mvpa2.misc.plot.lightbox.SpatialImage¶

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class
mvpa2.misc.plot.lightbox.
SpatialImage
(dataobj, affine, header=None, extra=None, file_map=None)¶ Template class for volumetric (3D/4D) images
Attributes
affine
dataobj
header
in_memory
True when any array data is in memory cache shape
Methods
as_reoriented
(ornt)Apply an orientation change and return a new image filespec_to_file_map
(klass, filespec)Make file_map
for this class from filenamefilespec
filespec_to_files
(*args, **kwargs)filespec_to_files class method is deprecated. from_file_map
(klass, file_map)from_filename
(klass, filename)from_files
(*args, **kwargs)from_files class method is deprecated. from_image
(klass, img)Class method to create new instance of own class from img
get_affine
(*args, **kwargs)Get affine from image get_data
([caching])Return image data from image with any necessary scaling applied get_data_dtype
()get_fdata
([caching, dtype])Return floating point image data with necessary scaling applied get_filename
()Fetch the image filename get_header
(*args, **kwargs)Get header from image get_shape
(*args, **kwargs)Return shape for image header_class
alias of SpatialHeader
instance_to_filename
(klass, img, filename)Save img
in our own format, to name implied byfilename
load
(klass, filename)make_file_map
(klass[, mapping])Class method to make files holder for this image type orthoview
()Plot the image using OrthoSlicer3D path_maybe_image
(klass, filename[, sniff, ...])Return True if filename
may be image matching this classset_data_dtype
(dtype)set_filename
(filename)Sets the files in the object from a given filename to_file_map
([file_map])to_filename
(filename)Write image to files implied by filename string to_files
(*args, **kwargs)to_files method is deprecated. to_filespec
(*args, **kwargs)to_filespec method is deprecated. uncache
()Delete any cached read of data from proxied data update_header
()Harmonize header with image data and affine Initialize image
The image is a combination of (array-like, affine matrix, header), with optional metadata in
extra
, and filename / file-like objects contained in thefile_map
mapping.Parameters: dataobj : object
Object containg image data. It should be some object that retuns an array from
np.asanyarray
. It should have ashape
attribute or propertyaffine : None or (4,4) array-like
homogenous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case,
obj.affine
also returns None, and the affine as written to disk will depend on the file format.header : None or mapping or header instance, optional
metadata for this image format
extra : None or mapping, optional
metadata to associate with image that cannot be stored in the metadata of this image type
file_map : mapping, optional
mapping giving file information for this image format
Attributes
affine
dataobj
header
in_memory
True when any array data is in memory cache shape
Methods
as_reoriented
(ornt)Apply an orientation change and return a new image filespec_to_file_map
(klass, filespec)Make file_map
for this class from filenamefilespec
filespec_to_files
(*args, **kwargs)filespec_to_files class method is deprecated. from_file_map
(klass, file_map)from_filename
(klass, filename)from_files
(*args, **kwargs)from_files class method is deprecated. from_image
(klass, img)Class method to create new instance of own class from img
get_affine
(*args, **kwargs)Get affine from image get_data
([caching])Return image data from image with any necessary scaling applied get_data_dtype
()get_fdata
([caching, dtype])Return floating point image data with necessary scaling applied get_filename
()Fetch the image filename get_header
(*args, **kwargs)Get header from image get_shape
(*args, **kwargs)Return shape for image header_class
alias of SpatialHeader
instance_to_filename
(klass, img, filename)Save img
in our own format, to name implied byfilename
load
(klass, filename)make_file_map
(klass[, mapping])Class method to make files holder for this image type orthoview
()Plot the image using OrthoSlicer3D path_maybe_image
(klass, filename[, sniff, ...])Return True if filename
may be image matching this classset_data_dtype
(dtype)set_filename
(filename)Sets the files in the object from a given filename to_file_map
([file_map])to_filename
(filename)Write image to files implied by filename string to_files
(*args, **kwargs)to_files method is deprecated. to_filespec
(*args, **kwargs)to_filespec method is deprecated. uncache
()Delete any cached read of data from proxied data update_header
()Harmonize header with image data and affine -
affine
¶
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as_reoriented
(ornt)¶ Apply an orientation change and return a new image
If ornt is identity transform, return the original image, unchanged
Parameters: ornt : (n,2) orientation array
orientation transform.
ornt[N,1]` is flip of axis N of the array implied by `shape`, where 1 means no flip and -1 means flip. For example, if ``N==0
andornt[0,1] == -1
, and there’s an arrayarr
of shapeshape
, the flip would correspond to the effect ofnp.flipud(arr)
.ornt[:,0]
is the transpose that needs to be done to the implied array, as inarr.transpose(ornt[:,0])
Notes
Subclasses should override this if they have additional requirements when re-orienting an image.
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classmethod
from_image
(klass, img)¶ Class method to create new instance of own class from
img
Parameters: img :
spatialimage
instanceIn fact, an object with the API of
spatialimage
- specificallydataobj
,affine
,header
andextra
.Returns: cimg :
spatialimage
instanceImage, of our own class
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get_affine
(*args, **kwargs)¶ Get affine from image
get_affine method is deprecated. Please use the
img.affine
property instead.- deprecated from version: 2.1
- Will raise <class ‘nibabel.deprecator.ExpiredDeprecationError’> as of version: 4.0
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get_data_dtype
()¶
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header_class
¶ alias of
SpatialHeader
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orthoview
()¶ Plot the image using OrthoSlicer3D
Returns: viewer : instance of OrthoSlicer3D
The viewer.
Notes
This requires matplotlib. If a non-interactive backend is used, consider using viewer.show() (equivalently plt.show()) to show the figure.
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set_data_dtype
(dtype)¶
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update_header
()¶ Harmonize header with image data and affine
>>> data = np.zeros((2,3,4)) >>> affine = np.diag([1.0,2.0,3.0,1.0]) >>> img = SpatialImage(data, affine) >>> img.shape == (2, 3, 4) True >>> img.update_header() >>> img.header.get_data_shape() == (2, 3, 4) True >>> img.header.get_zooms() (1.0, 2.0, 3.0)
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