Procedures

ProcedureLocationProcedure TypeDescription
abs vector_class Interface

Overload of the abs intrinsic for a vec3
abs_vec vector_class Function

Calculate the absoulte of a vector elementwise
alloc_array setupMod Subroutine

subroutine allocates allocatable arrays

annulus photonMod Subroutine

annular source
annulus_dect detectors Interface
aperture photonMod Subroutine

sample from square aperture to produce diff pattern
bend sdfModifiers Interface
bend_init sdfModifiers Function

Initialise the Bend modifier for a SDF.
box sdfs Interface

Interface to box SDF initialising function
box_init sdfs Function

Initalising function for Box SDF.
calcNormal sdf_baseMod Function

Calculate the surface normal of a SDF at the point p numerically.
camera detectors Interface
capsule sdfs Interface

Interface to capsule SDF initialising function
capsule_init sdfs Function

Initalising function for capsule SDF.
cart_grid gridMod Interface
check_file writer_mod Function

Functional wrapper around inquire to check if file exits
check_hit_annulus detectors Function

Check if a hitpoint is in the annulus
check_hit_camera detectors Function

Check if a hitpoint is in the camera detector ref
check_hit_circle detectors Function

Check if a hitpoint is in the circle
checkpoint writer_mod Subroutine
circle_dect detectors Interface
circular photonMod Subroutine

circular source
cone sdfs Interface

Interface to cone SDF initialising function
cone_init sdfs Function

Initalising function for Capped Cone SDF.
create_directory setupMod Subroutine

create directories if they don't exist
cylinder sdfs Interface

Interface to cylinder SDF initialising function
cylinder_init sdfs Function

Initalising function for Cylinder SDF.
dealloc_array setupMod Subroutine

deallocate data arrays
decode piecewiseMod Subroutine

Compute the 2 indices from a Morton index Adapted from archer2 cpp course
directory setupMod Subroutine

subroutine defines vars to hold paths to various folders

displacement sdfModifiers Interface
displacement_init sdfModifiers Function

Initialise the displacement modifier for a SDF.
display_settings kernels Subroutine

Displays the settings used in the current simulation run
dslit photonMod Subroutine

sample from double slit to produce diff pattern
egg sdfs Interface

Interface to egg SDF initialising function
egg_init sdfs Function

Initalising function for egg SDF. makes a Moss egg. ref.
elongate sdfModifiers Interface
elongate_init sdfModifiers Function

Initialise the elongate modifier for a SDF.
eval_bend sdfModifiers Function

Evaluation function for Bend modifier.
eval_disp sdfModifiers Function

Evaluation function for displacement modifier.
eval_elongate sdfModifiers Function

Evaluation function for Elongate modifier.
eval_extrude sdfModifiers Function

Evaluation function for Extrude modifier.
eval_model sdf_baseMod Function

Evaluate the model
eval_onion sdfModifiers Function

Evaluation function for Onion modifier.
eval_repeat sdfModifiers Function

Evaluation function for Repeat modifier.
eval_revolution sdfModifiers Function

Evaluation function for Revolution modifier.
eval_twist sdfModifiers Function

Evaluation function for Twist modifier.
evaluate_box sdfs Function

Evaluation function for Box SDF.
evaluate_capsule sdfs Function

Evaluation function for Capsule SDF.
evaluate_cone sdfs Function

Evaluation function for Cone SDF.
evaluate_cylinder sdfs Function

Evaluation function for Cylinder SDF.
evaluate_egg sdfs Function

Evaluation function for Egg SDF. ref
evaluate_plane sdfs Function

Evaluation function for Plane SDF.
evaluate_segment sdfs Function

Evaluation function for Segment SDF.
evaluate_sphere sdfs Function

Evaluation function for Sphere SDF.
evaluate_torus sdfs Function

Evaluation function for Torus SDF.
evaluate_triprism sdfs Function

Evaluation function for Triprisim SDF.
extrude sdfModifiers Interface
extrude_init sdfModifiers Function

