diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index 6c536ba109048b588ad1a9940563d61085c30027..a535ba92cfc20891164718280c053fe304433d8a 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -63,15 +63,14 @@ class FEATImage(fslimage.Image):
``<directory>.feat/filtered_func_data.nii.gz``.
"""
- featDir = featresults.getFEATDir(path)
-
- if featDir is None:
- raise ValueError('{} does not appear to be data from a '
- 'FEAT analysis'.format(path))
-
if op.isdir(path):
- path = op.join(featDir, 'filtered_func_data')
+ path = op.join(path, 'filtered_func_data')
+
+ if not featresults.isFEATImage(path):
+ raise ValueError('{} does not appear to be data '
+ 'from a FEAT analysis'.format(path))
+ featDir = op.dirname(path)
settings = featresults.loadSettings( featDir)
design = featresults.loadDesign( featDir)
names, cons = featresults.loadContrasts(featDir)
@@ -176,7 +175,7 @@ class FEATImage(fslimage.Image):
if self.__pes[ev] is None:
pefile = featresults.getPEFile(self.__featDir, ev)
- self.__pes[ev] = FEATImage(
+ self.__pes[ev] = fslimage.Image(
pefile,
name='{}: PE{} ({})'.format(
self.__analysisName,
@@ -191,7 +190,7 @@ class FEATImage(fslimage.Image):
if self.__residuals is None:
resfile = featresults.getResidualFile(self.__featDir)
- self.__residuals = FEATImage(
+ self.__residuals = fslimage.Image(
resfile,
name='{}: residuals'.format(self.__analysisName))
@@ -203,7 +202,7 @@ class FEATImage(fslimage.Image):
if self.__copes[con] is None:
copefile = featresults.getPEFile(self.__featDir, con)
- self.__copes[con] = FEATImage(
+ self.__copes[con] = fslimage.Image(
copefile,
name='{}: COPE{} ({})'.format(
self.__analysisName,
@@ -220,7 +219,7 @@ class FEATImage(fslimage.Image):
if self.__zstats[con] is None:
zfile = featresults.getZStatFile(self.__featDir, con)
- self.__zstats[con] = FEATImage(
+ self.__zstats[con] = fslimage.Image(
zfile,
name='{}: zstat{} ({})'.format(
self.__analysisName,
@@ -237,7 +236,7 @@ class FEATImage(fslimage.Image):
if self.__clustMasks[con] is None:
mfile = featresults.getClusterMaskFile(self.__featDir, con)
- self.__clustMasks[con] = FEATImage(
+ self.__clustMasks[con] = fslimage.Image(
mfile,
name='{}: cluster mask for zstat{} ({})'.format(
self.__analysisName,
diff --git a/fsl/data/featresults.py b/fsl/data/featresults.py
index 138c0379e11563504f39f4aac6ece0cb44db0036..5250788f65325f3762a46ecc9df442956e9c7915 100644
--- a/fsl/data/featresults.py
+++ b/fsl/data/featresults.py
@@ -13,8 +13,8 @@ following functions are provided:
.. autosummary::
:nosignatures:
+ isFEATImage
isFEATDir
- getFEATDir
hasMelodicDir
loadDesign
loadContrasts
@@ -51,59 +51,48 @@ import fsl.utils.transform as transform
log = logging.getLogger(__name__)
-def isFEATDir(path):
- """Returns ``True`` if the given path looks like a FEAT directory, or
- looks like the input data for a FEAT analysis, ``False`` otherwise.
-
- :arg path: A file / directory path.
+def isFEATImage(path):
+ """Returns ``True`` if the given path looks like it is the input data to
+ a FEAT analysis, ``False`` otherwise.
"""
+ dirname = op.dirname( path)
+ filename = op.basename(path)
- dirname, filename = op.split(path)
+ return filename.startswith('filtered_func_data') and isFEATDir(dirname)
- featDir = getFEATDir(dirname)
- isfeatdir = featDir is not None
-
- try:
- hasdesfsf = op.exists(op.join(featDir, 'design.fsf'))
- hasdesmat = op.exists(op.join(featDir, 'design.mat'))
- hasdescon = op.exists(op.join(featDir, 'design.con'))
-
- isfeat = (isfeatdir and
- hasdesmat and
- hasdescon and
- hasdesfsf)
-
- return isfeat
-
- except:
- return False
+def isFEATDir(path):
+ """Returns ``True`` if the given path looks like a FEAT directory, or
+ looks like the input data for a FEAT analysis, ``False`` otherwise. A
+ FEAT directory:
-def getFEATDir(path):
- """Given the path of any file/directory which is within a ``.feat`` or
- ``.gfeat`` directory, strips all trailing components of the path name,
- and returns the root FEAT directory.
-
- Returns ``None`` if the given path is not contained within a ``.feat``
- or ``.gfeat`` directory.
+ - Must be named ``*.feat``.
