def guessDataSourceType(path):
"""A convenience function which, given the name of a file or directory,
figures out a suitable overlay type.
Returns a tuple containing two values - a type which should be able to
load the path, and the path itself, possibly adjusted. If the type
is unrecognised, the first tuple value will be ``None``.
"""
import fsl.data.mesh as fslmesh
import fsl.data.gifti as fslgifti
import fsl.data.featimage as featimage
import fsl.data.melodicimage as melimage
import fsl.data.dtifit as dtifit
import fsl.data.melodicanalysis as melanalysis
import fsl.data.featanalysis as featanalysis
# Support files opened via fsleyes:// URL
if path.startswith('fsleyes://'):
path = path[10:]
path = op.abspath(path)
# VTK files are easy
if path.endswith('.vtk'):
return fslmesh.TriangleMesh, path
# So are GIFTIS
if path.endswith('.gii'):
return fslgifti.GiftiSurface, path
# Analysis directory?
if op.isdir(path):
if melanalysis.isMelodicDir(path):
return melimage.MelodicImage, path
elif featanalysis.isFEATDir(path):
return featimage.FEATImage, path
elif dtifit.isDTIFitPath(path):
return dtifit.DTIFitTensor, path
# Assume it's a NIFTI image
try:
path = fslimage.addExt(path, mustExist=True)
except fslimage.PathError:
return None, path
if melanalysis.isMelodicImage(path): return melimage.MelodicImage, path
elif featanalysis.isFEATImage(path): return featimage.FEATImage, path
else: return fslimage.Image, path
# Otherwise, I don't
# know what to do
return None, path
def test_isMelodicDir():
paths = ['analysis.ica/melodic_IC.nii.gz',
'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix']
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
assert mela.isMelodicDir(meldir)
# Directory must end in .ica
with tests.testdir([p.replace('.ica', '.blob') for p in paths]) as testdir:
meldir = op.join(testdir, 'analysis.blob')
assert not mela.isMelodicDir(meldir)
# Directory must exist!
assert not mela.isMelodicDir('non-existent.ica')
# Directory must contain all of the above files
perms = it.chain(it.combinations(paths, 1),
it.combinations(paths, 2))
for p in perms:
with tests.testdir(p) as testdir:
meldir = op.join(testdir, 'analysis.ica')
assert not mela.isMelodicDir(meldir)
def guessFlirtFiles(path):
"""Given a ``path`` to a NIFTI image file, tries to guess an appropriate
FLIRT transformation matrix file and reference image. The guess is based
on the path location (e.g. if it is a FEAT or MELODIC image).
Returns a tuple containing paths to the matrix file and reference image,
or ``(None, None)`` if a guess couldn't be made.
"""
import fsl.data.featanalysis as featanalysis
import fsl.data.melodicanalysis as melodicanalysis
if path is None:
return None, None
filename = op.basename(path)
dirname = op.dirname(path)
regDir = None
srcRefMap = {}
func2struc = 'example_func2highres.mat'
struc2std = 'highres2standard.mat'
featDir = featanalysis.getAnalysisDir(dirname)
melDir = melodicanalysis.getAnalysisDir(dirname)
# TODO more heuristics
if featDir is not None:
regDir = op.join(featDir, 'reg')
srcRefMap = {
'example_func': ('highres', func2struc),
'filtered_func_data': ('highres', func2struc),
'mean_func': ('highres', func2struc),
'thresh_zstat': ('highres', func2struc),
op.join('stats', 'zstat'): ('highres', func2struc),
op.join('stats', 'tstat'): ('highres', func2struc),
op.join('stats', 'cope'): ('highres', func2struc),
op.join('stats', 'pe'): ('highres', func2struc),
'highres': ('standard', struc2std),
'highres_head': ('standard', struc2std),
'struc': ('standard', struc2std),
'struct': ('standard', struc2std),
'struct_brain': ('standard', struc2std),
'struc_brain': ('standard', struc2std),
}
elif melodicanalysis.isMelodicDir(dirname):
if melDir.startswith('filtered_func_data'):
regDir = op.join(melDir, '..', 'reg')
else:
regDir = op.join(melDir, 'reg')
srcRefMap = {
'filtered_func_data': ('highres', func2struc),
'melodic_IC': ('highres', func2struc),
'example_func': ('highres', func2struc),
'mean_func': ('highres', func2struc),
'highres': ('standard', struc2std),
'highres_head': ('standard', struc2std),
'struc': ('standard', struc2std),
'struct': ('standard', struc2std),
'struct_brain': ('standard', struc2std),
'struc_brain': ('standard', struc2std),
}
matFile = None
refFile = None
for src, (ref, mat) in srcRefMap.items():
if not filename.startswith(src):
continue
mat = op.join(regDir, mat)
ref = op.join(regDir, ref)
try:
ref = fslimage.addExt(ref)
except Exception:
continue
if op.exists(mat):
matFile = mat
refFile = ref
break
return matFile, refFile
def guessDataSourceType(path):
"""A convenience function which, given the name of a file or directory,
figures out a suitable overlay type.
Returns a tuple containing two values - a type which should be able to
load the path, and the path itself, possibly adjusted. If the type
is unrecognised, the first tuple value will be ``None``.
"""
import fsl.data.vtk as fslvtk
import fsl.data.gifti as fslgifti
import fsl.data.freesurfer as fslfs
import fsl.data.mghimage as fslmgh
import fsl.data.featimage as featimage
import fsl.data.melodicimage as melimage
import fsl.data.dtifit as dtifit
import fsl.data.melodicanalysis as melanalysis
import fsl.data.featanalysis as featanalysis
# Support files opened via fsleyes:// URL
if path.startswith('fsleyes://'):
path = path[10:]
path = op.abspath(path)
# Accept images sans-extension
try:
path = fslimage.addExt(path, mustExist=True)
except fslimage.PathError:
pass
if op.isfile(path):
# Some types are easy - just check the extensions
if fslpath.hasExt(path, fslvtk.ALLOWED_EXTENSIONS):
return fslvtk.VTKMesh, path
elif fslpath.hasExt(path, fslgifti.ALLOWED_EXTENSIONS):
return fslgifti.GiftiMesh, path
elif fslfs.isGeometryFile(path):
return fslfs.FreesurferMesh, path
elif fslpath.hasExt(path, fslmgh.ALLOWED_EXTENSIONS):
return fslmgh.MGHImage, path
# Other specialised image types
elif melanalysis.isMelodicImage(path):
return melimage.MelodicImage, path
elif featanalysis.isFEATImage(path):
return featimage.FEATImage, path
elif fslimage.looksLikeImage(path):
return fslimage.Image, path
# Analysis directory?
elif op.isdir(path):
if melanalysis.isMelodicDir(path):
return melimage.MelodicImage, path
elif featanalysis.isFEATDir(path):
return featimage.FEATImage, path
elif dtifit.isDTIFitPath(path):
return dtifit.DTIFitTensor, path
# Otherwise, I don't
# know what to do
return None, path
