#include <nma_alignment.h>

Inheritance diagram for ProgNmaAlignment:

Collaboration diagram for ProgNmaAlignment:

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

	~ProgNmaAlignment ()
	Destructor. More...

void	defineParams ()
	Define params. More...

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

void	show ()
	Show. More...

FileName	createDeformedPDB (int pyramidLevel) const

void	performCompleteSearch (const FileName &fnRandom, int pyramidLevel) const

double	performContinuousAssignment (const FileName &fnRandom, int pyramidLevel) const

double	computeFitness (Matrix1D< double > &trial) const

void	updateBestFit (double fitness)

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
	Reference atomic or pseudo-atomic structure in PDB format. More...

FileName	fnOutDir
	Output directory. More...

FileName	fnModeList
	File with a list of mode filenames. More...

double	trustradius_scale
	Positive scaling factor to scale the initial trust region radius. More...

double	sampling_rate
	Pixel size in Angstroms. More...

FileName	fnmask
	Mask file for 2D masking of the projections of the deformed volume. More...

bool	do_centerPDB
	Center the PDB structure. More...

bool	projMatch
	Real-space instead of wavelet-space (default) projection matching (global matching) that is refined by local (Fourier central slice) projection matching. More...

double	discrAngStep
	Angular sampling step for computing the reference projections for global matching. More...

double	gaussian_DFT_sigma
	Sigma of Gaussian weigthing in Fourier space (parameter of central-slice method) More...

double	gaussian_Real_sigma
	Sigma of Gaussian weigthing in real space for spline interpolation in Fourier space (parameter of central-slice method) More...

double	weight_zero_freq
	Zero-frequency weight (parameter of central-slice method) More...

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

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

bool	useFixedGaussian
	Use pseudo-atoms instead of atoms. More...

double	sigmaGaussian
	Gaussian standard deviation for pseudo-atoms. More...

int	rangen

Matrix1D< double >	parameters

Matrix1D< double >	trial

Matrix1D< double >	trial_best

Matrix1D< double >	fitness_min

int	numberOfModes

int	imgSize

FileName	currentImgName

int	currentStage

Matrix1D< double >	bestStage1

MetaDataVec	DF_out

char	nameTemplate [256]

ProgPdbConverter *	progVolumeFromPDB

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 40 of file nma_alignment.h.

Constructor & Destructor Documentation

◆ ProgNmaAlignment()

ProgNmaAlignment::ProgNmaAlignment ( )

Empty constructor.

Definition at line 33 of file nma_alignment.cpp.

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

◆ ~ProgNmaAlignment()

ProgNmaAlignment::~ProgNmaAlignment ( )

Destructor.

Definition at line 43 of file nma_alignment.cpp.

                                     {
     delete progVolumeFromPDB;
 }

Member Function Documentation

◆ computeFitness()

double ProgNmaAlignment::computeFitness ( Matrix1D< double > & trial ) const

Computes the fitness of a set of trial parameters

◆ createDeformedPDB()

FileName ProgNmaAlignment::createDeformedPDB ( int pyramidLevel ) const

Create deformed PDB

Definition at line 146 of file nma_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 = 0; i < VEC_XSIZE(trial) - 5; ++i)
         arguments += floatToString(trial(i)) + " ";
     runSystem(program, arguments, false);
 
     program = "xmipp_volume_from_pdb";
     arguments = formatString(
             "-i %s_deformedPDB.pdb --size %i --sampling %f -v 0", randStr,
             imgSize, sampling_rate);
 
     if (do_centerPDB)
         arguments.append(" --centerPDB ");
 
     if (useFixedGaussian) {
         arguments.append(" --intensityColumn Bfactor --fixed_Gaussian ");
         if (sigmaGaussian >= 0)
             arguments += formatString("%f",sigmaGaussian);
     }
     //else
         //arguments +=" --poor_Gaussian"; // Otherwise, a detailed conversion of the atoms takes too long in this context
         
     progVolumeFromPDB->read(arguments);
     progVolumeFromPDB->tryRun();
 
     if (do_FilterPDBVol) {
         program = "xmipp_transform_filter";
         arguments = formatString(
                         "-i %s_deformedPDB.vol --sampling %f --fourier low_pass %f  -v 0",
                         randStr, sampling_rate, cutoff_LPfilter);
         runSystem(program, arguments, false);
     }
 
     if (pyramidLevel != 0) {
         Image<double> I;
         FileName fnDeformed = formatString("%s_deformedPDB.vol",randStr);
         I.read(fnDeformed);
         selfPyramidReduce(xmipp_transformation::BSPLINE3, I(), pyramidLevel);
         I.write(fnDeformed);
     }
     return fnRandom;
 }

◆ createWorkFiles()

virtual void ProgNmaAlignment::createWorkFiles ( )

inlineprotectedvirtual

Reimplemented in MpiProgNMA.

