PROJECT_Side_Info Class Reference

#include <project.h>

Collaboration diagram for PROJECT_Side_Info:

Public Types
enum	PhantomType { VOXEL, XMIPP, PDB }
	Types of phantom: voxel, Xmipp, PDB. More...

Public Member Functions
void	produce_Side_Info (ParametersProjection &prm, ProgProject &prog_prm)

Public Attributes
MetaDataVec	DF
	Document File for the projecting angles. Order: rot, tilt, psi. More...
PhantomType	phantomMode
	Projecting from a voxel volume, Xmipp description or PDB? More...
Image< double >	phantomVol
	Phantom Xmipp volume. More...
Phantom	phantomDescr
	Phantom mathematical description. More...
PDBPhantom	phantomPDB
	Phantom PDB. More...
AtomInterpolator	interpolator
	Atom interpolator. More...
double	paddFactor
	The padding factor for Fourier projection. More...
double	maxFrequency
	The maximum frequency for pixels. More...
int	BSplineDeg
	The type of interpolation (NEAR. More...
bool	doCrystal
	Is this a crystal projection. More...

Detailed Description

Project program Side information. This class contains side necessary information for the Project program. This information can be obtained from the parameters and is basically the Xmipp volume or phantom description plus a flag saying which of the two is valid.

Definition at line 215 of file project.h.

Member Enumeration Documentation

PhantomType

enum PROJECT_Side_Info::PhantomType

Types of phantom: voxel, Xmipp, PDB.

Enumerator
VOXEL
XMIPP
PDB

Definition at line 221 of file project.h.

{VOXEL, XMIPP, PDB};

Member Function Documentation

produce_Side_Info()

void PROJECT_Side_Info::produce_Side_Info	(	ParametersProjection &	prm,
		ProgProject &	prog_prm
	)

Produce Project Side information. This function produce the side information from the project program parameters. Basically it loads the phantom, sets the phantom mode to voxel or mathematical description and generates or read the projection angles.

Definition at line 871 of file project.cpp.

{
    // Generate Projection angles
    if (!prog_prm.singleProjection)
        Assign_angles(DF, prm, prog_prm.fn_sym);
    else
    {
        size_t DFid=DF.addObject();
        DF.setValue(MDL_ANGLE_ROT,prog_prm.rotSingle,DFid);
        DF.setValue(MDL_ANGLE_TILT,prog_prm.tiltSingle,DFid);
        DF.setValue(MDL_ANGLE_PSI,prog_prm.psiSingle,DFid);
        DF.setValue(MDL_SHIFT_X,prog_prm.xShift,DFid);
        DF.setValue(MDL_SHIFT_Y,prog_prm.yShift,DFid);
    }

    // Load Phantom and set working mode
    if (prog_prm.fnPhantom.isMetaData())
    {
        phantomDescr.read(prog_prm.fnPhantom);
        phantomMode = XMIPP;
        if (prog_prm.singleProjection)
        {
            if (prog_prm.projSize==-1)
                prm.proj_Xdim=prm.proj_Ydim=phantomDescr.xdim;
            else
                prm.proj_Xdim=prm.proj_Ydim=prog_prm.projSize;
        }
    }
    else if (prog_prm.fnPhantom.getExtension()=="pdb")
    {
        phantomPDB.read(prog_prm.fnPhantom);
        for (int i=0; i<phantomPDB.atomList.size(); i++)
        {
        phantomPDB.atomList[i].x /=prog_prm.samplingRate;
        phantomPDB.atomList[i].y /=prog_prm.samplingRate;
        phantomPDB.atomList[i].z /=prog_prm.samplingRate;
        }
        int M=ROUND(prog_prm.samplingRate/prog_prm.highTs);
        interpolator.setup(M,prog_prm.samplingRate/M,true);
        phantomMode = PDB;
        if (prog_prm.singleProjection)
        {
            if (prog_prm.projSize==-1)
                REPORT_ERROR(ERR_ARG_MISSING,"--xdim");
            else
                prm.proj_Xdim=prm.proj_Ydim=prog_prm.projSize;
        }
    }
    else
    {
        phantomVol.read(prog_prm.fnPhantom);
        phantomVol().setXmippOrigin();
        phantomMode = VOXEL;
        if (prog_prm.singleProjection)
        {
            if (prog_prm.projSize==-1)
                prm.proj_Xdim=prm.proj_Ydim=XSIZE(phantomVol());
            else
                prm.proj_Xdim=prm.proj_Ydim=prog_prm.projSize;
        }
    }
    paddFactor = prog_prm.paddFactor;
    maxFrequency = prog_prm.maxFrequency;
    BSplineDeg = prog_prm.BSplineDeg;
}

Member Data Documentation

BSplineDeg

int PROJECT_Side_Info::BSplineDeg

The type of interpolation (NEAR.

Definition at line 237 of file project.h.

DF

MetaDataVec PROJECT_Side_Info::DF

Document File for the projecting angles. Order: rot, tilt, psi.

Definition at line 219 of file project.h.

doCrystal

bool PROJECT_Side_Info::doCrystal

Is this a crystal projection.

Definition at line 239 of file project.h.

interpolator

AtomInterpolator PROJECT_Side_Info::interpolator

Atom interpolator.

Definition at line 231 of file project.h.

maxFrequency

double PROJECT_Side_Info::maxFrequency

The maximum frequency for pixels.

Definition at line 235 of file project.h.

paddFactor

double PROJECT_Side_Info::paddFactor

The padding factor for Fourier projection.

Definition at line 233 of file project.h.

phantomDescr

Phantom PROJECT_Side_Info::phantomDescr

Phantom mathematical description.

Definition at line 227 of file project.h.

phantomMode

PhantomType PROJECT_Side_Info::phantomMode

Projecting from a voxel volume, Xmipp description or PDB?

Definition at line 223 of file project.h.

phantomPDB

PDBPhantom PROJECT_Side_Info::phantomPDB

Phantom PDB.

Definition at line 229 of file project.h.

phantomVol

Image<double> PROJECT_Side_Info::phantomVol

Phantom Xmipp volume.

Definition at line 225 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