diff --git a/fsl/data/featresults.py b/fsl/data/featresults.py
index c2fddd25de2f70fe01e8b0d7078429bf11f2452f..4772f05b09c228f669a06c3d6dc8e62e6de2dcb9 100644
--- a/fsl/data/featresults.py
+++ b/fsl/data/featresults.py
@@ -43,7 +43,6 @@ The following functions return the names of various files of interest:
import logging
-import glob
import os.path as op
import numpy as np
@@ -104,11 +103,12 @@ def hasStats(featdir):
for the given FEAT analysis, ``False`` otherwise.
"""
- statdir = op.join(featdir, 'stats')
- statfiles = glob.glob(op.join(statdir, '*'))
-
- return op.exists(statdir) and len(statfiles) > 0
-
+ try:
+ getZStatFile(featdir, 0)
+ return True
+ except:
+ return False
+
def hasMelodicDir(featdir):
"""Returns ``True`` if the data for the given FEAT directory has had
@@ -465,71 +465,83 @@ 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.
+
:arg featdir: A FEAT directory.
"""
-
- # Assuming here that there is only
- # one file called filtered_func_data.*
- return glob.glob((op.join(featdir, 'filtered_func_data.*')))[0]
+ datafile = op.join(featdir, 'filtered_func_data')
+ return fslimage.addExt(datafile, mustExist=True)
def getMelodicFile(featdir):
- """Returns the name of the file in the FEAT results which contains the
- melodic components. This file can be loaded as a :class:`.MelodicImage`.
+ """Returns the name of the file in the FEAT results which contains the melodic
+ 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.
"""
- return op.join(featdir, 'filtered_func_data.ica', 'melodic_IC.nii.gz')
+ melfile = op.join(featdir, 'filtered_func_data.ica', 'melodic_IC')
+ return fslimage.addExt(melfile, mustExist=True)
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.
+
:arg featdir: A FEAT directory.
"""
-
- # Assuming here that there is only
- # one file called stats/res4d.*
- return glob.glob((op.join(featdir, 'stats', 'res4d.*')))[0]
+ resfile = op.join(featdir, 'stats', 'res4d')
+ return fslimage.addExt(resfile, mustExist=True)
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.
+
:arg featdir: A FEAT directory.
:arg ev: The EV number (0-indexed).
"""
- pefile = op.join(featdir, 'stats', 'pe{}.*'.format(ev + 1))
- return glob.glob(pefile)[0]
+ pefile = op.join(featdir, 'stats', 'pe{}'.format(ev + 1))
+ return fslimage.addExt(pefile, mustExist=True)
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.
+
:arg featdir: A FEAT directory.
:arg contrast: The contrast number (0-indexed).
"""
- copefile = op.join(featdir, 'stats', 'cope{}.*'.format(contrast + 1))
- return glob.glob(copefile)[0]
+ copefile = op.join(featdir, 'stats', 'cope{}'.format(contrast + 1))
+ return fslimage.addExt(copefile, mustExist=True)
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.
+
:arg featdir: A FEAT directory.
:arg contrast: The contrast number (0-indexed).
"""
- zfile = op.join(featdir, 'stats', 'zstat{}.*'.format(contrast + 1))
- return glob.glob(zfile)[0]
+ zfile = op.join(featdir, 'stats', 'zstat{}'.format(contrast + 1))
+ return fslimage.addExt(zfile, mustExist=True)
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.
+
:arg featdir: A FEAT directory.
:arg contrast: The contrast number (0-indexed).
"""
- mfile = op.join(featdir, 'cluster_mask_zstat{}.*'.format(contrast + 1))
- return glob.glob(mfile)[0]
+ mfile = op.join(featdir, 'cluster_mask_zstat{}'.format(contrast + 1))
+ return fslimage.addExt(mfile, mustExist=True)
def getEVNames(settings):
diff --git a/fsl/data/image.py b/fsl/data/image.py
index f122dcd7d7d7de1f107f52560a721e1084662734..d8dae6f625db57f8f3ccbb2950961f7740bff8bc 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -45,6 +45,8 @@ import props
import fsl.utils.transform as transform
import fsl.utils.status as status
+import fsl.utils.path as fslpath
+import fsl.data.strings as fslstrings
import fsl.data.constants as constants
@@ -604,97 +606,26 @@ def looksLikeImage(filename, allowedExts=None):
return any(map(lambda ext: filename.endswith(ext), allowedExts))
-def removeExt(filename, allowedExts=None):
+def removeExt(filename):
"""Removes the extension from the given file name. Returns the filename
unmodified if it does not have a supported extension.
- :arg filename: The file name to strip.
-
- :arg allowedExts: A list of strings containing the allowed file
- extensions.
