ProgReconsART Class Reference

#include <reconstruct_art.h>

Inheritance diagram for ProgReconsART:

Collaboration diagram for ProgReconsART:

Public Member Functions
	ProgReconsART ()
	~ProgReconsART ()
void	setIO (const FileName &fn_in, const FileName &fn_out)
	Functions of common reconstruction interface. More...
void	defineParams ()
void	readParams ()
void	show ()
void	run ()
Public Member Functions inherited from ProgReconsBase
virtual	~ProgReconsBase ()
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 Attributes
ARTReconsBase *	artRecons
bool	isMpi
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

Additional Inherited Members
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Detailed Description

Definition at line 38 of file reconstruct_art.h.

Constructor & Destructor Documentation

ProgReconsART()

ProgReconsART::ProgReconsART

(

)

Definition at line 32 of file reconstruct_art.cpp.

{
    isMpi = false;
    artRecons = nullptr;
}

~ProgReconsART()

ProgReconsART::~ProgReconsART

(

)

Definition at line 37 of file reconstruct_art.cpp.

{
    delete artRecons;
}

Member Function Documentation

defineParams()

void ProgReconsART::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 45 of file reconstruct_art.cpp.

{
    addUsageLine("Generate 3D reconstructions from projections using the ART algorithm (even with SIRT).");
    addUsageLine("+A history file with the information of the reconstruction process is created. You can ");
    addUsageLine("+also give symmetry elements to specify different points of view reusing the projections ");
    addUsageLine("+you have. The reconstruction is performed using some basis (blobs or voxels) in ");
    addUsageLine("+different grids (BCC (by default), FCC or CC).");

    ARTReconsBase::defineParams(this, isMpi);

    addParamsLine(" == Special Parameters for crystals == ");
    CrystalARTRecons::defineParams(this);

