project (Generate projections from a volume)

Collaboration diagram for project (Generate projections from a volume):

Classes
class	ProgProject
struct	Angle_range
class	ParametersProjection
class	PROJECT_Side_Info

Enumerations
enum	projectionType { REALSPACE, SHEARS, FOURIER }
	Type of projection. More...

Functions
int	PROJECT_Assign_angles (MetaData &DF, const ParametersProjection &prm)
int	PROJECT_Effectively_project (const FileName &fnOut, bool singleProjection, int projType, const ParametersProjection &prm, PROJECT_Side_Info &side, const Crystal_Projection_Parameters &prm_crystal, Projection &proj, MetaData &SF)
int	ROUT_project (ProgProject &prm, Projection &proj, MetaData &SF)

Detailed Description

Enumeration Type Documentation

projectionType

enum projectionType

Type of projection.

Enumerator
REALSPACE
SHEARS
FOURIER

Definition at line 42 of file project.h.

{REALSPACE, SHEARS, FOURIER};

Function Documentation

PROJECT_Assign_angles()

int PROJECT_Assign_angles	(	MetaData &	DF,
		const ParametersProjection &	prm
	)

Assign angles from the projection parameters to a Document file. Given a set of projection parameters this function returns a document file with a set of angles according to the specifications. The order in the output document file is rotational, tilting and psi angle.

The assignment can be done from another document file (with any angle order) or internally generated according to the ranges defined in the parameters.

The total number of angles is returned. The Document File is cleared, the first key in the document file is the starting key of the projection set. The current line of the document file is set to the beginning of the file.

PROJECT_Effectively_project()

int PROJECT_Effectively_project	(	const FileName &	fnOut,
		bool	singleProjection,
		int	projType,
		const ParametersProjection &	prm,
		PROJECT_Side_Info &	side,
		const Crystal_Projection_Parameters &	prm_crystal,
		Projection &	proj,
		MetaData &	SF
	)

Effectively project. This is the routine which effectively projects, it needs the projection parameters and the side information, ie, the loaded phantom and list of angles from which project. The Projection field will keep at the end the last projection, this is useful in case you want to project only one image, although it is also written to disk. The returned number is the total number of projections generated. A selection file with all images is also returned.

ROUT_project()

int ROUT_project	(	ProgProject &	prm,
		Projection &	proj,
		MetaData &	SF
	)

Main Project routine. Generate a set of projections given the projection parameters. This is the main projecting routine. This function generates a set of projections according to the projecting parameters defined. The projections are written to disk.

The Projection field will keep at the end the last projection, this is useful in case you want to project only one image, although it is also written to disk. The returned number is the total number of projections generated. A selection file with all images is also returned (and saved if any name has been given in the parameters).

Definition at line 1174 of file project.cpp.

{
    randomize_random_generator();
    // Read projection parameters and produce side information
    ParametersProjection proj_prm;
    PROJECT_Side_Info side;
    if (!prm.singleProjection)
        proj_prm.from_prog_params(prm);
    side.produce_Side_Info(proj_prm, prm);
    Crystal_Projection_Parameters crystal_proj_prm;

    side.doCrystal=false;
    if (prm.fn_proj_param != "")
    {
        MetaDataVec MD;
        size_t objId;
        MD.read(prm.fn_proj_param);
        objId = MD.firstRowId();
        MD.getValue(MDL_CRYSTAL_PROJ,side.doCrystal,objId);
    }
    if (side.doCrystal)
    {
        crystal_proj_prm.read(prm.fn_proj_param,
                              (side.phantomDescr).phantom_scale);
        // if not null read doc file with unitcell shift
        // format h, k, shift_X shift_Y shift_Z
        if (crystal_proj_prm.DF_shift_bool == true)
            crystal_proj_prm.DF_shift.read(crystal_proj_prm.fn_shift);
        double my_scale = (side.phantomDescr).phantom_scale;

        for (size_t objId : crystal_proj_prm.DF_shift.ids())
        {
            double xcell, ycell;
            crystal_proj_prm.DF_shift.getValue(MDL_CRYSTAL_CELLX,xcell,objId);
            crystal_proj_prm.DF_shift.getValue(MDL_CRYSTAL_CELLY,ycell,objId);
            crystal_proj_prm.DF_shift.setValue(MDL_CRYSTAL_CELLX,xcell*my_scale,objId);
            crystal_proj_prm.DF_shift.setValue(MDL_CRYSTAL_CELLY,ycell*my_scale,objId);

            double x,y,z;
            crystal_proj_prm.DF_shift.getValue(MDL_SHIFT_X,x,objId);
            crystal_proj_prm.DF_shift.getValue(MDL_SHIFT_Y,y,objId);
            crystal_proj_prm.DF_shift.getValue(MDL_SHIFT_Z,z,objId);
            crystal_proj_prm.DF_shift.setValue(MDL_SHIFT_X,x*my_scale,objId);
            crystal_proj_prm.DF_shift.setValue(MDL_SHIFT_Y,y*my_scale,objId);
            crystal_proj_prm.DF_shift.setValue(MDL_SHIFT_Z,z*my_scale,objId);

            crystal_proj_prm.DF_shift.getValue(MDL_CRYSTAL_SHIFTX,x,objId);
            crystal_proj_prm.DF_shift.getValue(MDL_CRYSTAL_SHIFTY,y,objId);
            crystal_proj_prm.DF_shift.getValue(MDL_CRYSTAL_SHIFTZ,z,objId);
            crystal_proj_prm.DF_shift.setValue(MDL_CRYSTAL_SHIFTX,x*my_scale,objId);
            crystal_proj_prm.DF_shift.setValue(MDL_CRYSTAL_SHIFTY,y*my_scale,objId);
            crystal_proj_prm.DF_shift.setValue(MDL_CRYSTAL_SHIFTZ,z*my_scale,objId);
        }
    }

    //#define DEBUG1
#ifdef DEBUG1
    if (crystal_proj_prm.DF_shift_bool == true)
        crystal_proj_prm.DF_shift.write("DEBUG1_shifts");
#endif
#undef DEBUG1


    int ProjNo = 0;
    if (!prm.only_create_angles)
    {
        // Really project
        if (prm.singleProjection)
            ProjNo = PROJECT_Effectively_project(prm.fnOut, prm.singleProjection, prm.projType,prm.samplingRate,
                                                 proj_prm, side, crystal_proj_prm, proj, SF);
        else
        {
            FileName stackName;
            if (prm.fnOut.hasStackExtension())
                stackName = prm.fnOut;
            else
                stackName = prm.fnOut.removeAllExtensions() + ".stk";
            FileName mdName = prm.fnOut.removeAllExtensions() + ".xmd";
            ProjNo = PROJECT_Effectively_project(stackName, prm.singleProjection, prm.projType,prm.samplingRate,
                                                 proj_prm, side, crystal_proj_prm, proj, SF);
            SF.setComment("Angles rot,tilt and psi contain noisy projection angles and rot2,tilt2 and psi2 contain actual projection angles");
            SF.write(mdName);
        }
    }
    else
        if (!prm.singleProjection)
            side.DF.write(prm.fnOut.removeAllExtensions()+".xmd");
    return ProjNo;
}