#include <volume_deform_sph_gpu.h>

Inheritance diagram for ProgVolumeDeformSphGpu:

Collaboration diagram for ProgVolumeDeformSphGpu:

Public Member Functions
void	defineParams ()
	Define params. More...

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

void	show () const override
	Show. More...

double	distance (double *pclnm)
	Distance. More...

void	run ()
	Run. More...

void	minimizepos (int L1, int l2, Matrix1D< double > &steps)
	Determine the positions to be minimize of a vector containing spherical harmonic coefficients. More...

void	numCoefficients (int l1, int l2, int &vecSize)
	Length of coefficients vector. More...

void	fillVectorTerms (int l1, int l2, Matrix1D< int > &vL1, Matrix1D< int > &vN, Matrix1D< int > &vL2, Matrix1D< int > &vM)
	Zernike and SPH coefficients allocation. More...

void	computeStrain ()
	Compute strain. More...

void	writeVector (std::string outPath, Matrix1D< double > v, bool append)
	Save vector to file. 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)

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	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
VolumeDeformSph	volDefSphGpu
	GPU computer. More...

FileName	fnVolI
	Volume to deform. More...

FileName	fnVolR
	Reference volume. More...

FileName	fnVolOut
	Output Volume (deformed input volume) More...

FileName	fnRoot
	Root name for several output files. More...

bool	analyzeStrain
	Save the deformation of each voxel for local strain and rotation analysis. More...

bool	optimizeRadius
	Radius optimization. More...

int	L1
	Degree of Zernike polynomials and spherical harmonics. More...

int	L2

Matrix1D< int >	vL1
	Zernike and SPH coefficients vectors. More...

Matrix1D< int >	vN

Matrix1D< int >	vL2

Matrix1D< int >	vM

std::vector< double >	sigma
	Gaussian width to filter the volumes. More...

std::vector< Image< double > >	volumesI
	Image Vector. More...

std::vector< Image< double > >	volumesR

double	Rmax
	Maximum radius for the transformation. More...

int	vecSize
	Coefficient vector size. More...

Image< double >	VI
	Images. More...

Image< double >	VR

Image< double >	VO

Image< double >	Gx

Image< double >	Gy

Image< double >	Gz

std::vector< double >	absMaxR_vec
	Maxima of reference volumes (in absolute value) More...

Matrix1D< double >	clnm

Matrix1D< double >	steps_cp

unsigned	onesInSteps

unsigned	Ncount

double	deformation

double	sumVI

double	sumVD

double	lambda

bool	applyTransformation

bool	saveDeformation

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

Sph Alignment Parameters.

Definition at line 39 of file volume_deform_sph_gpu.h.

Member Function Documentation

◆ computeStrain()

void ProgVolumeDeformSphGpu::computeStrain ( )

Compute strain.

Definition at line 515 of file volume_deform_sph_gpu.cpp.

 {
     Image<double> LS, LR;
     LS().initZeros(Gx());
     LR().initZeros(Gx());
 
     // Gaussian filter of the derivatives
     FourierFilter f;
     f.FilterBand=LOWPASS;
     f.FilterShape=REALGAUSSIAN;
     f.w1=2;
     f.applyMaskSpace(Gx());
     f.applyMaskSpace(Gy());
     f.applyMaskSpace(Gz());
 
     Gx.write(fnRoot+"_PPPGx.vol");
     Gy.write(fnRoot+"_PPPGy.vol");
     Gz.write(fnRoot+"_PPPGz.vol");
 
