From 5bf216bc8bc5f4508486896540235109ad124951 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 17 Nov 2016 16:14:47 +0000
Subject: [PATCH] imcp/immv moved into their own module. They now have an
option to honour the default file extensions (i.e. the FSLOUTPUTTYPE) - this
is used by the fslpy_immv/imcp command line scripts.
---
bin/fslpy_imcp | 37 +++------
bin/fslpy_immv | 43 ++++-------
fsl/data/image.py | 45 +++++------
fsl/utils/imcp.py | 193 ++++++++++++++++++++++++++++++++++++++++++++++
fsl/utils/path.py | 143 ++++------------------------------
5 files changed, 256 insertions(+), 205 deletions(-)
create mode 100644 fsl/utils/imcp.py
diff --git a/bin/fslpy_imcp b/bin/fslpy_imcp
index 85fa9a561..eb4441bdc 100755
--- a/bin/fslpy_imcp
+++ b/bin/fslpy_imcp
@@ -11,20 +11,8 @@ from __future__ import print_function
import os.path as op
import sys
import fsl.utils.path as fslpath
-
-
-SUPPORTED_EXTENSIONS = [
- '.nii', '.nii.gz',
- '.hdr', '.hdr.gz',
- '.img', '.img.gz',
- '.mnc', '.mnc.gz'
-]
-
-
-FILE_GROUPS = [
- ('.img', '.hdr'),
- ('.img.gz', '.hdr.gz')
-]
+import fsl.utils.imcp as imcp
+import fsl.data.image as fslimage
usage = """Usage:
@@ -37,35 +25,32 @@ Copy images from <file1> to <file2>, or copy all <file>s to <directory>
NB: filenames can be basenames or include an extension.
Recognised file extensions: {}
-""".format(', '.join(SUPPORTED_EXTENSIONS))
+""".format(', '.join(fslimage.ALLOWED_EXTENSIONS))
-def main():
+def main(argv=None):
"""Parses CLI arguments (see the usage string), and calls the
- fsl.utils.path.imcp function on each input.
+ :func:`fsl.utils.imcp.imcp` function on each input.
"""
- if len(sys.argv) < 2:
+ if len(argv) < 2:
print(usage)
sys.exit(1)
- srcs = sys.argv[1:-1]
- dest = sys.argv[ -1]
+ srcs = argv[:-1]
+ dest = argv[ -1]
if len(srcs) > 1 and not op.isdir(dest):
print(usage)
sys.exit(1)
srcs = fslpath.removeDuplicates(srcs,
- allowedExts=SUPPORTED_EXTENSIONS,
- fileGroups=FILE_GROUPS)
+ allowedExts=fslimage.ALLOWED_EXTENSIONS,
+ fileGroups=fslimage.FILE_GROUPS)
for src in srcs:
try:
- fslpath.imcp(src,
- dest,
- allowedExts=SUPPORTED_EXTENSIONS,
- fileGroups=FILE_GROUPS)
+ imcp.imcp(src, dest, useDefaultExt=True)
except Exception as e:
print(e)
diff --git a/bin/fslpy_immv b/bin/fslpy_immv
index f1f1baf08..0b5a5ae54 100755
--- a/bin/fslpy_immv
+++ b/bin/fslpy_immv
@@ -11,21 +11,8 @@ from __future__ import print_function
import os.path as op
import sys
import fsl.utils.path as fslpath
-
-
-SUPPORTED_EXTENSIONS = [
- '.nii', '.nii.gz',
- '.hdr', '.hdr.gz',
- '.img', '.img.gz',
- '.mnc', '.mnc.gz'
-]
-
-
-
-FILE_GROUPS = [
- ('.img', '.hdr'),
- ('.img.gz', '.hdr.gz')
-]
+import fsl.utils.imcp as imcp
+import fsl.data.image as fslimage
usage = """Usage:
@@ -38,35 +25,35 @@ Moves images from <file1> to <file2>, or move all <file>s to <directory>
NB: filenames can be basenames or include an extension.
Recognised file extensions: {}
-""".format(', '.join(SUPPORTED_EXTENSIONS))
+""".format(', '.join(fslimage.ALLOWED_EXTENSIONS))
-def main():
+def main(argv=None):
"""Parses CLI arguments (see the usage string), and calls the
- fsl.utils.path.immv function on each input.
- """
+ fsl.utils.imcp.immv function on each input.