Definition at line 187 of file nma_alignment.h.

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

◆ defineParams()

void ProgNmaAlignment::defineParams ( )

virtual

Define params.

Reimplemented from XmippMetadataProgram.

Definition at line 48 of file nma_alignment.cpp.

                                     {
     addUsageLine("Align images with an atomic or pseudo-atomic (from EM volume) structure by computing deformation amplitudes along normal modes, three Euler angles, and two in-plane shifts");
     addUsageLine("+See [[http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Nma_alignment_v3][here]] for further information about the parameters of this program.");
     defaultComments["-i"].clear();
     defaultComments["-i"].addComment("Metadata with image filenames");
     defaultComments["-o"].clear();
     defaultComments["-o"].addComment("Metadata with output Euler angles, shifts, and deformation amplitudes");
     XmippMetadataProgram::defineParams();
     addParamsLine("   --pdb <PDB_filename>                : Reference atomic or pseudo-atomic structure in PDB format");
     addParamsLine("  [--odir <outputDir=\".\">]           : Output directory");
     addParamsLine("  [--resume]                           : Resume processing");
     addParamsLine("==Generation of the deformed reference volumes==");
     addParamsLine("   --modes <filename>                  : File with a list of mode filenames");
     addParamsLine("  [--sampling_rate <Ts=1>]             : Pixel size in Angstroms");
     addParamsLine("  [--filterVol <cutoff=15.>]           : Filter the volume after deforming. If this option is used, the 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 the PDB file.");
     addParamsLine("==Combined elastic and rigid-body alignment==");
     addParamsLine("  [--trustradius_scale <s=1>]          : Positive scaling factor to scale the initial trust region radius");
     addParamsLine("  [--mask <m=\"\">]                    : 2D masking  of the projections of the deformed volume");
     addParamsLine("  [--projMatch]                        : Real-space instead of wavelet-space (default) projection matching (global matching) that is refined by local (Fourier central slice) projection matching");
     addParamsLine("                                       :+Note that wavelet-based method needs the image size to be power of 2");
     addParamsLine("  [--discrAngStep <ang=10>]            : Angular sampling step for computing the reference projections for global matching");
     addParamsLine("  [--gaussian_Fourier <s=0.5>]         : Sigma of Gaussian weigthing in Fourier space (parameter of central-slice method)");
     addParamsLine("  [--gaussian_Real    <s=0.5>]         : Sigma of Gaussian weigthing in real space for spline interpolation in Fourier space (parameter of central-slice method)");
     addParamsLine("  [--zerofreq_weight  <s=0.>]          : Zero-frequency weight (parameter of central-slice method)");
     addExampleLine("xmipp_nma_alignment -i images.sel --pdb 2tbv.pdb --modes modelist.xmd --trustradius_scale 1.2 --sampling_rate 3.2 -o output.xmd --resume");
 }

◆ finishProcessing()

void ProgNmaAlignment::finishProcessing ( )

virtual

Write the final parameters.

Reimplemented from XmippMetadataProgram.

Reimplemented in MpiProgNMA.

Definition at line 140 of file nma_alignment.cpp.

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

◆ performCompleteSearch()

void ProgNmaAlignment::performCompleteSearch	(	const FileName &	fnRandom,
		int	pyramidLevel
	)		const

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 199 of file nma_alignment.cpp.

