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STYLE: Super-resolution id as string
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@pdedumast
pdedumast committed Jun 10, 2020
1 parent e2875ee commit 319619c
Showing 1 changed file with 21 additions and 21 deletions.
42 changes: 21 additions & 21 deletions pymialsrtk/pipelines/anatomical/srr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,15 +48,15 @@ def create_workflow(bids_dir, process_dir, subject, p_stacksOrder, session=None,
wf_base_dir = os.path.join(process_dir, subject)
process_dir = os.path.join(process_dir, subject)
else:
wf_base_dir = os.path.join(process_dir, subject, str(srID))
process_dir = os.path.join(process_dir, subject, str(srID))
wf_base_dir = os.path.join(process_dir, subject, srID)
process_dir = os.path.join(process_dir, subject, srID)
else:
if srID is None:
wf_base_dir = os.path.join(process_dir, subject, session)
process_dir = os.path.join(process_dir, subject, session)
else:
wf_base_dir = os.path.join(process_dir, subject, session, str(srID))
process_dir = os.path.join(process_dir, subject, session, str(srID))
wf_base_dir = os.path.join(process_dir, subject, session, srID)
process_dir = os.path.join(process_dir, subject, session, srID)

if not os.path.exists(process_dir):
os.makedirs(process_dir)
Expand Down Expand Up @@ -226,7 +226,7 @@ def create_workflow(bids_dir, process_dir, subject, p_stacksOrder, session=None,
if srID is None:
dictsink.inputs.out_file = os.path.join(output_dir, 'anat', sub_ses+'_rec-SR_T2w.json')
else:
dictsink.inputs.out_file = os.path.join(output_dir, 'anat', sub_ses+'_rec-SR'+'_srID-'+str(int(srID))+'_T2w.json')
dictsink.inputs.out_file = os.path.join(output_dir, 'anat', sub_ses+'_rec-SR'+'_id-'+srID+'_T2w.json')


#
Expand Down Expand Up @@ -325,24 +325,24 @@ def create_workflow(bids_dir, process_dir, subject, p_stacksOrder, session=None,
else:
for stack in p_stacksOrder:

print( sub_ses+'_run-'+str(stack)+'_T2w_nlm_uni_bcorr_histnorm.nii.gz', ' ---> ',sub_ses+'_run-'+str(stack)+'_srID-'+str(int(srID))+'_T2w_preproc.nii.gz')
substitutions.append( ( sub_ses+'_run-'+str(stack)+'_T2w_nlm_uni_bcorr_histnorm.nii.gz', sub_ses+'_run-'+str(stack)+'_srID-'+str(int(srID))+'_T2w_preproc.nii.gz') )
print( sub_ses+'_run-'+str(stack)+'_T2w_nlm_uni_bcorr_histnorm.nii.gz', ' ---> ',sub_ses+'_run-'+str(stack)+'_id-'+srID+'_T2w_preproc.nii.gz')
substitutions.append( ( sub_ses+'_run-'+str(stack)+'_T2w_nlm_uni_bcorr_histnorm.nii.gz', sub_ses+'_run-'+str(stack)+'_id-'+srID+'_T2w_preproc.nii.gz') )

print( sub_ses+'_run-'+str(stack)+'_T2w_nlm_uni_bcorr_histnorm_transform_'+str(len(p_stacksOrder))+'V.txt', ' ---> ', sub_ses+'_run-'+str(stack)+'_srID-'+str(int(srID))+'_T2w_from-origin_to-SDI_mode-image_xfm.txt')
substitutions.append( ( sub_ses+'_run-'+str(stack)+'_T2w_nlm_uni_bcorr_histnorm_transform_'+str(len(p_stacksOrder))+'V.txt', sub_ses+'_run-'+str(stack)+'_srID-'+str(int(srID))+'_T2w_from-origin_to-SDI_mode-image_xfm.txt') )
print( sub_ses+'_run-'+str(stack)+'_T2w_nlm_uni_bcorr_histnorm_transform_'+str(len(p_stacksOrder))+'V.txt', ' ---> ', sub_ses+'_run-'+str(stack)+'_id-'+srID+'_T2w_from-origin_to-SDI_mode-image_xfm.txt')
substitutions.append( ( sub_ses+'_run-'+str(stack)+'_T2w_nlm_uni_bcorr_histnorm_transform_'+str(len(p_stacksOrder))+'V.txt', sub_ses+'_run-'+str(stack)+'_id-'+srID+'_T2w_from-origin_to-SDI_mode-image_xfm.txt') )