+ """
+
+ if argv is None:
+ argv = sys.argv[1:]
- if len(sys.argv) < 2:
+ if len(argv) < 2:
print(usage)
sys.exit(1)
- srcs = sys.argv[1:-1]
- dest = sys.argv[ -1]
+ srcs = argv[:-1]
+ dest = argv[ -1]
if len(srcs) > 1 and not op.isdir(dest):
print(usage)
sys.exit(1)
srcs = fslpath.removeDuplicates(srcs,
- allowedExts=SUPPORTED_EXTENSIONS,
- fileGroups=FILE_GROUPS)
+ allowedExts=fslimage.ALLOWED_EXTENSIONS,
+ fileGroups=fslimage.FILE_GROUPS)
for src in srcs:
try:
- fslpath.immv(src,
- dest,
- allowedExts=SUPPORTED_EXTENSIONS,
- fileGroups=FILE_GROUPS)
+ imcp.immv(src, dest, useDefaultExt=True, move=True)
except Exception as e:
print(e)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index c81acf89f..1ff4ee748 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -25,9 +25,10 @@ and file names:
:nosignatures:
looksLikeImage
- removeExt
+ addExt
splitExt
- addExt
+ getExt
+ removeExt
defaultExt
loadIndexedImageFile
"""
@@ -789,36 +790,36 @@ def looksLikeImage(filename, allowedExts=None):
return any([filename.endswith(ext) for ext in allowedExts])
-def removeExt(filename):
- """Removes the extension from the given file name. Returns the filename
- unmodified if it does not have a supported extension.
-
- See :func:`~fsl.utils.path.removeExt`.
-
- :arg filename: The file name to strip.
+def addExt(prefix, mustExist=True):
+ """Adds a file extension to the given file ``prefix``. See
+ :func:`~fsl.utils.path.addExt`.
"""
- return fslpath.removeExt(filename, ALLOWED_EXTENSIONS)
+ return fslpath.addExt(prefix,
+ ALLOWED_EXTENSIONS,
+ mustExist,
+ defaultExt(),
+ fileGroups=FILE_GROUPS)
def splitExt(filename):
- """Splits the base name and extension for the given ``filename``.
-
- See :func:`~fsl.utils.path.splitExt`.
+ """Splits the base name and extension for the given ``filename``. See
+ :func:`~fsl.utils.path.splitExt`.
"""
-
return fslpath.splitExt(filename, ALLOWED_EXTENSIONS)
-def addExt(prefix, mustExist=True):
- """Adds a file extension to the given file ``prefix``.
+def getExt(filename):
+ """Gets the extension for the given file name. See
+ :func:`~fsl.utils.path.getExt`.
+ """
+ return fslpath.getExt(filename, ALLOWED_EXTENSIONS)
+
- See :func:`~fsl.utils.path.addExt`.
+def removeExt(filename):
+ """Removes the extension from the given file name. See
+ :func:`~fsl.utils.path.removeExt`.
"""
- return fslpath.addExt(prefix,
- ALLOWED_EXTENSIONS,
- mustExist,
- defaultExt(),
- fileGroups=FILE_GROUPS)
+ return fslpath.removeExt(filename, ALLOWED_EXTENSIONS)
def defaultExt():
diff --git a/fsl/utils/imcp.py b/fsl/utils/imcp.py
new file mode 100644
index 000000000..47a509025
--- /dev/null
+++ b/fsl/utils/imcp.py
@@ -0,0 +1,193 @@
+#!/usr/bin/env python
+#
+# imcp.py - Functions for moving/copying NIFTI image files.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""
+
+.. autosummary::
+ :nosignatures:
+
+ imcp
+ immv
+"""
+
+
+import os
+import os.path as op
+import shutil
+
+import fsl.utils.path as fslpath
+import fsl.data.image as fslimage
+
+
+def imcp(src,
+ dest,
+ overwrite=False,
+ useDefaultExt=False,
+ move=False):
+ """Copy the given ``src`` file to destination ``dest``.
+
+ A :class:`.fsl.utils.path.PathError` is raised if anything goes wrong.
+
+ :arg src: Path to copy. If ``allowedExts`` is provided,
+ the file extension can be omitted.
+
+ :arg dest: Destination path. Can be an incomplete file
+ specification (i.e. without the extension), or a
+ directory.
+
+ :arg overwrite: If ``True`` this function will overwrite files that
+ already exist. Defaults to ``False``.
+
+ :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`.
+
+ :arg move: If ``True``, the files are moved, instead of being
+ copied. See :func:`immv`.
+ """
+
+ import nibabel as nib
+
+ if op.isdir(dest):
+ dest = op.join(dest, op.basename(src))
+
+ srcBase, srcExt = fslimage.splitExt(src)
+ destBase, destExt = fslimage.splitExt(dest)
+
+ # src was specified without an
+ # extension, or the specified
+ # src does not have an allowed
+ # extension.
+ if srcExt == '':
+
+ # Try to resolve the specified src
+ # path - if src does not exist, or
+ # does not have an allowed extension,
+ # addExt will raise an error
+ src = fslimage.addExt(src, mustExist=True)
+
+ # We've resolved src to a
+ # full filename - split it
+ # again to get its extension
+ srcBase, srcExt = fslimage.splitExt(src)
+
+ # Figure out the destination file
+ # extension/type. If useDefaultExt
+ # is True, we use the default
+ # extension. Otherwise, if no
+ # destination file extension is
+ # provided, we use the source
+ # extension.
