#include <tomo_extract_subvolume.h>

Inheritance diagram for ProgTomoExtractSubvolume:

Collaboration diagram for ProgTomoExtractSubvolume:

Public Member Functions
void	defineParams ()
	Define the arguments accepted. More...

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

void	show ()
	Show. More...

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

void	postProcess ()

void	preProcess ()

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_doc

FileName	fn_root

FileName	fn_sym

FileName	fn_missing

FileName	fn_mask

FileName	fn_aux

int	size

Matrix1D< double >	center_ref

std::vector< Matrix1D< double > >	centers_subvolumes

std::vector< Matrix2D< double > >	rotations_subvolumes

int	nr_exp_images

int	nr_output_volumes

MetaDataVec	DFout

double	mindist

int	symmetry

int	sym_order

SymList	SL

Image< double >	vol

Image< double >	volout

Matrix1D< double >	center

Matrix1D< double >	doccenter

Matrix2D< double >	A

Matrix2D< double >	R

Matrix2D< double >	I

double	rot

double	tilt

double	psi

double	rotp

double	tiltp

double	psip

int	x0

int	xF

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

tomo_extract_subvolume parameters.

Definition at line 49 of file tomo_extract_subvolume.h.

Member Function Documentation

◆ defineParams()

void ProgTomoExtractSubvolume::defineParams ( )

virtual

Define the arguments accepted.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgTomoExtractSubvolume >.

Definition at line 31 of file tomo_extract_subvolume.cpp.

 {
     defaultComments["-i"].addComment("Metadata file with input volumes (and rotations/shifts)");
 
     XmippMetadataProgram::defineParams();
     addUsageLine("Extract subvolumes of the asymmetric parts of each subtomogram");
 
     addUsageLine("+++This program works closely together with the ml_tomo program, which is used to align");
     addUsageLine("+++ (and classify) a series of subtomograms. Now, if each subtomogram contains some sort");
     addUsageLine("+++ of (pseudo-) symmetry, tomo_extract_subvolume can be used to extract subvolumes of the");
     addUsageLine("+++ asymmetric parts of each subtomogram. The metadata file that is output by this program orients");
     addUsageLine("+++ each subvolume and its missing wedge in the correct orientation, so that it can be fed");
     addUsageLine("+++ directly back into ml_tomo. There, the sub-subtomograms can be further aligned and/or classified");
     addParamsLine("[--oroot <rootname=\"\">]: Rootname for output stacks of subvolumes");
     addParamsLine("[-o <filename=\"\">]    : Name of output metadata (\"oroot\".xmd by default)");
     addParamsLine("--sym  <sym=\"c1\">     : Symmetry group");
     addParamsLine("--size     <dim>        : size output subvolumes");
     addParamsLine("[--mindist  <distance=-1>] : Minimum distance between subvolume centers, useful to avoid repetition of subvolumes place at simmetry axis");
     addParamsLine("                           : If set to -1 minsdist will be size/4");
     addParamsLine("--center  <x> <y> <z>   :  position of center of subvolume to be extracted");
     addExampleLine("Extract 12 vertices (subvolumes) in boxes of size 21x21x21 pixels from each subtomogram in the data set: ", false);
     addExampleLine("xmipp_extract_subvolume -i align/mltomo_1deg_it000001.doc -center 0 0 59 -size 21 -sym i3 -o vertices");
 
     addExampleLine("+++Imagine we have N subtomograms of a virus particle and we have aligned them",false);
     addExampleLine("+++ with respect to a reference structure (or we have aligned them in a reference-free manner).",false);
     addExampleLine("+++ Then, suppose we are interested in the vertices of the virus: perhaps because we suspect",false);
     addExampleLine("+++ that one of them is 'special': e.g. it is a portal. All we have to do is:",false);
 
     addExampleLine("+++* Pass the metadata of the aligned subtomograms of the ml_tomo prgram",false);
     addExampleLine("+++* Find the x,y,z coordinates of one of the vertices in the average (reference) map",false);
     addExampleLine("+++* Pass the (pseudo) symmetry description of the virus (icosahedral, see Symmetries)",false);
 
