03/'
for bdf in list_TSeries_folder(folder)[6:]:
fn = get_files_with_extension(bdf, extension='.xml')[0]
xml = bruker_xml_parser(fn)
binaryFile = os.path.join(bdf, 'suite2p', 'plane0', 'data.bin')
if len(xml['Ch1']['absoluteTime']) > 10 and os.path.isfile(binaryFile):
compress_FluorescenceMovie(bdf,
xml,
Nframe_per_file=1000,
max_file=1,
verbose=True,
subsampling=0,
smoothing=0)
os.system('ls -lh %s ' % os.path.join(bdf, 'suite2p', 'plane0'))
# import argparse
# parser=argparse.ArgumentParser()
def run(self):
if self.destination_folder == '':
self.destination_folder = FOLDERS[self.destBox.currentText()]
if self.source_folder == '':
self.source_folder = FOLDERS[self.sourceBox.currentText()]
if '10.0.0.' in self.destination_folder:
print('writing a bash script to be executed as: "bash temp.sh" ')
F = open('temp.sh', 'w')
F.write('echo "Password for %s ? "\n' % self.destination_folder)
F.write('read passwd\n')
else:
print('starting copy [...]')
if self.typeBox.currentText() == 'NWB':
##############################################
############# NWB file ##########
##############################################
FILES = get_files_with_extension(self.source_folder,
extension='.nwb',
recursive=True)
for f in FILES:
if '10.0.0.' in self.destination_folder:
F.write('sshpass -p $passwd rsync -avhP %s %s \n' %
(f, self.destination_folder))
else:
cmd = self.file_copy_command(f, self.destination_folder)
print('"%s" launched as a subprocess' % cmd)
p = subprocess.Popen(cmd, shell=True)
elif self.typeBox.currentText() == 'FULL':
if '10.0.0.' in self.destination_folder:
F.write('sshpass -p $passwd rsync -avhP %s %s \n' %
(self.source_folder, self.destination_folder))
else:
print(' copying "%s" [...]' % self.source_folder)
self.folder_copy_command(self.source_folder,
self.destination_folder)
elif ('Imaging' in self.typeBox.currentText()):
##############################################
############# Imaging ##########
##############################################
if 'TSeries' in str(self.source_folder):
folders = [self.source_folder]
else:
folders = get_TSeries_folders(self.source_folder)
print('processing: ', folders)
for f in folders:
new_folder = os.path.join(self.destination_folder,
'TSeries' + f.split('TSeries')[1])
if '10.0.0.' in self.destination_folder:
F.write('sshpass -p $passwd ssh %s mkdir %s \n' %
(self.destination_folder.split(':')[0],
new_folder.split(':')[1]))
F.write('sshpass -p $passwd ssh %s mkdir %s \n' %
(self.destination_folder.split(':')[0],
new_folder.split(':')[1] + '/suite2p'))
else:
pathlib.Path(new_folder).mkdir(parents=True, exist_ok=True)
# XML metadata file
xml = get_files_with_extension(f,
extension='.xml',
recursive=False)
if len(xml) > 0:
if '10.0.0.' in self.destination_folder:
F.write('sshpass -p $passwd rsync -avhP %s %s \n' %
(xml[0], new_folder))
else:
print(' copying "%s" [...]' % xml[0])
subprocess.Popen(self.file_copy_command(
xml[0], new_folder),
shell=True)
else:
print(' /!\ Problem no "xml" found !! /!\ ')
# XML metadata file
Fsuite2p = os.path.join(f, 'suite2p')
iplane = 0
while os.path.isdir(os.path.join(Fsuite2p,
'plane%i' % iplane)):
npys = get_files_with_extension(os.path.join(
Fsuite2p, 'plane%i' % iplane),
extension='.npy',
recursive=False)
