#include <transform_geometry.h>

Inheritance diagram for ProgTransformGeometry:

Collaboration diagram for ProgTransformGeometry:

Public Member Functions
	ProgTransformGeometry ()

	~ProgTransformGeometry ()

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	calculateRotationMatrix ()

void	preProcess ()

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

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
int	splineDegree

int	dim

bool	applyTransform

bool	inverse

bool	wrap

bool	isVol

bool	flip

bool	mdVol

Matrix2D< double >	R

Matrix2D< double >	A

Matrix2D< double >	B

Matrix2D< double >	T

ImageGeneric	img

ImageGeneric	imgOut

String	matrixStr

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 38 of file transform_geometry.h.

Constructor & Destructor Documentation

◆ ProgTransformGeometry()

ProgTransformGeometry::ProgTransformGeometry ( )

Constructor and destructor, just to avoid vtable undefined references errors

Definition at line 30 of file transform_geometry.cpp.

31 {}

◆ ~ProgTransformGeometry()

ProgTransformGeometry::~ProgTransformGeometry ( )

Definition at line 33 of file transform_geometry.cpp.

34 {}

Member Function Documentation

◆ calculateRotationMatrix()

void ProgTransformGeometry::calculateRotationMatrix ( )

protected

Calculate the rotation matrix according to the parameters

Definition at line 128 of file transform_geometry.cpp.

 {
     const char * rotateType = getParam("--rotate_volume");
     Matrix1D<double> xyz(3);
     if (!STR_EQUAL(rotateType, "icosahedral"))
     {   // params are char for icosahedral option
         XX(xyz) = getDoubleParam("--rotate_volume", 1); //rot
         YY(xyz) = getDoubleParam("--rotate_volume", 2); //tilt
         ZZ(xyz) = getDoubleParam("--rotate_volume", 3); //psi
     }
 
     if (STR_EQUAL(rotateType, "euler"))
         Euler_angles2matrix(XX(xyz), YY(xyz), ZZ(xyz), R, true);
     else if (STR_EQUAL(rotateType, "matrix"))
     {
         R.initZeros(4,4);
         MAT_ELEM(R, 3, 3) = 1;
         for (int i = 0; i < 9; ++i)
         {
             int r = i / 3;
             int c = i % 3;
             MAT_ELEM(R, r, c) =  getDoubleParam("--rotate_volume", i+1);
         }
     }
     else if (STR_EQUAL(rotateType, "alignZ"))
         alignWithZ(xyz, R);
     else if (STR_EQUAL(rotateType, "icosahedral"))
     {
         const char * icoFrom = getParam("--rotate_volume", 1);
         const char * icoTo = getParam("--rotate_volume", 2);
         rotation3DMatrixFromIcoOrientations(icoFrom, icoTo, R);
     }
     else
     {
         double ang = getDoubleParam("--rotate_volume", 1);
         XX(xyz) = getDoubleParam("--rotate_volume", 2); //axis x
         YY(xyz) = getDoubleParam("--rotate_volume", 3); //y
         ZZ(xyz) = getDoubleParam("--rotate_volume", 4);//z
         rotation3DMatrix(ang, xyz, R, true);
     }
 }

◆ defineParams()

void ProgTransformGeometry::defineParams ( )

protectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgTransformGeometry >.

Definition at line 36 of file transform_geometry.cpp.

