spm99analyze

Read / write access to SPM99 version of analyze image format

Spm99AnalyzeHeader([binaryblock, …])

Class for SPM99 variant of basic Analyze header

Spm99AnalyzeImage(dataobj, affine[, header, …])

Class for SPM99 variant of basic Analyze image

SpmAnalyzeHeader([binaryblock, endianness, …])

Basic scaling Spm Analyze header

Spm99AnalyzeHeader

class nibabel.spm99analyze.Spm99AnalyzeHeader(binaryblock=None, endianness=None, check=True)

Bases: nibabel.spm99analyze.SpmAnalyzeHeader

Class for SPM99 variant of basic Analyze header

SPM99 variant adds the following to basic Analyze format:

  • voxel origin;

  • slope scaling of data.

Initialize header from binary data block

Parameters
binaryblock{None, string} optional

binary block to set into header. By default, None, in which case we insert the default empty header block

endianness{None, ‘<’,’>’, other endian code} string, optional

endianness of the binaryblock. If None, guess endianness from the data.

checkbool, optional

Whether to check content of header in initialization. Default is True.

Examples

>>> hdr1 = AnalyzeHeader() # an empty header
>>> hdr1.endianness == native_code
True
>>> hdr1.get_data_shape()
(0,)
>>> hdr1.set_data_shape((1,2,3)) # now with some content
>>> hdr1.get_data_shape()
(1, 2, 3)

We can set the binary block directly via this initialization. Here we get it from the header we have just made

>>> binblock2 = hdr1.binaryblock
>>> hdr2 = AnalyzeHeader(binblock2)
>>> hdr2.get_data_shape()
(1, 2, 3)

Empty headers are native endian by default

>>> hdr2.endianness == native_code
True

You can pass valid opposite endian headers with the endianness parameter. Even empty headers can have endianness

>>> hdr3 = AnalyzeHeader(endianness=swapped_code)
>>> hdr3.endianness == swapped_code
True

If you do not pass an endianness, and you pass some data, we will try to guess from the passed data.

>>> binblock3 = hdr3.binaryblock
>>> hdr4 = AnalyzeHeader(binblock3)
>>> hdr4.endianness == swapped_code
True
__init__(binaryblock=None, endianness=None, check=True)

Initialize header from binary data block

Parameters
binaryblock{None, string} optional

binary block to set into header. By default, None, in which case we insert the default empty header block

endianness{None, ‘<’,’>’, other endian code} string, optional

endianness of the binaryblock. If None, guess endianness from the data.

checkbool, optional

Whether to check content of header in initialization. Default is True.

Examples

>>> hdr1 = AnalyzeHeader() # an empty header
>>> hdr1.endianness == native_code
True
>>> hdr1.get_data_shape()
(0,)
>>> hdr1.set_data_shape((1,2,3)) # now with some content
>>> hdr1.get_data_shape()
(1, 2, 3)

We can set the binary block directly via this initialization. Here we get it from the header we have just made

>>> binblock2 = hdr1.binaryblock
>>> hdr2 = AnalyzeHeader(binblock2)
>>> hdr2.get_data_shape()
(1, 2, 3)

Empty headers are native endian by default

>>> hdr2.endianness == native_code
True

You can pass valid opposite endian headers with the endianness parameter. Even empty headers can have endianness

>>> hdr3 = AnalyzeHeader(endianness=swapped_code)
>>> hdr3.endianness == swapped_code
True

If you do not pass an endianness, and you pass some data, we will try to guess from the passed data.

>>> binblock3 = hdr3.binaryblock
>>> hdr4 = AnalyzeHeader(binblock3)
>>> hdr4.endianness == swapped_code
True
get_best_affine()

Get affine from header, using SPM origin field if sensible

The default translations are got from the origin field, if set, or from the center of the image otherwise.

Examples

>>> hdr = Spm99AnalyzeHeader()
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.set_zooms((3, 2, 1))
>>> hdr.default_x_flip
True
>>> hdr.get_origin_affine() # from center of image
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
>>> hdr['origin'][:3] = [3,4,5]
>>> hdr.get_origin_affine() # using origin
array([[-3.,  0.,  0.,  6.],
       [ 0.,  2.,  0., -6.],
       [ 0.,  0.,  1., -4.],
       [ 0.,  0.,  0.,  1.]])
>>> hdr['origin'] = 0 # unset origin
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.get_origin_affine() # from center of image
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
get_origin_affine()

Get affine from header, using SPM origin field if sensible

The default translations are got from the origin field, if set, or from the center of the image otherwise.