inewfolder = os.path.join(new_folder, 'suite2p',
'plane%i' % iplane)
if '10.0.0.' in self.destination_folder:
F.write('sshpass -p $passwd ssh %s mkdir %s \n' %
(self.destination_folder.split(':')[0],
new_folder.split(':')[1] +
'/suite2p/plane%i' % iplane))
else:
pathlib.Path(inewfolder).mkdir(parents=True,
exist_ok=True)
for n in npys:
if '10.0.0.' in self.destination_folder:
F.write('sshpass -p $passwd rsync -avhP %s %s \n' %
(n, inewfolder))
else:
print(' copying "%s" [...]' % n)
subprocess.Popen(self.file_copy_command(
n, inewfolder),
shell=True)
if ('binary' in self.typeBox.currentText()) or (
'full' in self.typeBox.currentText()):
if os.path.isfile(
os.path.join(Fsuite2p, 'plane%i' % iplane,
'data.bin')):
print(' copying "%s" [...]' % os.path.join(
Fsuite2p, 'plane%i' % iplane, 'data.bin'))
if '10.0.0.' in self.destination_folder:
F.write(
'sshpass -p $passwd rsync -avhP %s %s \n' %
(os.path.join(Fsuite2p, 'plane%i' % iplane,
'data.bin'), inewfolder))
else:
print(' copying "%s" [...]' % n)
subprocess.Popen(self.file_copy_command(
os.path.join(Fsuite2p, 'plane%i' % iplane,
'data.bin'), inewfolder),
shell=True)
else:
print('In: "%s" ' % os.path.isfile(
os.path.join(Fsuite2p, 'plane%i' % iplane)))
print(
' /!\ Problem no "binary file" found !! /!\ ')
iplane += 1
if '10.0.0.' in self.destination_folder:
print('bash script "temp.sh" closed !')
F.close()
else:
print('done (but cmd likely still running as subprocesses)')
def __init__(self,
folder,
dt=None,
times=None,
frame_sampling=None,
extension='.npy',
lazy_loading=True,
compression_metadata=None,
t0=0):
"""
IMAGES can be initialized
"""
self.extension = extension
self.BINARY_IMAGES, self.VIDS, self.PICS = None, None, None
self.IMAGES = None
FILES = sorted(get_files_with_extension(folder, extension=extension))
### ASSOCIATING A TEMPORAL SAMPLING
# ---------------------------------------------
if times is not None:
self.t = times
else:
if dt is None:
dt = 1
self.t = np.arange(len(FILES)) * dt + t0
### DEALING WITH FRAME SAMPLING
# ---------------------------------------------
# you can specify a specific subsampling here !
if frame_sampling is not None and times is None:
print(
'/!\ Need to pass the specific times if you subsample the frames /!\ '
)
elif frame_sampling is None:
frame_sampling = np.arange(len(self.t))
### LOADING FRAMES
# ---------------------------------------------
if extension == '.npy':
self.BINARY_IMAGES = [FILES[f] for f in frame_sampling]
elif extension == '.npz':
self.VIDS = FILES
elif extension == '.avi':
self.VIDS = FILES
elif extension == '.mp4':
self.VIDS = FILES
elif extension == '.jpeg':
self.PICS = FILES
elif extension == '.tiff':
self.IMAGES = []
for fn in FILES:
self.IMAGES.append(np.array(Image.open(fn)))
else:
print('Extension', extension, ' not recognized !')
if lazy_loading and self.VIDS is not None:
# we just make a map between indices and videos/frames
self.index_frame_map = []
for i, fn in enumerate(self.VIDS):
s = fn.split('imgs-')[1].replace(extension, '').split('-')
i0, i1 = int(s[0]), int(s[1])
for i, iframe in enumerate(np.arange(i0, i1 + 1)):
if iframe in frame_sampling:
self.index_frame_map.append([fn, i])
elif (self.VIDS is not None):
print('Pre-loading the full-set of videos [...]')
self.IMAGES = []
if extension == '.npz':
