Flake8 cleanup workflows/anatomical

fmriprep/workflows/anatomical.py

@@ -11,8 +11,6 @@
 import os.path as op
 
 from nipype.interfaces import ants
-from nipype.interfaces import fsl
-from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 
@@ -25,7 +23,7 @@
 from fmriprep.interfaces import (DerivativesDataSink, IntraModalMerge)
 from fmriprep.interfaces.utils import reorient
 from fmriprep.utils.misc import fix_multi_T1w_source_name
-from fmriprep.viz import stripped_brain_overlay
+
 
 #  pylint: disable=R0914
 def t1w_preprocessing(name='t1w_preprocessing', settings=None):
@@ -144,7 +142,8 @@ def t1w_preprocessing(name='t1w_preprocessing', settings=None):
             name='DS_Report'
         )
         workflow.connect([
-            (inputnode, ds_t1_skull_strip_report, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
+            (inputnode, ds_t1_skull_strip_report, [
+                (('t1w', fix_multi_T1w_source_name), 'source_file')]),
             (asw, ds_t1_skull_strip_report, [('outputnode.out_report', 'in_file')])
         ])
 
@@ -264,7 +263,6 @@ def skullstrip_ants(name='ANTsBrainExtraction', settings=None):
         'T_template0_BrainCerebellumRegistrationMask.nii.gz'
     )
 
-
     workflow.connect([
         (inputnode, t1_skull_strip, [('in_file', 'anatomical_image')]),
         (t1_skull_strip, outputnode, [('BrainExtractionMask', 'out_mask'),

fmriprep/workflows/base.py

@@ -34,7 +34,7 @@ def base_workflow_enumerator(subject_list, task_id, settings):
                                                      settings=settings)
         if generated_workflow:
             cur_time = strftime('%Y%m%d-%H%M%S')
-            generated_workflow.config['execution']['crashdump_dir'] =(
+            generated_workflow.config['execution']['crashdump_dir'] = (
                 os.path.join(settings['output_dir'], 'log', subject, cur_time)
             )
             for node in generated_workflow._get_all_nodes():
@@ -51,15 +51,17 @@ def base_workflow_generator(subject_id, task_id, settings):
     settings["biggest_epi_file_size_gb"] = get_biggest_epi_file_size_gb(subject_data['func'])
 
     if subject_data['t1w'] == []:
-        raise Exception("No T1w images found for participant %s. All workflows require T1w images."%subject_id)
+        raise Exception("No T1w images found for participant {}. "
+                        "All workflows require T1w images.".format(subject_id))
 
-    if subject_data['fmap'] != [] and subject_data['sbref'] != [] and "fieldmaps" not in settings['ignore']:
+    if all((subject_data['fmap'] != [],
+            subject_data['sbref'] != [],
+            "fieldmaps" not in settings['ignore'])):
         return wf_ds054_type(subject_data, settings, name=subject_id)
     else:
         return wf_ds005_type(subject_data, settings, name=subject_id)
 
 
-
 def wf_ds054_type(subject_data, settings, name='fMRI_prep'):
     """
     The main fmri preprocessing workflow, for the ds054-type of data:
@@ -213,11 +215,12 @@ def wf_ds005_type(subject_data, settings, name='fMRI_prep'):
                              ('outputnode.t1_seg', 'inputnode.t1_seg')]),
 
         (t1w_pre, confounds_wf, [('outputnode.t1_tpms', 'inputnode.t1_tpms')]),
-        (hmcwf, confounds_wf, [('outputnode.movpar_file', 'inputnode.movpar_file'),
-                               ('outputnode.epi_hmc', 'inputnode.fmri_file'),
-                               ('outputnode.epi_mean', 'inputnode.reference_image'),
-                               ('outputnode.epi_mask', 'inputnode.epi_mask'),
-                               ('outputnode.motion_confounds_file', 'inputnode.motion_confounds_file')]),
+        (hmcwf, confounds_wf, [
+            ('outputnode.movpar_file', 'inputnode.movpar_file'),
+            ('outputnode.epi_hmc', 'inputnode.fmri_file'),
+            ('outputnode.epi_mean', 'inputnode.reference_image'),
+            ('outputnode.epi_mask', 'inputnode.epi_mask'),
+            ('outputnode.motion_confounds_file', 'inputnode.motion_confounds_file')]),
         (epi_2_t1, confounds_wf, [('outputnode.mat_t1_to_epi', 'inputnode.t1_transform')]),
         (hmcwf, confounds_wf, [('inputnode.epi', 'inputnode.source_file')]),
 

fmriprep/workflows/confounds.py

@@ -11,6 +11,7 @@
 from fmriprep.interfaces.bids import DerivativesDataSink
 from fmriprep.interfaces.utils import prepare_roi_from_probtissue
 
+
 def discover_wf(settings, name="ConfoundDiscoverer"):
     ''' All input fields are required.
 
