fixed white-space and extra indentations

Author: amygutierrez

CPAC/nuisance/nuisance.py

@@ -1714,7 +1714,7 @@ def ICA_AROMA_FSLreg(wf, cfg, strat_pool, pipe_num, opt=None):
      "inputs": [["desc-preproc_bold", "bold"],
                 "from-bold_to-T1w_mode-image_desc-linear_xfm",
                 "from-T1w_to-template_mode-image_xfm"],
-     "outputs": ["desc-preproc_bold", 
+     "outputs": ["desc-preproc_bold",
                  "desc-cleaned_bold"]}
     '''
 
@@ -1864,8 +1864,8 @@ def ICA_AROMA_FSLEPIreg(wf, cfg, strat_pool, pipe_num, opt=None):
     }
 
     return (wf, outputs)
-    
-    
+
+
 def ICA_AROMA_ANTsEPIreg(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     Node Block:
@@ -1891,7 +1891,7 @@ def ICA_AROMA_ANTsEPIreg(wf, cfg, strat_pool, pipe_num, opt=None):
 
     if reg_tool != 'ants':
         return (wf, None)
-        
+
     num_cpus = cfg.pipeline_setup['system_config'][
         'max_cores_per_participant']
 
@@ -1928,7 +1928,7 @@ def ICA_AROMA_ANTsEPIreg(wf, cfg, strat_pool, pipe_num, opt=None):
 
     node, out = strat_pool.get_data('from-EPItemplate_to-bold_mode-image_xfm')
     wf.connect(node, out, apply_xfm, 'inputspec.transform')
-    
+
     outputs = {
         'desc-preproc_bold': (apply_xfm, 'outputspec.output_image'),
         'desc-cleaned_bold': (apply_xfm, 'outputspec.output_image')
@@ -1962,7 +1962,7 @@ def erode_mask_T1w(wf, cfg, strat_pool, pipe_num, opt=None):
 
     node, out = strat_pool.get_data('space-T1w_desc-brain_mask')
     wf.connect(node, out, erode, 'inputspec.brain_mask')
-    
+
     node, out = strat_pool.get_data(['label-CSF_desc-preproc_mask',
                                      'label-CSF_mask'])
     wf.connect(node, out, erode, 'inputspec.mask')
@@ -2077,15 +2077,15 @@ def erode_mask_WM(wf, cfg, strat_pool, pipe_num, opt=None):
     erode.inputs.inputspec.erode_prop = cfg.nuisance_corrections[
         '2-nuisance_regression']['regressor_masks']['erode_wm'][
         'wm_erosion_prop']
-        
+
     erode.inputs.inputspec.mask_erode_mm = cfg.nuisance_corrections[
         '2-nuisance_regression']['regressor_masks']['erode_wm'][
         'wm_mask_erosion_mm']
 
     node, out = strat_pool.get_data(['label-WM_desc-preproc_mask',
                                      'label-WM_mask'])
     wf.connect(node, out, erode, 'inputspec.mask')
-    
+
     node, out = strat_pool.get_data('space-T1w_desc-brain_mask')
     wf.connect(node, out, erode, 'inputspec.brain_mask')
 
@@ -2094,8 +2094,8 @@ def erode_mask_WM(wf, cfg, strat_pool, pipe_num, opt=None):
     }
 
     return (wf, outputs)
-    
-    
+
+
 def nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     Node Block:
@@ -2130,9 +2130,11 @@ def nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt=None):
             'from-template_to-T1w_mode-image_desc-linear_xfm')
         reg_tool = check_prov_for_regtool(xfm_prov)
         use_ants = reg_tool == 'ants'
-    
+
     ventricle = strat_pool.check_rpool('lateral-ventricles-mask')
-    csf_mask = strat_pool.check_rpool(["label-CSF_desc-eroded_mask", "label-CSF_desc-preproc_mask", "label-CSF_mask"])
+    csf_mask = strat_pool.check_rpool(["label-CSF_desc-eroded_mask",
+                                        "label-CSF_desc-preproc_mask",
+                                        "label-CSF_mask"])
 
