ants.utils package

Submodules

ants.utils.bias_correction module

ants.utils.channels module

ants.utils.channels.merge_channels(image_list, channels_first=False)[source]

Merge channels of multiple scalar ANTsImage types into one multi-channel ANTsImage

ANTsR function: mergeChannels

Parameters:

image_list (list/tuple of ANTsImage python:types) – scalar images to merge

Return type:

ANTsImage

Example

>>> import ants
>>> image = ants.image_read(ants.get_ants_data('r16'))
>>> image2 = ants.image_read(ants.get_ants_data('r16'))
>>> image3 = ants.merge_channels([image,image2])
>>> image3 = ants.merge_channels([image,image2], channels_first=True)
>>> image3.numpy()
>>> image3.components == 2
ants.utils.channels.split_channels(image)[source]

Split channels of a multi-channel ANTsImage into a collection of scalar ANTsImage types

Parameters:

image (ANTsImage) – multi-channel image to split

Return type:

list of ANTsImage types

Example

>>> import ants
>>> image = ants.image_read(ants.get_ants_data('r16'), 'float')
>>> image2 = ants.image_read(ants.get_ants_data('r16'), 'float')
>>> imagemerge = ants.merge_channels([image,image2])
>>> imagemerge.components == 2
>>> images_unmerged = ants.split_channels(imagemerge)
>>> len(images_unmerged) == 2
>>> images_unmerged[0].components == 1

ants.utils.convert_nibabel module

ants.utils.crop_image module

ants.utils.denoise_image module

ants.utils.get_ants_data module

Get local ANTsPy data

ants.utils.get_ants_data.get_ants_data(file_id=None, target_file_name=None, antsx_cache_directory=None)

Get ANTsPy test data file

ANTsR function: getANTsRData

Parameters:

name (string) –

name of test image tag to retrieve Options:

  • ’r16’

  • ’r27’

  • ’r30’

  • ’r62’

  • ’r64’

  • ’r85’

  • ’ch2’

  • ’mni’

  • ’surf’

  • ’pcasl’

Returns:

filepath of test image

Return type:

string

Example

>>> import ants
>>> mnipath = ants.get_ants_data('mni')
ants.utils.get_ants_data.get_data(file_id=None, target_file_name=None, antsx_cache_directory=None)[source]

Get ANTsPy test data file

ANTsR function: getANTsRData

Parameters:

name (string) –

name of test image tag to retrieve Options:

  • ’r16’

  • ’r27’

  • ’r30’

  • ’r62’

  • ’r64’

  • ’r85’

  • ’ch2’

  • ’mni’

  • ’surf’

  • ’pcasl’

Returns:

filepath of test image

Return type:

string

Example

>>> import ants
>>> mnipath = ants.get_ants_data('mni')

ants.utils.get_centroids module

ants.utils.get_mask module

ants.utils.get_neighborhood module

ants.utils.iMath module

ants.utils.image_similarity module

ants.utils.image_to_cluster_images module

ants.utils.impute module

ants.utils.label_clusters module

ants.utils.label_image_centroids module

ants.utils.label_stats module

ants.utils.labels_to_matrix module

ants.utils.mask_image module

ants.utils.mni2tal module

ants.utils.mni2tal.mni2tal(xin)[source]

mni2tal for converting from ch2/mni space to tal - very approximate.

This is a standard approach but it’s not very accurate.

ANTsR function: mni2tal

Parameters:

xin (tuple) – point in mni152 space.

Return type:

tuple

Example

>>> import ants
>>> ants.mni2tal( (10,12,14) )

References

http://bioimagesuite.yale.edu/mni2tal/501_95733_More%20Accurate%20Talairach%20Coordinates%20SLIDES.pdf http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

ants.utils.morphology module

ants.utils.multi_label_morphology module

ants.utils.ndimage_to_list module

ants.utils.ndimage_to_list.list_to_ndimage(image, image_list)[source]

Merge list of multiple scalar ANTsImage types of dimension into one ANTsImage of dimension plus one

ANTsR function: mergeListToNDImage

Parameters:

  • image (target image space) –

  • image_list (list/tuple of ANTsImage python:types) – scalar images to merge into target image space

Return type:

