#include <transform_adjust_image_grey_levels.h>

Inheritance diagram for ProgTransformImageGreyLevels:

Collaboration diagram for ProgTransformImageGreyLevels:

Public Member Functions
	ProgTransformImageGreyLevels ()
	Empty constructor. More...

	~ProgTransformImageGreyLevels ()
	Destructor. More...

void	readParams ()
	Read argument from command line. More...

void	show ()
	Show. More...

void	defineParams ()
	Define parameters. 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
FileName	fnVol

double	maxResol

double	maxA

double	maxB

double	Ts

int	Rmax

int	pad

MultidimArray< int >	mask2D

double	iMask2Dsum

FourierProjector *	projector

size_t	Xdim

Image< double >	I

Image< double >	Ifiltered

Projection	P

FourierFilter	filter

double	Istddev

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

Transform image gray value Parameters.

Definition at line 38 of file transform_adjust_image_grey_levels.h.

Constructor & Destructor Documentation

◆ ProgTransformImageGreyLevels()

ProgTransformImageGreyLevels::ProgTransformImageGreyLevels ( )

Empty constructor.

Definition at line 30 of file transform_adjust_image_grey_levels.cpp.

 {
     produces_a_metadata = true;
     each_image_produces_an_output = true;
     projector = nullptr;
 }

◆ ~ProgTransformImageGreyLevels()

ProgTransformImageGreyLevels::~ProgTransformImageGreyLevels ( )

Destructor.

Definition at line 37 of file transform_adjust_image_grey_levels.cpp.

 {
     delete projector;
 }

Member Function Documentation

◆ defineParams()

void ProgTransformImageGreyLevels::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippMetadataProgram.

Definition at line 73 of file transform_adjust_image_grey_levels.cpp.

 {
     addUsageLine("Make a continuous angular assignment");
     defaultComments["-i"].clear();
     defaultComments["-i"].addComment("Metadata with images and alignment");
     defaultComments["-o"].clear();
     defaultComments["-o"].addComment("Stack of images prepared for 3D reconstruction");
     XmippMetadataProgram::defineParams();
     addParamsLine("   --ref <volume>              : Reference volume");
     addParamsLine("  [--max_resolution <f=4>]     : Maximum resolution (A)");
     addParamsLine("  [--max_gray_scale <a=0.05>]  : Maximum gray scale change");
     addParamsLine("  [--max_gray_shift <b=0.05>]  : Maximum gray shift change as a factor of the image standard deviation");
     addParamsLine("  [--sampling <Ts=1>]          : Sampling rate (A/pixel)");
     addParamsLine("  [--Rmax <R=-1>]              : Maximum radius (px). -1=Half of volume size");
     addParamsLine("  [--padding <p=2>]            : Padding factor");
 }

◆ preProcess()

void ProgTransformImageGreyLevels::preProcess ( )

virtual

Produce side info. An exception is thrown if any of the files is not found

Reimplemented from XmippMetadataProgram.

Definition at line 91 of file transform_adjust_image_grey_levels.cpp.

 {
     // Read the reference volume
     Image<double> V;
     V.read(fnVol);
     V().setXmippOrigin();
     Xdim=XSIZE(V());
 
     // Construct mask
     if (Rmax<0)
         Rmax=Xdim/2;
     Mask mask;
     mask.type = BINARY_CIRCULAR_MASK;
     mask.mode = INNER_MASK;
     mask.R1 = Rmax;
     mask.generate_mask(Xdim,Xdim);
     mask2D=mask.get_binary_mask();
     iMask2Dsum=1.0/mask2D.sum();
 
     // Construct projector
     projector = new FourierProjector(V(),pad,Ts/maxResol,xmipp_transformation::BSPLINE3);
 
     // Low pass filter
     filter.FilterBand=LOWPASS;
     filter.w1=Ts/maxResol;
     filter.raised_w=0.02;
 }

◆ processImage()

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

virtual

Predict angles and shift. At the input the pose parameters must have an initial guess of the parameters. At the output they have the estimated pose.

Implements XmippMetadataProgram.

Definition at line 154 of file transform_adjust_image_grey_levels.cpp.

 {
     rowOut=rowIn;
 
     // Read input image and initial parameters
     double rot, tilt, psi;
     rowIn.getValue(MDL_ANGLE_ROT,rot);
     rowIn.getValue(MDL_ANGLE_TILT,tilt);
     rowIn.getValue(MDL_ANGLE_PSI,psi);
 
     double olda=1.0, oldb=0.0;
     if (rowIn.containsLabel(MDL_CONTINUOUS_GRAY_A)){
         rowIn.getValue(MDL_CONTINUOUS_GRAY_A,olda);
         rowIn.getValue(MDL_CONTINUOUS_GRAY_B,oldb);
     }
 
     I.read(fnImg);
     I().setXmippOrigin();
     Istddev=I().computeStddev();
 