     MultidimArray<double> &mLS=LS();
     MultidimArray<double> &mLR=LR();
     MultidimArray<double> &mGx=Gx();
     MultidimArray<double> &mGy=Gy();
     MultidimArray<double> &mGz=Gz();
     Matrix2D<double> U(3,3), D(3,3), H(3,3);
     std::vector< std::complex<double> > eigs;
     H.initZeros();
     for (int k=STARTINGZ(mLS)+2; k<=FINISHINGZ(mLS)-2; ++k)
     {
         int km1=k-1;
         int kp1=k+1;
         int km2=k-2;
         int kp2=k+2;
         for (int i=STARTINGY(mLS)+2; i<=FINISHINGY(mLS)-2; ++i)
         {
             int im1=i-1;
             int ip1=i+1;
             int im2=i-2;
             int ip2=i+2;
             for (int j=STARTINGX(mLS)+2; j<=FINISHINGX(mLS)-2; ++j)
             {
                 int jm1=j-1;
                 int jp1=j+1;
                 int jm2=j-2;
                 int jp2=j+2;
                 MAT_ELEM(U,0,0)=Dx(mGx); MAT_ELEM(U,0,1)=Dy(mGx); MAT_ELEM(U,0,2)=Dz(mGx);
                 MAT_ELEM(U,1,0)=Dx(mGy); MAT_ELEM(U,1,1)=Dy(mGy); MAT_ELEM(U,1,2)=Dz(mGy);
                 MAT_ELEM(U,2,0)=Dx(mGz); MAT_ELEM(U,2,1)=Dy(mGz); MAT_ELEM(U,2,2)=Dz(mGz);
 
                 MAT_ELEM(D,0,0) = MAT_ELEM(U,0,0);
                 MAT_ELEM(D,0,1) = MAT_ELEM(D,1,0) = 0.5*(MAT_ELEM(U,0,1)+MAT_ELEM(U,1,0));
                 MAT_ELEM(D,0,2) = MAT_ELEM(D,2,0) = 0.5*(MAT_ELEM(U,0,2)+MAT_ELEM(U,2,0));
                 MAT_ELEM(D,1,1) = MAT_ELEM(U,1,1);
                 MAT_ELEM(D,1,2) = MAT_ELEM(D,2,1) = 0.5*(MAT_ELEM(U,1,2)+MAT_ELEM(U,2,1));
                 MAT_ELEM(D,2,2) = MAT_ELEM(U,2,2);
 
                 MAT_ELEM(H,0,1) = 0.5*(MAT_ELEM(U,0,1)-MAT_ELEM(U,1,0));
                 MAT_ELEM(H,0,2) = 0.5*(MAT_ELEM(U,0,2)-MAT_ELEM(U,2,0));
                 MAT_ELEM(H,1,2) = 0.5*(MAT_ELEM(U,1,2)-MAT_ELEM(U,2,1));
                 MAT_ELEM(H,1,0) = -MAT_ELEM(H,0,1);
                 MAT_ELEM(H,2,0) = -MAT_ELEM(H,0,2);
                 MAT_ELEM(H,2,1) = -MAT_ELEM(H,1,2);
 
                 A3D_ELEM(mLS,k,i,j)=fabs(D.det());
                 allEigs(H,eigs);
                 for (size_t n=0; n < eigs.size(); n++)
                 {
                     double imagabs=fabs(eigs[n].imag());
                     if (imagabs>1e-6)
                     {
                         A3D_ELEM(mLR,k,i,j)=imagabs*180/PI;
                         break;
                     }
                 }
             }
         }
         LS.write(fnVolOut.withoutExtension()+"_strain.mrc");
         LR.write(fnVolOut.withoutExtension()+"_rotation.mrc");
     }
 }

◆ defineParams()

void ProgVolumeDeformSphGpu::defineParams ( )

virtual

Define params.

Reimplemented from XmippProgram.

Definition at line 34 of file volume_deform_sph_gpu.cpp.

                                           {
     addUsageLine("Compute the deformation that properly fits two volumes using spherical harmonics (GPU accelerated)");
     addParamsLine("   -i <volume>                         : Volume to deform");
     addParamsLine("   -r <volume>                         : Reference volume");
     addParamsLine("  [-o <volume=\"\">]                   : Output volume which is the deformed input volume");
     addParamsLine("  [--oroot <rootname=\"Volumes\">]     : Root name for output files");
     addParamsLine("                                       : By default, the input file is rewritten");
     addParamsLine("  [--sigma <Matrix1D=\"\">]            : Sigma values to filter the volume to perform a multiresolution analysis");
     addParamsLine("  [--analyzeStrain]                    : Save the deformation of each voxel for local strain and rotation analysis");
     addParamsLine("  [--optimizeRadius]                   : Optimize the radius of each spherical harmonic");
     addParamsLine("  [--l1 <l1=3>]                        : Degree Zernike Polynomials=1,2,3,...");
     addParamsLine("  [--l2 <l2=2>]                        : Harmonical depth of the deformation=1,2,3,...");
     addParamsLine("  [--regularization <l=0.00025>]       : Regularization weight");
     addParamsLine("  [--Rmax <r=-1>]                      : Maximum radius for the transformation");
     addExampleLine("xmipp_volume_deform_sph -i vol1.vol -r vol2.vol -o vol1DeformedTo2.vol");
 }

◆ distance()

double ProgVolumeDeformSphGpu::distance ( double * pclnm )

Distance.

