NiBabel

Access a cacophony of neuro-imaging file formats

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minc2

Reggie -- the one

minc1

Read MINC1 format images

Minc1File(mincfile) Class to wrap MINC1 format opened netcdf object
Minc1Image(dataobj, affine[, header, extra, ...]) Class for MINC1 format images
MincError Error when reading MINC files
MincFile(*args, **kwargs) Deprecated alternative name for Minc1File
MincHeader([data_dtype, shape, zooms]) Class to contain header for MINC formats
MincImage(*args, **kwargs) Deprecated alternative name for Minc1Image
MincImageArrayProxy(minc_file) 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:

sliceobj : tuple, optional

slice definition. If not specified, return whole array

Returns:

scaled_arr : array

array from minc file with scaling applied

get_zooms()

Get real-world sizes of voxels

Minc1Image

class nibabel.minc1.Minc1Image(dataobj, affine, header=None, extra=None, file_map=None)

Bases: nibabel.spatialimages.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, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters:

dataobj : object

Object containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affine : 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

__init__(dataobj, affine, header=None, extra=None, file_map=None)

Initialize image

The image is a combination of (array, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters:

dataobj : object

Object containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affine : 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

ImageArrayProxy

alias of MincImageArrayProxy

files_types = (('image', '.mnc'),)
classmethod from_file_map(klass, file_map)
header_class

alias of MincHeader

MincError

class nibabel.minc1.MincError

Bases: exceptions.Exception

Error when reading MINC files

__init__()

x.__init__(...) initializes x; see help(type(x)) for signature

MincFile

class nibabel.minc1.MincFile(*args, **kwargs)

Bases: nibabel.deprecated.FutureWarningMixin, nibabel.minc1.Minc1File

Deprecated alternative name for Minc1File

__init__(*args, **kwargs)
warn_message = 'MincFile is deprecated; please use Minc1File instead'

MincHeader

class nibabel.minc1.MincHeader(data_dtype=<type 'numpy.float32'>, shape=(0, ), zooms=None)

Bases: nibabel.spatialimages.Header

Class to contain header for MINC formats

__init__(data_dtype=<type 'numpy.float32'>, shape=(0, ), zooms=None)
data_from_fileobj(fileobj)

See Header class for an implementation we can’t use

data_layout = 'C'
data_to_fileobj(data, fileobj, rescale=True)

See Header class for an implementation we can’t use

MincImage

class nibabel.minc1.MincImage(*args, **kwargs)

Bases: nibabel.deprecated.FutureWarningMixin, nibabel.minc1.Minc1Image

Deprecated alternative name for Minc1Image

__init__(*args, **kwargs)
warn_message = 'MincImage is deprecated; please use Minc1Image instead'

MincImageArrayProxy

class nibabel.minc1.MincImageArrayProxy(minc_file)

Bases: object

MINC implementation of array proxy protocol

The array proxy allows us to freeze the passed fileobj and header such that it returns the expected data array.

__init__(minc_file)
is_proxy
shape