+ if useDefaultExt: destExt = fslimage.defaultExt()
+ elif destExt == '': destExt = srcExt
+
+ # Resolve any file group differences
+ # e.g. we don't care if the src is
+ # specified as file.hdr, and the dest
+ # is specified as file.img - if src
+ # and dest are part of the same file
+ # group, we replace the dest extension
+ # with the src extension.
+ if srcExt != destExt:
+ for group in fslimage.FILE_GROUPS:
+ if srcExt in group and destExt in group:
+ destExt = srcExt
+ break
+
+ dest = destBase + destExt
+
+ # Give up if we don't have permission.
+ if not os.access(op.dirname(dest), os.W_OK | os.X_OK):
+ raise fslpath.PathError('imcp error - cannot write to {}'.format(dest))
+
+ if move and not os.access(op.dirname(src), os.W_OK | os.X_OK):
+ raise fslpath.PathError('imcp error - cannot move from {}'.format(src))
+
+ # If the source file type does not
+ # match the destination file type,
+ # we need to perform a conversion.
+ #
+ # This is expensive in terms of io
+ # and cpu, but programmatically
+ # very easy - nibabel does all the
+ # hard work.
+ if srcExt != destExt:
+
+ if not overwrite and op.exists(dest):
+ raise fslpath.PathError('imcp error - destination already '
+ 'exists ({})'.format(dest))
+
+ img = nib.load(src)
+ nib.save(img, dest)
+
+ if move:
+ os.remove(src)
+
+ return
+
+ # Otherwise we do a file copy. This
+ # is actually more complicated than
+ # conveting the file type due to
+ # hdr/img pairs ...
+ #
+ # If the source is part of a file group,
+ # e.g. src.img/src.hdr), we need to copy
+ # the whole set of files. So here we
+ # build a list of source files that need
+ # to be copied/moved. The getFileGroup
+ # function returns all other files that
+ # are associated with this file (i.e.
+ # part of the same group).
+ #
+ # We store the sources as separate
+ # (base, ext) tuples, so we don't
+ # have to re-split when creating
+ # destination paths.
+ copySrcs = fslpath.getFileGroup(src,
+ fslimage.ALLOWED_EXTENSIONS,
+ fslimage.FILE_GROUPS,
+ fullPaths=False)
+
+ copySrcs = [(srcBase, e) for e in copySrcs]
+
+ # Note that these additional files
+ # do not have to exist, e.g.
+ # imcp('blah.img', ...) will still
+ # work if there is no blah.hdr
+ copySrcs = [(b, e) for (b, e) in copySrcs if op.exists(b + e)]
+
+ # Build a list of destinations for each
+ # copy source - we build this list in
+ # advance, so we can fail if any of the
+ # destinations already exist. We also
+ # re-combine the source bases/extensions.
+ copyDests = [destBase + e for (b, e) in copySrcs]
+ copySrcs = [b + e for (b, e) in copySrcs]
+
+ # Fail if any of the destination
+ # paths already exist
+ if not overwrite and any([op.exists(d) for d in copyDests]):
+ raise fslpath.PathError('imcp error - a destination path already '
+ 'exists ({})'.format(', '.join(copyDests)))
+
+ # Do the copy/move
+ for src, dest in zip(copySrcs, copyDests):
+ if move: shutil.move(src, dest)
+ else: shutil.copy(src, dest)
+
+
+def immv(src,
+ dest,
+ overwrite=False,
+ useDefaultExt=True):
+ """Move the specified ``src`` to the specified ``dest``. See :func:`imcp`.
+ """
+ imcp(src,
+ dest,
+ overwrite=overwrite,
+ useDefaultExt=useDefaultExt,
+ move=True)
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 464c0b892..cbd9fd8bd 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -18,13 +18,10 @@ paths.
getExt
splitExt
getFileGroup
- imcp
- immv
"""
import os.path as op
-import shutil
class PathError(Exception):
@@ -231,23 +228,23 @@ def removeDuplicates(paths, allowedExts=None, fileGroups=None):
001.img
002.hdr
002.img
- 003.img
+ 003.hdr
003.img
And you call ``removeDuplicates`` like so::
- paths = ['001.img', '001.hdr',
- '002.img', '002.hdr',
- '003.img', '003.hdr']
+ paths = ['001.img', '001.hdr',
+ '002.img', '002.hdr',
+ '003.img', '003.hdr']
- allowedExts = ['.img', '.hdr']
- fileGroups = [('.img', '.hdr')]
+ allowedExts = ['.img', '.hdr']
+ fileGroups = [('.img', '.hdr')]
removeDuplicates(paths, allowedExts, fileGroups)
The returned list will be::
- ['001.img', '003.img', '003.img']
+ ['001.img', '002.img', '003.img']
:arg paths: List of paths to reduce.