     regressors = create_regressor_workflow(opt, use_ants,
                                            ventricle_mask_exist=ventricle,
@@ -2161,7 +2163,7 @@ def nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt=None):
                                "label-CSF_desc-preproc_mask",
                                "label-CSF_mask"]):
         node, out = strat_pool.get_data(["label-CSF_desc-eroded_mask",
-                                         "label-CSF_desc-preproc_mask", 
+                                         "label-CSF_desc-preproc_mask",
                                          "label-CSF_mask"])
         wf.connect(node, out, regressors, 'inputspec.csf_mask_file_path')
 
@@ -2174,10 +2176,10 @@ def nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt=None):
         wf.connect(node, out, regressors, 'inputspec.wm_mask_file_path')
 
     if strat_pool.check_rpool(["label-GM_desc-eroded_mask",
-                               "label-GM_desc-preproc_mask", 
+                               "label-GM_desc-preproc_mask",
                                "label-GM_mask"]):
         node, out = strat_pool.get_data(["label-GM_desc-eroded_mask",
-                                         "label-GM_desc-preproc_mask", 
+                                         "label-GM_desc-preproc_mask",
                                          "label-GM_mask"])
         wf.connect(node, out, regressors, 'inputspec.gm_mask_file_path')
 
@@ -2253,10 +2255,10 @@ def nuisance_regression(wf, cfg, strat_pool, pipe_num, opt=None):
                  "desc-cleaned_bold",
                  "regressors"]}
     '''
-    
+
     regressor_prov = strat_pool.get_cpac_provenance('regressors')
     regressor_strat_name = regressor_prov[-1].split('_')[-1]
-    
+
     for regressor_dct in cfg['nuisance_corrections']['2-nuisance_regression'][
         'Regressors']:
         if regressor_dct['Name'] == regressor_strat_name:
@@ -2316,7 +2318,7 @@ def nuisance_regression(wf, cfg, strat_pool, pipe_num, opt=None):
 
         elif cfg.nuisance_corrections['2-nuisance_regression'][
             'bandpass_filtering_order'] == 'Before':
-            
+
             node, out = strat_pool.get_data("desc-preproc_bold")
             wf.connect(node, out, filt, 'inputspec.functional_file_path')
 
@@ -2332,7 +2334,7 @@ def nuisance_regression(wf, cfg, strat_pool, pipe_num, opt=None):
     else:
         node, out = strat_pool.get_data("desc-preproc_bold")
         wf.connect(node, out, nuis, 'inputspec.functional_file_path')
-        
+
         outputs = {
             'desc-preproc_bold': (nuis, 'outputspec.residual_file_path'),
             'desc-cleaned_bold': (nuis, 'outputspec.residual_file_path')
@@ -2366,7 +2368,7 @@ def erode_mask_bold(wf, cfg, strat_pool, pipe_num, opt=None):
 
     node, out = strat_pool.get_data('space-bold_desc-brain_mask')
     wf.connect(node, out, erode, 'inputspec.brain_mask')
-    
+
     node, out = strat_pool.get_data(['space-bold_label-CSF_desc-preproc_mask',
                                      'space-bold_label-CSF_mask'])
     wf.connect(node, out, erode, 'inputspec.mask')
@@ -2376,8 +2378,8 @@ def erode_mask_bold(wf, cfg, strat_pool, pipe_num, opt=None):
     }
 
     return (wf, outputs)
-    
-    
+
+
 def erode_mask_boldCSF(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     {"name": "erode_mask_boldCSF",
@@ -2481,15 +2483,15 @@ def erode_mask_boldWM(wf, cfg, strat_pool, pipe_num, opt=None):
     erode.inputs.inputspec.erode_prop = cfg.nuisance_corrections[
         '2-nuisance_regression']['regressor_masks']['erode_wm'][
         'wm_erosion_prop']
-        
+
     erode.inputs.inputspec.mask_erode_mm = cfg.nuisance_corrections[
         '2-nuisance_regression']['regressor_masks']['erode_wm'][
         'wm_mask_erosion_mm']
 
