minc1
¶
Read MINC1 format images
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Class to wrap MINC1 format opened netcdf object |
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Class for MINC1 format images |
Error when reading MINC files |
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Class to contain header for MINC formats |
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MINC implementation of array proxy protocol |
Minc1File
¶
- class nibabel.minc1.Minc1File(mincfile)¶
Bases:
object
Class to wrap MINC1 format opened netcdf object
Although it has some of the same methods as a
Header
, we use this only when reading a MINC file, to pull out useful header information, and for the method of reading the data out- __init__(mincfile)¶
- get_affine()¶
- get_data_dtype()¶
- get_data_shape()¶
- get_scaled_data(sliceobj=())¶
Return scaled data for slice definition sliceobj
- Parameters:
- sliceobjtuple, optional
slice definition. If not specified, return whole array
- Returns:
- scaled_arrarray
array from minc file with scaling applied
- get_zooms()¶
Get real-world sizes of voxels
Minc1Header
¶
- class nibabel.minc1.Minc1Header(data_dtype: npt.DTypeLike = <class 'numpy.float32'>, shape: Sequence[int] = (0, ), zooms: Sequence[float] | None = None)¶
Bases:
MincHeader
- __init__(data_dtype: npt.DTypeLike = <class 'numpy.float32'>, shape: Sequence[int] = (0, ), zooms: Sequence[float] | None = None)¶
- classmethod may_contain_header(binaryblock)¶
Minc1Image
¶
- class nibabel.minc1.Minc1Image(dataobj: ArrayLike, affine: np.ndarray | None, header: FileBasedHeader | ty.Mapping | None = None, extra: ty.Mapping | None = None, file_map: FileMap | None = None)¶
Bases:
SpatialImage
Class for MINC1 format images
The MINC1 image class uses the default header type, rather than a specific MINC header type - and reads the relevant information from the MINC file on load.
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:
- dataobjobject
Object containing image data. It should be some object that returns an array from
np.asanyarray
. It should have ashape
attribute or property- affineNone 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.- headerNone or mapping or header instance, optional
metadata for this image format
- extraNone or mapping, optional
metadata to associate with image that cannot be stored in the metadata of this image type
- file_mapmapping, optional
mapping giving file information for this image format
- __init__(dataobj: ArrayLike, affine: np.ndarray | None, header: FileBasedHeader | ty.Mapping | None = None, extra: ty.Mapping | None = None, file_map: FileMap | None = None)¶
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:
- dataobjobject
Object containing image data. It should be some object that returns an array from
np.asanyarray
. It should have ashape
attribute or property- affineNone 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.- headerNone or mapping or header instance, optional
metadata for this image format
- extraNone or mapping, optional
metadata to associate with image that cannot be stored in the metadata of this image type
- file_mapmapping, optional
mapping giving file information for this image format
- ImageArrayProxy¶
alias of
MincImageArrayProxy
- classmethod from_file_map(file_map, *, mmap=True, keep_file_open=None)¶
Class method to create image from mapping in
file_map
- Parameters:
- file_mapdict
Mapping with (key, value) pairs of (
file_type
, FileHolder instance giving file-likes for each file needed for this image type.- mmap{True, False, ‘c’, ‘r’}, optional, keyword only
mmap controls the use of numpy memory mapping for reading image array data. If False, do not try numpy
memmap
for data array. If one of {‘c’, ‘r’}, try numpy memmap withmode=mmap
. A mmap value of True gives the same behavior asmmap='c'
. If image data file cannot be memory-mapped, ignore mmap value and read array from file.- keep_file_open{ None, True, False }, optional, keyword only
keep_file_open controls whether a new file handle is created every time the image is accessed, or a single file handle is created and used for the lifetime of this
ArrayProxy
. IfTrue
, a single file handle is created and used. IfFalse
, a new file handle is created every time the image is accessed. Iffile_map
refers to an open file handle, this setting has no effect. The default value (None
) will result in the value ofnibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT
being used.
- Returns:
- imgDataobjImage instance
- header_class¶
alias of
Minc1Header
MincError
¶
MincHeader
¶
- class nibabel.minc1.MincHeader(data_dtype: npt.DTypeLike = <class 'numpy.float32'>, shape: Sequence[int] = (0, ), zooms: Sequence[float] | None = None)¶
Bases:
SpatialHeader
Class to contain header for MINC formats
- __init__(data_dtype: npt.DTypeLike = <class 'numpy.float32'>, shape: Sequence[int] = (0, ), zooms: Sequence[float] | None = None)¶
- data_from_fileobj(fileobj)¶
See Header class for an implementation we can’t use
- data_layout: Literal['F', 'C'] = 'C'¶
- data_to_fileobj(data, fileobj, rescale=True)¶
See Header class for an implementation we can’t use