#include <flexible_alignment.h>

Inheritance diagram for ProgFlexibleAlignment:

Collaboration diagram for ProgFlexibleAlignment:

Public Member Functions
	ProgFlexibleAlignment ()
	Empty constructor. More...

void	defineParams ()
	Define params. More...

void	readParams ()
	Read arguments from command line. More...

void	show ()
	Show. More...

FileName	createDeformedPDB () const

void	performCompleteSearch (int pyramidLevel)

double	performContinuousAssignment (int pyramidLevel)

double	eval ()

virtual void	preProcess ()

virtual void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)

virtual void	finishProcessing ()

virtual void	writeImageParameters (const FileName &fnImg)

Public Member Functions inherited from XmippMetadataProgram
MetaData *	getInputMd ()

MetaDataVec &	getOutputMd ()

	XmippMetadataProgram ()
	Empty constructor. More...

virtual int	tryRead (int argc, const char **argv, bool reportErrors=true)

virtual void	init ()

virtual void	setup (MetaData *md, const FileName &o="", const FileName &oroot="", bool applyGeo=false, MDLabel label=MDL_IMAGE)

virtual	~XmippMetadataProgram ()

void	setMode (WriteModeMetaData _mode)

void	setupRowOut (const FileName &fnImgIn, const MDRow &rowIn, const FileName &fnImgOut, MDRow &rowOut) const
	Prepare rowout. More...

virtual void	wait ()
	Wait for the distributor to finish. More...

virtual void	checkPoint ()
	For very long programs, it may be needed to write checkpoints. More...

virtual void	run ()
	Run over all images. More...

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)

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	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
bool	MPIversion

bool	resume

FileName	fnPDB
	PDB file. More...

FileName	fnModeList
	File zith a list of modes. More...

FileName	fnOutDir
	Output directory. More...

double	maxdefamp
	Maximum deformation amplitude. More...

double	defampsampling
	Deformation sampling. More...

double	scale_defamp
	Temporary. More...

double	scdefamp
	Scaling factor to scale deformation amplitude. More...

double	translsampling
	Translation sampling. More...

double	maxtransl
	Maximum translation. More...

double	sampling_rate
	Sampling rate. More...

FileName	fnmask
	Mask file. More...

bool	do_centerPDB
	Center PDB. More...

bool	projMatch
	ProjMatch. More...

double	minAngularSampling
	Min angular sampling rate. More...

double	gaussian_Real_sigma
	Gaussian weight sigma in real space. More...

double	weight_zero_freq
	Weight for zero frequency. More...

bool	do_FilterPDBVol
	Low-pass filter the volume from PDB. More...

double	cutoff_LPfilter
	Low-pass cut-off frequency. More...

bool	useFixedGaussian
	Use fixed Gaussian instead of scattering factors. More...

double	sigmaGaussian
	Fixed Gaussian standard deviation. More...

double	costfunctionvalue

double	costfunctionvalue_cst

double	sigma
	Sigma. More...

int	max_no_iter
	Max iteration number. More...

std::vector< std::string >	modeList

int	rangen

Matrix1D< double >	parameters

Matrix1D< double >	trial

Matrix1D< double >	trial_best

int	numberOfModes

int	imgSize

FileName	currentImgName

int	currentStage

Matrix1D< double >	bestStage1

MetaDataVec	DF_out

char	nameTemplate [256]

FileName	fnDown

Public Attributes inherited from XmippMetadataProgram
FileName	fn_in
	Filenames of input and output Metadata. More...

FileName	fn_out

FileName	baseName

FileName	pathBaseName

FileName	oextBaseName

bool	apply_geo
	Apply geo. More...

size_t	ndimOut
	Output dimensions. More...

size_t	zdimOut

size_t	ydimOut

size_t	xdimOut

DataType	datatypeOut

size_t	mdInSize
	Number of input elements. More...

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Protected Member Functions
virtual void	createWorkFiles ()

Protected Member Functions inherited from XmippMetadataProgram
virtual void	initComments ()

virtual void	postProcess ()

virtual bool	getImageToProcess (size_t &objId, size_t &objIndex)

void	show () const override

virtual void	startProcessing ()

virtual void	writeOutput ()

virtual void	showProgress ()

virtual void	defineLabelParam ()

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Member Functions inherited from Rerunable
	Rerunable (const FileName &fn)

virtual void	createWorkFiles (bool resume, MetaData *md)

const FileName &	getFileName () const

void	setFileName (const FileName &fn)

Additional Inherited Members
Protected Attributes inherited from XmippMetadataProgram
WriteModeMetaData	mode
	Metadata writing mode: OVERWRITE, APPEND. More...