     node, out = strat_pool.get_data(['space-bold_label-WM_desc-preproc_mask',
                                      'space-bold_label-WM_mask'])
     wf.connect(node, out, erode, 'inputspec.mask')
-    
+
     node, out = strat_pool.get_data('space-bold_desc-brain_mask')
     wf.connect(node, out, erode, 'inputspec.brain_mask')
 
@@ -2516,7 +2518,7 @@ def nuisance_regressors_generation_EPItemplate(wf, cfg, strat_pool, pipe_num, op
                  "framewise-displacement-power",
                  "dvars",
                  ["space-bold_desc-eroded_mask", "space-bold_desc-brain_mask"],
-                 ["space-bold_label-CSF_desc-eroded_mask", "space-bold_label-CSF_desc-preproc_mask", 
+                 ["space-bold_label-CSF_desc-eroded_mask", "space-bold_label-CSF_desc-preproc_mask",
                   "space-bold_label-CSF_mask"],
                  ["space-bold_label-WM_desc-eroded_mask", "space-bold_label-WM_desc-preproc_mask",
                   "space-bold_label-WM_mask"],
@@ -2535,7 +2537,9 @@ def nuisance_regressors_generation_EPItemplate(wf, cfg, strat_pool, pipe_num, op
 
     use_ants = reg_tool == 'ants'
     ventricle = strat_pool.check_rpool('lateral-ventricles-mask')
-    csf_mask = strat_pool.check_rpool([ "space-bold_label-CSF_desc-eroded_mask", "space-bold_label-CSF_desc-preproc_mask", "space-bold_label-CSF_mask"])
+    csf_mask = strat_pool.check_rpool(["space-bold_label-CSF_desc-eroded_mask",
+                                        "space-bold_label-CSF_desc-preproc_mask",
+                                        "space-bold_label-CSF_mask"])
 
     regressors = create_regressor_workflow(opt, use_ants,
                                            ventricle_mask_exist=ventricle,
@@ -2596,15 +2600,15 @@ def nuisance_regressors_generation_EPItemplate(wf, cfg, strat_pool, pipe_num, op
         wf.connect(node, out, regressors, 'inputspec.anat_to_mni_linear_xfm_file_path')
         wf.connect(node, out, regressors, 'inputspec.func_to_anat_linear_xfm_file_path')
 
-    if strat_pool.check_rpool('movement-parameters'):    
+    if strat_pool.check_rpool('movement-parameters'):
         node, out = strat_pool.get_data('movement-parameters')
         wf.connect(node, out, regressors, 'inputspec.motion_parameters_file_path')
 
-    if strat_pool.check_rpool('framewise-displacement-jenkinson'):    
+    if strat_pool.check_rpool('framewise-displacement-jenkinson'):
         node, out = strat_pool.get_data('framewise-displacement-jenkinson')
         wf.connect(node, out, regressors, 'inputspec.fd_j_file_path')
 
-    if strat_pool.check_rpool('framewise-displacement-power'):    
+    if strat_pool.check_rpool('framewise-displacement-power'):
         node, out = strat_pool.get_data('framewise-displacement-power')
         wf.connect(node, out, regressors, 'inputspec.fd_p_file_path')
 
@@ -2619,4 +2623,4 @@ def nuisance_regressors_generation_EPItemplate(wf, cfg, strat_pool, pipe_num, op
         'regressors': (regressors, 'outputspec.regressors_file_path')
     }
 
-    return (wf, outputs)
+    return (wf, outputs)

