Added package_check for nipy in new Similarity4D

Additionally, docstrings have been improved for several methods,
especially indicating deprecated classes.

Author: oesteban

nipype/algorithms/metrics.py

@@ -28,6 +28,7 @@
 import scipy.stats as stats
 
 from .. import logging
+from ..utils.misc import package_check
 
 from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
                                InputMultiPath, OutputMultiPath,
@@ -69,9 +70,8 @@ class DistanceOutputSpec(TraitedSpec):
 
 
 class Distance(BaseInterface):
-    '''
-    Calculates distance between two volumes.
-    '''
+    """Calculates distance between two volumes.
+    """
     input_spec = DistanceInputSpec
     output_spec = DistanceOutputSpec
 
@@ -232,8 +232,7 @@ class OverlapOutputSpec(TraitedSpec):
 
 
 class Overlap(BaseInterface):
-    """
-    Calculates various overlap measures between two maps.
+    """Calculates various overlap measures between two maps.
 
     Example
     -------
@@ -313,7 +312,7 @@ class FuzzyOverlapOutputSpec(TraitedSpec):
 
 
 class FuzzyOverlap(BaseInterface):
-    """ Calculates various overlap measures between two maps, using the fuzzy
+    """Calculates various overlap measures between two maps, using the fuzzy
     definition proposed in: Crum et al., Generalized Overlap Measures for
     Evaluation and Validation in Medical Image Analysis, IEEE Trans. Med.
     Ima. 25(11),pp 1451-1461, Nov. 2006.
@@ -524,8 +523,9 @@ class Similarity(BaseInterface):
     the same coordinate system, same space within that coordinate system and
     with the same voxel dimensions.
 
-    .. note:: This interface is an extension of nipype.interfaces.nipy.utils.Similarity
-              to support 4D files.
+    .. note:: This interface is an extension of
+              :py:class:`nipype.interfaces.nipy.utils.Similarity` to support 4D files.
+              Requires :py:mod:`nipy`
 
     Example
     -------
@@ -541,8 +541,22 @@ class Similarity(BaseInterface):
 
     input_spec = SimilarityInputSpec
     output_spec = SimilarityOutputSpec
+    _have_nipy = True
+
+    def __init__(self, **inputs):
+        try:
+            package_check('nipy')
+        except Exception, e:
+            self._have_nipy = False
+        super(Similarity,self).__init__(**inputs)
+
 
     def _run_interface(self, runtime):
+        if not self._have_nipy:
+            raise RuntimeError('nipy is not installed')
+
+        from nipy.algorithms.registration.histogram_registration import HistogramRegistration
+        from nipy.algorithms.registration.affine import Affine
 
         vol1_nii = nb.load(self.inputs.volume1)
         vol2_nii = nb.load(self.inputs.volume2)

nipype/algorithms/misc.py

@@ -64,10 +64,10 @@ class PickAtlasOutputSpec(TraitedSpec):
 
 
 class PickAtlas(BaseInterface):
-    '''
-    Returns ROI masks given an atlas and a list of labels. Supports dilation
+    """Returns ROI masks given an atlas and a list of labels. Supports dilation
     and left right masking (assuming the atlas is properly aligned).
-    '''
+    """
+
     input_spec = PickAtlasInputSpec
     output_spec = PickAtlasOutputSpec
 
@@ -132,6 +132,8 @@ class SimpleThresholdOutputSpec(TraitedSpec):
 
 
 class SimpleThreshold(BaseInterface):
+    """Applies a threshold to input volumes
+    """
     input_spec = SimpleThresholdInputSpec
     output_spec = SimpleThresholdOutputSpec
 
@@ -182,10 +184,9 @@ class ModifyAffineOutputSpec(TraitedSpec):
 
 
 class ModifyAffine(BaseInterface):
-    '''
-    Left multiplies the affine matrix with a specified values. Saves the volume
+    """Left multiplies the affine matrix with a specified values. Saves the volume
     as a nifti file.
-    '''
+    """
     input_spec = ModifyAffineInputSpec
     output_spec = ModifyAffineOutputSpec
 
