make flake8 happy

Author: chrisgorgo

fmriprep/interfaces/images.py

@@ -345,7 +345,6 @@ class ValidateImage(SimpleInterface):
     def _run_interface(self, runtime):
 
         def deoblique(img):
-            import os
             import nibabel as nb
             import numpy as np
             affine = img.affine
@@ -381,7 +380,8 @@ def deoblique(img):
         # Both match, qform valid (implicit with match), codes okay -> do nothing, empty report
         if matching_affines and qform_code > 0 and sform_code > 0:
             if self.inputs.deoblique:
-                out_fname = fname_presuffix(self.inputs.in_file, suffix='_valid', newpath=runtime.cwd)
+                out_fname = fname_presuffix(self.inputs.in_file, suffix='_valid',
+                                            newpath=runtime.cwd)
                 img = deoblique(img)
                 img.to_filename(out_fname)
                 self._results['out_file'] = out_fname

fmriprep/utils/misc.py

@@ -14,18 +14,17 @@ def split_and_deoblique_func(in_file):
     import numpy as np
     out_files = []
     for i, img in enumerate(iter_img(in_file)):
-        out_file = os.path.abspath('vol%04d.nii.gz'%i)
+        out_file = os.path.abspath('vol%04d.nii.gz' % i)
         affine = img.affine
-        affine[:3,:3] = np.diag(np.diag(affine[:3, :3]))
+        affine[:3, :3] = np.diag(np.diag(affine[:3, :3]))
         nb.Nifti1Image(np.asanyarray(img.dataobj), affine, img.header).to_filename(out_file)
         out_files.append(out_file)
     return out_files
 
 
 def afni2itk_func(in_file):
     import os
-    from scipy.io import loadmat, savemat
-    from numpy import loadtxt, around, hstack, vstack, zeros, float64
+    from numpy import loadtxt, hstack, vstack, zeros, float64
 
     def read_afni_affine(input_file, debug=False):
         orig_afni_mat = loadtxt(input_file)
@@ -34,13 +33,13 @@ def read_afni_affine(input_file, debug=False):
 
         output = []
         for i in range(orig_afni_mat.shape[0]):
-            output.append(vstack((orig_afni_mat[i,:].reshape(3, 4, order='C'), [0, 0, 0, 1])))
+            output.append(vstack((orig_afni_mat[i, :].reshape(3, 4, order='C'), [0, 0, 0, 1])))
         return output
 
     def get_ants_dict(affine, debug=False):
         out_dict = {}
-        out_dict['AffineTransform_double_3_3'] = hstack(
-            (affine[:3, :3].reshape(1, -1), affine[:3, 3].reshape(1, -1))).reshape(-1, 1).astype(float64)
+        ants_affine_2d = hstack((affine[:3, :3].reshape(1, -1), affine[:3, 3].reshape(1, -1)))
+        out_dict['AffineTransform_double_3_3'] = ants_affine_2d.reshape(-1, 1).astype(float64)
         out_dict['fixed'] = zeros((3, 1))
         if debug:
             print(out_dict)
@@ -51,11 +50,18 @@ def get_ants_dict(affine, debug=False):
     with open(out_file, 'w') as fp:
         fp.write("#Insight Transform File V1.0\n")
         for i, affine in enumerate(read_afni_affine(in_file)):
-            fp.write("#Transform %d\n"%i)
+            fp.write("#Transform %d\n" % i)
             fp.write("Transform: AffineTransform_double_3_3\n")
             trans_dict = get_ants_dict(affine)
-            fp.write("Parameters: " + ' '.join(["%g"%i for i in list(trans_dict['AffineTransform_double_3_3'])]) + "\n")
-            fp.write("FixedParameters: " + ' '.join(["%g"%i for i in list(trans_dict['fixed'])]) + "\n")
+
+            params_list = ["%g" % i for i in list(trans_dict['AffineTransform_double_3_3'])]
+            params_str = ' '.join(params_list)
+            fp.write("Parameters: " + params_str + "\n")
+
+            fixed_params_list = ["%g" % i for i in list(trans_dict['fixed'])]
+            fixed_params_str = ' '.join(fixed_params_list)
+            fp.write("FixedParameters: " + ' '.join(fixed_params_str) + "\n")
+
     return out_file
 
 

fmriprep/workflows/bold/base.py

@@ -15,7 +15,6 @@
 import nibabel as nb
 from nipype import logging
 
-from nipype.interfaces.fsl import Split as FSLSplit
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
 

fmriprep/workflows/bold/hmc.py

@@ -14,7 +14,6 @@
 from niworkflows.interfaces import NormalizeMotionParams
 from fmriprep.utils.misc import afni2itk_func
 from ...engine import Workflow
-from ...interfaces import MCFLIRT2ITK
 
 DEFAULT_MEMORY_MIN_GB = 0.01
 

fmriprep/workflows/bold/util.py

@@ -104,7 +104,8 @@ def init_bold_reference_wf(omp_nthreads, bold_file=None, name='bold_reference_wf
     gen_ref = pe.Node(EstimateReferenceImage(), name="gen_ref",
                       mem_gb=1)  # OE: 128x128x128x50 * 64 / 8 ~ 900MB.
     # Re-run validation; no effect if no sbref; otherwise apply same validation to sbref as bold
-    validate_ref = pe.Node(ValidateImage(deoblique=True), name='validate_ref', mem_gb=DEFAULT_MEMORY_MIN_GB)
+    validate_ref = pe.Node(ValidateImage(deoblique=True), name='validate_ref',
+                           mem_gb=DEFAULT_MEMORY_MIN_GB)
     enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads)
 
     workflow.connect([