From 8ce305993639f91c272ff87ca0225550fb040ad7 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 7 Jan 2015 12:17:16 +0000
Subject: [PATCH] Moved file extension stuff back out of image module, and into
a new module called imageio, which also contains functions for loading/saving
images. Skeleton for saveImage function.
---
fsl/data/image.py | 337 ++++--------------------------
fsl/data/imageio.py | 367 +++++++++++++++++++++++++++++++++
fsl/tools/bet.py | 7 +-
fsl/tools/fslview_parseargs.py | 3 +-
4 files changed, 410 insertions(+), 304 deletions(-)
create mode 100644 fsl/data/imageio.py
diff --git a/fsl/data/image.py b/fsl/data/image.py
index c2c60329a..7e0a42e99 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -1,28 +1,33 @@
#!/usr/bin/env python
-#
+#
# image.py - Classes for representing 3D/4D images and collections of said
# images.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""Classes for representing 3D/4D images and collections of said images."""
+"""Classes for representing 3D/4D images and collections of said images.
+
+See the :mod:`fsl.data.imageio` module for image loading/saving
+functionality.
+
+"""
-import os
import logging
-import tempfile
import collections
-import subprocess as sp
-import os.path as op
+import os.path as op
-import numpy as np
-import nibabel as nib
+import numpy as np
+import nibabel as nib
import props
-import fsl.utils.transform as transform
+
+import fsl.utils.transform as transform
+import fsl.data.imageio as iio
log = logging.getLogger(__name__)
+
# Constants which represent the orientation
# of an axis, in either voxel or world space.
ORIENT_UNKNOWN = -1
@@ -33,6 +38,7 @@ ORIENT_A2P = 3
ORIENT_I2S = 4
ORIENT_S2I = 5
+
# Constants from the NIFTI1 specification that define
# the 'space' in which an image is assumed to be.
NIFTI_XFORM_UNKNOWN = 0
@@ -42,228 +48,6 @@ NIFTI_XFORM_TALAIRACH = 3
NIFTI_XFORM_MNI_152 = 4
-# TODO The wx.FileDialog does not
-# seem to handle wildcards with
-# multiple suffixes (e.g. '.nii.gz'),
-# so i'm just providing '*.gz'for now
-ALLOWED_EXTENSIONS = ['.nii', '.img', '.hdr', '.gz']
-"""The file extensions which we understand. This list is used as the default
-if if the ``allowedExts`` parameter is not passed to any of the functions in
-this module.
-"""
-
-EXTENSION_DESCRIPTIONS = ['NIFTI1 images',
- 'ANALYZE75 images',
- 'NIFTI1/ANALYZE75 headers',
- 'Compressed images']
-"""Descriptions for each of the extensions in :data:`ALLOWED_EXTENSIONS`. """
-
-
-DEFAULT_EXTENSION = '.nii.gz'
-"""The default file extension (TODO read this from ``$FSLOUTPUTTYPE``)."""
-
-
-def makeWildcard(allowedExts=None):
- """Returns a wildcard string for use in a file dialog, to limit
- the acceptable file types.
-
- :arg allowedExts: A list of strings containing the allowed file
- extensions.
- """
-
- if allowedExts is None:
- allowedExts = ALLOWED_EXTENSIONS
- descs = EXTENSION_DESCRIPTIONS
- else:
- descs = allowedExts
-
- exts = ['*{}'.format(ext) for ext in allowedExts]
-
- allDesc = 'All supported files'
- allExts = ';'.join(exts)
-
- wcParts = ['|'.join((desc, ext)) for (desc, ext) in zip(descs, exts)]
- wcParts = ['|'.join((allDesc, allExts))] + wcParts
-
- return '|'.join(wcParts)
-
-
-def isSupported(filename, allowedExts=None):
- """
- Returns ``True`` if the given file has a supported extension, ``False``
- otherwise.
-
- :arg filename: The file name to test.
-
- :arg allowedExts: A list of strings containing the allowed file
- extensions.
- """
-
- if allowedExts is None: allowedExts = ALLOWED_EXTENSIONS
-
- return any(map(lambda ext: filename.endswith(ext, allowedExts)))
-
-
-def removeExtension(filename, allowedExts=None):
- """
- Removes the extension from the given file name. Raises a :exc:`ValueError`
- if the file has an unsupported 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):
- raise ValueError('Unsupported file type')
-
- # 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]
-
-
-def addExtension(
- prefix,
- mustExist=False,
- allowedExts=None,
- defaultExt=None):
- """Adds a file extension to the given file ``prefix``.