    addExampleLine("+++* Basis volume definition: The basis volume is defined internally such that it should cover ",false);
    addExampleLine("+++the space cube corresponding to =(-Xdim/2,-Xdim/2,-Xdim/2)= to =(X dim /2,Xdim/2,Xdim/2)= where Xdim  ",false);
    addExampleLine("+++is the X dimension of the projections.", false);
    addExampleLine("+++* Voxel volume definition: The final reconstructed volume is defined in such a way that it ", false);
    addExampleLine("+++covers the whole basis volume. For these two definitions and the fact that the basis has got ", false);
    addExampleLine("+++some radius (normally 2) the final reconstructions are a little wider than the original ",false);
    addExampleLine("+++projections (usually =2*radius+1=)",false);
    addExampleLine("+++* Crystal reconstructions: Crystal projections must be the deformed projections of the ",false);
    addExampleLine("+++deformed volume. I mean, the lattice vectors of the volume to reconstruct need not to lie ",false);
    addExampleLine("+++on a grid point inside the BCC, FCC or CC grid. If we ant to force that they lie on a grid ",false);
    addExampleLine("+++point we have to deform the volume. When he have this deformed volume and we project it, the ",false);
    addExampleLine("+++two 3D lattice vectors project to two different 2D lattice vectors, that in principle there ",false);
    addExampleLine("+++is no relationship between them. We must force this two 2D lattice vectors to align with ",false);
    addExampleLine("+++=a=(Xdim,0)= and =b=(0,Ydim)= by deforming the projection. This is the second deformation. ",false);
    addExampleLine("+++This complex projections are either generated from phantoms using the program Project or ",false);
    addExampleLine("+++from lists of Fourier spots coming out from MRC as APH files by applying the program ",false);
    addExampleLine("+++Spots2RealSpace2D.",false);
    addExampleLine("+++* Surface constraints: These constraints force the volume to be 0 at known places. ",false);
    addExampleLine("+++This has got the beneficial consequence that mass tends to be compacted where it should be.",false);
    addExampleLine("+++* Grids: This program defines three grids for working with data. The typical simple cubic grid, ",false);
    addExampleLine("+++the face-centered grid (fcc) and the body-centered cubic grid (bcc). We define these grids as follows: ",false);
    addExampleLine("+++|  Simple Cubic Grid  |  %ATTACHURL%/image004.gif  |",false);
    addExampleLine("+++|  Face-centered cubic grid  |  %ATTACHURL%/image008.gif  |",false);
    addExampleLine("+++|  Body-centered cubic grid  |  %ATTACHURL%/image006.gif  |",false);
    addExampleLine("+++where %ATTACHURL%/image010.gif is the set of integers and %ATTACHURL%/image002.gif is a positive ",false);
    addExampleLine("+++real number called sampling distance. See =Gabor H., Geometry of Digital Spaces, Birkhauser, 1998, Massachussets=",false);
    addExampleLine("+++Spots2RealSpace2D. %BR%",false);
    addExampleLine("+++In the case of the simple cubic grid the voxels are cubes of volume %ATTACHURL%/image013.gif ³",false);
    addExampleLine("+++. The voxels associated to the bcc grid are truncated octahedra, polyhedra of 8 hexagonal ",false);
    addExampleLine("+++faces and 6 square faces, of volume 4 %ATTACHURL%/image013.gif ³ .Finally, the voxels associated ",false);
    addExampleLine("+++to the fcc grid are rhombic dodacehedra, polyhedra of 12 identical rhombic faces, of volume 2 ",false);
    addExampleLine("+++%ATTACHURL%/image013.gif ³. However, in practice the above definitions are implemented using a ",false);
    addExampleLine("+++combination of simple cubic grids. Clearly, a simple cubic grid defines the complex simple cubic ",false);
    addExampleLine("+++grid and thus the relative size used in the implementation is exactly the %ATTACHURL%/image013.gif ³. ",false);
    addExampleLine("+++For defining the bcc grid two simple cubic grids are used, it can be seen from the definition for ",false);
    addExampleLine("+++the bcc above that the valid positions for even values of =z=, =x= and =y= have to be also even, ",false);
    addExampleLine("+++in the case of odd values of =z= , =x= and =y= have to be odd. Consequently, the relative size used ",false);
    addExampleLine("+++in the BCC grid is equivalent to 2 %ATTACHURL%/image013.gif above. For defining the fcc grid four ",false);
    addExampleLine("+++simple cubic grids are used, it can be seen from the definition for the fcc above that the valid ",false);
    addExampleLine("+++positions for even values of =z=, the sum of =x= and =y= has to be even; in the case of odd values ",false);
    addExampleLine("+++of =z= the sum of =x= and =y= has to be odd. Consequently, the relative size used in the FCC grid ",false);
    addExampleLine("+++is equivalent to 2 %ATTACHURL%/image013.gif above. %BR%",false);
    addExampleLine(" ",false); // For style twiki reasons
    addExampleLine("Basic reconstructing commands:",false);
    addExampleLine("reconstruct_art -i projections.sel -o artrec");
    addExampleLine("Create the equivalent noisy reconstruction:",false);
    addExampleLine("reconstruct_art -i projections.sel -o artrec --noisy_reconstruction");
    //    addExampleLine("Reconstruct using SIRT parallelization algorithm for five iterations:",false);
    //    addExampleLine("reconstruct_art -i projections.sel -o artrec -n 5 --parallel_mode SIRT");
    addExampleLine("Save the basis information at each iteration:",false);
    addExampleLine("reconstruct_art -i projections.sel -o artrec -n 3 --save_basis");
}

readParams()

void ProgReconsART::readParams ( )

virtual

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 111 of file reconstruct_art.cpp.

{


      if (checkParam("--crystal"))
          artRecons = new CrystalARTRecons;
      else
          artRecons = new SinPartARTRecons;

    artRecons->readParams(this);

    if (artRecons->artPrm.threads > 1 && isMpi)
        REPORT_ERROR(ERR_ARG_BADCMDLINE, "Threads not compatible in mpi version.");
    if (!isMpi && artRecons->artPrm.parallel_mode != BasicARTParameters::ART)
        REPORT_ERROR(ERR_ARG_BADCMDLINE, "If --parallel_mode is passed, then mpi version must be used.");

}

run()

void ProgReconsART::run ( )

virtual

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

Reimplemented from XmippProgram.

Definition at line 146 of file reconstruct_art.cpp.

