flake8

Macatools · Feb 28, 2024 · 473b36c · 473b36c
1 parent a151856
commit 473b36c
Show file tree

Hide file tree

Showing 3 changed files with 22 additions and 31 deletions.
diff --git a/macapype/pipelines/prepare.py b/macapype/pipelines/prepare.py
@@ -736,29 +736,33 @@ def create_short_preparation_pipe(params, params_template={},
 
             if "use_T2" in params.keys():
 
-
                 if "crop_z_T1" in params.keys():
-                    data_preparation_pipe.connect(crop_z_T1, "out_roi",
-                                                outputnode, 'preproc_T2')
+                    data_preparation_pipe.connect(
+                        crop_z_T1, "out_roi",
+                        outputnode, 'preproc_T2')
                 else:
-                    data_preparation_pipe.connect(crop_aladin_T1, "res_file",
-                                                outputnode, 'preproc_T2')
+                    data_preparation_pipe.connect(
+                        crop_aladin_T1, "res_file",
+                        outputnode, 'preproc_T2')
 
-                data_preparation_pipe.connect(apply_crop_aladin_T2, 'out_file',
-                                            outputnode, 'preproc_T1')
+                data_preparation_pipe.connect(
+                    apply_crop_aladin_T2, 'out_file',
+                    outputnode, 'preproc_T1')
 
             else:
 
-
                 if "crop_z_T1" in params.keys():
-                    data_preparation_pipe.connect(crop_z_T1, "out_roi",
-                                                outputnode, 'preproc_T1')
+                    data_preparation_pipe.connect(
+                        crop_z_T1, "out_roi",
+                        outputnode, 'preproc_T1')
                 else:
-                    data_preparation_pipe.connect(crop_aladin_T1, "res_file",
-                                                outputnode, 'preproc_T1')
+                    data_preparation_pipe.connect(
+                        crop_aladin_T1, "res_file",
+                        outputnode, 'preproc_T1')
 
-                data_preparation_pipe.connect(apply_crop_aladin_T2, 'out_file',
-                                            outputnode, 'preproc_T2')
+                data_preparation_pipe.connect(
+                    apply_crop_aladin_T2, 'out_file',
+                    outputnode, 'preproc_T2')
 
     return data_preparation_pipe
 

diff --git a/macapype/pipelines/register.py b/macapype/pipelines/register.py
@@ -15,6 +15,7 @@
                               NMTSubjectAlign2, NwarpApplyPriors,
                               animal_warper)
 
+
 def create_iterative_register_pipe(
         template_file, template_brain_file, template_mask_file, gm_prob_file,
         wm_prob_file, csf_prob_file, n_iter, name="register_pipe"):
@@ -504,22 +505,6 @@ def create_native_to_stereo_pipe(name="native_to_stereo_pipe", params={}):
                                       'native_to_stereo_trans']),
         name='outputnode')
 
-    ## pad_stereo_T1
-    #pad_template_T1 = NodeParams(
-        #interface=niu.Function(
-            #input_names=["img_file", "pad_val"],
-            #output_names=["img_padded_file"],
-            #function=pad_zero_mri),
-        #params=parse_key(params, "pad_template_T1"),
-        #name="pad_template_T1")
-
-    #reg_pipe.connect(inputnode, 'stereo_T1',
-                     #pad_template_T1, "img_file")
-
-    ## outputnode
-    #reg_pipe.connect(pad_template_T1, 'img_padded_file',
-                     #outputnode, "padded_stereo_T1")
-
     if "pre_crop_z_T1" in params.keys():
 
         print('pre_crop_z_T1')

diff --git a/macapype/pipelines/rename.py b/macapype/pipelines/rename.py
@@ -7,7 +7,9 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe,
                                  datasink, pref_deriv, parse_str,
                                  space, ssoft, datatypes):
 
-    if "fast" in params or "N4debias" in params or "correct_bias_pipe" in params:
+    if ("fast" in params
+            or "N4debias" in params
+            or "correct_bias_pipe" in params):
 
         # rename debiased_T1
         rename_debiased_T1 = pe.Node(