FileName	oext
	Output extension and root. More...

FileName	oroot

MDLabel	image_label
	MDLabel to be used to read/write images, usually will be MDL_IMAGE. More...

bool	produces_an_output
	Indicate that a unique final output is produced. More...

bool	produces_a_metadata
	Indicate that the unique final output file is a Metadata. More...

bool	each_image_produces_an_output
	Indicate that an output is produced for each image in the input. More...

bool	allow_apply_geo

bool	decompose_stacks
	Input Metadata will treat a stack file as a set of images instead of a unique file. More...

bool	delete_output_stack
	Delete previous output stack file prior to process images. More...

bool	get_image_info
	Get the input image file dimensions to further operations. More...

bool	save_metadata_stack
	Save the associated output metadata when output file is a stack. More...

bool	track_origin
	Include the original input image filename in the output stack. More...

bool	keep_input_columns
	Keep input metadata columns. More...

bool	remove_disabled
	Remove disabled images from the input selfile. More...

bool	allow_time_bar
	Show process time bar. More...

bool	input_is_metadata
	Input is a metadata. More...

bool	single_image
	Input is a single image. More...

bool	input_is_stack
	Input is a stack. More...

bool	output_is_stack
	Output is a stack. More...

bool	create_empty_stackfile

bool	delete_mdIn

size_t	time_bar_step
	Some time bar related counters. More...

size_t	time_bar_size

size_t	time_bar_done

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

NMA Alignment Parameters.

Definition at line 37 of file flexible_alignment.h.

Constructor & Destructor Documentation

◆ ProgFlexibleAlignment()

ProgFlexibleAlignment::ProgFlexibleAlignment ( )

Empty constructor.

Definition at line 40 of file flexible_alignment.cpp.

                                              : Rerunable("")
 {
     rangen = 0;
     resume = false;
     currentImgName = "";
     each_image_produces_an_output = false;
     produces_an_output = true;
 }

Member Function Documentation

◆ createDeformedPDB()

FileName ProgFlexibleAlignment::createDeformedPDB ( ) const

Create deformed PDB

Definition at line 174 of file flexible_alignment.cpp.

                                                         {
     String program;
     String arguments;
     FileName fnRandom;
     fnRandom.initUniqueName(nameTemplate, fnOutDir);
     const char *randStr = fnRandom.c_str();
     program = "xmipp_pdb_nma_deform";
     arguments = formatString(
             "--pdb %s -o %s_deformedPDB.pdb --nma %s --deformations ",
             fnPDB.c_str(), randStr, fnModeList.c_str());
     for (size_t i = 5; i < VEC_XSIZE(trial); i++)
         arguments += floatToString(trial(i)) + " ";
     runSystem(program, arguments, false);
 
     return fnRandom;
 }

◆ createWorkFiles()

virtual void ProgFlexibleAlignment::createWorkFiles ( )

inlineprotectedvirtual

Definition at line 200 of file flexible_alignment.h.

                                    {
       return Rerunable::createWorkFiles(resume, getInputMd());
     }

◆ defineParams()

void ProgFlexibleAlignment::defineParams ( )

virtual

Define params.

Reimplemented from XmippMetadataProgram.

Definition at line 50 of file flexible_alignment.cpp.

