ProgWindow Class Reference

Inheritance diagram for ProgWindow:

Collaboration diagram for ProgWindow:

Public Types
enum	WindowMode { CORNERMODE, SIZEMODE, CROPMODE, UNITCELLMODE }

Public Member Functions
void	defineParams ()
void	readParams ()
void	show ()
void	preProcess ()
void	unitcell (ImageGeneric &in3Dmap, ImageGeneric &out3DDmap)
void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)
void	postProcess ()
Public Member Functions inherited from XmippMetadataProgram
MetaData *	getInputMd ()
MetaDataVec &	getOutputMd ()
	XmippMetadataProgram ()
	Empty constructor. More...
virtual int	tryRead (int argc, const char **argv, bool reportErrors=true)
virtual void	init ()
virtual void	setup (MetaData *md, const FileName &o="", const FileName &oroot="", bool applyGeo=false, MDLabel label=MDL_IMAGE)
virtual	~XmippMetadataProgram ()
void	setMode (WriteModeMetaData _mode)
void	setupRowOut (const FileName &fnImgIn, const MDRow &rowIn, const FileName &fnImgOut, MDRow &rowOut) const
	Prepare rowout. More...
virtual void	wait ()
	Wait for the distributor to finish. More...
virtual void	checkPoint ()
	For very long programs, it may be needed to write checkpoints. More...
virtual void	run ()
	Run over all images. More...
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)
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
bool	physical_coords
int	sizeX
int	sizeY
int	sizeZ
int	cropX
int	cropY
int	cropZ
int	x0
int	y0
int	z0
int	xF
int	yF
int	zF
String	sym
double	rmin
double	rmax
double	expand
double	offset
double	sampling
double	x_origin
double	y_origin
double	z_origin
double	padValue
String	padType
WindowMode	windowMode
FileName	tempFn
bool	renameTempFn
Public Attributes inherited from XmippMetadataProgram
FileName	fn_in
	Filenames of input and output Metadata. More...
FileName	fn_out
FileName	baseName
FileName	pathBaseName
FileName	oextBaseName
bool	apply_geo
	Apply geo. More...
size_t	ndimOut
	Output dimensions. More...
size_t	zdimOut
size_t	ydimOut
size_t	xdimOut
DataType	datatypeOut
size_t	mdInSize
	Number of input elements. More...
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippMetadataProgram
virtual void	initComments ()
virtual bool	getImageToProcess (size_t &objId, size_t &objIndex)
void	show () const override
virtual void	startProcessing ()
virtual void	finishProcessing ()
virtual void	writeOutput ()
virtual void	showProgress ()
virtual void	defineLabelParam ()
Protected Member Functions inherited from XmippProgram
void	defineCommons ()
Protected Attributes inherited from XmippMetadataProgram
WriteModeMetaData	mode
	Metadata writing mode: OVERWRITE, APPEND. More...
FileName	oext
	Output extension and root. More...
FileName	oroot
MDLabel	image_label
	MDLabel to be used to read/write images, usually will be MDL_IMAGE. More...
bool	produces_an_output
	Indicate that a unique final output is produced. More...
bool	produces_a_metadata
	Indicate that the unique final output file is a Metadata. More...
bool	each_image_produces_an_output
	Indicate that an output is produced for each image in the input. More...
bool	allow_apply_geo
bool	decompose_stacks
	Input Metadata will treat a stack file as a set of images instead of a unique file. More...
bool	delete_output_stack
	Delete previous output stack file prior to process images. More...
bool	get_image_info
	Get the input image file dimensions to further operations. More...
bool	save_metadata_stack
	Save the associated output metadata when output file is a stack. More...
bool	track_origin
	Include the original input image filename in the output stack. More...
bool	keep_input_columns
	Keep input metadata columns. More...
bool	remove_disabled
	Remove disabled images from the input selfile. More...
bool	allow_time_bar
	Show process time bar. More...
bool	input_is_metadata
	Input is a metadata. More...
bool	single_image
	Input is a single image. More...
bool	input_is_stack
	Input is a stack. More...
bool	output_is_stack
	Output is a stack. More...
bool	create_empty_stackfile
bool	delete_mdIn
size_t	time_bar_step
	Some time bar related counters. More...
size_t	time_bar_size
size_t	time_bar_done
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 29 of file transform_window.cpp.