Initialise the extrude modifier for a SDF.
finalise kernels Subroutine

Routine writes out simulation data, deallocates arrays and prints total runtime
find inttau2 Function

searches for bracketing indices for a value value in an array a
focus photonMod Subroutine
fresnel surfaces Function

calculates the fresnel coefficents
get_new_file_name writer_mod Function

If file exits, get numeral to append to filename

get_vector parse_HelpersMod Function

Vector helper function for parsing toml
get_vessels setupGeometry Function

setup blood vessel scene
get_voxel gridMod Function

get current voxel the photon packet is in
getAlbedo sdf_baseMod Function

Return albedo for the current SDF.
getg2 sdf_baseMod Function

Return factor for the current SDF.
gethgg sdf_baseMod Function

Return g-factor for the current SDF.
getKappa sdf_baseMod Function

Return for the current SDF
getMua sdf_baseMod Function

Return for the current SDF.
getN sdf_baseMod Function

Return refractive index for the current SDF.
getValue piecewiseMod Subroutine

The constant version of sample
handle_annulus_dect parse_detectorsMod Subroutine

Read in Annulus_detector settings and initalise variable
handle_camera parse_detectorsMod Subroutine

Read in Camera settings and initalise variable
handle_circle_dect parse_detectorsMod Subroutine

Read in Circle_detector settings and initalise variable
histempty_fn historyStack Function
histfinish_sub historyStack Subroutine
history_stack_t historyStack Interface
histpeek_fn historyStack Function
histpop_fn historyStack Function
histpush_sub historyStack Subroutine
histwrite_sub historyStack Subroutine
histzero_sub historyStack Subroutine
hit_init detector_mod Function
hit_t detector_mod Interface
identity sdfHelpers Function

Returns the identity transformation matrix
init_annulus_dect detectors Function

Initalise Annular detector
init_camera detectors Function

Initalise Camera detector
init_circle_dect detectors Function

Initalise Circle detector
init_grid gridMod Function

setup grid
init_historyStack historyStack Function
init_mono opticalProperties Function
init_photon photonMod Function

set up all the variables in the photon object
init_piecewise1D piecewiseMod Function

initalise the piecewise1D type with an array size (n, 2). Calculates the CDF of this array. Input array
init_piecewise2D piecewiseMod Function

Initalise the piecewise2D type with a given cell_width, cell_height and input image
init_rng random Subroutine

initiate RNG state with reproducible state
init_source photonMod Function

Bind emission function to photon object
init_spectral opticalProperties Function
init_vec4_vector_real vec4_class Function

Initalise vec4 from a vec3 and Scalar e.g vec4 = [vec3%x, vec3%y, vec3%z, scalar]
intersectCircle geometry Function

ref
intersectCone geometry Function

calculates where a line, with origin:orig and direction:dir hits a cone, radius:radius and height:height with centre:centre. centre is the point under the apex at the cone's base. returns true if intersection exists returns t, the paramertised parameter of the line equation adapted from scratchapixel and pbrt need to check z height after moving ray if not this is an infinte cone cone lies height ways along z-axis
intersectCylinder geometry Function

calculates where a line, with origin:orig and direction:dir hits a cylinder, centre:centre and radius:radius This solves for an infinitely long cylinder centered on the z axis with radius radius returns true if intersection exists returns t, the paramertised parameter of the line equation adapted from scratchapixel need to check z height after moving ray if not this is an infinite cylinder
intersectEllipse geometry Function

calculates where a line, with origin:orig and direction:dir hits a ellipse, centre:centre and axii:semia, semib returns true if intersection exists returns t, the paramertised parameter of the line equation adapted from scratchapixel and pbrt need to check z height after moving ray if not this is an infinte ellipse-cylinder ellipse lies length ways along z-axis semia and semib are the semimajor axis which are the half width and height.
intersection sdfModifiers Function