print( sub_ses+'_run-'+str(stack)+'_T2w_uni_bcorr_histnorm_LRmask.nii.gz', ' ---> ', sub_ses+'_run-'+str(stack)+'_srID-'+str(int(srID))+'_T2w_desc-LRmask.nii.gz')
substitutions.append( ( sub_ses+'_run-'+str(stack)+'_T2w_uni_bcorr_histnorm_LRmask.nii.gz', sub_ses+'_run-'+str(stack)+'_srID-'+str(int(srID))+'_T2w_desc-LRmask.nii.gz') )
print( sub_ses+'_run-'+str(stack)+'_T2w_uni_bcorr_histnorm_LRmask.nii.gz', ' ---> ', sub_ses+'_run-'+str(stack)+'_id-'+srID+'_T2w_desc-LRmask.nii.gz')
substitutions.append( ( sub_ses+'_run-'+str(stack)+'_T2w_uni_bcorr_histnorm_LRmask.nii.gz', sub_ses+'_run-'+str(stack)+'_id-'+srID+'_T2w_desc-LRmask.nii.gz') )


print( 'SDI_'+sub_ses+'_'+str(len(p_stacksOrder))+'V_rad1.nii.gz', ' ---> ', sub_ses+'_rec-SDI'+'_srID-'+str(int(srID))+'_T2w.nii.gz')
substitutions.append( ( 'SDI_'+sub_ses+'_'+str(len(p_stacksOrder))+'V_rad1.nii.gz', sub_ses+'_rec-SDI'+'_srID-'+str(int(srID))+'_T2w.nii.gz') )
print( 'SDI_'+sub_ses+'_'+str(len(p_stacksOrder))+'V_rad1.nii.gz', ' ---> ', sub_ses+'_rec-SDI'+'_id-'+srID+'_T2w.nii.gz')
substitutions.append( ( 'SDI_'+sub_ses+'_'+str(len(p_stacksOrder))+'V_rad1.nii.gz', sub_ses+'_rec-SDI'+'_id-'+srID+'_T2w.nii.gz') )

print( 'SRTV_'+sub_ses+'_'+str(len(p_stacksOrder))+'V_rad1_gbcorr.nii.gz', ' ---> ', sub_ses+'_rec-SR'+'_srID-'+str(int(srID))+'_T2w.nii.gz')
substitutions.append( ( 'SRTV_'+sub_ses+'_'+str(len(p_stacksOrder))+'V_rad1_gbcorr.nii.gz', sub_ses+'_rec-SR'+'_srID-'+str(int(srID))+'_T2w.nii.gz') )
print( 'SRTV_'+sub_ses+'_'+str(len(p_stacksOrder))+'V_rad1_gbcorr.nii.gz', ' ---> ', sub_ses+'_rec-SR'+'_id-'+srID+'_T2w.nii.gz')
substitutions.append( ( 'SRTV_'+sub_ses+'_'+str(len(p_stacksOrder))+'V_rad1_gbcorr.nii.gz', sub_ses+'_rec-SR'+'_id-'+srID+'_T2w.nii.gz') )

print( sub_ses+'_T2w_uni_bcorr_histnorm_srMask.nii.gz', ' ---> ', sub_ses+'_rec-SR'+'_srID-'+str(int(srID))+'_T2w_desc-brain_mask.nii.gz')
substitutions.append( ( sub_ses+'_T2w_uni_bcorr_histnorm_srMask.nii.gz', sub_ses+'_rec-SR'+'_srID-'+str(int(srID))+'_T2w_desc-SRmask.nii.gz') )
print( sub_ses+'_T2w_uni_bcorr_histnorm_srMask.nii.gz', ' ---> ', sub_ses+'_rec-SR'+'_id-'+srID+'_T2w_desc-brain_mask.nii.gz')
substitutions.append( ( sub_ses+'_T2w_uni_bcorr_histnorm_srMask.nii.gz', sub_ses+'_rec-SR'+'_id-'+srID+'_T2w_desc-SRmask.nii.gz') )



Expand Down Expand Up @@ -449,14 +449,14 @@ def get_parser():
continue

if 'paramTV' in sr_params.keys():
if 'srID' in sr_params.keys():
if 'sr-id' in sr_params.keys():
main(bids_dir=args.bids_dir,
process_dir=args.output_dir,
subject=sub,
p_stacksOrder=sr_params['stacksOrder'],
session=ses,
paramTV=sr_params['paramTV'],
srID=sr_params['srID'])
srID=sr_params['sr-id'])
else:
main(bids_dir=args.bids_dir,
process_dir=args.output_dir,
Expand All @@ -466,13 +466,13 @@ def get_parser():
paramTV=sr_params['paramTV'])

else:
if 'srID' in sr_params.keys():
if 'sr-id' in sr_params.keys():
main(bids_dir=args.bids_dir,
process_dir=args.output_dir,
subject=sub,
p_stacksOrder=sr_params['stacksOrder'],
session=ses,
srID=sr_params['srID'])
srID=sr_params['sr-id'])
else:
main(bids_dir=args.bids_dir,
process_dir=args.output_dir,
Expand Down

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