New dipy interfaces

Author: oesteban

nipype/interfaces/dipy/__init__.py

@@ -1,3 +1,4 @@
-from .tracks import TrackDensityMap
+from .tracks import StreamlineTractography, TrackDensityMap
 from .tensors import TensorMode
 from .preprocess import Resample, Denoise
+from .reconstruction import RESTORE, EstimateResponseSH, CSD

nipype/interfaces/dipy/base.py

@@ -0,0 +1,38 @@
+# -*- coding: utf-8 -*-
+
+
+class DipyBaseInterfaceInputSpec(BaseInterfaceInputSpec):
+    in_file = File(exists=True, mandatory=True, desc=('input diffusion data'))
+    in_bval = File(exists=True, mandatory=True, desc=('input b-values table'))
+    in_bvec = File(exists=True, mandatory=True, desc=('input b-vectors table'))
+    out_prefix = traits.Str(desc=('output prefix for file names'))
+
+
+class DipyBaseInterface(BaseInterface):
+
+    """
+    A base interface for py:mod:`dipy` computations
+    """
+    input_spec = DipyBaseInterfaceInputSpec
+
+    def _get_gradient_table(self):
+        gtab = GradientTable(np.loadtxt(self.inputs.in_bvec).T)
+        gtab.b0_threshold = 700
+        gtab.bvals = np.loadtxt(self.inputs.in_bval)
+        return gtab
+
+    def _gen_filename(self, name, ext=None):
+        fname, fext = op.splitext(op.basename(self.inputs.in_file))
+        if fext == '.gz':
+            fname, fext2 = op.splitext(fname)
+            fext = fext2 + fext
+
+        if not isdefined(self.inputs.out_prefix):
+            out_prefix = op.abspath(fname)
+        else:
+            out_prefix = self.inputs.out_prefix
+
+        if ext is None:
+            ext = fext
+
+        return out_prefix + '_' + name + ext

nipype/interfaces/dipy/preprocess.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-"""Change directory to provide relative paths for doctests
+"""
+Change directory to provide relative paths for doctests
    >>> import os
    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
@@ -36,15 +37,17 @@ class ResampleInputSpec(TraitedSpec):
                                   ' is set, then isotropic regridding will '
                                   'be performed, with spacing equal to the '
                                   'smallest current zoom.'))
-    interp = traits.Int(1, mandatory=True, usedefault=True, desc=('order of '
-                        'the interpolator (0 = nearest, 1 = linear, etc.'))
+    interp = traits.Int(
+        1, mandatory=True, usedefault=True,
+        desc=('order of the interpolator (0 = nearest, 1 = linear, etc.'))
 
 
 class ResampleOutputSpec(TraitedSpec):
     out_file = File(exists=True)
 
 
 class Resample(BaseInterface):
+
     """
     An interface to reslicing diffusion datasets.
     See
@@ -106,6 +109,7 @@ class DenoiseOutputSpec(TraitedSpec):
 
 
 class Denoise(BaseInterface):
+
     """
     An interface to denoising diffusion datasets [Coupe2008]_.
     See
@@ -152,7 +156,7 @@ def _run_interface(self, runtime):
                              noise_mask=noise_mask,
                              out_file=out_file)
         iflogger.info(('Denoised image saved as {i}, estimated '
-                      'sigma={s}').format(i=out_file, s=s))
+                       'sigma={s}').format(i=out_file, s=s))
         return runtime
 
     def _list_outputs(self):