Intersection operator. Returns the intersection of two SDFs.
intersectPlane geometry Function

ref
intersectSphere geometry Function

calculates where a line, with origin:orig and direction:dir hits a sphere, centre:centre and radius:radius returns true if intersection exists returns t, the paramertised parameter of the line equation adapted from scratchapixel
invert mat_class Function

Performs a direct calculation of the inverse of a 4×4 matrix. from http://fortranwiki.org/fortran/show/Matrix+inversion
json_writer historyStack Subroutine
length vector_class Function

Returns the length of a vec3
length vec4_class Function

Returns the length of a vec4
magnitude vector_class Function

Returns the magnitude of a vec3
magnitude_fn vec4_class Function

Returns the magnitude of a vec4
mat mat_class Interface

Intalise Matrix with 1D Array
mat_add_scal mat_class Function

Matrix + Scalar = Matrix
mat_div_scal mat_class Function

Matrix / scalar
mat_init mat_class Function

Initalise matrix type from 1D array
mat_minus_scal mat_class Function

Matrix - Scalar
mat_mult_mat mat_class Function

Matrix * vec4
mat_mult_scal mat_class Function

Matrix * Scalar
max vector_class Interface

Overload of the max intrinsic for a vec3
max_vec vector_class Function

Get the max value elementwise between a vec3 and a scalar
maxval_vec vector_class Function

Get the max value in a vec3
min vector_class Interface

Overload of the min intrinsic for a vec3
min_vec vector_class Function

Get the min value elementwise between a vec3 and a scalar
minval_vec vector_class Function

Get the min value in a vec3
model sdf_baseMod Interface
model_init sdf_baseMod Function

Initalise the model type.
mono opticalProperties Interface
next random Function
nextpwr2 piecewiseMod Function

Get the next power of 2. i.e given 5 will return 8 (4^2) only works on 32bit ints ref
nint vector_class Interface

Overload of the nint intrinsic for a vec3
nint_vec vector_class Function

Overload the nint intrinsic for a vec3 elementwise
normalise_fluence writer_mod Subroutine

normalise fluence in the Lucy 1999 way
nrrd_write writer_mod Interface
obj_writer historyStack Subroutine
onion sdfModifiers Interface
onion_init sdfModifiers Function

Initialise the Onion modifier for a SDF.
opticalProp_t opticalProperties Interface
opticalProp_t_assign opticalProperties Subroutine
opticaProp_new opticalProperties Function
pack_bits piecewiseMod Function

Reverse the split function. I.e go from 0a0b0c0d to abcd Adapted from archer2 cpp course
parse_detectors parse_detectorsMod Subroutine

parse the detectors
parse_geometry parse_mod Subroutine

parse geometry information
parse_grid parse_mod Subroutine

parse grid input data
parse_output parse_mod Subroutine

parse output file information
parse_params parse_mod Subroutine

entry point for parsing toml file
parse_simulation parse_mod Subroutine

parse simulation information
parse_source parse_sourcesMod Subroutine

Parse sources any updates here MUST be reflected in docs/config.md
parse_spectrum parse_SpectrumMod Subroutine

Parse spectrums to be used
pathlength_scatter kernels Subroutine
pencil photonMod Subroutine

pencil beam source
photon photonMod Interface
piecewise1D piecewiseMod Interface
piecewise2D piecewiseMod Interface
plane sdfs Interface

Interface to plane SDF initialising function
plane_init sdfs Function

Initalising function for plane SDF.
ply_writer historyStack Subroutine
point photonMod Subroutine

isotropic point source
ran2 random Function

wrapper for call random number
randint random Function

sample a random integer between [a, b]
rang random Subroutine

sample a 2D Guassian distribution
ranu random Function

uniformly sample in range[a, b)
raw_write writer_mod Interface
record_hit_1D_sub detector_mod Subroutine

check if a hit is on the detector and record it if so
record_hit_2D_sub detector_mod Subroutine

check if a hit is on the detector and record it if so
reflect surfaces Subroutine

get vector of reflected photon
reflect_refract surfaces Subroutine

wrapper routine for fresnel calculation
refract surfaces Subroutine

get vector of refracted photon
render sdf_baseMod Interface
render_sub sdf_baseMod Subroutine