# we pre-load the video !
for i, fn in enumerate(self.VIDS):
s = fn.split('imgs-')[1].replace(extension, '').split('-')
i0, i1 = int(s[0]), int(s[1])
x = np.load(fn)
for i, iframe in enumerate(np.arange(i0, i1 + 1)):
if iframe in frame_sampling:
self.IMAGES.append(x[i, :, :, 0])
else:
for i, fn in enumerate(self.VIDS):
s = fn.split('imgs-')[1].replace(extension, '').split('-')
i0, i1 = int(s[0]), int(s[1])
x = skvideo.io.vread(fn)
for i, iframe in enumerate(np.arange(i0, i1 + 1)):
if iframe in frame_sampling:
self.IMAGES.append(x[i, :, :, 0])
def add_ophys(nwbfile,
args,
metadata=None,
with_raw_CaImaging=True,
with_processed_CaImaging=True,
Ca_Imaging_options={
'Suite2P-binary-filename': 'data.bin',
'plane': 0
}):
if metadata is None:
metadata = ast.literal_eval(nwbfile.session_description)
try:
CaFn = get_files_with_extension(
args.CaImaging_folder, extension='.xml')[0] # get Tseries metadata
except BaseException as be:
print(be)
print('\n /!\ Problem with the CA-IMAGING data in %s /!\ ' %
args.datafolder)
raise Exception
xml = bruker_xml_parser(CaFn) # metadata
onset = (metadata['STEP_FOR_CA_IMAGING_TRIGGER']['onset']
if 'STEP_FOR_CA_IMAGING_TRIGGER' in metadata else 0)
CaImaging_timestamps = onset+xml['Ch1']['relativeTime']+\
float(xml['settings']['framePeriod'])/2. # in the middle in-between two time stamps
device = pynwb.ophys.Device('Imaging device with settings: \n %s' %
str(xml['settings'])) # TO BE FILLED
nwbfile.add_device(device)
optical_channel = pynwb.ophys.OpticalChannel(
'excitation_channel 1', 'Excitation 1',
float(xml['settings']['laserWavelength']['Excitation 1']))
imaging_plane = nwbfile.create_imaging_plane(
'my_imgpln',
optical_channel,
description='Depth=%.1f[um]' %
float(xml['settings']['positionCurrent']['ZAxis']),
device=device,
excitation_lambda=float(
xml['settings']['laserWavelength']['Excitation 1']),
imaging_rate=1. / float(xml['settings']['framePeriod']),
indicator='GCamp',
location='V1',
# reference_frame='A frame to refer to',
grid_spacing=(float(xml['settings']['micronsPerPixel']['YAxis']),
float(xml['settings']['micronsPerPixel']['XAxis'])))
Ca_data = None
if with_raw_CaImaging:
if args.verbose:
print('=> Storing Calcium Imaging data [...]')
Ca_data = BinaryFile(
Ly=int(xml['settings']['linesPerFrame']),
Lx=int(xml['settings']['pixelsPerLine']),
read_filename=os.path.join(
args.CaImaging_folder, 'suite2p',
'plane%i' % Ca_Imaging_options['plane'],
Ca_Imaging_options['Suite2P-binary-filename']))
CA_SUBSAMPLING = build_subsampling_from_freq(\
subsampled_freq=args.CaImaging_frame_sampling,
original_freq=1./float(xml['settings']['framePeriod']),
N=Ca_data.shape[0], Nmin=3)
if args.CaImaging_frame_sampling > 0:
dI = int(1. / args.CaImaging_frame_sampling /
float(xml['settings']['framePeriod']))
else:
dI = 1
def Ca_frame_generator():
for i in CA_SUBSAMPLING:
yield Ca_data.data[i:i + dI, :, :].mean(axis=0).astype(
np.uint8)
Ca_dataI = DataChunkIterator(data=Ca_frame_generator(),
maxshape=(None, Ca_data.shape[1],
Ca_data.shape[2]),
dtype=np.dtype(np.uint8))
if args.compression > 0:
Ca_dataC = H5DataIO(
data=Ca_dataI, # with COMPRESSION
compression='gzip',
compression_opts=args.compression)
image_series = pynwb.ophys.TwoPhotonSeries(
name='CaImaging-TimeSeries',
dimension=[2],
data=Ca_dataC,
imaging_plane=imaging_plane,
unit='s',
timestamps=CaImaging_timestamps[CA_SUBSAMPLING])
else:
image_series = pynwb.ophys.TwoPhotonSeries(
name='CaImaging-TimeSeries',
dimension=[2],
data=Ca_dataI,
# data = Ca_data.data[:].astype(np.uint8),
imaging_plane=imaging_plane,
unit='s',
timestamps=CaImaging_timestamps[CA_SUBSAMPLING])
else:
image_series = pynwb.ophys.TwoPhotonSeries(name='CaImaging-TimeSeries',
dimension=[2],
data=np.ones((2, 2, 2)),
imaging_plane=imaging_plane,
unit='s',
timestamps=1. *
np.arange(2))
nwbfile.add_acquisition(image_series)
if with_processed_CaImaging and os.path.isdir(
os.path.join(args.CaImaging_folder, 'suite2p')):
print('=> Adding the suite2p processing [...]')