{
    BasicARTParameters &artPrm = artRecons->artPrm;

    Image<double> vol_voxels;
    GridVolume vol_basis;
    // Configure time clock
    time_config();

    struct timeval start_time, end_time;
    long int init_usecs, process_usecs, finish_usecs;

    gettimeofday(&start_time, nullptr);

    show();
    // Produce side information and initial volume
    artRecons->preProcess(vol_basis);
    if (verbose > 0)
    {
        std::cout << " ---------------------------------------------------------------------" << std::endl;
        std::cout << " Projections                  : "  << artRecons->artPrm.numIMG << std::endl;
        std::cout << " ---------------------------------------------------------------------" << std::endl;
    }
    // Show parameters and initiate history
    artRecons->initHistory(vol_basis);

    gettimeofday(&end_time, nullptr);

    init_usecs = (end_time.tv_sec-start_time.tv_sec)*1000000+(end_time.tv_usec-start_time.tv_usec);

    gettimeofday(&start_time,nullptr);

    // Iterations
    artRecons->iterations(vol_basis);


    gettimeofday(&end_time,nullptr);

    process_usecs = (end_time.tv_sec-start_time.tv_sec)*1000000+(end_time.tv_usec-start_time.tv_usec);

    gettimeofday(&start_time,nullptr);

    // Finish iterations
    artRecons->postProcess(vol_basis);

    // Write final volume
    int Xoutput_volume_size=(artPrm.Xoutput_volume_size==0) ?
                            artPrm.projXdim:artPrm.Xoutput_volume_size;
    int Youtput_volume_size=(artPrm.Youtput_volume_size==0) ?
                            artPrm.projYdim:artPrm.Youtput_volume_size;
    int Zoutput_volume_size=(artPrm.Zoutput_volume_size==0) ?
                            artPrm.projXdim:artPrm.Zoutput_volume_size;

    //   int min_distance = ceil( ( 2 * artPrm.grid_relative_size ) / artPrm.basis.blob.radius) + 1;

    artPrm.basis.changeToVoxels(vol_basis, &(vol_voxels()),
                                Zoutput_volume_size, Youtput_volume_size, Xoutput_volume_size,artPrm.threads);

    vol_voxels.write(artPrm.fn_out);

    if (artPrm.tell&TELL_SAVE_BASIS)
        vol_basis.write(artPrm.fn_root+".basis");
    artPrm.fh_hist->close();

    gettimeofday(&end_time,nullptr);

    finish_usecs = (end_time.tv_sec-start_time.tv_sec)*1000000+(end_time.tv_usec-start_time.tv_usec);

    std::cout << "INIT_TIME: " << (double)init_usecs/(double)1000000 << std::endl;
    std::cout << "PROCESS_TIME: " << (double)process_usecs/(double)1000000 << std::endl;
    std::cout << "FINISH_TIME: " << (double)finish_usecs/(double)1000000 << std::endl;

}

setIO()

void ProgReconsART::setIO ( const FileName &  fn_in, const FileName &  fn_out  )

virtual

Functions of common reconstruction interface.

Implements ProgReconsBase.

Definition at line 42 of file reconstruct_art.cpp.

{}

show()

void ProgReconsART::show

(

)

Definition at line 129 of file reconstruct_art.cpp.

{
    if (verbose > 0)
    {
        std::cout << " =====================================================================" << std::endl;
        std::cout << " ART reconstruction method " << std::endl;
        std::cout << " =====================================================================" << std::endl;
        std::cout << " Projections file             : "  << artRecons->artPrm.fn_sel << std::endl;
        std::cout << " Output rootname              : "  << artRecons->artPrm.fn_root << std::endl;
        std::cout << " Iterations                   : "  << artRecons->artPrm.no_it << std::endl;
        std::cout << " Lambda                       : "  << artRecons->artPrm.lambda_list(0) << std::endl;
        std::cout << std::endl;
        std::cout << " More info in the history file: "  << artRecons->artPrm.fn_root + ".hist" << std::endl;
        std::cout << " ---------------------------------------------------------------------\n" << std::endl;
    }
}

Member Data Documentation

artRecons

ARTReconsBase* ProgReconsART::artRecons

protected

Definition at line 41 of file reconstruct_art.h.

isMpi

bool ProgReconsART::isMpi

protected

Definition at line 42 of file reconstruct_art.h.

---

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

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