                                          {
     addUsageLine(
             "Compute deformation parameters according to a set of NMA modes");
     defaultComments["-o"].clear();
     defaultComments["-o"].addComment(
             "Metadata with output alignment and deformations");
     XmippMetadataProgram::defineParams();
     addParamsLine(
             "   --pdb <PDB_filename>                : PDB Model to compute NMA");
     addParamsLine("  [--odir <outputDir=\".\">]           : Output directory");
     addParamsLine("  [--resume]                           : Resume processing");
     addParamsLine("==Generation of the deformed volumes==");
     addParamsLine(
             "   --modes <filename>                  : File with a list of mode filenames");
     addParamsLine(
             "  [--defampsampling <s=200>]           : Deformation sampling");
     addParamsLine(
             "  [--maxdefamp <s=2000>]               : Maximum deformation amplitude");
     addParamsLine(
             "  [--translsampling <s=2>]             : Translational sampling");
     addParamsLine(
             "  [--maxtransl <max=10>]               : Maximum translation");
     addParamsLine(
             "  [--sampling_rate <Ts=1>]             : in Angstroms/pixel");
     addParamsLine(
             "  [--filterVol <cutoff=15.>]           : Filter the volume after deforming. Default cut-off is 15 A.");
     addParamsLine(
             "  [--centerPDB]                        : Center the PDB structure");
     addParamsLine(
             "  [--fixed_Gaussian <std=-1>]          : For pseudo atoms fixed_Gaussian must be used.");
     addParamsLine(
             "                                       : Default standard deviation <std> is read from PDB file.");
     addParamsLine("==Angular assignment and mode detection==");
     addParamsLine(
             "  [--mask <m=\"\">]                    : 2D Mask applied to the reference images of the deformed volume");
     addParamsLine(
             "                                       :+Note that wavelet assignment needs the input images to be of a size power of 2");
     addParamsLine(
             "  [--minAngularSampling <ang=3>]       : Minimum angular sampling rate");
     addParamsLine(
             "  [--gaussian_Real    <s=0.5>]         : Weighting sigma in Real space");
     addParamsLine(
             "  [--zerofreq_weight  <s=0.>]          : Zero-frequency weight");
     addParamsLine("  [--sigma    <s=10>]                  : Sigma");
     addParamsLine(
             "  [--max_iter  <N=60>]                 : Maximum number of iterations");
     addExampleLine(
             "xmipp_nma_alignment -i images.sel --pdb 2tbv.pdb --modes modelist.xmd --sampling_rate 6.4 -o output.xmd --resume");
     Rerunable::setFileName(fnOutDir+"/nmaDone.xmd");
 }

◆ eval()

double ProgFlexibleAlignment::eval ( )

Alignment

Definition at line 1192 of file flexible_alignment.cpp.

                                    {
     int pyramidLevelDisc = 1;
     int pyramidLevelCont = (currentStage == 1) ? 1 : 0;
 
     if (currentStage == 1) {
         performCompleteSearch(pyramidLevelDisc);
     } else {
         //link(currentImgName.c_str(), fnDown.c_str());
     }
     double fitness = performContinuousAssignment(pyramidLevelCont);
 
     std::cout << "Fitness" << std::endl;
     return fitness;
 }

◆ finishProcessing()

void ProgFlexibleAlignment::finishProcessing ( )

virtual

Write the final parameters.

Reimplemented from XmippMetadataProgram.

Definition at line 168 of file flexible_alignment.cpp.

                                              {
     XmippMetadataProgram::finishProcessing();
     rename(Rerunable::getFileName().c_str(), fn_out.c_str());
 }

◆ performCompleteSearch()

void ProgFlexibleAlignment::performCompleteSearch ( int pyramidLevel )

Perform a complete search with the given image and reference volume at the given level of pyramid. Return the values in the last five positions of trial.

Definition at line 968 of file flexible_alignment.cpp.

                                                                   {
 
     int dim = numberOfModes;
     int ModMaxdeDefamp, ModpowDim, help;
     double SinPhi, CosPhi, SinPsi, CosPsi;
     double S_muMin = 1e30;
     //double    *cost;
     costfunctionvalue = 0.0;
     Matrix1D<double> Parameters(dim + 5);
     Matrix1D<double> limit0(3), limitF(3), centerOfMass(3);
     const char *intensityColumn = "Bfactor";
     computePDBgeometry(fnPDB, centerOfMass, limit0, limitF, intensityColumn);
     centerOfMass = (limit0 + limitF) / 2;
 
     FileName fnRandom;
     fnRandom.initUniqueName(nameTemplate, fnOutDir);
     std::string command;
 
     // Reduce the image
     fnDown = formatString("%s_downimg.xmp", fnRandom.c_str());
     if (pyramidLevel != 0) {
         Image<double> I;
         I.read(currentImgName);
         selfPyramidReduce(xmipp_transformation::BSPLINE3, I(), pyramidLevel);
         I.write(fnDown);
     }
     Image<double> imgtemp;
     imgtemp.read(fnDown);
 
     imgtemp().setXmippOrigin();
     MultidimArray<double> P_mu_image;
     P_mu_image.resize(imgtemp());
     int Xwidth = XSIZE(imgtemp());
     int Ywidth = YSIZE(imgtemp());
     double reduce_rate = 1;
 
