#include <tomo_align_refinement.h>

Inheritance diagram for ProgTomoAlignRefinement:

Collaboration diagram for ProgTomoAlignRefinement:

Public Member Functions
void	readParams ()
	Read arguments from command line. More...

void	show ()
	Show. More...

void	defineParams ()
	Define parameters. More...

void	produce_side_info ()

void	predict_angles (size_t i, const FileName &fnImgOut)

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_ref

FileName	fn_sel

FileName	fn_out

double	max_rot_change

double	max_tilt_change

double	max_psi_change

double	rot_step

double	tilt_step

double	psi_step

double	max_shift_change

double	shift_step

bool	adjustGray

bool	generateAligned

Image< double >	V

std::vector< AlignmentTomography >	list_of_assigned

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

Angular Predict parameters.

Definition at line 53 of file tomo_align_refinement.h.

Member Function Documentation

◆ defineParams()

void ProgTomoAlignRefinement::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 75 of file tomo_align_refinement.cpp.

 {
     addUsageLine("Realign a tilt series with respect to a volume following a single ");
     addUsageLine("particles approach, i.e., the volume is reprojected and the alignment");
     addUsageLine("parameters are reoptimized.");
     addParamsLine("   --ref <volume>             : Reference volume");
     addParamsLine("   --sel <selfile>            : Images to align");
     addParamsLine("   --oroot <rootname>         : rootname for the output");
     addParamsLine("                              : rootname.doc contains a selfile with the");
     addParamsLine("                              : images realigned");
     addParamsLine("                              : rootname.stk contains the aligned and");
     addParamsLine("                              : adjusted images in case --adjustGray or");
     addParamsLine("                              : --generateAligned are given");
     addParamsLine("  [--max_rot_change <ang=2>]  : Maximum change allowed in rot");
     addParamsLine("  [--max_tilt_change <ang=2>] : Maximum change allowed in tilt");
     addParamsLine("  [--max_psi_change <ang=2>]  : Maximum change allowed in psi");
     addParamsLine("  [--max_shift_change <r=10>] : Maximum change allowed in shift");
     addParamsLine("  [--rot_step <ang=0.25>]     : Rot search step");
     addParamsLine("  [--tilt_step <ang=0.25>]    : Tilt search step");
     addParamsLine("  [--psi_step <ang=0.25>]     : Psi search step");
     addParamsLine("  [--shift_step <r=2>]        : Step in shift in pixels");
     addParamsLine("  [--adjustGray]              : Adjust also gray values");
     addParamsLine("  [--generateAligned]         : Generate aligned images");
 }

◆ predict_angles()

void ProgTomoAlignRefinement::predict_angles	(	size_t	i,
		const FileName &	fnImgOut
	)

Predict angles and shift. This function searches in the shift-psi space and for each combination it correlates with the whole reference set.

Definition at line 132 of file tomo_align_refinement.cpp.

 {
     AlignmentTomography newAlignment=list_of_assigned[idx];
     Image<double> I, Ip;
     MultidimArray<int> mask;
     I.read(list_of_assigned[idx].fn_img);
     I().setXmippOrigin();
     mask.resizeNoCopy(I());
 
     double rot0=list_of_assigned[idx].rot-max_rot_change;
     double rotF=list_of_assigned[idx].rot+max_rot_change;
     double tilt0=list_of_assigned[idx].tilt-max_tilt_change;
     double tiltF=list_of_assigned[idx].tilt+max_tilt_change;
     if (idx>0)
         tilt0=XMIPP_MAX(tilt0,
                         (list_of_assigned[idx].tilt+list_of_assigned[idx-1].tilt)/2);
     if (idx<list_of_assigned.size()-1)
         tiltF=XMIPP_MIN(tiltF,
                         (list_of_assigned[idx].tilt+list_of_assigned[idx+1].tilt)/2);
 
     Projection theo;
     Matrix2D<double> M;
 #ifdef DEBUG
 
     std::cout << "original idx,rot,tilt,psi,x,y=" << idx << " "
     << newAlignment.rot << " " << newAlignment.tilt
     << " " << newAlignment.psi << " "
     << newAlignment.x << " " << newAlignment.y << std::endl;
 #endif
 
     for (double rot = rot0; rot <= rotF; rot += rot_step)
         for (double tilt = tilt0; tilt <= tiltF; tilt += tilt_step)
         {
             Ip()=I();
             // Take a projection from the given direction
             projectVolume(V(), theo, YSIZE(V()), XSIZE(V()), rot, tilt, 0);
             mask.initConstant(1);
             FOR_ALL_ELEMENTS_IN_ARRAY2D(mask)
             if (IMGPIXEL(theo,i,j)==0 || IMGPIXEL(Ip,i,j)==0)
             {
                 A2D_ELEM(mask,i,j)=0;
                 IMGPIXEL(Ip,i,j)=0;
             }
             double newCorr=correlationIndex(theo(),Ip(),&mask);
             if (newCorr>newAlignment.corr)
             {
                 newAlignment.rot = rot;
                 newAlignment.tilt = tilt;
                 newAlignment.corr=newCorr;
                 if (adjustGray)
                     Ip().rangeAdjust(theo(),&mask);
                 if (adjustGray || generateAligned)
                     Ip.write(fnImgOut);
 #ifdef DEBUG
 
