ProgAngResAlign Class Reference

#include <angular_resolution_alignment.h>

Inheritance diagram for ProgAngResAlign:

Collaboration diagram for ProgAngResAlign:

Public Member Functions
void	defineParams ()
void	readParams ()
void	run ()
Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)
const char *	getParam (const char *param, const char *subparam, int arg=0)
int	getIntParam (const char *param, int arg=0)
int	getIntParam (const char *param, const char *subparam, int arg=0)
double	getDoubleParam (const char *param, int arg=0)
double	getDoubleParam (const char *param, const char *subparam, int arg=0)
float	getFloatParam (const char *param, int arg=0)
float	getFloatParam (const char *param, const char *subparam, int arg=0)
void	getListParam (const char *param, StringVector &list)
int	getCountParam (const char *param)
bool	checkParam (const char *param)
bool	existsParam (const char *param)
void	addParamsLine (const String &line)
void	addParamsLine (const char *line)
ParamDef *	getParamDef (const char *param) const
virtual void	quit (int exit_code=0) const
virtual int	tryRun ()
void	initProgress (size_t total, size_t stepBin=60)
void	setProgress (size_t value=0)
void	endProgress ()
void	processDefaultComment (const char *param, const char *left)
void	setDefaultComment (const char *param, const char *comment)
virtual void	initComments ()
void	setProgramName (const char *name)
void	addUsageLine (const char *line, bool verbatim=false)
void	clearUsage ()
void	addExampleLine (const char *example, bool verbatim=true)
void	addSeeAlsoLine (const char *seeAlso)
void	addKeywords (const char *keywords)
const char *	name () const
virtual void	usage (int verb=0) const
virtual void	usage (const String &param, int verb=2)
int	version () const
virtual void	show () const
virtual void	read (int argc, const char **argv, bool reportErrors=true)
virtual void	read (int argc, char **argv, bool reportErrors=true)
void	read (const String &argumentsLine)
	XmippProgram ()
	XmippProgram (int argc, const char **argv)
virtual	~XmippProgram ()

Additional Inherited Members
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug
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

Definition at line 36 of file angular_resolution_alignment.h.

Member Function Documentation

defineParams()

void ProgAngResAlign::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 34 of file angular_resolution_alignment.cpp.

{
    addUsageLine("This algorithm estimates the existence of angular alignment errors by measuring a set of directional FSC.");
    addUsageLine("To do that, the method only makes use of two half maps, but it does not use the set of particles.");
    addUsageLine("The result is a plot resolution-radius. When this plot presents a slope the map has angular assignment error.");
    addUsageLine("In contrast, if the curve is flat, the map is error free or there is shift errors in the particle alignment.");
    addUsageLine("Reference: J.L. Vilas, et. al, XXXXX (2023)");
    addUsageLine("+ The optimal con angle is 17 degree.", true);
    addUsageLine(" This fact was proved in J.L Vilas & H.D. Tagare Nat. Meth 2023. Other values can be used,");
    addUsageLine(" and this parameter does not seems to affect in a significative manner");
    addUsageLine("+* On the helix", true);
    addUsageLine(" If the map is a helix, the helix option should be activated. This option ensures a better estimation of the angular");
    addUsageLine(" assignment errors. The helix is assumen that is oriented along the z-axis. This flag modifies the shape of the ");
    addUsageLine("gaussian mask usign a cylinder.");
    addUsageLine(" ");
    addUsageLine(" ");
    addSeeAlsoLine("resolution_fsc");

    addParamsLine("   --half1 <input_file>               : Input Half map 1");
    addParamsLine("   --half2 <input_file>               : Input Half map 2");
    addParamsLine("   [--directional_resolution]         : (Optional) Uses direcitonal FSC instead of global FSC shell ");
    addParamsLine("   [--limit_radius]                   : (Optional) Limits the maximum radius ");

    addParamsLine("   [-o <output_folder=\"\">]          : Folder where the results will be stored.");

    addParamsLine("   [--sampling <Ts=1>]                : (Optical) Pixel size (Angstrom). If it is not provided by default will be 1 A/px.");
    addParamsLine("   [--mask <input_file=\"\">]         : (Optional) Smooth mask to remove noise. If it is not provided, the computation will be carried out without mask.");

    addParamsLine("   [--anglecone <ang_con=17>]         : (Optional) Angle Cone (angle between the axis and the  generatrix) for estimating the directional FSC");
    addParamsLine("   [--threshold <thrs=0.143>]         : (Optional) Threshold for the FSC/directionalFSC estimation ");
    addParamsLine("   [--helix]                          : (Optional) If the reconstruction is a helix put this flag. The axis of the helix must be along the z-axis");
    addParamsLine("   [--threads <Nthreads=1>]           : (Optional) Number of threads to be used");

    addExampleLine("Resolution of two half maps half1.mrc and half2.mrc with a sampling rate of 2 A/px", false);
    addExampleLine("xmipp_angular_resolution_alignment --half1 half1.mrc --half2 half2.mrc --sampling 2 ");
    addExampleLine("Resolution of two half maps half1.mrc and half2.mrc with a sampling rate of 2 A/px and a mask mask.mrc", false);
    addExampleLine("xmipp_angular_resolution_alignment --half1 half1.mrc --half2 half2.mrc --mask mask.mrc --sampling 2 ");
}

readParams()

void ProgAngResAlign::readParams ( )

virtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippProgram.

