[ENH] Ensure that headers are consistent along the process

fmriprep/info.py

@@ -67,14 +67,14 @@
     'grabbit',
     'pybids>=0.3',
     'nitime',
-    'niworkflows>=0.1.7',
+    'niworkflows>=0.1.8',
     'statsmodels',
     'nipype',
     'seaborn',
-    'joblib',
 ]
 
-LINKS_REQUIRES = []
+LINKS_REQUIRES = [
+]
 
 TESTS_REQUIRES = [
     "mock",

fmriprep/interfaces/bids.py

@@ -6,7 +6,7 @@
 # @Author: oesteban
 # @Date:   2016-06-03 09:35:13
 # @Last Modified by:   oesteban
-# @Last Modified time: 2017-02-13 11:44:23
+# @Last Modified time: 2017-10-10 15:37:47
 """
 Interfaces for handling BIDS-like neuroimaging structures
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -35,11 +35,10 @@
 from niworkflows.nipype import logging
 from niworkflows.nipype.interfaces.base import (
     traits, isdefined, TraitedSpec, BaseInterfaceInputSpec,
-    File, Directory, InputMultiPath, OutputMultiPath, Str
+    File, Directory, InputMultiPath, OutputMultiPath, Str,
+    SimpleInterface
 )
 
-from niworkflows.interfaces.base import SimpleInterface
-
 LOGGER = logging.getLogger('interface')
 BIDS_NAME = re.compile(
     '^(.*\/)?(?P<subject_id>sub-[a-zA-Z0-9]+)(_(?P<session_id>ses-[a-zA-Z0-9]+))?'

fmriprep/interfaces/confounds.py

@@ -15,9 +15,9 @@
 import pandas as pd
 from niworkflows.nipype import logging
 from niworkflows.nipype.interfaces.base import (
-    traits, TraitedSpec, BaseInterfaceInputSpec, File, Directory, isdefined
+    traits, TraitedSpec, BaseInterfaceInputSpec, File, Directory, isdefined,
+    SimpleInterface
 )
-from niworkflows.interfaces.base import SimpleInterface
 
 LOGGER = logging.getLogger('interface')
 

fmriprep/interfaces/fmap.py

@@ -12,8 +12,8 @@
 from niworkflows.nipype import logging
 from niworkflows.nipype.utils.filemanip import fname_presuffix
 from niworkflows.nipype.interfaces.base import (
-    BaseInterfaceInputSpec, TraitedSpec, File, isdefined, traits)
-from niworkflows.interfaces.base import SimpleInterface
+    BaseInterfaceInputSpec, TraitedSpec, File, isdefined, traits,
+    SimpleInterface)
 
 LOGGER = logging.getLogger('interface')
 

fmriprep/interfaces/freesurfer.py

@@ -30,8 +30,7 @@
     isdefined, InputMultiPath, BaseInterfaceInputSpec, TraitedSpec, File, traits, Directory
 )
 from niworkflows.nipype.interfaces import freesurfer as fs
-
-from niworkflows.interfaces.base import SimpleInterface
+from niworkflows.nipype.interfaces.base import SimpleInterface
 
 
 class StructuralReference(fs.RobustTemplate):

fmriprep/interfaces/images.py

@@ -20,36 +20,11 @@
     traits, TraitedSpec, BaseInterfaceInputSpec,
     File, InputMultiPath, OutputMultiPath)
 from niworkflows.nipype.interfaces import fsl
-from niworkflows.interfaces.base import SimpleInterface
-
+from niworkflows.nipype.interfaces.base import SimpleInterface
 
 LOGGER = logging.getLogger('interface')
 
 
-class GenerateSamplingReferenceInputSpec(BaseInterfaceInputSpec):
-    fixed_image = File(exists=True, mandatory=True, desc='the reference file')
-    moving_image = File(exists=True, mandatory=True, desc='the pixel size reference')
-
-
-class GenerateSamplingReferenceOutputSpec(TraitedSpec):
-    out_file = File(exists=True, desc='one file with all inputs flattened')
-
-
-class GenerateSamplingReference(SimpleInterface):
-    """
-    Generates a reference grid for resampling one image keeping original resolution,
-    but moving data to a different space (e.g. MNI)
-    """
-
-    input_spec = GenerateSamplingReferenceInputSpec
-    output_spec = GenerateSamplingReferenceOutputSpec
-
-    def _run_interface(self, runtime):
-        self._results['out_file'] = _gen_reference(self.inputs.fixed_image,
-                                                   self.inputs.moving_image)
-        return runtime
-
-
 class IntraModalMergeInputSpec(BaseInterfaceInputSpec):
     in_files = InputMultiPath(File(exists=True), mandatory=True,
                               desc='input files')
@@ -468,18 +443,6 @@ def _flatten_split_merge(in_files):
     return merged, flat_split
 
 
-def _gen_reference(fixed_image, moving_image, out_file=None):
-    if out_file is None:
-        out_file = fname_presuffix(fixed_image, suffix='_reference', newpath=os.getcwd())
-    new_zooms = nli.load_img(moving_image).header.get_zooms()[:3]
-    # Avoid small differences in reported resolution to cause changes to
-    # FOV. See https://github.com/poldracklab/fmriprep/issues/512
-    new_zooms_round = np.round(new_zooms, 3)
-    nli.resample_img(fixed_image, target_affine=np.diag(new_zooms_round),
-                     interpolation='nearest').to_filename(out_file)
-    return out_file
-
-
 def extract_wm(in_seg, wm_label=3):
     import os.path as op
     import nibabel as nb