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Commit 5d7de43e authored by Paul McCarthy's avatar Paul McCarthy
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Nifti1 related stuff has been moved out of the Image class, and into 

a general base class. Will be used by TensorImage.
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fsl/data/image.py
+ 159
− 133
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......@@ -37,6 +37,9 @@ import os
import os.path as op
import subprocess as sp
import numpy as np
import nibabel as nib
import props
import fsl.utils.transform as transform
......@@ -47,58 +50,38 @@ import fsl.data.constants as constants
log = logging.getLogger(__name__)
class Image(props.HasProperties):
"""Class which represents a 3D/4D image. Internally, the image is
loaded/stored using :mod:`nibabel`.
class Nifti1(object):
"""The ``Nifti1`` class is intended to be used as a base class for
things which either are, or are associated with, a NIFTI1 image.
In addition to the :attr:`name`, :attr:`data`, and :attr:`saved`
properties, the following attributes are present on an ``Image`` instance:
When a ``Nifti1`` instance is created, it adds the following attributes
to itself:
================= ====================================================
``nibImage`` The :mod:`nibabel` image object.
``dataSource`` The name of the file that the image was loaded from.
``dataSource`` The name of the file that the image was loaded from.
``tempFile`` The name of the temporary file which was created (in
the event that the image was large and was gzipped -
see :func:`loadImage`).
``shape`` A list/tuple containing the number of voxels along
each image dimension.
``pixdim`` A list/tuple containing the size of one voxel along
each image dimension.
each image dimension.
``voxToWorldMat`` A 4*4 array specifying the affine transformation
for transforming voxel coordinates into real world
coordinates.
``worldToVoxMat`` A 4*4 array specifying the affine transformation
for transforming real world coordinates into voxel
coordinates.
================= ====================================================
"""
name = props.String()
"""The name of this image."""
data = props.Object()
"""The image data. This is a read-only :mod:`numpy` array - all changes
to the image data must be via the :meth:`applyChange` method.
"""
saved = props.Boolean(default=False)
"""A read-only property (not enforced) which is ``True`` if the image,
as stored in memory, is saved to disk, ``False`` otherwise.
================= ====================================================
"""
def __init__(self,
image,
xform=None,
name=None,
header=None,
loadData=True):
"""Create an ``Image`` object with the given image data or file name.
"""Create a ``Nifti1`` object.
:arg image: A string containing the name of an image file to load,
or a :mod:`numpy` array, or a :mod:`nibabel` image
......@@ -108,8 +91,6 @@ class Image(props.HasProperties):
which transforms voxel coordinates into real world
coordinates.
:arg name: A name for the image.
:arg header: If not ``None``, assumed to be a
:class:`nibabel.nifti1.Nifti1Header` to be used as the
image header. Not applied to images loaded from file,
......@@ -119,9 +100,9 @@ class Image(props.HasProperties):
not loaded - this is useful if you're only interested
in the header data, as the file will be loaded much
more quickly. The image data may subsequently be loaded
via the :meth:`loadData` method.
via the :meth:`loadData` method.
"""
self.nibImage = None
self.dataSource = None
self.tempFile = None
......@@ -133,54 +114,35 @@ class Image(props.HasProperties):
if header is not None:
header = header.copy()
import numpy as np
import nibabel as nib
# The image parameter may be the name of an image file
if isinstance(image, basestring):
nibImage, filename = loadImage(addExt(image))
self.nibImage = nibImage
self.dataSource = op.abspath(image)
self.dataSource = op.abspath(image)
# if the returned file name is not the same as
# the provided file name, that means that the
# image was opened from a temporary file
if filename != image:
filepref = removeExt(op.basename(self.dataSource))
self.tempFile = nibImage.get_filename()
else:
filepref = removeExt(op.basename(self.dataSource))
if name is None:
name = filepref
self.name = name
self.saved = True
# Or a numpy array - we wrap it in a nibabel image,
# with an identity transformation (each voxel maps
# to 1mm^3 in real world space)
elif isinstance(image, np.ndarray):
if xform is None:
if header is None: xform = np.identity(4)
else: xform = header.get_best_affine()
if name is None: name = 'Numpy array'
self.nibImage = nib.nifti1.Nifti1Image(image,
xform,
header=header)
self.name = name
# otherwise, we assume that it is a nibabel image
else:
if name is None:
name = 'Nibabel image'
self.nibImage = image
self.name = name
self.shape = self.nibImage.get_shape()
self.pixdim = self.nibImage.get_header().get_zooms()
......@@ -194,34 +156,8 @@ class Image(props.HasProperties):
if len(self.shape) < 3 or len(self.shape) > 4:
raise RuntimeError('Only 3D or 4D images are supported')
log.memory('{}.init ({})'.format(type(self).__name__, id(self)))
def __del__(self):
"""Prints a log message. """
log.memory('{}.del ({})'.format(type(self).__name__, id(self)))
def __hash__(self):
"""Returns a number which uniquely idenfities this ``Image`` instance
(the result of ``id(self)``).
"""
return id(self)
def __str__(self):
"""Return a string representation of this ``Image`` instance."""
return '{}({}, {})'.format(self.__class__.__name__,
self.name,
self.dataSource)
def __repr__(self):
"""See the :meth:`__str__` method."""
return self.__str__()
def loadData(self):
"""Loads the image data from the file. This method only needs to
be called if the ``loadData`` parameter passed to :meth:`__init__`
......@@ -243,7 +179,7 @@ class Image(props.HasProperties):
log.debug('Loaded image data ({}) - original '
'shape {}, squeezed shape {}'.format(
self.name,
self.dataSource,
shape,
data.shape))
......@@ -252,58 +188,12 @@ class Image(props.HasProperties):
self.pixdim = self.pixdim[:len(data.shape)]
def applyChange(self, offset, newVals, vol=None):
"""Changes the image data according to the given new values.