-
- If ``mustExist`` is False (the default), 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 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 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]
-
-
-def _loadImageFile(filename):
- """Given the name of an image file, loads it using nibabel.
-
- If the file is large, and is gzipped, it is decompressed to a temporary
- location, so that it can be memory-mapped. A tuple is returned,
- consisting of the nibabel image object, and the name of the file that it
- was loaded from (either the passed-in file name, or the name of the
- temporary decompressed file).
- """
-
- # If we have a GUI, we can display a dialog
- # message. Otherwise we print a log message
- haveGui = False
- try:
- import wx
- if wx.GetApp() is not None:
- haveGui = True
- except:
- pass
-
- realFilename = filename
- mbytes = op.getsize(filename) / 1048576.0
-
- # The mbytes limit is arbitrary
- if filename.endswith('.nii.gz') and mbytes > 512:
-
- unzipped, filename = tempfile.mkstemp(suffix='.nii')
-
- unzipped = os.fdopen(unzipped)
-
- msg = '{} is a large file ({} MB) - decompressing ' \
- 'to {}, to allow memory mapping...'.format(realFilename,
- mbytes,
- filename)
-
- if not haveGui:
- log.info(msg)
- else:
- busyDlg = wx.BusyInfo(msg, wx.GetTopLevelWindows()[0])
-
- gzip = ['gzip', '-d', '-c', realFilename]
- log.debug('Running {} > {}'.format(' '.join(gzip), filename))
-
- # If the gzip call fails, revert to loading from the gzipped file
- try:
- sp.call(gzip, stdout=unzipped)
- unzipped.close()
-
- except OSError as e:
- log.warn('gzip call failed ({}) - cannot memory '
- 'map file: {}'.format(e, realFilename),
- exc_info=True)
- unzipped.close()
- os.remove(filename)
- filename = realFilename
-
- if haveGui:
- busyDlg.Destroy()
-
- return nib.load(filename), filename
-
-
class Image(props.HasProperties):
"""Class which represents a 3D/4D image. Internally, the image is
loaded/stored using :mod:`nibabel`.
@@ -279,20 +63,20 @@ class Image(props.HasProperties):
:ivar shape: A list/tuple containing the number of voxels
along each image dimension.
-
+
:ivar pixdim: A list/tuple containing the size of one voxel
along each image dimension.
-
+
:ivar voxToWorldMat: A 4*4 array specifying the affine transformation
for transforming voxel coordinates into real world
coordinates.
:ivar worldToVoxMat: A 4*4 array specifying the affine transformation
for transforming real world coordinates into voxel
- coordinates.
+ coordinates.
:ivar imageFile: The name of the file that the image was loaded from.
-
+
:ivar tempFile: The name of the temporary file which was created (in
the event that the image was large and was gzipped -
see :func:`_loadImageFile`).
@@ -306,7 +90,7 @@ class Image(props.HasProperties):
default='volume')
"""This property defines the type of image data."""
-
+
name = props.String()
"""The name of this image."""
@@ -322,7 +106,7 @@ class Image(props.HasProperties):
as stored in memory, is saved to disk, ``False`` otherwise.
"""
-
+
def __init__(self, image, xform=None, name=None):
"""Initialise an Image object with the given image data or file name.
@@ -333,7 +117,7 @@ class Image(props.HasProperties):
# The image parameter may be the name of an image file
if isinstance(image, basestring):
- nibImage, filename = _loadImageFile(addExtension(image))
+ nibImage, filename = iio.loadImage(iio.addExt(image))
self.nibImage = nibImage
self.imageFile = image
@@ -341,10 +125,10 @@ class Image(props.HasProperties):
# the provided file name, that means that the
# image was opened from a temporary file
if filename != image:
- self.name = removeExtension(op.basename(self.imageFile))
+ self.name = iio.removeExt(op.basename(self.imageFile))
self.tempFile = nibImage.get_filename()
else:
- self.name = removeExtension(op.basename(self.imageFile))
+ self.name = iio.removeExt(op.basename(self.imageFile))
self.saved = True
@@ -402,7 +186,7 @@ class Image(props.HasProperties):
:arg volume: If this is a 4D image, the volume index.
"""
-
+
if self.is4DImage() and volume is None:
raise ValueError('Volume must be specified for 4D images')
@@ -426,10 +210,13 @@ class Image(props.HasProperties):
def save(self):
+ """Convenience method to save any changes made to the :attr:`data` of
+ this :class:`Image` instance.
+
+ See the :func:`fsl.data.imageio.save` function.