     ModMaxdeDefamp = (int) floor(maxdefamp / defampsampling) + 1;
     ModpowDim = (int) pow(ModMaxdeDefamp, dim);
 
     std::vector<double> Rz1(16,0);
     std::vector<double> Ry(16,0);
     std::vector<double> Rz2(16,0);
     std::vector<double> R(16,0);
     std::vector<double> Tr(16,0);
 
     int phiSteps=360/minAngularSampling;
     int thetaSteps=180/minAngularSampling;
     int psiSteps=360/minAngularSampling;
     int transSteps=maxtransl/translsampling;
     for (int iphi = 0; iphi <= phiSteps; iphi++) {
         double phi=iphi*minAngularSampling;
         Parameters(0) = phi;
         trial(0) = phi;
         SinPhi = sin(phi / 180 * PI);
         CosPhi = cos(phi / 180 * PI);
 
         GetIdentitySquareMatrix(Ry.data(), 4L);
 
         double *hlp = Ry.data();
         *hlp = CosPhi;
         hlp += (std::ptrdiff_t) 2L;
         *hlp = -SinPhi;
         hlp += (std::ptrdiff_t) 6L;
         *hlp = SinPhi;
         hlp += (std::ptrdiff_t) 2L;
         *hlp = CosPhi;
 
         for (int itheta = 0; itheta <=thetaSteps; itheta++) {
             double theta=itheta*minAngularSampling;
             Parameters(1) = theta;
             trial(1) = theta;
 
             GetIdentitySquareMatrix(Rz1.data(), 4L);
 
             hlp = Rz1.data();
             *hlp++ = CosPhi;
             *hlp = SinPhi;
             hlp += (std::ptrdiff_t) 3L;
             *hlp++ = -SinPhi;
             *hlp = CosPhi;
 
             for (int ipsi = 0; ipsi<=psiSteps; ipsi++) {
                 double psi=ipsi*minAngularSampling;
                 Parameters(2) = psi;
                 trial(2) = psi;
                 SinPsi = sin(psi / 180 * PI);
                 CosPsi = cos(psi / 180 * PI);
 
                 GetIdentitySquareMatrix(Rz2.data(), 4L);
 
                 hlp = Rz2.data();
                 *hlp++ = CosPsi;
                 *hlp = SinPsi;
                 hlp += (std::ptrdiff_t) 3L;
                 *hlp++ = -SinPsi;
                 *hlp = CosPsi;
 
                 multiply_3Matrices(Rz2.data(), Ry.data(), Rz1.data(), R.data(), 4L, 4L, 4L, 4L);
 
                 for (int ix0=0; ix0<=transSteps; ix0++) {
                     double x0=ix0*translsampling;
                     Parameters(3) = x0 / reduce_rate;
                     trial(3) = x0;
                     for (int iy0=0; iy0<=transSteps; iy0++) {
                         double y0=iy0*translsampling;
                         Parameters(4) = y0 / reduce_rate;
                         trial(4) = y0;
 
                         GetIdentitySquareMatrix(Tr.data(), 4L);
                         hlp = Tr.data();
                         hlp += (std::ptrdiff_t) 3L;
                         *hlp = -x0;
                         hlp += (std::ptrdiff_t) 5L;
                         *hlp = -y0;
 
                         MatrixMultiply(R.data(), Tr.data(), Tr.data(), 4L, 4L, 4L);
 
                         for (int i = 0; i < ModpowDim; i++) {
                             help = i;
                             for (int j = dim - 1; j >= 0; j--) {
                                 Parameters(j + 5) = (double) (help
                                         % ModMaxdeDefamp) * defampsampling;
                                 trial(j + 5) = (double) (help % ModMaxdeDefamp)
                                         * defampsampling;
                                 help = (int) floor(help / ModMaxdeDefamp);
 
                             }
 
                             ProjectionRefencePoint(Parameters, dim, R.data(), Tr.data(),
                                     P_mu_image, imgtemp(), Xwidth, Ywidth,
                                     sigma);
 
