ProgHistogram Class Reference

Inheritance diagram for ProgHistogram:

Collaboration diagram for ProgHistogram:

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 ()

Public Attributes
Image< double >	image
MetaDataVec	mdIn
FileName	fn_in
FileName	fn_out
FileName	fn_sel
Mask	mask
MultidimArray< int >	maskArray
bool	automatic_range
bool	do_normalize
bool	apply_mask
double	m
double	M
int	StepsNo
Histogram1D	hist
Histogram1D	histb
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

Definition at line 31 of file image_histogram.cpp.

Member Function Documentation

defineParams()

void ProgHistogram::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 44 of file image_histogram.cpp.

    {
        addUsageLine("Calculate histogram from a list of images/volumes");
        addParamsLine("   -i <input_file>              : input metadata, image, volume or stack");
        addParamsLine("  [-o <text_file>]              : output text file with histogram");
        addParamsLine("  [--range <m> <M>]             : range for the histogram, automatic calculated if not provided");
        addParamsLine("  [--steps <N=100>]             : number of subdivisions");
        addParamsLine("  [--norm]                      : normalize histogram ");
        mask.defineParams(this, INT_MASK, nullptr, "Histogram constrained to the mask area.");

        addExampleLine("Create the histogram from an stack setting number of steps to 20", false);
        addExampleLine("xmipp_histogram -i input/images_some.stk -o hist.txt --steps 20");
        addExampleLine("You can use the =hist.txt= file with =gnuplot= to produce graphical histogram", false);
        addExampleLine("After you enter =gnuplot= terminal you can use:", false);
        addExampleLine("gnuplot> plot \"kk.txt\" using 1:2 title \"Histogram\" with steps");

        addSeeAlsoLine("metadata_histogram");
    }

readParams()

void ProgHistogram::readParams ( )

inlinevirtual

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 63 of file image_histogram.cpp.

    {
        fn_in = getParam("-i");
        mdIn.read(fn_in);

        if (mdIn.isEmpty())
            REPORT_ERROR(ERR_PARAM_INCORRECT, "Can't calculate histogram from empty metadata");

        if (checkParam("-o"))
            fn_out = getParam("-o");

        StepsNo = getIntParam("--steps");
        do_normalize = checkParam("--norm");
        automatic_range = true;

        if (checkParam("--range"))
        {
            m = getDoubleParam("--range", 0);
            M = getDoubleParam("--range", 1);
            automatic_range = false;
        }

        mask.allowed_data_types = INT_MASK;
        if ((apply_mask = checkParam("--mask")))
            mask.readParams(this);

        //todo: check this
        //        if (fn_sel!="" && automatic_range)
        //            REPORT_ERROR(ERR_ARG_INCORRECT,"Only use selfile in combination with fixed range!");
        //
        //        mask_prm.read(argc, argv);

    }

run()

void ProgHistogram::run ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 97 of file image_histogram.cpp.

    {
        auto iterId = mdIn.ids().begin();
        image.readApplyGeo(mdIn, *iterId);
        image().setXmippOrigin();
        double dummy;

        // Generate mask if necessary
        if (apply_mask)
        {
            mask.generate_mask(image());
            maskArray = mask.get_binary_mask();
            if (automatic_range)
                computeStats_within_binary_mask(maskArray, image(), m, M, dummy, dummy);
        }
        else if (automatic_range)
            image().computeDoubleMinMax(m, M);

        if (automatic_range)
        {
            m *= 1.5;
            M *= 1.5;
        }

        if (apply_mask)
          compute_hist_within_binary_mask(maskArray, image(), histb, m, M, StepsNo);
        else
          compute_hist(image(), histb, m, M, StepsNo);

        const auto totalSize = mdIn.ids().end();
        while (++iterId != totalSize)
        {
            image.readApplyGeo(mdIn, *iterId);
            image().setXmippOrigin();
            // Compute histogram ----------------------------------------------------
            if (apply_mask)
              compute_hist_within_binary_mask(maskArray, image(), hist, m, M, StepsNo);
            else
              compute_hist(image(), hist, m, M, StepsNo);
            histb += hist;
        }

        if (do_normalize)
            histb *= 1.0 / (histb.sum() * histb.step_size);

        if (!fn_out.empty())
            histb.write(fn_out);
        else
            std::cout << histb;
    }

Member Data Documentation

apply_mask

bool ProgHistogram::apply_mask

Definition at line 39 of file image_histogram.cpp.

automatic_range

bool ProgHistogram::automatic_range

Definition at line 39 of file image_histogram.cpp.

do_normalize

bool ProgHistogram::do_normalize

Definition at line 39 of file image_histogram.cpp.

fn_in

FileName ProgHistogram::fn_in

Definition at line 36 of file image_histogram.cpp.

fn_out

FileName ProgHistogram::fn_out

Definition at line 36 of file image_histogram.cpp.

fn_sel

FileName ProgHistogram::fn_sel

Definition at line 36 of file image_histogram.cpp.

hist

Histogram1D ProgHistogram::hist

Definition at line 42 of file image_histogram.cpp.

histb

Histogram1D ProgHistogram::histb

Definition at line 42 of file image_histogram.cpp.

image

Image<double> ProgHistogram::image

Definition at line 34 of file image_histogram.cpp.

m

double ProgHistogram::m

Definition at line 40 of file image_histogram.cpp.

M

double ProgHistogram::M

Definition at line 40 of file image_histogram.cpp.

mask

Mask ProgHistogram::mask

Definition at line 37 of file image_histogram.cpp.

maskArray

MultidimArray<int> ProgHistogram::maskArray

Definition at line 38 of file image_histogram.cpp.

mdIn

MetaDataVec ProgHistogram::mdIn

Definition at line 35 of file image_histogram.cpp.

StepsNo

int ProgHistogram::StepsNo

Definition at line 41 of file image_histogram.cpp.

---

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

• xmipp/libraries/reconstruction/image_histogram.cpp