ProgMicrographScissor Class Reference

Inheritance diagram for ProgMicrographScissor:

Collaboration diagram for ProgMicrographScissor:

Public Member Functions
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 ()

Protected Member Functions
void	defineParams ()
void	readParams ()
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes
FileName	fn_micrograph
FileName	fn_out
FileName	fn_tilted
FileName	fn_out_tilted
FileName	fn_angles
FileName	fn_tilt_pos
FileName	fn_orig
FileName	fn_pos
bool	pair_mode
int	Ydim
int	Xdim
bool	reverse_endian
bool	compute_transmitance
bool	compute_inverse
double	down_transform
bool	rmStack
bool	fillBorders
int	Nnoise
bool	extractNoise
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

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

Detailed Description

Definition at line 32 of file micrograph_scissor.cpp.

Member Function Documentation

defineParams()

void ProgMicrographScissor::defineParams ( )

inlineprotectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 37 of file micrograph_scissor.cpp.

    {
        addUsageLine ("Extract particles from a micrograph");
        addSeeAlsoLine("micrograph_mark");

        addParamsLine(" == General Options == ");
        addParamsLine("  -i <input_untilted_micrograph>     : From which the untilted images will be cutted");
        addParamsLine("     alias --untilted;");
        addParamsLine("  [--orig <original_micrograph>]      : unless this parameter is specified");
        addParamsLine("  -o <output_stack>                   : Name for the particle images");
        addParamsLine("                                      :+ Two files will be created: output_stack with the particles in a Spider stack an output_stack.xmd with the list of image names, the micrograph they were taken from, and their coordinates");
        addParamsLine("     alias --untiltfn;");
        addParamsLine("  [--pos <position_file>]             : file with particle coordinates");
        addParamsLine("     alias --untiltPos;");
        addParamsLine("  [--extractNoise <n=-1>]             : extract noise particles instead of true particles");
        addParamsLine("                                      : n is the number of noise particles to extract");
        addParamsLine("                                      : If n=-1, then the number of noise particles is the number of coordinates in the pos file");
        addParamsLine("                                      : The input posfile WILL be rewritten with the noise coordinates");

        addParamsLine(" == Processing Options == ");
        addParamsLine("  --Xdim <window_X_dim>               : In pixels");
        addParamsLine("  [--downsampling <float=1.>]         : The positions were determined with this downsampling rate");
        addParamsLine("  [--Ydim <window_Y_dim>]             : If not given Ydim=Xdim");
        addParamsLine("  [--invert]                          : Invert contrast");
        addParamsLine("  [--log]                             : Take logarithm (compute transmitance)");
        addParamsLine("  [--appendToStack]                   : The output stack is deleted.");
        addParamsLine("                                      : Use this option to add the new images to the stack");
        addParamsLine("  [--fillBorders]                     : If the box is outside the micrograph, fill the missing pixels");
        addParamsLine("                                      : instead of setting the whole image to blank");

        addParamsLine(" == Options for tilt pairs == ");
        addParamsLine("  [-t <input_tilted_micrograph>]      : From which the   tilted images will be cutted");
        addParamsLine("     alias --tilted;");
        addParamsLine("  [--tiltfn <output_stack>]           : Name for tilted images (Stack FileName)");
        addParamsLine("     requires --untiltfn;                                                         ");
        addParamsLine("  [--tiltAngles <angles_file>]        : Name of the estimated tilt angles");
        addParamsLine("                                      :  Angle from the Y axis to the tilt axis. Both (tilted and untilted) must be cut with its corresponding angle. Cut images are rotated so that the tilt axis is parallel to Y axis.");
        addParamsLine("     requires --tiltfn;                                                         ");
        addParamsLine("  [--tiltPos <position_file>]         : file with particle coordinates");
        addParamsLine("     requires --tiltfn;                                                         ");
        addParamsLine("  [--ctfparam <ctfparam>]             : metadata with ctf parameters for the micrograph.");

        addExampleLine ("   xmipp_micrograph_scissor -i g7107.raw --pos g7107.raw.Common.pos --oroot images --Xdim 64");
        addExampleLine ("   xmipp_micrograph_scissor --untilted Preprocessing/untilt/down1_untilt.raw --tilted Preprocessing/tilt/down1_tilt.raw --untiltfn untilt --tiltfn tilt --Xdim 60 --tiltAngles ParticlePicking/down1_untilt.raw.angles.txt --pos ParticlePicking/down1_untilt.raw.Common.pos --tiltPos ParticlePicking/down1_untilt.raw.tilted.Common.pos");
    }

readParams()

void ProgMicrographScissor::readParams ( )

inlineprotectedvirtual

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 96 of file micrograph_scissor.cpp.

    {
        fn_micrograph = getParam  ("-i");
        pair_mode     = checkParam("--tilted");
        fn_out        = getParam  ("-o");
        fn_pos        = getParam  ("--pos");
        Xdim          = getIntParam("--Xdim");
        if (checkParam("--Ydim"))
            Ydim      = getIntParam("--Ydim");
        else
            Ydim = Xdim;

        compute_inverse      = checkParam("--invert");
        compute_transmitance = checkParam("--log");
        rmStack              = !checkParam("--appendToStack");

        if (!pair_mode)
        {
            if (checkParam("--orig"))
                fn_orig       = getParam("--orig");
        }
        else
        {
            fn_out_tilted = getParam("--tiltfn");
            fn_tilted      = getParam("--tilted");
            fn_angles      = getParam("--tiltAngles");
            fn_tilt_pos    = getParam("--tiltPos");
        }
        down_transform = getDoubleParam("--downsampling");
        fillBorders = checkParam("--fillBorders");
        extractNoise = checkParam("--extractNoise");
        if (extractNoise)
        {
            randomize_random_generator();
            Nnoise = getIntParam("--extractNoise",0);
        }
    }

run()

void ProgMicrographScissor::run ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 134 of file micrograph_scissor.cpp.