                             if (costfunctionvalue < S_muMin) { //2
                                 S_muMin = costfunctionvalue;
                                 for (int k = 0; k < dim + 5; k++) {
                                     trial_best(k) = trial(k);
                                 }
 
                             }
                             std::cout << "trial" << trial << "  cost="
                                     << costfunctionvalue << std::endl;
                             std::cout << "trial_best" << trial_best
                                     << "  cost_best=" << S_muMin << std::endl;
                         }
                     }
                 }
             }
         }
 
     }
 
     std::cout << "trial" << trial << costfunctionvalue << std::endl;
     std::cout << "trial_best" << trial_best << S_muMin << std::endl;
     for (int i = 0; i < dim + 5; i++) {
         trial(i) = trial_best(i);
         parameters(i) = trial_best(i);
     }
 
     MetaDataVec DF_out_discrete;
     size_t id = DF_out_discrete.addObject();
     DF_out_discrete.setValue(MDL_IMAGE, currentImgName, id);
     std::vector<double> aux;
     aux.resize(VEC_XSIZE(parameters));
     FOR_ALL_ELEMENTS_IN_MATRIX1D(parameters)
         aux[i] = parameters(i);
     DF_out_discrete.setValue(MDL_NMA, aux, id);
     DF_out_discrete.write("result_angular_discrete.xmd");
 }

◆ performContinuousAssignment()

double ProgFlexibleAlignment::performContinuousAssignment ( int pyramidLevel )

Perform a continuous search with the given image and reference volume at the given pyramid level. Return the values in the last five positions of trial.

Definition at line 1138 of file flexible_alignment.cpp.

                                                                           {
     costfunctionvalue = 0.0;
     costfunctionvalue_cst = 0.0;
 
     Matrix1D<double> Parameters;
 
     Parameters = trial_best;
 
     std::string command;
     if (pyramidLevel == 0) {
         // Make links
         FileName fnRandom;
         fnRandom.initUniqueName(nameTemplate, fnOutDir);
         fnDown = formatString("%s_downimg.xmp", fnRandom.c_str());
 
         Image<double> I;
         I.read(currentImgName);
         selfPyramidReduce(xmipp_transformation::BSPLINE3, I(), pyramidLevel);
         I.write(fnDown);
     }
 
     //std::string arguments;
     //arguments = formatString("%s_downimg.xmp",fnRandom.c_str());
     Image<double> imgtemp;
     imgtemp.read(fnDown);
 
     imgtemp().setXmippOrigin();
     MultidimArray<double> P_mu_image, P_esp_image;
     P_esp_image = imgtemp();
     P_mu_image.resize(imgtemp());
     int Xwidth = XSIZE(imgtemp());
     int Ywidth = YSIZE(imgtemp());
     //double P_mu_image[Xwidth*Xwidth];
     Matrix1D<double> limit0(3), limitF(3), centerOfMass(3);
     const char *intensityColumn = "Bfactor";
     //Matrix1D<double> test=centerOfMass;
     computePDBgeometry(fnPDB, centerOfMass, limit0, limitF, intensityColumn);
 
     centerOfMass = (limit0 + limitF) / 2;
 
     cstregistrationcontinuous(centerOfMass, Parameters, P_mu_image, P_esp_image,
             Xwidth, Ywidth);
     /* Insert code for continious alignment */
 
     trial(3) *= pow(2.0, (double) pyramidLevel);
     trial(4) *= pow(2.0, (double) pyramidLevel);
 
     trial_best = trial;
 
     double outcost = costfunctionvalue_cst;
     return outcost;
 }

◆ preProcess()

void ProgFlexibleAlignment::preProcess ( )

virtual

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

Reimplemented from XmippMetadataProgram.

Definition at line 155 of file flexible_alignment.cpp.

                                        {
     MetaDataVec SF(fnModeList);
     numberOfModes = SF.size();
     SF.getColumnValues(MDL_NMA_MODEFILE, modeList);
 
     // Get the size of the images in the selfile
     imgSize = xdimOut;
     // Set the pointer of the program to this object
     global_flexible_prog = this;
     //create some neededs files
     createWorkFiles();
 }

◆ processImage()

void ProgFlexibleAlignment::processImage	(	const FileName &	fnImg,
		const FileName &	fnImgOut,
		const MDRow &	rowIn,
		MDRow &	rowOut
	)

virtual

Assign NMA and Alignment parameters to an image

Implements XmippMetadataProgram.

