ProgProjectTomography Class Reference

#include <project_tomography.h>

Inheritance diagram for ProgProjectTomography:

Collaboration diagram for ProgProjectTomography:

Public Member Functions
virtual void	run ()
Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)
const char *	getParam (const char *param, const char *subparam, int arg=0)
int	getIntParam (const char *param, int arg=0)
int	getIntParam (const char *param, const char *subparam, int arg=0)
double	getDoubleParam (const char *param, int arg=0)
double	getDoubleParam (const char *param, const char *subparam, int arg=0)
float	getFloatParam (const char *param, int arg=0)
float	getFloatParam (const char *param, const char *subparam, int arg=0)
void	getListParam (const char *param, StringVector &list)
int	getCountParam (const char *param)
bool	checkParam (const char *param)
bool	existsParam (const char *param)
void	addParamsLine (const String &line)
void	addParamsLine (const char *line)
ParamDef *	getParamDef (const char *param) const
virtual void	quit (int exit_code=0) const
virtual int	tryRun ()
void	initProgress (size_t total, size_t stepBin=60)
void	setProgress (size_t value=0)
void	endProgress ()
void	processDefaultComment (const char *param, const char *left)
void	setDefaultComment (const char *param, const char *comment)
virtual void	initComments ()
void	setProgramName (const char *name)
void	addUsageLine (const char *line, bool verbatim=false)
void	clearUsage ()
void	addExampleLine (const char *example, bool verbatim=true)
void	addSeeAlsoLine (const char *seeAlso)
void	addKeywords (const char *keywords)
const char *	name () const
virtual void	usage (int verb=0) const
virtual void	usage (const String &param, int verb=2)
int	version () const
virtual void	show () const
virtual void	read (int argc, const char **argv, bool reportErrors=true)
virtual void	read (int argc, char **argv, bool reportErrors=true)
void	read (const String &argumentsLine)
	XmippProgram ()
	XmippProgram (int argc, const char **argv)
virtual	~XmippProgram ()

Public Attributes
FileName	fn_proj_param
	Filename with the Projection_Parameters. More...
FileName	fn_sel_file
	Selection file with all projections. More...
ParametersProjectionTomography	projParam
	Projection parameters. More...
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Protected Member Functions
virtual void	defineParams ()
virtual void	readParams ()
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Additional Inherited Members
Protected Attributes inherited from XmippProgram
int	errorCode
ProgramDef *	progDef
	Program definition and arguments parser. More...
std::map< String, CommentList >	defaultComments
int	argc
	Original command line arguments. More...
const char **	argv

Detailed Description

Definition at line 36 of file project_tomography.h.

Member Function Documentation

defineParams()

void ProgProjectTomography::defineParams ( )

protectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 30 of file project_tomography.cpp.

{
    addUsageLine("Generate projections as if it were a single axis tomographic series.");
    addSeeAlsoLine("phantom_create, phantom_project");
    //Params
    projParam.defineParams(this);
    //Examples
    addExampleLine("Generating a set of projections using a projection parameter:", false);
    addExampleLine("Generating a single projection at 45 degrees around X axis:", false);
    addExampleLine("Generating a single projection at 45 degrees around Y axis:", false);
    //Example projection file
    addExampleLine("In the following link you can find an example of projection parameter file:",false);
    addExampleLine(" ",false);
    addExampleLine("https://sourceforge.net/p/testxmipp/code/ci/master/tree/input/tomoProjection.param?format=raw",false);
}

readParams()

void ProgProjectTomography::readParams ( )

protectedvirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippProgram.

Definition at line 46 of file project_tomography.cpp.

{
    projParam.readParams(this);
}

run()

void ProgProjectTomography::run ( )

virtual

Main Project routine. Generate a set of projections given the projection parameters. This is the main projecting routine. This function generates a set of projections according to the projecting parameters defined. The projections are written to disk.

The Projection field will keep at the end the last projection, this is useful in case you want to project only one image, although it is also written to disk. The returned number is the total number of projections generated. A selection file with all images is also returned (and saved if any name has been given in the parameters).

Reimplemented from XmippProgram.

Definition at line 51 of file project_tomography.cpp.