Render the SDFs onto a voxel grid
render_vec sdf_baseMod Subroutine

Render the SDF Wrapper around the render function to allow ease of use
repeat sdfModifiers Interface
repeat_init sdfModifiers Function

Initialise the Repeat modifier for a SDF.
revolution sdfModifiers Interface
revolution_init sdfModifiers Function

Initialise the Revolution modifier for a SDF.
rotate_x sdfHelpers Function

rotation in the x-axis function from here
rotate_y sdfHelpers Function

rotation in the y-axis function from here
rotate_z sdfHelpers Function

rotation in the z-axis function from here
rotationAlign sdfHelpers Function

Calculate the rotation matrix to rotate vector a onto b ref1 ref2
rotmat sdfHelpers Function

Rotate around around an axis by a given angle taken from here
sample1D piecewiseMod Subroutine

Randomly sample from 1D array
sample2D piecewiseMod Subroutine
scal_add_mat mat_class Function

Scaler + Matrix
scal_add_vec vector_class Function

vec3 + scalar
scal_add_vec vec4_class Function

Elementwise scalar + vec4
scal_minus_vec vector_class Function

scalar - vec3
scal_minus_vec vec4_class Function

Elementwise Scalar - vec4
scal_mult_mat mat_class Function

Matrix * Scalar
scal_mult_vec vector_class Function

Scalar * vec3 elementwise
scal_mult_vec vec4_class Function

Elementwise Scalar * vec4
scatter photonMod Subroutine

Scattering routine. Implments both isotropic and henyey-greenstein scattering taken from mcxyz
sdf sdf_baseMod Interface
sdf_assign sdf_baseMod Subroutine

sdf initializer
sdf_evaluate sdf_baseMod Function

Evaluate the SDF at a given position.
sdf_new sdf_baseMod Function

sdf initializer
search_1D piecewiseMod Subroutine

search by bisection for 1D array
search_2D piecewiseMod Subroutine

search by bisection for 1D array
segment sdfs Interface

Interface to segment SDF initialising function
segment_init sdfs Function

Initalising function for segment SDF. Note this is a 2D function
set_photon photonMod Subroutine
setup kernels Subroutine

setup simulation by reading in setting file, and setup variables to be used.
setup_egg setupGeometry Function

setup an egg, with yolk, albumen and shell
setup_exp setupGeometry Function

Setup experimental geometry from Georgies paper. i.e a glass bottle with contents
setup_logo setupGeometry Function

setup uni crest geometry
setup_omg_sdf setupGeometry Function

setup OMG scene
setup_scat_test setupGeometry Function

set up scattering test scene with user defined tau
setup_scat_test2 setupGeometry Function

set up scattering test scene 2 with user defined tau and hgg
setup_simulation setupMod Subroutine

Read in parameters Setup up various simulation parameters and routines
setup_sphere setupGeometry Function

setup the sphere test case from tran and jacques paper.
setup_sphere_scene setupGeometry Function

setup a test scene with user defined spheres
sin vec4_class Interface

Vec4 overload of the sin intrinsic

sin_vec vec4_class Function

Sine of a vec4, elementwise
skewSymm sdfHelpers Function

Calculate the Skew Symmetric matrix for a given vector
slm photonMod Subroutine

image source
SmoothUnion sdfModifiers Function

Smooth union. Joins two SDFs together smoothly
solveQuadratic geometry Function

solves quadratic equation given coeffs a, b, and c returns true if real solution returns x0 and x1 adapted from scratchapixel
spectral opticalProperties Interface
sphere sdfs Interface
sphere_init sdfs Function

Initalising function for Sphere SDF.
subtraction sdfModifiers Function

Subtraction operator. Takes one SDF from another. Take the first SDF from the 2nd SDF
tauint2 inttau2 Subroutine

optical depth integration subroutine Moves photons to interaction location Calculated is any reflection or refraction happens whilst moving
test_kernel kernels Subroutine
torus sdfs Interface

