ProgProject Class Reference

#include <project.h>

Inheritance diagram for ProgProject:

Collaboration diagram for ProgProject:

Public Member Functions
void	readParams ()
void	defineParams ()
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	fnPhantom
FileName	fnOut
	Output filename (used for a singleProjection or a stack) More...
FileName	fn_crystal
FileName	fn_sym
	Symmetry file. More...
int	projSize
	Projection size when fnOut is given. More...
double	samplingRate
	Sampling rate: Only used for PDB projections. More...
double	highTs
	High sampling rate: Only used for PDB projections. More...
bool	only_create_angles
	Only create angles, do not project. More...
bool	singleProjection
	Single projection. More...
double	rotSingle
	Rotational angle of a single projection. More...
double	tiltSingle
	Tilt angle of a single projection. More...
double	psiSingle
	Psi angle of a single projection. More...
double	xShift
double	yShift
projectionType	projType
	Type of projection algorithm. More...
double	paddFactor
	The padding factor for Fourier projection. More...
double	maxFrequency
	The maximum frequency for Fourier projection. More...
int	BSplineDeg
	The type of interpolation (NEAR. More...
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()
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

Parameter class for the project program

Definition at line 45 of file project.h.

Member Function Documentation

defineParams()

void ProgProject::defineParams ( )

virtual

Define parameters

Reimplemented from XmippProgram.

Definition at line 91 of file project.cpp.

{
    addUsageLine("This program is able to generate a set of projections from a volume. ");
    addUsageLine("++The projection is done using the information directly or from a file.");
    addSeeAlsoLine("tomo_project,phantom_create");

    addParamsLine("   -i <volume_file>                           : Voxel volume, PDB or description file");
    addParamsLine("   -o <image_file>                            : Output stack or image");
    addParamsLine("  [--sampling_rate <Ts=1>]                    : It is only used for PDB phantoms");
    addParamsLine("  [--high_sampling_rate <highTs=0.08333333>]  : Sampling rate before downsampling. It is only used for PDB phantoms");
    addParamsLine("  [--method <method=real_space>]              : Projection method");
    addParamsLine("        where <method>");
    addParamsLine("                real_space                    : Makes projections by ray tracing in real space");
    addParamsLine("                shears                        : Use real-shears algorithm");
    addParamsLine("                                              :+This algorithm is slower but more accurate. For a full description see");
    addParamsLine("               fourier <pad=2> <maxfreq=0.25> <interp=bspline> : Takes a central slice in Fourier space");
    addParamsLine("                                              :+++                        %BR% ");
    addParamsLine("                                              : pad: controls the padding factor.");
    addParamsLine("                                              :+++                        %BR% ");
    addParamsLine("                                              : maxfreq: is the maximum frequency for the pixels and by default ");
    addParamsLine("                                              : pixels with frequency more than 0.25 are not considered.");
    addParamsLine("                                              :+++                        %BR% ");
    addParamsLine("                                              : interp: is the method for interpolation and the values can be: ");
    addParamsLine("                                              :+++                        %BR% ");
    addParamsLine("                                              : nearest:          Nearest Neighborhood  ");