    {
        if (!pair_mode)
        {
            Micrograph m;
            m.open_micrograph(fn_micrograph);
            m.set_window_size(Xdim, Ydim);
            m.read_coordinates(0, fn_pos);
            if (down_transform != 1.)
                m.scale_coordinates(1./down_transform);
            m.add_label("");
            m.set_transmitance_flag(compute_transmitance);
            m.set_inverse_flag(compute_inverse);

            if (checkParam("--ctfparam"))
            {
              MetaDataVec ctfparam(getParam("--ctfparam"));
              MDRowVec ctfRow;
              ctfparam.getRow(ctfRow, ctfparam.firstRowId());
              m.set_ctfparams(ctfRow);
            }
            m.produce_all_images(0, -1, fn_out, fn_orig, 0., rmStack, fillBorders, extractNoise, Nnoise);
            if (extractNoise)
            {
                MDRowVec row=firstRow(fn_pos);
                size_t micId=0;
                if (row.containsLabel(MDL_MICROGRAPH_ID))
                    row.getValue(MDL_MICROGRAPH_ID,micId);

                // Rewrite the input posfile with the true noise coordinates
                MetaDataVec MD;
                for (size_t i=0; i<m.coords.size(); i++)
                {
                    size_t id=MD.addObject();
                    MD.setValue(MDL_XCOOR, m.coords[i].X, id);
                    MD.setValue(MDL_YCOOR, m.coords[i].Y, id);
                    MD.setValue(MDL_MICROGRAPH_ID, micId, id);
                }
                MD.write(fn_pos);
            }
        }
        else
        {
            MetaDataVec auxMd;
            // Read angles
            double alpha_u, alpha_t, tilt_angle;
            auxMd.read(fn_angles);
            size_t objId = auxMd.firstRowId();
            auxMd.getValue(MDL_ANGLE_Y, alpha_u, objId);
            auxMd.getValue(MDL_ANGLE_Y2, alpha_t, objId);
            auxMd.getValue(MDL_ANGLE_TILT, tilt_angle, objId);

            // Generate the images for the untilted image
            Micrograph m;
            m.open_micrograph(fn_micrograph);
            m.set_window_size(Xdim, Ydim);
            m.read_coordinates(0, fn_pos);
            m.add_label("");
            m.set_transmitance_flag(compute_transmitance);
            m.set_inverse_flag(compute_inverse);
            m.produce_all_images(0, -1, fn_out, "", alpha_u, rmStack);
            m.close_micrograph();

            // Generate the images for the tilted image
            Micrograph mt;
            mt.open_micrograph(fn_tilted);
            mt.set_window_size(Xdim, Ydim);
            mt.read_coordinates(0, fn_tilt_pos);
            mt.add_label("");
            mt.set_transmitance_flag(compute_transmitance);
            mt.set_inverse_flag(compute_inverse);
            mt.produce_all_images(0, -1, fn_out_tilted, "", 0., rmStack);
            mt.close_micrograph();
        }
    }

Member Data Documentation

compute_inverse

bool ProgMicrographScissor::compute_inverse

protected

Definition at line 89 of file micrograph_scissor.cpp.

compute_transmitance

bool ProgMicrographScissor::compute_transmitance

protected

Definition at line 88 of file micrograph_scissor.cpp.

down_transform

double ProgMicrographScissor::down_transform

protected

Definition at line 90 of file micrograph_scissor.cpp.

extractNoise

bool ProgMicrographScissor::extractNoise

protected

Definition at line 94 of file micrograph_scissor.cpp.

fillBorders

bool ProgMicrographScissor::fillBorders

protected

Definition at line 92 of file micrograph_scissor.cpp.

fn_angles

FileName ProgMicrographScissor::fn_angles

protected

Definition at line 83 of file micrograph_scissor.cpp.

fn_micrograph

FileName ProgMicrographScissor::fn_micrograph

protected

Definition at line 82 of file micrograph_scissor.cpp.

fn_orig

FileName ProgMicrographScissor::fn_orig

protected

Definition at line 84 of file micrograph_scissor.cpp.

fn_out

FileName ProgMicrographScissor::fn_out

protected

Definition at line 82 of file micrograph_scissor.cpp.

fn_out_tilted

FileName ProgMicrographScissor::fn_out_tilted

protected

Definition at line 83 of file micrograph_scissor.cpp.

fn_pos

FileName ProgMicrographScissor::fn_pos

protected

Definition at line 84 of file micrograph_scissor.cpp.

fn_tilt_pos

FileName ProgMicrographScissor::fn_tilt_pos

protected

Definition at line 83 of file micrograph_scissor.cpp.

fn_tilted

FileName ProgMicrographScissor::fn_tilted

protected

Definition at line 83 of file micrograph_scissor.cpp.

Nnoise

int ProgMicrographScissor::Nnoise

protected

Definition at line 93 of file micrograph_scissor.cpp.

pair_mode

bool ProgMicrographScissor::pair_mode

protected

Definition at line 85 of file micrograph_scissor.cpp.

reverse_endian

bool ProgMicrographScissor::reverse_endian

protected

Definition at line 87 of file micrograph_scissor.cpp.

rmStack

bool ProgMicrographScissor::rmStack

protected

Definition at line 91 of file micrograph_scissor.cpp.

Xdim

int ProgMicrographScissor::Xdim

protected

Definition at line 86 of file micrograph_scissor.cpp.

Ydim

int ProgMicrographScissor::Ydim

protected

Definition at line 86 of file micrograph_scissor.cpp.

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

• xmipp/libraries/reconstruction/micrograph_scissor.cpp