Definition at line 1207 of file flexible_alignment.cpp.

                                                                      {
     static size_t imageCounter = 0;
     ++imageCounter;
 
     int dim = numberOfModes;
 
     parameters.initZeros(dim + 5);
     currentImgName = fnImg;
     snprintf(nameTemplate, 256, "_node%d_img%ld_XXXXXX", rangen,
             (long int) imageCounter);
 
     trial.initZeros(dim + 5);
     trial_best.initZeros(dim + 5);
 
     currentStage = 1;
 #ifdef DEBUG
 
               std::cerr << std::endl << "DEBUG: ===== Node: " << rangen
               <<" processing image " << fnImg <<"(" << objId << ")"
               << " at stage: " << currentStage << std::endl;
 #endif
 
     eval(); // FIXME is this call necessary?
     bestStage1 = trial = parameters = trial_best;
 
     currentStage = 2;
 #ifdef DEBUG
 
               std::cerr << std::endl << "DEBUG: ===== Node: " << rangen
               <<" processing image " << fnImg <<"(" << objId << ")"
               << " at stage: " << currentStage << std::endl;
 #endif
 
     double fitness = eval();
 
     trial = trial_best;
     parameters = trial_best;
 
     parameters.resize(VEC_XSIZE(parameters) + 1);
     parameters(VEC_XSIZE(parameters) - 1) = fitness;
 
     writeImageParameters(fnImg);
 }

◆ readParams()

void ProgFlexibleAlignment::readParams ( )

virtual

Read arguments from command line.

Reimplemented from XmippMetadataProgram.

Definition at line 102 of file flexible_alignment.cpp.

                                        {
     XmippMetadataProgram::readParams();
     fnPDB = getParam("--pdb");
     fnOutDir = getParam("--odir");
     fnModeList = getParam("--modes");
     resume = checkParam("--resume");
     maxdefamp = getDoubleParam("--maxdefamp");
     defampsampling = getDoubleParam("--defampsampling");
     translsampling = getDoubleParam("--translsampling");
     maxtransl = getDoubleParam("--maxtransl");
     sampling_rate = getDoubleParam("--sampling_rate");
     fnmask = getParam("--mask");
     gaussian_Real_sigma = getDoubleParam("--gaussian_Real");
     weight_zero_freq = getDoubleParam("--zerofreq_weight");
     do_centerPDB = checkParam("--centerPDB");
     do_FilterPDBVol = checkParam("--filterVol");
     if (do_FilterPDBVol)
         cutoff_LPfilter = getDoubleParam("--filterVol");
     useFixedGaussian = checkParam("--fixed_Gaussian");
     //if (useFixedGaussian)
     sigmaGaussian = getDoubleParam("--fixed_Gaussian");
     minAngularSampling = getDoubleParam("--minAngularSampling");
     sigma = getDoubleParam("--sigma");
     max_no_iter = getIntParam("--max_iter");
 }

◆ show()

void ProgFlexibleAlignment::show ( )

Show.

Definition at line 129 of file flexible_alignment.cpp.

                                  {
     XmippMetadataProgram::show();
     std::cout << "Output directory:     " << fnOutDir << std::endl
             << "PDB:                  " << fnPDB << std::endl
             << "Resume:               " << resume << std::endl
             << "Mode list:            " << fnModeList << std::endl
             << "Deformation sampling: " << defampsampling << std::endl
             << "Maximum amplitude:    " << maxdefamp << std::endl
             << "Transl. sampling:     " << translsampling << std::endl
             << "Max. Translation:     " << maxtransl << std::endl
             << "Sampling rate:        " << sampling_rate << std::endl
             << "Mask:                 " << fnmask << std::endl
             << "Center PDB:           " << do_centerPDB << std::endl
             << "Filter PDB volume     " << do_FilterPDBVol << std::endl
             << "Use fixed Gaussian:   " << useFixedGaussian << std::endl
             << "Sigma of Gaussian:    " << sigmaGaussian << std::endl
             << "minAngularSampling:   " << minAngularSampling << std::endl
             << "Gaussian Real:        " << gaussian_Real_sigma << std::endl
             << "Zero-frequency weight:" << weight_zero_freq << std::endl
             << "Sigma:                " << sigma << std::endl
             << "Max. Iter:            " << max_no_iter << std::endl;
 }

◆ writeImageParameters()

void ProgFlexibleAlignment::writeImageParameters ( const FileName & fnImg )

virtual

Write the parameters found for one image

Definition at line 1252 of file flexible_alignment.cpp.

