modelarrayio.utils.mif_image.MifImage

class modelarrayio.utils.mif_image.MifImage(dataobj, affine, header=None, extra=None, file_map=None)[source]

Nibabel-style image class for MIF (.mif / .mif.gz) files.

Supports reading and writing the MRtrix Image Format, including gzip compression. The public API mirrors standard nibabel images:

img = MifImage.load('image.mif')
data = img.get_fdata()
affine = img.affine

new_img = MifImage(data, affine)
new_img.to_filename('output.mif')
new_img.to_filename('output.mif.gz')

The MIF layout field (e.g. -0,-1,+2) describes which axis varies fastest on disk and in which direction. get_fdata() always returns a C-contiguous array indexed as data[x, y, z, ...] regardless of the on-disk layout.

__init__(dataobj, affine, header=None, extra=None, file_map=None)[source]

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) – Object containing image data. It should be some object that returns an array from np.asanyarray. It should have a shape attribute or property
affine (None or (4,4) array-like) – homogeneous 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

Methods

`__init__`(dataobj, affine[, header, extra, ...])	Initialize image
`as_reoriented`(ornt)	Apply an orientation change and return a new image
`filespec_to_file_map`(filespec)	Make file_map for this class from filename filespec
`from_file_map`(file_map, *[, mmap, ...])	Load a MIF image from a nibabel file_map dict.
`from_filename`(filename, *[, mmap, ...])	Class method to create image from filename filename
`from_image`(img)	Class method to create new instance of own class from img
`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
`instance_to_filename`(img, filename)	Save img in our own format, to name implied by filename
`load`(filename, *[, mmap, keep_file_open])	Class method to create image from filename filename
`make_file_map`([mapping])	Class method to make files holder for this image type
`orthoview`()	Plot the image using OrthoSlicer3D
`path_maybe_image`(filename[, sniff, sniff_max])	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, dtype])	Save the image to the files described by file_map.
`to_filename`(filename, **kwargs)	Write image to files implied by filename string
`uncache`()	Delete any cached read of data from proxied data
`update_header`()	Harmonize header with image data and affine

Attributes

`affine`
`dataobj`
`files_types`
`header`
`in_memory`	True when any array data is in memory cache
`makeable`
`ndim`
`rw`
`shape`
`slicer`	Slicer object that returns cropped and subsampled images
`valid_exts`