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Commit 8ce30599 authored by Paul McCarthy's avatar Paul McCarthy
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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.
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fsl/data/image.py
+ 37
− 300
View file @ 8ce30599
#!/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
......
fsl/data/imageio.py 0 → 100644
+ 367
− 0
View file @ 8ce30599
#!/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
fsl/tools/bet.py
+ 4
− 3
View file @ 8ce30599
......@@ -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'
......
fsl/tools/fslview_parseargs.py
+ 2
− 1
View file @ 8ce30599
......@@ -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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