CPAC/nuisance/utils/__init__.py

@@ -323,14 +323,13 @@ def generate_summarize_tissue_mask(nuisance_wf,
 
             if all_bold:
                 pass
-            
+
             if csf_mask_exist:
                 mask_to_epi = pe.Node(interface=fsl.FLIRT(),
-                                    name='{}_flirt'
-                                        .format(node_mask_key),
-                            mem_gb=3.63,
-                            mem_x=(3767129957844731 / 1208925819614629174706176,
-                               'in_file'))
+                                name='{}_flirt'.format(node_mask_key),
+                                mem_gb=3.63,
+                                mem_x=(3767129957844731 / 1208925819614629174706176,
+                                    'in_file'))
 
                 mask_to_epi.inputs.interp = 'nearestneighbour'
 
@@ -445,13 +444,19 @@ def generate_summarize_tissue_mask_ventricles_masking(nuisance_wf,
 
                     nuisance_wf.connect(*(pipeline_resource_pool['Ventricles'] + (lat_ven_mni_to_anat, 'input_image')))
                     resolution = regressor_selector['extraction_resolution']
-                    
+
                     if csf_mask_exist:
-                        nuisance_wf.connect(*(pipeline_resource_pool[mask_key] + (lat_ven_mni_to_anat, 'reference_image')))
+                        nuisance_wf.connect(*(
+                            pipeline_resource_pool[mask_key] +
+                            (lat_ven_mni_to_anat, 'reference_image')))
                     elif resolution == 'Functional':
-                        nuisance_wf.connect(*(pipeline_resource_pool['Functional_mean'] + (lat_ven_mni_to_anat, 'reference_image')))
+                        nuisance_wf.connect(*(
+                            pipeline_resource_pool['Functional_mean'] +
+                            (lat_ven_mni_to_anat, 'reference_image')))
                     else:
-                        nuisance_wf.connect(*(pipeline_resource_pool['Anatomical_{}mm'.format(resolution)] + (lat_ven_mni_to_anat, 'reference_image')))
+                        nuisance_wf.connect(*(
+                            pipeline_resource_pool['Anatomical_{}mm'.format(resolution)] + 
+                            (lat_ven_mni_to_anat, 'reference_image')))
 
                     pipeline_resource_pool[ventricles_key] = (lat_ven_mni_to_anat, 'output_image')
 
@@ -469,18 +474,19 @@ def generate_summarize_tissue_mask_ventricles_masking(nuisance_wf,
 
             if csf_mask_exist:
                 # reduce CSF mask to the lateral ventricles
-                mask_csf_with_lat_ven = pe.Node(interface=afni.Calc(outputtype='NIFTI_GZ'), name='{}_Ventricles'.format(mask_key))
+                mask_csf_with_lat_ven = pe.Node(interface=afni.Calc(outputtype='NIFTI_GZ'),
+                                                name='{}_Ventricles'.format(mask_key))
                 mask_csf_with_lat_ven.inputs.expr = 'a*b'
                 mask_csf_with_lat_ven.inputs.out_file = 'csf_lat_ven_mask.nii.gz'
-                
+
                 nuisance_wf.connect(*(pipeline_resource_pool[ventricles_key] + (mask_csf_with_lat_ven, 'in_file_a')))
                 nuisance_wf.connect(*(pipeline_resource_pool[mask_key] + (mask_csf_with_lat_ven, 'in_file_b')))
 
                 pipeline_resource_pool['{}_Unmasked'.format(mask_key)] = pipeline_resource_pool[mask_key]
                 pipeline_resource_pool[mask_key] = (mask_csf_with_lat_ven, 'out_file')
 
             else:
-                pipeline_resource_pool[mask_key] = pipeline_resource_pool[ventricles_key]  
+                pipeline_resource_pool[mask_key] = pipeline_resource_pool[ventricles_key]
 
         return pipeline_resource_pool
 
@@ -694,4 +700,4 @@ def encode(selector):
         return "_".join(selectors_representations)
 
     def __repr__(self):
-        return NuisanceRegressor.encode(self.selector)
+        return NuisanceRegressor.encode(self.selector)