diff --git a/fsl/data/featanalysis.py b/fsl/data/featanalysis.py
index 75fe43a61a9d2a58347455f2e50e46e3ea9e9b60..c1fd09557903580e36ed6d3de26a04d3dc68da1c 100644
--- a/fsl/data/featanalysis.py
+++ b/fsl/data/featanalysis.py
@@ -90,7 +90,7 @@ def isFEATDir(path):
try:
fslimage.addExt(op.join(path, 'filtered_func_data'), mustExist=True)
- except ValueError:
+ except fslimage.PathError:
return False
if not op.exists(op.join(dirname, 'design.fsf')): return False
@@ -451,7 +451,7 @@ def getDataFile(featdir):
"""Returns the name of the file in the FEAT directory which contains
the model input data (typically called ``filtered_func_data.nii.gz``).
- Raises a :exc:`ValueError` if the file does not exist.
+ Raises a :exc:`.PathError` if the file does not exist.
:arg featdir: A FEAT directory.
"""
@@ -464,7 +464,7 @@ def getMelodicFile(featdir):
components (if melodic ICA was performed as part of the FEAT
analysis). This file can be loaded as a :class:`.MelodicImage`.
- Raises a :exc:`ValueError` if the file does not exist.
+ Raises a :exc:`.PathError` if the file does not exist.
"""
melfile = op.join(featdir, 'filtered_func_data.ica', 'melodic_IC')
return fslimage.addExt(melfile, mustExist=True)
@@ -474,7 +474,7 @@ def getResidualFile(featdir):
"""Returns the name of the file in the FEAT results which contains
the model fit residuals (typically called ``res4d.nii.gz``).
- Raises a :exc:`ValueError` if the file does not exist.
+ Raises a :exc:`.PathError` if the file does not exist.
:arg featdir: A FEAT directory.
"""
@@ -485,7 +485,7 @@ def getResidualFile(featdir):
def getPEFile(featdir, ev):
"""Returns the path of the PE file for the specified EV.
- Raises a :exc:`ValueError` if the file does not exist.
+ Raises a :exc:`.PathError` if the file does not exist.
:arg featdir: A FEAT directory.
:arg ev: The EV number (0-indexed).
@@ -497,7 +497,7 @@ def getPEFile(featdir, ev):
def getCOPEFile(featdir, contrast):
"""Returns the path of the COPE file for the specified contrast.
- Raises a :exc:`ValueError` if the file does not exist.
+ Raises a :exc:`.PathError` if the file does not exist.
:arg featdir: A FEAT directory.
:arg contrast: The contrast number (0-indexed).
@@ -509,7 +509,7 @@ def getCOPEFile(featdir, contrast):
def getZStatFile(featdir, contrast):
"""Returns the path of the Z-statistic file for the specified contrast.
- Raises a :exc:`ValueError` if the file does not exist.
+ Raises a :exc:`.PathError` if the file does not exist.
:arg featdir: A FEAT directory.
:arg contrast: The contrast number (0-indexed).
@@ -521,7 +521,7 @@ def getZStatFile(featdir, contrast):
def getClusterMaskFile(featdir, contrast):
"""Returns the path of the cluster mask file for the specified contrast.
- Raises a :exc:`ValueError` if the file does not exist.
+ Raises a :exc:`.PathError` if the file does not exist.
:arg featdir: A FEAT directory.
:arg contrast: The contrast number (0-indexed).
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 696ebd855a92b0dd67b0a257cef5e9ab2193db13..384768aab24bbfdbf3404e2b2292f28c9461cd90 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -769,10 +769,22 @@ EXTENSION_DESCRIPTIONS = ['Compressed NIFTI images',
"""Descriptions for each of the extensions in :data:`ALLOWED_EXTENSIONS`. """
+REPLACEMENTS = {'.hdr' : ['.img', '.img.gz']}
+"""Suffix replacements used by :func:`addExt` to resolve file path
+ambiguities - see :func:`fsl.utils.path.addExt`.
+"""
+
+
DEFAULT_EXTENSION = '.nii.gz'
"""The default file extension (TODO read this from ``$FSLOUTPUTTYPE``)."""
+PathError = fslpath.PathError
+"""Error raised by :mod:`fsl.utils.path` functions when an error occurs.