Examples

>>> hdr = Spm99AnalyzeHeader()
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.set_zooms((3, 2, 1))
>>> hdr.default_x_flip
True
>>> hdr.get_origin_affine() # from center of image
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
>>> hdr['origin'][:3] = [3,4,5]
>>> hdr.get_origin_affine() # using origin
array([[-3.,  0.,  0.,  6.],
       [ 0.,  2.,  0., -6.],
       [ 0.,  0.,  1., -4.],
       [ 0.,  0.,  0.,  1.]])
>>> hdr['origin'] = 0 # unset origin
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.get_origin_affine() # from center of image
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
set_origin_from_affine(affine)

Set SPM origin to header from affine matrix.

The origin field was read but not written by SPM99 and 2. It was used for storing a central voxel coordinate, that could be used in aligning the image to some standard position - a proxy for a full translation vector that was usually stored in a separate matlab .mat file.

Nifti uses the space occupied by the SPM origin field for important other information (the transform codes), so writing the origin will make the header a confusing Nifti file. If you work with both Analyze and Nifti, you should probably avoid doing this.

Parameters
affinearray-like, shape (4,4)

Affine matrix to set

Returns
None

Examples

>>> hdr = Spm99AnalyzeHeader()
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.set_zooms((3,2,1))
>>> hdr.get_origin_affine()
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
>>> affine = np.diag([3,2,1,1])
>>> affine[:3,3] = [-6, -6, -4]
>>> hdr.set_origin_from_affine(affine)
>>> np.all(hdr['origin'][:3] == [3,4,5])
True
>>> hdr.get_origin_affine()
array([[-3.,  0.,  0.,  6.],
       [ 0.,  2.,  0., -6.],
       [ 0.,  0.,  1., -4.],
       [ 0.,  0.,  0.,  1.]])

Spm99AnalyzeImage

class nibabel.spm99analyze.Spm99AnalyzeImage(dataobj, affine, header=None, extra=None, file_map=None)

Bases: nibabel.analyze.AnalyzeImage

Class for SPM99 variant of basic Analyze image

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

affineNone 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.

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, affine, header=None, extra=None, file_map=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 containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affineNone 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.

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

files_types = (('image', '.img'), ('header', '.hdr'), ('mat', '.mat'))
classmethod from_file_map(file_map, mmap=True, keep_file_open=None)

Class method to create image from mapping in file_map

Deprecated since version 2.4.1: keep_file_open='auto' is redundant with False and has been deprecated. It will raise an error in nibabel 3.0.

Parameters
file_mapdict

Mapping with (kay, 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 with mode=mmap. A mmap value of True gives the same behavior as mmap='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. If True, a single file handle is created and used. If False, a new file handle is created every time the image is accessed. If file_map refers to an open file handle, this setting has no effect. The default value (None) will result in the value of nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT being used.

Returns
imgSpm99AnalyzeImage instance
has_affine = True
header_class

alias of Spm99AnalyzeHeader

makeable = True
rw = True
to_file_map(file_map=None)

Write image to file_map or contained self.file_map

Extends Analyze to_file_map method by writing mat file

Parameters
file_mapNone or mapping, optional

files mapping. If None (default) use object’s file_map attribute instead

SpmAnalyzeHeader

class nibabel.spm99analyze.SpmAnalyzeHeader(binaryblock=None, endianness=None, check=True)

Bases: nibabel.analyze.AnalyzeHeader

Basic scaling Spm Analyze header

Initialize header from binary data block

Parameters
binaryblock{None, string} optional

binary block to set into header. By default, None, in which case we insert the default empty header block

endianness{None, ‘<’,’>’, other endian code} string, optional

endianness of the binaryblock. If None, guess endianness from the data.

checkbool, optional

Whether to check content of header in initialization. Default is True.