{

    Projection         proj;
    MetaDataVec        projMD;

    randomize_random_generator();

    TomoProjectSideInfo side;
    side.produceSideInfo(projParam);

    // Project
    int expectedNumProjs = FLOOR((projParam.tiltF-projParam.tilt0)/projParam.tiltStep);
    int numProjs=0;

    std::cerr << "Projecting ...\n";
    if (!(projParam.show_angles))
        init_progress_bar(expectedNumProjs);

    projMD.setComment("True rot, tilt and psi; rot, tilt, psi, X and Y shifts applied");
    double tRot,tTilt,tPsi,rot,tilt,psi;
    FileName fn_proj;              // Projection name
    int idx = 1;
    size_t objId;

    int iterAngle=static_cast<int>((projParam.tiltF - projParam.tilt0) / projParam.tiltStep);
    for (int iangle=0; iangle<=iterAngle; iangle++)
    {
        double angle=projParam.tilt0+iangle*projParam.tiltStep;
        if (projParam.singleProjection)
            fn_proj = projParam.fnOut;
        else
            fn_proj.compose(idx, projParam.fnRoot + ".stk");

        // Choose Center displacement ........................................
        double shiftX     = rnd_gaus(projParam.Ncenter_avg, projParam.Ncenter_dev);
        double shiftY    = rnd_gaus(projParam.Ncenter_avg, projParam.Ncenter_dev);
        Matrix1D<double> inPlaneShift(3);
        VECTOR_R3(inPlaneShift,shiftX,shiftY,0);

        projParam.calculateProjectionAngles(proj,angle, 0,inPlaneShift);

        // Really project ....................................................
        if (!projParam.only_create_angles)
            projectVolumeOffCentered(side.phantomVol(), proj,
                                     projParam.proj_Ydim, projParam.proj_Xdim);

        // Add noise in angles and voxels ....................................
        proj.getEulerAngles(tRot, tTilt,tPsi);

        rot  = tRot  + rnd_gaus(projParam.Nangle_avg,  projParam.Nangle_dev);
        tilt = tTilt + rnd_gaus(projParam.Nangle_avg,  projParam.Nangle_dev);
        psi  = tPsi  + rnd_gaus(projParam.Nangle_avg,  projParam.Nangle_dev);

        proj.setEulerAngles(rot,tilt,psi);

        objId = projMD.addObject();
        if (!projParam.only_create_angles)
        {
            proj.write(fn_proj, ALL_IMAGES, !projParam.singleProjection, WRITE_REPLACE);
            projMD.setValue(MDL_IMAGE,fn_proj,objId);
        }

        projMD.setValue(MDL_ANGLE_ROT,rot,objId);
        projMD.setValue(MDL_ANGLE_TILT,tilt,objId);
        projMD.setValue(MDL_ANGLE_PSI,psi,objId);
        projMD.setValue(MDL_ANGLE_ROT2,tRot,objId);
        projMD.setValue(MDL_ANGLE_TILT2,tTilt,objId);
        projMD.setValue(MDL_ANGLE_PSI2,tPsi,objId);
        projMD.setValue(MDL_SHIFT_X,shiftX,objId);
        projMD.setValue(MDL_SHIFT_Y,shiftY,objId);

        IMGMATRIX(proj).addNoise(projParam.Npixel_avg, projParam.Npixel_dev, "gaussian");

        // Save ..............................................................
        if (projParam.show_angles)
            std::cout << idx << "\t" << tRot << "\t"
            << tTilt << "\t" << tPsi << std::endl;
        else if ((expectedNumProjs % XMIPP_MAX(1, numProjs / 60))
                 == 0)
            progress_bar(numProjs);

        numProjs++;
        idx++;
    }
    if (!projParam.show_angles)
        progress_bar(expectedNumProjs);

    if (!projParam.singleProjection)
    {
        projMD.setComment("Angles rot,tilt and psi contain noisy projection angles and rot2,tilt2 and psi2 contain actual projection angles");
        projMD.write(projParam.fnRoot + ".sel");
    }

    return;
}

Member Data Documentation

fn_proj_param

FileName ProgProjectTomography::fn_proj_param

Filename with the Projection_Parameters.

Definition at line 40 of file project_tomography.h.

fn_sel_file

FileName ProgProjectTomography::fn_sel_file

Selection file with all projections.

Definition at line 42 of file project_tomography.h.

projParam

ParametersProjectionTomography ProgProjectTomography::projParam

Projection parameters.

Definition at line 44 of file project_tomography.h.

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

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