#include <transform_downsample.h>

Inheritance diagram for ProgTransformDownsample:

Collaboration diagram for ProgTransformDownsample:

Public Types
enum	TDownsamplingMethod { KER_RECTANGLE, FOURIER, SMOOTH }

Public Member Functions
void	readParams ()

void	defineParams ()
	Define params. More...

void	preProcess ()

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

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
double	step
	Downsampling factor. More...

TDownsamplingMethod	method

int	nThreads
	Number of Threads used in the Fourier Transform. More...

MultidimArray< double >	kernel

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 void	postProcess ()

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

Downsample parameters.

Definition at line 38 of file transform_downsample.h.

Member Enumeration Documentation

◆ TDownsamplingMethod

enum ProgTransformDownsample::TDownsamplingMethod

Enumerator
KER_RECTANGLE
FOURIER
SMOOTH

Definition at line 44 of file transform_downsample.h.

44 {KER_RECTANGLE, FOURIER, SMOOTH} TDownsamplingMethod;

ProgTransformDownsample::SMOOTH

Definition: transform_downsample.h:44

ProgTransformDownsample::FOURIER

Definition: transform_downsample.h:44

ProgTransformDownsample::TDownsamplingMethod

TDownsamplingMethod

Definition: transform_downsample.h:44

ProgTransformDownsample::KER_RECTANGLE

Definition: transform_downsample.h:44

Member Function Documentation

◆ defineParams()

void ProgTransformDownsample::defineParams ( )

virtual

Define params.

Reimplemented from XmippMetadataProgram.

Definition at line 50 of file transform_downsample.cpp.

 {
     each_image_produces_an_output = true;
     addUsageLine("Downsample a micrograph. For volumes use xmipp_transform_geometry.");
     addUsageLine("+There are several downsampling methods. The most general and recommended is Fourier.");
     addUsageLine("+Fourier downsampling puts a window in Fourier space. This is the best downsampling that can be performed.");
     addUsageLine("+Altermatively, smoothing makes color dithering which is pretty good for visualization, ");
     addUsageLine("+but it modifies the particle spectrum. Binning with a rectangle kernel modifies the ");
     addUsageLine("+spectrum of the micrographs and is not recommended. You may see the effects of the different ");
     addUsageLine("+downsampling schemes at [[http://biocomp.cnb.csic.es/~coss/Articulos/Sorzano2009d.pdf][this article]].");
     addUsageLine("+ ");
     addUsageLine("+The downsampling factor (--step) is the factor by which the micrograph will be reduced.");
     addUsageLine("+For instance, a downsampling by 2 will reduce the image size to one half. Using Fourier and smooth ");
     addUsageLine("+you may use non-integer downsampling factors, and the image size will be reduced by 1/factor");
     addSeeAlsoLine("transform_geometry");
     XmippMetadataProgram::defineParams();
     addParamsLine("  --step <factor>    : Downsampling factor. factor=2 reduces the image size to one half.");
     addParamsLine("                     :+Fourier and smooth support non-integer downsampling factors.");
     addParamsLine("                     :+Rectangular binning must use integer factors.");
     addParamsLine(" [--method <mth=fourier>]  : Method for making the downsampling");
     addParamsLine("         where <mth>");
     addParamsLine("               fourier <numThreads=1>: Fourier supports non-integer downsampling factors");
     addParamsLine("                                     :+This is the best choice.");
     addParamsLine("               rectangle: This is simple binning in a square of size factor x factor");
     addParamsLine("                        :+This is not a good choice since it creates aliasing and ");
     addParamsLine("                        :+unequal frequency damping.");
     addParamsLine("               smooth: smooth and colordither");
     addParamsLine("                     :+ Both input and output micrographs must be 8 bits, unsigned char");
     addExampleLine("xmipp_transform_downsample -i micrograph.tif -o downsampledMicrograph.tif --step 2");
 }

◆ preProcess()

void ProgTransformDownsample::preProcess ( )

inlinevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 62 of file transform_downsample.h.

     {
         create_empty_stackfile = false;
     }

◆ processImage()

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

virtual

Really downsample.

Implements XmippMetadataProgram.

Definition at line 82 of file transform_downsample.cpp.

 {
     // Open input data
     ImageGeneric M_in;
     M_in.readOrReadMapped(fnImg);
     size_t Zdim, Ydim, Xdim;
     M_in.getDimensions(Xdim,Ydim,Zdim);
     if (Zdim!=1)
         REPORT_ERROR(ERR_MULTIDIM_DIM,"This program is not intended for volumes");
 
     // Open output data, mapped file
     auto Xpdim = (int)floor(Xdim/step);
     auto Ypdim = (int)floor(Ydim/step);
     ImageGeneric M_out;
     if (method==SMOOTH)
         M_out.setDatatype(DT_UChar);
     else
         M_out.setDatatype(DT_Float);
     M_out.mapFile2Write(Xpdim, Ypdim, 1, fnImgOut,fnImg==fnImgOut);
 
     // Downsample
     if (method==KER_RECTANGLE)
         downsampleKernel(M_in,step,M_out);
     else if (method==FOURIER)
         downsampleFourier(M_in,step,M_out,nThreads);
     else
         downsampleSmooth(M_in,M_out);
 
     M_out.write(fnImgOut);
 }

◆ readParams()

void ProgTransformDownsample::readParams ( )

virtual

Read input parameters.

Reimplemented from XmippMetadataProgram.

Definition at line 32 of file transform_downsample.cpp.

 {
 
     XmippMetadataProgram::readParams();
     step=getDoubleParam("--step");
     String strMethod=getParam("--method");
     if (strMethod=="fourier")
     {
         nThreads=getIntParam("--method",1);
         method=FOURIER;
     }
     else if (strMethod=="smooth")
         method=SMOOTH;
     else
         method=KER_RECTANGLE;
 }

Member Data Documentation

◆ kernel

MultidimArray<double> ProgTransformDownsample::kernel

Definition at line 54 of file transform_downsample.h.

◆ method

TDownsamplingMethod ProgTransformDownsample::method

Downsampling method

Definition at line 47 of file transform_downsample.h.

◆ nThreads

int ProgTransformDownsample::nThreads

Number of Threads used in the Fourier Transform.

Definition at line 50 of file transform_downsample.h.

◆ step

double ProgTransformDownsample::step

Downsampling factor.

Definition at line 42 of file transform_downsample.h.

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

xmipp/libraries/data/transform_downsample.h
xmipp/libraries/data/transform_downsample.cpp

Public Types

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ TDownsamplingMethod

Member Function Documentation

◆ defineParams()

◆ preProcess()

◆ processImage()

◆ readParams()

Member Data Documentation

◆ kernel

◆ method

◆ nThreads

◆ step