#include <project_xray.h>

Inheritance diagram for ProgXrayProject:

Collaboration diagram for ProgXrayProject:

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...

FileName	fn_psf_xr
	Filename with the Microscope Parameters. More...

ParametersProjectionTomography	projParam

XRayPSF	psf

double	psfThr
	threshold for psfSlabs More...

double	dxo

int	nThr
	Number of threads;. More...

bool	save_std_projs
	Save standard projections. More...

XrayProjPhantom	phantom

Projection	proj

Projection	stdProj

MetaDataVec	projMD

ParallelTaskDistributor *	td

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 ()

void	preRun ()

void	postRun ()

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

Program class for the project program

Definition at line 82 of file project_xray.h.

Member Function Documentation

◆ defineParams()

void ProgXrayProject::defineParams ( )

protectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Reimplemented in ProgMPIXrayProject.

Definition at line 28 of file project_xray.cpp.

 {
     addUsageLine("Generate projections as in a X-ray microscope from a 3D Xmipp volume.");
     addSeeAlsoLine("phantom_create");
     //Params
     projParam.defineParams(this); // Projection parameters
     addParamsLine("== Xray options == ");
     addParamsLine(" [--sampling_rate <Ts>]       : Sampling rate of the volume to be projected (nm).");
     addParamsLine("                              : If empty, same value as X-Y plane sampling from PSF.");
     addParamsLine("alias -s;");
     addParamsLine("[--psf <psf_param_file=\"\">] : XRay-Microscope parameters file. If not set, then default parameters are chosen.");
     addParamsLine("[--focal_shift+ <delta_z=0.0>] : Shift along optical axis between the center of the phantom and the center of the psf in microns");
     addParamsLine("alias -f;");
     addParamsLine("[--threshold+ <thr=0.0>]     : Normalized threshold relative to maximum of PSF to reduce the volume into slabs");
     addParamsLine("[--std_proj]                  : Save also standard projections, adding _std suffix to filenames");
     addParamsLine("[--thr <threads=1>]           : Number of concurrent threads");
     //Examples
     //Example projection file
     addExampleLine("In the following link you can find an example of projection parameter file:",false);
     addExampleLine(" ",false);
     addExampleLine("http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/tomoProjection.param?format=raw",false);
     addExampleLine(" ",false);
     addExampleLine("In the following link you can find an example of X-ray microscope parameters file:",false);
     addExampleLine(" ",false);
     addExampleLine("http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/xray_psf.xmd?format=raw",false);
 
 }

◆ postRun()

void ProgXrayProject::postRun ( )

protected

Definition at line 99 of file project_xray.cpp.

 {
     //Terminate threads and free memory
     //    if (td != NULL)
     //        delete td;
     delete thMgr;
     delete barrier;
 }

◆ preRun()

void ProgXrayProject::preRun ( )

protected

Definition at line 81 of file project_xray.cpp.

 {
     randomize_random_generator();
 
     psf.calculateParams(dxo, -1, psfThr);
     phantom.read(projParam);
     //Correct the rotation axis displacement in projectionParams from pixels to meters
     projParam.raxis *= psf.dxo;
 
     // Threads stuff
 
     barrier = new Barrier(nThr);
 
     //Create threads to start working
     thMgr = new ThreadManager(nThr);
 
 }

◆ readParams()

void ProgXrayProject::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 57 of file project_xray.cpp.

 {
     //    fn_proj_param = getParam("-i");
     //    fn_sel_file   = getParam("-o");
     projParam.readParams(this);
 
     fn_psf_xr = getParam("--psf");
     dxo  = (checkParam("-s"))? getDoubleParam("-s")*1e-9 : -1 ;
     psfThr = getDoubleParam("--threshold");
     nThr = getIntParam("--thr");
     save_std_projs = checkParam("--std_proj");
 
     psf.read(fn_psf_xr);
     psf.setFocalShift(getDoubleParam("--focal_shift")*1e-6);
     psf.verbose = verbose;
     psf.nThr = nThr;
 }

◆ run()

void ProgXrayProject::run ( )

virtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Reimplemented in ProgMPIXrayProject.

Definition at line 108 of file project_xray.cpp.

 {
     preRun();
 
     int expectedNumProjs = FLOOR((projParam.tiltF-projParam.tilt0)/projParam.tiltStep);
     int numProjs=0;
 
     if (verbose > 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
     size_t idx = FIRST_IMAGE;
 
     // Project
     for (double angle=projParam.tilt0; angle<=projParam.tiltF; angle+=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);
 
         //Reset thread task distributor
         //        td->clear();
 
         // Really project ....................................................
         if (!projParam.only_create_angles)
             XrayRotateAndProjectVolumeOffCentered(phantom, psf, proj, stdProj, 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);
 
         size_t objId = projMD.addObject();
         if (!projParam.only_create_angles)
         {
             // Here we subtract the differences to the background illumination (at this moment normalized to 1) //TODO
             MULTIDIM_ARRAY(proj) = 1.0 - MULTIDIM_ARRAY(proj);
             proj.write(fn_proj, ALL_IMAGES, !projParam.singleProjection, WRITE_REPLACE);
 
             if (save_std_projs)
                 stdProj.write(fn_proj.insertBeforeExtension("_std"), 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 << "N      Rot     Tilt     Psi" <<std::endl;
             std::cout << idx << "\t" << proj.rot() << "\t"
             << proj.tilt() << "\t" << proj.psi() << std::endl;
         }
         else if ((expectedNumProjs % XMIPP_MAX(1, numProjs / 60))  == 0 && verbose > 0)
             progress_bar(numProjs);
 
         numProjs++;
         idx++;
     }
     if (!(projParam.show_angles))
         progress_bar(expectedNumProjs);
 
     // Save metadata file with angles and shift info
     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 + ".xmd");
     }
 
     postRun();
 
     return;
 }

Member Data Documentation

◆ dxo

double ProgXrayProject::dxo

Definition at line 99 of file project_xray.h.

◆ fn_proj_param

FileName ProgXrayProject::fn_proj_param

Filename with the Projection_Parameters.

Definition at line 87 of file project_xray.h.

◆ fn_psf_xr

FileName ProgXrayProject::fn_psf_xr

Filename with the Microscope Parameters.

Definition at line 91 of file project_xray.h.

◆ fn_sel_file

FileName ProgXrayProject::fn_sel_file

Selection file with all projections.

Definition at line 89 of file project_xray.h.

◆ nThr

int ProgXrayProject::nThr

Number of threads;.

Definition at line 101 of file project_xray.h.

◆ phantom

XrayProjPhantom ProgXrayProject::phantom

Definition at line 105 of file project_xray.h.

◆ proj

Projection ProgXrayProject::proj

Definition at line 106 of file project_xray.h.

◆ projMD

MetaDataVec ProgXrayProject::projMD

Definition at line 107 of file project_xray.h.

◆ projParam

ParametersProjectionTomography ProgXrayProject::projParam

Definition at line 93 of file project_xray.h.

◆ psf

XRayPSF ProgXrayProject::psf

Definition at line 95 of file project_xray.h.

◆ psfThr

double ProgXrayProject::psfThr

threshold for psfSlabs

Definition at line 97 of file project_xray.h.

◆ save_std_projs

bool ProgXrayProject::save_std_projs

Save standard projections.

Definition at line 103 of file project_xray.h.

◆ stdProj

Projection ProgXrayProject::stdProj

Definition at line 106 of file project_xray.h.

◆ td

ParallelTaskDistributor* ProgXrayProject::td

Definition at line 108 of file project_xray.h.

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

xmipp/legacy/libraries/reconstruction/project_xray.h
xmipp/legacy/libraries/reconstruction/project_xray.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ postRun()

◆ preRun()

◆ readParams()

◆ run()

Member Data Documentation

◆ dxo

◆ fn_proj_param

◆ fn_psf_xr

◆ fn_sel_file

◆ nThr

◆ phantom

◆ proj

◆ projMD

◆ projParam

◆ psf

◆ psfThr

◆ save_std_projs

◆ stdProj

◆ td