Merge pull request #1523 from TheChymera/bru

new bru2nii PR

Author: satra

nipype/interfaces/bru2nii.py

@@ -0,0 +1,54 @@
+
+"""The bru2nii module provides basic functions for dicom conversion
+
+	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 (CommandLine, CommandLineInputSpec, traits, TraitedSpec, isdefined, File, Directory)
+import os
+
+
+
+class Bru2InputSpec(CommandLineInputSpec):
+	input_dir = Directory(desc = "Input Directory", exists=True, mandatory=True, position=-1, argstr="%s")
+	actual_size = traits.Bool(argstr='-a', desc="Keep actual size - otherwise x10 scale so animals match human.")
+	force_conversion = traits.Bool(argstr='-f', desc="Force conversion of localizers images (multiple slice orientations).")
+	append_protocol_name = traits.Bool(argstr='-p', desc="Append protocol name to output filename.")
+	output_filename = traits.Str(argstr="-o %s", desc="Output filename ('.nii' will be appended)", genfile=True)
+
+class Bru2OutputSpec(TraitedSpec):
+	nii_file = File(exists=True)
+
+class Bru2(CommandLine):
+	"""Uses bru2nii's Bru2 to convert Bruker files
+
+	Examples
+	========
+
+	>>> from nipype.interfaces.bru2nii import Bru2
+	>>> converter = Bru2()
+	>>> converter.inputs.input_dir = "brukerdir"
+	>>> converter.cmdline  # doctest: +ELLIPSIS
+	'Bru2 -o .../nipype/nipype/testing/data/brukerdir brukerdir'
+	"""
+	input_spec = Bru2InputSpec
+	output_spec = Bru2OutputSpec
+	_cmd = "Bru2"
+
+	def _list_outputs(self):
+		outputs = self._outputs().get()
+		if isdefined(self.inputs.output_filename):
+			output_filename1 = self.inputs.output_filename
+		else:
+			output_filename1 = self._gen_filename('output_filename')
+		outputs["nii_file"] = output_filename1+".nii"
+		return outputs
+
+	def _gen_filename(self, name):
+		if name == 'output_filename':
+			outfile = os.path.join(os.getcwd(),os.path.basename(os.path.normpath(self.inputs.input_dir)))
+			return outfile

nipype/interfaces/tests/test_auto_Bru2.py

@@ -0,0 +1,45 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ...testing import assert_equal
+from ..bru2nii import Bru2
+
+
+def test_Bru2_inputs():
+    input_map = dict(actual_size=dict(argstr='-a',
+    ),
+    append_protocol_name=dict(argstr='-p',
+    ),
+    args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    force_conversion=dict(argstr='-f',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    input_dir=dict(argstr='%s',
+    mandatory=True,
+    position=-1,
+    ),
+    output_filename=dict(argstr='-o %s',
+    genfile=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = Bru2.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+
+def test_Bru2_outputs():
+    output_map = dict(nii_file=dict(),
+    )
+    outputs = Bru2.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value