linting

PennLINC · Aug 17, 2024 · bd32719 · bd32719
1 parent 1fa7373
commit bd32719
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Showing 3 changed files with 9 additions and 6 deletions.
diff --git a/qsirecon/interfaces/anatomical.py b/qsirecon/interfaces/anatomical.py
@@ -190,7 +190,8 @@ def _run_interface(self, runtime):
         self._results["t1_brain_mask"] = conformed_mask_file
 
         return runtime
-
+
+
 class HCPAnatomicalIngressInputSpec(QSIReconAnatomicalIngressInputSpec):
     recon_input_dir = traits.Directory(
         exists=True, mandatory=True, help="directory containing a single subject's results"

diff --git a/qsirecon/interfaces/ingress.py b/qsirecon/interfaces/ingress.py
@@ -178,6 +178,7 @@ def _run_interface(self, runtime):
         self._results["dwi_ref"] = dwiref_file
         return runtime
 
+
 class _HCPDWIIngressInputSpec(QsiReconDWIIngressInputSpec):
     dwi_file = File(exists=False, help="The name of what a BIDS dwi file may have been")
     data_dir = traits.Directory(
@@ -198,7 +199,7 @@ def _run_interface(self, runtime):
         hcp_bval_file = op.join(dwi_dir, "bvals")
         hcp_bvec_file = op.join(dwi_dir, "bvecs")  # These are the same as eddy rotated
         hcp_dwi_file = op.join(dwi_dir, "data.nii.gz")
-        #hcp_dwiref_file = op.join(dwi_dir, "dti_FA.nii.gz")
+        # hcp_dwiref_file = op.join(dwi_dir, "dti_FA.nii.gz")
 
         # The bids_name is what the images will be renamed to
         bids_name = Path(self.inputs.dwi_file).name.replace(".nii.gz", "")
@@ -207,7 +208,7 @@ def _run_interface(self, runtime):
         bvec_file = str(runpath / (bids_name + ".bvec"))
         b_file = str(runpath / (bids_name + ".b"))
         btable_file = str(runpath / (bids_name + "btable.txt"))
-        #dwiref_file = str(runpath / (bids_name.replace("_dwi", "_dwiref") + ".nii.gz"))
+        # dwiref_file = str(runpath / (bids_name.replace("_dwi", "_dwiref") + ".nii.gz"))
 
         dwi_conform = ConformDwi(
             dwi_file=str(hcp_dwi_file), bval_file=str(hcp_bval_file), bvec_file=str(hcp_bvec_file)
@@ -231,6 +232,6 @@ def _run_interface(self, runtime):
         self._results["b_file"] = b_file
 
         # Create a dwi ref file
-        #to_lps(nb.load(hcp_dwiref_file)).to_filename(dwiref_file)
-        #self._results["dwi_ref"] = dwiref_file
+        # to_lps(nb.load(hcp_dwiref_file)).to_filename(dwiref_file)
+        # self._results["dwi_ref"] = dwiref_file
         return runtime
diff --git a/qsirecon/workflows/base.py b/qsirecon/workflows/base.py
@@ -47,6 +47,7 @@ def init_qsirecon_wf():
         )
     elif config.workflow.recon_input_pipeline == "hcpya":
         from ..utils.ingress import collect_hcp_participants, create_hcp_layout
+
         # The hcp input will always be specified as the bids input - we can't preproc it first
         hcp_layout = create_hcp_layout(config.execution.bids_dir)
         to_recon_list = collect_hcp_participants(
@@ -321,7 +322,7 @@ def _get_iterable_dwi_inputs(subject_id):
 
     elif config.workflow.recon_input_pipeline == "ukb":
         return create_ukb_layout(ukb_dir=config.execution.bids_dir, participant_label=subject_id)
-    
+
     elif config.workflow.recon_input_pipeline == "hcpya":
         return create_hcp_layout(hcp_dir=config.execution.bids_dir, participant_label=subject_id)