+Made available in this module for convenience.
+"""
+
+
def looksLikeImage(filename, allowedExts=None):
"""Returns ``True`` if the given file looks like an image, ``False``
otherwise.
@@ -810,7 +822,8 @@ def addExt(prefix, mustExist=True):
return fslpath.addExt(prefix,
ALLOWED_EXTENSIONS,
mustExist,
- DEFAULT_EXTENSION)
+ DEFAULT_EXTENSION,
+ replace=REPLACEMENTS)
def loadIndexedImageFile(filename):
diff --git a/fsl/data/melodicanalysis.py b/fsl/data/melodicanalysis.py
index 9de847d439741b64a980bf34355dcca1693bdbfe..6bb63b7000578ea36c084e1ef9eb2e2d0cfaf5ec 100644
--- a/fsl/data/melodicanalysis.py
+++ b/fsl/data/melodicanalysis.py
@@ -77,7 +77,7 @@ def isMelodicDir(path):
# Must contain an image file called melodic_IC
try:
fslimage.addExt(op.join(dirname, 'melodic_IC'), mustExist=True)
- except ValueError:
+ except fslimage.PathError:
return False
# Must contain files called
@@ -124,8 +124,8 @@ def getDataFile(meldir):
dataFile = op.join(topDir, 'filtered_func_data')
- try: return fslimage.addExt(dataFile, mustExist=True)
- except ValueError: return None
+ try: return fslimage.addExt(dataFile, mustExist=True)
+ except fslimage.PathErrpr: return None
def getMeanFile(meldir):
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 408b77c23ba7eed3579c7d4876caa5052dce546a..ef628918c1df60ce98985a69879a73d52a394153 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -15,12 +15,18 @@ paths.
shallowest
addExt
removeExt
+ getExt
"""
import os.path as op
+class PathError(Exception):
+ """``Exception`` class raised by :func:`addExt` and :func:`getExt`. """
+ pass
+
+
def deepest(path, suffixes):
"""Finds the deepest directory which ends with one of the given
sequence of suffixes, or returns ``None`` if no directories end
@@ -64,7 +70,11 @@ def shallowest(path, suffixes):
return None
-def addExt(prefix, allowedExts, mustExist=True, defaultExt=None):
+def addExt(prefix,
+ allowedExts,
+ mustExist=True,
+ defaultExt=None,
+ replace=None):
"""Adds a file extension to the given file ``prefix``.
If ``mustExist`` is False, and the file does not already have a
@@ -77,17 +87,47 @@ def addExt(prefix, allowedExts, mustExist=True, defaultExt=None):
extension. A :exc:`ValueError` is raised if:
- No files exist with the given prefix and a supported extension.
- - More than one file exists with the given prefix, and a supported
- extension.
+
+ - ``replace`` is ``None``, and more than one file exists with the
+ given prefix, and a supported extension.
Otherwise the full file name is returned.
- :arg prefix: The file name refix to modify.
- :arg mustExist: Whether the file must exist or not.
+ :arg prefix: The file name prefix to modify.
+
:arg allowedExts: List of allowed file extensions.
+
+ :arg mustExist: Whether the file must exist or not.
+
:arg defaultExt: Default file extension to use.
+
+ :arg replace: If multiple files exist with the same ``prefix`` and
+ supported extensions (e.g. ``file.hdr`` and
+ ``file.img``), this dictionary can be used to resolve
+ ambiguities. It must have the structure::
+
+ {
+ suffix : [replacement, ...],
+ ...
+ }
+
+ If files with ``suffix`` and one of the ``replacement``
+ suffixes exists, the ``suffix`` file will
+ be ignored, and replaced with the ``replacement`` file.
+ If multiple ``replacement`` files exist alongside the
+ ``suffix`` file, a ``PathError`` is raised.
+
+ .. note:: The primary use-case of the ``replace`` parameter is to resolve
+ ambiguity with respect to NIFTI and ANALYSE75 image pairs. By
+ specifying ``replace={'.hdr' : ['.img'. '.img.gz'}``, the
+ ``addExt`` function is able to figure out what you mean when you
+ wish to add an extension to ``file``, and ``file.hdr`` and
+ either ``file.img`` or ``file.img.gz`` (but not both) exist.