Definition at line 99 of file volume_deform_sph_gpu.cpp.

 {
     if (applyTransformation)
     {
         VO().initZeros(VR());
         VO().setXmippOrigin();
     }
 
     FOR_ALL_ELEMENTS_IN_MATRIX1D(clnm)
         VEC_ELEM(clnm,i)=pclnm[i+1];
 #ifdef DEBUG
     std::cout << "Starting to evaluate\n" << clnm << std::endl;
 #endif
 
     double diff2=0.0;
     sumVD = 0.0;
     double modg=0.0;
 
 // GPU computation 
     volDefSphGpu.setupChangingParameters();
 
     volDefSphGpu.runKernel();
 
     volDefSphGpu.transferResults();
 
     auto result = volDefSphGpu.getOutputs();
     diff2 = result.diff2;
     modg = result.modg;
     sumVD = result.sumVD;
 // GPU computation end
 
     deformation=std::sqrt(modg/Ncount);
 
 #ifdef DEBUG
     Image<double> save;
     save() = VI();
     save.write(fnRoot+"_PPPIdeformed.vol");
     save()-=VR();
     save.write(fnRoot+"_PPPdiff.vol");
     save()=VR();
     save.write(fnRoot+"_PPPR.vol");
     if (saveDeformation)
     {
         save() = Gx();
         save.write(fnRoot+"_PPPGx.vol");
         save() = Gy();
         save.write(fnRoot+"_PPPGy.vol");
         save() = Gz();
         save.write(fnRoot+"_PPPGz.vol");
     }
     std::cout << "Error=" << deformation << " " << std::sqrt(diff2/totalVal) << std::endl;
     std::cout << "Press any key\n";
     char c; std::cin >> c;
 #endif
 
     if (applyTransformation)
         VO.write(fnVolOut);
 
     double massDiff=std::abs(sumVI-sumVD)/sumVI;
     return std::sqrt(diff2/Ncount)+lambda*(deformation+massDiff);
 }

◆ fillVectorTerms()

void ProgVolumeDeformSphGpu::fillVectorTerms	(	int	l1,
		int	l2,
		Matrix1D< int > &	vL1,
		Matrix1D< int > &	vN,
		Matrix1D< int > &	vL2,
		Matrix1D< int > &	vM
	)

Zernike and SPH coefficients allocation.

Definition at line 467 of file volume_deform_sph_gpu.cpp.

 {
     int idx = 0;
     vL1.initZeros(vecSize);
     vN.initZeros(vecSize);
     vL2.initZeros(vecSize);
     vM.initZeros(vecSize);
     for (int h=0; h<=l2; h++)
     {
         int totalSPH = 2*h+1;
         int aux = std::floor(totalSPH/2);
         for (int l=h; l<=l1; l+=2)
         {
             for (int m=0; m<totalSPH; m++)
             {
                 VEC_ELEM(vL1,idx) = l;
                 VEC_ELEM(vN,idx) = h;
                 VEC_ELEM(vL2,idx) = h;
                 VEC_ELEM(vM,idx) = m-aux;
                 idx++;
             }
         }
     }
 }

◆ minimizepos()

void ProgVolumeDeformSphGpu::minimizepos	(	int	L1,
		int	l2,
		Matrix1D< double > &	steps
	)

Determine the positions to be minimize of a vector containing spherical harmonic coefficients.

Definition at line 417 of file volume_deform_sph_gpu.cpp.

