def find(self):
self.clean(self.job.data_container, u'peripheral')
transaction.commit()
DBSession.add(self.job)
dc = self.job.data_container
ds = self.job.data_container.primary_dataset
if dc.physio_recorded:
physio_files = nimsutil.find_ge_physio(self.physio_path, dc.timestamp+dc.prescribed_duration, dc.psd.encode('utf-8'))
if physio_files:
physio = nimsdata.nimsphysio.NIMSPhysio(physio_files, dc.tr, dc.num_timepoints)
if physio.is_valid():
self.job.activity = u'valid physio found'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
# Computing the slice-order can be expensive, so we didn't do it when we instantiated.
# But now that we know physio is valid, we need to do it.
ni = nimsdata.parse(os.path.join(self.nims_path, ds.primary_file_relpath))
physio.slice_order = ni.get_slice_order() # TODO: should probably write a set method
dataset = Dataset.at_path(self.nims_path, u'physio')
DBSession.add(self.job)
DBSession.add(self.job.data_container)
dataset.kind = u'peripheral'
dataset.container = self.job.data_container
with nimsutil.TempDir(dir=self.tempdir) as tempdir_path:
arcdir_path = os.path.join(tempdir_path, '%s_physio' % self.job.data_container.name)
os.mkdir(arcdir_path)
for f in physio_files:
shutil.copy2(f, arcdir_path)
filename = '%s_physio.tgz' % self.job.data_container.name
dataset.filenames = [filename]
with tarfile.open(os.path.join(self.nims_path, dataset.relpath, filename), 'w:gz', compresslevel=6) as archive:
archive.add(arcdir_path, arcname=os.path.basename(arcdir_path))
try:
reg_filename = '%s_physio_regressors.csv.gz' % self.job.data_container.name
physio.write_regressors(os.path.join(self.nims_path, dataset.relpath, reg_filename))
except nimsdata.nimsphysio.NIMSPhysioError:
self.job.activity = u'error generating regressors from physio data'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
else:
dataset.filenames += [reg_filename]
else:
self.job.activity = u'invalid physio found and discarded'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
else:
self.job.activity = u'no physio files found'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
else:
self.job.activity = u'physio not recorded'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
transaction.commit()
DBSession.add(self.job)
def find(self):
dc = self.job.data_container
ds = self.job.data_container.primary_dataset
if dc.physio_flag:
physio_files = nimsutil.find_ge_physio(self.physio_path, dc.timestamp+dc.duration, dc.psd.encode('utf-8'))
if physio_files:
self.job.activity = u'physio found %s' % (', '.join([os.path.basename(pf) for pf in physio_files]))
self.log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
dataset = Dataset.at_path(self.nims_path, None, u'Physio Data')
DBSession.add(self.job)
DBSession.add(self.job.data_container)
dataset.file_cnt_act = 0
dataset.file_cnt_tgt = len(physio_files)
dataset.kind = u'secondary'
dataset.container = self.job.data_container
for f in physio_files:
shutil.copy2(f, os.path.join(self.nims_path, dataset.relpath))
dataset.file_cnt_act += 1
else:
self.job.activity = u'no physio files found'
self.log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
transaction.commit()
DBSession.add(self.job)
def find(self, slice_order, num_slices):
"""
Locate physio and generate physio regressors.
Find is called from within each pipeline's process() method after the file's slice_order
and num_slices attributes have been set, but before preparing the data to be written out.
This will use the num_slice and slice_order to create an array of the slice numbers in the
sequence they were acquired. Nimsphysio will use both the current data containers metadata,
like timestamp and duration, and metadata obtained by parsing the primary dataset file to
determine if physio is valid.
This method should never raise any exceptions.