    addParamsLine("                                              :+++                        %BR% ");
    addParamsLine("                                              : linear:           Linear BSpline  ");
    addParamsLine("                                              :+++                        %BR% ");
    addParamsLine("                                              : bspline:          Cubic BSpline  ");
    addParamsLine("== Generating a set of projections == ");
    addParamsLine("  [--params <parameters_file>]           : File containing projection parameters");
    addParamsLine("                                         : Check the manual for a description of the parameters");
    addParamsLine("                                         : tilt angle should be in the range [0-180]");
    addParamsLine("  [--sym <sym_file>]                     : It is used for computing the asymmetric unit");
    addParamsLine("  [--only_create_angles]                 : Do not create projections");
    addParamsLine("== Generating a single projection == ");
    addParamsLine("  [--angles <rot> <tilt> <psi> <x=0.> <y=0.>]: Angles and shifts for a single projection");
    addParamsLine("  [--xdim <size=-1>]                     : Size of the projection");
    addParamsLine("                                         : For geometric descriptions and voxel volumes");
    addParamsLine("                                         : this parameter is not necessary");
    addExampleLine("Generating a set of projections using fourier method",false);
    addExampleLine("xmipp_phantom_project -i volume.vol -o images.stk --method fourier 3 0.25 bspline --params uniformProjection_xmd.param");
    addExampleLine("Generating a set of projections using shears method",false);
    addExampleLine("xmipp_phantom_project -i volume.vol -o images.stk --method shears --params uniformProjection_xmd.param");
    addExampleLine("Generating a top view from Z",false);
    addExampleLine("xmipp_phantom_project -i volume.vol -o image.xmp --angles 0 0 0");
    addExampleLine("Generating a side view from Y",false);
    addExampleLine("xmipp_phantom_project -i volume.vol -o image.xmp --angles 90 90 0");
    addExampleLine("Generating a side view from X",false);
    addExampleLine("xmipp_phantom_project -i volume.vol -o image.xmp --angles 0 90 0");
    addExampleLine("+++In the following links you can find some examples of projection parameter files",false);
    addExampleLine("+++",false);
    addExampleLine("+++http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/phantomProject.param?format=raw",false);
    addExampleLine("+++",false);
    addExampleLine("+++http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/uniformProjection_xmd.param?format=raw",false);
    addExampleLine("+++",false);
    addExampleLine("+++http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/clusterProjection_xmd.param?format=raw",false);
    addExampleLine("+++",false);
    addExampleLine("+++Creating a 2D crystal",false);
    addExampleLine("+In order to create a 2D crystal, you can pass --params as a projection file with a second block for crystal projection.: ",false);
    addExampleLine("+xmipp_phantom_project   -i cylinder_with_axis.descr --oroot MRCproj --params MRCCrystalProj_xmd.param");
    addExampleLine("+++In the following links you can find some examples of projection parameter files",false);
    addExampleLine("+++",false);
    addExampleLine("+++http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/Crystal/MRCCrystalProj_xmd.param?format=raw",false);
    addExampleLine("+++",false);
    addExampleLine("+++ http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/Crystal/cylinder_with_axis.descr?format=raw",false);
    addExampleLine("+++",false);
    addExampleLine("+++http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/Crystal/MRC_crystal_projection_xmd.param?format=raw",false);