@@ -225,6 +226,8 @@ class CreateNiftiOutputSpec(TraitedSpec):
 
 
 class CreateNifti(BaseInterface):
+    """Creates a nifti volume
+    """
     input_spec = CreateNiftiInputSpec
     output_spec = CreateNiftiOutputSpec
 
@@ -344,8 +347,7 @@ class GunzipOutputSpec(TraitedSpec):
 
 
 class Gunzip(BaseInterface):
-    """
-
+    """Gunzip wrapper
     """
     input_spec = GunzipInputSpec
     output_spec = GunzipOutputSpec
@@ -409,8 +411,7 @@ class Matlab2CSVOutputSpec(TraitedSpec):
 
 
 class Matlab2CSV(BaseInterface):
-    """
-    Simple interface to save the components of a MATLAB .mat file as a text
+    """Simple interface to save the components of a MATLAB .mat file as a text
     file with comma-separated values (CSVs).
 
     CSV files are easily loaded in R, for use in statistical processing.
@@ -602,8 +603,7 @@ class MergeCSVFilesOutputSpec(TraitedSpec):
 
 
 class MergeCSVFiles(BaseInterface):
-    """
-    This interface is designed to facilitate data loading in the R environment.
+    """This interface is designed to facilitate data loading in the R environment.
     It takes input CSV files and merges them into a single CSV file.
     If provided, it will also incorporate column heading names into the
     resulting CSV file.
@@ -738,8 +738,7 @@ class AddCSVColumnOutputSpec(TraitedSpec):
 
 
 class AddCSVColumn(BaseInterface):
-    """
-    Short interface to add an extra column and field to a text file
+    """Short interface to add an extra column and field to a text file
 
     Example
     -------
@@ -799,8 +798,7 @@ class CalculateNormalizedMomentsOutputSpec(TraitedSpec):
 
 
 class CalculateNormalizedMoments(BaseInterface):
-    """
-    Calculates moments of timeseries.
+    """Calculates moments of timeseries.
 
     Example
     -------
@@ -827,8 +825,7 @@ def _list_outputs(self):
 
 
 def calc_moments(timeseries_file, moment):
-    """
-    Returns nth moment (3 for skewness, 4 for kurtosis) of timeseries
+    """Returns nth moment (3 for skewness, 4 for kurtosis) of timeseries
     (list of values; one per timeseries).
 
     Keyword arguments:
@@ -844,13 +841,23 @@ def calc_moments(timeseries_file, moment):
 
 # Deprecated interfaces ---------------------------------------------------------
 class Distance( nam.Distance ):
+    """Calculates distance between two volumes.
+
+    .. deprecated:: 0.10.0
+       Use :py:class:`nipype.algorithms.metrics.Distance` instead.
+    """
     def __init__(self, **inputs):
         super(nam.Distance, self).__init__(**inputs)
         warnings.warn(("This interface has been deprecated since 0.10.0,"
                       " please use nipype.algorithms.metrics.Distance"),
                       DeprecationWarning)
 
 class Overlap( nam.Overlap ):
+    """Calculates various overlap measures between two maps.
+
+    .. deprecated:: 0.10.0
+       Use :py:class:`nipype.algorithms.metrics.Overlap` instead.
+    """
     def __init__(self, **inputs):
         super(nam.Overlap, self).__init__(**inputs)
         warnings.warn(("This interface has been deprecated since 0.10.0,"
@@ -859,6 +866,12 @@ def __init__(self, **inputs):
 
 
 class FuzzyOverlap( nam.FuzzyOverlap ):
+    """Calculates various overlap measures between two maps, using a fuzzy
+    definition.
+
+    .. deprecated:: 0.10.0
+       Use :py:class:`nipype.algorithms.metrics.FuzzyOverlap` instead.
+    """
     def __init__(self, **inputs):
         super(nam.FuzzyOverlap, self).__init__(**inputs)
         warnings.warn(("This interface has been deprecated since 0.10.0,"

nipype/interfaces/nipy/utils.py

@@ -51,6 +51,9 @@ class Similarity(BaseInterface):
     the same coordinate system, same space within that coordinate system and
     with the same voxel dimensions.
 
+    .. deprecated:: 0.10.0
+       Use :py:class:`nipype.algorithms.metrics.Similarity` instead.
+
     Example
     -------
     >>> from nipype.interfaces.nipy.utils import Similarity