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Commit a22fb99e authored by Paul McCarthy's avatar Paul McCarthy
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All imagefile functionality is now in image module.

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fsl/data/image.py
+ 158
− 5
View file @ a22fb99e
......@@ -18,7 +18,6 @@ import numpy as np
import nibabel as nib
import props
import fsl.data.imagefile as imagefile
import fsl.utils.transform as transform
......@@ -43,6 +42,160 @@ NIFTI_XFORM_TALAIRACH = 3
NIFTI_XFORM_MNI_152 = 4
ALLOWED_EXTENSIONS = ['.nii', '.img', '.hdr', '.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 NIFTI1 images',
'Compressed ANALYZE75/NIFTI1 images']
"""Descriptions for each of the extensions in :data:`_allowedExts`. """
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]
wcParts = ['|'.join((desc, ext)) for (desc, ext) in zip(descs, exts)]
print '|'.join(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.
......@@ -174,7 +327,7 @@ class Image(props.HasProperties):
# The image parameter may be the name of an image file
if isinstance(image, basestring):
nibImage, filename = _loadImageFile(imagefile.addExt(image))
nibImage, filename = _loadImageFile(addExtension(image))
self.nibImage = nibImage
self.imageFile = image
......@@ -182,10 +335,10 @@ class Image(props.HasProperties):
# the provided file name, that means that the
# image was opened from a temporary file
if filename != image:
self.name = op.basename(self.imageFile)
self.name = removeExtension(op.basename(self.imageFile))
self.tempFile = nibImage.get_filename()
else:
self.name = op.basename(self.imageFile)
self.name = removeExtension(op.basename(self.imageFile))
self.saved = True
......@@ -459,7 +612,7 @@ class ImageList(props.HasProperties):
# TODO wx wildcard handling is buggy,
# so i'm disabling it for now
# wildcard = imagefile.wildcard()
# wildcard = wildcard()
dlg = wx.FileDialog(app.GetTopWindow(),
message='Open image file',
defaultDir=fromDir,
......
fsl/data/imagefile.py deleted 100644 → 0
+ 0
− 170
View file @ b53cb687
#!/usr/bin/env python
#
# imagefile.py - Convenience functions for adding/stripping supported
# file extensions to/from image file names.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""Convenience functions for adding/stripping supported
file extensions to/from image file names.
"""
import os
import os.path as op
_allowedExts = ['.nii', '.img', '.hdr', '.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.
"""
_descriptions = ['NIFTI1 images',
'ANALYZE75 images',
'NIFTI1/ANALYZE75 headers',
'Compressed NIFTI1 images',
'Compressed ANALYZE75/NIFTI1 images']
"""Descriptions for each of the extensions in :data:`_allowedExts`. """
_defaultExt = '.nii.gz'
"""The default file extension (TODO read this from ``$FSLOUTPUTTYPE``)."""
def wildcard(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 = _allowedExts
descs = _descriptions
else:
descs = allowedExts
exts = ['*{}'.format(ext) for ext in allowedExts]
wcParts = ['|'.join((desc, ext)) for (desc, ext) in zip(descs, exts)]
print '|'.join(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 = _allowedExts
return any(map(lambda ext: filename.endswith(ext, allowedExts)))
def removeExt(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 = _allowedExts
# 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 addExt(
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 = _allowedExts
if defaultExt is None: defaultExt = _defaultExt
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]
fsl/fslview/actions/copyimage.py
+ 1
− 1
View file @ a22fb99e
......@@ -25,7 +25,7 @@ class CopyImageAction(actions.Action):
data = np.copy(image.data)
xform = image.voxToWorldMat
name = '{} copy'.format(image.name)
name = '{}_copy'.format(image.name)
copy = fslimage.Image(data, xform, name)
self._imageList.insert(imageIdx + 1, copy)
fsl/tools/bet.py
+ 3
− 4
View file @ a22fb99e
......@@ -9,7 +9,6 @@ from collections import OrderedDict
import props
import fsl.data.imagefile as imagefile
import fsl.data.image as fslimage
import fsl.utils.transform as transform
import fsl.fslview.displaycontext as displaycontext
......@@ -34,12 +33,12 @@ class Options(props.HasProperties):
inputImage = props.FilePath(
exists=True,
suffixes=imagefile._allowedExts,
suffixes=fslimage.ALLOWED_EXTENSIONS,
required=True)
outputImage = props.FilePath(required=True)
t2Image = props.FilePath(
exists=True,
suffixes=imagefile._allowedExts,
suffixes=fslimage.ALLOWED_EXTENSIONS,
required=lambda i: i.runChoice == '-A2')
runChoice = props.Choice(runChoices)
......@@ -66,7 +65,7 @@ class Options(props.HasProperties):
"""
if not valid: return
value = imagefile.removeExt(value)
value = fslimage.removeExtension(value)
self.outputImage = value + '_brain'
......
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