 {
     int size = 0;
     numCoefficients(L1,l2,size);
     onesInSteps = size;
     int totalSize = steps.size()/3;
     for (int idx=0; idx<size; idx++)
     {
         VEC_ELEM(steps,idx) = 1;
         VEC_ELEM(steps,idx+totalSize) = 1;
         VEC_ELEM(steps,idx+2*totalSize) = 1;
     }   
 }

◆ numCoefficients()

void ProgVolumeDeformSphGpu::numCoefficients	(	int	l1,
		int	l2,
		int &	vecSize
	)

Length of coefficients vector.

Definition at line 453 of file volume_deform_sph_gpu.cpp.

 {
     for (int h=0; h<=l2; h++)
     {
         int numSPH = 2*h+1;
         int count=l1-h+1;
         int numEven=(count>>1)+(count&1 && !(h&1));
         if (h%2 == 0)
             vecSize += numSPH*numEven;
         else
             vecSize += numSPH*(l1-h+1-numEven);
     }
 }

◆ readParams()

void ProgVolumeDeformSphGpu::readParams ( )

virtual

Read arguments from command line.

Reimplemented from XmippProgram.

Definition at line 52 of file volume_deform_sph_gpu.cpp.

                                         {
     std::string aux;
     fnVolI = getParam("-i");
     fnVolR = getParam("-r");
     L1 = getIntParam("--l1");
     L2 = getIntParam("--l2");
     fnRoot = getParam("--oroot");
     
     aux = getParam("--sigma");
     // Transform string ov values separated by white spaces into substrings stored in a vector
     std::stringstream ss(aux);
     std::istream_iterator<std::string> begin(ss);
     std::istream_iterator<std::string> end;
     std::vector<std::string> vstrings(begin, end);
     sigma.resize(vstrings.size());
     std::transform(vstrings.begin(), vstrings.end(), sigma.begin(), [](const std::string& val)
     {
         return std::stod(val);
     });
 
     fnVolOut = getParam("-o");
     if (fnVolOut=="")
         fnVolOut=fnVolI;
     analyzeStrain=checkParam("--analyzeStrain");
     optimizeRadius=checkParam("--optimizeRadius");
     lambda = getDoubleParam("--regularization");
     Rmax = getDoubleParam("--Rmax");
     applyTransformation = false;
 }

◆ run()

void ProgVolumeDeformSphGpu::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 169 of file volume_deform_sph_gpu.cpp.

                                  {
 
     saveDeformation=false;
 
     VI.read(fnVolI);
     VR.read(fnVolR);
     sumVI = 0.0;
     if (Rmax<0)
         Rmax=XSIZE(VI())/2;
 
     VI().setXmippOrigin();
     VR().setXmippOrigin();
 
     //GPU preparation
     volDefSphGpu.associateWith(this);
     //GPU preparation end
 
     // Filter input and reference volumes according to the values of sigma
     FourierFilter filter;
     filter.FilterShape = REALGAUSSIAN;
     filter.FilterBand = LOWPASS;
     filter.generateMask(VI());
 
     // We need also to normalized the filtered volumes to compare them appropiately
     Image<double> auxI = VI;
     Image<double> auxR = VR;
 
     MultidimArray<int> bg_mask;
     bg_mask.resizeNoCopy(VI().zdim, VI().ydim, VI().xdim);
     bg_mask.setXmippOrigin();
     normalize_Robust(auxI(), bg_mask, true);
     bg_mask *= 0;
     normalize_Robust(auxR(), bg_mask, true);
 
     FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(auxI())
     {
         if (DIRECT_A3D_ELEM(auxI(),k,i,j) >= 0.0)
             sumVI += DIRECT_A3D_ELEM(auxI(),k,i,j);
     }
 
     if (sigma.size() == 1 && sigma[0] == 0)
     {
         volumesI.push_back(auxI());
         volumesR.push_back(auxR());
     }
     else
     {
         volumesI.push_back(auxI());
         volumesR.push_back(auxR());
         for (unsigned ids=0; ids<sigma.size(); ids++)
         {
             Image<double> auxI = VI;
             Image<double> auxR = VR;
             filter.w1 = sigma[ids];
 