                 std::cout << "    Improved " << idx << " rot=" << rot << " tilt=" << tilt
                 << " x,y="
                 << newAlignment.x << " " << newAlignment.y << " psi="
                 << newAlignment.psi << " corr="
                 << newCorr << std::endl;
                 Image<double> save;
                 save()=Ip();
                 save.write("PPPexp.xmp");
                 save()=theo();
                 save.write("PPPtheo.xmp");
                 typeCast(mask,save());
                 save.write("PPPmask.xmp");
                 save()=theo()-Ip();
                 save.write("PPPdiff.xmp");
 #endif
 
             }
 
             // Look for better alignment
             alignImages(theo(),Ip(),M, xmipp_transformation::DONT_WRAP);
 
             // Measure the new correlation
             newCorr=correlationIndex(theo(),Ip(),&mask);
 
             // Keep the value
             if (newCorr>newAlignment.corr)
             {
                 newAlignment.rot = rot;
                 newAlignment.tilt = tilt;
                 bool flip;
                 double scale;
                 newAlignment.M=M;
                 transformationMatrix2Parameters2D(M, flip, scale, newAlignment.x, newAlignment.y,
                                                 newAlignment.psi);
                 if (adjustGray)
                     Ip().rangeAdjust(theo(),&mask);
                 if (adjustGray || generateAligned)
                     Ip.write(fnImgOut);
 #ifdef DEBUG
 
                 std::cout << "    Improved " << idx << " rot=" << rot << " tilt=" << tilt
                 << " x,y="
                 << newAlignment.x << " " << newAlignment.y << " psi="
                 << newAlignment.psi << " corr="
                 << newCorr << std::endl;
                 newAlignment.corr = newCorr;
                 Image<double> save;
                 save() = Ip();
                 save.write("PPPexpRealigned.xmp");
                 save()=theo()-Ip();
                 save.write("PPPdiffRealigned.xmp");
                 std::cout << "Press any key\n";
                 char c;
                 std::cin >> c;
 #endif
 
             }
         }
 
     // Select best alignment
     list_of_assigned[idx]=newAlignment;
 }

◆ produce_side_info()

void ProgTomoAlignRefinement::produce_side_info ( )

Produce side info. An exception is thrown if any of the files is not found

Definition at line 102 of file tomo_align_refinement.cpp.

 {
     V.read(fn_ref);
     V().setXmippOrigin();
     MetaDataVec SF(fn_sel);
     Image<double> I;
     FileName fnImg;
     ApplyGeoParams params;
     params.datamode = HEADER;
 
     for (size_t objId : SF.ids())
     {
         AlignmentTomography dummy;
         SF.getValue(MDL_IMAGE,fnImg,objId);
         I.readApplyGeo(fnImg,SF,objId, params);
         I().setXmippOrigin();
         dummy.rot=I.rot();
         dummy.tilt=I.tilt();
         dummy.psi=I.psi();
         dummy.x=I.Xoff();
         dummy.y=I.Yoff();
         dummy.fn_img=fnImg;
         dummy.corr=-1;
         list_of_assigned.push_back(dummy);
     }
 }

◆ readParams()

void ProgTomoAlignRefinement::readParams ( )

virtual

Read arguments from command line.

Reimplemented from XmippProgram.

Definition at line 41 of file tomo_align_refinement.cpp.

 {
     fn_ref = getParam("--ref");
     fn_sel = getParam("--sel");
     fn_out = getParam("--oroot");
     max_rot_change = getDoubleParam("--max_rot_change");
     max_tilt_change = getDoubleParam("--max_tilt_change");
     max_psi_change = getDoubleParam("--max_psi_change");
     rot_step = getDoubleParam("--rot_step");
     tilt_step = getDoubleParam("--tilt_step");
     psi_step = getDoubleParam("--psi_step");
     max_shift_change = getDoubleParam("--max_shift_change");
     shift_step = getDoubleParam("--shift_step");
     adjustGray = checkParam("--adjustGray");
     generateAligned = checkParam("--generateAligned");
 }

◆ run()

void ProgTomoAlignRefinement::run ( )

virtual

Run the algorithm over all images

Reimplemented from XmippProgram.

Definition at line 253 of file tomo_align_refinement.cpp.