Any listeners registered on the :attr:`data` property will be
notified of the change.
:arg offset: A tuple of three values, containing the xyz
offset of the image region to be changed.
:arg newVals: A 3D numpy array containing the new image values.
:arg vol: If this is a 4D image, the volume index.
"""
if self.is4DImage() and vol is None:
raise ValueError('Volume must be specified for 4D images')
data = self.data
xlo, ylo, zlo = offset
xhi = xlo + newVals.shape[0]
yhi = ylo + newVals.shape[1]
zhi = zlo + newVals.shape[2]
try:
data.flags.writeable = True
if self.is4DImage(): data[xlo:xhi, ylo:yhi, zlo:zhi, vol] = newVals
else: data[xlo:xhi, ylo:yhi, zlo:zhi] = newVals
data.flags.writeable = False
except:
data.flags.writeable = False
raise
# Force a notification on the 'data' property
# by assigning its value back to itself
self.data = data
self.saved = False
def save(self):
"""Convenience method to save any changes made to the :attr:`data` of
this :class:`Image` instance.
See the :func:`saveImage` function.
"""
return saveImage(self)
# TODO: Remove this method, and use the shape attribute directly
def is4DImage(self):
"""Returns ``True`` if this image is 4D, ``False`` otherwise. """
return len(self.shape) > 3 and self.shape[3] > 1
return len(self.shape) > 3 and self.shape[3] > 1
def getXFormCode(self, code=None):
"""This method returns the code contained in the NIFTI1 header,
indicating the space to which the (transformed) image is oriented.
......@@ -372,7 +262,143 @@ class Image(props.HasProperties):
(constants.ORIENT_A2P, constants.ORIENT_P2A),
(constants.ORIENT_S2I, constants.ORIENT_I2S)))[axis]
return code
return code
class Image(Nifti1, props.HasProperties):
"""Class which represents a 3D/4D NIFTI1 image. Internally, the image
is loaded/stored using :mod:`nibabel`.
In addition to the :attr:`data`, and :attr:`saved` properties, and
the attributes added by the :meth:`Nifti1.__init__` method, the
following attributes are present on an ``Image`` instance:
================= ====================================================
``name`` the name of this ``Image`` - defaults to the image
file name, sans-suffix.
================= ====================================================
"""
data = props.Object()
"""The image data. This is a read-only :mod:`numpy` array - all changes
to the image data must be via the :meth:`applyChange` method.
"""
saved = props.Boolean(default=False)
"""A read-only property (not enforced) which is ``True`` if the image,
as stored in memory, is saved to disk, ``False`` otherwise.
"""
def __init__(self, image, name=None, **kwargs):
"""Create an ``Image`` object with the given image data or file name.
:arg image: A string containing the name of an image file to load,
or a :mod:`numpy` array, or a :mod:`nibabel` image
object.
:arg name: A name for the image.
All other arguments are passed through to :meth:`Nifti1.__init__`.
"""
Nifti1.__init__(self, image, **kwargs)
# Figure out the name of this image.
# It might have been explicitly passed in
if name is not None:
self.name = name
# Or, if this image was loaded
# from disk, use the file name
elif isinstance(image, basestring):
self.name = removeExt(op.basename(self.dataSource))
self.saved = True
# Or the image was created from a numpy array
elif isinstance(image, np.ndarray):
self.name = 'Numpy array'
# Or image from a nibabel image
else:
self.name = 'Nibabel image'
log.memory('{}.init ({})'.format(type(self).__name__, id(self)))
def __del__(self):
"""Prints a log message. """
log.memory('{}.del ({})'.format(type(self).__name__, id(self)))
def __hash__(self):
"""Returns a number which uniquely idenfities this ``Image`` instance
(the result of ``id(self)``).
"""
return id(self)
def __str__(self):
"""Return a string representation of this ``Image`` instance."""
return '{}({}, {})'.format(self.__class__.__name__,
self.name,
self.dataSource)
def __repr__(self):
"""See the :meth:`__str__` method."""
return self.__str__()
def applyChange(self, offset, newVals, vol=None):
"""Changes the image data according to the given new values.
Any listeners registered on the :attr:`data` property will be
notified of the change.
:arg offset: A tuple of three values, containing the xyz
offset of the image region to be changed.
:arg newVals: A 3D numpy array containing the new image values.
:arg vol: If this is a 4D image, the volume index.
"""
if self.is4DImage() and vol is None:
raise ValueError('Volume must be specified for 4D images')
data = self.data
xlo, ylo, zlo = offset
xhi = xlo + newVals.shape[0]
yhi = ylo + newVals.shape[1]
zhi = zlo + newVals.shape[2]
try:
data.flags.writeable = True
if self.is4DImage(): data[xlo:xhi, ylo:yhi, zlo:zhi, vol] = newVals
else: data[xlo:xhi, ylo:yhi, zlo:zhi] = newVals
data.flags.writeable = False
except:
data.flags.writeable = False
raise
# Force a notification on the 'data' property
# by assigning its value back to itself
self.data = data
self.saved = False
def save(self):
"""Convenience method to save any changes made to the :attr:`data` of
this :class:`Image` instance.
See the :func:`saveImage` function.
"""
return saveImage(self)
# TODO The wx.FileDialog does not
......
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