             // Filer input vol
             filter.do_generate_3dmask = true;
             filter.applyMaskSpace(auxI());
             bg_mask *= 0;
             normalize_Robust(auxI(), bg_mask, true);
             volumesI.push_back(auxI);
             FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(auxI())
             {
                 if (DIRECT_A3D_ELEM(auxI(),k,i,j) >= 0.0)
                     sumVI += DIRECT_A3D_ELEM(auxI(),k,i,j);
             }
             filter.applyMaskSpace(auxR());
             bg_mask *= 0;
             normalize_Robust(auxR(), bg_mask, true);
             volumesR.push_back(auxR);
         }
     }
 
     Matrix1D<double> x;
     Matrix1D<double> steps;
     vecSize = 0;
     numCoefficients(L1,L2,vecSize);
     size_t totalSize = 3*vecSize;
     fillVectorTerms(L1,L2,vL1,vN,vL2,vM);
     clnm.initZeros(totalSize);
     x.initZeros(totalSize);
 
     // GPU preparation
     volDefSphGpu.setupConstantParameters();
     Ncount = volumesR.size() * VR().getSize();
     // GPU preparation end
 
     for (int h=0;h<=L2;h++)
     {
         steps.clear();
         steps.initZeros(totalSize);
         minimizepos(L1,h,steps);
         steps_cp = steps;
 
         std::cout<<std::endl;
         std::cout<<"-------------------------- Basis Degrees: ("<<L1<<","<<h<<") --------------------------"<<std::endl;
         // if (h==0)
         // {
 
         // }
         // else
         // {
         //  x.resize(VEC_XSIZE(steps),false);
         //  copyvectors(clnm,x);
         //  clnm=x;
         // }
 
         // for(int d=VEC_XSIZE(x)-L+prevL;d<VEC_XSIZE(x);d++)
         // {
         //  x(d)=Rmax;
         //  clnm(d)=Rmax;
         // }
 #ifdef NEVERDEFINED
         for (int d=0;d<VEC_XSIZE(x);d++)
         {
             if (x(d)==0)
             {
                 steps(d) = 1;
             }
             else if (d>=VEC_XSIZE(steps)+nh(h)-nh(h+1)&d<VEC_XSIZE(steps)+nh(h+1))
             {
                 steps(d) = 1;
             }
             else
             {
                 steps(d) = 0;
             }
             //std::cout<<steps(d)<<" ";
         }
         //std::cout<<std::endl;
 #endif
         // if (h!=0)
         // {
         //     minimizepos(steps,prevsteps);
         // }
         // else
         // {
         //  steps(VEC_XSIZE(steps)-1)=0;
         // }
         int iter;
         double fitness;
         powellOptimizer(x, 1, totalSize, &volDeformSphGoal, this,
                         0.01, fitness, iter, steps, true);
 
         std::cout<<std::endl;
         std::cout << "Deformation " << deformation << std::endl;
         std::ofstream deformFile;
         deformFile.open (fnRoot+"_deformation.txt");
         deformFile << deformation;
         deformFile.close();
 
 // #define DEBUG
 #ifdef DEBUG
     Image<double> save;
     save() = VI();
     save.write(fnRoot+"_PPPIdeformed.vol");
     save()-=VR();
     save.write(fnRoot+"_PPPdiff.vol");
     save()=VR();
     save.write(fnRoot+"_PPPR.vol");
     std::cout << "Error=" << deformation << std::endl;
     std::cout << "Press any key\n";
     char c; std::cin >> c;
 #endif
 
     }
     applyTransformation=true;
     // x.write(fnRoot+"_clnm.txt");
     Matrix1D<double> degrees;
     degrees.initZeros(3);
     VEC_ELEM(degrees,0) = L1;
     VEC_ELEM(degrees,1) = L2;
     VEC_ELEM(degrees,2) = Rmax;
     writeVector(fnRoot+"_clnm.txt", degrees, false);
     writeVector(fnRoot+"_clnm.txt", x, true);
     if (analyzeStrain)
     {
         saveDeformation=true;
         Gx().initZeros(VR());
         Gy().initZeros(VR());
         Gz().initZeros(VR());
         Gx().setXmippOrigin();
         Gy().setXmippOrigin();
         Gz().setXmippOrigin();
     }
 
     distance(x.adaptForNumericalRecipes()); // To save the output volume
 
 #ifdef DEBUG
         Image<double> save;
         save() = Gx();
         save.write(fnRoot+"_PPPGx.vol");
         save() = Gy();
         save.write(fnRoot+"_PPPGy.vol");
         save() = Gz();
         save.write(fnRoot+"_PPPGz.vol");
 #endif
 
     if (analyzeStrain)
         computeStrain();
 }

◆ show()

void ProgVolumeDeformSphGpu::show ( ) const

overridevirtual

Show.

