adding trim interface that keeps the original dtype storage

Author: bpinsard

nipype/interfaces/nipy/preprocess.py

@@ -5,7 +5,7 @@
 import numpy as np
 
 from ...utils.misc import package_check
-from ...utils.filemanip import split_filename
+from ...utils.filemanip import split_filename, fname_presuffix
 
 
 try:
@@ -181,3 +181,53 @@ def _list_outputs(self):
         outputs['out_file'] = self._out_file_path
         outputs['par_file'] = self._par_file_path
         return outputs
+
+
+class TrimInputSpec(BaseInterfaceInputSpec):
+    in_file = File(
+        exists=True, mandatory=True,
+        desc="EPI image to trim")
+    begin_index = traits.Int(
+        0,usedefault=True,
+        desc='first volume')
+    end_index = traits.Int(
+        0,usedefault=True,
+        desc='last volume indexed as in python (and 0 for last)')
+    out_file = File(desc='output filename')
+    suffix = traits.Str(
+        '_trim',usedefault=True,
+        desc='suffix for out_file to use if no out_file provided')
+
+class TrimOutputSpec(TraitedSpec):
+    out_file = File(exists=True)
+
+class Trim(BaseInterface):
+    input_spec = TrimInputSpec
+    output_spec = TrimOutputSpec
+
+    def _run_interface(self, runtime):
+        out_file = self._list_outputs()['out_file']
+        nii = nb.load(self.inputs.in_file)
+        if self.inputs.end_index == 0:
+            s = slice(self.inputs.begin_index,nii.shape[3])
+        else:
+            s = slice(self.inputs.begin_index,self.inputs.end_index)
+        nii2 = nb.Nifti1Image(
+            nii.get_data()[...,s],
+            nii.get_affine(),
+            nii.get_header())
+        nb.save(nii2,out_file)
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = self.inputs.out_file
+        if not isdefined(outputs['out_file']):
+            outputs['out_file'] = fname_presuffix(
+                self.inputs.in_file,
+                newpath=os.getcwd(),
+                suffix=self.inputs.suffix)
+        outputs['out_file'] = os.path.abspath(outputs['out_file'])
+        return outputs
+
+