def check_input(self, layout, gui=True):
"""Method that checks if inputs of the diffusion pipeline are available in the datasets.
Parameters
-----------
layout : bids.BIDSLayout
BIDSLayout object used to query
gui : bool
If True, display message in GUI
Returns
-------
valid_inputs : bool
True in all inputs of the anatomical pipeline are available
"""
print('**** Check Inputs ****')
diffusion_available = False
bvecs_available = False
bvals_available = False
valid_inputs = False
if self.global_conf.subject_session == '':
subject = self.subject
else:
subject = "_".join(
(self.subject, self.global_conf.subject_session))
dwi_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.nii.gz')
bval_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.bval')
bvec_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.bvec')
subjid = self.subject.split("-")[1]
try:
layout = BIDSLayout(self.base_directory)
print("Valid BIDS dataset with %s subjects" %
len(layout.get_subjects()))
for subj in layout.get_subjects():
self.global_conf.subjects.append('sub-' + str(subj))
# self.global_conf.subjects = ['sub-'+str(subj) for subj in layout.get_subjects()]
# self.global_conf.modalities = [
# str(mod) for mod in layout.get_modalities()]
# mods = layout.get_modalities()
types = layout.get_modalities()
# print "Available modalities :"
# for mod in mods:
# print "-%s" % mod
if self.global_conf.subject_session == '':
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.nii.gz')
if len(files) > 0:
dwi_file = os.path.join(files[0].dirname,
files[0].filename)
print(dwi_file)
else:
error(message="Diffusion image not found for subject %s." %
subjid,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bval')
if len(files) > 0:
bval_file = os.path.join(files[0].dirname,
files[0].filename)
print(bval_file)
else:
error(
message="Diffusion bval image not found for subject %s."
% subjid,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bvec')
if len(files) > 0:
bvec_file = os.path.join(files[0].dirname,
files[0].filename)
print(bvec_file)
else:
error(
message="Diffusion bvec image not found for subject %s."
% subjid,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
else:
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
dwi_file = os.path.join(files[0].dirname,
files[0].filename)
print(dwi_file)
else:
error(
message=
"Diffusion image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bval',
session=sessid)
if len(files) > 0:
bval_file = os.path.join(files[0].dirname,
files[0].filename)
print(bval_file)
else:
error(
message=
"Diffusion bval image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bvec',
session=sessid)
if len(files) > 0:
bvec_file = os.path.join(files[0].dirname,
files[0].filename)
print(bvec_file)
else:
error(
message=
"Diffusion bvec image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
print("Looking for....")
print("dwi_file : %s" % dwi_file)
print("bvecs_file : %s" % bvec_file)
print("bvals_file : %s" % bval_file)
if os.path.isfile(dwi_file):
print("DWI available")
diffusion_available = True
except Exception:
error(
message=
"Invalid BIDS dataset. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
if os.path.isfile(bval_file):
bvals_available = True
if os.path.isfile(bvec_file):
bvecs_available = True
if diffusion_available:
if bvals_available and bvecs_available:
self.stages[
'Diffusion'].config.diffusion_imaging_model_choices = self.diffusion_imaging_model
# Copy diffusion data to derivatives / cmp / subject / dwi
if self.global_conf.subject_session == '':
out_dwi_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.nii.gz')
out_bval_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.bval')
out_bvec_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.bvec')
else:
out_dwi_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.nii.gz')
out_bval_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.bval')
out_bvec_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.bvec')
if not os.path.isfile(out_dwi_file):
shutil.copy(src=dwi_file, dst=out_dwi_file)
if not os.path.isfile(out_bvec_file):
shutil.copy(src=bvec_file, dst=out_bvec_file)
if not os.path.isfile(out_bval_file):
shutil.copy(src=bval_file, dst=out_bval_file)
valid_inputs = True
input_message = 'Inputs check finished successfully.\nDiffusion and morphological data available.'
else:
input_message = 'Error during inputs check.\nDiffusion bvec or bval files not available.'
else:
if self.global_conf.subject_session == '':
input_message = 'Error during inputs check. No diffusion data available in folder ' + os.path.join(
self.base_directory, self.subject, 'dwi') + '!'
else:
input_message = 'Error during inputs check. No diffusion data available in folder ' + os.path.join(
self.base_directory, self.subject,
self.global_conf.subject_session, 'dwi') + '!'
if gui:
# input_notification = Check_Input_Notification(message=input_message,
# diffusion_imaging_model_options=diffusion_imaging_model,
# diffusion_imaging_model=diffusion_imaging_model)
# input_notification.configure_traits()
print(input_message)
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
else:
print(input_message)
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
if diffusion_available:
valid_inputs = True
else:
print("Missing required inputs.")
error(
message=
"Missing diffusion inputs. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
# for stage in self.stages.values():
# if stage.enabled:
# print stage.name
# print stage.stage_dir
# self.fill_stages_outputs()
return valid_inputs
from bids import BIDSLayout bids_dataset = '/home/emdupre/Desktop/ds000007' # Change to your dataset location ! # first, we want to make sure we have a valid BIDS dataset ! # let's navigate to : # https://bids-standard.github.io/bids-validator/ layout = BIDSLayout(bids_dataset) # Let's learn a little about the data we have layout.description layout.get_modalities() layout.get_tasks()