     addExampleLine("+++The program will then extract all symmetry-related vertices in each of the N aligned subtomograms.",false);
     addExampleLine("+++Each icosahedral has 12 vertices, so if the x,y,z coordinates coincided with a vertex (with an accuracy ",false);
     addExampleLine("+++given by the --mindist option, see below)",false);
     addExampleLine("+++, then we will end up with 12*N sub-subtomograms. The sub-subtomograms are not rotated ",false);
     addExampleLine("+++to avoid interpolation. Instead, the output metadata holds the correct orientations ",false);
     addExampleLine("+++and translation for each of them to subsequently superimpose them in the ml_tomo program. ",false);
     addExampleLine("+++Also the missing wedges of all sub-subtomograms will be treated correctly in this way. Then, in the ",false);
     addExampleLine("+++ml_tomo program one could attempt to classify the 12*N vertices, in an attempt to 'fish out' the N ",false);
     addExampleLine("+++supposed portal structures.",false);
 
     addExampleLine("+++The format of the input and output files is as described for the ml_tomo program.",false);
 
     addExampleLine("+++ First, lets align our set of virus subtomograms (images.sel, with missing wedges defined ",false);
     addExampleLine("+++ in images.doc and wedges.doc, see ml_tomo for details) ",false);
     addExampleLine("+++. We will use a known virus structure (myreference.vol) as reference and will use ",false);
     addExampleLine("+++ maximum cross-correlation (rather than maximum likelihood) to avoid problems with absolute ",false);
     addExampleLine("+++ greyscales and the standard deviation in the noise. ",false);
 
     addExampleLine("+++ ml_tomo -i images.sel -doc images.doc                      -ref myreference.vol --oroot align/mltomo_10deg -missing wedges.doc -iter 1 -ang 10");
     addExampleLine("+++ ml_tomo -i images.sel -doc align/mltomo_10deg_it000001.doc -ref myreference.vol --oroot align/mltomo_5deg  -missing wedges.doc -iter 1 -ang 5 -ang_search 20");
     addExampleLine("+++ ml_tomo -i images.sel -doc align/mltomo_5deg_it000001.doc  -ref myreference.vol --oroot align/mltomo_2deg  -missing wedges.doc -iter 1 -ang 2 -ang_search 8");
     addExampleLine("+++ ml_tomo -i images.sel -doc align/mltomo_2deg_it000001.doc  -ref myreference.vol --oroot align/mltomo_1deg  -missing wedges.doc -iter 1 -ang 1 -ang_search 3");
 
     addExampleLine("+++ Now, we will identify the x,y,z coordinates of the vertex in the reference structure (which has symmetry i3): ",false);
     addExampleLine("+++ -center 0 0 59. And we will extract 12 vertices (subvolumes) in boxes of size 12x12x12 pixels ",false);
     addExampleLine("+++ from each subtomogram in the data set: ",false);
 
     addExampleLine("+++ xmipp_extract_subvolume -doc align/mltomo_1deg_it000001.doc -center 0 0 59 -size 21 -sym i3 -o vertices ",false);
 
     addExampleLine("+++ his has generated subvolumes in the same directory as the original subtomograms. For each subtomogram 12  ",false);
     addExampleLine("+++ subvolumes, which are named in the same way as the original subtomograms, but ending in _sub000001.vol etc. ",false);
     addExampleLine("+++ The orientations and translations are in a file called vertices.doc, the selection file is called vertices.sel.  ",false);
     addExampleLine("+++ These files are already in the correct format for the ml_tomo program. Therefore, classifying the vertices into  ",false);
     addExampleLine("+++ 4 classes using ML is now straightforward (see ml_tomo for details again) ",false);
     addExampleLine("+++ : ",false);
 
     addExampleLine("+++ xmipp_ml_tomo -i vertices.sel -doc vertices.doc -dont_align -keep_angles -missing wedges.doc -nref 4 -reg0 5 -iter 25");
 
     addExampleLine("+++ Note that the whole functionality of ml_tomo can be employed on the sub-subtomograms: alignment, ",false);
     addExampleLine("+++ classification, local angular searches, symmetry, etc. For example, in case of the vertices, on ",false);
     addExampleLine("+++ could apply -sym c5, and/or one could allow the vertices to re-orient slightly (with respect ",false);
     addExampleLine("+++ to the i3 symmetry) by using -ang 5 ang_search 15. ",false);
 }

