Merge pull request #818 from mick-d/caminostats

New camino interface for ImageStats

Author: satra

nipype/interfaces/camino/__init__.py

@@ -13,3 +13,4 @@
                   ComputeTensorTrace,  ComputeEigensystem, DTMetric)
 from .calib import (SFPICOCalibData, SFLUTGen)
 from .odf import (QBallMX, LinRecon, SFPeaks, MESD)
+from .utils import ImageStats

nipype/interfaces/camino/tests/test_auto_ImageStats.py

@@ -0,0 +1,46 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.camino.utils import ImageStats
+
+def test_ImageStats_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_files=dict(argstr='-images %s',
+    mandatory=True,
+    position=-1,
+    ),
+    out_type=dict(argstr='-outputdatatype %s',
+    usedefault=True,
+    ),
+    output_root=dict(argstr='-outputroot %s',
+    mandatory=True,
+    ),
+    stat=dict(argstr='-stat %s',
+    mandatory=True,
+    units='NA',
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    )
+    inputs = ImageStats.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_ImageStats_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = ImageStats.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/camino/utils.py

@@ -0,0 +1,63 @@
+"""
+    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 nipype.interfaces.base import (traits, TraitedSpec, File,
+                                    CommandLine, CommandLineInputSpec, isdefined,
+                                    InputMultiPath)
+from nipype.utils.filemanip import split_filename
+import os
+
+class ImageStatsInputSpec(CommandLineInputSpec):
+    in_files = InputMultiPath(File(exists=True), argstr='-images %s', mandatory=True,
+                              position=-1, desc=('List of images to process. They must '
+                                                 'be in the same space and have the same '
+                                                 'dimensions.'))
+    stat = traits.Enum("min", "max", "mean", "median", "sum", "std", "var",
+                       argstr='-stat %s', units='NA', mandatory=True,
+                       desc="The statistic to compute.")
+
+    out_type = traits.Enum("float", "char", "short", "int", "long", "double",
+                           argstr='-outputdatatype %s', usedefault=True,
+                           desc=('A Camino data type string, default is "float". '
+                                 'Type must be signed.'))
+    output_root = File(argstr='-outputroot %s', mandatory=True,
+                       desc=('Filename root prepended onto the names of the output '
+                             ' files. The extension will be determined from the input.'))
+
+class ImageStatsOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='Path of the file computed with the statistic chosen')
+
+class ImageStats(CommandLine):
+    """
+    This program computes voxelwise statistics on a series of 3D images. The images
+    must be in the same space; the operation is performed voxelwise and one output
+    is produced per voxel.
+
+    Examples
+    --------
+
+    >>> import nipype.interfaces.camino as cam
+    >>> imstats = cam.ImageStats()
+    >>> imstats.inputs.in_files = ['im1.nii','im2.nii','im3.nii']
+    >>> imstats.inputs.stat = 'max'
+    >>> imstats.run()                  # doctest: +SKIP
+    """
+    _cmd = 'imagestats'
+    input_spec = ImageStatsInputSpec
+    output_spec = ImageStatsOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = os.path.abspath(self._gen_outfilename())
+        return outputs
+
+    def _gen_outfilename(self):
+        output_root = self.inputs.output_root
+        first_file = self.inputs.in_files[0]
+        _, _ , ext = split_filename(first_file)
+        return output_root + ext