Fixes for PR #847

Added a test: #847 (comment)

Changed interface name

Author: oesteban

nipype/algorithms/misc.py

@@ -1207,32 +1207,34 @@ def calc_moments(timeseries_file, moment):
     return np.where(zero, 0, m3 / m2**(moment/2.0))
 
 
-class NormalizeMapsInputSpec(TraitedSpec):
+class NormalizeProbabilityMapSetInputSpec(TraitedSpec):
     in_files = InputMultiPath(File(exists=True, mandatory=True,
                     desc='The tpms to be normalized') )
     in_mask = File(exists=True, mandatory=False,
                     desc='Masked voxels must sum up 1.0, 0.0 otherwise.')
 
-class NormalizeMapsOutputSpec(TraitedSpec):
+class NormalizeProbabilityMapSetOutputSpec(TraitedSpec):
     out_files = OutputMultiPath(File(exists=True),
                                 desc="normalized maps")
 
 
-class NormalizeMaps(BaseInterface):
+class NormalizeProbabilityMapSet(BaseInterface):
     """ Returns the input tissue probability maps (tpms, aka volume fractions)
     normalized to sum up 1.0 at each voxel within the mask.
 
+    .. note:: Please recall this is not a spatial normalization algorithm
+
     Example
     -------
 
     >>> import nipype.algorithms.misc as misc
-    >>> normalize = misc.NormalizeMaps()
+    >>> normalize = misc.NormalizeProbabilityMapSet()
     >>> normalize.inputs.in_files = [ 'csf.nii', 'wm.nii', 'gm.nii' ]
     >>> normalize.inputs.in_mask = [ 'brain.nii' ]
     >>> normalize.run() # doctest: +SKIP
     """
-    input_spec = NormalizeMapsInputSpec
-    output_spec = NormalizeMapsOutputSpec
+    input_spec = NormalizeProbabilityMapSetInputSpec
+    output_spec = NormalizeProbabilityMapSetOutputSpec
 
     def _run_interface(self, runtime):
         mask = None

nipype/algorithms/tests/test_normalize_tpms.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# @Author: oesteban - [email protected]
+# @Date:   2014-05-28 17:57:20
+# @Last Modified by:   oesteban
+# @Last Modified time: 2014-05-28 18:55:27
+
+import os
+from shutil import rmtree
+from tempfile import mkdtemp
+
+
+import numpy as np
+import nibabel as nb
+import nipype.testing as nit
+
+from nipype.algorithms.misc import normalize_tpms
+
+def test_normalize_tpms():
+    tempdir = mkdtemp()
+
+    in_mask = os.path.join(nit.basedir, 'data' , 'tpms_msk.nii.gz' )
+    mskdata = nb.load( in_mask ).get_data()
+    mskdata[mskdata>0.0] = 1.0
+
+    mapdata = []
+    in_files = []
+    out_files = []
+
+    for i in range(3):
+        mapname = os.path.join(nit.basedir, 'data' , 'tpm_%02d.nii.gz' % i)
+        filename =  os.path.join(tempdir, 'modtpm_%02d.nii.gz' % i )
+        out_files.append(os.path.join(tempdir, 'normtpm_%02d.nii.gz' % i ))
+
+        im = nb.load(mapname)
+        data = im.get_data()
+        mapdata.append( data.copy() )
+
+        nb.Nifti1Image(2.0 * (data * mskdata), im.get_affine(),
+                    im.get_header() ).to_filename(filename)
+        in_files.append( filename )
+
+    normalize_tpms( in_files, in_mask, out_files=out_files )
+
+    sumdata = np.zeros_like(mskdata)
+
+    for i,tstfname in enumerate( out_files ):
+        normdata = nb.load( tstfname ).get_data()
+        sumdata+=normdata
+        yield assert_equal, np.all( normdata[mskdata==0]==0 ), True
+        yield assert_equal, np.allclose( normdata, mapdata[i] ), True
+
+    yield assert_equal, np.allclose( sumdata, mskdata ), True
+
+    rmtree(tempdir)