Inheritance diagram for ProgAngularDistributionShow:

Collaboration diagram for ProgAngularDistributionShow:

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	fnIn

FileName	fnOut

String	type

double	R

double	rmax

int	shift_center

int	solid_sphere

int	steps

double	rot_view

double	tilt_view

bool	up_down_correction

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

Definition at line 34 of file angular_distribution_show.cpp.

Member Function Documentation

◆ defineParams()

void ProgAngularDistributionShow::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 68 of file angular_distribution_show.cpp.

     {
         addUsageLine("Shows which is the angular distribution of a set of projections.");
         addUsageLine("+There are three kinds of outputs: a bild file (chimera understands this format), a distance histogram and a postscript file. ");
         addUsageLine("+In postcript, each projection is represented by a small isosceles triangles (the longest part is pointing to Y in the projection plane). ");
         addUsageLine("+In chimera, each projection direction has a sphere whose radius is proportional to the number of images assigned to it");
         addUsageLine("+The histogram output is the histogram of the minimum distance (in degrees) among projections. The distance is measured on the sphere surface. This gives an idea of how compact is the angular distribution.");
         addParamsLine(" -i <metadata>                 : Metadata file with the angles");
         addParamsLine(" -o <file> <type>              : Output file");
         addParamsLine("    where <type>");
         addParamsLine("          chimera <R=60> <rmax=1.5> <shift_center=0>               : R=sphere radius, rmax=maximum point radius, shift_center=shift in pixels applied to all coordinates");
         addParamsLine("                                                                   : shift_center should be half the volume size and R should be 2/3 the volume size");
         addParamsLine("          ps <R=60> <rmax=1.5> <rot=0> <tilt=30> <solid_sphere=0>  : R=sphere radius, rmax=maximum point radius, rot and tilt defines the point of view, solid_sphere=0 (=no) or 1 (=yes)");
         addParamsLine("                                                                : If the sphere is solid, projections in the back plane are not shown");
         addParamsLine("          histogram <stepno=100> : Number of divisions in the histogram");
         addParamsLine("[--up_down_correction]         : correct angles so that a semisphere is shown");
     }

◆ readParams()

void ProgAngularDistributionShow::readParams ( )

inlinevirtual

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 44 of file angular_distribution_show.cpp.

     {
         fnIn = getParam("-i");
         fnOut = getParam("-o");
         type = getParam("-o",1);
         if (type=="chimera")
         {
             R=getDoubleParam("-o",2);
             rmax=getDoubleParam("-o",3);
             shift_center=getIntParam("-o",4);
         }
         else if (type=="ps")
         {
             R=getDoubleParam("-o",2);
             rmax=getDoubleParam("-o",3);
             rot_view=getDoubleParam("-o",4);
             tilt_view=getDoubleParam("-o",5);
             solid_sphere=getIntParam("-o",6);
         }
         else if (type=="histogram")
             steps = getIntParam("-o",2);
         up_down_correction = checkParam("--up_down_correction");
     }

◆ run()

void ProgAngularDistributionShow::run ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 86 of file angular_distribution_show.cpp.

     {
         // Get angles ==============================================================
         MetaDataVec angles;
         angles.read(fnIn);
         size_t AngleNo = angles.size();
         if (AngleNo == 0 || !angles.containsLabel(MDL_ANGLE_ROT))
             REPORT_ERROR(ERR_MD_BADLABEL, "Input file doesn't contain angular information");
 
         double maxWeight = -99.e99;
         MultidimArray<double> weight;
         weight.initZeros(AngleNo);
         if (angles.containsLabel(MDL_WEIGHT))
         {
             // Find maximum weight
             int i=0;
             for (size_t objId : angles.ids())
             {
                 double w;
                 angles.getValue(MDL_WEIGHT,w,objId);
                 DIRECT_A1D_ELEM(weight,i++)=w;
                 maxWeight=XMIPP_MAX(w,maxWeight);
             }
         }
         double imaxWeight=1.0/maxWeight;
 
         // Build vector tables ======================================================
         std::vector< Matrix1D<double> > v, v_ang;
         v.reserve(AngleNo);
         v_ang.reserve(AngleNo);
         Matrix1D<double> aux(3);
         Matrix1D<double> aux_ang(3);
         for (size_t objId : angles.ids())
         {
             double rot, tilt, psi;
             angles.getValue(MDL_ANGLE_ROT,rot,objId);
             angles.getValue(MDL_ANGLE_TILT,tilt,objId);
             angles.getValue(MDL_ANGLE_PSI,psi,objId);
             if (up_down_correction && fabs(tilt)>90)
                 \
                 Euler_up_down(rot,tilt,psi,rot,tilt,psi);
             Euler_direction(rot, tilt, psi, aux);
             v.push_back(aux);
             VECTOR_R3(aux_ang, rot, tilt, psi);
             v_ang.push_back(aux_ang);
         }
 
         if (type=="histogram")
         {
             // Compute minimum distance table
             MultidimArray<double> dist;
             dist.initZeros(AngleNo);
             for (size_t i = 0; i < AngleNo; i++)
             {
                 const Matrix1D<double> &vi=v[i];
                 for (size_t j = i + 1; j < AngleNo; j++)
                 {
                     const Matrix1D<double> &vj=v[j];
                     // Since the two vectors are in the unit sphere, the spherical distance
                     // is simply the arc cosine
                     double d = acos(XX(vi)*XX(vj) + YY(vi)*YY(vj) + ZZ(vi)*ZZ(vj));
                     d=RAD2DEG(d);
                     if (DIRECT_A1D_ELEM(dist,i) == 0 || d < DIRECT_A1D_ELEM(dist,i))
                         DIRECT_A1D_ELEM(dist,i) = d;
                     if (DIRECT_A1D_ELEM(dist,j) == 0 || d < DIRECT_A1D_ELEM(dist,j))
                         DIRECT_A1D_ELEM(dist,j) = d;
                 }
             }
 