 {
     produce_side_info();
     MetaDataVec DF;
     FileName fnMaskOut, fnImgOut;
     Projection theo;
     Image<double> Imask, I;
     FileName fn_tmp(fn_out + ".stk");
     if (adjustGray)
       fn_tmp.deleteFile();
 
     for (size_t i=0; i<list_of_assigned.size(); i++)
     {
         if (adjustGray || generateAligned)
             fnImgOut.compose(i+1,fn_out+".stk");
         else
             fnImgOut=list_of_assigned[i].fn_img;
 
         // Get angles and shifts
         predict_angles(i,fnImgOut);
 
         // Store them in the output docfile
         size_t id = DF.addObject();
         DF.setValue(MDL_IMAGE,fnImgOut,id);
         DF.setValue(MDL_IMAGE_ORIGINAL,list_of_assigned[i].fn_img,id);
         DF.setValue(MDL_ANGLE_ROT,list_of_assigned[i].rot,id);
         DF.setValue(MDL_ANGLE_TILT,list_of_assigned[i].tilt,id);
         DF.setValue(MDL_ANGLE_PSI,list_of_assigned[i].psi,id);
         DF.setValue(MDL_SHIFT_X,list_of_assigned[i].x,id);
         DF.setValue(MDL_SHIFT_Y,list_of_assigned[i].y,id);
         DF.setValue(MDL_MAXCC,list_of_assigned[i].corr,id);
     }
     DF.write(fn_out+".doc");
 }

◆ show()

void ProgTomoAlignRefinement::show ( )

Show.

Definition at line 59 of file tomo_align_refinement.cpp.

 {
     std::cout
     << "Reference images:   " << fn_ref           << std::endl
     << "Input images:       " << fn_sel           << std::endl
     << "Ouput rootname:     " << fn_out           << std::endl
     << "Max rot change:     " << max_rot_change   << " step: " << rot_step << std::endl
     << "Max tilt change:    " << max_tilt_change  << " step: " << tilt_step << std::endl
     << "Max psi change:     " << max_psi_change   << " step: " << psi_step << std::endl
     << "Max shift change:   " << max_shift_change << " step: " << shift_step << std::endl
     << "Adjust gray:        " << adjustGray       << std::endl
     << "Generate aligned:   " << generateAligned  << std::endl
     ;
 }

Member Data Documentation

◆ adjustGray

bool ProgTomoAlignRefinement::adjustGray

Adjust gray

Definition at line 79 of file tomo_align_refinement.h.

◆ fn_out

FileName ProgTomoAlignRefinement::fn_out

Root filename for the output

Definition at line 61 of file tomo_align_refinement.h.

◆ fn_ref

FileName ProgTomoAlignRefinement::fn_ref

Filename of the reference volume

Definition at line 57 of file tomo_align_refinement.h.

◆ fn_sel

FileName ProgTomoAlignRefinement::fn_sel

Filename of the images

Definition at line 59 of file tomo_align_refinement.h.

◆ generateAligned

bool ProgTomoAlignRefinement::generateAligned

Generate output images

Definition at line 81 of file tomo_align_refinement.h.

◆ list_of_assigned

std::vector<AlignmentTomography> ProgTomoAlignRefinement::list_of_assigned

Definition at line 84 of file tomo_align_refinement.h.

◆ max_psi_change

double ProgTomoAlignRefinement::max_psi_change

Maximum psi change.

Definition at line 67 of file tomo_align_refinement.h.

◆ max_rot_change

double ProgTomoAlignRefinement::max_rot_change

Maximum rotation change.

Definition at line 63 of file tomo_align_refinement.h.

◆ max_shift_change

double ProgTomoAlignRefinement::max_shift_change

Maximum shift change

Definition at line 75 of file tomo_align_refinement.h.

◆ max_tilt_change

double ProgTomoAlignRefinement::max_tilt_change

Max tilt change

Definition at line 65 of file tomo_align_refinement.h.

◆ psi_step

double ProgTomoAlignRefinement::psi_step

Psi step

Definition at line 73 of file tomo_align_refinement.h.

◆ rot_step

double ProgTomoAlignRefinement::rot_step

Rot step

Definition at line 69 of file tomo_align_refinement.h.

◆ shift_step

double ProgTomoAlignRefinement::shift_step

Shift step

Definition at line 77 of file tomo_align_refinement.h.

◆ tilt_step

double ProgTomoAlignRefinement::tilt_step

Tilt step

Definition at line 71 of file tomo_align_refinement.h.

◆ V

Image<double> ProgTomoAlignRefinement::V

Definition at line 83 of file tomo_align_refinement.h.

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

xmipp/legacy/libraries/reconstruction/tomo_align_refinement.h
xmipp/legacy/libraries/reconstruction/tomo_align_refinement.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ predict_angles()

◆ produce_side_info()

◆ readParams()

◆ run()

◆ show()

Member Data Documentation

◆ adjustGray

◆ fn_out

◆ fn_ref

◆ fn_sel

◆ generateAligned

◆ list_of_assigned

◆ max_psi_change

◆ max_rot_change

◆ max_shift_change

◆ max_tilt_change

◆ psi_step

◆ rot_step

◆ shift_step

◆ tilt_step

◆ V