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Commit ea619b7f authored by Paul McCarthy's avatar Paul McCarthy
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Some small fixes and some re-orgnisation

parent 09fe6e28
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fsl/scripts/imcp.py
View file @ ea619b7f
......@@ -58,7 +58,7 @@ def main(argv=None):
fileGroups=fslimage.FILE_GROUPS)
for src in srcs:
imcp.imcp(src, dest, useDefaultExt=True)
imcp.imcp(src, dest, useDefaultExt=True, overwrite=True)
if __name__ == '__main__':
......
fsl/scripts/immv.py
View file @ ea619b7f
......@@ -59,7 +59,7 @@ def main(argv=None):
fileGroups=fslimage.FILE_GROUPS)
for src in srcs:
imcp.immv(src, dest, useDefaultExt=True)
imcp.immv(src, dest, useDefaultExt=True, overwrite=True)
if __name__ == '__main__':
......
fsl/utils/imcp.py
View file @ ea619b7f
......@@ -44,7 +44,10 @@ def imcp(src,
:arg useDefaultExt: Defaults to ``False``. If ``True``, the destination
file type will be set according to the default
extension, specified by
:func:`~fsl.data.image.defaultExt`.
:func:`~fsl.data.image.defaultExt`. If the source
file does not have the same type as the default
extension, it will be converted. If ``False``, the
source file type is not changed.
:arg move: If ``True``, the files are moved, instead of being
copied. See :func:`immv`.
......@@ -187,7 +190,7 @@ def imcp(src,
def immv(src,
dest,
overwrite=False,
useDefaultExt=True):
useDefaultExt=False):
"""Move the specified ``src`` to the specified ``dest``. See :func:`imcp`.
"""
imcp(src,
......
fsl/utils/path.py
View file @ ea619b7f
......@@ -18,6 +18,7 @@ paths.
getExt
splitExt
getFileGroup
removeDuplicates
"""
......@@ -75,7 +76,7 @@ def shallowest(path, suffixes):
def addExt(prefix,
allowedExts,
allowedExts=None,
mustExist=True,
defaultExt=None,
fileGroups=None):
......@@ -108,8 +109,11 @@ def addExt(prefix,
:arg fileGroups: Recognised file groups - see :func:`getFileGroup`.
"""
if fileGroups is None:
fileGroups = {}
if allowedExts is None: allowedExts = []
if fileGroups is None: fileGroups = {}
if defaultExt is not None and defaultExt not in allowedExts:
allowedExts.append(defaultExt)
if not mustExist:
......@@ -119,11 +123,15 @@ def addExt(prefix,
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([prefix.endswith(ext) for ext in allowedExts]):
else: return prefix
# If no allowed extensions were
# provided, or the provided prefix
# already ends with a supported
# extension, check to see that it
# exists.
if len(allowedExts) == 0 or \
any([prefix.endswith(ext) for ext in allowedExts]):
allPaths = [prefix]
# Otherwise, make a bunch of file names, one per
......@@ -218,72 +226,17 @@ def splitExt(filename, allowedExts=None):
return filename[:-extLen], filename[-extLen:]
def removeDuplicates(paths, allowedExts=None, fileGroups=None):
"""Reduces the list of ``paths`` down to those which are unique with
respect to the specified ``fileGroups``.
For example, if you have a directory containing::
001.hdr
001.img
002.hdr
002.img
003.hdr
003.img
And you call ``removeDuplicates`` like so::
paths = ['001.img', '001.hdr',
'002.img', '002.hdr',
'003.img', '003.hdr']
allowedExts = ['.img', '.hdr']
fileGroups = [('.img', '.hdr')]
removeDuplicates(paths, allowedExts, fileGroups)
The returned list will be::
['001.img', '002.img', '003.img']
A :exc:`PathError` is raised if any of the paths do not exist.
:arg paths: List of paths to reduce. If ``allowedExts`` is not
``None``, may be incomplete.
