#include <image_resize.h>

Inheritance diagram for ProgImageResize:

Collaboration diagram for ProgImageResize:

Public Member Functions
	ProgImageResize ()

	~ProgImageResize ()

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 ()

Protected Member Functions
void	defineParams ()

void	readParams ()

void	preProcess ()

void	postProcess ()

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

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
ScaleType	scale_type

int	splineDegree

int	dim

int	pyramid_level

int	fourier_threads

bool	isVol

bool	temporaryOutput

Matrix1D< double >	resizeFactor

ImageGeneric	img

ImageGeneric	imgOut

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

Additional Inherited Members
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

Detailed Description

Definition at line 40 of file image_resize.h.

Constructor & Destructor Documentation

◆ ProgImageResize()

ProgImageResize::ProgImageResize ( )

Constructor and destructor, just to avoid vtable undefined references errors

Definition at line 30 of file image_resize.cpp.

31 {}

◆ ~ProgImageResize()

ProgImageResize::~ProgImageResize ( )

Definition at line 33 of file image_resize.cpp.

34 {}

Member Function Documentation

◆ defineParams()

void ProgImageResize::defineParams ( )

protectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgImageResize >.

Definition at line 36 of file image_resize.cpp.

 {
     each_image_produces_an_output = true;
     save_metadata_stack = true;
     keep_input_columns = true;
     allow_apply_geo = true;
     temporaryOutput = false;
     XmippMetadataProgram::defineParams();
     //usage
     addUsageLine("Resize image or volume dimensions.");
     addUsageLine("+You can select different ways to resize your image/volumes.");
     //keywords
     addKeywords("transform, dimension, pyramid, fourier, scale");
     //examples
     addExampleLine("Resize a group of images to half size", false);
     addExampleLine("xmipp_image_resize -i images.xmd --factor 0.5 --oroot halvedOriginal");
     addExampleLine("For pyramid resizing(increase volume size 4 times):", false);
     addExampleLine("xmipp_image_resize -i input/bacteriorhodopsin.vol --pyramid 2 -o bdr_x4.vol");
     addExampleLine("Resize from 128 to 64 using Fourier", false);
     addExampleLine("xmipp_image_resize -i images.xmd --fourier 64 --oroot halvedFourierDim");
     //params
     addParamsLine("--factor <n=0.5>                 : Resize a factor of dimensions, 0.5 halves and 2 doubles (uses splines or linear interpolation).");
     addParamsLine(" alias -n;");
     addParamsLine("or --dim <x> <y=x> <z=x>         : New x,y and z dimensions (uses splines / linear interpolation or nearest neighbour method).");
     addParamsLine(" alias -d;");
     addParamsLine("or --fourier <x> <y=x> <z=x> <thr=1>   : Use padding/windowing in Fourier Space to resize. thr=number of threads");
     addParamsLine(" alias -f;");
     addParamsLine("or --pyramid <levels=1>          : Use positive value to expand and negative to reduce");
     addParamsLine(" alias -p;");
     addParamsLine(" [--interp <interpolation_type=spline>] : Interpolation type to be used. ");
     addParamsLine("      where <interpolation_type>");
     addParamsLine("        spline          : Use spline interpolation");
     addParamsLine("        linear          : Use bilinear/trilinear interpolation");
     addParamsLine("        nearest         : Use nearest neighbour to set new value");
 }

◆ postProcess()

void ProgImageResize::postProcess ( )

protectedvirtual

Reimplemented from XmippMetadataProgram.

Definition at line 236 of file image_resize.cpp.

 {
     if (temporaryOutput)
         std::rename(fn_out.c_str(),fn_in.c_str());
 }

◆ preProcess()

void ProgImageResize::preProcess ( )

protectedvirtual

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgImageResize >.

Definition at line 88 of file image_resize.cpp.

