added an anisotropic power interface to dipy

Author: Kesshi jordan

nipype/interfaces/dipy/__init__.py

@@ -4,3 +4,4 @@
 from .preprocess import Resample, Denoise
 from .reconstruction import RESTORE, EstimateResponseSH, CSD
 from .simulate import SimulateMultiTensor
+from .anisotropic_power import APMQball

nipype/interfaces/dipy/anisotropic_power.py

@@ -0,0 +1,76 @@
+# -*- coding: utf-8 -*-
+"""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'))
+   >>> os.chdir(datadir)
+"""
+
+from __future__ import print_function, division, unicode_literals, absolute_import
+
+import nibabel as nb
+
+from ... import logging
+from ..base import TraitedSpec, File, isdefined
+from .base import DipyDiffusionInterface, DipyBaseInterfaceInputSpec
+
+IFLOGGER = logging.getLogger('interface')
+
+class APMQballInputSpec(DipyBaseInterfaceInputSpec):
+    mask_file = File(exists=True,
+                     desc='An optional brain mask')
+
+
+class APMQballOutputSpec(TraitedSpec):
+    out_file = File(exists=True)
+
+class APMQball(DipyDiffusionInterface):
+    """
+    Calculates the anisotropic power map 
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.dipy as dipy
+    >>> apm = dipy.APMQball()
+    >>> apm.inputs.in_file = 'diffusion.nii'
+    >>> apm.inputs.in_bvec = 'bvecs'
+    >>> apm.inputs.in_bval = 'bvals'
+    >>> apm.run()                                   # doctest: +SKIP
+    """
+    input_spec = APMQballInputSpec
+    output_spec = APMQballOutputSpec
+
+    def _run_interface(self, runtime):
+        from dipy.reconst import shm
+        from dipy.io.utils import nifti1_symmat
+	from dipy.data import get_sphere
+	from dipy.reconst.peaks import peaks_from_model
+
+        gtab = self._get_gradient_table()
+
+        img = nb.load(self.inputs.in_file)
+        data = img.get_data()
+        affine = img.affine
+        mask = None
+        if isdefined(self.inputs.mask_file):
+            mask = nb.load(self.inputs.mask_file).get_data()
+
+        # Fit it
+        model = shm.QballModel(gtab,8)
+	sphere = get_sphere('symmetric724')
+        fit = model.fit(data, mask)
+	peaks = peaks_from_model(model=model, data=data, relative_peak_threshold=.5, min_separation_angle=25, sphere=sphere, mask=mask)
+        apm = shm.anisotropic_power(peaks.shm_coeff)
+	out_file = self._gen_filename('apm')
+	nb.Nifti1Image(apm.astype("float32"), affine).to_filename(out_file)
+        IFLOGGER.info('APM qball image saved as {i}'.format(i=out_file))
+
+
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['out_file'] = self._gen_filename('apm')
+
+        return outputs