"""
+ if replace is None:
+ replace = {}
+
if not mustExist:
# the provided file name already
@@ -101,31 +141,74 @@ def addExt(prefix, allowedExts, mustExist=True, defaultExt=None):
# If the provided prefix already ends with a
# supported extension , check to see that it exists
if any([prefix.endswith(ext) for ext in allowedExts]):
- extended = [prefix]
+ allPaths = [prefix]
# Otherwise, make a bunch of file names, one per
# supported extension, and test to see if exactly
# one of them exists.
else:
- extended = [prefix + ext for ext in allowedExts]
+ allPaths = [prefix + ext for ext in allowedExts]
- exists = [op.isfile(e) for e in extended]
+ exists = [op.isfile(e) for e in allPaths]
+ nexists = sum(exists)
# Could not find any supported file
# with the specified prefix
- if not any(exists):
- raise ValueError(
- 'Could not find a supported file with prefix {}'.format(prefix))
+ if nexists == 0:
+ raise PathError('Could not find a supported file '
+ 'with prefix {}'.format(prefix))
# Ambiguity! More than one supported
- # file with the specified prefix
- if sum(exists) > 1:
- raise ValueError('More than one file with prefix {}'.format(prefix))
+ # file with the specified prefix.
+ elif nexists > 1:
+
+ # Remove non-existent paths from the
+ # extended list, get all their
+ # suffixes, and potential replacements
+ allPaths = [allPaths[i] for i in range(len(allPaths)) if exists[i]]
+ suffixes = [getExt(e, allowedExts) for e in allPaths]
+ replacements = [replace.get(s) for s in suffixes]
+ hasReplace = [r is not None for r in replacements]
+
+ for p, r in zip(allPaths, replacements):
+ print ' {} replacements: {}'.format(p, r)
+
+ # If any replacement has been specified
+ # for any of the existing suffixes,
+ # see if we have a unique match for
+ # exactly one existing suffix, the
+ # one to be ignored/replaced.
+ if sum(hasReplace) == 1:
+
+ # Make sure there is exactly one potential
+ # replacement for this suffix. If there's
+ # more than one (e.g. file.hdr plus both
+ # file.img and file.img.gz) we can't resolve
+ # the ambiguity. In this case the code will
+ # fall through to the raise statement below.
+ toReplace = allPaths[hasReplace.index(True)]
+ replacements = replacements[hasReplace.index(True)]
+ replacements = [prefix + ext for ext in replacements]
+ replExists = [r in allPaths for r in replacements]
+
+ if sum(replExists) == 1:
+
+ replacedBy = replacements[replExists.index(True)]
+ allPaths[allPaths.index(toReplace)] = replacedBy
+ allPaths = list(set(allPaths))
+
+ exists = [True] * len(allPaths)
+
+ # There's more than one path match -
+ # we can't resolve the ambiguity
+ if len(allPaths) > 1:
+ raise PathError('More than one file with '
+ 'prefix {}'.format(prefix))
# Return the full file name of the
# supported file that was found
extIdx = exists.index(True)
- return extended[extIdx]
+ return allPaths[extIdx]
def removeExt(filename, allowedExts):
@@ -151,3 +234,32 @@ def removeExt(filename, allowedExts):
# and trim it from the file name
return filename[:-extLen]
+
+
+def getExt(filename, allowedExts=None):
+ """Returns the extension from the given file name.
+
+ If ``allowedExts`` is ``None``, this function is equivalent to using::
+
+ os.path.splitext(filename)[1]
+
+ If ``allowedExts`` is provided, but the file does not end with an allowed
+ extension, a :exc:`PathError` is raised.
+
+ :arg allowedExts: Allowed/recognised file extensions.
+ """
+
+ # If allowedExts is not specified,
+ # we just use op.splitext
+ if allowedExts is None:
+ return op.splitext(filename)[1]
+
+ # Otherwise, try and find a suffix match
+ extMatches = [filename.endswith(ext) for ext in allowedExts]
+
+ if not any(extMatches):
+ raise PathError('{} does not end in a supported extension ({})'.format(
+ filename, ', '.join(allowedExts)))
+
+ extIdx = extMatches.index(True)
+ return allowedExts[extIdx]