 {
     each_image_produces_an_output = true;
     save_metadata_stack = true;
     keep_input_columns = true;
     allow_apply_geo = true;
     mdVol = false;
     XmippMetadataProgram::defineParams();
     //usage
     addUsageLine("Apply geometric transformations to images. You can shift, rotate and scale a group of images/volumes.");
     addUsageLine("+ By default the geometric transformations will be read from a metadata, if provided. Also, ");
     addUsageLine("+ the original images will be preserved if possible, trying to write out transformations to ");
     addUsageLine("+ the output metadata. If output is not specified, the original files will be overwritten.");
     addUsageLine("+ When output param -o is a stack file, associated metadata file is also generated using same rootname.");
     addUsageLine("+ If geometrical transformation are applied, involved labels are reset in output metadata.");
     //keywords
     addKeywords("transform, geometry, shift, rotate, scale, flip");
     //params
     addParamsLine("== Transformations ==");
     addParamsLine("[--rotate <ang=0>]   : Inplane rotation in 2D images.");
     addParamsLine("               : Positive angle is a clockwise rotation");
     addParamsLine("[--rotate_volume <rotation_type>]   : Rotation of volumes.");
     addParamsLine("         where <rotation_type>");
     addParamsLine("             euler <rot> <tilt> <psi>     : Rotate with these Euler angles (ZYZ convention)");
     addParamsLine("             matrix <r11> <r12> <r13> <r21> <r22> <r23> <r31> <r32> <r33>    : 3x3 rotation matrix, first index is row");
     addParamsLine("             alignZ <x> <y> <z>           : Align (x,y,z) with Z axis");
     addParamsLine("             axis <ang> <x=0> <y=0> <z=1> : Rotate <ang> degrees around (x,y,z)");
     addParamsLine("             icosahedral <from> <to>      : Rotate an icosahedral volume from i1 to i2, for instance");
     addParamsLine("                                          : valid symmetries are i1, i2, i3 and i4");
     addParamsLine("[--scale <factor=1>]                      : Perfom Scaling. Factor 0.5 halves and 2 doubles");
     addParamsLine(" alias -s;");
     addParamsLine("[--shift <x=0> <y=0> <z=0>]               : Shift by x, y and z");
     addParamsLine("[--flip]                                  : Flip images, only valid for 2D");
     addParamsLine("[--matrix <...>]                 : Apply directly the matrix transformation");
     addParamsLine("== Other options ==");
     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("[--inverse]                         : Apply inverse transformations");
     addParamsLine("[--apply_transform]                 : By default, the original images are preserved");
     addParamsLine("                                    : and the alignment information is stored in metadata");
     addParamsLine("[--dont_wrap]                       : By default, the image/volume is wrapped");
     addParamsLine("[--write_matrix]                    : Print transformation matrix to screen");
     addParamsLine("[--shift_to <x=0> <y=0> <z=0>]      : Shift each particle to x,y,z position");
     //examples
     addExampleLine("Write a metadata with geometrical transformations keeping the reference to original images:", false);
     addExampleLine("xmipp_transform_geometry -i mD1.xmd --shift 2 3 4 --scale 1.2 --rotate 23 -o newGeo.xmd");
     addExampleLine("Write a metadata with geometrical transformations copying original images to new stack file:", false);
     addExampleLine("xmipp_transform_geometry -i mD1.xmd --shift 2 3 4 --scale 1.2 --rotate 23 -o newGeo.stk");
     addExampleLine("Apply geometrical transformations to images ,reset involved labels and save in new metadata and stack files:", false);
     addExampleLine("xmipp_transform_geometry -i mD1.xmd --shift 2 3 4 --scale 1.2 --rotate 23 -o newGeo.xmd --apply_transform");
     addExampleLine("To simply apply the transformations in a metadata to the images:", false);
     addExampleLine("xmipp_transform_geometry -i mD1.xmd --apply_transform");
     addExampleLine("Shift a volume by 10, 5 and -10 in x,y and z and do not wrap", false);
     addExampleLine("xmipp_transform_geometry -i a.vol --shift 10 5 -10 -o b.vol --dont_wrap");
     addExampleLine("Scale a group of images to half size, not modifying image dimensions neither original image files", false);
     addExampleLine("xmipp_transform_geometry -i images.xmd --scale 0.5 -o halvedOriginal.xmd");
 
 }

◆ preProcess()

void ProgTransformGeometry::preProcess ( )

protectedvirtual

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgTransformGeometry >.