+ - Must contain a file called ``filtered_func_data.nii.gz``.
+ - Must contain a file called ``design.fsf``.
+ - Must contain a file called ``design.mat``.
+ - Must contain a file called ``design.con``.
:arg path: A file / directory path.
"""
- sufs = ['.feat', '.gfeat']
- idxs = [(path.rfind(s), s) for s in sufs]
- idx, suf = max(idxs, key=lambda (i, s): i)
-
- if idx == -1:
- return None
-
- idx += len(suf)
- path = path[:idx]
+ path = op.abspath(path)
+
+ if op.isdir(path): dirname = path
+ else: dirname = op.dirname(path)
+
+ if not dirname.endswith('.feat'):
+ return False
- if path.endswith(suf) or path.endswith('{}{}'.format(suf, op.sep)):
- return path
-
- return None
+ try:
+ fslimage.addExt(op.join(path, 'filtered_func_data'), mustExist=True)
+ except ValueError:
+ return False
+
+ if not op.exists(op.join(dirname, 'design.fsf')): return False
+ if not op.exists(op.join(dirname, 'design.mat')): return False
+ if not op.exists(op.join(dirname, 'design.con')): return False
+
+ return True
def hasMelodicDir(featdir):
diff --git a/fsl/data/melodicimage.py b/fsl/data/melodicimage.py
index 7e3d7a0f2acee1e660a8e0be4de0ca59fd5d94d1..fd9772744611064de5dd9b37f09c27abfd7e1a6c 100644
--- a/fsl/data/melodicimage.py
+++ b/fsl/data/melodicimage.py
@@ -59,31 +59,18 @@ class MelodicImage(fslimage.Image):
"""
if op.isdir(path):
- dirname = path
- filename = 'melodic_IC'
+ path = op.join(path, 'melodic_IC')
- else:
- dirname = op.dirname( path)
- filename = op.basename(path)
-
- dirname = dirname.rstrip(op.sep)
-
- if not melresults.isMelodicDir(dirname):
+ if not melresults.isMelodicImage(path):
raise ValueError('{} does not appear to be a '
- 'MELODIC directory'.format(dirname))
-
- if not filename.startswith('melodic_IC'):
- raise ValueError('{} does not appear to be a MELODIC '
- 'component file'.format(filename))
+ 'MELODIC component file'.format(path))
- fslimage.Image.__init__(self,
- op.join(dirname, filename),
- *args,
- **kwargs)
-
- self.__meldir = dirname
- self.__melmix = melresults.getComponentTimeSeries( dirname)
- self.__melFTmix = melresults.getComponentPowerSpectra(dirname)
+ fslimage.Image.__init__(self, path, *args, **kwargs)
+
+ meldir = op.dirname(path)
+ self.__meldir = meldir
+ self.__melmix = melresults.getComponentTimeSeries( meldir)
+ self.__melFTmix = melresults.getComponentPowerSpectra(meldir)
self.__melICClass = melresults.MelodicClassification( self)
# Automatically set the
diff --git a/fsl/data/melodicresults.py b/fsl/data/melodicresults.py
index 3b8d8dc33be34509741543a5957e873935898fc2..46e78a624a2ceec41a30836976907e3f2000e0cf 100644
--- a/fsl/data/melodicresults.py
+++ b/fsl/data/melodicresults.py
@@ -14,8 +14,8 @@ following functions are provided:
.. autosummary::
:nosignatures:
+ isMelodicImage
isMelodicDir
- getMelodicDir
getTopLevelAnalysisDir
getDataFile
getICFile
@@ -38,62 +38,54 @@ import numpy as np
import props
-import fsl.data.image as fslimage
-import fsl.data.featresults as featresults
+import fsl.data.image as fslimage
log = logging.getLogger(__name__)
-def isMelodicDir(path):
- """Returns ``True`` if the given path looks like it is contained within
- a MELODIC directory, ``False`` otherwise.
+def isMelodicImage(path):
+ """Returns ``True`` if the given path looks like it is a melodic
+ component image file, ``False`` otherwise.
"""
- # Must be named *.ica or *.gica
- return getMelodicDir(path) is not None
-
-def getMelodicDir(path):
- """Returns the MELODIC directory in which the given path is contained,
- or ``None`` if it is not contained within a MELODIC directory. A melodic
- directory:
-
- - Must be named ``*.ica`` or ``*.gica``
- - Must contain a file called ``melodic_IC.nii.gz``
- - Must contain a file called ``melodic_mix``.
- """
+ dirname = op.dirname( path)
+ filename = op.basename(path)
- # TODO This code is identical to featresults.getFEATDir.
- # Can you generalise it and put it somewhere in fsl.utils?