Examples

>>> hdr1 = AnalyzeHeader() # an empty header
>>> hdr1.endianness == native_code
True
>>> hdr1.get_data_shape()
(0,)
>>> hdr1.set_data_shape((1,2,3)) # now with some content
>>> hdr1.get_data_shape()
(1, 2, 3)

We can set the binary block directly via this initialization. Here we get it from the header we have just made

>>> binblock2 = hdr1.binaryblock
>>> hdr2 = AnalyzeHeader(binblock2)
>>> hdr2.get_data_shape()
(1, 2, 3)

Empty headers are native endian by default

>>> hdr2.endianness == native_code
True

You can pass valid opposite endian headers with the endianness parameter. Even empty headers can have endianness

>>> hdr3 = AnalyzeHeader(endianness=swapped_code)
>>> hdr3.endianness == swapped_code
True

If you do not pass an endianness, and you pass some data, we will try to guess from the passed data.

>>> binblock3 = hdr3.binaryblock
>>> hdr4 = AnalyzeHeader(binblock3)
>>> hdr4.endianness == swapped_code
True
__init__(binaryblock=None, endianness=None, check=True)

Initialize header from binary data block

Parameters
binaryblock{None, string} optional

binary block to set into header. By default, None, in which case we insert the default empty header block

endianness{None, ‘<’,’>’, other endian code} string, optional

endianness of the binaryblock. If None, guess endianness from the data.

checkbool, optional

Whether to check content of header in initialization. Default is True.

Examples

>>> hdr1 = AnalyzeHeader() # an empty header
>>> hdr1.endianness == native_code
True
>>> hdr1.get_data_shape()
(0,)
>>> hdr1.set_data_shape((1,2,3)) # now with some content
>>> hdr1.get_data_shape()
(1, 2, 3)

We can set the binary block directly via this initialization. Here we get it from the header we have just made

>>> binblock2 = hdr1.binaryblock
>>> hdr2 = AnalyzeHeader(binblock2)
>>> hdr2.get_data_shape()
(1, 2, 3)

Empty headers are native endian by default

>>> hdr2.endianness == native_code
True

You can pass valid opposite endian headers with the endianness parameter. Even empty headers can have endianness

>>> hdr3 = AnalyzeHeader(endianness=swapped_code)
>>> hdr3.endianness == swapped_code
True

If you do not pass an endianness, and you pass some data, we will try to guess from the passed data.

>>> binblock3 = hdr3.binaryblock
>>> hdr4 = AnalyzeHeader(binblock3)
>>> hdr4.endianness == swapped_code
True
classmethod default_structarr(endianness=None)

Create empty header binary block with given endianness

get_slope_inter()

Get scalefactor and intercept

If scalefactor is 0.0 return None to indicate no scalefactor. Intercept is always None because SPM99 analyze cannot store intercepts.

has_data_intercept = False
has_data_slope = True
set_slope_inter(slope, inter=None)

Set slope and / or intercept into header

Set slope and intercept for image data, such that, if the image data is arr, then the scaled image data will be (arr * slope) + inter

The SPM Analyze header can’t save an intercept value, and we raise an error unless inter is None, NaN or 0

Parameters
slopeNone or float

If None, implies slope of NaN. NaN is a signal to the image writing routines to rescale on save. 0, Inf, -Inf are invalid and cause a HeaderDataError

interNone or float, optional

intercept. Must be None, NaN or 0, because SPM99 cannot store intercepts.

template_dtype = dtype([('sizeof_hdr', '<i4'), ('data_type', 'S10'), ('db_name', 'S18'), ('extents', '<i4'), ('session_error', '<i2'), ('regular', 'S1'), ('hkey_un0', 'S1'), ('dim', '<i2', (8,)), ('vox_units', 'S4'), ('cal_units', 'S8'), ('unused1', '<i2'), ('datatype', '<i2'), ('bitpix', '<i2'), ('dim_un0', '<i2'), ('pixdim', '<f4', (8,)), ('vox_offset', '<f4'), ('scl_slope', '<f4'), ('funused2', '<f4'), ('funused3', '<f4'), ('cal_max', '<f4'), ('cal_min', '<f4'), ('compressed', '<i4'), ('verified', '<i4'), ('glmax', '<i4'), ('glmin', '<i4'), ('descrip', 'S80'), ('aux_file', 'S24'), ('orient', 'S1'), ('origin', '<i2', (5,)), ('generated', 'S10'), ('scannum', 'S10'), ('patient_id', 'S10'), ('exp_date', 'S10'), ('exp_time', 'S10'), ('hist_un0', 'S3'), ('views', '<i4'), ('vols_added', '<i4'), ('start_field', '<i4'), ('field_skip', '<i4'), ('omax', '<i4'), ('omin', '<i4'), ('smax', '<i4'), ('smin', '<i4')])