scipy#

dbdicom.wrappers.scipy.array(series, on=None, **kwargs)[source]#: Return the array overlaid on another series

dbdicom.wrappers.scipy.binary_fill_holes(input, **kwargs)[source]#

Fill holes in an existing segmentation.

Wrapper for scipy.ndimage.binary_fill_holes function.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.distance_transform_edt_3d(input, **kwargs)[source]#

Euclidian distance transform in 3D

Wrapper for scipy.ndimage.distance_transform_edt function.

Parameters:

input (dbdicom series) –
markers (dbdicom series of the same dimensions as series) –

Returns:

filtered

Return type:

dbdicom series

dbdicom.wrappers.scipy.extract_largest_cluster_3d(input, **kwargs)[source]#

Label structures in 3D and then extract the largest cluster, return as a mask.

Parameters:: input (dbdicom series) –
Return type:: dbdicom series

dbdicom.wrappers.scipy.fourier_ellipsoid(input, size, **kwargs)[source]#

wrapper for scipy.ndimage.fourier_ellipsoid

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.fourier_gaussian(input, sigma, **kwargs)[source]#

wrapper for scipy.ndimage.fourier_gaussian.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.fourier_shift(input, shift, **kwargs)[source]#

wrapper for scipy.ndimage.fourier_shift.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.fourier_uniform(input, size, **kwargs)[source]#

wrapper for scipy.ndimage.fourier_uniform

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.gaussian_filter(input, sigma, **kwargs)[source]#

wrapper for scipy.ndimage.gaussian_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.gaussian_filter_3d(input, sigma, **kwargs)[source]#

wrapper for scipy.ndimage.gaussian_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.gaussian_gradient_magnitude(input, sigma, **kwargs)[source]#

wrapper for scipy.ndimage.gaussian_gradient_magnitude.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.gaussian_laplace(input, sigma, **kwargs)[source]#

wrapper for scipy.ndimage.gaussian_laplace.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.image_calculator(series1, series2, operation='series 1 - series 2', integer=False)[source]#

dbdicom.wrappers.scipy.label_2d(input, **kwargs)[source]#

Labels structures in an image

Wrapper for scipy.ndimage.label function.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.label_3d(input, **kwargs)[source]#

Labels structures in a 3D volume

Wrapper for scipy.ndimage.label function.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.laplace(input, **kwargs)[source]#

wrapper for scipy.ndimage.sobel.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.map_to(source, target, **kwargs)[source]#: Map non-zero pixels onto another series

dbdicom.wrappers.scipy.mask_array(mask, on=None, dim='InstanceNumber')[source]#: Map non-zero pixels onto another series

dbdicom.wrappers.scipy.mask_curve_3d(masks, images, **kwargs)[source]#

dbdicom.wrappers.scipy.mask_statistics(masks, images)[source]#

dbdicom.wrappers.scipy.maximum_filter(input, size=3, **kwargs)[source]#

wrapper for scipy.ndimage.maximum_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.median_filter(input, size=3, **kwargs)[source]#

wrapper for scipy.ndimage.median_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.minimum_filter(input, size=3, **kwargs)[source]#

wrapper for scipy.ndimage.minimum_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.n_images_calculator(series, operation='mean')[source]#

dbdicom.wrappers.scipy.overlay(features)[source]#: Ensure all the features are in the same geometry as the reference feature

dbdicom.wrappers.scipy.percentile_filter(input, percentile, **kwargs)[source]#

wrapper for scipy.ndimage.percentile_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.prewitt_filter(input, axis=-1, **kwargs)[source]#

wrapper for scipy.ndimage.prewitt.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.rank_filter(input, rank, **kwargs)[source]#

wrapper for scipy.ndimage.rank_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.resample(series, voxel_size=[1.0, 1.0, 1.0])[source]#

dbdicom.wrappers.scipy.reslice(series, orientation='axial')[source]#

dbdicom.wrappers.scipy.series_calculator(series, operation='1 - series')[source]#

dbdicom.wrappers.scipy.sobel_filter(input, axis=-1, **kwargs)[source]#

wrapper for scipy.ndimage.sobel.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.uniform_filter(input, size=3, **kwargs)[source]#

wrapper for scipy.ndimage.uniform_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.uniform_filter_3d(input, size=3, **kwargs)[source]#

wrapper for scipy.ndimage.uniform_filter.

Parameters:: input (dbdicom series) –
Returns:: filtered
Return type:: dbdicom series

dbdicom.wrappers.scipy.zoom(input, zoom, **kwargs)[source]#

wrapper for scipy.ndimage.zoom.

Parameters:: input (dbdicom series) –
Returns:: zoomed
Return type:: dbdicom series