v0.14.0 |
Load data from MetaImage file, translate grayscale values to densities. More...
#include <users_modules/bone_remodelling/src/DensityMaps.hpp>
Public Member Functions | |
DataFromMetaIO (MetaImage &metaFile) | |
PetscErrorCode | fromOptions () |
PetscErrorCode | getDataForGiveIndex (const vector< int > &vec_idx, vector< double > &vec_data) |
PetscErrorCode | getInidcesForGivenCoordinate (const double x, const double y, const double z, const double dx, const double dy, const double dz, vector< int > &vec_ix, vector< int > &vec_iy, vector< int > &vec_iz, vector< int > &vec_idx, vector< double > &vec_dist) |
double | getAverage (const vector< double > &vec_data) |
Averages data within given vector. More... | |
PetscErrorCode | mapDensityLinear (double *paramDensity, const vector< double > &vec_data, vector< double > &vec_density) |
Transform data to densities. More... | |
PetscErrorCode | mapDensityLinear (const vector< double > &vec_data, vector< double > &vec_density) |
double | getElasticMod (double *param, double rho) |
Transform densities to Youngs modulus. More... | |
double | getElasticMod (double rho) |
double | medianFilter (const vector< double > &vec_density) |
function returns median of data from given vector More... | |
double | mapGaussSmooth (const double sigma, const vector< double > &vec_density, const vector< double > &vec_dist) |
function smooths values in a given vector depending on distance from center (vec_dist) More... | |
double | mapGaussSmooth (const vector< double > &vec_density, const vector< double > &vec_dist) |
Public Attributes | |
MetaImage & | metaFile |
double | sIgma |
double | cUbe_size |
int | fIlter |
double | sCale |
double | dIst_tol |
double | tHreshold |
double | paramElastic [2] |
double | paramDensity [2] |
double | lAmbda |
vector< double > | kErnel |
Load data from MetaImage file, translate grayscale values to densities.
Definition at line 205 of file DensityMaps.hpp.
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Definition at line 208 of file DensityMaps.hpp.
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Definition at line 223 of file DensityMaps.hpp.
Averages data within given vector.
vector | data from metaFile |
Definition at line 485 of file DensityMaps.hpp.
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returns vertors of data for given index of the point
vec_idx | reference vector of indices |
vec_data | reference vector of data (colors) |
Definition at line 302 of file DensityMaps.hpp.
Transform densities to Youngs modulus.
a,b | parameter for relation of density - density, b * density ^ a = E |
rho | density |
param | parameters a,b for density-elasticity relation |
rho | density |
Definition at line 538 of file DensityMaps.hpp.
Definition at line 545 of file DensityMaps.hpp.
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returns vertors of coordinates and indices for given coordinate
x | coordinate of point x |
y | coordinate of point y |
z | coordinate of point z |
dx | dimension of the block in x direction |
dy | dimension of the block in y direction |
dz | dimension of the block in z direction |
vec_ix | reference vector of x coordinates |
vec_iy | reference vector of y coordinates |
vec_iz | reference vector of z coordinates |
vec_idx | reference vector of indices |
z | center of the cube |
dz | size of the cube |
vec_ix | vectors of coord points inside cube |
vec_idx | indices of inside cube with dimensions dx dy dz |
vec_dist | vector of squared distances between center of the cube and points |
Definition at line 334 of file DensityMaps.hpp.
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Definition at line 523 of file DensityMaps.hpp.
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Transform data to densities.
a | array of parameters a,b for linear relation of grayscale - density, a * HU + b = density |
vec_data | data from metaFile |
vec_density | output vector with density |
Definition at line 508 of file DensityMaps.hpp.
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function smooths values in a given vector depending on distance from center (vec_dist)
< normalisation of kernel and smooting values
< avoid division by zero (ad exception) this should not happen /FIXME
sigma | sigma parameter for gausssian smoothing |
vec_density | vector with non-smoothed densities |
vec_dist | vector with squared distances form center of the cubes |
Definition at line 581 of file DensityMaps.hpp.
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vec_density | vector with non-smoothed densities |
vec_dist | vector with distances form center of the cubes |
Definition at line 614 of file DensityMaps.hpp.
function returns median of data from given vector
vec_density | vector with densities |
< copy of the vector to allow sorting data
< applying threshold
< sorting vector
Definition at line 553 of file DensityMaps.hpp.
double BoneRemodeling::DataFromMetaIO::cUbe_size |
Definition at line 214 of file DensityMaps.hpp.
double BoneRemodeling::DataFromMetaIO::dIst_tol |
Definition at line 217 of file DensityMaps.hpp.
int BoneRemodeling::DataFromMetaIO::fIlter |
Definition at line 215 of file DensityMaps.hpp.
vector<double> BoneRemodeling::DataFromMetaIO::kErnel |
Definition at line 575 of file DensityMaps.hpp.
double BoneRemodeling::DataFromMetaIO::lAmbda |
Definition at line 221 of file DensityMaps.hpp.
MetaImage& BoneRemodeling::DataFromMetaIO::metaFile |
Definition at line 207 of file DensityMaps.hpp.
double BoneRemodeling::DataFromMetaIO::paramDensity[2] |
Definition at line 220 of file DensityMaps.hpp.
double BoneRemodeling::DataFromMetaIO::paramElastic[2] |
Definition at line 219 of file DensityMaps.hpp.
double BoneRemodeling::DataFromMetaIO::sCale |
Definition at line 216 of file DensityMaps.hpp.
double BoneRemodeling::DataFromMetaIO::sIgma |
Definition at line 213 of file DensityMaps.hpp.
double BoneRemodeling::DataFromMetaIO::tHreshold |
Definition at line 218 of file DensityMaps.hpp.