Parameters
----------
slice_order : int
integer that corresponds to the appropriate NIFTI slice order code. 0 for unknown.
num_slices : int
number of slices
"""
self.clean(self.job.data_container, u'peripheral')
transaction.commit()
DBSession.add(self.job)
if self.physio_path is None: return # can't search w/o phys path
if not slice_order or not num_slices: return # need both slice order AND num_slices to create regressors
if self.job.data_container.scanner_name == 'IRC MRC35068': return # hack to ignore Davis files
dc = self.job.data_container
if dc.physio_recorded:
# 2015.02.03 RFD: apparently the old rule was incorrect. The physio files are not timestamped
# sometime after the Rxed duration, but rather sometime after the actual duration! We don't yet
# know the actual duration, so we'll just make shit up and hope for the best.
physio_lag = datetime.timedelta(seconds=30)
physio_files = nimsutil.find_ge_physio(self.physio_path, dc.timestamp+physio_lag, dc.psd.encode('utf-8'))
#physio_files = nimsutil.find_ge_physio(self.physio_path, dc.timestamp+dc.prescribed_duration, dc.psd.encode('utf-8'))
if physio_files:
physio = nimsphysio.NIMSPhysio(physio_files, dc.tr, dc.num_timepoints, nimsdata.medimg.medimg.get_slice_order(slice_order, num_slices))
if physio.is_valid():
self.job.activity = u'valid physio found (%s...)' % os.path.basename(physio_files[0])
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
dataset = Dataset.at_path(self.nims_path, u'physio')
DBSession.add(self.job)
DBSession.add(self.job.data_container)
dataset.kind = u'peripheral'
dataset.container = self.job.data_container
with nimsutil.TempDir(dir=self.tempdir) as tempdir_path:
arcdir_path = os.path.join(tempdir_path, '%s_physio' % self.job.data_container.name)
os.mkdir(arcdir_path)
for f in physio_files:
shutil.copy2(f, arcdir_path)
filename = '%s_physio.tgz' % self.job.data_container.name
dataset.filenames = [filename]
with tarfile.open(os.path.join(self.nims_path, dataset.relpath, filename), 'w:gz', compresslevel=6) as archive:
archive.add(arcdir_path, arcname=os.path.basename(arcdir_path))
try:
reg_filename = '%s_physio_regressors.csv.gz' % self.job.data_container.name
physio.write_regressors(os.path.join(self.nims_path, dataset.relpath, reg_filename))
self.job.activity = u'physio regressors %s written' % reg_filename
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
except nimsphysio.NIMSPhysioError:
self.job.activity = u'error generating regressors from physio data'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
else:
dataset.filenames += [reg_filename]
else:
self.job.activity = u'invalid physio found and discarded'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
else:
self.job.activity = u'no physio files found'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
else:
self.job.activity = u'physio not recorded'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
transaction.commit()
DBSession.add(self.job)
def find(self, slice_order, num_slices):
"""
Locate physio and generate physio regressors.
Find is called from within each pipeline's process() method after the file's slice_order
and num_slices attributes have been set, but before preparing the data to be written out.
This will use the num_slice and slice_order to create an array of the slice numbers in the
sequence they were acquired. Nimsphysio will use both the current data containers metadata,
like timestamp and duration, and metadata obtained by parsing the primary dataset file to
determine if physio is valid.
This method should never raise any exceptions.
Parameters
----------
slice_order : int
integer that corresponds to the appropriate NIFTI slice order code. 0 for unknown.
num_slices : int
number of slices
"""
self.clean(self.job.data_container, u'peripheral')
transaction.commit()
DBSession.add(self.job)
if self.physio_path is None: return # can't search w/o phys path
if not slice_order or not num_slices:
return # need both slice order AND num_slices to create regressors
if self.job.data_container.scanner_name == 'IRC MRC35068':
return # hack to ignore Davis files
dc = self.job.data_container
if dc.physio_recorded:
# 2015.02.03 RFD: apparently the old rule was incorrect. The physio files are not timestamped
# sometime after the Rxed duration, but rather sometime after the actual duration! We don't yet
# know the actual duration, so we'll just make shit up and hope for the best.
physio_lag = datetime.timedelta(seconds=30)
physio_files = nimsutil.find_ge_physio(self.physio_path,
dc.timestamp + physio_lag,
dc.psd.encode('utf-8'))
#physio_files = nimsutil.find_ge_physio(self.physio_path, dc.timestamp+dc.prescribed_duration, dc.psd.encode('utf-8'))
if physio_files:
physio = nimsphysio.NIMSPhysio(
physio_files, dc.tr, dc.num_timepoints,
nimsdata.medimg.medimg.get_slice_order(
slice_order, num_slices))
if physio.is_valid():
self.job.activity = u'valid physio found (%s...)' % os.path.basename(
physio_files[0])
log.info(u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
dataset = Dataset.at_path(self.nims_path, u'physio')
DBSession.add(self.job)
DBSession.add(self.job.data_container)
dataset.kind = u'peripheral'
dataset.container = self.job.data_container
with nimsutil.TempDir(dir=self.tempdir) as tempdir_path:
arcdir_path = os.path.join(
tempdir_path,
'%s_physio' % self.job.data_container.name)
os.mkdir(arcdir_path)
for f in physio_files:
shutil.copy2(f, arcdir_path)
filename = '%s_physio.tgz' % self.job.data_container.name
dataset.filenames = [filename]
with tarfile.open(os.path.join(self.nims_path,
dataset.relpath,
filename),
'w:gz',
compresslevel=6) as archive:
archive.add(arcdir_path,
arcname=os.path.basename(arcdir_path))
try:
reg_filename = '%s_physio_regressors.csv.gz' % self.job.data_container.name
physio.write_regressors(
os.path.join(self.nims_path, dataset.relpath,
reg_filename))
self.job.activity = u'physio regressors %s written' % reg_filename
log.info(
u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
except nimsphysio.NIMSPhysioError:
self.job.activity = u'error generating regressors from physio data'
log.info(
u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
else:
dataset.filenames += [reg_filename]
else:
self.job.activity = u'invalid physio found and discarded'
log.info(u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
else:
self.job.activity = u'no physio files found'
log.info(u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
else:
self.job.activity = u'physio not recorded'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
transaction.commit()
DBSession.add(self.job)
def find(self):
self.clean(self.job.data_container, u'peripheral')
transaction.commit()
DBSession.add(self.job)
dc = self.job.data_container
ds = self.job.data_container.primary_dataset
if dc.physio_recorded:
physio_files = nimsutil.find_ge_physio(
self.physio_path, dc.timestamp + dc.prescribed_duration,
dc.psd.encode('utf-8'))
if physio_files:
physio = nimsdata.nimsphysio.NIMSPhysio(
physio_files, dc.tr, dc.num_timepoints)
if physio.is_valid():
self.job.activity = u'valid physio found'
log.info(u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
# Computing the slice-order can be expensive, so we didn't do it when we instantiated.
# But now that we know physio is valid, we need to do it.
ni = nimsdata.parse(
os.path.join(self.nims_path, ds.primary_file_relpath))
physio.slice_order = ni.get_slice_order(
) # TODO: should probably write a set method
dataset = Dataset.at_path(self.nims_path, u'physio')
DBSession.add(self.job)
DBSession.add(self.job.data_container)
dataset.kind = u'peripheral'
dataset.container = self.job.data_container
with nimsutil.TempDir(dir=self.tempdir) as tempdir_path:
arcdir_path = os.path.join(
tempdir_path,
'%s_physio' % self.job.data_container.name)
os.mkdir(arcdir_path)
for f in physio_files:
shutil.copy2(f, arcdir_path)
filename = '%s_physio.tgz' % self.job.data_container.name
dataset.filenames = [filename]
with tarfile.open(os.path.join(self.nims_path,
dataset.relpath,
filename),
'w:gz',
compresslevel=6) as archive:
archive.add(arcdir_path,
arcname=os.path.basename(arcdir_path))
try:
reg_filename = '%s_physio_regressors.csv.gz' % self.job.data_container.name
physio.write_regressors(
os.path.join(self.nims_path, dataset.relpath,
reg_filename))
except nimsdata.nimsphysio.NIMSPhysioError:
self.job.activity = u'error generating regressors from physio data'
log.info(
u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
else:
dataset.filenames += [reg_filename]
else:
self.job.activity = u'invalid physio found and discarded'
log.info(u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
else:
self.job.activity = u'no physio files found'
log.info(u'%d %s %s' %
(self.job.id, self.job, self.job.activity))
else:
self.job.activity = u'physio not recorded'
log.info(u'%d %s %s' % (self.job.id, self.job, self.job.activity))
transaction.commit()
DBSession.add(self.job)
