Basis Class Reference

#include <basis.h>

Collaboration diagram for Basis:

Public Types
enum	tBasisFunction { blobs, voxels, splines }
	Type of basis function. More...

Public Member Functions
	Basis ()
	Empty constructor. By default, blobs. More...
void	setDefault ()
	Default values. More...
String	basisName () const
	Basis name. More...
void	read (int argc, char **argv)
void	read (const FileName &fn)
void	readParams (XmippProgram *program)
void	produceSideInfo (const Grid &grid)
void	setSamplingRate (double _Tm)
void	setD (Matrix2D< double > *_D)
double	maxLength () const
void	changeToVoxels (GridVolume &vol_basis, MultidimArray< double > *vol_voxels, int Zdim, int Ydim, int Xdim, int threads=1) const
void	changeFromVoxels (const MultidimArray< double > &vol_voxels, GridVolume &vol_basis, int grid_type, double grid_relative_size, const MultidimArray< double > *vol_mask, const Matrix2D< double > *D, double R, int threads=1) const
double	valueAt (const Matrix1D< double > &r) const
double	projectionAt (const Matrix1D< double > &u, const Matrix1D< double > &r) const

Static Public Member Functions
static void	defineParams (XmippProgram *program, const char *prefix=NULL, const char *comment=NULL)

Public Attributes
tBasisFunction	type
	Basis function to use. More...
MultidimArray< double > *	VolPSF
	Footprint is convolved with a volume PSF // At this moment only used with blobs. More...
double	Tm
	Sampling rate. More...
struct blobtype	blob
	Blob parameters. More...
double	grid_relative_size
	Relative size for the grid. More...
Matrix2D< double > *	D
ImageOver	blobprint
	Blob footprint. More...
ImageOver	blobprint2
	Square of the footprint. More...
double	sum_on_grid
	Sum of the basis on the grid points. More...
Matrix1D< double >	aux
	Auxiliary vector for projections. More...

Friends
std::ostream &	operator<< (std::ostream &out, const Basis &basis)
	Show. More...

Detailed Description

Basis class.

Definition at line 45 of file basis.h.

Member Enumeration Documentation

tBasisFunction

enum Basis::tBasisFunction

Type of basis function.

Enumerator
blobs
voxels
splines

Definition at line 49 of file basis.h.

{blobs, voxels, splines} tBasisFunction;

Constructor & Destructor Documentation

Basis()

Basis::Basis

(

)

Empty constructor. By default, blobs.

Definition at line 30 of file basis.cpp.

{
    setDefault();
}

Member Function Documentation

basisName()

String Basis::basisName

(

)

const

Basis name.

Definition at line 50 of file basis.cpp.

{
    switch (type)
    {
    case Basis::blobs:
        return "blobs";
        break;
    case Basis::voxels:
        return "voxels";
        break;
    case Basis::splines:
        return "splines";
        break;
    default:
        return "Unknown";
        break;
    }
}

changeFromVoxels()

void Basis::changeFromVoxels	(	const MultidimArray< double > &	vol_voxels,
		GridVolume &	vol_basis,
		int	grid_type,
		double	grid_relative_size,
		const MultidimArray< double > *	vol_mask,
		const Matrix2D< double > *	D,
		double	R,
		int	threads = 1
	)		const

Change basis from voxels. A voxel volume is provided, then the output vol_basis will be shaped to represent this voxel volume. If the volume is already in voxels, then the mask and the radius mask are applied.

Definition at line 292 of file basis.cpp.

{
    Grid grid;
    Matrix1D<double> corner1(3);
    Matrix1D<double> corner2(3);
    double R2 = R * R;
    switch (type)
    {
    case blobs:
        voxels2blobs(&vol_voxels, blob, vol_basis,
                     grid_type, grid_relative_size, 0.05, vol_mask,
                     D, 0.01, 0, R, threads);
        break;
    case voxels:
        VECTOR_R3(corner1, STARTINGX(vol_voxels),
                  STARTINGY(vol_voxels), STARTINGZ(vol_voxels));
        VECTOR_R3(corner2, FINISHINGX(vol_voxels),
                  FINISHINGY(vol_voxels), FINISHINGZ(vol_voxels));
        grid = Create_CC_grid(1, corner1, corner2);
        vol_basis.adapt_to_grid(grid);
        vol_basis(0)() = vol_voxels;
        if (R != -1)
            FOR_ALL_ELEMENTS_IN_ARRAY3D(vol_voxels)
            if (k*k + i*i + j*j > R2)
                vol_basis(0)()(k, i, j) = 0;
        if (vol_mask != nullptr)
            FOR_ALL_ELEMENTS_IN_ARRAY3D(vol_voxels)
            if ((*vol_mask)(k, i, j) == 0)
                vol_basis(0)()(k, i, j) = 0;
        break;
    case splines:
        REPORT_ERROR(ERR_NOT_IMPLEMENTED,"");
        /* TODO */
        break;
    }
}

changeToVoxels()

void Basis::changeToVoxels	(	GridVolume &	vol_basis,
		MultidimArray< double > *	vol_voxels,
		int	Zdim,
		int	Ydim,
		int	Xdim,
		int	threads = 1
	)		const