"""
- """
- pass
-
+ return iio.saveImage(self)
+
def __hash__(self):
"""Returns a number which uniquely idenfities this :class:`Image`
@@ -440,7 +227,9 @@ class Image(props.HasProperties):
def __str__(self):
"""Return a string representation of this :class:`Image`."""
- return '{}("{}")'.format(self.__class__.__name__, self.imageFile)
+ return '{}({}, {})'.format(self.__class__.__name__,
+ self.name,
+ self.imageFile)
def __repr__(self):
@@ -560,6 +349,7 @@ class ImageList(props.HasProperties):
as if it were a list itself.
"""
+
def _validateImage(self, atts, images):
"""Returns ``True`` if all objects in the given ``images`` list are
:class:`Image` objects, ``False`` otherwise.
@@ -576,69 +366,16 @@ class ImageList(props.HasProperties):
:class:`Image` objects."""
if images is None: images = []
-
self.images.extend(images)
- # set the _lastDir attribute,
- # used by the addImages method
- if len(images) == 0: self._lastDir = os.getcwd()
- else: self._lastDir = op.dirname(images[-1].imageFile)
-
def addImages(self, fromDir=None, addToEnd=True):
"""Convenience method for interactively adding images to this
:class:`ImageList`.
- If the :mod:`wx` package is available, pops up a file dialog
- prompting the user to select one or more images to append to the
- image list.
-
- :param str fromDir: Directory in which the file dialog should start.
- If ``None``, the most recently visited directory
- (via this method) is used, or a directory from
- an already loaded image, or the current working
- directory.
-
- :param bool addToEnd: If True (the default), the new images are added
- to the end of the list. Otherwise, they are added
- to the beginning of the list.
-
- Returns: True if images were successfully added, False if no images
- were added.
-
- :raise ImportError: if :mod:`wx` is not present.
- :raise RuntimeError: if a :class:`wx.App` has not been created.
-
+ See the :func:`fsl.data.imageio.addImages` function.
"""
- import wx
-
- app = wx.GetApp()
-
- if app is None:
- raise RuntimeError('A wx.App has not been created')
-
- saveLastDir = False
- if fromDir is None:
- fromDir = self._lastDir
- saveLastDir = True
-
- dlg = wx.FileDialog(app.GetTopWindow(),
- message='Open image file',
- defaultDir=fromDir,
- wildcard=makeWildcard(),
- style=wx.FD_OPEN | wx.FD_MULTIPLE)
-
- if dlg.ShowModal() != wx.ID_OK: return False
-
- paths = dlg.GetPaths()
- images = map(Image, paths)
-
- if saveLastDir: self._lastDir = op.dirname(paths[-1])
-
- if addToEnd: self.extend( images)
- else: self.insertAll(0, images)
-
- return True
+ return iio.addImages(self, fromDir, addToEnd)
# Wrappers around the images list property, allowing this
diff --git a/fsl/data/imageio.py b/fsl/data/imageio.py
new file mode 100644
index 000000000..75a3bd652
--- /dev/null
+++ b/fsl/data/imageio.py
@@ -0,0 +1,367 @@
+#!/usr/bin/env python
+#
+# imageio.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import logging
+log = logging.getLogger(__name__)
+
+import os
+import os.path as op
+import subprocess as sp
+import tempfile
+
+import nibabel as nib
+
+import image as fslimage
+
+
+# TODO The wx.FileDialog does not
+# seem to handle wildcards with
+# multiple suffixes (e.g. '.nii.gz'),
+# so i'm just providing '*.gz'for now
+ALLOWED_EXTENSIONS = ['.nii', '.img', '.hdr', '.gz', '.nii.gz', '.img.gz']
+"""The file extensions which we understand. This list is used as the default
+if if the ``allowedExts`` parameter is not passed to any of the functions in
+this module.
+"""
+
+EXTENSION_DESCRIPTIONS = ['NIFTI1 images',
+ 'ANALYZE75 images',
+ 'NIFTI1/ANALYZE75 headers',
+ 'Compressed images',
+ 'Compressed images',
+ 'Compressed images']
+"""Descriptions for each of the extensions in :data:`ALLOWED_EXTENSIONS`. """
+
+
+DEFAULT_EXTENSION = '.nii.gz'
+"""The default file extension (TODO read this from ``$FSLOUTPUTTYPE``)."""
+
+
+def makeWildcard(allowedExts=None):
+ """Returns a wildcard string for use in a file dialog, to limit
+ the acceptable file types.
+
+ :arg allowedExts: A list of strings containing the allowed file
+ extensions.