:arg allowedExts: Allowed/recognised file extensions.
:arg fileGroups: Recognised file groups - see :func:`getFileGroup`.
"""
unique = []
for path in paths:
path = addExt(path,
mustExist=True,
allowedExts=allowedExts,
fileGroups=fileGroups)
groupFiles = getFileGroup(path, allowedExts, fileGroups)
if len(groupFiles) == 0:
if path not in unique:
unique.append(path)
elif not any([p in unique for p in groupFiles]):
unique.append(groupFiles[0])
return unique
def getFileGroup(path, allowedExts=None, fileGroups=None, fullPaths=True):
"""If the given ``path`` is part of a ``fileGroup``, returns a list
containing the paths to all other files in the group (including the
``path`` itself).
If the ``path`` does not appear to be part of a file group, a list
containing only the ``path`` is returned.
If the ``path`` does not appear to be part of a file group, or appears to
be part of an incomplete file group, a list containing only the ``path``
is returned.
If the ``path`` does not exist, or appears to be part of more than one
file group, a :exc:`PathError` is raised.
File groups can be used to specify a collection of file suffixes which
should always exist alongside each other. This can be used to resolve
......@@ -322,10 +275,12 @@ def getFileGroup(path, allowedExts=None, fileGroups=None, fullPaths=True):
extensions in the group are returned.
"""
if fileGroups is None:
return [path]
path = addExt(path, allowedExts, mustExist=True, fileGroups=fileGroups)
base, ext = splitExt(path, allowedExts)
if fileGroups is None:
if fullPaths: return [path]
else: return [ext]
matchedGroups = []
matchedGroupFiles = []
......@@ -343,12 +298,75 @@ def getFileGroup(path, allowedExts=None, fileGroups=None, fullPaths=True):
matchedGroups .append(group)
matchedGroupFiles.append(groupFiles)
if len(matchedGroupFiles) == 1:
if fullPaths: return matchedGroupFiles[0]
else: return matchedGroups[ 0]
# Path is not part of any group
elif len(matchedGroupFiles) == 0:
if fullPaths: return [path]
else: return [ext]
# If the given path is part of more
# than one existing file group, we
# can't resolve this ambiguity.
if len(matchedGroupFiles) != 1:
if fullPaths: return [path]
else: return [ext]
else:
if fullPaths: return matchedGroupFiles[0]
else: return matchedGroups[ 0]
raise PathError('Path is part of multiple '
'file groups: {}'.format(path))
def removeDuplicates(paths, allowedExts=None, fileGroups=None):
"""Reduces the list of ``paths`` down to those which are unique with
respect to the specified ``fileGroups``.
For example, if you have a directory containing::
001.hdr
001.img
002.hdr
002.img
003.hdr
003.img
And you call ``removeDuplicates`` like so::
paths = ['001.img', '001.hdr',
'002.img', '002.hdr',
'003.img', '003.hdr']
allowedExts = ['.img', '.hdr']
fileGroups = [('.img', '.hdr')]
removeDuplicates(paths, allowedExts, fileGroups)
The returned list will be::
['001.img', '002.img', '003.img']
If you provide ``allowedExts``, you may specify incomplete ``paths`` (i.e.
without extensions), as long as there are no path ambiguities.
A :exc:`PathError` will be raised if any of the ``paths`` do not exist,
or if there are any ambiguities with respect to incomplete paths.
:arg paths: List of paths to reduce.
:arg allowedExts: Allowed/recognised file extensions.
:arg fileGroups: Recognised file groups - see :func:`getFileGroup`.
"""
unique = []
for path in paths:
groupFiles = getFileGroup(path, allowedExts, fileGroups)
if len(groupFiles) == 0:
if path not in unique:
unique.append(path)
elif not any([p in unique for p in groupFiles]):
unique.append(groupFiles[0])
return unique
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