- """
-
- if allowedExts is None: allowedExts = ALLOWED_EXTENSIONS
-
- # figure out the extension of the given file
- extMatches = map(lambda ext: filename.endswith(ext), allowedExts)
-
- # the file does not have a supported extension
- if not any(extMatches):
- return filename
+ See :func:`~fsl.utils.path.removeExt`.
- # figure out the length of the matched extension
- extIdx = extMatches.index(True)
- extLen = len(allowedExts[extIdx])
-
- # and trim it from the file name
- return filename[:-extLen]
+ :arg filename: The file name to strip.
+ """
+ return fslpath.removeExt(filename, ALLOWED_EXTENSIONS)
-def addExt(prefix, mustExist=True, allowedExts=None, defaultExt=None):
+def addExt(prefix, mustExist=True):
"""Adds a file extension to the given file ``prefix``.
- If ``mustExist`` is False, and the file does not already have a
- supported extension, the default extension is appended and the new
- file name returned. If the prefix already has a supported extension,
- it is returned unchanged.
-
- If ``mustExist`` is ``True`` (the default), the function checks to see
- if any files exist that have the given prefix, and a supported file
- 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.
-
- 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 allowedExts: List of allowed file extensions.
- :arg defaultExt: Default file extension to use.
+ See :func:`~fsl.utils.path.addExt`.
"""
-
- if allowedExts is None: allowedExts = ALLOWED_EXTENSIONS
- if defaultExt is None: defaultExt = DEFAULT_EXTENSION
-
- if not mustExist:
-
- # the provided file name already
- # ends with a supported extension
- if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
- return prefix
-
- return prefix + defaultExt
-
- # If the provided prefix already ends with a
- # supported extension , check to see that it exists
- if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
- extended = [prefix]
-
- # Otherwise, make a bunch of file names, one per
- # supported extension, and test to see if exactly
- # one of them exists.
- else:
- extended = map(lambda ext: prefix + ext, allowedExts)
-
- exists = map(op.isfile, extended)
-
- # 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))
-
- # Ambiguity! More than one supported
- # file with the specified prefix
- if len(filter(bool, exists)) > 1:
- raise ValueError('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 fslpath.addExt(prefix,
+ ALLOWED_EXTENSIONS,
+ mustExist,
+ DEFAULT_EXTENSION)
def loadImage(filename):
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 4c22cd41034676fce4dcc02fa18de2d55c56c9a4..cacc25b0f9756e4055bad480efc21c0166c2ec04 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -12,7 +12,9 @@ paths.
:nosignatures:
deepest
- shallowest
+ shallowest
+ addExt
+ removeExt
"""
@@ -60,3 +62,92 @@ def shallowest(path, suffixes):
return path
return None
+
+
+def addExt(prefix, allowedExts, mustExist=True, defaultExt=None):
+ """Adds a file extension to the given file ``prefix``.
+
+ If ``mustExist`` is False, and the file does not already have a
+ supported extension, the default extension is appended and the new
+ file name returned. If the prefix already has a supported extension,
+ it is returned unchanged.
+
+ If ``mustExist`` is ``True`` (the default), the function checks to see
+ if any files exist that have the given prefix, and a supported file
+ 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.
+
+ 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 allowedExts: List of allowed file extensions.
+ :arg defaultExt: Default file extension to use.
+ """
+
+ if not mustExist:
+
+ # the provided file name already
+ # ends with a supported extension
+ if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
+ return prefix
+
+ if defaultExt is not None: return prefix + defaultExt
+ else: return None
+
+ # If the provided prefix already ends with a
+ # supported extension , check to see that it exists
+ if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
+ extended = [prefix]
+
+ # Otherwise, make a bunch of file names, one per
+ # supported extension, and test to see if exactly
+ # one of them exists.
+ else:
+ extended = map(lambda ext: prefix + ext, allowedExts)
+
+ exists = map(op.isfile, extended)
+
+ # 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))
+
+ # Ambiguity! More than one supported
+ # file with the specified prefix
+ if len(filter(bool, exists)) > 1:
+ raise ValueError('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]
+
+
+def removeExt(filename, allowedExts):
+ """Removes the extension from the given file name. Returns the filename
+ unmodified if it does not have a supported extension.
+
+ :arg filename: The file name to strip.
+
+ :arg allowedExts: A list of strings containing the allowed file
+ extensions.
+ """
+
+ # figure out the extension of the given file
+ extMatches = map(lambda ext: filename.endswith(ext), allowedExts)
+
+ # the file does not have a supported extension
+ if not any(extMatches):
+ return filename
+
+ # figure out the length of the matched extension
+ extIdx = extMatches.index(True)
+ extLen = len(allowedExts[extIdx])
+
+ # and trim it from the file name
+ return filename[:-extLen]