@@ -67,7 +68,7 @@ def discover_wf(settings, name="ConfoundDiscoverer"):
                                                    'epi_mask_erosion_mm'],
                                       output_names=['roi_file', 'eroded_mask'],
                                       function=prepare_roi_from_probtissue),
-                      name='WM_roi')
+                     name='WM_roi')
     WM_roi.inputs.erosion_mm = 6
     WM_roi.inputs.epi_mask_erosion_mm = 10
 

fmriprep/workflows/epi.py

@@ -15,7 +15,6 @@
 from nipype.interfaces import ants
 from nipype.interfaces import c3
 from nipype.interfaces import fsl
-from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
 from niworkflows.interfaces.masks import ComputeEPIMask, BETRPT
 from niworkflows.interfaces.registration import FLIRTRPT
@@ -25,7 +24,6 @@
 from fmriprep.interfaces.utils import nii_concat
 from fmriprep.utils.misc import fix_multi_T1w_source_name, _first
 from fmriprep.workflows.fieldmap import sdc_unwarp
-from fmriprep.viz import stripped_brain_overlay
 from fmriprep.workflows.sbref import _extract_wm
 
 
@@ -243,13 +241,13 @@ def epi_sbref_registration(settings, name='EPI_SBrefRegistration'):
 
     ds_report = pe.Node(
         DerivativesDataSink(base_directory=settings['output_dir'],
-                            suffix='epi_sbref', out_path_base='reports'), 
+                            suffix='epi_sbref', out_path_base='reports'),
         name="DS_Report")
 
     workflow.connect([
         (inputnode, epi_split, [('epi', 'in_file')]),
         (inputnode, epi_sbref, [('sbref', 'reference'),
-                                ('sbref_mask', 'ref_weight'),]),
+                                ('sbref_mask', 'ref_weight')]),
         (inputnode, epi_xfm, [('sbref', 'reference')]),
         (inputnode, epi_sbref, [('epi_mean', 'in_file'),
                                 ('epi_mask', 'in_weight')]),

fmriprep/workflows/fieldmap/base.py

@@ -21,6 +21,7 @@
 
 LOGGER = logging.getLogger('workflow')
 
+
 def is_fmap_type(fmap_type, filename):
     from fmriprep.utils import misc
     import re

fmriprep/workflows/fieldmap/phase_diff_and_magnitudes.py

@@ -9,20 +9,17 @@
 """
 from __future__ import print_function, division, absolute_import, unicode_literals
 
-import logging
 import os.path as op
 
 from nipype.interfaces import ants
 from nipype.interfaces import fsl
 from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
-from nipype.workflows.dmri.fsl.utils import (siemens2rads, demean_image, cleanup_edge_pipeline,
-                                             rads2radsec)
+from nipype.workflows.dmri.fsl.utils import siemens2rads, demean_image, cleanup_edge_pipeline
 from niworkflows.interfaces.masks import BETRPT
 
 from fmriprep.interfaces import ReadSidecarJSON, IntraModalMerge
-from fmriprep.utils.misc import fieldmap_suffixes
 from fmriprep.viz import stripped_brain_overlay
 
 

fmriprep/workflows/fieldmap/se_fmap_workflow.py

@@ -10,9 +10,8 @@
 from nipype.pipeline import engine as pe
 from niworkflows.interfaces.masks import BETRPT
 
-from fmriprep.utils.misc import _first, gen_list
+from fmriprep.utils.misc import gen_list
 from fmriprep.interfaces import ReadSidecarJSON
-from fmriprep.viz import stripped_brain_overlay
 from fmriprep.workflows.fieldmap.utils import create_encoding_file
 
 WORKFLOW_NAME = 'Fieldmap_SEs'

fmriprep/workflows/fieldmap/unwarp.py

@@ -11,11 +11,8 @@
 from nipype.pipeline import engine as pe
 from nipype.interfaces import fsl
 from nipype.interfaces import ants
-from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
-from niworkflows.interfaces.masks import BETRPT
 
-from fmriprep.utils.misc import gen_list
 from fmriprep.interfaces.bids import ReadSidecarJSON
 from fmriprep.workflows.fieldmap.utils import create_encoding_file
 
@@ -137,7 +134,6 @@ def _multiple_pe_hmc(in_files, in_movpar, in_ref=None):
 
     It just forwards the two inputs otherwise.
     """
-    import os
     from six import string_types
     from nipype.interfaces import fsl
     from nipype.interfaces import ants

fmriprep/workflows/fieldmap/utils.py

@@ -14,7 +14,6 @@ def create_encoding_file(input_images, in_dict):
     """
     Creates a valid encoding file for topup
     """
-    import json
     import nibabel as nb
     import numpy as np
     import os
@@ -68,6 +67,7 @@ def create_encoding_file(input_images, in_dict):
                fmt=['%0.1f', '%0.1f', '%0.1f', '%0.20f'])
     return os.path.abspath('parameters.txt')
 
+
 def mcflirt2topup(in_files, in_mats, out_movpar=None):
     """
     Converts a list of matrices from MCFLIRT to the movpar input

fmriprep/workflows/sbref.py

@@ -9,21 +9,17 @@
 Originally coded by Craig Moodie. Refactored by the CRN Developers.
 """
 
-import os
 import os.path as op
 
 from nipype.pipeline import engine as pe
 from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
-from nipype.interfaces import fsl, c3
+from nipype.interfaces import fsl
 from nipype.interfaces import ants
 from niworkflows.interfaces.masks import ComputeEPIMask
-from niworkflows.interfaces.registration import FLIRTRPT
 
-from fmriprep.utils.misc import _first, gen_list
-from fmriprep.interfaces.utils import reorient
-from fmriprep.interfaces import (ReadSidecarJSON, IntraModalMerge,
-                                 DerivativesDataSink)
+from fmriprep.utils.misc import _first
+from fmriprep.interfaces import DerivativesDataSink
 from fmriprep.workflows.fieldmap import sdc_unwarp
 from fmriprep.viz import stripped_brain_overlay
 

tox.ini

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 99