fix pep8

scilpy/denoise/asym_filtering.py

@@ -536,7 +536,8 @@ def cosine_filtering(in_sh, sh_order=8, sh_basis='descoteaux07',
 
     # We want a B matrix to project on an inverse sphere to have the sf on
     # the opposite hemisphere for a given vertice
-    neg_B = sh_to_sf_matrix(Sphere(xyz=-sphere.vertices), sh_order_max=sh_order,
+    neg_B = sh_to_sf_matrix(Sphere(xyz=-sphere.vertices),
+                            sh_order_max=sh_order,
                             basis_type=sh_basis, return_inv=False,
                             full_basis=in_full_basis, legacy=is_legacy)
 

scilpy/image/volume_operations.py

@@ -272,7 +272,8 @@ def register_image(static, static_grid2world, moving, moving_grid2world,
 
     sigmas = [8.0, 4.0, 2.0, 1.0] if fine else [8.0, 4.0, 2.0]
     factors = [8, 4, 2, 1.0] if fine else [8, 4, 2]
-    metric = MutualInformationMetric(nbins=nbins, sampling_proportion=sampling_prop)
+    metric = MutualInformationMetric(nbins=nbins,
+                                     sampling_proportion=sampling_prop)
     reg_obj = AffineRegistration(metric=metric, level_iters=level_iters,
                                  sigmas=sigmas, factors=factors, verbosity=0)
 

scilpy/reconst/frf.py

@@ -10,8 +10,7 @@
 from dipy.segment.mask import applymask
 import numpy as np
 
-from scilpy.gradients.bvec_bval_tools import (check_b0_threshold,
-                                              is_normalized_bvecs,
+from scilpy.gradients.bvec_bval_tools import (is_normalized_bvecs,
                                               normalize_bvecs,
                                               DEFAULT_B0_THRESHOLD)
 

scilpy/reconst/sh.py

@@ -160,7 +160,8 @@ def compute_rish(sh, mask=None, full_basis=False):
     n_indices_per_order = np.bincount(order_ids)[::step]
 
     # Get start index of each order (e.g. for order 6 : [0,1,6,15])
-    order_positions = np.concatenate([[0], np.cumsum(n_indices_per_order)])[:-1]
+    order_positions = np.concatenate([[0],
+                                      np.cumsum(n_indices_per_order)])[:-1]
 
     # Get paired indices for np.add.reduceat, specifying where to reduce.
     # The last index is omitted, it is automatically replaced by len(array)-1

scilpy/segment/recobundlesx.py

@@ -129,9 +129,10 @@ def _cluster_model_bundle(self, model_clust_thr, identifier):
         len_centroids = len(self.model_centroids)
         if len_centroids > 1000:
             logging.warning('Model {0} simplified at threshold '
-                            '{1}mm with {2} centroids'.format(identifier,
-                                                              str(model_clust_thr),
-                                                              str(len_centroids)))
+                            '{1}mm with '
+                            '{2} centroids'.format(identifier,
+                                                   str(model_clust_thr),
+                                                   str(len_centroids)))
 
     def _reduce_search_space(self, neighbors_reduction_thr=18):
         """
@@ -195,7 +196,8 @@ def _register_model_to_neighb(self, select_model=1000, select_target=1000,
         slr_transform_type_id = possible_slr_transform_type[slr_transform_type]
         if slr_transform_type_id >= 0:
             init_transfo_dof = np.zeros(3)
-            slr = StreamlineLinearRegistration(metric=metric, method="L-BFGS-B",
+            slr = StreamlineLinearRegistration(metric=metric,
+                                               method="L-BFGS-B",
                                                x0=init_transfo_dof,
                                                bounds=bounds_dof[:3],
                                                num_threads=1)

scilpy/tractanalysis/afd_along_streamlines.py

@@ -52,8 +52,8 @@ def afd_map_along_streamlines(sft, fodf, fodf_basis, length_weighting,
 def afd_and_rd_sums_along_streamlines(sft, fodf, fodf_basis,
                                       length_weighting, is_legacy=True):
     """
-    Compute the mean Apparent Fiber Density (AFD) and mean Radial fODF (radfODF)
-    maps along a bundle.
+    Compute the mean Apparent Fiber Density (AFD) and
+    mean Radial fODF (radfODF) maps along a bundle.
 
     Parameters
     ----------

scilpy/tractograms/tractogram_operations.py

@@ -1047,7 +1047,8 @@ def cut_streamlines_alter(sft, min_dice=0.90, epsilon=0.01, from_end=False):
     """
     Cut streamlines based on a dice similarity metric.
     The function will keep removing points from the streamlines until the dice
-    similarity between the original and the cut tractogram is close to min_dice.
+    similarity between the original and the cut tractogram is close
+    to min_dice.
 
     Parameters
     ----------
@@ -1059,8 +1060,8 @@ def cut_streamlines_alter(sft, min_dice=0.90, epsilon=0.01, from_end=False):
         Stopping criteria for convergence. The maximum difference between the
         dice similarity and min_dice.
     from_end: bool
-        If True, the streamlines will be cut from the end. Else, the streamlines
-        will be cut from the start.
+        If True, the streamlines will be cut from the end. Else,
+        the streamlines will be cut from the start.
 
     Returns
     -------
@@ -1321,8 +1322,8 @@ def transform_streamlines_alter(sft, min_dice=0.90, epsilon=0.01):
         curr_density_map = compute_tract_counts_map(curr_sft.streamlines,
                                                     sft.dimensions)
         dice, _ = compute_dice_voxel(original_density_map, curr_density_map)
-        logging.debug(f'Transformed {np.round(to_pick * 360, 6)} degree on axis '
-                      f'{axis}, dice: {dice}')
+        logging.debug(f'Transformed {np.round(to_pick * 360, 6)} degree '
+                      f'on axis {axis}, dice: {dice}')
         last_pick[axis] = to_pick
 
         if dice < min_dice:

scripts/scil_bundle_clean_qbx_clusters.py

@@ -177,9 +177,6 @@ def keypress_callback(obj, _):
     sft_rejected_on_size, filename_rejected_on_size = [], []
     concat_streamlines = []
 
-    ref_bundle = load_tractogram_with_reference(
-        parser, args, args.in_bundles[0])
-
     for filename in args.in_bundles:
         basename = os.path.basename(filename)
         sft = load_tractogram_with_reference(parser, args, filename)

scripts/scil_fibertube_score_tractogram.py

@@ -55,7 +55,6 @@
 
 import os
 import json
-import numba
 import argparse
 import logging
 import numpy as np

scripts/tests/test_tracking_local.py

@@ -59,7 +59,7 @@ def test_execution_tracking_ptt(script_runner, monkeypatch):
     assert ret.success
 
 
-def test_execution_sphere_subdivide(n=script_runner, monkeypatch):
+def test_execution_sphere_subdivide(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_fodf = os.path.join(SCILPY_HOME, 'tracking', 'fodf.nii.gz')
     in_mask = os.path.join(SCILPY_HOME, 'tracking', 'seeding_mask.nii.gz')
@@ -172,7 +172,7 @@ def test_execution_tracking_fodf_prob_pmf_mapping(script_runner, monkeypatch):
     assert ret.success
 
 
-def test_execution_tracking_ptt(script_runner, monkeypatch):
+def test_execution_tracking_ptt_with_probe(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_fodf = os.path.join(SCILPY_HOME, 'tracking', 'fodf.nii.gz')
     in_mask = os.path.join(SCILPY_HOME, 'tracking', 'seeding_mask.nii.gz')