PREDICT.helpers package¶
Submodules¶
PREDICT.helpers.contour_functions module¶
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PREDICT.helpers.contour_functions.
cmp
(a, b)¶ Built in in python 2, but defined for python 3
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PREDICT.helpers.contour_functions.
convex_hull
(contour)¶ Returns points on convex hull for contour, uses Graham Scan
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PREDICT.helpers.contour_functions.
convex_hull_points
(points)¶ Returns points on convex hull of an array of points in CCW order. Uses Graham Scan
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PREDICT.helpers.contour_functions.
get_contour_boundary
(contour)¶ Labels pixels on edge of boundary
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PREDICT.helpers.contour_functions.
get_contour_boundary_points
(contour)¶ Get boundary coordinates from contour
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PREDICT.helpers.contour_functions.
get_not_voi_voxels
(contour, image)¶ Sets all voxels within VOI to 0
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PREDICT.helpers.contour_functions.
get_smooth_contour
(mask, N_min, N_max)¶ Find local convex hull for given contour
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PREDICT.helpers.contour_functions.
get_voi_voxels
(contour, image)¶ Gives back VOI (non-zero slices), and indices of slices
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PREDICT.helpers.contour_functions.
local_convex_hull
(contour, N_min, N_max)¶ Find local convex hull for given contour
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PREDICT.helpers.contour_functions.
local_convex_hull_points
(points, N_min, N_max)¶ Find local convex points, can be used for smoothing boundary
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PREDICT.helpers.contour_functions.
sort_points
(points)¶ Order supplied points in clockwise order
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PREDICT.helpers.contour_functions.
turn
(p, q, r)¶
PREDICT.helpers.contour_functions_3d module¶
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PREDICT.helpers.contour_functions_3d.
cmp
(a, b)¶ Built in in python 2, but defined for python 3
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PREDICT.helpers.contour_functions_3d.
convex_hull
(contour)¶ Returns points on convex hull for contour, uses Graham Scan
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PREDICT.helpers.contour_functions_3d.
convex_hull_points
(points)¶ Returns points on convex hull of an array of points in CCW order. Uses Graham Scan
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PREDICT.helpers.contour_functions_3d.
get_contour_boundary
(contour)¶ Labels pixels on edge of boundary
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PREDICT.helpers.contour_functions_3d.
get_contour_boundary_points
(contour)¶ Get boundary coordinates from contour
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PREDICT.helpers.contour_functions_3d.
get_not_voi_voxels
(contour, image)¶ Sets all voxels within VOI to 0
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PREDICT.helpers.contour_functions_3d.
get_smooth_contour
(mask, N_min, N_max)¶ Find local convex hull for given contour
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PREDICT.helpers.contour_functions_3d.
get_voi_voxels
(contour, image)¶ Gives back VOI (non-zero slices), and indices of slices
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PREDICT.helpers.contour_functions_3d.
local_convex_hull
(contour, N_min, N_max)¶ Find local convex hull for given contour
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PREDICT.helpers.contour_functions_3d.
local_convex_hull_points
(points, N_min, N_max)¶ Find local convex points, can be used for smoothing boundary
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PREDICT.helpers.contour_functions_3d.
sort_points
(points)¶ Order supplied points in clockwise order
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PREDICT.helpers.contour_functions_3d.
turn
(p, q, r)¶
PREDICT.helpers.image_helper module¶
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PREDICT.helpers.image_helper.
get_masked_slices_image
(image_array, mask_array)¶ For a 3-D array, get only those axial slices which contains non-zero numbers in the mask.
- image_array: numpy array, mandatory
- Array containing the array to be masked.
- mask_array: numpy array, mandatory
- Array containing the mask.
- image_array: numpy array, mandatory
- Array containing the masked image array.
- mask_array: numpy array, mandatory
- Array containing the masked mask array.
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PREDICT.helpers.image_helper.
get_masked_slices_mask
(mask_image)¶ Remove the axial slices in a 3-D mask array for which there are non-zero elements.
- mask_image: numpy array, mandatory
- Boolean 3D array.
- mask_sliced: numpy array, mandatory
- Array containing only those slices of which there are non-zero elements in the mask.
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PREDICT.helpers.image_helper.
get_masked_voxels
(image_array, mask_array)¶ Returns only those voxels of an array for which the mask array value is True.
- image_array: numpy array, mandatory
- Array containing the array to be masked.
- mask_array: numpy array, mandatory
- Array containing the mask.
- masked_voxels: numpy array
- 1D Array containing only those voxels for which the mask was True.
PREDICT.helpers.orientation_functions module¶
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PREDICT.helpers.orientation_functions.
data_regularize
(data, type='spheric', divs=10)¶
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PREDICT.helpers.orientation_functions.
ellipsoid_fit
(X)¶
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PREDICT.helpers.orientation_functions.
ellipsoid_plot
(center, radii, rotation, ax, plotAxes=False, cageColor='b', cageAlpha=0.2)¶ Plot an ellipsoid
PREDICT.helpers.sitk_helper module¶
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PREDICT.helpers.sitk_helper.
GetArrayFromImage
(image)¶ GetArrayFromImage converts an ITK image to a numpy array, while ensuring the orientation is kept the same.
- Args:
- image (ITK image): 2D or 3D ITK image
- Returns:
- numpy array
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PREDICT.helpers.sitk_helper.
GetImageFromArray
(array)¶ GetImageFromArray converts a numpy array to an ITK image, while ensuring the orientation is kept the same.
- Args:
- array (numpy array): 2D or 3D array of image
- Returns:
- ITK image