Member Enumeration Documentation

WindowMode

enum ProgWindow::WindowMode

Enumerator
CORNERMODE
SIZEMODE
CROPMODE
UNITCELLMODE

Definition at line 31 of file transform_window.cpp.

                 {
        CORNERMODE, SIZEMODE, CROPMODE, UNITCELLMODE
    } WindowMode;

Member Function Documentation

defineParams()

void ProgWindow::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Definition at line 49 of file transform_window.cpp.

                        {
        each_image_produces_an_output = true;
        allow_apply_geo = true;
        XmippMetadataProgram::defineParams();
        addUsageLine("This program takes a region from the input images");
        addUsageLine(" ");
        addUsageLine(
                "But... what is windowing? Let's suppose we have an image 32x32,");
        addUsageLine(
                "and we window it to 16x16, then the central part which contains");
        addUsageLine(
                "this 16x16 square is returned, but if we window to 64x64 then the");
        addUsageLine(
                "image is kept in the center of the final image and it is padded");
        addUsageLine(
                "with 0's until the new size is reached (the padding value may be");
        addUsageLine(
                "modified using --pad_value, --corner_pad_value or --average_pad_value).");
        addUsageLine(" ");
        addUsageLine(
                "With this idea in mind of padding or cutting, if you define two");
        addUsageLine(
                "logical corners in the input image (the most negative -the top");
        addUsageLine(
                "left in an image- and the most positive -bottom right in an image-)");
        addUsageLine(
                "you can store the new image or volume generated by windowing with");
        addUsageLine("a square box.");
        addParamsLine(
                "  --corners <...>                        : Windows corners (by default indexes are logical)");
        addParamsLine(
                "                                         : 2D: <x0> <y0> <xF> <yF>");
        addParamsLine(
                "                                         : 3D: <x0> <y0> <z0> <xF> <yF> <zF>");
        addParamsLine(
                "  or --size <sizeX> <sizeY=0> <sizeZ=0>  : Output dimension. The volume is windowed");
        addParamsLine(
                "                                         : (expanded or cutted) in all directions such");
        addParamsLine(
                "                                         : that the origin of the volume remains the");
        addParamsLine(
                "                                         : same. If the Y and Z dimensions are not");
        addParamsLine(
                "                                         : specified they are assumed to be the same as");
        addParamsLine(
                "                                         : the X dimension.");
        addParamsLine(
                "  or --crop <sizeX> <sizeY=0> <sizeZ=0>  : Crop this amount of pixels in each direction.");
        addParamsLine(
                "                                         : Half of the pixels will be cropped from the left");
        addParamsLine(
                "                                         : and the other half from the right");
        addParamsLine(
                "                                         : if only one is given, the other two");
        addParamsLine(
                "                                         : are supposed to be the same");
        addParamsLine(
                "  or --unitcell <sym> <rmin=0> <rmax=0> <expandFactor=0> <offset=0> <sampling=1.> <x_origin=-1.> <y_origin=-1.> <z_origin=-1.> : Extract a unit cell from volume");
        addParamsLine(
                "                                         : sym = particle symmetry");
        addParamsLine(
                "                                         : expandFactor = expand unitcell by this factor");
        addParamsLine(
                "                                         : rmax, rmin = cut a shell with these radii (pixels)");
        addParamsLine(
                "                                         : offset= for CN symmetry rotate unit cell by this angle");
        addParamsLine(
                "                                         : sampling=if the output is a mrc file it will use this value to fill the header");
        addParamsLine(
                "                                         : x_origin = origin x coordinate introduced by the user with the input volume (in pixels)");
        addParamsLine(
                "                                         : y_origin = origin y coordinate introduced by the user with the input volume (in pixels)");
        addParamsLine(
                "                                         : z_origin = origin z coordinate introduced by the user with the input volume (in pixels)");
        addParamsLine(
                "  [--physical]                           : use physical instead of logical coordinates");
        addParamsLine("    requires --corners;");
        addParamsLine(
                "  [--pad <padtype=value>]                : value used for padding");
        addParamsLine("   where <padtype>");
        addParamsLine(
                "         value <v=0>                     : use this value for padding");
        addParamsLine(
                "         corner                          : use the top-left corner for padding");
        addParamsLine(
                "         avg                             : use the image average for padding");
        addExampleLine(
                "Window a single image to 16x16, overwriting input image",
                false);
        addExampleLine("xmipp_transform_window -i g0ta0001.xmp --size 16");
        addExampleLine("Window a single volume to 32x64x64", false);
        addExampleLine("xmipp_transform_window -i g0ta.vol --size 64 64 32");
        addExampleLine("The same using logical indexes", false);
        addExampleLine(
                "xmipp_transform_window -i g0ta.vol --corners -32 -32 -16 31 31 15");
        addExampleLine(
                "Note that r0 and rF are not symmetric because the volume is of an",
                false);
        addExampleLine(
                "even size, if we wanted to get a 33x65x65 volume, the right indexes",
                false);
        addExampleLine("would be", false);
        addExampleLine(
                "xmipp_transform_window -i g0ta.vol --corners -32 -32 -16 32 32 16");
        addExampleLine("Reduce the volume by 10 pixels on each direction",
                false);
        addExampleLine("xmipp_transform_window -i g0ta.vol --crop 10");
        addExampleLine(
                "Enlarge the volume by 10 pixels on each direction (negative crop)",
                false);
        addExampleLine("xmipp_transform_window -i g0ta.vol --crop -10");
        addExampleLine("scipion xmipp_transform_window -i postprocess.mrc:mrc  -o postprocess_win.mrc  --unitcell i2 0 300 20 0 0.34");
        addKeywords("window, crop, resize, corner, padding");
    }

