STYLE: Cleaning for codacy

Medical-Image-Analysis-Laboratory · Nov 24, 2020 · 95fd1c0 · 95fd1c0
1 parent d1f9ebc
commit 95fd1c0
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Showing 3 changed files with 4 additions and 8 deletions.
diff --git a/pymialsrtk/interfaces/preprocess.py b/pymialsrtk/interfaces/preprocess.py
@@ -1368,7 +1368,8 @@ def _compute_motion_index(self, in_file):
 
         img = nibabel.load(in_file)
 
-        voxelspacing = img.header['pixdim'][2]
+        # Todo: Compute centroid displacement as a distance instead of a number of voxel
+        # voxelspacing = img.header['pixdim'][2]
         data = img.get_fdata()
 
         z = np.where(data)[2]

diff --git a/pymialsrtk/interfaces/reconstruction.py b/pymialsrtk/interfaces/reconstruction.py
@@ -376,7 +376,8 @@ def _run_interface(self, runtime):
         cmd += ['--outer-thresh', str(self.inputs.in_outer_thresh)]
 
         # JSON file SRTV
-        self.m_output_dict["Description"] = "Isotropic high-resolution image reconstructed using the Total-Variation Super-Resolution algorithm provided by MIALSRTK"
+        self.m_output_dict["Description"] = "Isotropic high-resolution image reconstructed using the Total-Variation" \
+                                            " Super-Resolution algorithm provided by MIALSRTK"
         self.m_output_dict["Input sources run order"] = self.inputs.stacks_order
         self.m_output_dict["CustomMetaData"] = {}
         self.m_output_dict["CustomMetaData"]["Number of scans used"] = str(len(self.inputs.stacks_order))

diff --git a/pymialsrtk/pipelines/anatomical/srr.py b/pymialsrtk/pipelines/anatomical/srr.py
@@ -320,8 +320,6 @@ def create_workflow(self):
         srtkTVSuperResolution.inputs.in_lambda = self.lambdaTV
         srtkTVSuperResolution.inputs.use_manual_masks = self.use_manual_masks
 
-        srTVdictSink = Node(JSONFileSink(),name='srtv_json_sinker')
-
         srtkRefineHRMaskByIntersection = Node(interface=postprocess.MialsrtkRefineHRMaskByIntersection(), name='srtkRefineHRMaskByIntersection')
         srtkRefineHRMaskByIntersection.inputs.bids_dir = self.bids_dir
 
@@ -408,9 +406,6 @@ def create_workflow(self):
         self.wf.connect(srtkImageReconstruction, ("output_transforms", utils.sort_ascending), srtkRefineHRMaskByIntersection, "input_transforms")
         self.wf.connect(srtkTVSuperResolution, "output_sr", srtkRefineHRMaskByIntersection, "input_sr")
 
-        # self.wf.connect(srtkTVSuperResolution, "output_dict", srTVdictSink, "in_dict")
-        # self.wf.connect(srtkTVSuperResolution, "output_json_path", srTVdictSink, "out_file")
-
         self.wf.connect(srtkTVSuperResolution, "output_sr", srtkMaskImage02, "in_file")
         self.wf.connect(srtkRefineHRMaskByIntersection, "output_srmask", srtkMaskImage02, "in_mask")
 
@@ -427,7 +422,6 @@ def create_workflow(self):
 
         self.wf.connect(srtkImageReconstruction, "output_sdi", datasink, 'anat.@SDI')
         self.wf.connect(srtkN4BiasFieldCorrection, "output_image", datasink, 'anat.@SR')
-        # self.wf.connect(srTVdictSink, "out_file", datasink, 'anat.@SRjson')
         self.wf.connect(srtkTVSuperResolution, "output_json_path", datasink, 'anat.@SRjson')
         self.wf.connect(srtkRefineHRMaskByIntersection, "output_srmask", datasink, 'anat.@SRmask')