ProgVolumeSegment Class Reference

#include <volume_segment.h>

Inheritance diagram for ProgVolumeSegment:

Collaboration diagram for ProgVolumeSegment:

Public Member Functions
void	readParams ()
	Read arguments. More...
void	show () const
	Show. More...
void	defineParams ()
	Define parameters. More...
void	produce_side_info ()
void	segment (Image< double > &mask)
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	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
FileName	fn_vol
	Input volume. More...
String	method
	Segmentation method. More...
double	voxel_mass
double	dalton_mass
	Desired mass (in Daltons). Not necessary if voxel_mass is provided. More...
double	aa_mass
	Desired mass (in aminoacids). Not necessary if voxel_mass is provided. More...
double	sampling_rate
	Sampling rate (in A/pixel). Not necessary if voxel_mass is provided. More...
FileName	fn_mask
	Output mask. If not given it is not written. More...
bool	en_threshold
	Enable a single threshold measure. More...
double	threshold
	Threshold. More...
bool	otsu
	Use Otse. More...
bool	do_prob
	From here on by Sjors. More...
int	wang_radius
	radius for B.C. Wang-like smoothing procedure More...
Image< double >	V
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

Segment parameters.

Definition at line 37 of file volume_segment.h.

Member Function Documentation

defineParams()

void ProgVolumeSegment::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 90 of file volume_segment.cpp.

{
    addParamsLine("   -i <volume>              : Volume to segment");
    addParamsLine("  [-o <mask=\"\">]          : Output mask");
    addParamsLine("   --method <method>        : Segmentation method");
    addParamsLine("      where <method>");
    addParamsLine("            voxel_mass  <mass>        : Mass in voxels");
    addParamsLine("            dalton_mass <mass> <Tm=1> : Mass in daltons");
    addParamsLine("                                      : Tm is the sampling rate (A/pixel)");
    addParamsLine("            aa_mass     <mass> <Tm=1> : Mass in aminoacids");
    addParamsLine("                                      : Tm is the sampling rate (A/pixel)");
    addParamsLine("            threshold   <th>          : Thresholding");
    addParamsLine("            otsu                      : Otsu's method segmentation");
    addParamsLine("            prob        <radius=-1>   : Probabilistic solvent mask (typical value 3)");
    addParamsLine("                                      : Radius [pix] is used for B.C. Wang cone smoothing");
}

produce_side_info()

void ProgVolumeSegment::produce_side_info

(

)

Produce side info. Read the input volume, and compute the number of voxels if not given. An exception is thrown if no way is given to compute the voxel mass

Definition at line 108 of file volume_segment.cpp.

{
    V.read(fn_vol);
    if (method=="dalton_mass" || method=="aa_mass")
    {
        if ((dalton_mass == -1 && aa_mass == -1) || sampling_rate == -1)
            REPORT_ERROR(ERR_VALUE_INCORRECT, "No way to compute voxel mass");
        double sampling_rate3 = sampling_rate * sampling_rate * sampling_rate;
        if (dalton_mass != -1)
            voxel_mass = dalton_mass * 1.207 / sampling_rate3;
        else
            voxel_mass = aa_mass * 110 * 1.207 / sampling_rate3;
        std::cout << std::endl << "Derived voxel_mass=" << voxel_mass << std::endl;
    }
}

readParams()

void ProgVolumeSegment::readParams ( )

virtual

Read arguments.

Reimplemented from XmippProgram.

Definition at line 32 of file volume_segment.cpp.

{
    voxel_mass=dalton_mass=aa_mass=-1;
    sampling_rate=-1;
    threshold=-1;
    wang_radius=-1;
    en_threshold=false;
    do_prob=false;
    otsu=false;

    fn_vol = getParam("-i");
    fn_mask = getParam("-o");
    method=getParam("--method");
    if (method=="voxel_mass")
        voxel_mass = getDoubleParam("--method", 1);
    else if (method=="dalton_mass")
    {
        dalton_mass = getDoubleParam("--method", 1);
        sampling_rate = getDoubleParam("--method", 2);
    }
    else if (method=="aa_mass")
    {
        aa_mass = getDoubleParam("--method", 1);
        sampling_rate = getDoubleParam("--method", 2);
    }
    else if (method=="threshold")
    {
        en_threshold = true;
        threshold = getDoubleParam("--method", 1);
    }
    else if (method=="otsu")
        otsu=true;
    else if (method=="prob")
    {
        do_prob = true;
        wang_radius = getIntParam("--method", 1);
    }
}

run()

void ProgVolumeSegment::run ( )

virtual

Run

Reimplemented from XmippProgram.

Definition at line 369 of file volume_segment.cpp.

{
    Image<double> mask;
    show();
    produce_side_info();
    segment(mask);
}

segment()

void ProgVolumeSegment::segment

(

Image< double > &

mask

)

Really compute the mask. If a mask name is given then it is written to disk.