+ """
+
+ if allowedExts is None:
+ allowedExts = ALLOWED_EXTENSIONS
+ descs = EXTENSION_DESCRIPTIONS
+ else:
+ descs = allowedExts
+
+ exts = ['*{}'.format(ext) for ext in allowedExts]
+
+ allDesc = 'All supported files'
+ allExts = ';'.join(exts)
+
+ wcParts = ['|'.join((desc, ext)) for (desc, ext) in zip(descs, exts)]
+ wcParts = ['|'.join((allDesc, allExts))] + wcParts
+
+ return '|'.join(wcParts)
+
+
+def isSupported(filename, allowedExts=None):
+ """
+ Returns ``True`` if the given file has a supported extension, ``False``
+ otherwise.
+
+ :arg filename: The file name to test.
+
+ :arg allowedExts: A list of strings containing the allowed file
+ extensions.
+ """
+
+ if allowedExts is None: allowedExts = ALLOWED_EXTENSIONS
+
+ return any(map(lambda ext: filename.endswith(ext, allowedExts)))
+
+
+def removeExt(filename, allowedExts=None):
+ """
+ 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
+
+ # 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]
+
+
+def addExt(
+ prefix,
+ mustExist=True,
+ allowedExts=None,
+ 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 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]
+
+
+def loadImage(filename):
+ """Given the name of an image file, loads it using nibabel.
+
+ If the file is large, and is gzipped, it is decompressed to a temporary
+ location, so that it can be memory-mapped. A tuple is returned,
+ consisting of the nibabel image object, and the name of the file that it
+ was loaded from (either the passed-in file name, or the name of the
+ temporary decompressed file).
+ """
+
+ # If we have a GUI, we can display a dialog
+ # message. Otherwise we print a log message
+ haveGui = False
+ try:
+ import wx
+ if wx.GetApp() is not None:
+ haveGui = True
+ except:
+ pass
+
+ realFilename = filename
+ mbytes = op.getsize(filename) / 1048576.0
+
+ # The mbytes limit is arbitrary
+ if filename.endswith('.nii.gz') and mbytes > 512:
+
+ unzipped, filename = tempfile.mkstemp(suffix='.nii')
+
+ unzipped = os.fdopen(unzipped)
+
+ msg = '{} is a large file ({} MB) - decompressing ' \
+ 'to {}, to allow memory mapping...'.format(realFilename,
+ mbytes,
+ filename)
+
+ if not haveGui:
+ log.info(msg)
+ else:
+ busyDlg = wx.BusyInfo(msg, wx.GetTopLevelWindows()[0])
+
+ gzip = ['gzip', '-d', '-c', realFilename]
+ log.debug('Running {} > {}'.format(' '.join(gzip), filename))
+
+ # If the gzip call fails, revert to loading from the gzipped file
+ try:
+ sp.call(gzip, stdout=unzipped)
+ unzipped.close()
+
+ except OSError as e:
+ log.warn('gzip call failed ({}) - cannot memory '
+ 'map file: {}'.format(e, realFilename),
+ exc_info=True)
+ unzipped.close()
+ os.remove(filename)
+ filename = realFilename
+
+ if haveGui:
+ busyDlg.Destroy()
+
+ return nib.load(filename), filename
+
+
+def saveImage(image, imageList=None, fromDir=None):
+ """Convenience method for interactively saving changes to an image.
+
+ If the :mod:`wx` package is available, a dialog is popped up, prompting
+ the user to select a destination. Or, if the image has been loaded
+ from a file, the user is prompted to confirm that they want to overwrite
+ the image.
+
+
+ :param image: The :class:`~fsl.data.image.Image` instance to
+ be saved.
+
+
+ :param imageList: The :class:`~fsl.data.image.ImageList` instance
+ which contains the given image.
+
+
+ :param str fromDir: Directory in which the file dialog should start.
+ If ``None``, the most recently visited directory
+ (via this method) is used, or the directory from
+ the given image, or the current working directory.
+
+ :raise ImportError: if :mod:`wx` is not present.
+ :raise RuntimeError: if a :class:`wx.App` has not been created.