             Histogram1D dist_hist;
             compute_hist(dist, dist_hist, steps);
             dist_hist.write(fnOut);
         }
         else if (type=="chimera")
         {
             std::ofstream fh_bild;
             fh_bild.open(fnOut.c_str(), std::ios::out);
             if (!fh_bild)
                 REPORT_ERROR(ERR_IO_NOWRITE, fnOut);
             fh_bild << ".color 1 0 0" << std::endl;
 
             int imax=v.size();
             for (int i=0; i<imax; i++)
             {
                 double r=rmax;
                 if (maxWeight>0)
                     r *= DIRECT_A1D_ELEM(weight,i)*imaxWeight;
                 fh_bild
                 << ".sphere "
                 << R*XX(v[i])  + shift_center << " "
                 << R*YY(v[i])  + shift_center << " "
                 << R*ZZ(v[i])  + shift_center << " "
                 << r
                 <<"\n";
             }
             fh_bild.close();
         }
         else if (type=="ps")
         {
             std::ofstream fh_ps;
             fh_ps.open(fnOut.c_str(), std::ios::out);
             if (!fh_ps)
                 REPORT_ERROR(ERR_IO_NOWRITE, fnOut);
 
             fh_ps << "%%!PS-Adobe-2.0\n";
             fh_ps << "%% Creator: Angular Distribution\n";
             fh_ps << "%% Title: Angular distribution of " << fnIn << "\n";
             fh_ps << "%% Pages: 1\n";
 
 #define TO_PS(x,y) \
         tmp=y; \
         y=400.0f-x*250.0f/60; \
         x=300.0f+tmp*250.0f/60;
 
             Matrix1D<double> p0(4), p1(4), p2(4), p3(4), view_direction, pp(3);
             Matrix2D<double> A, euler_view;
             Euler_angles2matrix(rot_view, tilt_view, 0., euler_view);
             euler_view.getRow(2, view_direction);
             double tmp;
             int imax=v.size();
             for (int i=0; i<imax; i++)
             {
                 double r=rmax;
                 if (maxWeight>0)
                     r *= DIRECT_A1D_ELEM(weight,i)*imaxWeight;
 
                 // Initially the triangle is on the floor of the projection plane
                 VECTOR_R3(p0,    0   ,      0        , 0);
                 VECTOR_R3(p1,    0   , r*2 / 3*SIND(60), 0);
                 VECTOR_R3(p2, r / 2*0.6, -r*1 / 3*SIND(60), 0);
                 VECTOR_R3(p3, -r / 2*0.6, -r*1 / 3*SIND(60), 0);
 
                 // Convert to homogeneous coordinates
                 p0(3) = 1;
                 p1(3) = 1;
                 p2(3) = 1;
                 p3(3) = 1;
 
                 // Compute Transformation matrix
                 const Matrix1D<double> &v_angi=v_ang[i];
                 const Matrix1D<double> &vi=v[i];
                 Euler_angles2matrix(VEC_ELEM(v_angi,1), VEC_ELEM(v_angi,2),
                                     VEC_ELEM(v_angi,3), A, true);
                 A = A.transpose(); // We go from the projection plane to the universal coordinates
 
                 // Apply a translation to the sphere of radius R
                 MAT_ELEM(A, 0, 3) = R * XX(vi);
                 MAT_ELEM(A, 1, 3) = R * YY(vi);
                 MAT_ELEM(A, 2, 3) = R * ZZ(vi);
 
                 // Convert triangle coordinates to universal ones
                 p0 = A * p0;
                 p1 = A * p1;
                 p2 = A * p2;
                 p3 = A * p3;
 
                 // Check if this triangle must be drawn
                 if (solid_sphere)
                 {
                     // Point-plane distance
                     double d=XX(p0)*XX(view_direction)+
                              YY(p0)*YY(view_direction)+
                              ZZ(p0)*ZZ(view_direction);
                     if (d < 0)
                         continue;
                 }
 
                 // Project this triangle onto the view plane and write in PS
                 Uproject_to_plane(p1, euler_view, pp);
                 TO_PS(XX(pp), YY(pp));
                 fh_ps << "newpath\n";
                 fh_ps << XX(pp) << " " << YY(pp) << " moveto\n";
 
                 Uproject_to_plane(p2, euler_view, pp);
                 TO_PS(XX(pp), YY(pp));
                 fh_ps << XX(pp) << " " << YY(pp) << " lineto\n";
 
                 Uproject_to_plane(p3, euler_view, pp);
                 TO_PS(XX(pp), YY(pp));
                 fh_ps << XX(pp) << " " << YY(pp) << " lineto\n";
 
                 Uproject_to_plane(p1, euler_view, pp);
                 TO_PS(XX(pp), YY(pp));
                 fh_ps << XX(pp) << " " << YY(pp) << " lineto\n";
 
                 fh_ps << "closepath\nstroke\n";
             }
             fh_ps << "showpage\n";
             fh_ps.close();
         }
     }