    addExampleLine("+++",false);
    addExampleLine("+++Figures (a) and (b) show the achievable resolution for different methods of projection. ",false);
    addExampleLine("+++",false);
    addExampleLine("+++<img width='100%' alt='Test_Resolution_Small.jpg' src='%ATTACHURLPATH%/Test_Resolution_Small.jpg' height='100%' />");
    addExampleLine("+++",false);
    addExampleLine("+++(a) The achievable resolution for different methods for a volume of size 64*64",false);
    addExampleLine("+++",false);
    addExampleLine("+++ <img width='100%' alt='Test_Resolution_Big.jpg' src='%ATTACHURLPATH%/Test_Resolution_Big.jpg' height='100%' />");
    addExampleLine("+++",false);
    addExampleLine("+++(b) The achievable resolution for different methods for a volume of size 400*400",false);
    addExampleLine("+++",false);
    addExampleLine("+++As it can be seen in these two figures, Fourier method with cubic B-Spline interpolation for both padding two and padding one provides the best resolution. However, there is a preference on padding one because of less memory and time complexity.",false);
}

readParams()

void ProgProject::readParams ( )

virtual

Read parameters.

Reimplemented from XmippProgram.

Definition at line 35 of file project.cpp.

{
    fnPhantom = getParam("-i");
    fnOut = getParam("-o");
    samplingRate  = getDoubleParam("--sampling_rate");
    highTs = getDoubleParam("--high_sampling_rate");
    singleProjection = false;
    if (STR_EQUAL(getParam("--method"), "real_space"))
        projType = REALSPACE;
    if (STR_EQUAL(getParam("--method"), "shears"))
        projType = SHEARS;
    if (STR_EQUAL(getParam("--method"), "fourier"))
    {
        projType = FOURIER;
        paddFactor = getDoubleParam("--method", 1);
        maxFrequency = getDoubleParam("--method", 2);
        String degree = getParam("--method", 3);
        if (degree == "nearest")
            BSplineDeg = xmipp_transformation::NEAREST;
        else if (degree == "linear")
            BSplineDeg = xmipp_transformation::LINEAR;
        else if (degree == "bspline")
            BSplineDeg = xmipp_transformation::BSPLINE3;
        else
            REPORT_ERROR(ERR_ARG_BADCMDLINE, "The values for interpolation can be : nearest, linear, bspline");

    }
    bool doParams = checkParam("--params");
    bool doAngles = checkParam("--angles");

    if (doParams && doAngles)
        REPORT_ERROR(ERR_ARG_BADCMDLINE, "--params and --angles are mutually exclusive");
    else if (!doParams && !doAngles)
        REPORT_ERROR(ERR_ARG_BADCMDLINE, "You should provide --params or --angles");

    if (doParams)
    {
        fn_proj_param = getParam("--params");
        if (checkParam("--sym"))
            fn_sym        = getParam("--sym");
        only_create_angles = checkParam("--only_create_angles");
    }
    else //doAngles = true
    {
        singleProjection = true;
        only_create_angles = false;
        projSize = getIntParam("--xdim");
        rotSingle  = getDoubleParam("--angles",0);
        tiltSingle = getDoubleParam("--angles",1);
        psiSingle  = getDoubleParam("--angles",2);
        xShift  = getDoubleParam("--angles",3);
        yShift  = getDoubleParam("--angles",4);
    }
}

run()

void ProgProject::run ( )

virtual

Run

Reimplemented from XmippProgram.

Definition at line 175 of file project.cpp.

{
    Projection proj;
    MetaDataVec SF;
    ROUT_project(*this, proj, SF);
}

Member Data Documentation

BSplineDeg

int ProgProject::BSplineDeg

The type of interpolation (NEAR.

Definition at line 87 of file project.h.

fn_crystal

FileName ProgProject::fn_crystal

Filename with the special crystal parameters (Crystal_Projection_Parameters )

Definition at line 57 of file project.h.

fn_proj_param

FileName ProgProject::fn_proj_param

Filename with the Projection_Parameters.

Definition at line 49 of file project.h.

fn_sym

FileName ProgProject::fn_sym

Symmetry file.

Definition at line 59 of file project.h.

fnOut

FileName ProgProject::fnOut

Output filename (used for a singleProjection or a stack)

Definition at line 54 of file project.h.

fnPhantom

FileName ProgProject::fnPhantom

Phantom filename. It can be a Xmipp volume or a mathematically defined phantom.

Definition at line 52 of file project.h.

highTs

double ProgProject::highTs

High sampling rate: Only used for PDB projections.

Definition at line 65 of file project.h.

maxFrequency

double ProgProject::maxFrequency

The maximum frequency for Fourier projection.

Definition at line 85 of file project.h.

only_create_angles

bool ProgProject::only_create_angles

Only create angles, do not project.

Definition at line 67 of file project.h.

paddFactor

double ProgProject::paddFactor

The padding factor for Fourier projection.

Definition at line 83 of file project.h.

projSize

int ProgProject::projSize

Projection size when fnOut is given.

Definition at line 61 of file project.h.

projType

projectionType ProgProject::projType

Type of projection algorithm.

Definition at line 81 of file project.h.

psiSingle

double ProgProject::psiSingle

Psi angle of a single projection.

Definition at line 75 of file project.h.

rotSingle

double ProgProject::rotSingle

Rotational angle of a single projection.

Definition at line 71 of file project.h.

samplingRate

double ProgProject::samplingRate

Sampling rate: Only used for PDB projections.

Definition at line 63 of file project.h.

singleProjection

bool ProgProject::singleProjection

Single projection.

Definition at line 69 of file project.h.

tiltSingle

double ProgProject::tiltSingle

Tilt angle of a single projection.

Definition at line 73 of file project.h.

xShift

double ProgProject::xShift

Definition at line 77 of file project.h.

yShift

double ProgProject::yShift

Definition at line 79 of file project.h.

---

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

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