+ """
+
+ if image.saved:
+ return
+
+ import wx
+
+ app = wx.GetApp()
+
+ if app is None:
+ raise RuntimeError('A wx.App has not been created')
+
+ lastDir = getattr(saveImage, 'lastDir', None)
+
+ if lastDir is None:
+ if image.imageFile is None: lastDir = os.cwd()
+ else: lastDir = op.dirname(image.imageFile)
+
+ if image.imageFile is None: filename = os.cwd()
+ else: filename = op.basename(image.imageFile)
+
+ saveLastDir = False
+ if fromDir is None:
+ fromDir = lastDir
+ saveLastDir = True
+
+ dlg = wx.FileDialog(app.GetTopWindow(),
+ message='Save image file',
+ defaultDir=fromDir,
+ defaultFile=filename,
+ wildcard=makeWildcard(),
+ style=wx.FD_SAVE)
+
+ if dlg.ShowModal() != wx.ID_OK: return False
+
+ if saveLastDir: saveImage.lastDir = lastDir
+
+
+
+def addImages(imageList, fromDir=None, addToEnd=True):
+ """Convenience method for interactively adding images to an
+ :class:`fsl.data.image.ImageList`.
+ If the :mod:`wx` package is available, pops up a file dialog
+ prompting the user to select one or more images to append to the
+ image list.
+
+ :param str fromDir: Directory in which the file dialog should start.
+ If ``None``, the most recently visited directory
+ (via this method) is used, or a directory from
+ an already loaded image, or the current working
+ directory.
+
+ :param bool addToEnd: If True (the default), the new images are added
+ to the end of the list. Otherwise, they are added
+ to the beginning of the list.
+
+ Returns: True if images were successfully added, False if no images
+ were added.
+
+ :raise ImportError: if :mod:`wx` is not present.
+ :raise RuntimeError: if a :class:`wx.App` has not been created.
+ """
+ import wx
+
+ app = wx.GetApp()
+
+ if app is None:
+ raise RuntimeError('A wx.App has not been created')
+
+ lastDir = getattr(addImages, 'lastDir', None)
+
+ if lastDir is None:
+ if len(imageList) > 0 and imageList[-1].imageFile is not None:
+ lastDir = op.dirname(imageList[-1].imageFile)
+ else:
+ lastDir = os.cwd()
+
+ saveLastDir = False
+ if fromDir is None:
+ fromDir = lastDir
+ saveLastDir = True
+
+ dlg = wx.FileDialog(app.GetTopWindow(),
+ message='Open image file',
+ defaultDir=fromDir,
+ wildcard=makeWildcard(),
+ style=wx.FD_OPEN | wx.FD_MULTIPLE)
+
+ if dlg.ShowModal() != wx.ID_OK: return False
+
+ paths = dlg.GetPaths()
+ images = map(fslimage.Image, paths)
+
+ if saveLastDir: addImages.lastDir = op.dirname(paths[-1])
+
+ if addToEnd: imageList.extend( images)
+ else: imageList.insertAll(0, images)
+
+ return True
diff --git a/fsl/tools/bet.py b/fsl/tools/bet.py
index 85af2b83b..797ba782c 100644
--- a/fsl/tools/bet.py
+++ b/fsl/tools/bet.py
@@ -10,6 +10,7 @@ from collections import OrderedDict
import props
import fsl.data.image as fslimage
+import fsl.data.imageio as iio
import fsl.utils.transform as transform
import fsl.fslview.displaycontext as displaycontext
@@ -33,12 +34,12 @@ class Options(props.HasProperties):
inputImage = props.FilePath(
exists=True,
- suffixes=fslimage.ALLOWED_EXTENSIONS,
+ suffixes=iio.ALLOWED_EXTENSIONS,
required=True)
outputImage = props.FilePath(required=True)
t2Image = props.FilePath(
exists=True,
- suffixes=fslimage.ALLOWED_EXTENSIONS,
+ suffixes=iio.ALLOWED_EXTENSIONS,
required=lambda i: i.runChoice == '-A2')
runChoice = props.Choice(runChoices)
@@ -65,7 +66,7 @@ class Options(props.HasProperties):
"""
if not valid: return
- value = fslimage.removeExtension(value)
+ value = iio.removeExt(value)
self.outputImage = value + '_brain'
diff --git a/fsl/tools/fslview_parseargs.py b/fsl/tools/fslview_parseargs.py
index 893e97f3b..6c4b6e475 100644
--- a/fsl/tools/fslview_parseargs.py
+++ b/fsl/tools/fslview_parseargs.py
@@ -18,6 +18,7 @@ import argparse
import props
import fsl.data.image as fslimage
+import fsl.data.imageio as iio
import fsl.utils.transform as transform
import fsl.fslview.displaycontext as displaycontext
@@ -233,7 +234,7 @@ def parseArgs(mainParser, argv, name, desc, toolOptsDesc='[options]'):
# an -i with something that is
# not a file following it
- if not op.isfile(imgFile):
+ if not op.isfile(iio.addExt(imgFile, True)):
print_help()
sys.argv(1)
--
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