Voxel Array

Purpose

This class is creates a 3D array of voxels. It is used to create your phantom from various shapes and materials.

Properties

array_position: (3x1 double) The position of the top left corner of the voxel array in the world coordinate system.

num_planes: (3x1 double) The number of planes in the voxel array.

dimensions: (3x1 double) The dimensions of each voxel in the voxel array.

voxel_objs: (1xN cell) A cell array of all the voxel objects in the voxel array (see Voxel Objects).

nobj: (double) The number of voxel objects in the array, equivalent to length(voxel_objs) + 1. The last element is the world material.

world_material: (material_attenuation) The material of the world in the array that is not occupied by any voxel objects.

Functions

voxel_array(centre, object_dims, voxel_size, voxel_objs, world_material=material_attenuation("air"))

The constructor for the voxel array. The arguments are as follows:

Parameters:

centre (3x1 double) – The position of the centre of the array in the world coordinate system. Used to calculate the position of the top left corner of the array.
object_dims (3x1 double) – The dimensions of the array in the x, y and z directions.
voxel_size (double) – The dimensions of each voxel in the array in the x, y and z directions, currently must be the same for all voxels, so is given as a single number.
voxel_objs (voxel_object cell array) – A cell array of all the voxel objects in the array (see Voxel Objects).
world_material (material_attenuation) – The material of the world in the array that is not occupied by any voxel objects, defaults to air.

Returns:

Voxel array – An instance of the voxel array class.

Return type:

voxel_array

Methods

update_voxel_size(obj, new_voxel_size)

Updates the voxel size of the array to new_voxel_size by changing the number of planes and the dimensions of the array.

Parameters:: new_voxel_size (double) – The new dimensions of each voxel in the array in the x, y and z directions.
Returns:: Voxel array – An instance of the voxel array class with the updated voxel size.
Return type:: voxel_array

precalculate_mus(obj, nrj_arr)

Pre-calculates the linear attenuation coefficient for each voxel object in voxel_objs for each energy in nrjs.

Parameters:: nrj_arr – An array of energies in keV. This is an n-Dimensional array of energies, the output is the same shape as the input.
Returns:: mu_dict – A PxMxN double with the first dimension representing the index of the voxel object in your array, the other dimensions are the same as the input nrj_arr. The values are the linear attenuation coefficients for each voxel object in voxel_objs at each energy in nrj_arr. P is the number of voxel objects + 1, the last element is the linear attenuation coefficient of the world material.
Return type:: PxMxN double

precalculate_mfps(obj, nrj_arr)

Pre-calculates the Compton mean free path for each voxel object in voxel_objs for each energy in nrjs.

Parameters:: nrj_arr – An array of energies in keV. This is an n-Dimensional array of energies, the output is the same shape as the input.
Returns:: mfp_dict – A PxMxN double with the first dimension representing the index of the voxel object in your array, the other dimensions are the same as the input nrj_arr. The values are the Compton mean free paths for each voxel object in voxel_objs at each energy in nrj_arr. P is the number of voxel objects + 1, the last element is the Compton mean free path of the world material.
Return type:: PxMxN double

get_object_idxs(obj, indices)

Obtain the indices of the voxel objects at the indices in indices.

Parameters:: indices (3xN double) – List of indices of voxels to obtain which voxel object they belong to.
Returns:: iobj – A 1xN array of the identifiers of the voxel objects at the indices in indices. This is used along with the output of precalculate_mus() and precalculate_mfps() to obtain the linear attenuation coefficients and Compton mean free paths at the indices in indices.
Return type:: 1xN double

get_mu_arr(obj, nrj)

Obtain all the linear attenuation coefficients for each voxel object in voxel_objs at the energy nrj.

Parameters:: nrj (double) – The photon energy (in \(keV\)).
Returns:: mu_arr – A 1D array of the linear attenuation coefficients for each voxel object in voxel_objs at the energy nrj.
Return type:: 1xN double

get_mfp_arr(obj, nrj)

Obtain all the Compton mean free paths for each voxel object in voxel_objs at the energy nrj.

Parameters:: nrj (double) – The energy in keV.
Returns:: mfp_arr – A 1D array of the Compton mean free paths for each voxel object in voxel_objs at the energy nrj.
Return type:: 1xN double

get_saved_mu(obj, indices, dict)

Obtain the linear attenuation coefficients at the indices in indices from the list of linear attenuation coefficients in dict.

Parameters:

indices (3xN double) – List of indices of voxels to obtain the linear attenuation coefficients for.
dict (double) – A list of linear attenuation coefficients, as returned by a single energy from the dictionary returned by precalculate_mus().

Returns:

mus – A 1D array of the linear attenuation coefficients at the indices in indices. It is the same length as the number of indices in indices.

Return type:

1xN double

get_saved_mfp(obj, indices, dict)

Obtain the Compton mean free paths at the indices in indices from the list of Compton mean free paths in dict.

Parameters:

indices (3xN double) – List of indices of voxels to obtain the Compton mean free paths for.
dict (double) – A list of Compton mean free paths, as returned by a single energy from the dictionary returned by precalculate_mfps().

Returns:

mfps - A 1D array of the Compton mean free paths at the indices in indices. It is the same length as the number of indices in indices.

Return type:

1xN double