Interface to torus SDF initialising function
torus_init sdfs Function

Initalising function for Torus SDF.
translate sdfHelpers Function

Returns the Translation matrix for a given vector translation.
triprism sdfs Interface

Interface to triprisim SDF initialising function
triprism_init sdfs Function

Initalising function for triprisim SDF.
twist sdfModifiers Interface
twist_init sdfModifiers Function

Initialise the twist modifier for a SDF.
uniform photonMod Subroutine

uniformly illuminate a surface of the simulation media
union sdfModifiers Function

Union operation. Joins two SDFs together
update_grids inttau2 Subroutine

record fluence using path length estimators. Uses voxel grid
update_opticalProp_t opticalProperties Subroutine
update_pos inttau2 Subroutine

routine that updates positions of photon and calls Fresnel routines if photon leaves current voxel
update_voxels inttau2 Subroutine

updates the current voxel based upon position
updateMono opticalProperties Subroutine
updateSpectral opticalProperties Subroutine
vec4 vec4_class Interface

Initalise a vec4 from a vec3 and a scalar
vec_add_scal vector_class Function

vec3 + scalar
vec_add_scal vec4_class Function

Elementwise vec4 + scalar
vec_add_vec vector_class Function

vec3 + vec3
vec_add_vec vec4_class Function

Elementwise vec4 + vec4
vec_cross_vec vector_class Function

vec3 x vec3
vec_div_scal_int vector_class Function

vec3 / scalar elementwise. Scalar is an integer
vec_div_scal_int vec4_class Function

Elementwise vec4 / Scalar. Scalar is an integer
vec_div_scal_r4 vector_class Function

vec3 / scalar elementwise. Scalar is a 32-bit float
vec_div_scal_r4 vec4_class Function

Elementwise vec4 / Scalar. Scalar is 32-bit float
vec_div_scal_r8 vector_class Function

vec3 / scalar elementwise. Scalar is a 64-bit float
vec_div_scal_r8 vec4_class Function

Elementwise vec4 / Scalar. Scalar is 32-bit float
vec_dot_mat vector_class Function

vec3 . matrix
vec_dot_vec vector_class Function

vec3 . vec3
vec_dot_vec vec4_class Function

dot product between two vec4s
vec_equal_vec vector_class Function

vec3 == vec3
vec_minus_scal vector_class Function

vec3 - scalar
vec_minus_scal vec4_class Function

Elementwise vec4 - scalar
vec_minus_vec vector_class Function

vec3 - vec3
vec_minus_vec vec4_class Function

Elementwise vec4 - vec4
vec_mult_exp_scal_int vector_class Function

vec3**scalar for integer scalar
vec_mult_exp_scal_r4 vector_class Function

vec3**scalar for 32-bit float scalar
vec_mult_exp_scal_r8 vector_class Function

vec3**scalar for 64-bit float scalar
vec_mult_scal vector_class Function

vec3 * scalar elementwise
vec_mult_scal vec4_class Function

Elementwise vec4 * Scalar
vec_mult_vec vector_class Function

vec3 * vec3 elementwise
vec_mult_vec vec4_class Function

Elementwise vec4 * vec4
wall_dist inttau2 Function

funtion that returns distant to nearest wall and which wall that is (x, y, or z)
weight_scatter kernels Subroutine
write_3d_r4_nrrd writer_mod Subroutine

write 3D array of float32's to .nrrd fileformat
write_3d_r4_raw writer_mod Subroutine

write 3D array of float32's to disk as raw binary data
write_3d_r8_nrrd writer_mod Subroutine

write 3D array of float64's to .nrrd fileformat
write_3d_r8_raw writer_mod Subroutine

write 3D array of float64s to disk as raw binary data
write_data writer_mod Subroutine

routine automatically selects which way to write out results based upon file extension
write_detected_photons writer_mod Subroutine
write_hdr writer_mod Subroutine

write out header information for .nrrd file format
zarray setupMod Subroutine

zero data arrays