Crystal_Projection_Parameters Class Reference

#include <project_crystal.h>

Collaboration diagram for Crystal_Projection_Parameters:

Public Member Functions
	Crystal_Projection_Parameters ()
void	read (const FileName &fn_crystal, double scale=1.0)
void	write (const FileName &fn_crystal)

Public Attributes
int	crystal_Xdim
	Crystal X dimension. More...
int	crystal_Ydim
	Crystal Y dimension. More...
bool	orthogonal
	Orthogonalize projections. More...
Matrix1D< double >	a
	Crystal vector a. More...
Matrix1D< double >	b
	Crustal vector b. More...
double	Nshift_avg
	Bias to apply to the magnitude shift. More...
double	Nshift_dev
	Standard deviation of the magnitude shift. More...
double	disappearing_th
	Disappearing threshold. More...
FileName	fn_shift
	file with shifts More...
MetaDataVec	DF_shift
	Document File for shifts. Order: H K x_SHIFT y_SHIFT z_SHIFT. More...
bool	DF_shift_bool
	is doc file with shifts available More...

Detailed Description

Crystal Projecting parameters. This class reads a set of projection parameters in a file (see the user guide of the projection program for more information about the file structure) and extract the useful information from it. This class allows also to write in the same file format, for doing so you must first introduce the right values in the class fields, and the call to the procedure write.

A crystal is supposed to have two lattice vectors: a and b as follows

^ b
|
|
|
-----------> a

Definition at line 56 of file project_crystal.h.

Constructor & Destructor Documentation

Crystal_Projection_Parameters()

Crystal_Projection_Parameters::Crystal_Projection_Parameters

(

)

Empty constructor

Definition at line 32 of file project_crystal.cpp.

{
    crystal_Xdim = 0;
    crystal_Ydim = 0;
    orthogonal = false;
    a.clear();
    b.clear();
    Nshift_avg = 0;
    Nshift_dev = 0;
    disappearing_th = 0;
    DF_shift_bool = false;
    DF_shift.clear();
}

Member Function Documentation

read()

void Crystal_Projection_Parameters::read	(	const FileName &	fn_crystal,
		double	scale = 1.0
	)

Read projection parameters from a file. An exception is thrown if the file is not found or any of the parameters is not found in the right place.

Definition at line 47 of file project_crystal.cpp.

{
    MetaDataVec MD;
    size_t objId;
    FileName fn_crystal = fn.removeBlockName();
    MD.read(formatString("crystal@%s", fn_crystal.c_str()));
    if (MD.isEmpty())
        REPORT_ERROR(ERR_IO_NOTOPEN,
                     (String)"Prog_Project_Parameters::read: There is a problem "
                     "opening the file " + fn_crystal);

    std::vector <double> ParamVec;
    objId = MD.firstRowId();
    MD.getValue(MDL_DIMENSIONS_2D, ParamVec, objId);
    crystal_Xdim = (int)ParamVec[0];
    crystal_Ydim = (int)ParamVec[1];
    crystal_Xdim = ROUND(scale * crystal_Xdim);
    crystal_Ydim = ROUND(scale * crystal_Ydim);
    MD.getValue(MDL_CRYSTAL_LATTICE_A, ParamVec, objId);
    a.resize(3);
    XX(a) = scale * ParamVec[0];
    YY(a) = scale * ParamVec[1];
    ZZ(a) = 0;
    MD.getValue(MDL_CRYSTAL_LATTICE_B, ParamVec, objId);
    b.resize(3);
    XX(b) = scale * ParamVec[0];
    YY(b) = scale * ParamVec[1];
    ZZ(b) = 0;
    MD.getValue(MDL_CRYSTAL_NOISE_SHIFT,ParamVec, objId);
    Nshift_dev = scale *  ParamVec[0];
    if (ParamVec.size() < 2)
        Nshift_avg = 0;
    else
        Nshift_avg = scale * ParamVec[1];
    MD.getValue(MDL_CRYSTAL_DISAPPEAR_THRE,disappearing_th, objId);
    MD.getValue(MDL_CRYSTAL_ORTHO_PRJ,orthogonal, objId);
    if (MD.getValue(MDL_CRYSTAL_SHFILE, fn_shift, objId))
        DF_shift_bool = true;
    //#define DEBUG
#ifdef DEBUG

    std::cerr << "crystal_Xdim"   << crystal_Xdim<<std::endl;
    std::cerr << "crystal_Ydim"   << crystal_Ydim<<std::endl;
    std::cerr << "a vector"  << a <<std::endl;
    std::cerr << "b vector"  << b <<std::endl;
    std::cerr << "Nshift_devr"  << Nshift_dev <<std::endl;
    std::cerr << "Nshift_avg"  << Nshift_avg <<std::endl;
#endif
#undef DEBUG
}

write()

void Crystal_Projection_Parameters::write

(

const FileName &

fn_crystal

)

Write projection parameters to a file. The projection parameters are written into a file wth the same structure as always. If the file cannot be openned for output an exception is thrown.