◆ postProcess()

void ProgTomoExtractSubvolume::postProcess ( )

virtual

Reimplemented from XmippMetadataProgram.

Definition at line 349 of file tomo_extract_subvolume.cpp.

350 {}

◆ preProcess()

void ProgTomoExtractSubvolume::preProcess ( )

virtual

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgTomoExtractSubvolume >.

Definition at line 153 of file tomo_extract_subvolume.cpp.

 {
     //    produceSideInfo();
 #ifdef  DEBUG
     std::cerr<<"Start produceSideInfo"<<std::endl;
 #endif
 
     //    //Read in Docfile
     //    DF.read(fn_doc);
     //    nr_exp_images = DF.size();
 
     // Setup symmetry
     if (!SL.isSymmetryGroup(fn_sym, symmetry, sym_order))
         REPORT_ERROR(ERR_PARAM_INCORRECT, "tomo_extract_subvolume: Invalid symmetry " +  fn_sym);
     SL.readSymmetryFile(fn_sym);
 
     // Check which symmetry operators give unique output points
     centers_subvolumes.clear();
     rotations_subvolumes.clear();
     Matrix2D<double>  L(4, 4), R(4, 4);
     Matrix2D<double>  Iref(3,3);
     Matrix1D<double>  newcenter(3), distcenter(3);
     double dist;
     bool is_uniq;
     Iref.initIdentity();
 
     centers_subvolumes.push_back(center_ref);
     rotations_subvolumes.push_back(Iref);
 
     for (int isym = 0; isym < SL.symsNo(); isym++)
     {
         SL.getMatrices(isym, L, R);
         L.resize(3,3);
         R.resize(3,3);
         newcenter = L * (center_ref.transpose() * R).transpose();
         is_uniq=true;
         for (size_t i = 0; i < centers_subvolumes.size(); i++)
         {
             distcenter = centers_subvolumes[i] - newcenter;
             dist = sqrt(distcenter.sum2());
             if (dist < mindist)
             {
                 is_uniq=false;
                 break;
             }
         }
         if (is_uniq)
         {
             centers_subvolumes.push_back(newcenter);
             rotations_subvolumes.push_back(R);
         }
     }
 //#define DEBUG
 #ifdef  DEBUG
     for (int isym = 0; isym < SL.symsNo(); isym++)
     {
     std::cerr << "centers_subvolumes" << centers_subvolumes[isym] << std::endl;
     std::cerr << "rotations_subvolumes" << rotations_subvolumes[isym] << std::endl;
     }    std::cerr<<"End produceSideInfo"<<std::endl;
 #endif
 
     center.resizeNoCopy(3);
     doccenter.resizeNoCopy(3);
     A.resizeNoCopy(3,3);
     R.resizeNoCopy(3,3);
     I.resizeNoCopy(3,3);
     I.initIdentity();
 }

◆ processImage()

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

virtual

Implements XmippMetadataProgram.

Definition at line 222 of file tomo_extract_subvolume.cpp.

