Symmetrize Parameters. More...

#include <symmetrize.h>

Inheritance diagram for ProgSymmetrize:

Collaboration diagram for ProgSymmetrize:

Public Member Functions
void	readParams ()

void	defineParams ()

void	show ()

void	preProcess ()

void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)
	Process image or volume. More...

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	fn_sym
	symmetry file More...

FileName	fn_sym2

FileName	fn_Maskin
	mask file (mask what is inside) More...

FileName	fn_Maskout
	mask file (mask what is outside) More...

bool	doMask
	set to true is we should mask More...

double	rotHelical
	Helical rotation. More...

double	rotPhaseHelical
	Helical phase. More...

double	zHelical
	Helical shift. More...

double	heightFraction
	Helical height fraction. More...

double	Ts
	Sampling rate (used for helical) More...

bool	do_not_generate_subgroup
	Do not generate subgroup. More...

bool	wrap
	wrap or don't wrap input file during symmetrisation More...

bool	sum
	Sum or average the result. More...

int	splineOrder
	Spline order. More...

int	Cn
	Cn for helical or helicalDihedral. More...

SymList	SL

int	symorder

bool	helical

bool	dihedral

bool	helicalDihedral

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

Symmetrize Parameters.

Definition at line 39 of file symmetrize.h.

Member Function Documentation

◆ defineParams()

void ProgSymmetrize::defineParams ( )

virtual

Define Parameters

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgSymmetrize >.

Definition at line 63 of file symmetrize.cpp.

 {
     addUsageLine("Symmetrize volumes and images ");
     each_image_produces_an_output=true;
     XmippMetadataProgram::defineParams();
     addParamsLine("    --sym <symmetry>     : For 2D images: a number");
     addParamsLine("                         : For 3D volumes: a symmetry file or point-group description");
     addParamsLine("                         : Valid point-group descriptions are:");
     addParamsLine("                         : C1, Ci, Cs, Cn (from here on n must be an integer number with no more than 2 digits)");
     addParamsLine("                         : Cnv, Cnh, Sn, Dn, Dnv, Dnh, T, Td, Th, O, Oh");
     addParamsLine("                         : I, I1, I2, I3, I4, I5, Ih, helical, dihedral, helicalDihedral");
     addParamsLine("                         :+ For a full description of symmetries look at");
     addParamsLine("                         :+ http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry");
     addParamsLine("   [--sym2 <sym2=C1>]    : Only for helical, or helicalDihedral");
     addParamsLine("                         : You may use any other Cn symmetry");
     addParamsLine("   [--helixParams <z> <rot> <rotPhase=0>]: Helical parameters z(Angstroms), rot(degrees), rotPhase(degrees)");
     addParamsLine("                         :+ V(r,theta,z)=V(r,theta+rotHelix+rotPhase,z+zHelix)");
     addParamsLine("   [--heightFraction <f=0.95>]: Height fraction used for symmetrizing a helix");
     addParamsLine("   [--sampling <T=1>]    : Sampling rate (A/pixel). Used only for helical parameters");
     addParamsLine("   [--no_group]          : For 3D volumes: do not generate symmetry subgroup");
     addParamsLine("   [--dont_wrap]         : by default, the image/volume is wrapped");
     addParamsLine("   [--sum]               : compute the sum of the images/volumes instead of the average. This is useful for symmetrizing pieces");
     addParamsLine("   [--mask_in <fileName>]: symmetrize only in the masked area");
     addParamsLine("   [--spline <order=3>]  : Spline order for the interpolation (valid values are 1 and 3)");
     addExampleLine("Symmetrize a list of images with 6 fold symmetry",false);
     addExampleLine("   xmipp_transform_symmetrize -i input.sel --sym 6");
     addExampleLine("Symmetrize with i3 symmetry and the volume is not wrapped",false);
     addExampleLine("   xmipp_transform_symmetrize -i input.vol --sym i3 --dont_wrap");
 }

◆ preProcess()

void ProgSymmetrize::preProcess ( )

virtual

Run

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgSymmetrize >.

Definition at line 217 of file symmetrize.cpp.

 {
     if (!helical && !dihedral & !helicalDihedral)
     {
         if (!fn_sym.exists() && isdigit(fn_sym[0]))
             symorder=textToInteger(fn_sym);
         else
         {
             double accuracy = do_not_generate_subgroup ? -1 : 1e-6;
             SL.readSymmetryFile(fn_sym, accuracy);
             symorder=-1;
         }
     }
 }

◆ processImage()

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

virtual

Process image or volume.

Implements XmippMetadataProgram.

Definition at line 233 of file symmetrize.cpp.

 {
     Image<double> Iin;
     Image<double> Iout;
     Image<double> mask;
     MultidimArray<double> *mmask=nullptr;
 
     Iin.readApplyGeo(fnImg, rowIn);
     Iin().setXmippOrigin();
     Iout().resize(Iin());
 
     if (doMask)
     {
         mask.read(fn_Maskin);
         mmask=&(mask());
     }
 
     if (ZSIZE(Iin())==1)
     {
         if (helical)
             REPORT_ERROR(ERR_ARG_INCORRECT,"Helical symmetrization is not meant for images");
         if (symorder!=-1)
             symmetrizeImage(symorder,Iin(),Iout(),splineOrder,wrap,!wrap,sum,mmask);
         else
             REPORT_ERROR(ERR_ARG_MISSING,"The symmetry order is not valid for images");
     }
     else
     {
         if (SL.symsNo()>0 || helical || dihedral || helicalDihedral)
         {
             symmetrizeVolume(SL,Iin(),Iout(),splineOrder,wrap,!wrap,
                              sum,helical,dihedral,helicalDihedral,rotHelical,rotPhaseHelical,zHelical,heightFraction,mmask,Cn);
         }
         else
             REPORT_ERROR(ERR_ARG_MISSING,"The symmetry description is not valid for volumes");
     }
     Iout.write(fnImgOut);
 }

◆ readParams()

void ProgSymmetrize::readParams ( )

virtual

Read parameters from command line.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgSymmetrize >.

