CellEngineering::DataFromFiles Struct Reference

#include <users_modules/cell_engineering/src/DispMap.hpp>

Collaboration diagram for CellEngineering::DataFromFiles:

Public Member Functions
	DataFromFiles (string &file)
MoFEMErrorCode	loadFileData ()
MoFEMErrorCode	fromOptions ()
double	getDataForGivenCoordinate (const double x, const double y, vector< vector< double >> &main_vector, const double sCale, const double cUbe_size)

Public Attributes
string &	fIle
double	sCale
double	cUbe_size
vector< vector< double > >	main_vector
double	lAmbda

Detailed Description

Definition at line 29 of file DispMap.hpp.

Constructor & Destructor Documentation

DataFromFiles()

CellEngineering::DataFromFiles::DataFromFiles ( string &  file )

inline

Definition at line 38 of file DispMap.hpp.

: fIle(file) {}

Member Function Documentation

fromOptions()

MoFEMErrorCode CellEngineering::DataFromFiles::fromOptions ( )

inline

Definition at line 68 of file DispMap.hpp.

                               {
    MoFEMFunctionBegin;
    CHKERR PetscOptionsBegin(PETSC_COMM_WORLD, "", "Get parameters", "none");
 
    cUbe_size = 4;
    CHKERR PetscOptionsScalar("-cube_size", "get cube size for the averaging",
                              "", 0, &cUbe_size, PETSC_NULL);
 
    sCale = 1;
    CHKERR PetscOptionsScalar(
        "-scale", "scale the distance between voxels (eg. from mm to m)", "",
        sCale, &sCale, PETSC_NULL);
 
    ierr = PetscOptionsEnd();
    CHKERRQ(ierr);
 
    MoFEMFunctionReturn(0);
  }

getDataForGivenCoordinate()

double CellEngineering::DataFromFiles::getDataForGivenCoordinate ( const double  x, const double  y, vector< vector< double >> &  main_vector, const double  sCale, const double  cUbe_size  )

inline

returns vertors of data for given index of the point

Parameters

vec_idx	reference vector of indices
vec_data	reference vector of data (colors)

Returns

error code

Definition at line 94 of file DispMap.hpp.

                                                                               {
 
    const int size_y = main_vector.size(); // flip
    const int size_x = main_vector.begin()->size();
    double data = 0;
 
    vector<int> vec_ix;
    vector<int> vec_iy;
    vector<double> vec_data;
    vector<double> vec_dist;
 
    int nx = ceil(cUbe_size);
    int ny = ceil(cUbe_size);
 
    int ix = ceil(x / sCale);
    int iy = ceil(y / sCale);
 
    vec_ix.resize(2 * nx);
    vec_iy.resize(2 * ny);
 
    int ii = 0;
    for (int i = 0; i < 2 * nx; i++) {
      int idx = ix - nx + i;
      if (idx >= size_x / 2 || idx < -size_x / 2)
        continue;
      vec_ix[ii++] = idx;
    }
    vec_ix.resize(ii);
    ii = 0;
    for (int i = 0; i < 2 * ny; i++) {
      int idx = iy - ny + i;
      if (idx >= size_y / 2 || idx < -size_y / 2)
        continue;
      vec_iy[ii++] = idx;
    }
    vec_iy.resize(ii);
    ii = 0;
 
    vec_data.resize(vec_iy.size() * vec_ix.size());
    vec_dist.resize(vec_iy.size() * vec_ix.size());
 
    for (vector<int>::iterator it_iy = vec_iy.begin(); it_iy != vec_iy.end();
         it_iy++) {
      for (vector<int>::iterator it_ix = vec_ix.begin(); it_ix != vec_ix.end();
           it_ix++) {
        vec_data[ii] =
            main_vector[*it_iy + size_y / 2][*it_ix + size_x / 2]; // flip
        vec_dist[ii] = ((*it_iy * sCale - y) * (*it_iy * sCale - y) +
                        (*it_ix * sCale - x) * (*it_ix * sCale - x));
 
        ii++;
      }
    }
 
    // gaussian smoothing
    vector<double> kernel;
    kernel.resize(vec_data.size());
    int i = 0;
    double sigma = 10;
    double sum = 0;
    const double m = (1 / sqrt(M_PI * 2 * sigma * sigma));
    for (int ii = 0; ii < vec_dist.size(); ii++) {
      kernel[i] = m * exp(-(vec_dist[ii]) /
                          (2 * sigma * sigma)); // distance is already squared
      sum += kernel[i++];
    }
    ii = 0;
    for (vector<double>::iterator vec_itr = vec_data.begin();
         vec_itr != vec_data.end(); vec_itr++) {
      kernel[ii] /= sum;
      data += (*vec_itr) * kernel[ii++];
    }
    return data;
  }

loadFileData()

MoFEMErrorCode CellEngineering::DataFromFiles::loadFileData ( )

inline

Definition at line 40 of file DispMap.hpp.

                                {
    MoFEMFunctionBegin;
    ifstream in(fIle.c_str());
    if (!in.is_open()) {
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
              "file with data points not found");
      //  cout << ">> couldn't read the file <<"<< endl;
    }
 
    typedef boost::tokenizer<boost::escaped_list_separator<char>> Tokenizer;
 
    string line;
 
    main_vector.clear();
    while (getline(in, line)) {
      vector<double> vec;
      Tokenizer tok(line);
      for (Tokenizer::iterator it(tok.begin()), end(tok.end()); it != end;
           ++it) {
        vec.push_back(atof(it->c_str()));
      }
 
      main_vector.push_back(vec);
    }
    reverse(main_vector.begin(), main_vector.end());
    MoFEMFunctionReturn(0);
  }

Member Data Documentation

cUbe_size

double CellEngineering::DataFromFiles::cUbe_size

Definition at line 34 of file DispMap.hpp.

fIle

string& CellEngineering::DataFromFiles::fIle

Definition at line 31 of file DispMap.hpp.

lAmbda

double CellEngineering::DataFromFiles::lAmbda

Definition at line 36 of file DispMap.hpp.

main_vector

vector<vector<double> > CellEngineering::DataFromFiles::main_vector

Definition at line 35 of file DispMap.hpp.

sCale

double CellEngineering::DataFromFiles::sCale

Definition at line 33 of file DispMap.hpp.

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The documentation for this struct was generated from the following file:

• users_modules/cell_engineering/src/DispMap.hpp