postProcess()

void ProgWindow::postProcess ( )

inlinevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 352 of file transform_window.cpp.

                       {
        /* Since dimensions are usually changed in this program, we cannot reuse the same file
         * but we can create a temporary file. Now it must be deleted */
        if (renameTempFn) {
            if (std::rename(fn_out.c_str(), fn_in.c_str()) != 0)
                REPORT_ERROR(ERR_IO,
                        formatString("Error renaming file '%s' to '%s'.",
                                fn_out.c_str(), fn_in.c_str()));
        }
    }

preProcess()

void ProgWindow::preProcess ( )

inlinevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 264 of file transform_window.cpp.

                      {
        create_empty_stackfile = false;
        renameTempFn = false;

        /* Since dimensions are usually changed in this program, we cannot reuse the same file
         * but we can create a temporary file */
        if (input_is_stack && fn_out.empty()) {
//            tempFn.initUniqueName("temp_XXXXXX");
            fn_out = fn_in + "xtw_tmpfile" + "." + fn_in.getExtension();
            renameTempFn = true;
        }
    }

processImage()

void ProgWindow::processImage ( const FileName &  fnImg, const FileName &  fnImgOut, const MDRow &  rowIn, MDRow &  rowOut  )

inlinevirtual

Implements XmippMetadataProgram.

Definition at line 286 of file transform_window.cpp.

                                               {
        ImageGeneric Iin;
        bool createTempFile = (fnImg == fnImgOut);
        if (apply_geo) {
            Iin.readApplyGeo(fnImg, rowIn);
        } else {
            Iin.read(fnImg, DATA, ALL_IMAGES, true);
        }

        double init_value(padValue);
        if (padType == "avg")
            init_value = Iin().computeAvg();
        else if (padType == "corner")
            init_value = Iin()(0, 0, 0, 0);

        Iin().setXmippOrigin();
        if (ZSIZE(Iin()()) == 1)
            zF = z0 = 0;

        String oext = fnImgOut.getExtension();
        DataType dataType = Iin.getDatatype();
        ImageGeneric result(dataType);
        if (windowMode == UNITCELLMODE) {
            Iin.convert2Datatype(DT_Float);
            unitcell(Iin, result);
        } else if (windowMode == CROPMODE) {
            int xl = cropX / 2;
            int xr = cropX - xl;
            int yl = cropY / 2;
            int yr = cropY - yl;
            int zl = cropZ / 2;
            int zr = cropZ - zl;
            if (ZSIZE(Iin()()) == 1) {
                zl = zr = 0;
            }
            //call to a generic 4D function;
            result.mapFile2Write(
            FINISHINGX(Iin()()) - xr - (STARTINGX(Iin()()) + xl) + 1,
            FINISHINGY(Iin()()) - yr - (STARTINGY(Iin()()) + yl) + 1,
            FINISHINGZ(Iin()()) - zr - (STARTINGZ(Iin()()) + zl) + 1, fnImgOut,
                    createTempFile);
            Iin().window(result(),
            STARTINGZ(Iin()()) + zl, STARTINGY(Iin()()) + yl,
            STARTINGX(Iin()()) + xl,
            FINISHINGZ(Iin()()) - zr, FINISHINGY(Iin()()) - yr,
            FINISHINGX(Iin()()) - xr);
        } else if (!physical_coords) {
            result.mapFile2Write(xF - x0 + 1, yF - y0 + 1, zF - z0 + 1,
                    fnImgOut, createTempFile);
            Iin().window(result(), z0, y0, x0, zF, yF, xF, init_value);
        } else {
            result.mapFile2Write(xF - x0 + 1, yF - y0 + 1, zF - z0 + 1,
                    fnImgOut, createTempFile);
            Iin().window(result(),
            STARTINGZ(Iin()()) + z0,
            STARTINGY(Iin()()) + y0,
            STARTINGX(Iin()()) + x0,
            STARTINGZ(Iin()()) + zF,
            STARTINGY(Iin()()) + yF,
            STARTINGX(Iin()()) + xF, init_value);
        }
        Iin.clear(); // Close the input file
        result.write(fnImgOut);
    }