Definition at line 99 of file project_crystal.cpp.

{
    if (fn_crystal.isMetaData())
    {
        MetaDataVec MD1;  //MetaData for crystal projection parameters
        std::vector<double> FCVect(2);  //For the center of feature
        size_t id;
        std::vector<double> TVector;  //For general use
        MD1.setColumnFormat(false);
        id = MD1.addObject();
        TVector[0] = crystal_Xdim;
        TVector[1] = crystal_Ydim;
        MD1.setValue(MDL_DIMENSIONS_2D, TVector, id);
        TVector[0] = XX(a);
        TVector[1] = YY(a);
        MD1.setValue(MDL_CRYSTAL_LATTICE_A, TVector, id);
        TVector[0] = XX(b);
        TVector[1] = YY(b);
        MD1.setValue(MDL_CRYSTAL_LATTICE_B, TVector, id);
        TVector[0] = Nshift_dev;
        TVector[1] = Nshift_avg;
        MD1.setValue(MDL_NOISE_PIXEL_LEVEL, TVector, id);
        MD1.setValue(MDL_CRYSTAL_DISAPPEAR_THRE, disappearing_th, id);
        MD1.setValue(MDL_CRYSTAL_ORTHO_PRJ, orthogonal, id);
        MD1.setValue(MDL_CRYSTAL_SHFILE, fn_shift.c_str(), id);
        //MD1.write(fn_crystal, MD_OVERWRITE);
    }
    else
    {
        FILE *fh_param;

        if ((fh_param = fopen(fn_crystal.c_str(), "w")) == nullptr)
            REPORT_ERROR(ERR_IO_NOTOPEN,
                         (std::string)"Prog_Project_Parameters::write: There is a problem "
                         "opening the file " + fn_crystal + " for output");

        fprintf(fh_param, "# Crystal dimensions (X, Y)\n");
        fprintf(fh_param, "%d %d\n", crystal_Xdim, crystal_Ydim);
        fprintf(fh_param, "# Crystal a lattice vector (X, Y)\n");
        fprintf(fh_param, "%f %f\n", XX(a), YY(a));
        fprintf(fh_param, "# Crystal b lattice vector (X, Y)\n");
        fprintf(fh_param, "%f %f\n", XX(b), YY(b));

        fprintf(fh_param, "#     Noise (and bias) applied to the magnitude shift\n");
        fprintf(fh_param, "%f ", Nshift_dev);
        if (Nshift_avg != 0)
            fprintf(fh_param, "%f \n", Nshift_avg);
        else
            fprintf(fh_param, "\n");

        fprintf(fh_param, "# Disappearing threshold\n");
        fprintf(fh_param, "%f\n", disappearing_th);

        fprintf(fh_param, "# Orthogonal Projections\n");
        if (orthogonal)
            fprintf(fh_param, "Yes\n");
        else
            fprintf(fh_param, "No\n");

        //   fprintf(fh_param,"# Grid relative size\n");

        fprintf(fh_param, "# File with shifts for each unit cell\n");
        fprintf(fh_param, "%s", fn_shift.c_str());

        fclose(fh_param);
    }
}

Member Data Documentation

a

Matrix1D<double> Crystal_Projection_Parameters::a

Crystal vector a.

Definition at line 66 of file project_crystal.h.

b

Matrix1D<double> Crystal_Projection_Parameters::b

Crustal vector b.

Definition at line 68 of file project_crystal.h.

crystal_Xdim

int Crystal_Projection_Parameters::crystal_Xdim

Crystal X dimension.

Definition at line 60 of file project_crystal.h.

crystal_Ydim

int Crystal_Projection_Parameters::crystal_Ydim

Crystal Y dimension.

Definition at line 62 of file project_crystal.h.

DF_shift

MetaDataVec Crystal_Projection_Parameters::DF_shift

Document File for shifts. Order: H K x_SHIFT y_SHIFT z_SHIFT.

Definition at line 78 of file project_crystal.h.

DF_shift_bool

bool Crystal_Projection_Parameters::DF_shift_bool

is doc file with shifts available

Definition at line 80 of file project_crystal.h.

disappearing_th

double Crystal_Projection_Parameters::disappearing_th

Disappearing threshold.

Definition at line 74 of file project_crystal.h.

fn_shift

FileName Crystal_Projection_Parameters::fn_shift

file with shifts

Definition at line 76 of file project_crystal.h.

Nshift_avg

double Crystal_Projection_Parameters::Nshift_avg

Bias to apply to the magnitude shift.

Definition at line 70 of file project_crystal.h.

Nshift_dev

double Crystal_Projection_Parameters::Nshift_dev

Standard deviation of the magnitude shift.

Definition at line 72 of file project_crystal.h.

orthogonal

bool Crystal_Projection_Parameters::orthogonal

Orthogonalize projections.

Definition at line 64 of file project_crystal.h.

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The documentation for this class was generated from the following files:

• xmipp/libraries/reconstruction/project_crystal.h
• xmipp/libraries/reconstruction/project_crystal.cpp