ctf_estimate_from_micrograph (CTF estimation from a micrograph)

Collaboration diagram for ctf_estimate_from_micrograph (CTF estimation from a micrograph):

Classes
class	ProgCTFEstimateFromMicrograph

Functions
void	fastEstimateEnhancedPSD (const FileName &fnMicrograph, double downsampling, MultidimArray< double > &enhancedPSD, int numberOfThreads)

Detailed Description

This program assign different CTFs to the particles in a micrograph

Function Documentation

fastEstimateEnhancedPSD()

void fastEstimateEnhancedPSD	(	const FileName &	fnMicrograph,
		double	downsampling,
		MultidimArray< double > &	enhancedPSD,
		int	numberOfThreads
	)

Fast estimate enhanced PSD. Set downsampling to 2 for halving the image size.

Definition at line 924 of file ctf_estimate_from_micrograph.cpp.

{
    size_t Xdim, Ydim, Zdim, Ndim;
    getImageSizeFromFilename(fnMicrograph, Xdim, Ydim, Zdim, Ndim);
    int minSize = 2 * (std::max(Xdim, Ydim) / 10);
    minSize = (int)std::min((double) std::min(Xdim, Ydim), NEXT_POWER_OF_2(minSize));
    minSize = std::min(1024, minSize);

    /*
     ProgCTFEstimateFromMicrograph prog1;
     prog1.fn_micrograph=fnMicrograph;
     prog1.fn_root=fnMicrograph.withoutExtension()+"_tmp";
     prog1.pieceDim=(int)(minSize*downsampling);
     prog1.PSDEstimator_mode=ProgCTFEstimateFromMicrograph::Periodogram;
     prog1.Nsubpiece=1;
     prog1.psd_mode=ProgCTFEstimateFromMicrograph::OnePerMicrograph;
     prog1.estimate_ctf=false;
     prog1.bootstrapN=-1;
     prog1.verbose=1;
     prog1.overlap=0;
     prog1.run();
     */
    // Prepare auxiliary variables
    ImageGeneric I;
    I.read(fnMicrograph);

    MultidimArray<double> PSD;
    PSD.initZeros(minSize, minSize);

    MultidimArray<int> pieceMask;
    pieceMask.resizeNoCopy(PSD);
    pieceMask.initConstant(1);

    MultidimArray<double> pieceSmoother;
    ProgCTFEstimateFromMicrograph::constructPieceSmoother(PSD, pieceSmoother);

    // Prepare thread arguments
    Mutex mutex;
    ThreadFastEstimateEnhancedPSDParams args;
    args.I = &I;
    args.PSD = &PSD;
    args.pieceMask = &pieceMask;
    args.pieceSmoother = &pieceSmoother;
    args.Nprocessed = 0;
    args.mutex = &mutex;
    auto thMgr = std::unique_ptr<ThreadManager>(std::make_unique<ThreadManager>(numberOfThreads, &args));
    thMgr->run(threadFastEstimateEnhancedPSD);
    if (args.Nprocessed != 0)
        *(args.PSD) /= args.Nprocessed;

    ProgCTFEnhancePSD prog2;
    prog2.filter_w1 = 0.02;
    prog2.filter_w2 = 0.2;
    prog2.decay_width = 0.02;
    prog2.mask_w1 = 0.005;
    prog2.mask_w2 = 0.5;

    prog2.applyFilter(*(args.PSD));
    enhancedPSD = *(args.PSD);

    auto downXdim = (int) ((double)XSIZE(enhancedPSD) / downsampling);
    int firstIndex = FIRST_XMIPP_INDEX(downXdim);
    int lastIndex = LAST_XMIPP_INDEX(downXdim);
    enhancedPSD.setXmippOrigin();
    enhancedPSD.selfWindow(firstIndex, firstIndex, lastIndex, lastIndex);
}