 {
     double factor=1.0;
     double oxdim = xdimOut;
     auto oydim = (double)ydimOut;
     auto ozdim = (double)zdimOut;
 
     //If zdimOut greater than 1, is a volume and should apply transform
     dim = (isVol = (zdimOut > 1)) ? 3 : 2;
 
     resizeFactor.resizeNoCopy(dim);
     resizeFactor.initConstant(1.);
 
     if (fn_out.empty() && oroot.empty())
     {
         fn_out=fn_in+"_tmp";
         fn_out=fn_out.addExtension(fn_in.getExtension());
         temporaryOutput=true;
         create_empty_stackfile=true;
     }
 
     if (checkParam("--factor") || checkParam("--dim"))
     {
         //Calculate scale factor from images sizes and given dimensions
         //this approach assumes that all images have equal size
         if (checkParam("--dim"))
         {
             xdimOut = getIntParam("--dim", 0);
             ydimOut = STR_EQUAL(getParam("--dim", 1), "x") ? xdimOut : getIntParam("--dim", 1);
             XX(resizeFactor) = (double)xdimOut / oxdim;
             YY(resizeFactor) = (double)ydimOut / oydim;
         }
         else
         {
             factor = getDoubleParam("--factor");
             if (factor <= 0)
                 REPORT_ERROR(ERR_VALUE_INCORRECT,"Resize factor must be a positive number");
             xdimOut = (int) (xdimOut * factor);
             ydimOut = (int) (ydimOut * factor);
             resizeFactor.initConstant(factor);
         }
 
         //if scale factor is large splines s not the way to go, print a warning
         if( fabs(1.0-XX(resizeFactor)) > 0.1 )
         {
             reportWarning("Do not apply large scale factor using B-splines "
                           "choose fourier option.");
         }
 
         if (isVol)
         {
             if (checkParam("--dim"))
             {
                 zdimOut = STR_EQUAL(getParam("--dim", 2), "x")
                           ? xdimOut : getIntParam("--dim", 2);
                 ZZ(resizeFactor) = (double)zdimOut / ozdim;
             }
             else
                 zdimOut = (int) (zdimOut * factor);
         }
         scale_type = RESIZE_FACTOR;
     }
     else if (checkParam("--fourier"))
     {
         //        if (isVol)
         //            REPORT_ERROR(ERR_PARAM_INCORRECT, "The 'fourier' scaling type is only valid for images");
         auto oxdim2 = xdimOut;
         auto oydim2 = ydimOut;
         auto ozdim2 = zdimOut;
         scale_type = RESIZE_FOURIER;
 
         xdimOut = getIntParam("--fourier", 0);
         ydimOut = STR_EQUAL(getParam("--fourier", 1), "x") ? xdimOut : getIntParam("--fourier", 1);
         if (isVol)
             zdimOut = STR_EQUAL(getParam("--fourier", 2), "x") ? xdimOut : getIntParam("--fourier", 2);
         else
             zdimOut=1;
         fourier_threads = getIntParam("--fourier", 3);
         XX(resizeFactor) = (double)xdimOut / oxdim2;
         YY(resizeFactor) = (double)ydimOut / oydim2;
         if (isVol)
             ZZ(resizeFactor) = (double)zdimOut / ozdim2;
         //Do not think this is true
         //            if (oxdim < xdimOut || oydim < ydimOut)
         //                REPORT_ERROR(ERR_PARAM_INCORRECT, "The 'fourier' scaling type can only be used for reducing size");
     }
     else if (checkParam("--pyramid"))
     {
         scale_type = RESIZE_PYRAMID_EXPAND;
         pyramid_level = getIntParam("--pyramid", 0);
         factor = (double)(pow(2.0, pyramid_level));
         xdimOut = (size_t)(xdimOut*factor);
         ydimOut = (size_t)(ydimOut*factor);
         if (isVol)
             zdimOut = (size_t)(zdimOut*factor);
         if (pyramid_level < 0)
         {
             pyramid_level *= -1; //change sign, negative means reduce operation
             scale_type = RESIZE_PYRAMID_REDUCE;
         }
         resizeFactor.initConstant(factor);
     }
 }

◆ processImage()

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

protectedvirtual

Implements XmippMetadataProgram.

