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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 ...@@ -37,6 +37,9 @@ import os
import os.path as op import os.path as op
import subprocess as sp import subprocess as sp
import numpy as np
import nibabel as nib
import props import props
import fsl.utils.transform as transform import fsl.utils.transform as transform
...@@ -47,58 +50,38 @@ import fsl.data.constants as constants ...@@ -47,58 +50,38 @@ import fsl.data.constants as constants
log = logging.getLogger(__name__) log = logging.getLogger(__name__)
class Image(props.HasProperties): class Nifti1(object):
"""Class which represents a 3D/4D image. Internally, the image is """The ``Nifti1`` class is intended to be used as a base class for
loaded/stored using :mod:`nibabel`. 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. ``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 ``tempFile`` The name of the temporary file which was created (in
the event that the image was large and was gzipped - the event that the image was large and was gzipped -
see :func:`loadImage`). see :func:`loadImage`).
``shape`` A list/tuple containing the number of voxels along ``shape`` A list/tuple containing the number of voxels along
each image dimension. each image dimension.
``pixdim`` A list/tuple containing the size of one voxel along
each image dimension.
``voxToWorldMat`` A 4*4 array specifying the affine transformation ``voxToWorldMat`` A 4*4 array specifying the affine transformation
for transforming voxel coordinates into real world for transforming voxel coordinates into real world
coordinates. coordinates.
``worldToVoxMat`` A 4*4 array specifying the affine transformation ``worldToVoxMat`` A 4*4 array specifying the affine transformation
for transforming real world coordinates into voxel for transforming real world coordinates into voxel
coordinates. 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, def __init__(self,
image, image,
xform=None, xform=None,
name=None,
header=None, header=None,
loadData=True): 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, :arg image: A string containing the name of an image file to load,
or a :mod:`numpy` array, or a :mod:`nibabel` image or a :mod:`numpy` array, or a :mod:`nibabel` image
...@@ -108,8 +91,6 @@ class Image(props.HasProperties): ...@@ -108,8 +91,6 @@ class Image(props.HasProperties):
which transforms voxel coordinates into real world which transforms voxel coordinates into real world
coordinates. coordinates.
:arg name: A name for the image.
:arg header: If not ``None``, assumed to be a :arg header: If not ``None``, assumed to be a
:class:`nibabel.nifti1.Nifti1Header` to be used as the :class:`nibabel.nifti1.Nifti1Header` to be used as the
image header. Not applied to images loaded from file, image header. Not applied to images loaded from file,
...@@ -119,9 +100,9 @@ class Image(props.HasProperties): ...@@ -119,9 +100,9 @@ class Image(props.HasProperties):
not loaded - this is useful if you're only interested not loaded - this is useful if you're only interested
in the header data, as the file will be loaded much in the header data, as the file will be loaded much
more quickly. The image data may subsequently be loaded more quickly. The image data may subsequently be loaded
via the :meth:`loadData` method. via the :meth:`loadData` method.
""" """
self.nibImage = None self.nibImage = None
self.dataSource = None self.dataSource = None
self.tempFile = None self.tempFile = None
...@@ -133,54 +114,35 @@ class Image(props.HasProperties): ...@@ -133,54 +114,35 @@ class Image(props.HasProperties):
if header is not None: if header is not None:
header = header.copy() header = header.copy()
import numpy as np
import nibabel as nib
# The image parameter may be the name of an image file # The image parameter may be the name of an image file
if isinstance(image, basestring): if isinstance(image, basestring):
nibImage, filename = loadImage(addExt(image)) nibImage, filename = loadImage(addExt(image))
self.nibImage = nibImage self.nibImage = nibImage
self.dataSource = op.abspath(image) self.dataSource = op.abspath(image)
# if the returned file name is not the same as # if the returned file name is not the same as
# the provided file name, that means that the # the provided file name, that means that the
# image was opened from a temporary file # image was opened from a temporary file
if filename != image: if filename != image:
filepref = removeExt(op.basename(self.dataSource))
self.tempFile = nibImage.get_filename() 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, # Or a numpy array - we wrap it in a nibabel image,
# with an identity transformation (each voxel maps # with an identity transformation (each voxel maps
# to 1mm^3 in real world space) # to 1mm^3 in real world space)
elif isinstance(image, np.ndarray): elif isinstance(image, np.ndarray):
if xform is None: if xform is None:
if header is None: xform = np.identity(4) if header is None: xform = np.identity(4)
else: xform = header.get_best_affine() else: xform = header.get_best_affine()
if name is None: name = 'Numpy array'
self.nibImage = nib.nifti1.Nifti1Image(image, self.nibImage = nib.nifti1.Nifti1Image(image,
xform, xform,
header=header) header=header)
self.name = name
# otherwise, we assume that it is a nibabel image # otherwise, we assume that it is a nibabel image
else: else:
if name is None:
name = 'Nibabel image'
self.nibImage = image self.nibImage = image
self.name = name
self.shape = self.nibImage.get_shape() self.shape = self.nibImage.get_shape()
self.pixdim = self.nibImage.get_header().get_zooms() self.pixdim = self.nibImage.get_header().get_zooms()
...@@ -194,34 +156,8 @@ class Image(props.HasProperties): ...@@ -194,34 +156,8 @@ class Image(props.HasProperties):
if len(self.shape) < 3 or len(self.shape) > 4: if len(self.shape) < 3 or len(self.shape) > 4:
raise RuntimeError('Only 3D or 4D images are supported') 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): def loadData(self):
"""Loads the image data from the file. This method only needs to """Loads the image data from the file. This method only needs to
be called if the ``loadData`` parameter passed to :meth:`__init__` be called if the ``loadData`` parameter passed to :meth:`__init__`
...@@ -243,7 +179,7 @@ class Image(props.HasProperties): ...@@ -243,7 +179,7 @@ class Image(props.HasProperties):
log.debug('Loaded image data ({}) - original ' log.debug('Loaded image data ({}) - original '
'shape {}, squeezed shape {}'.format( 'shape {}, squeezed shape {}'.format(
self.name, self.dataSource,
shape, shape,
data.shape)) data.shape))
...@@ -252,58 +188,12 @@ class Image(props.HasProperties): ...@@ -252,58 +188,12 @@ class Image(props.HasProperties):
self.pixdim = self.pixdim[:len(data.shape)] self.pixdim = self.pixdim[:len(data.shape)]
def applyChange(self, offset, newVals, vol=None): # TODO: Remove this method, and use the shape attribute directly
"""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)
def is4DImage(self): def is4DImage(self):
"""Returns ``True`` if this image is 4D, ``False`` otherwise. """ """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): def getXFormCode(self, code=None):
"""This method returns the code contained in the NIFTI1 header, """This method returns the code contained in the NIFTI1 header,
indicating the space to which the (transformed) image is oriented. indicating the space to which the (transformed) image is oriented.
...@@ -372,7 +262,143 @@ class Image(props.HasProperties): ...@@ -372,7 +262,143 @@ class Image(props.HasProperties):
(constants.ORIENT_A2P, constants.ORIENT_P2A), (constants.ORIENT_A2P, constants.ORIENT_P2A),
(constants.ORIENT_S2I, constants.ORIENT_I2S)))[axis] (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 # TODO The wx.FileDialog does not
......
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