def test_getAnalysisDir():
paths = ['analysis.feat/filtered_func_data.nii.gz',
'analysis.feat/design.fsf',
'analysis.feat/design.mat',
'analysis.feat/design.con']
testpaths = ['analysis.feat/filtered_func_data.nii.gz',
'analysis.feat/stats/zstat1.nii.gz',
'analysis.feat/logs/feat4_post',
'analysis.feat/.ramp.gif']
with tests.testdir(paths) as testdir:
expected = op.join(testdir, 'analysis.feat')
for t in testpaths:
t = op.join(testdir, t)
assert featanalysis.getAnalysisDir(t) == expected
def findFEATImage(overlayList, overlay):
"""Searches the given :class:`.OverlayList` to see if there is a
:class:`.FEATImage` associated with the given ``overlay``. Returns the
``FEATImage`` if found, otherwise returns ``None``.
"""
import fsl.data.featanalysis as featanalysis
import fsl.data.featimage as featimage
if isinstance(overlay, featimage.FEATImage): return overlay
if overlay is None: return None
if overlay.dataSource is None: return None
featPath = featanalysis.getAnalysisDir(overlay.dataSource)
if featPath is None:
return None
dataPath = featanalysis.getDataFile(featPath)
featImage = overlayList.find(dataPath)
return featImage
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 __selectedOverlayChanged(self, *a):
"""Called when the :attr:`.DisplayContext.selectedOverlay` changes,
and by the :meth:`__overlayListChanged` method.
If the newly selected overlay is a :class:`.FEATImage` (or is otherwise
associated with a FEAT analysis) which has cluster results, they are
loaded in, and displayed on a :class:`.WidgetGrid`.
"""
prevOverlay = self.__selectedOverlay
self.__selectedOverlay = None
# No overlays are loaded
if len(self.overlayList) == 0:
self.__disable(strings.messages[self, 'noOverlays'])
return
overlay = self.displayCtx.getSelectedOverlay()
# Overlay is in-memory
if overlay.dataSource is None:
self.__disable(strings.messages[self, 'notFEAT'])
return
featDir = featanalysis.getAnalysisDir(overlay.dataSource)
# No FEAT analysis, or not an Image,
# can't do anything with that
if featDir is None or not isinstance(overlay, fslimage.Nifti):
log.debug('Overlay {} is not part of a feat '
'analysis, or is not Nifti'.format(overlay))
self.__disable(strings.messages[self, 'notFEAT'])
return
# Selected overlay is either the
# same one (maybe the overlay list,
# rather than the selected overlay,
# changed) or the newly selected
# overlay is from the same FEAT
# analysis. No need to do anything.
if prevOverlay is not None:
prevFeatImage = self.__featImages.get(prevOverlay)
if prevOverlay is overlay or \
(prevFeatImage is not None and
featDir == prevFeatImage.getFEATDir()):
log.debug('Overlay {} is already selected.'.format(overlay))
# Make sure the overlay -> FEATImage
# mapping is present, and (re-)cache
# a reference to the selected overlay.
self.__featImages[overlay] = prevFeatImage
self.__selectedOverlay = overlay
return
# We're in business. The newly selected
# overlay is a part of a FEAT analysis
# which is not currently being displayed.
self.__selectedOverlay = overlay
# Clear the stat selection combo box.
self.__statSelect.Clear()
# Get the FEATImage associated with
# this overlay, so we can get
# information about the FEAT analysis
featImage = self.__featImages.get(overlay)
if featImage is None:
# If the overlay itself is a FEATImage,
# then we have nothing to do.
if isinstance(overlay, featimage.FEATImage):
featImage = overlay
else:
# The FEATImage might already
# be in the overlay list -
# let's search for it.
for ovl in self.overlayList:
if isinstance(ovl, featimage.FEATImage) and \
ovl.getFEATDir() == featDir:
featImage = ovl
# As a last resort, if the FEATImage is not
# in the overlay list, we'll create one.
if featImage is None:
featImage = featimage.FEATImage(featDir,
loadData=False,
calcRange=False)
self.__featImages[overlay] = featImage
log.debug('Identified FEAT analysis associated with overlay '
'{}: {}'.format(overlay, featImage.getFEATDir()))
# Get the contrast and cluster
# information for the FEAT analysis.
display = self.displayCtx.getDisplay(overlay)
numCons = featImage.numContrasts()
conNames = featImage.contrastNames()
try:
# clusts is a list of (contrast, clusterList) tuples
clusts = [(c, featImage.clusterResults(c)) for c in range(numCons)]
clusts = [c for c in clusts if c[1] is not None]
# Error parsing the cluster data
except Exception as e:
log.warning('Error parsing cluster data for '
'{}: {}'.format(featImage.name, str(e)),
exc_info=True)
self.__disable(strings.messages[self, 'badData'])
return
# No cluster results exist
# for any contrast
if len(clusts) == 0:
self.__disable(strings.messages[self, 'noClusters'])
return
# Populate the stat selection combo box
for contrast, clusterList in clusts:
name = conNames[contrast]
name = strings.labels[self, 'clustName'].format(contrast + 1, name)
self.__statSelect.Append(name, clusterList)
self.__overlayName.SetLabel(display.name)
# Refresh the widget grid
self.__statSelect.SetSelection(0)
self.__statSelected()
self.Layout()