                                                                       {
 
     MetaDataVec md;
     size_t objId = md.addObject();
     md.setValue(MDL_IMAGE, fnImg, objId);
     md.setValue(MDL_ENABLED, 1, objId);
     md.setValue(MDL_ANGLE_ROT, parameters(0), objId);
     md.setValue(MDL_ANGLE_TILT, parameters(1), objId);
     md.setValue(MDL_ANGLE_PSI, parameters(2), objId);
     md.setValue(MDL_SHIFT_X, parameters(3), objId);
     md.setValue(MDL_SHIFT_Y, parameters(4), objId);
 
     int dim = numberOfModes;
     std::vector<double> vectortemp;
 
     for (int j = 5; j < 5 + dim; j++)
         vectortemp.push_back(parameters(j));
     md.setValue(MDL_NMA, vectortemp, objId);
     md.setValue(MDL_COST, parameters(5 + dim), objId);
     md.append(Rerunable::getFileName());
 }

Member Data Documentation

◆ bestStage1

Matrix1D<double> ProgFlexibleAlignment::bestStage1

Definition at line 147 of file flexible_alignment.h.

◆ costfunctionvalue

double ProgFlexibleAlignment::costfunctionvalue

Definition at line 107 of file flexible_alignment.h.

◆ costfunctionvalue_cst

double ProgFlexibleAlignment::costfunctionvalue_cst

Definition at line 110 of file flexible_alignment.h.

◆ currentImgName

FileName ProgFlexibleAlignment::currentImgName

Definition at line 141 of file flexible_alignment.h.

◆ currentStage

int ProgFlexibleAlignment::currentStage

Definition at line 144 of file flexible_alignment.h.

◆ cutoff_LPfilter

double ProgFlexibleAlignment::cutoff_LPfilter

Low-pass cut-off frequency.

Definition at line 98 of file flexible_alignment.h.

◆ defampsampling

double ProgFlexibleAlignment::defampsampling

Deformation sampling.

Definition at line 59 of file flexible_alignment.h.

◆ DF_out

MetaDataVec ProgFlexibleAlignment::DF_out

Definition at line 150 of file flexible_alignment.h.

◆ do_centerPDB

bool ProgFlexibleAlignment::do_centerPDB

Center PDB.

Definition at line 80 of file flexible_alignment.h.

◆ do_FilterPDBVol

bool ProgFlexibleAlignment::do_FilterPDBVol

Low-pass filter the volume from PDB.

Definition at line 95 of file flexible_alignment.h.

◆ fnDown

FileName ProgFlexibleAlignment::fnDown

Definition at line 156 of file flexible_alignment.h.

◆ fnmask

FileName ProgFlexibleAlignment::fnmask

Mask file.

Definition at line 77 of file flexible_alignment.h.

◆ fnModeList

FileName ProgFlexibleAlignment::fnModeList

File zith a list of modes.

Definition at line 50 of file flexible_alignment.h.

◆ fnOutDir

FileName ProgFlexibleAlignment::fnOutDir

Output directory.

Definition at line 53 of file flexible_alignment.h.

◆ fnPDB

FileName ProgFlexibleAlignment::fnPDB

PDB file.

Definition at line 47 of file flexible_alignment.h.

◆ gaussian_Real_sigma

double ProgFlexibleAlignment::gaussian_Real_sigma

Gaussian weight sigma in real space.

Definition at line 89 of file flexible_alignment.h.

◆ imgSize

int ProgFlexibleAlignment::imgSize

Definition at line 138 of file flexible_alignment.h.

◆ max_no_iter

int ProgFlexibleAlignment::max_no_iter

Max iteration number.

Definition at line 116 of file flexible_alignment.h.

◆ maxdefamp

double ProgFlexibleAlignment::maxdefamp

Maximum deformation amplitude.

Definition at line 56 of file flexible_alignment.h.