                                 {
     String program;
     String arguments;
     const char * randStr = fnRandom.c_str();
 
     // Reduce the image
     FileName 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);
     } else
         copyImage(currentImgName.c_str(), fnDown.c_str());
 
     mkdir((fnRandom+"_ref").c_str(), S_IRWXU);
 
     double angSampling=2*RAD2DEG(atan(1.0/((double) imgSize / pow(2.0, (double) pyramidLevel+1))));
     angSampling=std::max(angSampling,discrAngStep);
     program = "xmipp_angular_project_library";
     arguments = formatString(
             "-i %s_deformedPDB.vol -o %s_ref/ref.stk --sampling_rate %f -v 0",
             randStr, randStr, angSampling);
     if (projMatch)
         arguments +=formatString(
                         " --compute_neighbors --angular_distance -1 --experimental_images %s_downimg.xmp", randStr);
 
     runSystem(program, arguments, false);
 
     String refSelStr = formatString("%s_ref/ref.doc", randStr);
 
     if (fnmask != "") {
         program = "xmipp_transform_mask";
         arguments = formatString("-i %s --mask binary_file %s", refSelStr.c_str(),
                 fnmask.c_str());
         runSystem(program, arguments, false);
     }
 
     // Perform alignment
     String fnOut=formatString("%s_angledisc.xmd",randStr);
     if (!projMatch) {
         program = "xmipp_angular_discrete_assign";
         arguments = formatString(
                         "-i %s_downimg.xmp --ref %s -o %s --psi_step 5 --max_shift_change %d --search5D -v 0",
                         randStr, refSelStr.c_str(), fnOut.c_str(), (int)round((double) imgSize / (10.0 * pow(2.0, (double) pyramidLevel))));
     } else {
         String refStkStr = formatString("%s_ref/ref.stk", randStr);
         program = "xmipp_angular_projection_matching";
         arguments = formatString(
                         "-i %s_downimg.xmp --ref %s -o %s --search5d_step 1  --search5d_shift %d -v 0",
                         randStr, refStkStr.c_str(), fnOut.c_str(), (int)round((double) imgSize / (10.0 * pow(2.0, (double) pyramidLevel))));
     }
     runSystem(program, arguments, false);
     if (projMatch)
     {
         MetaDataVec MD;
         MD.read(fnOut);
         bool flip;
         size_t id=MD.firstRowId();
         MD.getValue(MDL_FLIP,flip,id);
         if (flip)
         {
             // This is because continuous assignment does not understand flips
 
             double shiftX, rot, tilt, psi, newrot, newtilt, newpsi;
             // Change sign in shiftX
             MD.getValue(MDL_SHIFT_X,shiftX,id);
             MD.setValue(MDL_SHIFT_X,-shiftX,id);
 
             // Change Euler angles
             MD.getValue(MDL_ANGLE_ROT,rot,id);
             MD.getValue(MDL_ANGLE_TILT,tilt,id);
             MD.getValue(MDL_ANGLE_PSI,psi,id);
             Euler_mirrorY(rot,tilt,psi,newrot,newtilt,newpsi);
             MD.setValue(MDL_ANGLE_ROT,newrot,id);
             MD.setValue(MDL_ANGLE_TILT,newtilt,id);
             MD.setValue(MDL_ANGLE_PSI,newpsi,id);
             MD.write(fnOut);
         }
     }
 }

◆ performContinuousAssignment()

double ProgNmaAlignment::performContinuousAssignment	(	const FileName &	fnRandom,
		int	pyramidLevel
	)		const

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 283 of file nma_alignment.cpp.

                                 {
     // Perform alignment
     const char * randStr = fnRandom.c_str();
     String fnResults=formatString("%s_anglecont.xmd", randStr);
     bool costSource=true;
     String program = "xmipp_angular_continuous_assign";
     String arguments =
             formatString(
                     "-i %s_angledisc.xmd --ref %s_deformedPDB.vol -o %s --gaussian_Fourier %f --gaussian_Real %f --zerofreq_weight %f -v 0",
                     randStr, randStr, fnResults.c_str(), gaussian_DFT_sigma,
                     gaussian_Real_sigma, weight_zero_freq);
     runSystem(program, arguments, false);
 
     // Pick up results
     MetaDataVec DF(fnResults);
     MDRowVec row;
     DF.getRow(row, DF.firstRowId());
     row.getValue(MDL_ANGLE_ROT, trial(VEC_XSIZE(trial) - 5));
     row.getValue(MDL_ANGLE_TILT, trial(VEC_XSIZE(trial) - 4));
     row.getValue(MDL_ANGLE_PSI, trial(VEC_XSIZE(trial) - 3));
     row.getValue(MDL_SHIFT_X, trial(VEC_XSIZE(trial) - 2));
     trial(VEC_XSIZE(trial) - 2) *= pow(2.0, (double) pyramidLevel);
     row.getValue(MDL_SHIFT_Y, trial(VEC_XSIZE(trial) - 1));
     trial(VEC_XSIZE(trial) - 1) *= pow(2.0, (double) pyramidLevel);
     double tempvar;
     if (!costSource) {
         row.getValue(MDL_MAXCC, tempvar);
         tempvar = -tempvar;
     } else
         row.getValue(MDL_COST, tempvar);
     return tempvar;
 }

◆ preProcess()

void ProgNmaAlignment::preProcess ( )

virtual

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

Reimplemented from XmippMetadataProgram.

