Template class for volumetric (3D/4D) images
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 filename filespec |
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 by filename |
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 class |
set_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 the file_map mapping.
Parameters: | dataobj : object
affine : None or (4,4) array-like
header : None or mapping or header instance, optional
extra : None or mapping, optional
file_map : mapping, optional
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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 filename filespec |
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 by filename |
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 class |
set_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 |
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
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Notes
Subclasses should override this if they have additional requirements when re-orienting an image.
Class method to create new instance of own class from img
Parameters: | img : spatialimage instance
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Returns: | cimg : spatialimage instance
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Get affine from image
get_affine method is deprecated. Please use the img.affine property instead.
alias of SpatialHeader
Plot the image using OrthoSlicer3D
Returns: | viewer : instance of OrthoSlicer3D
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Notes
This requires matplotlib. If a non-interactive backend is used, consider using viewer.show() (equivalently plt.show()) to show the figure.
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)