Reimplemented from XmippProgram.

Definition at line 83 of file volume_deform_sph_gpu.cpp.

                                         {
     if (verbose==0)
         return;
     std::cout
             << "Volume to deform:     " << fnVolI         << std::endl
             << "Reference volume:     " << fnVolR         << std::endl
             << "Output volume:        " << fnVolOut       << std::endl
             << "Zernike Degree:       " << L1             << std::endl
             << "SH Degree:            " << L2             << std::endl
             << "Save deformation:     " << analyzeStrain  << std::endl
             << "Regularization:       " << lambda         << std::endl
     ;
 }

◆ writeVector()

void ProgVolumeDeformSphGpu::writeVector	(	std::string	outPath,
		Matrix1D< double >	v,
		bool	append
	)

Save vector to file.

Definition at line 596 of file volume_deform_sph_gpu.cpp.

 {
     std::ofstream outFile;
     if (append == false)
         outFile.open(outPath);
     else
         outFile.open(outPath, std::ios_base::app);
     FOR_ALL_ELEMENTS_IN_MATRIX1D(v)
         outFile << VEC_ELEM(v,i) << " ";
     outFile << std::endl;
 }

Member Data Documentation

◆ absMaxR_vec

std::vector<double> ProgVolumeDeformSphGpu::absMaxR_vec

Maxima of reference volumes (in absolute value)

Definition at line 86 of file volume_deform_sph_gpu.h.

◆ analyzeStrain

bool ProgVolumeDeformSphGpu::analyzeStrain

Save the deformation of each voxel for local strain and rotation analysis.

Definition at line 58 of file volume_deform_sph_gpu.h.

◆ applyTransformation

bool ProgVolumeDeformSphGpu::applyTransformation

Definition at line 107 of file volume_deform_sph_gpu.h.

◆ clnm

Matrix1D<double> ProgVolumeDeformSphGpu::clnm

Definition at line 89 of file volume_deform_sph_gpu.h.

◆ deformation

double ProgVolumeDeformSphGpu::deformation

Definition at line 101 of file volume_deform_sph_gpu.h.

◆ fnRoot

FileName ProgVolumeDeformSphGpu::fnRoot

Root name for several output files.

Definition at line 55 of file volume_deform_sph_gpu.h.

◆ fnVolI

FileName ProgVolumeDeformSphGpu::fnVolI

Volume to deform.

Definition at line 46 of file volume_deform_sph_gpu.h.

◆ fnVolOut

FileName ProgVolumeDeformSphGpu::fnVolOut

Output Volume (deformed input volume)

Definition at line 52 of file volume_deform_sph_gpu.h.

◆ fnVolR

FileName ProgVolumeDeformSphGpu::fnVolR

Reference volume.

Definition at line 49 of file volume_deform_sph_gpu.h.

◆ Gx

Image<double> ProgVolumeDeformSphGpu::Gx

Definition at line 83 of file volume_deform_sph_gpu.h.

◆ Gy

Image<double> ProgVolumeDeformSphGpu::Gy

Definition at line 83 of file volume_deform_sph_gpu.h.

◆ Gz

Image<double> ProgVolumeDeformSphGpu::Gz

Definition at line 83 of file volume_deform_sph_gpu.h.

◆ L1

int ProgVolumeDeformSphGpu::L1

Degree of Zernike polynomials and spherical harmonics.

Definition at line 64 of file volume_deform_sph_gpu.h.

◆ L2

int ProgVolumeDeformSphGpu::L2

Definition at line 64 of file volume_deform_sph_gpu.h.

◆ lambda

double ProgVolumeDeformSphGpu::lambda

Definition at line 104 of file volume_deform_sph_gpu.h.

◆ Ncount

unsigned ProgVolumeDeformSphGpu::Ncount

Definition at line 98 of file volume_deform_sph_gpu.h.