ANTsImage

Example

>>> import ants
>>> image = ants.image_read(ants.get_ants_data('r16'))
>>> image2 = ants.image_read(ants.get_ants_data('r16'))
>>> imageTar = ants.make_image( ( *image2.shape, 2 ) )
>>> image3 = ants.list_to_ndimage( imageTar, [image,image2])
>>> image3.dimension == 3
ants.utils.ndimage_to_list.ndimage_to_list(image)[source]

Split a n dimensional ANTsImage into a list of n-1 dimensional ANTsImages

Parameters:

image (ANTsImage) – n-dimensional image to split

Return type:

list of ANTsImage types

Example

>>> import ants
>>> image = ants.image_read(ants.get_ants_data('r16'))
>>> image2 = ants.image_read(ants.get_ants_data('r16'))
>>> imageTar = ants.make_image( ( *image2.shape, 2 ) )
>>> image3 = ants.list_to_ndimage( imageTar, [image,image2])
>>> image3.dimension == 3
>>> images_unmerged = ants.ndimage_to_list( image3 )
>>> len(images_unmerged) == 2
>>> images_unmerged[0].dimension == 2

ants.utils.pad_image module

ants.utils.process_args module

ants.utils.quantile module

ants.utils.scalar_rgb_vector module

ants.utils.scalar_rgb_vector.rgb_to_vector(image)[source]

Convert an RGB ANTsImage to a Vector ANTsImage

Parameters:

image (ANTsImage) – RGB image to be converted

Return type:

ANTsImage

Example

>>> import ants
>>> mni = ants.image_read(ants.get_data('mni'))
>>> mni_rgb = ants.scalar_to_rgb(mni)
>>> mni_vector = mni.rgb_to_vector()
>>> mni_rgb2 = mni.vector_to_rgb()
ants.utils.scalar_rgb_vector.scalar_to_rgb(image, mask=None, filename=None, cmap='red', custom_colormap_file=None, min_input=None, max_input=None, min_rgb_output=None, max_rgb_output=None, vtk_lookup_table=None)[source]

Usage: ConvertScalarImageToRGB imageDimension inputImage outputImage mask colormap [customColormapFile] [minimumInput] [maximumInput] [minimumRGBOutput=0] [maximumRGBOutput=255] <vtkLookupTable> Possible colormaps: grey, red, green, blue, copper, jet, hsv, spring, summer, autumn, winter, hot, cool, overunder, custom

Example

>>> import ants
>>> img = ants.image_read(ants.get_data('r16'))
>>> img_color = ants.scalar_to_rgb(img, cmap='jet')
ants.utils.scalar_rgb_vector.vector_to_rgb(image)[source]

Convert an Vector ANTsImage to a RGB ANTsImage

Parameters:

image (ANTsImage) – RGB image to be converted

Return type:

ANTsImage

Example

>>> import ants
>>> img = ants.image_read(ants.get_data('r16'), pixeltype='unsigned char')
>>> img_rgb = ants.scalar_to_rgb(img.clone())
>>> img_vec = img_rgb.rgb_to_vector()
>>> img_rgb2 = img_vec.vector_to_rgb()

ants.utils.slice_image module

ants.utils.smooth_image module

ants.utils.threshold_image module

ants.utils.sitk_to_ants module

ants.utils.sitk_to_ants.from_sitk(sitk_image: SimpleITK.Image) → ANTsImage[source]

Converts a SimpleITK image into an ANTsPy image. Requires SimpleITK.

Parameters:

sitk_image (SimpleITK.Image) – The SimpleITK image to convert.

Returns:

ants_image – The converted ANTsPy image.

Return type:

ANTsImage

Raises:

ValueError – If the image dimensionality is unsupported.

Examples

>>> import SimpleITK as sitk
>>> import ants
>>> img = sitk.ReadImage('brain.nii.gz')
>>> ants_img = from_sitk(img)
ants.utils.sitk_to_ants.to_sitk(ants_image: ANTsImage) → SimpleITK.Image[source]

Converts an ANTsPy image into a SimpleITK image. Requires SimpleITK.

Parameters:

ants_image (ANTsImage) – The ANTsPy image to convert.

Returns:

sitk_image – The converted SimpleITK image.

Return type:

SimpleITK.Image

Raises:

ValueError – If the image dimensionality is unsupported.

Examples

>>> import ants
>>> ants_img = ants.image_read('brain.nii.gz')
>>> sitk_img = ants.to_sitk(ants_img)
… automodule:: ants.utils.ants_to_sitk
members:

undoc-members:

show-inheritance:

ants.utils.weingarten_image_curvature module

Module contents