Definition at line 32 of file symmetrize.cpp.

 {
     XmippMetadataProgram::readParams();
     fn_sym = getParam("--sym");
     fn_sym2 = getParam("--sym2");
     doMask = false;
     if (checkParam("--mask_in"))
     {
         fn_Maskin = getParam("--mask_in");
         doMask = true;
     }
     helical=(fn_sym=="helical");
     dihedral=(fn_sym=="dihedral");
     helicalDihedral=(fn_sym=="helicalDihedral");
     if (helical || helicalDihedral)
     {
         Ts=getDoubleParam("--sampling");
         zHelical=getDoubleParam("--helixParams",0)/Ts;
         rotHelical=DEG2RAD(getDoubleParam("--helixParams",1));
         rotPhaseHelical=DEG2RAD(getDoubleParam("--helixParams",2));
 
         Cn=std::stoi(fn_sym2.substr(1));
     }
     do_not_generate_subgroup = checkParam("--no_group");
     wrap = !checkParam("--dont_wrap");
     sum = checkParam("--sum");
     heightFraction = getDoubleParam("--heightFraction");
     splineOrder = getIntParam("--spline");
 }

◆ show()

void ProgSymmetrize::show ( )

Show parameters

Definition at line 94 of file symmetrize.cpp.

 {
     if (verbose==0)
         return;
     XmippMetadataProgram::show();
     std::cout
     << "Symmetry: " << fn_sym << std::endl
     << "No group: " << do_not_generate_subgroup << std::endl
     << "Wrap:     " << wrap << std::endl
     << "Sum:      " << sum << std::endl
     << "Spline:   " << splineOrder << std::endl;
     if (doMask)
         std::cout << "mask_in    " << fn_Maskin << std::endl;
     if (helical)
         std::cout << "RotHelical: " << RAD2DEG(rotHelical) << std::endl
         << "RotPhaseHelical: " << RAD2DEG(rotPhaseHelical) << std::endl
         << "ZHelical:   " << zHelical*Ts
         << "Height fraction: " << heightFraction << std::endl;
     if (helical || helicalDihedral)
         std::cout << "Symmetry2: " << fn_sym2 << std::endl;
 }

Member Data Documentation

◆ Cn

int ProgSymmetrize::Cn

Cn for helical or helicalDihedral.

Definition at line 69 of file symmetrize.h.

◆ dihedral

bool ProgSymmetrize::dihedral

Definition at line 93 of file symmetrize.h.

◆ do_not_generate_subgroup

bool ProgSymmetrize::do_not_generate_subgroup

Do not generate subgroup.

Definition at line 61 of file symmetrize.h.

◆ doMask

bool ProgSymmetrize::doMask

set to true is we should mask

Definition at line 49 of file symmetrize.h.

◆ fn_Maskin

FileName ProgSymmetrize::fn_Maskin

mask file (mask what is inside)

Definition at line 45 of file symmetrize.h.

◆ fn_Maskout

FileName ProgSymmetrize::fn_Maskout

mask file (mask what is outside)

Definition at line 47 of file symmetrize.h.

◆ fn_sym

FileName ProgSymmetrize::fn_sym

symmetry file

Definition at line 43 of file symmetrize.h.

◆ fn_sym2

FileName ProgSymmetrize::fn_sym2

Definition at line 43 of file symmetrize.h.

◆ heightFraction

double ProgSymmetrize::heightFraction

Helical height fraction.

Definition at line 57 of file symmetrize.h.

◆ helical

bool ProgSymmetrize::helical

Definition at line 91 of file symmetrize.h.

◆ helicalDihedral

bool ProgSymmetrize::helicalDihedral

Definition at line 95 of file symmetrize.h.

◆ rotHelical

double ProgSymmetrize::rotHelical

Helical rotation.

Definition at line 51 of file symmetrize.h.

◆ rotPhaseHelical

double ProgSymmetrize::rotPhaseHelical

Helical phase.

Definition at line 53 of file symmetrize.h.

◆ SL

SymList ProgSymmetrize::SL

Definition at line 87 of file symmetrize.h.

◆ splineOrder

int ProgSymmetrize::splineOrder

Spline order.

Definition at line 67 of file symmetrize.h.

◆ sum

bool ProgSymmetrize::sum

Sum or average the result.

Definition at line 65 of file symmetrize.h.

◆ symorder

int ProgSymmetrize::symorder

Definition at line 89 of file symmetrize.h.

◆ Ts

double ProgSymmetrize::Ts

Sampling rate (used for helical)

Definition at line 59 of file symmetrize.h.

◆ wrap

bool ProgSymmetrize::wrap

wrap or don't wrap input file during symmetrisation

Definition at line 63 of file symmetrize.h.

◆ zHelical

double ProgSymmetrize::zHelical

Helical shift.

Definition at line 55 of file symmetrize.h.

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

xmipp/libraries/reconstruction/symmetrize.h
xmipp/libraries/reconstruction/symmetrize.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ show()

Member Data Documentation

◆ Cn

◆ dihedral

◆ do_not_generate_subgroup

◆ doMask

◆ fn_Maskin

◆ fn_Maskout

◆ fn_sym

◆ fn_sym2

◆ heightFraction

◆ helical

◆ helicalDihedral

◆ rotHelical

◆ rotPhaseHelical

◆ SL

◆ splineOrder

◆ sum

◆ symorder

◆ Ts

◆ wrap

◆ zHelical