     Ifiltered()=I();
     filter.applyMaskSpace(Ifiltered());
 
     projectVolume(*projector, P, (int)XSIZE(I()), (int)XSIZE(I()),  rot, tilt, psi);
 
 #ifdef DEBUG
     Image<double> save;
     save()=P();
     std::cout << "P: "; P().printStats(); std::cout << std::endl;
     save.write("PPPprojection.xmp");
     save()=I();
     std::cout << "I: "; I().printStats(); std::cout << std::endl;
     save.write("PPPexperimental.xmp");
     save()=P()-I();
     std::cout << "P-I init: "; save().printStats(); std::cout << std::endl;
     save.write("PPPdiffInit.xmp");
 #endif
 
     Matrix1D<double> pAB(2), steps(2), pBA(2), p(2);
     steps.initConstant(1);
 
     // Optimize
     double costAB=-1, costBA=-1;
     int iter;
     try
     {
         costAB=1e38;
         pAB(0)=olda; // a in I'=a*I+b
         pAB(1)=oldb; // b in I'=a*I+b
         powellOptimizer(pAB, 1, 2, &transformImageGrayCostAB, this, 0.01, costAB, iter, steps, verbose>=2);
         if (costAB>1e30)
         {
             rowOut.setValue(MDL_ENABLED,-1);
             pAB.initZeros();
             pAB(0)=1; // a in I'=a*I+b
             pAB(1)=0; // b in I'=a*I+b
         }
 
         costBA=1e38;
         pBA(0)=oldb; // a in I'=a*I+b
         pBA(1)=olda; // b in I'=a*I+b
         powellOptimizer(pBA, 1, 2, &transformImageGrayCostBA, this, 0.01, costBA, iter, steps, verbose>=2);
         if (costBA>1e30)
         {
             rowOut.setValue(MDL_ENABLED,-1);
             pBA.initZeros();
             pBA(0)=0; // a in I'=a*I+b
             pBA(1)=1; // b in I'=a*I+b
         }
 
         // Decide
         if (costAB<costBA)
             p=pAB;
         else
         {
             p(0)=pBA(1);
             p(1)=pBA(0);
         }
 
         // Apply
         MultidimArray<double> &mI=I();
         double ia=1.0/p(0);
         double b=p(1);
         FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mI)
         {
             if (DIRECT_MULTIDIM_ELEM(mask2D,n) || true)
                 DIRECT_MULTIDIM_ELEM(mI,n)=ia*(DIRECT_MULTIDIM_ELEM(mI,n)-b);
             else
                 DIRECT_MULTIDIM_ELEM(mI,n)=0.0;
         }
         rowOut.setValue(MDL_IMAGE,fnImgOut);
         I.write(fnImgOut);
     }
     catch (XmippError XE)
     {
         std::cerr << XE.what() << std::endl;
         std::cerr << "Warning: Cannot refine " << fnImg << std::endl;
         rowOut.setValue(MDL_ENABLED,-1);
     }
     rowOut.setValue(MDL_CONTINUOUS_GRAY_A,p(0));
     rowOut.setValue(MDL_CONTINUOUS_GRAY_B,p(1));
 
 #ifdef DEBUG
     save()=I();
     save.write("PPPexperimentalCorrected.xmp");
     std::cout << "I corrected: "; I().printStats(); std::cout << std::endl;
     save()=P()-I();
     std::cout << "P-I final: "; save().printStats(); std::cout << std::endl;
     save.write("PPPdiff.xmp");
     std::cout << fnImgOut << " rewritten\n";
     std::cout << "Press any key" << std::endl;
     char c; std::cin >> c;
 #endif
 }

◆ readParams()

void ProgTransformImageGreyLevels::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippMetadataProgram.

Definition at line 43 of file transform_adjust_image_grey_levels.cpp.

 {
     XmippMetadataProgram::readParams();
     fnVol = getParam("--ref");
     maxResol = getDoubleParam("--max_resolution");
     maxA = getDoubleParam("--max_gray_scale");
     maxB = getDoubleParam("--max_gray_shift");
     Ts = getDoubleParam("--sampling");
     Rmax = getIntParam("--Rmax");
     pad = getIntParam("--padding");
 }

◆ show()

void ProgTransformImageGreyLevels::show ( )

Show.

Definition at line 56 of file transform_adjust_image_grey_levels.cpp.

 {
     if (!verbose)
         return;
     XmippMetadataProgram::show();
     std::cout
     << "Reference volume:    " << fnVol              << std::endl
     << "Max. Resolution:     " << maxResol           << std::endl
     << "Max. Gray Scale:     " << maxA               << std::endl
     << "Max. Gray Shift:     " << maxB               << std::endl
     << "Sampling:            " << Ts                 << std::endl
     << "Max. Radius:         " << Rmax               << std::endl
     << "Padding factor:      " << pad                << std::endl
     ;
 }