readParams()

void ProgWindow::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 XmippMetadataProgram.

Definition at line 164 of file transform_window.cpp.

                      {
        XmippMetadataProgram::readParams();
        padType = getParam("--pad");
        if (padType == "value")
            padValue = getDoubleParam("--pad", "value");
        if (checkParam("--corners")) {
            int nparams = getCountParam("--corners");
            if (nparams == 4 || nparams == 6) {
                x0 = getIntParam("--corners", 0);
                y0 = getIntParam("--corners", 1);
                if (nparams == 4) {
                    xF = getIntParam("--corners", 2);
                    yF = getIntParam("--corners", 3);
                    zF = z0 = 0;
                } else {
                    z0 = getIntParam("--corners", 2);
                    xF = getIntParam("--corners", 3);
                    yF = getIntParam("--corners", 4);
                    zF = getIntParam("--corners", 5);
                }
            } else
                REPORT_ERROR(ERR_ARG_INCORRECT,
                        "Incorrect number of arguments after --corners");
            physical_coords = checkParam("--physical");
            windowMode = CORNERMODE;
        } else if (checkParam("--size")) {
            sizeX = getIntParam("--size", 0);
            sizeY = getIntParam("--size", 1);
            sizeZ = getIntParam("--size", 2);
            if (sizeY == 0)
                sizeY = sizeX;
            if (sizeZ == 0)
                sizeZ = sizeX;
            x0 = FIRST_XMIPP_INDEX(sizeX);
            y0 = FIRST_XMIPP_INDEX(sizeY);
            z0 = FIRST_XMIPP_INDEX(sizeZ);
            xF = LAST_XMIPP_INDEX(sizeX);
            yF = LAST_XMIPP_INDEX(sizeY);
            zF = LAST_XMIPP_INDEX(sizeZ);
            windowMode = SIZEMODE;
            physical_coords = false;
        }
        //<sym> <rmin=0> <rmax=0> <expandFactor=0> <offset=0> <x_offset=-1.> <y_offset=-1.> <z_offset=-1.>: Extract a unit cell from volume");

        else if (checkParam("--crop")) {
            cropX = getIntParam("--crop", 0);
            cropY = getIntParam("--crop", 1);
            cropZ = getIntParam("--crop", 2);
            if (cropY == 0)
                cropY = cropX;
            if (cropZ == 0)
                cropZ = cropX;
            windowMode = CROPMODE;
            physical_coords = false;
        } else if (checkParam("--unitcell")) {
            int nparams = getCountParam("--unitcell");
            if (nparams != 9) REPORT_ERROR(ERR_ARG_INCORRECT, "Incorrect number of arguments after --unitcell");
            sym = getParam("--unitcell", 0);
            rmin = getDoubleParam("--unitcell", 1);
            rmax = getDoubleParam("--unitcell", 2);
            expand = getDoubleParam("--unitcell", 3);
            offset = DEG2RAD(getDoubleParam("--unitcell", 4));
            sampling = getDoubleParam("--unitcell", 5);
            x_origin = getDoubleParam("--unitcell", 6);
            y_origin = getDoubleParam("--unitcell", 7);
            z_origin = getDoubleParam("--unitcell", 8);

            windowMode = UNITCELLMODE;
        }
    }

show()

void ProgWindow::show ( )

inline

Definition at line 235 of file transform_window.cpp.