Definition at line 128 of file nma_alignment.cpp.

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

◆ processImage()

void ProgNmaAlignment::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 380 of file nma_alignment.cpp.

                                                                      {
     static size_t imageCounter = 0;
     ++imageCounter;
 
     double rhoStart=trustradius_scale*250.;
     double rhoEnd=trustradius_scale*50.;
 
     int niter=10000;
 
     ObjectiveFunction *of;
 
     int dim = numberOfModes;
 
     parameters.initZeros(dim + 5);
     currentImgName = fnImg;
     sprintf(nameTemplate, "_node%d_img%lu_XXXXXX", rangen, (long unsigned int)imageCounter);
 
     trial.initZeros(dim + 5);
     trial_best.initZeros(dim + 5);
 
     fitness_min.initZeros(1);
     fitness_min(0) = 1000000.0;
 
     currentStage = 1;
 #ifdef DEBUG
     std::cerr << std::endl << "DEBUG: ===== Node: " << rangen
     <<" processing image " << fnImg <<"(" << objId << ")"
     << " at stage: " << currentStage << std::endl;
 #endif
     of = new ObjFunc_nma_alignment(1, dim);
 
     of->xStart.setSize(dim);
     for (int i = 0; i < dim; i++)
         of->xStart[i] = 0.;
 
 #ifdef DEBUG
     strcpy(of->name,("OF1_"+integerToString(rangen)).c_str());
     of->setSaveFile();
 #endif
 
     CONDOR(rhoStart, rhoEnd, niter, of);
 #ifdef DEBUG
     of->printStats();
     FILE *ff = fopen(("res1_"+integerToString(rangen)+".xmd").c_str(),"w");
     fprintf(ff,"%s & %i & %i & (%i) & %e \\\\\n", of->name, of->dim(), of->getNFE(), of->getNFE2(), of->valueBest);
     fclose(ff);
 #endif
 
     bestStage1 = trial = parameters = trial_best;
 
     delete of;
 
     currentStage = 2;
 #ifdef DEBUG
     std::cerr << std::endl << "DEBUG: ===== Node: " << rangen
     <<" processing image " << fnImg <<"(" << objId << ")"
     << " at stage: " << currentStage << std::endl;
 #endif
 
     fitness_min(0) = 1000000.0;
 
     of = new ObjFunc_nma_alignment(1, dim);
 
     of->xStart.setSize(dim);
     for (int i = 0; i < dim; i++)
         of->xStart[i] = parameters(i);
 #ifdef DEBUG
     strcpy(of->name,("OF2_"+integerToString(rangen)).c_str());
     of->setSaveFile();
 #endif
 
     rhoStart=trustradius_scale*50.-1., rhoEnd=0.5;
     CONDOR(rhoStart, rhoEnd, niter, of);
 #ifdef DEBUG
     of->printStats();
     ff=fopen(("res2_"+integerToString(rangen)+".xmd").c_str(),"w");
     fprintf(ff,"%s & %i & %i & (%i) & %e \\\\\n", of->name, of->dim(), of->getNFE(), of->getNFE2(), of->valueBest);
     fclose(ff);
 #endif
 
 #ifdef DEBUG
     std::cout << "Best fitness = " << fitness << std::endl;
     for (int i=0; i<dim; i++)
     {
         std::cout << "Best deformations = " << dd[i] << std::endl;
     }
 #endif
 
     trial = trial_best;
 
     for (int i = dim; i < dim + 5; i++) {
         parameters(i - dim) = trial_best(i);
     }
 
     for (int i = 0; i < dim; i++) {
         parameters(5 + i) = trial_best(i);
     }
 
     parameters.resize(VEC_XSIZE(parameters) + 1);
     parameters(VEC_XSIZE(parameters) - 1) = fitness_min(0);
 
     writeImageParameters(fnImg);
     delete of;
 }

◆ readParams()

void ProgNmaAlignment::readParams ( )

virtual

Read arguments from command line.

