enh: calcmedian interface

Author: mgxd

nipype/algorithms/misc.py

@@ -33,7 +33,7 @@
                                InputMultiPath, OutputMultiPath,
                                BaseInterfaceInputSpec, isdefined,
                                DynamicTraitedSpec, Undefined)
-from ..utils.filemanip import fname_presuffix, split_filename
+from ..utils.filemanip import fname_presuffix, split_filename, filename_to_list
 from ..utils import NUMPY_MMAP
 
 from . import confounds
@@ -1380,6 +1380,51 @@ def merge_rois(in_files, in_idxs, in_ref,
     return out_file
 
 
+class CalculateMedianInputSpec(BaseInterfaceInputSpec):
+    in_file = InputMultiPath(File(exists=True, mandatory=True,
+      desc="One or more realigned Nifti 4D timeseries"))
+    median_file = traits.Str('median.nii.gz', usedefault=True,
+      desc="Filename to store median image")
+
+class CalculateMedianOutputSpec(TraitedSpec):
+    median_file = File(exists=True)
+
+class CalculateMedian(BaseInterface):
+    """
+    Computes an average of the median across one or more 4D Nifti timeseries
+
+    Example
+    -------
+
+    >>> from nipype.algorithms.misc import CalculateMedian
+    >>> mean = CalculateMedian()
+    >>> mean.inputs.in_file = 'functional.nii'
+    >>> mean.run() # doctest: +SKIP
+
+    """
+    input_spec = CalculateMedianInputSpec
+    output_spec = CalculateMedianOutputSpec
+
+    def _run_interface(self, runtime):
+        total = None
+        for idx, fname in enumerate(filename_to_list(self.inputs.in_file)):
+            img = nb.load(fname, mmap=NUMPY_MMAP)
+            data = np.median(img.get_data(), axis=3)
+            if total is None:
+                total = data
+            else:
+                total += data
+        median_img = nb.Nifti1Image(total/(idx + 1), img.affine, img.header)
+        filename = os.path.join(os.getcwd(), self.inputs.median_file)
+        median_img.to_filename(filename)
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['median_file'] = os.path.abspath(self.inputs.median_file)
+        return outputs
+
+
 # Deprecated interfaces ------------------------------------------------------
 
 class Distance(nam.Distance):

nipype/algorithms/tests/test_misc.py

@@ -9,6 +9,7 @@
 from nipype.algorithms import misc
 from nipype.utils.filemanip import fname_presuffix
 from nipype.testing.fixtures import create_analyze_pair_file_in_directory
+from nipype.utils import NUMPY_MMAP
 
 
 def test_CreateNifti(create_analyze_pair_file_in_directory):
@@ -31,4 +32,18 @@ def test_CreateNifti(create_analyze_pair_file_in_directory):
     result = create_nifti.run()
 
     assert os.path.exists(result.outputs.nifti_file)
-    assert nb.load(result.outputs.nifti_file)
+    assert nb.load(result.outputs.nifti_file, mmap=NUMPY_MMAP)
+
+def test_CalculateMedian(create_analyze_pair_file_in_directory):
+
+    filelist, outdir = create_analyze_pair_file_in_directory
+
+    mean = misc.CalculateMedian()
+
+    with pytest.raises(TypeError): mean.run()
+
+    mean.inputs.in_file = filelist[0]
+    eg = mean.run()
+
+    assert os.path.exists(eg.outputs.median_file)
+    assert nb.load(eg.outputs.median_file, mmap=NUMPY_MMAP)