Change basis to voxels. This function takes a grid volume in the basis indicated in this object and translates it into voxels of the given size. If the volume is already in voxels a padding is done so that the output is of the given size and the basis volume is in the center.

Definition at line 261 of file basis.cpp.

{
    int xdiff;
    int ydiff;
    int zdiff;
    switch (type)
    {
    case blobs:
        blobs2voxels(vol_basis, blob, vol_voxels, D, threads , Zdim, Ydim, Xdim );
        break;
    case voxels:
        *vol_voxels = vol_basis(0)();
        xdiff = (Xdim - XSIZE(*vol_voxels)) / 2;
        ydiff = (Ydim - YSIZE(*vol_voxels)) / 2;
        zdiff = (Zdim - ZSIZE(*vol_voxels)) / 2;
        vol_voxels->selfWindow(
            STARTINGZ(*vol_voxels) - zdiff,
            STARTINGY(*vol_voxels) - ydiff,
            STARTINGX(*vol_voxels) - xdiff,
            (int)(FINISHINGZ(*vol_voxels) + Zdim - ZSIZE(*vol_voxels) - zdiff),
            (int)(FINISHINGY(*vol_voxels) + Ydim - YSIZE(*vol_voxels) - ydiff),
            (int)(FINISHINGX(*vol_voxels) + Xdim - XSIZE(*vol_voxels) - xdiff));
        break;
    case splines:
        spatial_Bspline032voxels(vol_basis, vol_voxels, Zdim, Ydim, Xdim);
        break;
    }
}

defineParams()

void Basis::defineParams ( XmippProgram *  program, const char *  prefix = NULL, const char *  comment = NULL  )

static

Definition of paramaters

Definition at line 69 of file basis.cpp.

{
    char tempLine[256];
    char lineOut[512];

    if(prefix == nullptr)
        sprintf(tempLine, "  [--basis <basis_type=blobs>] ");
    else
        sprintf(tempLine,"%s --basis <basis_type=blobs> ", prefix);

    //std::cerr << "DEBUG_JM: tempLine: " << tempLine << std::endl;


    if (comment != nullptr)
        sprintf(lineOut, "%s : %s", tempLine, comment);
    else
        sprintf(lineOut, "%s : Basis function to use for the reconstruction", tempLine);

    program->addParamsLine(lineOut);

    //std::cerr << "DEBUG_JM: tempLine: " << lineOut << std::endl;

    program->addParamsLine("    where <basis_type>");
    program->addParamsLine("      blobs <radius=2> <Bessel_order=2> <alpha_param=10.4> : Default blob parameters and grid relative size adjusted to use small blobs");
    program->addParamsLine("     voxels");
    program->addParamsLine("     splines");
    program->addParamsLine(" or   --big_blobs    : blob parameters and grid relative size adjusted to use big blobs (r=2, m=2, alpha=2.26, g=2.26)");
    program->addParamsLine(" or   --visual_blobs : blobs optimal for direct visualization (r=2.4, m=2, alpha=13.3633, g=1.41)");
    program->addParamsLine(" or   --tomo_blobs   : blobs with high overlapping (r=3.469269, m=2, alpha=13.7385, g=1/sqrt(2))");
}

maxLength()

double Basis::maxLength

(

)

const

Max length of the basis. This is the maximum distance between the center of the basis and its further point.

Definition at line 242 of file basis.cpp.

{
    switch (type)
    {
    case blobs:
        return blob.radius;
        break;
    case voxels:
        return sqrt(3.0) * 0.5;
        break;
    case splines:
        return sqrt(3.0) * 2.0;
        break;
    }
    return 0.0;
}

produceSideInfo()

void Basis::produceSideInfo

(

const Grid &

grid

)

Produce side information. You must provide the grid in which this basis function will live

Definition at line 162 of file basis.cpp.

