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fix: make dcm2nii compatible with node for efficient execution, improve docs #782

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Merged
merged 4 commits into from
Feb 1, 2014
Merged

fix: make dcm2nii compatible with node for efficient execution, improve docs #782

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969d326
fix: make dcm2nii compatible with node for efficient execution, impro…
satra Jan 31, 2014
d0e0990
fix: use two files
satra Jan 31, 2014
12c03b8
doc: no support for directories
satra Jan 31, 2014
8aa9aa8
Merge remote-tracking branch 'upstream/master' into enh/dcm2nii
satra Jan 31, 2014
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30 changes: 28 additions & 2 deletions nipype/interfaces/dcm2nii.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,12 @@
"""The dcm2nii 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,
InputMultiPath, traits, TraitedSpec,
OutputMultiPath, isdefined,
Expand All @@ -8,7 +17,8 @@
import re

class Dcm2niiInputSpec(CommandLineInputSpec):
source_names = InputMultiPath(File(exists=True), argstr="%s", position=10, mandatory=True)
source_names = InputMultiPath(File(exists=True), argstr="%s", position=10,
copyfile=False, mandatory=True)
gzip_output = traits.Bool(False, argstr='-g', position=0, usedefault=True)
nii_output = traits.Bool(True, argstr='-n', position=1, usedefault=True)
anonymize = traits.Bool(argstr='-a', position=2)
Expand All @@ -18,7 +28,8 @@ class Dcm2niiInputSpec(CommandLineInputSpec):
output_dir = Directory(exists=True, argstr='-o %s', genfile=True, position=6)
config_file = File(exists=True, argstr="-b %s", genfile=True, position=7)
convert_all_pars = traits.Bool(argstr='-v', position=8)
args = traits.Str(argstr='%s', desc='Additional parameters to the command', position=9)
args = traits.Str(argstr='%s', desc='Additional parameters to the command',
position=9)

class Dcm2niiOutputSpec(TraitedSpec):
converted_files = OutputMultiPath(File(exists=True))
Expand All @@ -28,6 +39,21 @@ class Dcm2niiOutputSpec(TraitedSpec):
bvals = OutputMultiPath(File(exists=True))

class Dcm2nii(CommandLine):
"""Uses MRICRON's dcm2nii to convert dicom files

Examples
========

>>> from nipype.interfaces.dcm2nii import Dcm2nii
>>> converter = Dcm2nii()
>>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
>>> converter.inputs.gzip_output = True
>>> converter.inputs.output_dir = '.'
>>> converter.cmdline #doctest: +ELLIPSIS
'dcm2nii -g y -n y -i n -o . -b config.ini functional_1.dcm functional_2.dcm'
>>> converter.run() # doctest: +SKIP
"""

input_spec=Dcm2niiInputSpec
output_spec=Dcm2niiOutputSpec

Expand Down
1 change: 1 addition & 0 deletions nipype/interfaces/tests/test_auto_Dcm2nii.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ def test_Dcm2nii_inputs():
position=5,
),
source_names=dict(argstr='%s',
copyfile=False,
mandatory=True,
position=10,
),
Expand Down