add_ophys_processing_from_suite2p(
os.path.join(args.CaImaging_folder, 'suite2p'),
nwbfile,
CaImaging_timestamps,
device=device,
optical_channel=optical_channel,
imaging_plane=imaging_plane,
image_series=image_series) # ADD UPDATE OF starting_time
elif with_processed_CaImaging:
print('\n /!\ no "suite2p" folder found in "%s" /!\ ' %
args.CaImaging_folder)
return Ca_data
def add_ophys(nwbfile,
args,
metadata=None,
with_raw_CaImaging=True,
with_processed_CaImaging=True,
Ca_Imaging_options={
'Suite2P-binary-filename': 'data.bin',
'plane': 0
}):
#########################################
########## Loading metadata ############
#########################################
if metadata is None:
metadata = ast.literal_eval(nwbfile.session_description)
try:
CaFn = get_files_with_extension(
args.CaImaging_folder, extension='.xml')[0] # get Tseries metadata
except BaseException as be:
print(be)
print('\n /!\ Problem with the CA-IMAGING data in %s /!\ ' %
args.datafolder)
raise Exception
xml = bruker_xml_parser(CaFn) # metadata
##################################################
########## setup-specific quantities ############
##################################################
if 'A1-2P' in metadata['Rig']:
functional_chan = 'Ch2' # green channel is channel 2 downstairs
laser_key = 'Laser'
Depth = float(xml['settings']['positionCurrent']['ZAxis']['Z Focus']
[0]) # center depth only !
else:
functional_chan = 'Ch1'
laser_key = 'Excitation 1'
Depth = float(xml['settings']['positionCurrent']['ZAxis'])
##################################################
########## setup-specific quantities ############
##################################################
device = pynwb.ophys.Device('Imaging device with settings: \n %s' %
str(xml['settings'])) # TO BE FILLED
nwbfile.add_device(device)
optical_channel = pynwb.ophys.OpticalChannel(
'excitation_channel 1', laser_key,
float(xml['settings']['laserWavelength'][laser_key]))
multiplane = (True if len(np.unique(xml['depth_shift'])) > 1 else False)
if not multiplane:
imaging_plane = nwbfile.create_imaging_plane(
'my_imgpln',
optical_channel,
description='Depth=%.1f[um]' %
(float(metadata['Z-sign-correction-for-rig']) * Depth),
device=device,
excitation_lambda=float(
xml['settings']['laserWavelength'][laser_key]),
imaging_rate=1. / float(xml['settings']['framePeriod']),
indicator='GCamp',
location='V1', # ADD METADATA HERE
# reference_frame='A frame to refer to',
grid_spacing=(float(xml['settings']['micronsPerPixel']['YAxis']),
float(xml['settings']['micronsPerPixel']['XAxis'])))
else:
# DESCRIBE THE MULTIPLANES HERE !!!!
imaging_plane = nwbfile.create_imaging_plane(
'my_imgpln',
optical_channel,
description='Depth=%.1f[um]' %
(float(metadata['Z-sign-correction-for-rig']) * Depth),
device=device,
excitation_lambda=float(
xml['settings']['laserWavelength'][laser_key]),
imaging_rate=1. / float(xml['settings']['framePeriod']),
indicator='GCamp',
location='V1', # ADD METADATA HERE
# reference_frame='A frame to refer to',
grid_spacing=(float(xml['settings']['micronsPerPixel']['YAxis']),
float(xml['settings']['micronsPerPixel']['XAxis'])))