 {
 
 #ifdef  DEBUG
     std::cerr<<"Start processImages"<<std::endl;
 #endif
 
     //    for (int imgno=imgno_start; imgno <imgno_end; imgno++)
     rot = rowIn.getValueOrDefault(MDL_ANGLE_ROT, 0.);
     tilt = rowIn.getValueOrDefault(MDL_ANGLE_TILT, 0.);
     psi = rowIn.getValueOrDefault(MDL_ANGLE_PSI, 0.);
 
     double auxD;
     rowIn.getValue(MDL_ORIGIN_X,auxD);
     XX(doccenter) = auxD;
     rowIn.getValue(MDL_ORIGIN_Y,auxD);
     YY(doccenter) = auxD;
     rowIn.getValue(MDL_ORIGIN_Z,auxD);
     ZZ(doccenter) = auxD;
 
     // Read volume
     vol.read(fnImg2);
     vol().setXmippOrigin();
     FileName fnImg;
     fnImg = fnImg2.removeFileFormat().removeLastExtension();
 
     x0 = FIRST_XMIPP_INDEX(size);
     xF = LAST_XMIPP_INDEX(size);
 
     FileName fnOutStack, fnOutMd;
 
     size_t image_num = 0;
     FileName dump;
     if (mdInSize > 1)// Other case, is a unique volume name so there is no need to add the number
     {
         if (oroot.empty())
         {
             fn_aux = fnImg.removePrefixNumber().removeLastExtension()+ "_sub";
 
             if  (fnImg.isInStack())
             {
                 fnImg.decompose(image_num, dump);
                 fn_aux.compose(fn_aux,image_num);
             }
         }
         else if (fnImg.isInStack())
         {
             fnImg.decompose(image_num, dump);
             fn_aux.compose(oroot,image_num);
         }
         else
             fn_aux = oroot + "_" + fnImg.afterLastOf("/");
     }
     else if (!oroot.empty())
         fn_aux = oroot;
     else
         fn_aux = fnImg+"_sub";
 
     if (mdInSize > 1)
     {
         if (fn_out.empty())
             fnOutMd = fn_aux.addExtension("xmd");
         else if (fnImg.isInStack())
             fnOutMd.compose(fn_out.removeLastExtension(), image_num, fn_out.getExtension());
         else
             fnOutMd = fn_out.insertBeforeExtension("_" + fnImg.getBaseName());
     }
     else if (!fn_out.empty())
         fnOutMd = fn_out;
     else
         fnOutMd = fn_aux.addExtension("xmd");
 
      // Tomo_Extract each of the unique subvolumes
     size_t oId;
     SPEED_UP_temps012;
     for (size_t i = 0; i < centers_subvolumes.size(); i++)
     {
         center=centers_subvolumes[i];
 
         // 1. rotate center
         Euler_angles2matrix(-psi,-tilt,-rot,A,false);
         M3x3_BY_V3x1(center, A, center);
         // 2. translate center
         center -= doccenter;
         // 3. Apply possible non-integer center to volume
         //translations may be non-integer
         translate(xmipp_transformation::BSPLINE3,volout(),vol(),center);
 
         //vol().translate(-center, volout(), DONT_WRAP);
         //4. Window operation and write subvolume to disc
         volout().selfWindow(x0,x0,x0,xF,xF,xF);
         //remove type if present
         fnOutStack.compose(i+1,fn_aux,"stk");
         volout.write(fnOutStack);
 
 
         // 5. Calculate output angles: apply symmetry rotation to rot,tilt and psi
         Euler_apply_transf(rotations_subvolumes[i], I, rot, tilt, psi, rotp, tiltp, psip);
         oId=DFout.addObject();
 
         DFout.setValue(MDL_IMAGE,fnOutStack,oId);
         DFout.setValue(MDL_ANGLE_ROT,rotp,oId);
         DFout.setValue(MDL_ANGLE_TILT,tiltp,oId);
         DFout.setValue(MDL_ANGLE_PSI,psip,oId);
         DFout.setValue(MDL_SHIFT_X,XX(center),oId);
         DFout.setValue(MDL_SHIFT_Y,YY(center),oId);
         DFout.setValue(MDL_SHIFT_Z,ZZ(center),oId);
     }
     // 6. Output translations will be zero because subvolumes are centered by definition
     DFout.setValueCol(MDL_ORIGIN_X,0.);
     DFout.setValueCol(MDL_ORIGIN_Y,0.);
     DFout.setValueCol(MDL_ORIGIN_Z,0.);
     
     DFout.setComment("shift keeps the center of the box in the original virus");
     DFout.write(fnOutMd);
     DFout.clear();
 
 
 
 #ifdef  DEBUG
 
     std::cerr<<"end processImages"<<std::endl;
 #endif
 }

◆ readParams()

void ProgTomoExtractSubvolume::readParams ( )

virtual

Read arguments from command line.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgTomoExtractSubvolume >.

Definition at line 107 of file tomo_extract_subvolume.cpp.

 {
     XmippMetadataProgram::readParams();
     oroot = getParam("--oroot");
     fn_out = getParam("-o");
     // Read command line
     fn_sym  = getParam( "--sym");
     center_ref.resize(3);
     size = getIntParam("--size");
     XX(center_ref) = getIntParam( "--center",0);
     YY(center_ref) = getIntParam( "--center",1);
     ZZ(center_ref) = getIntParam( "--center",2);
     mindist = getDoubleParam("--mindist");
     if (mindist == -1)
         mindist = size/4.;
 }

◆ show()

void ProgTomoExtractSubvolume::show ( )

Show.

Definition at line 125 of file tomo_extract_subvolume.cpp.

 {
 #ifdef DEBUG
     std::cerr << "start show" <<std::endl;
 #endif
 
     if (verbose)
     {
         std::cout << " -----------------------------------------------------------------" << std::endl;
         std::cout << " | Read more about this program in the following publication:    |" << std::endl;
         std::cout << " |  Scheres ea.  (2009) Structure, 17, 1563-1572                 |" << std::endl;
         std::cout << " |                                                               |" << std::endl;
         std::cout << " |   *** Please cite it if this program is of use to you! ***    |" << std::endl;
         std::cout << " -----------------------------------------------------------------" << std::endl;
 
         std::cout << "Input  Metadata File " <<  fn_in       << std::endl;
         std::cout << "Output volume root   " <<  oroot      << std::endl;
         std::cout << "Output metadata file " <<  fn_out      << std::endl;
         std::cout << "Coordenate center    " <<  center_ref   << std::endl;
         std::cout << "Size subvolume       " <<  size         << std::endl;
         std::cout << "Symmetry group       " <<  fn_sym       << std::endl;
         std::cout << "Minimum distance between subvolumes " << mindist << std::endl;
     }
 #ifdef DEBUG
     std::cerr << "end show" <<std::endl;
 #endif
 }

Member Data Documentation

◆ A

Matrix2D<double> ProgTomoExtractSubvolume::A

Definition at line 91 of file tomo_extract_subvolume.h.

◆ center

Matrix1D<double> ProgTomoExtractSubvolume::center

Definition at line 90 of file tomo_extract_subvolume.h.

◆ center_ref

Matrix1D<double> ProgTomoExtractSubvolume::center_ref

Coordinates of the center of the subvolume in the reference

Definition at line 59 of file tomo_extract_subvolume.h.

◆ centers_subvolumes

std::vector<Matrix1D<double> > ProgTomoExtractSubvolume::centers_subvolumes

Coordinates of the unique symmetry related centers in the reference

Definition at line 62 of file tomo_extract_subvolume.h.

◆ DFout

MetaDataVec ProgTomoExtractSubvolume::DFout

Definition at line 76 of file tomo_extract_subvolume.h.

◆ doccenter

Matrix1D<double> ProgTomoExtractSubvolume::doccenter

Definition at line 90 of file tomo_extract_subvolume.h.

◆ fn_aux

FileName ProgTomoExtractSubvolume::fn_aux

Definition at line 53 of file tomo_extract_subvolume.h.

◆ fn_doc

FileName ProgTomoExtractSubvolume::fn_doc

Filenames reference selfile/image, fraction metadata & output rootname

Definition at line 53 of file tomo_extract_subvolume.h.

◆ fn_mask

FileName ProgTomoExtractSubvolume::fn_mask

Definition at line 53 of file tomo_extract_subvolume.h.

◆ fn_missing

FileName ProgTomoExtractSubvolume::fn_missing

Definition at line 53 of file tomo_extract_subvolume.h.