◆ onesInSteps

unsigned ProgVolumeDeformSphGpu::onesInSteps

Definition at line 95 of file volume_deform_sph_gpu.h.

◆ optimizeRadius

bool ProgVolumeDeformSphGpu::optimizeRadius

Radius optimization.

Definition at line 61 of file volume_deform_sph_gpu.h.

◆ Rmax

double ProgVolumeDeformSphGpu::Rmax

Maximum radius for the transformation.

Definition at line 76 of file volume_deform_sph_gpu.h.

◆ saveDeformation

bool ProgVolumeDeformSphGpu::saveDeformation

Definition at line 110 of file volume_deform_sph_gpu.h.

◆ sigma

std::vector<double> ProgVolumeDeformSphGpu::sigma

Gaussian width to filter the volumes.

Definition at line 70 of file volume_deform_sph_gpu.h.

◆ steps_cp

Matrix1D<double> ProgVolumeDeformSphGpu::steps_cp

Definition at line 92 of file volume_deform_sph_gpu.h.

◆ sumVD

double ProgVolumeDeformSphGpu::sumVD

Definition at line 101 of file volume_deform_sph_gpu.h.

◆ sumVI

double ProgVolumeDeformSphGpu::sumVI

Definition at line 101 of file volume_deform_sph_gpu.h.

◆ vecSize

int ProgVolumeDeformSphGpu::vecSize

Coefficient vector size.

Definition at line 80 of file volume_deform_sph_gpu.h.

◆ VI

Image<double> ProgVolumeDeformSphGpu::VI

Images.

Definition at line 83 of file volume_deform_sph_gpu.h.

◆ vL1

Matrix1D<int> ProgVolumeDeformSphGpu::vL1

Zernike and SPH coefficients vectors.

Definition at line 67 of file volume_deform_sph_gpu.h.

◆ vL2

Matrix1D<int> ProgVolumeDeformSphGpu::vL2

Definition at line 67 of file volume_deform_sph_gpu.h.

◆ vM

Matrix1D<int> ProgVolumeDeformSphGpu::vM

Definition at line 67 of file volume_deform_sph_gpu.h.

◆ vN

Matrix1D<int> ProgVolumeDeformSphGpu::vN

Definition at line 67 of file volume_deform_sph_gpu.h.

◆ VO

Image<double> ProgVolumeDeformSphGpu::VO

Definition at line 83 of file volume_deform_sph_gpu.h.

◆ volDefSphGpu

VolumeDeformSph ProgVolumeDeformSphGpu::volDefSphGpu

GPU computer.

Definition at line 43 of file volume_deform_sph_gpu.h.

◆ volumesI

std::vector<Image<double> > ProgVolumeDeformSphGpu::volumesI

Image Vector.

Definition at line 73 of file volume_deform_sph_gpu.h.

◆ volumesR

std::vector<Image<double> > ProgVolumeDeformSphGpu::volumesR

Definition at line 73 of file volume_deform_sph_gpu.h.

◆ VR

Image<double> ProgVolumeDeformSphGpu::VR

Definition at line 83 of file volume_deform_sph_gpu.h.

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

xmipp/libraries/reconstruction_adapt_cuda/volume_deform_sph_gpu.h
xmipp/libraries/reconstruction_adapt_cuda/volume_deform_sph_gpu.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ computeStrain()

◆ defineParams()

◆ distance()

◆ fillVectorTerms()

◆ minimizepos()

◆ numCoefficients()

◆ readParams()

◆ run()

◆ show()

◆ writeVector()

Member Data Documentation

◆ absMaxR_vec

◆ analyzeStrain

◆ applyTransformation

◆ clnm

◆ deformation

◆ fnRoot

◆ fnVolI

◆ fnVolOut

◆ fnVolR

◆ Gx

◆ Gy

◆ Gz

◆ L1

◆ L2

◆ lambda

◆ Ncount

◆ onesInSteps

◆ optimizeRadius

◆ Rmax

◆ saveDeformation

◆ sigma

◆ steps_cp

◆ sumVD

◆ sumVI

◆ vecSize

◆ VI

◆ vL1

◆ vL2

◆ vM

◆ vN

◆ VO

◆ volDefSphGpu

◆ volumesI

◆ volumesR

◆ VR