Reimplemented from XmippMetadataProgram.

Definition at line 79 of file nma_alignment.cpp.

                                   {
     XmippMetadataProgram::readParams();
     fnPDB = getParam("--pdb");
     fnOutDir = getParam("--odir");
     Rerunable::setFileName(fnOutDir + "/nmaDone.xmd");
     fnModeList = getParam("--modes");
     resume = checkParam("--resume");
     trustradius_scale = std::abs(getDoubleParam("--trustradius_scale"));
     sampling_rate = getDoubleParam("--sampling_rate");
     fnmask = getParam("--mask");
     gaussian_DFT_sigma = getDoubleParam("--gaussian_Fourier");
     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");
     projMatch = checkParam("--projMatch");
     discrAngStep = getDoubleParam("--discrAngStep");
 }

◆ show()

void ProgNmaAlignment::show ( )

Show.

Definition at line 104 of file nma_alignment.cpp.

                             {
     XmippMetadataProgram::show();
     std::cout
             << "Output directory:     " << fnOutDir << std::endl
             << "PDB:                  " << fnPDB << std::endl
             << "Resume:               " << resume << std::endl
             << "Mode list:            " << fnModeList << std::endl
             << "Trust-region scale:   " << trustradius_scale << std::endl
             << "Pixel size:           " << sampling_rate << std::endl
             << "Mask:                 " << fnmask << std::endl
             << "Center PDB:           " << do_centerPDB << std::endl
             << "Filter PDB volume:    " << do_FilterPDBVol << std::endl
             << "Use pseudo-atoms:     " << useFixedGaussian << std::endl
             << "Pseudo-atom sigma:    " << sigmaGaussian << std::endl
             << "Projection matching:  " << projMatch << std::endl
             << "AngularSamplingStep:  " << discrAngStep << std::endl
                     << "Gaussian Fourier:     " << gaussian_DFT_sigma << std::endl
             << "Gaussian Real:        " << gaussian_Real_sigma << std::endl
             << "Zero-frequency weight:" << weight_zero_freq << std::endl;
 }

◆ updateBestFit()

void ProgNmaAlignment::updateBestFit ( double fitness )

Update the best fitness and the corresponding best trial

Definition at line 317 of file nma_alignment.cpp.

                                                    {
     if (fitness < fitness_min(0)) {
         fitness_min(0) = fitness;
         trial_best = trial;
     }
 }

◆ writeImageParameters()

void ProgNmaAlignment::writeImageParameters ( const FileName & fnImg )

virtual

Write the parameters found for one image

Reimplemented in MpiProgNMA.

Definition at line 486 of file nma_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> ProgNmaAlignment::bestStage1

Definition at line 127 of file nma_alignment.h.

◆ currentImgName

FileName ProgNmaAlignment::currentImgName

Definition at line 121 of file nma_alignment.h.

◆ currentStage

int ProgNmaAlignment::currentStage

Definition at line 124 of file nma_alignment.h.

◆ cutoff_LPfilter

double ProgNmaAlignment::cutoff_LPfilter

Low-pass cut-off frequency.

Definition at line 89 of file nma_alignment.h.

◆ DF_out

MetaDataVec ProgNmaAlignment::DF_out

Definition at line 130 of file nma_alignment.h.

◆ discrAngStep

double ProgNmaAlignment::discrAngStep

Angular sampling step for computing the reference projections for global matching.

Definition at line 74 of file nma_alignment.h.

◆ do_centerPDB

bool ProgNmaAlignment::do_centerPDB

Center the PDB structure.

Definition at line 68 of file nma_alignment.h.

◆ do_FilterPDBVol

bool ProgNmaAlignment::do_FilterPDBVol

Low-pass filter the volume from PDB.

Definition at line 86 of file nma_alignment.h.

◆ fitness_min

Matrix1D<double> ProgNmaAlignment::fitness_min

Definition at line 112 of file nma_alignment.h.

◆ fnmask

FileName ProgNmaAlignment::fnmask

Mask file for 2D masking of the projections of the deformed volume.

Definition at line 65 of file nma_alignment.h.

◆ fnModeList

FileName ProgNmaAlignment::fnModeList

File with a list of mode filenames.

Definition at line 56 of file nma_alignment.h.

◆ fnOutDir

FileName ProgNmaAlignment::fnOutDir

Output directory.

Definition at line 53 of file nma_alignment.h.