◆ maxtransl

double ProgFlexibleAlignment::maxtransl

Maximum translation.

Definition at line 71 of file flexible_alignment.h.

◆ minAngularSampling

double ProgFlexibleAlignment::minAngularSampling

Min angular sampling rate.

Definition at line 86 of file flexible_alignment.h.

◆ modeList

std::vector<std::string> ProgFlexibleAlignment::modeList

Definition at line 120 of file flexible_alignment.h.

◆ MPIversion

bool ProgFlexibleAlignment::MPIversion

MPI version

Definition at line 41 of file flexible_alignment.h.

◆ nameTemplate

char ProgFlexibleAlignment::nameTemplate[256]

Definition at line 153 of file flexible_alignment.h.

◆ numberOfModes

int ProgFlexibleAlignment::numberOfModes

Definition at line 135 of file flexible_alignment.h.

◆ parameters

Matrix1D<double> ProgFlexibleAlignment::parameters

Definition at line 126 of file flexible_alignment.h.

◆ projMatch

bool ProgFlexibleAlignment::projMatch

ProjMatch.

Definition at line 83 of file flexible_alignment.h.

◆ rangen

int ProgFlexibleAlignment::rangen

Definition at line 123 of file flexible_alignment.h.

◆ resume

bool ProgFlexibleAlignment::resume

Resume computations

Definition at line 44 of file flexible_alignment.h.

◆ sampling_rate

double ProgFlexibleAlignment::sampling_rate

Sampling rate.

Definition at line 74 of file flexible_alignment.h.

◆ scale_defamp

double ProgFlexibleAlignment::scale_defamp

Temporary.

Definition at line 62 of file flexible_alignment.h.

◆ scdefamp

double ProgFlexibleAlignment::scdefamp

Scaling factor to scale deformation amplitude.

Definition at line 65 of file flexible_alignment.h.

◆ sigma

double ProgFlexibleAlignment::sigma

Sigma.

Definition at line 113 of file flexible_alignment.h.

◆ sigmaGaussian

double ProgFlexibleAlignment::sigmaGaussian

Fixed Gaussian standard deviation.

Definition at line 104 of file flexible_alignment.h.

◆ translsampling

double ProgFlexibleAlignment::translsampling

Translation sampling.

Definition at line 68 of file flexible_alignment.h.

◆ trial

Matrix1D<double> ProgFlexibleAlignment::trial

Definition at line 129 of file flexible_alignment.h.

◆ trial_best

Matrix1D<double> ProgFlexibleAlignment::trial_best

Definition at line 132 of file flexible_alignment.h.

◆ useFixedGaussian

bool ProgFlexibleAlignment::useFixedGaussian

Use fixed Gaussian instead of scattering factors.

Definition at line 101 of file flexible_alignment.h.

◆ weight_zero_freq

double ProgFlexibleAlignment::weight_zero_freq

Weight for zero frequency.

Definition at line 92 of file flexible_alignment.h.

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

xmipp/libraries/reconstruction/flexible_alignment.h
xmipp/libraries/reconstruction/flexible_alignment.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgFlexibleAlignment()

Member Function Documentation

◆ createDeformedPDB()

◆ createWorkFiles()

◆ defineParams()

◆ eval()

◆ finishProcessing()

◆ performCompleteSearch()

◆ performContinuousAssignment()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ show()

◆ writeImageParameters()

Member Data Documentation

◆ bestStage1

◆ costfunctionvalue

◆ costfunctionvalue_cst

◆ currentImgName

◆ currentStage

◆ cutoff_LPfilter

◆ defampsampling

◆ DF_out

◆ do_centerPDB

◆ do_FilterPDBVol

◆ fnDown

◆ fnmask

◆ fnModeList

◆ fnOutDir

◆ fnPDB

◆ gaussian_Real_sigma

◆ imgSize

◆ max_no_iter

◆ maxdefamp

◆ maxtransl

◆ minAngularSampling

◆ modeList

◆ MPIversion

◆ nameTemplate

◆ numberOfModes

◆ parameters

◆ projMatch

◆ rangen

◆ resume

◆ sampling_rate

◆ scale_defamp

◆ scdefamp

◆ sigma

◆ sigmaGaussian

◆ translsampling

◆ trial

◆ trial_best

◆ useFixedGaussian

◆ weight_zero_freq