def main(argv=None):
"""``imln`` - create sym-links to images. """
if argv is None:
argv = sys.argv[1:]
if len(argv) != 2:
print(usage)
return 1
target, linkbase = argv
target = fslpath.removeExt(target, exts)
linkbase = fslpath.removeExt(linkbase, exts)
# Target must exist, so we can
# infer the correct extension(s).
# Error on incomplete file groups
# (e.g. a.img without a.hdr).
try:
targets = fslpath.getFileGroup(target,
allowedExts=exts,
fileGroups=groups,
unambiguous=True)
except Exception as e:
print(f'Error: {e}')
return 1
for target in targets:
if not op.exists(target):
continue
ext = fslpath.getExt(target, exts)
link = f'{linkbase}{ext}'
try:
# emulate old imln behaviour - if
# link already exists, it is removed
if op.exists(link):
os.remove(link)
os.symlink(target, link)
except Exception as e:
print(f'Error: {e}')
return 1
return 0
def parseFilename(filename):
"""Parses a BIDS-like file name, returning the entities and suffix encoded
in the name. See the :func:`isBIDSFile` function for an explanation of
what is considered to be a valid BIDS file name.
.. note:: This function assumes that no period (``.``) characters occur in
the body of a BIDS filename.
:returns: A tuple containing:
- A dict containing the entities
- The suffix
"""
if not isBIDSFile(filename, strict=False):
raise ValueError('Does not look like a BIDS '
'file: {}'.format(filename))
suffix = None
entities = []
filename = op.basename(filename)
filename = fslpath.removeExt(filename, firstDot=True)
parts = filename.split('_')
for part in parts[:-1]:
entities.append(part.split('-'))
suffix = parts[-1]
entities = dict(entities)
return entities, suffix
def main(argv=None):
"""Test if an image path exists, and prints ``'1'`` if it does or ``'0'``
if it doesn't.
"""
if argv is None:
argv = sys.argv[1:]
# emulate old fslio/imtest - always return 0
if len(argv) != 1:
print('0')
return 0
path = fslpath.removeExt(argv[0], exts)
path = op.realpath(path)
# getFileGroup will raise an error
# if the image (including all
# components - i.e. header and
# image) does not exist
try:
fslpath.getFileGroup(path,
allowedExts=exts,
fileGroups=groups,
unambiguous=True)
print('1')
except fslpath.PathError:
print('0')
return 0
def save(self, filename=None):
"""Overrides :meth:`.Image.save`. If a ``filename`` is not provided,
converts the original (MGH) file name into a NIFTI filename, before
passing it to the :meth:`.Image.save` method.
"""
if filename is None:
filename = self.dataSource
filename = fslpath.removeExt(filename, ALLOWED_EXTENSIONS)
return fslimage.Image.save(self, filename)
def imglob(paths, output=None):
"""Given a list of file names, identifies and returns the unique
NIFTI/ANALYZE image files that exist.
:arg paths: Sequence of paths/prefixes to glob.
:arg output: One of ``'prefix'`` (the default), ``'all'``, or
``'primary'``:
- ``'prefix'``: Returns the files without extensions.
- ``'all'``: Returns all files that match (e.g. both
``.img`` and ``.hdr`` files will be
returned).
- ``'primary'``: Returns only the primary file of each
matching file group, e.g. only the
``.hdr`` file would be returned from
an ``.img``/``.hdr`` pair.
:returns: A sequence of resolved path names, in the form specified
by the ``output`` parameter.
"""
if output is None:
output = 'prefix'
if output not in ('prefix', 'all', 'primary'):
raise ValueError('Unsupported output format: {}'.format(output))
imgfiles = []
# Build a list of all image files (both
# hdr and img and otherwise) that match
for path in paths:
try:
path = fslimage.removeExt(path)
imgfiles.extend(fslimage.addExt(path, unambiguous=False))
except fslpath.PathError:
continue
if output == 'prefix':
imgfiles = fslpath.removeDuplicates(imgfiles,
allowedExts=exts,
fileGroups=groups)
imgfiles = [fslpath.removeExt(f, exts) for f in imgfiles]
elif output == 'primary':
imgfiles = fslpath.removeDuplicates(imgfiles,
allowedExts=exts,
fileGroups=groups)
return list(sorted(set(imgfiles)))
def main(argv=None):
"""Removes file extensions from all paths which are specified on the
command line.
