cmtklib.interfaces.misc module
ConcatOutputsAsTuple
Bases: nipype.interfaces.base.core.BaseInterface
Concatenate 2 different output file as a Tuple of 2 files.
Examples
>>> from cmtklib.interfaces.misc import ConcatOutputsAsTuple >>> concat_outputs = ConcatOutputsAsTuple() >>> concat_outputs.inputs.input1 = 'output_interface1.nii.gz' >>> concat_outputs.inputs.input2 = 'output_interface2.nii.gz' >>> concat_outputs.run()input1 : a pathlike object or string representing an existing file input2 : a pathlike object or string representing an existing file
out_tuple : a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)
ExtractHeaderVoxel2WorldMatrix
Bases: nipype.interfaces.base.core.BaseInterface
Write in a text file the voxel-to-world transform matrix from the heaer of a Nifti image.
Examples
>>> from cmtklib.interfaces.misc import ExtractHeaderVoxel2WorldMatrix >>> extract_mat = ExtractHeaderVoxel2WorldMatrix() >>> extract_mat.inputs.in_file = 'sub-01_T1w.nii.gz' >>> extract_mat.run()
- in_filea pathlike object or string representing an existing file
Input image file.
- out_matrixa pathlike object or string representing an existing file
Output voxel to world affine transform file.
ExtractImageVoxelSizes
Bases: nipype.interfaces.base.core.BaseInterface
Returns a list of voxel sizes from an image.
Examples
>>> from cmtklib.interfaces.misc import ExtractImageVoxelSizes >>> extract_voxel_sizes = ExtractImageVoxelSizes() >>> extract_voxel_sizes.inputs.in_file = 'sub-01_T1w.nii.gz' >>> extract_voxel_sizes.run()in_file : a pathlike object or string representing an existing file
voxel_sizes : a list of items which are any value
Rename001
Bases: nipype.interfaces.utility.base.Rename
Change the name of a file based on a mapped format string.
To use additional inputs that will be defined at run-time, the class constructor must be called with the format template, and the fields identified will become inputs to the interface. Additionally, you may set the parse_string input, which will be run over the input filename with a regular expressions search, and will fill in additional input fields from matched groups. Fields set with inputs have precedence over fields filled in with the regexp match.
It corresponds to the
nipype.interfaces.utility.base.Rename
interface that has been modified to force hard link during copyExamples
>>> from nipype.interfaces.utility import Rename >>> rename1 = Rename() >>> rename1.inputs.in_file = os.path.join(datadir, "zstat1.nii.gz") # datadir is a directory with exemplary files, defined in conftest.py >>> rename1.inputs.format_string = "Faces-Scenes.nii.gz" >>> res = rename1.run() >>> res.outputs.out_file 'Faces-Scenes.nii.gz">>> rename2 = Rename(format_string="%(subject_id)s_func_run%(run)02d") >>> rename2.inputs.in_file = os.path.join(datadir, "functional.nii") >>> rename2.inputs.keep_ext = True >>> rename2.inputs.subject_id = "subj_201" >>> rename2.inputs.run = 2 >>> res = rename2.run() >>> res.outputs.out_file 'subj_201_func_run02.nii'>>> rename3 = Rename(format_string="%(subject_id)s_%(seq)s_run%(run)02d.nii") >>> rename3.inputs.in_file = os.path.join(datadir, "func_epi_1_1.nii") >>> rename3.inputs.parse_string = r"func_(?P<seq>\w*)_.*" >>> rename3.inputs.subject_id = "subj_201" >>> rename3.inputs.run = 2 >>> res = rename3.run() >>> res.outputs.out_file 'subj_201_epi_run02.nii'References
- format_stringa string
Python formatting string for output template.
- in_filea pathlike object or string representing an existing file
File to rename.
- keep_exta boolean
Keep in_file extension, replace non-extension component of name.
- parse_stringa string
Python regexp parse string to define replacement inputs.
- use_fullpatha boolean
Use full path as input to regex parser. (Nipype default value:
False
)
- out_filea pathlike object or string representing an existing file
Softlink to original file with new name.