                {
        if (verbose == 0)
            return;
        XmippMetadataProgram::show();
        switch (windowMode) {
        case SIZEMODE:
            std::cout << "New size: (XxYxZ)=" << sizeX << "x" << sizeY << "x"
                    << sizeZ << std::endl;
            break;
        case CROPMODE:
            std::cout << "Crop: (XxYxZ)=" << cropX << "x" << cropY << "x"
                    << cropZ << std::endl;
            break;
        case CORNERMODE:
            std::cout << "New window: from (z0,y0,x0)=(" << z0 << "," << y0
                    << "," << x0 << ") to (zF,yF,xF)=(" << zF << "," << yF
                    << "," << xF << ")\n" << "Physical: " << physical_coords
                    << std::endl;
            break;
        case UNITCELLMODE:
            std::cout << "Sym: " << sym << ", rmin: " << rmin << ", rmax: " << rmax
                      << ", Expand Factor: " << expand << ", offset: " << offset
                      << ", sampling: " << sampling << "; Origin in Angstroms: "
                      << " x: " << x_origin * sampling << ", y: " << y_origin * sampling << ", z: " << z_origin * sampling
                      << std::endl;
            break;
        }
    }

unitcell()

void ProgWindow::unitcell ( ImageGeneric &  in3Dmap, ImageGeneric &  out3DDmap  )

inline

Definition at line 277 of file transform_window.cpp.

                                            {
        //1) init class and compute auxiliary vectors
        UnitCell UC(sym, rmin, rmax, expand, offset, sampling, x_origin, y_origin, z_origin);
        //2) mask image
        UC.maskUnitCell(in3Dmap,out3DDmap);
        //3) shift them
        //4) retain only positive cases
    }

Member Data Documentation

cropX

int ProgWindow::cropX

Definition at line 37 of file transform_window.cpp.

cropY

int ProgWindow::cropY

Definition at line 37 of file transform_window.cpp.

cropZ

int ProgWindow::cropZ

Definition at line 37 of file transform_window.cpp.

expand

double ProgWindow::expand

Definition at line 42 of file transform_window.cpp.

offset

double ProgWindow::offset

Definition at line 42 of file transform_window.cpp.

padType

String ProgWindow::padType

Definition at line 44 of file transform_window.cpp.

padValue

double ProgWindow::padValue

Definition at line 43 of file transform_window.cpp.

physical_coords

bool ProgWindow::physical_coords

Definition at line 35 of file transform_window.cpp.

renameTempFn

bool ProgWindow::renameTempFn

Definition at line 47 of file transform_window.cpp.

rmax

double ProgWindow::rmax

Definition at line 42 of file transform_window.cpp.

rmin

double ProgWindow::rmin

Definition at line 42 of file transform_window.cpp.

sampling

double ProgWindow::sampling

Definition at line 42 of file transform_window.cpp.

sizeX

int ProgWindow::sizeX

Definition at line 36 of file transform_window.cpp.

sizeY

int ProgWindow::sizeY

Definition at line 36 of file transform_window.cpp.

sizeZ

int ProgWindow::sizeZ

Definition at line 36 of file transform_window.cpp.

sym

String ProgWindow::sym

Definition at line 40 of file transform_window.cpp.

tempFn

FileName ProgWindow::tempFn

Definition at line 46 of file transform_window.cpp.

windowMode

WindowMode ProgWindow::windowMode

Definition at line 45 of file transform_window.cpp.

x0

int ProgWindow::x0

Definition at line 38 of file transform_window.cpp.

x_origin

double ProgWindow::x_origin

Definition at line 42 of file transform_window.cpp.

xF

int ProgWindow::xF

Definition at line 39 of file transform_window.cpp.

y0

int ProgWindow::y0

Definition at line 38 of file transform_window.cpp.

y_origin

double ProgWindow::y_origin

Definition at line 42 of file transform_window.cpp.

yF

int ProgWindow::yF

Definition at line 39 of file transform_window.cpp.

z0

int ProgWindow::z0

Definition at line 38 of file transform_window.cpp.

z_origin

double ProgWindow::z_origin

Definition at line 42 of file transform_window.cpp.

zF

int ProgWindow::zF

Definition at line 39 of file transform_window.cpp.

---

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

• xmipp/libraries/reconstruction/transform_window.cpp