Definition at line 195 of file image_resize.cpp.

 {
     double aux;
     if (apply_geo)
     {
         SCALE_SHIFT(MDL_SHIFT_X, XX(resizeFactor));
         SCALE_SHIFT(MDL_SHIFT_Y, YY(resizeFactor));
         if (isVol)
             SCALE_SHIFT(MDL_SHIFT_Z, ZZ(resizeFactor));
     }
     else
         rowOut.resetGeo(false);
 
     img.read(fnImg);
     img().setXmippOrigin();
     imgOut.setDatatype(img.getDatatype());
 
     switch (scale_type)
     {
     case RESIZE_FACTOR:
         //selfScaleToSize(splineDegree, img(), xdimOut, ydimOut, zdimOut);
         scaleToSize(splineDegree, imgOut(), img(), xdimOut, ydimOut, zdimOut);
         break;
     case RESIZE_PYRAMID_EXPAND:
         pyramidExpand(splineDegree, imgOut(), img(), pyramid_level);
         //selfPyramidExpand(splineDegree, img(), pyramid_level);
         break;
     case RESIZE_PYRAMID_REDUCE:
         pyramidReduce(splineDegree, imgOut(), img(), pyramid_level);
         //selfPyramidReduce(splineDegree, img(), pyramid_level);
         break;
     case RESIZE_FOURIER:
         selfScaleToSizeFourier(zdimOut, ydimOut, xdimOut, img(), fourier_threads);
         img.write(fnImgOut);
         return;
     case RESIZE_NONE:
         break;
     }
     imgOut.write(fnImgOut);
 }

◆ readParams()

void ProgImageResize::readParams ( )

protectedvirtual

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

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgImageResize >.

Definition at line 72 of file image_resize.cpp.

 {
     XmippMetadataProgram::readParams();
     String degree = getParam("--interp");
 
     if (degree == "spline")
         splineDegree = xmipp_transformation::BSPLINE3;
     else if (degree == "linear")
         splineDegree = xmipp_transformation::LINEAR;
     else if (degree == "nearest")
         splineDegree = xmipp_transformation::NEAREST;
 
     scale_type = RESIZE_NONE;
 }

Member Data Documentation

◆ dim

int ProgImageResize::dim

protected

Definition at line 51 of file image_resize.h.

◆ fourier_threads

int ProgImageResize::fourier_threads

protected

Definition at line 53 of file image_resize.h.

◆ img

ImageGeneric ProgImageResize::img

protected

Definition at line 58 of file image_resize.h.

◆ imgOut

ImageGeneric ProgImageResize::imgOut

protected

Definition at line 59 of file image_resize.h.

◆ isVol

bool ProgImageResize::isVol

protected

Definition at line 54 of file image_resize.h.

◆ pyramid_level

int ProgImageResize::pyramid_level

protected

Definition at line 52 of file image_resize.h.

◆ resizeFactor

Matrix1D<double> ProgImageResize::resizeFactor

protected

Definition at line 57 of file image_resize.h.

◆ scale_type

ScaleType ProgImageResize::scale_type

protected

Definition at line 48 of file image_resize.h.

◆ splineDegree

int ProgImageResize::splineDegree

protected

Definition at line 50 of file image_resize.h.

◆ temporaryOutput

bool ProgImageResize::temporaryOutput

protected

Definition at line 55 of file image_resize.h.

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

xmipp/libraries/data/image_resize.h
xmipp/libraries/data/image_resize.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgImageResize()

◆ ~ProgImageResize()

Member Function Documentation

◆ defineParams()

◆ postProcess()

◆ preProcess()

◆ processImage()

◆ readParams()

Member Data Documentation

◆ dim

◆ fourier_threads

◆ img

◆ imgOut

◆ isVol

◆ pyramid_level

◆ resizeFactor

◆ scale_type

◆ splineDegree

◆ temporaryOutput