◆ fn_root

FileName ProgTomoExtractSubvolume::fn_root

Definition at line 53 of file tomo_extract_subvolume.h.

◆ fn_sym

FileName ProgTomoExtractSubvolume::fn_sym

Definition at line 53 of file tomo_extract_subvolume.h.

◆ I

Matrix2D<double> ProgTomoExtractSubvolume::I

Definition at line 91 of file tomo_extract_subvolume.h.

◆ mindist

double ProgTomoExtractSubvolume::mindist

Minimum distance between unique subvolumes

Definition at line 82 of file tomo_extract_subvolume.h.

◆ nr_exp_images

int ProgTomoExtractSubvolume::nr_exp_images

Number of input volumes

Definition at line 66 of file tomo_extract_subvolume.h.

◆ nr_output_volumes

int ProgTomoExtractSubvolume::nr_output_volumes

Number of subvolumes per input volume

Definition at line 69 of file tomo_extract_subvolume.h.

◆ psi

double ProgTomoExtractSubvolume::psi

Definition at line 92 of file tomo_extract_subvolume.h.

◆ psip

double ProgTomoExtractSubvolume::psip

Definition at line 92 of file tomo_extract_subvolume.h.

◆ R

Matrix2D<double> ProgTomoExtractSubvolume::R

Definition at line 91 of file tomo_extract_subvolume.h.

◆ rot

double ProgTomoExtractSubvolume::rot

Definition at line 92 of file tomo_extract_subvolume.h.

◆ rotations_subvolumes

std::vector<Matrix2D<double> > ProgTomoExtractSubvolume::rotations_subvolumes

Definition at line 63 of file tomo_extract_subvolume.h.

◆ rotp

double ProgTomoExtractSubvolume::rotp

Definition at line 92 of file tomo_extract_subvolume.h.

◆ size

int ProgTomoExtractSubvolume::size

Size of the output subvolume

Definition at line 56 of file tomo_extract_subvolume.h.

◆ SL

SymList ProgTomoExtractSubvolume::SL

Definition at line 86 of file tomo_extract_subvolume.h.

◆ sym_order

int ProgTomoExtractSubvolume::sym_order

Definition at line 85 of file tomo_extract_subvolume.h.

◆ symmetry

int ProgTomoExtractSubvolume::symmetry

Definition at line 85 of file tomo_extract_subvolume.h.

◆ tilt

double ProgTomoExtractSubvolume::tilt

Definition at line 92 of file tomo_extract_subvolume.h.

◆ tiltp

double ProgTomoExtractSubvolume::tiltp

Definition at line 92 of file tomo_extract_subvolume.h.

◆ vol

Image<double> ProgTomoExtractSubvolume::vol

Definition at line 89 of file tomo_extract_subvolume.h.

◆ volout

Image<double> ProgTomoExtractSubvolume::volout

Definition at line 89 of file tomo_extract_subvolume.h.

◆ x0

int ProgTomoExtractSubvolume::x0

Definition at line 93 of file tomo_extract_subvolume.h.

◆ xF

int ProgTomoExtractSubvolume::xF

Definition at line 93 of file tomo_extract_subvolume.h.

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

xmipp/legacy/libraries/reconstruction/tomo_extract_subvolume.h
xmipp/legacy/libraries/reconstruction/tomo_extract_subvolume.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ postProcess()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ show()

Member Data Documentation

◆ A

◆ center

◆ center_ref

◆ centers_subvolumes

◆ DFout

◆ doccenter

◆ fn_aux

◆ fn_doc

◆ fn_mask

◆ fn_missing

◆ fn_root

◆ fn_sym

◆ I

◆ mindist

◆ nr_exp_images

◆ nr_output_volumes

◆ psi

◆ psip

◆ R

◆ rot

◆ rotations_subvolumes

◆ rotp

◆ size

◆ SL

◆ sym_order

◆ symmetry

◆ tilt

◆ tiltp

◆ vol

◆ volout

◆ x0

◆ xF