Definition at line 73 of file angular_resolution_alignment.cpp.

{
    fnhalf1 = getParam("--half1");
    fnhalf2 = getParam("--half2");
    fnOut = getParam("-o");

    sampling = getDoubleParam("--sampling");
    fnmask = getParam("--mask");
    directionalRes = checkParam("--directional_resolution");
    limRad = checkParam("--limit_radius");
    isHelix = checkParam("--helix");
    ang_con = getDoubleParam("--anglecone");
    thrs = getDoubleParam("--threshold");
    
    Nthreads = getIntParam("--threads");
}

run()

void ProgAngResAlign::run ( )

virtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 1068 of file angular_resolution_alignment.cpp.

    {
        std::cout << "Starting ... " << std::endl << std::endl;

        //This read the data and applies a fftshift to in the next step compute the fft
        // The maps half1_aux, and half2_aux are used to recover the initial maps after masking in each iteration
        MultidimArray<double> half1, half2;
        MultidimArray<double> &phalf1 = half1, &phalf2 = half2;
        readData(phalf1, phalf2);

        // Defining frequencies freq_fourier_x,y,z and freqMap
        // The number of frequencies in each shell freqElem is determined
        defineFrequenciesSimple(phalf1);

        //Define shell Mask
        MultidimArray<double> shellMask;
        shellMask.resizeNoCopy(phalf1);

        // Generating the set of directions to be analyzed
        // And converting the cone angle to radians
        generateDirections(angles, false);
        ang_con = ang_con*PI/180.0;

        MultidimArray<double> half1_aux; 
        MultidimArray<double> half2_aux;

        //Generate shell mask and computing radial resolution
        
        MetaDataVec mdOut;

        //std::cout << "max radius  = " << maxRadius << std::endl;

        for (size_t shellRadius = 0; shellRadius<maxRadius; shellRadius++) 
        {
            shellMask.initZeros();
            shellMask.setXmippOrigin();
            generateShellMask(shellMask, shellRadius, isHelix);

            // Image<double> img;
            // img() = shellMask;
            // FileName fn;
            // fn = formatString("mk_%i.mrc", shellRadius);
            // img.write(fn);

            applyShellMask(half1, half2, shellMask, half1_aux, half2_aux);

                    //Computing the FFT
            FourierTransformer transformer2(FFTW_BACKWARD), transformer1(FFTW_BACKWARD);
            //transformer1.setThreadsNumber(Nthreads);
            //transformer2.setThreadsNumber(Nthreads);

            transformer1.FourierTransform(half1_aux, FT1, false);
            transformer2.FourierTransform(half2_aux, FT2, false);

            // Storing the shell of both maps as vectors global
            // The global FSC is also computed
            
            arrangeFSC_and_fscGlobal();


            double res;
            if (directionalRes)
            {
                std::vector<double> radialResolution(angles.mdimx);

                for (size_t k = 0; k<angles.mdimx; k++)
                {
                    float rot  = MAT_ELEM(angles, 0, k);
                    float tilt = MAT_ELEM(angles, 1, k);

                    double resInterp = -1;  
                    MultidimArray<float> fsc;

                    // Estimating the direction FSC along the direction given by rot and tilt
                    fscDir_fast(fsc, rot, tilt, thrs, resInterp);

                    radialResolution[k] = resInterp;
                }

                std::sort(radialResolution.begin(),radialResolution.end());

                res = radialResolution[round(0.5*angles.mdimx)];
                radialResolution.clear();
            }
            else
            {
                fscGlobal(thrs, res);
            }

            std::cout << "Radius "<< shellRadius << "/" << maxRadius << " " << res << "A" << std::endl;

            MDRowVec row;
            row.setValue(MDL_RESOLUTION_FRC, res);
            row.setValue(MDL_IDX, shellRadius);
            mdOut.addRow(row);
            
        }

        mdOut.write(fnOut);
}

---

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

• xmipp/libraries/reconstruction/angular_resolution_alignment.h
• xmipp/libraries/reconstruction/angular_resolution_alignment.cpp