◆ fnPDB

FileName ProgNmaAlignment::fnPDB

Reference atomic or pseudo-atomic structure in PDB format.

Definition at line 50 of file nma_alignment.h.

◆ gaussian_DFT_sigma

double ProgNmaAlignment::gaussian_DFT_sigma

Sigma of Gaussian weigthing in Fourier space (parameter of central-slice method)

Definition at line 77 of file nma_alignment.h.

◆ gaussian_Real_sigma

double ProgNmaAlignment::gaussian_Real_sigma

Sigma of Gaussian weigthing in real space for spline interpolation in Fourier space (parameter of central-slice method)

Definition at line 80 of file nma_alignment.h.

◆ imgSize

int ProgNmaAlignment::imgSize

Definition at line 118 of file nma_alignment.h.

◆ MPIversion

bool ProgNmaAlignment::MPIversion

MPI version

Definition at line 44 of file nma_alignment.h.

◆ nameTemplate

char ProgNmaAlignment::nameTemplate[256]

Definition at line 133 of file nma_alignment.h.

◆ numberOfModes

int ProgNmaAlignment::numberOfModes

Definition at line 115 of file nma_alignment.h.

◆ parameters

Matrix1D<double> ProgNmaAlignment::parameters

Definition at line 103 of file nma_alignment.h.

◆ progVolumeFromPDB

ProgPdbConverter* ProgNmaAlignment::progVolumeFromPDB

Definition at line 136 of file nma_alignment.h.

◆ projMatch

bool ProgNmaAlignment::projMatch

Real-space instead of wavelet-space (default) projection matching (global matching) that is refined by local (Fourier central slice) projection matching.

Definition at line 71 of file nma_alignment.h.

◆ rangen

int ProgNmaAlignment::rangen

Definition at line 100 of file nma_alignment.h.

◆ resume

bool ProgNmaAlignment::resume

Resume computations

Definition at line 47 of file nma_alignment.h.

◆ sampling_rate

double ProgNmaAlignment::sampling_rate

Pixel size in Angstroms.

Definition at line 62 of file nma_alignment.h.

◆ sigmaGaussian

double ProgNmaAlignment::sigmaGaussian

Gaussian standard deviation for pseudo-atoms.

Definition at line 95 of file nma_alignment.h.

◆ trial

Matrix1D<double> ProgNmaAlignment::trial

Definition at line 106 of file nma_alignment.h.

◆ trial_best

Matrix1D<double> ProgNmaAlignment::trial_best

Definition at line 109 of file nma_alignment.h.

◆ trustradius_scale

double ProgNmaAlignment::trustradius_scale

Positive scaling factor to scale the initial trust region radius.

Definition at line 59 of file nma_alignment.h.

◆ useFixedGaussian

bool ProgNmaAlignment::useFixedGaussian

Use pseudo-atoms instead of atoms.

Definition at line 92 of file nma_alignment.h.

◆ weight_zero_freq

double ProgNmaAlignment::weight_zero_freq

Zero-frequency weight (parameter of central-slice method)

Definition at line 83 of file nma_alignment.h.

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

xmipp/libraries/reconstruction/nma_alignment.h
xmipp/libraries/reconstruction/nma_alignment.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgNmaAlignment()

◆ ~ProgNmaAlignment()

Member Function Documentation

◆ computeFitness()

◆ createDeformedPDB()

◆ createWorkFiles()

◆ defineParams()

◆ finishProcessing()

◆ performCompleteSearch()

◆ performContinuousAssignment()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ show()

◆ updateBestFit()

◆ writeImageParameters()

Member Data Documentation

◆ bestStage1

◆ currentImgName

◆ currentStage

◆ cutoff_LPfilter

◆ DF_out

◆ discrAngStep

◆ do_centerPDB

◆ do_FilterPDBVol

◆ fitness_min

◆ fnmask

◆ fnModeList

◆ fnOutDir

◆ fnPDB

◆ gaussian_DFT_sigma

◆ gaussian_Real_sigma

◆ imgSize

◆ MPIversion

◆ nameTemplate

◆ numberOfModes

◆ parameters

◆ progVolumeFromPDB

◆ projMatch

◆ rangen

◆ resume

◆ sampling_rate

◆ sigmaGaussian

◆ trial

◆ trial_best

◆ trustradius_scale

◆ useFixedGaussian

◆ weight_zero_freq