"""
if argv is None:
argv = sys.argv[1:]
if len(argv) < 1:
print(usage)
return 1
removed = []
for path in argv:
removed.append(fslpath.removeExt(path, ALLOWED_EXTENSIONS))
print(' '.join(removed))
return 0
def __init__(self, infile, fixWinding=False):
"""Load the given GIFTI file using ``nibabel``, and extracts surface
data using the :func:`loadGiftiSurface` function.
:arg infile: A GIFTI surface file (``*.surf.gii``).
.. todo:: Allow loading from a ``.topo.gii`` and ``.coord.gii`` file?
Maybe.
"""
surfimg, vertices, indices = loadGiftiSurface(infile)
mesh.TriangleMesh.__init__(self, vertices, indices, fixWinding)
name = fslpath.removeExt(op.basename(infile), ALLOWED_EXTENSIONS)
infile = op.abspath(infile)
self.name = name
self.dataSource = infile
self.surfImg = surfimg
def main(argv=None):
"""Removes all images which are specified on the command line. """
if argv is None:
argv = sys.argv[1:]
if len(argv) < 1:
print(usage)
return 1
prefixes = [fslpath.removeExt(p, exts) for p in argv]
for prefix, ext in it.product(prefixes, exts):
path = f'{prefix}{ext}'
if op.exists(path):
os.remove(path)
return 0
def parseFilename(filename):
"""Parses a BIDS-like file name. The file name must consist of zero or more
"entities" (alpha-numeric ``name-value`` pairs), a "suffix", all separated
by underscores, and a regular file extension. For example, the following
file::
sub-01_ses-01_task-stim_bold.nii.gz
has suffix ``bold``, entities ``sub=01``, ``ses=01`` and ``task=stim``, and
extension ``.nii.gz``.
.. note:: This function assumes that no period (``.``) characters occur in
the body of a BIDS filename.
:returns: A tuple containing:
- A dict containing the entities
- The suffix
"""
if not isBIDSFile(filename, strict=False):
raise ValueError('Does not look like a BIDS '
'file: {}'.format(filename))
suffix = None
entities = []
filename = op.basename(filename)
filename = fslpath.removeExt(filename, firstDot=True)
parts = filename.split('_')
for part in parts[:-1]:
entities.append(part.split('-'))
suffix = parts[-1]
entities = dict(entities)
return entities, suffix
def __init__(self, infile, fixWinding=False, loadAll=False):
"""Load the given GIFTI file using ``nibabel``, and extracts surface
data using the :func:`loadGiftiMesh` function.
If the file contains more than one set of vertices, the additional
ones are added with keys of the form ``infile_i``, where ``infile`` is
the absolute path to the file, and ``i`` is an index number, starting
from 1. See the :meth:`.addVertices` method.
:arg infile: A GIFTI file (``*.gii``) which contains a surface
definition.
:arg fixWinding: Passed through to the :meth:`addVertices` method
for the first vertex set.
:arg loadAll: If ``True``, the ``infile`` directory is scanned
for other surface files which are then loaded
as additional vertex sets.
.. todo:: Allow loading from a ``.topo.gii`` and ``.coord.gii`` file?
Maybe.
"""
name = fslpath.removeExt(op.basename(infile), ALLOWED_EXTENSIONS)
infile = op.abspath(infile)
surfimg, indices, vertices, vdata = loadGiftiMesh(infile)
fslmesh.Mesh.__init__(self, indices, name=name, dataSource=infile)
for i, v in enumerate(vertices):
if i == 0: key = infile
else: key = '{}_{}'.format(infile, i)
self.addVertices(v, key, select=(i == 0), fixWinding=fixWinding)
self.setMeta(infile, surfimg)
if vdata is not None:
self.addVertexData(infile, vdata)
# Find and load all other
# surfaces in the same directory
# as the specfiied one.
if loadAll:
# Only attempt to auto-load sensibly
# named gifti files (i.e. *.surf.gii,
# rather than *.gii).
surfFiles = relatedFiles(infile, [ALLOWED_EXTENSIONS[0]])
nvertices = vertices[0].shape[0]
for sfile in surfFiles:
try:
surfimg, _, vertices, _ = loadGiftiMesh(sfile)
except Exception:
continue
if vertices[0].shape[0] != nvertices:
continue
self.addVertices(vertices[0], sfile, select=False)
self.setMeta(sfile, surfimg)