@@ -290,16 +287,17 @@ def getFileGroup(path, allowedExts=None, fileGroups=None, fullPaths=True):
return ``file.img`` (i.e. the file which matches the first extension in
the group).
- Similarly, if you call the :func:`imcp` or :func:`immv` functions with the
- above parameters, both ``file.img`` and ``file.hdr`` will be moved.
+ Similarly, if you call the :func:`.imcp.imcp` or :func:`.imcp.immv`
+ functions with the above parameters, both ``file.img`` and ``file.hdr``
+ will be moved.
.. note:: The primary use-case of file groups is to resolve ambiguity with
respect to NIFTI and ANALYSE75 image pairs. By specifying
``fileGroups=[('.img', '.hdr'), ('.img.gz', '.hdr.gz')]``, the
- :func:`addExt`, :func:`immv` and :func:`imcp` functions are able
- to figure out what you mean when you specify ``file``, and both
- ``file.hdr`` and ``file.img`` (or ``file.hdr.gz`` and
- ``file.img.gz``) exist.
+ :func:`addExt`, :func:`.imcp.immv` and :func:`.imcp.imcp`
+ functions are able to figure out what you mean when you specify
+ ``file``, and both ``file.hdr`` and ``file.img`` (or
+ ``file.hdr.gz`` and ``file.img.gz``) exist.
:arg path: Path to the file. Must contain the file extension.
@@ -342,116 +340,3 @@ def getFileGroup(path, allowedExts=None, fileGroups=None, fullPaths=True):
else:
if fullPaths: return matchedGroupFiles[0]
else: return matchedGroups[ 0]
-
-
-def imcp(src,
- dest,
- allowedExts=None,
- fileGroups=None,
- overwrite=False,
- move=False):
- """Copy the given ``src`` file to destination ``dest``.
-
- :arg src: Path to copy. If ``allowedExts`` is provided,
- the file extension can be omitted.
-
- :arg dest: Destination path. Can be an incomplete file
- specification (i.e. without the extension), or a
- directory.
-
- :arg allowedExts: Allowed/recognised file extensions.
-
- :arg fileGroups: Recognised file groups - see the :func:`getFileGroup`
- documentation.
-
- :arg overwrite: If ``True`` this function will overwrite files that
- already exist. Defaults to ``False``.
-
- :arg move: If ``True``, the files are moved, instead of being
- copied.
- """
-
- base, ext = splitExt(src, allowedExts)
- destIsDir = op.isdir(dest)
-
- # If dest has been specified
- # as a file name, we don't
- # care about its extension.
- if not destIsDir:
- dest = removeExt(dest, allowedExts)
-
- # src was specified without an
- # extension, or the specitifed
- # src does not have an allowed
- # extension.
- if ext == '':
-
- # Try to resolve the specified src
- # path - if src does not exist, or
- # does not have an allowed extension,
- # addExt will raise an error
- src = addExt(src,
- allowedExts,
- mustExist=True,
- fileGroups=fileGroups)
-
- # We've resolved src to a
- # full filename - split it
- # again to get its extension
- base, ext = splitExt(src, allowedExts)
-
- # If the source is part of a file group,
- # e.g. src.img/src.hdr, we want to copy
- # the whole set of files. So here we
- # build a list of source files that need
- # to be copied/moved. The getFileGroup
- # function returns all other files that
- # are associated with this file (i.e.
- # part of the same group).
- #
- # We store the sources as separate
- # (base, ext) tuples, so we don't
- # have to re-split when creating
- # destination paths.
- copySrcs = getFileGroup(src, allowedExts, fileGroups, fullPaths=False)
- copySrcs = [(base, e) for e in copySrcs]
-
- # Note that these additional files
- # do not have to exist, e.g.
- # imcp('blah.img', ...) will still
- # work if there is no blah.hdr
- copySrcs = [(b, e) for (b, e) in copySrcs if op.exists(b + e)]
-
- # Build a list of destinations for each
- # copy source - we build this list in
- # advance, so we can fail if any of the
- # destinations already exist.
- copyDests = []
- for i, (base, ext) in enumerate(copySrcs):
-
- # We'll also take this opportunity
- # to re-combine the source paths
- copySrcs[i] = base + ext
-
- 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 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):
-
- if move: shutil.move(src, dest)
- else: shutil.copy(src, dest)
-
-
-def immv(src, dest, allowedExts=None, fileGroups=None, overwrite=False):
- """Move the specified ``src`` to the specified ``dest``. See :func:`imcp`.
- """
- imcp(src, dest, allowedExts, fileGroups, overwrite, move=True)
--
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