/usr/share/pyshared/nipype/interfaces/dcm2nii.py is in python-nipype 0.5.3-2wheezy2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 | from nipype.interfaces.base import (CommandLine, CommandLineInputSpec,
InputMultiPath, traits, TraitedSpec,
OutputMultiPath, isdefined,
File, Directory)
import os
from copy import deepcopy
from nipype.utils.filemanip import split_filename
class Dcm2niiInputSpec(CommandLineInputSpec):
source_names = InputMultiPath(File(exists=True), argstr="%s", position=8, 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)
id_in_filename = traits.Bool(False, argstr='-i', usedefault=True, position=3)
reorient = traits.Bool(argstr='-r', position=4)
reorient_and_crop = traits.Bool(argstr='-x', position=5)
output_dir = Directory(exists=True, argstr='-o %s', genfile=True, position=6)
config_file = File(exists=True, argstr="-b %s", genfile=True, position=7)
class Dcm2niiOutputSpec(TraitedSpec):
converted_files = OutputMultiPath(File(exists=True))
reoriented_files = OutputMultiPath(File(exists=True))
reoriented_and_cropped_files = OutputMultiPath(File(exists=True))
bvecs = OutputMultiPath(File(exists=True))
bvals = OutputMultiPath(File(exists=True))
class Dcm2nii(CommandLine):
input_spec=Dcm2niiInputSpec
output_spec=Dcm2niiOutputSpec
_cmd = 'dcm2nii'
def _format_arg(self, opt, spec, val):
if opt in ['gzip_output', 'nii_output', 'anonymize', 'id_in_filename']:
spec = deepcopy(spec)
if val:
spec.argstr += ' y'
else:
spec.argstr += ' n'
val = True
return super(Dcm2nii, self)._format_arg(opt, spec, val)
def _run_interface(self, runtime):
new_runtime = super(Dcm2nii, self)._run_interface(runtime)
(self.output_files,
self.reoriented_files,
self.reoriented_and_cropped_files,
self.bvecs, self.bvals) = self._parse_stdout(new_runtime.stdout)
return new_runtime
def _parse_stdout(self, stdout):
files = []
reoriented_files = []
reoriented_and_cropped_files = []
bvecs = []
bvals = []
skip = False
last_added_file = None
for line in stdout.split("\n"):
if not skip:
file = None
if line.startswith("Saving "):
file = line[len("Saving "):]
elif line.startswith("GZip..."):
#for gzipped outpus files are not absolute
if isdefined(self.inputs.output_dir):
output_dir = self.inputs.output_dir
else:
output_dir = self._gen_filename('output_dir')
file = os.path.abspath(os.path.join(output_dir,
line[len("GZip..."):]))
elif line.startswith("Number of diffusion directions "):
if last_added_file:
base, filename, ext = split_filename(last_added_file)
bvecs.append(os.path.join(base,filename + ".bvec"))
bvals.append(os.path.join(base,filename + ".bval"))
if file:
files.append(file)
last_added_file = file
continue
if line.startswith("Reorienting as "):
reoriented_files.append(line[len("Reorienting as "):])
skip = True
continue
elif line.startswith("Cropping NIfTI/Analyze image "):
base, filename = os.path.split(line[len("Cropping NIfTI/Analyze image "):])
filename = "c" + filename
reoriented_and_cropped_files.append(os.path.join(base, filename))
skip = True
continue
skip = False
return files, reoriented_files, reoriented_and_cropped_files, bvecs, bvals
def _list_outputs(self):
outputs = self.output_spec().get()
outputs['converted_files'] = self.output_files
outputs['reoriented_files'] = self.reoriented_files
outputs['reoriented_and_cropped_files'] = self.reoriented_and_cropped_files
outputs['bvecs'] = self.bvecs
outputs['bvals'] = self.bvals
return outputs
def _gen_filename(self, name):
if name == 'output_dir':
return os.getcwd()
elif name == 'config_file':
config_file = "config.ini"
f = open(config_file, "w")
# disable interactive mode
f.write("[BOOL]\nManualNIfTIConv=0\n")
f.close()
return config_file
return None
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