{
    switch (type)
    {
    case blobs:
        {
            int subsampling = (VolPSF == nullptr )? BLOB_SUBSAMPLING : PIXEL_SUBSAMPLING;

            footprint_blob(blobprint, blob, subsampling);
            sum_on_grid = sum_blob_Grid(blob, grid, D);
            blobprint()  /= sum_on_grid;

            if (VolPSF != nullptr)
            {
                // let adjust to the same resolution and size both blobprint and VolPSF
                //                selfScaleToSize(LINEAR, *VolPSF, XSIZE(*VolPSF)*BLOB_SUBSAMPLING,
                //                                YSIZE(*VolPSF)*BLOB_SUBSAMPLING, ZSIZE(*VolPSF));

                blobprint().setXmippOrigin();

                if (XSIZE(blobprint()) < XSIZE(*VolPSF))
                    blobprint().selfWindow(STARTINGY(*VolPSF),
                                           STARTINGX(*VolPSF),
                                           STARTINGY(*VolPSF)+YSIZE(*VolPSF)-1,
                                           STARTINGX(*VolPSF)+XSIZE(*VolPSF)-1);
                else if (XSIZE(blobprint()) > XSIZE(*VolPSF))
                    VolPSF->selfWindow(STARTINGY(blobprint()),
                                       STARTINGX(blobprint()),
                                       STARTINGY(blobprint())+YSIZE(blobprint())-1,
                                       STARTINGX(blobprint())+XSIZE(blobprint())-1);

                // creation of the 3D blobprint from convolution of blobprint and PSF
                ImageOver footprintT;
                footprintT.init(*VolPSF, subsampling);

                convolutionFFTStack(*VolPSF, blobprint(), footprintT());

                blobprint = footprintT;
            }

            blobprint2()  = blobprint();
            blobprint2() *= blobprint();
            break;
        }
    case voxels:  sum_on_grid = 1;
        break;
    case splines: sum_on_grid = sum_spatial_Bspline03_Grid(grid);
        break;
    }

#ifdef DEBUG
    std::cout << "Sum of a basis on the grid=" << sum_on_grid << std::endl;
    std::cout << "D\n" << D << std::endl;
    ImageXmipp save;
    save() = blobprint();
    save.write("footprint.xmp");
#endif
}

projectionAt()

double Basis::projectionAt	(	const Matrix1D< double > &	u,
		const Matrix1D< double > &	r
	)		const

Projection at a given direction (u) with a given point (r).

Definition at line 367 of file basis.cpp.

{
    const double p0 = 1.0 / (2 * PIXEL_SUBSAMPLING) - 0.5;
    const double pStep = 1.0 / PIXEL_SUBSAMPLING;
    const double pAvg = 1.0 / (PIXEL_SUBSAMPLING * PIXEL_SUBSAMPLING);
    double module_r;
    double px;
    double py;
    int i;
    int j;
    switch (type)
    {
    case blobs:
        module_r = sqrt(XX(r) * XX(r) + YY(r) * YY(r) + ZZ(r) * ZZ(r));
        return blob_proj(module_r, blob);
        break;
    case voxels:
        {
            double retval = 0;
            ZZ(aux) = ZZ(r);
            for (i = 0, px = p0; i < PIXEL_SUBSAMPLING; i++, px += pStep)
            {
                XX(aux) = XX(r) + px;
                for (j = 0, py = p0; j < PIXEL_SUBSAMPLING; j++, py += pStep)
                {
                    YY(aux) = YY(r) + py;
                    retval += intersection_unit_cube(u, aux);
                }
            }
            return retval*pAvg;
            break;
        }
    case splines:
        return spatial_Bspline03_proj(r, u);
        break;
    }
    return 0.0;
}

read() [1/2]

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

Read parameters from a command line. This function reads the parameters from a command line defined by argc and argv. An exception might be thrown by any of the internal conversions, this would mean that there is an error in the command line and you might show a usage message.

read() [2/2]

void Basis::read

(

const FileName &

fn

)

Read parameters from a file. An exception is thrown if the file cannot be open

readParams()

void Basis::readParams

(

XmippProgram *

program

)

Read the parameters from the command line

Definition at line 100 of file basis.cpp.