-
- path = op.abspath(path)
+ return filename.startswith('melodic_IC') and isMelodicDir(dirname)
+
- sufs = ['.ica', '.gica']
- idxs = [(path.rfind(s), s) for s in sufs]
- idx, suf = max(idxs, key=lambda (i, s): i)
+def isMelodicDir(path):
+ """Returns ``True`` if the given path looks like it is contained within
+ a MELODIC directory, ``False`` otherwise. A melodic directory:
- if idx == -1:
- return None
+ - Must be named ``*.ica``.
+ - Must contain a file called ``melodic_IC.nii.gz``.
+ - Must contain a file called ``melodic_mix``.
+ - Must contain a file called ``melodic_FTmix``.
+ """
- idx += len(suf)
- path = path[:idx].rstrip(op.sep)
+ path = op.abspath(path)
+
+ if op.isdir(path): dirname = path
+ else: dirname = op.dirname(path)
- if not path.endswith(suf):
- return None
+ if not dirname.endswith('.ica'):
+ return False
# Must contain an image file called melodic_IC
try:
- fslimage.addExt(op.join(path, 'melodic_IC'), mustExist=True)
+ fslimage.addExt(op.join(dirname, 'melodic_IC'), mustExist=True)
except ValueError:
- return None
+ return False
# Must contain files called
# melodic_mix and melodic_FTmix
- if not op.exists(op.join(path, 'melodic_mix')): return None
- if not op.exists(op.join(path, 'melodic_FTmix')): return None
-
- return path
+ if not op.exists(op.join(dirname, 'melodic_mix')): return False
+ if not op.exists(op.join(dirname, 'melodic_FTmix')): return False
+
+ return True
def getTopLevelAnalysisDir(path):
@@ -102,30 +94,24 @@ def getTopLevelAnalysisDir(path):
directory is returned. Otherwise, ``None`` is returned.
"""
- meldir = getMelodicDir(path)
- sufs = ['.feat', '.gfeat', '.ica', '.gica']
-
- if meldir is None:
- return None
+ path = path.strip()
- if featresults.isFEATDir(meldir):
- return featresults.getFEATDir(meldir)
+ # We've reached the root of the file system
+ if path == op.sep or path == '':
+ return None
- parentDir = op.dirname(meldir)
- parentDir = parentDir.rstrip(op.sep)
+ path = path.rstrip(op.sep)
+ parent = getTopLevelAnalysisDir(op.dirname(path))
- if not any([parentDir.endswith(s) for s in sufs]):
- return None
+ if parent is not None:
+ return parent
- # Must contain a file called filtered_func_data.nii.gz
- dataFile = op.join(parentDir, 'filtered_func_data')
+ sufs = ['.ica', '.gica', '.feat', '.gfeat']
- try:
- dataFile = fslimage.addExt(dataFile, mustExist=True)
- except ValueError:
- return None
+ if any([path.endswith(suf) for suf in sufs]):
+ return path
- return parentDir
+ return None
def getDataFile(meldir):
diff --git a/fsl/fsleyes/overlay.py b/fsl/fsleyes/overlay.py
index 053801d5f8db5d2e1667920a47045449a2a696af..1ede376e0f14418db55981c6f2431c992a9aac5a 100644
--- a/fsl/fsleyes/overlay.py
+++ b/fsl/fsleyes/overlay.py
@@ -204,37 +204,21 @@ def guessDataSourceType(path):
if path.endswith('.vtk'):
return fslmodel.Model, path
- # Now, we check to see if the given
- # path is part of a FEAT or MELODIC
- # analysis. The way we go about this is
- # a bit silly, but is necessary due to
- # the fact thet a melodic analysis can
- # be contained within a feat analysis
- # (or another melodic analysis). So we
- # check for all analysis types and, if
- # more than one analysis type matches,
- # we return the one with the longest
- # path name.
- analyses = [
- (fslfeatimage.FEATImage, featresults.getFEATDir( path)),
- (fslmelimage .MelodicImage, melresults .getMelodicDir(path))]
-
- # Remove the analysis types that didn't match
- # (the get*Dir function returned None)
- analyses = [(t, d) for (t, d) in analyses if d is not None]
-
- # If we have one or more matches for
- # an analysis directory, we return
- # the one with the longest path
- if len(analyses) > 0:
-
- dirlens = map(len, [d for (t, d) in analyses])
- maxidx = dirlens.index(max(dirlens))
-
- return analyses[maxidx]
- # If the path is not an analysis directory,
- # see if it is a regular nifti image
+ if op.isdir(path):
+ if melresults.isMelodicDir(path):
+ return fslmelimage.MelodicImage, path
+
+ if featresults.isFEATDir(path):
+ return fslfeatimage.FEATImage, path
+
+ elif melresults.isMelodicImage(path):
+ return fslmelimage.MelodicImage, path
+
+ elif featresults.isFEATImage(path):
+ return fslfeatimage.FEATImage, path
+
+ # A regular NIFTI image?
try:
path = fslimage.addExt(path, mustExist=True)
return fslimage.Image, path