Definition at line 293 of file volume_segment.cpp.

{
    double th_min, th_max, val_min=0., val_max=0.;
    V().computeDoubleMinMax(val_min, val_max);
    th_min = val_min;
    th_max = val_max;

    bool ok = false;
    if (!otsu)
    {
        if (!en_threshold)
        {
            // Perform a bracketing search until the mass is
            // within a 0.1% of the desired mass
            do
            {
                double th_med = (th_min + th_max) * 0.5;
                double mass_med = segment_threshold(&V, &mask, th_med, do_prob);
                std::cout << "Threshold= " << th_med
                << " mass of the main piece= " << mass_med << std::endl;
                if (ABS(mass_med - voxel_mass) / voxel_mass < 0.001)
                {
                    ok = true;
                    break;
                }
                if ((th_max - th_min) / (val_max - val_min) < 0.0001)
                    break;
                if (mass_med < voxel_mass)
                {
                    th_max = th_med;
                }
                else
                {
                    th_min = th_med;
                }
            }
            while (true);
        }
        else
        {
            // Perform a single thresholding
            double mass_med = segment_threshold(&V, &mask, threshold, do_prob);
            std::cout << "Threshold= " << threshold
            << " mass of the main piece= " << mass_med << std::endl;
            ok = true;
        }
    }

    if (otsu)
    {
        mask()=V();
        double th=EntropyOtsuSegmentation(mask());
        std::cout << "Threshold " << th << std::endl;
        ok=true;
    }

    if (do_prob)
    {
        // Wang-Leslie like modification of the input volume
        if (wang_radius >= 3)
        {
            Image<double> Vwang;
            wang_smoothing(&V, &Vwang, wang_radius);
            V = Vwang;
        }
        // Terwilliger-like calculation of P(solv|x) through P(x|solv) & P(x|prot)
        probabilistic_solvent(&V, &mask);
    }

    // Save mask if necessary
    if (fn_mask != "" && (ok || do_prob))
        mask.write(fn_mask);
    if (!ok && !do_prob)
        std::cout << "Segment: Cannot find an appropriate threshold\n";
}

show()

void ProgVolumeSegment::show ( ) const

virtual

Show.

Reimplemented from XmippProgram.

Definition at line 72 of file volume_segment.cpp.

{
    std::cout
    << "Input file   : " << fn_vol        << std::endl
    << "Voxel mass   : " << voxel_mass    << std::endl
    << "Dalton mass  : " << dalton_mass   << std::endl
    << "AA mass      : " << aa_mass       << std::endl
    << "Sampling rate: " << sampling_rate << std::endl
    << "Output mask  : " << fn_mask       << std::endl
    << "Enable thres.: " << en_threshold  << std::endl
    << "Threshold    : " << threshold     << std::endl
    << "Otsu         : " << otsu          << std::endl
    << "Wang radius  : " << wang_radius   << std::endl
    << "Probabilistic: " << do_prob       << std::endl
    ;
}

Member Data Documentation

aa_mass

double ProgVolumeSegment::aa_mass

Desired mass (in aminoacids). Not necessary if voxel_mass is provided.

Definition at line 50 of file volume_segment.h.

dalton_mass

double ProgVolumeSegment::dalton_mass

Desired mass (in Daltons). Not necessary if voxel_mass is provided.

Definition at line 48 of file volume_segment.h.

do_prob

bool ProgVolumeSegment::do_prob

From here on by Sjors.

Definition at line 64 of file volume_segment.h.

en_threshold

bool ProgVolumeSegment::en_threshold

Enable a single threshold measure.

Definition at line 56 of file volume_segment.h.

fn_mask

FileName ProgVolumeSegment::fn_mask

Output mask. If not given it is not written.

Definition at line 54 of file volume_segment.h.

fn_vol

FileName ProgVolumeSegment::fn_vol

Input volume.

Definition at line 41 of file volume_segment.h.

method

String ProgVolumeSegment::method

Segmentation method.

Definition at line 43 of file volume_segment.h.

otsu

bool ProgVolumeSegment::otsu

Use Otse.

Definition at line 60 of file volume_segment.h.

sampling_rate

double ProgVolumeSegment::sampling_rate

Sampling rate (in A/pixel). Not necessary if voxel_mass is provided.

Definition at line 52 of file volume_segment.h.

threshold

double ProgVolumeSegment::threshold

Threshold.

Definition at line 58 of file volume_segment.h.

V

Image<double> ProgVolumeSegment::V

Definition at line 70 of file volume_segment.h.

voxel_mass

double ProgVolumeSegment::voxel_mass

Desired mass (in voxels), if not given computed from the mass and the sampling rate by produce_info.

Definition at line 46 of file volume_segment.h.

wang_radius

int ProgVolumeSegment::wang_radius

radius for B.C. Wang-like smoothing procedure

Definition at line 66 of file volume_segment.h.

---

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

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