From 90466b63358ab24db9befb3ef0f6524b1c98a3ca Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 14 Nov 2016 18:54:54 +0000
Subject: [PATCH] New function removeDuplicates, so immv/imcp scripts can
reduce redundant copies/overwrite errors. Made imcp overwrite check more
robust.
---
bin/imcp | 4 ++++
bin/immv | 4 ++++
fsl/utils/path.py | 58 +++++++++++++++++++++++++++++++++++++++++++----
3 files changed, 61 insertions(+), 5 deletions(-)
diff --git a/bin/imcp b/bin/imcp
index bef56cc74..af65e4cef 100755
--- a/bin/imcp
+++ b/bin/imcp
@@ -56,6 +56,10 @@ def main():
print(usage)
sys.exit(1)
+ srcs = fslpath.removeDuplicates(srcs,
+ allowedExts=SUPPORTED_EXTENSIONS,
+ fileGroups=FILE_GROUPS)
+
for src in srcs:
try:
fslpath.imcp(src,
diff --git a/bin/immv b/bin/immv
index 6054693e4..503326b8f 100755
--- a/bin/immv
+++ b/bin/immv
@@ -57,6 +57,10 @@ def main():
print(usage)
sys.exit(1)
+ srcs = fslpath.removeDuplicates(srcs,
+ allowedExts=SUPPORTED_EXTENSIONS,
+ fileGroups=FILE_GROUPS)
+
for src in srcs:
try:
fslpath.immv(src,
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 1c15fe964..464c0b892 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -221,6 +221,53 @@ 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.img
+ 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', '003.img', '003.img']
+
+ :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 not any([g in unique for g in groupFiles]):
+ unique.append(path)
+
+ 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
@@ -386,15 +433,16 @@ def imcp(src,
# to re-combine the source paths
copySrcs[i] = base + ext
- if destIsDir: copyDests.append(dest)
+ basename = op.basename(base)
+
+ if destIsDir: copyDests.append(op.join(dest, basename + ext))
else: copyDests.append(dest + ext)
# Fail if any of the destination
# paths already exist
- if not overwrite:
- if not destIsDir and any([op.exists(d) for d in copyDests]):
- raise PathError('imcp error - a destination path already '
- 'exists ({})'.format(', '.join(copyDests)))
+ if not overwrite and any([op.exists(d) for d in copyDests]):
+ raise PathError('imcp error - a destination path already '
+ 'exists ({})'.format(', '.join(copyDests)))
# Do the copy/move
for src, dest in zip(copySrcs, copyDests):
--
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