diff --git a/fsl/data/image.py b/fsl/data/image.py
index 3dda62827dec53ca10ec928cf5cbaea68875a5f0..7f235b8cb291acb14bb6b5cdf0d8e58b3f2e6001 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -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