{
    String basisType = program->getParam("--basis");

    if (basisType == "blobs")
    {
        blob.radius = program->getDoubleParam("--basis", "blobs", 0);
        blob.order  = program->getIntParam("--basis", "blobs", 1);
        blob.alpha  = program->getDoubleParam("--basis", "blobs", 2);
    }
    if (!program->checkParam("--basis")) // Default is for small blobs
        grid_relative_size = 1.41;

    if (program->checkParam("--big_blobs"))
    {
        blob.radius = 2;
        blob.order  = 2;
        blob.alpha  = 3.6;

        grid_relative_size = 2.26;
    }
    else if (program->checkParam("--visual_blobs"))
    {
        blob.radius = 2.4;
        blob.order  = 2;
        blob.alpha  = 13.3633;

        grid_relative_size = 1.41;
    }
    else if (program->checkParam("--tomo_blobs"))
    {
        blob.radius = 3.469269392209083;
        blob.order  = 2;
        blob.alpha  = 13.7385068372842;

        grid_relative_size = 1.0/sqrt(2);
    }
    else
    {
        if (basisType == "voxels")
        {
            type = voxels;
            grid_relative_size = 1;
        }
        else if (basisType == "splines")
        {
            type = splines;
            grid_relative_size = 1;
        }
    }
}

setD()

void Basis::setD ( Matrix2D< double > *  _D )

inline

Set D. D is the deformation matrix used for crystals.

Definition at line 123 of file basis.h.

    {
        D = _D;
    }

setDefault()

void Basis::setDefault

(

)

Default values.

Definition at line 36 of file basis.cpp.

{
    type        = blobs;
    blob.radius = 2;
    blob.order  = 2;
    blob.alpha  = 10.4;
    VolPSF   = nullptr;
    D           = nullptr;
    blobprint.clear();
    blobprint2.clear();
    aux.resizeNoCopy(3);
}

setSamplingRate()

void Basis::setSamplingRate

(

double

_Tm

)

Set sampling rate.

Definition at line 153 of file basis.cpp.

{
    if (_Tm == 0)
        REPORT_ERROR(ERR_VALUE_INCORRECT, "Basis::set_sampling_rate: Sampling rate cannot be 0");
    Tm = _Tm;
    blob.radius /= Tm;
}

valueAt()

double Basis::valueAt

(

const Matrix1D< double > &

r

)

const

Basis value at a given point.

Definition at line 332 of file basis.cpp.

{
    double module_r;
    switch (type)
    {
    case  blobs:
        {
            module_r = sqrt(XX(r) * XX(r) + YY(r) * YY(r) + ZZ(r) * ZZ(r));
            return blob_val(module_r, blob);
            break;
        }
    case voxels:
        {
            if (-0.5 <= XX(r) && XX(r) < 0.5 &&
                -0.5 <= YY(r) && YY(r) < 0.5 &&
                -0.5 <= ZZ(r) && ZZ(r) < 0.5)
                return 1.0;
            else
                return 0.0;
            break;
        }
    case splines:
        {
            if (-2 <= XX(r) && XX(r) < 2 &&
                -2 <= YY(r) && YY(r) < 2 &&
                -2 <= ZZ(r) && ZZ(r) < 2)
                return spatial_Bspline03LUT(r);
            else
                return 0.0;
            break;
        }
    }
    return 0.0;
}

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  out, const Basis &  basis  )

friend

Show.

Definition at line 223 of file basis.cpp.

{
    switch (basis.type)
    {
    case Basis::blobs:
        out << " Blobs:         radius=" << basis.blob.radius << " pixels"
        << " alpha=" << basis.blob.alpha
        << " order=" << basis.blob.order << std::endl;
        break;
    case Basis::voxels:
        out << "Voxels\n";
        break;
    case Basis::splines:
        out << "Splines\n";
        break;
    }
    return out;
}

Member Data Documentation

aux

Matrix1D<double> Basis::aux

Auxiliary vector for projections.

Definition at line 80 of file basis.h.

blob

struct blobtype Basis::blob

Blob parameters.

Definition at line 61 of file basis.h.

blobprint

ImageOver Basis::blobprint

Blob footprint.

Definition at line 71 of file basis.h.

blobprint2

ImageOver Basis::blobprint2

Square of the footprint.

Definition at line 74 of file basis.h.

D

Matrix2D<double>* Basis::D

Volume deformation matrix. See the documentation of BasicARTParameters for further explanation.

Definition at line 68 of file basis.h.

grid_relative_size

double Basis::grid_relative_size

Relative size for the grid.

Definition at line 64 of file basis.h.

sum_on_grid

double Basis::sum_on_grid

Sum of the basis on the grid points.

Definition at line 77 of file basis.h.

Tm

double Basis::Tm

Sampling rate.

Definition at line 58 of file basis.h.

type

tBasisFunction Basis::type

Basis function to use.

Definition at line 52 of file basis.h.

VolPSF

MultidimArray<double>* Basis::VolPSF

Footprint is convolved with a volume PSF // At this moment only used with blobs.

Definition at line 55 of file basis.h.

---

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

• xmipp/libraries/data/basis.h
• xmipp/libraries/data/basis.cpp