########################################
##### --- DEPRECATED to be fixed ... ##
########################################
Ca_data = None
# if with_raw_CaImaging:
# if args.verbose:
# print('=> Storing Calcium Imaging data [...]')
# Ca_data = BinaryFile(Ly=int(xml['settings']['linesPerFrame']),
# Lx=int(xml['settings']['pixelsPerLine']),
# read_filename=os.path.join(args.CaImaging_folder,
# 'suite2p', 'plane%i' % Ca_Imaging_options['plane'],
# Ca_Imaging_options['Suite2P-binary-filename']))
# CA_SUBSAMPLING = build_subsampling_from_freq(\
# subsampled_freq=args.CaImaging_frame_sampling,
# original_freq=1./float(xml['settings']['framePeriod']),
# N=Ca_data.shape[0], Nmin=3)
# if args.CaImaging_frame_sampling>0:
# dI = int(1./args.CaImaging_frame_sampling/float(xml['settings']['framePeriod']))
# else:
# dI = 1
# def Ca_frame_generator():
# for i in CA_SUBSAMPLING:
# yield Ca_data.data[i:i+dI, :, :].mean(axis=0).astype(np.uint8)
# Ca_dataI = DataChunkIterator(data=Ca_frame_generator(),
# maxshape=(None, Ca_data.shape[1], Ca_data.shape[2]),
# dtype=np.dtype(np.uint8))
# if args.compression>0:
# Ca_dataC = H5DataIO(data=Ca_dataI, # with COMPRESSION
# compression='gzip',
# compression_opts=args.compression)
# image_series = pynwb.ophys.TwoPhotonSeries(name='CaImaging-TimeSeries',
# dimension=[2],
# data = Ca_dataC,
# imaging_plane=imaging_plane,
# unit='s',
# timestamps = CaImaging_timestamps[CA_SUBSAMPLING])
# else:
# image_series = pynwb.ophys.TwoPhotonSeries(name='CaImaging-TimeSeries',
# dimension=[2],
# data = Ca_dataI,
# # data = Ca_data.data[:].astype(np.uint8),
# imaging_plane=imaging_plane,
# unit='s',
# timestamps = CaImaging_timestamps[CA_SUBSAMPLING])
# else:
# image_series = pynwb.ophys.TwoPhotonSeries(name='CaImaging-TimeSeries',
# dimension=[2],
# data = np.ones((2,2,2)),
# imaging_plane=imaging_plane,
# unit='s',
# timestamps = 1.*np.arange(2))
# just a dummy version for now
image_series = pynwb.ophys.TwoPhotonSeries(
name='CaImaging-TimeSeries\n raw-data-folder=%s' %
args.CaImaging_folder.replace('/', '_'),
dimension=[2],
data=np.ones((2, 2, 2)),
imaging_plane=imaging_plane,
unit='s',
timestamps=1. * np.arange(2)) # TEMPORARY
nwbfile.add_acquisition(image_series)
if with_processed_CaImaging and os.path.isdir(
os.path.join(args.CaImaging_folder, 'suite2p')):
print('=> Adding the suite2p processing [...]')
add_ophys_processing_from_suite2p(
os.path.join(args.CaImaging_folder, 'suite2p'),
nwbfile,
xml,
device=device,
optical_channel=optical_channel,
imaging_plane=imaging_plane,
image_series=image_series) # ADD UPDATE OF starting_time
elif with_processed_CaImaging:
print('\n /!\ no "suite2p" folder found in "%s" /!\ ' %
args.CaImaging_folder)
return Ca_data
default=['protocols'],
help='')
parser.add_argument("--remove_all_pdfs",
help="remove all pdfs of previous analysis in folder",
action="store_true")
parser.add_argument('-nmax', "--Nmax", type=int, default=1000000)
parser.add_argument("-v",
"--verbose",
help="increase output verbosity",
action="store_true")
args = parser.parse_args()
if args.remove_all_pdfs and os.path.isdir(args.datafile):
FILES = get_files_with_extension(args.datafile,
extension='.pdf',
recursive=True)
for f in FILES:
print('removing', f)
os.remove(f)
elif os.path.isdir(args.datafile):
FILES = get_files_with_extension(args.datafile,
extension='.nwb',
recursive=True)
for f in FILES:
try:
make_summary_pdf(f,
include=args.ops,
Nmax=args.Nmax,
verbose=args.verbose)
except BaseException as be:
