#include <mpi_project_XR.h>

Inheritance diagram for ProgMPIXrayProject:

Collaboration diagram for ProgMPIXrayProject:

Public Member Functions
void	read (int argc, char **argv)

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 ()

Protected Member Functions
void	defineParams ()

Protected Member Functions inherited from ProgXrayProject
virtual void	readParams ()

void	preRun ()

void	postRun ()

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Additional Inherited Members
Public Attributes inherited from ProgXrayProject
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 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 37 of file mpi_project_XR.h.

Member Function Documentation

◆ defineParams()

void ProgMPIXrayProject::defineParams ( )

protectedvirtual

Function in which the param of each Program are defined.

Reimplemented from ProgXrayProject.

Definition at line 42 of file mpi_project_XR.cpp.

 {
     ProgXrayProject::defineParams();
     clearUsage();
     addUsageLine("MPI Generate projections as in a X-ray microscope from a 3D Xmipp volume.");
 
 }

◆ read()

void ProgMPIXrayProject::read	(	int	argc,
		char **	argv
	)

Definition at line 49 of file mpi_project_XR.cpp.

 {
     node = std::make_shared<MpiNode>(argc, argv);
     if (!node->isMaster())
         verbose = 0;
     ProgXrayProject::read(argc, (const char **)argv);
 }

◆ run()

void ProgMPIXrayProject::run ( )

virtual

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

Reimplemented from ProgXrayProject.

Definition at line 57 of file mpi_project_XR.cpp.

 {
     preRun();
 
     // Project
     projMD.setComment("True rot, tilt and psi; rot, tilt, psi, X and Y shifts applied");
 
     //    // Assign mpi node information
     //    MpiNode & node = *node;
 
     // Calculation of data to be distributed in nodes -----------------------------------------
     std::vector<mpiProjData> mpiData;
     mpiProjData data;
 
     size_t idx = FIRST_IMAGE;
     size_t id;
 
     double angle=projParam.tilt0;
     while (angle <= projParam.tiltF)
     {
         if (projParam.singleProjection)
             data.fn_proj = projParam.fnOut;
         else
             data.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);
         proj.getEulerAngles(data.tRot, data.tTilt,data.tPsi);
         proj.getShifts(data.xShift, data.yShift, data.zShift);
 
         // Add noise in angles and voxels ....................................
 
         data.rot  = data.tRot  + rnd_gaus(projParam.Nangle_avg,  projParam.Nangle_dev);
         data.tilt = data.tTilt + rnd_gaus(projParam.Nangle_avg,  projParam.Nangle_dev);
         data.psi  = data.tPsi  + rnd_gaus(projParam.Nangle_avg,  projParam.Nangle_dev);
 
         //MPI            proj.setEulerAngles(rot,tilt,psi);
 
         if (node->isMaster())
         {
             id = projMD.addObject();
             projMD.setValue(MDL_IMAGE,data.fn_proj, id);
 
             projMD.setValue(MDL_ANGLE_ROT,data.tRot, id);
             projMD.setValue(MDL_ANGLE_TILT,data.tTilt, id);
             projMD.setValue(MDL_ANGLE_PSI,data.tPsi, id);
             projMD.setValue(MDL_ANGLE_ROT2,data.rot, id);
             projMD.setValue(MDL_ANGLE_TILT2,data.tilt, id);
             projMD.setValue(MDL_ANGLE_PSI2,data.psi, id);
             projMD.setValue(MDL_SHIFT_X,shiftX, id);
             projMD.setValue(MDL_SHIFT_Y,shiftY, id);
         }
 
         mpiData.push_back(data);
         idx++;
         angle += projParam.tiltStep;
     }
 
     // Creation of MPI Job Handler file
 
     long long int nodeBlockSize = 1;
     std::unique_ptr<MpiTaskDistributor>jobHandler = std::make_unique<MpiTaskDistributor>(mpiData.size(), nodeBlockSize, node);
 
     size_t first = 0, last = 0;
 
     if (node->isMaster())
     {
         // Save metadata file with angles and shift info
         if (!projParam.singleProjection)
             projMD.write(projParam.fnRoot + ".sel");
 
         if (!(projParam.show_angles))
             init_progress_bar(mpiData.size());
 
         // Creation of output file to reserve space
         createEmptyFile(mpiData[mpiData.size()-1].fn_proj,
                         XMIPP_MIN(XSIZE(MULTIDIM_ARRAY(phantom.iniVol)),(size_t)projParam.proj_Xdim),
                         XMIPP_MIN(YSIZE(MULTIDIM_ARRAY(phantom.iniVol)),(size_t)projParam.proj_Ydim));
 
         std::cout << "Projecting ...\n";
     }
 
     node->barrierWait();
 
     MPI_Barrier(MPI_COMM_WORLD);
 
     // Parallel node jobs
     while (jobHandler->getTasks(first, last))
     {
         for (size_t k = first; k <= last; k++)
         {
             std::cout << "Node: " << node->rank << " - Task: " << k <<std::endl;
             proj.setEulerAngles(mpiData[k].tRot, mpiData[k].tTilt,mpiData[k].tPsi);
             proj.setShifts(mpiData[k].xShift, mpiData[k].yShift, mpiData[k].zShift);
 
             //Reset thread task distributor
             td->clear();
 
             // Really project ....................................................
             if (!projParam.only_create_angles)
             {
                 XrayRotateAndProjectVolumeOffCentered(phantom, psf, proj, stdProj, projParam.proj_Ydim, projParam.proj_Xdim);
                 proj.write(mpiData[k].fn_proj);
             }
 
             // Add noise in angles and voxels ....................................
             //            proj.setEulerAngles(mpiData[k].rot,mpiData[k].tilt,mpiData[k].psi); // Geo info is not stored in header file
             IMGMATRIX(proj).addNoise(projParam.Npixel_avg, projParam.Npixel_dev, "gaussian");
 
             if (projParam.show_angles)
                 std::cout << "Node: " << node->rank << "\t" << proj.rot() << "\t"
                 << proj.tilt() << "\t" << proj.psi() << std::endl;
 
             if (node->isMaster() && !(projParam.show_angles))
                 progress_bar(k+1);
         }
     }
     jobHandler->wait();
 
     postRun();
 
     return;
 }

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

xmipp/legacy/libraries/parallel/mpi_project_XR.h
xmipp/legacy/libraries/parallel/mpi_project_XR.cpp

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ read()

◆ run()