Definition at line 170 of file transform_geometry.cpp.

 {
     //If zdimOut greater than 1, is a volume and should apply transform
     dim = (isVol = (zdimOut > 1)) ? 3 : 2;
 
     applyTransform = applyTransform || isVol || mdInSize == 1;
     R.initIdentity(dim + 1);
     A.initIdentity(dim + 1);
 
     MDRowVec rowGeo;
     rowGeo.setValue(MDL_SHIFT_X, getDoubleParam("--shift", 0));
     rowGeo.setValue(MDL_SHIFT_Y, getDoubleParam("--shift", 1));
     rowGeo.setValue(MDL_SCALE, getDoubleParam("--scale"));
 
     if (isVol)
     {
         if (checkParam("--rotate_volume"))
             calculateRotationMatrix();
         else
             mdVol = true;
         rowGeo.setValue(MDL_SHIFT_Z, getDoubleParam("--shift", 2));
 
     }
     else
         rowGeo.setValue(MDL_ANGLE_PSI, getDoubleParam("--rotate"));
 
     geo2TransformationMatrix(rowGeo, A);
 
     A = A * R;
 
     if (flip)
     {
         MAT_ELEM(A, 0, 0) *= -1.;
         MAT_ELEM(A, 0, 1) *= -1.;
         if (dim == 3)
             MAT_ELEM(A, 0, 2) *= -1.;
     }
     if (inverse)
         A = A.inv();
 }

◆ processImage()

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

protectedvirtual

Implements XmippMetadataProgram.

Definition at line 211 of file transform_geometry.cpp.

 {
 
     if (checkParam("--matrix"))
     {
       // In this case we are directly reading the transformation matrix
       // from the arguments passed
       matrixStr = getParam("--matrix");
       string2TransformationMatrix(matrixStr, T);
     }
     else
     {
       B.initIdentity(dim + 1);
 
 
     if (apply_geo || mdVol || applyTransform)
         geo2TransformationMatrix(rowOut, B);
 
       T = A * B;
     }
 
     if (checkParam("--write_matrix"))
         std::cerr << T << std::endl;
 
     if (applyTransform || fnImg != fnImgOut)
         img.read(fnImg);
 
 
     if (checkParam("--shift_to"))
     {
         double rot, tilt, psi;
         rowIn.getValue(MDL_ANGLE_ROT, rot);
         rowIn.getValue(MDL_ANGLE_TILT, tilt);
         rowIn.getValue(MDL_ANGLE_PSI, psi);
         Matrix1D<double> pos, posp;
         pos.initZeros(3);
         posp.initZeros(3);
         pos(0) = getDoubleParam("--shift_to", 0);
         pos(1) = getDoubleParam("--shift_to", 1);
         pos(2) = getDoubleParam("--shift_to", 2);
         R.initIdentity(3);
         Euler_angles2matrix(rot, tilt, psi, R, false);
         if (checkParam("--inverse"))
             R = R.inv();
         posp = R * pos;
         rowOut.setValue(MDL_SHIFT_X, -posp(0));
         rowOut.setValue(MDL_SHIFT_Y, -posp(1));
         T.initIdentity(3);
         int nx;
         rowIn.getValue(MDL_XCOOR, nx);
         nx += int(-posp(0));
         rowOut.setValue(MDL_XCOOR, nx);
         int ny;
         rowIn.getValue(MDL_YCOOR, ny);
         ny += int(-posp(1));
         rowOut.setValue(MDL_YCOOR, ny);
         geo2TransformationMatrix(rowOut, T, true);
     }
 
     if (applyTransform)
     {
         img().setXmippOrigin();
         imgOut.setDatatype(img.getDatatype());
         imgOut().resize(1, zdimOut, ydimOut, xdimOut, false);
         imgOut().setXmippOrigin();
         applyGeometry(splineDegree, imgOut(), img(), T, xmipp_transformation::IS_NOT_INV, wrap, 0.);
         imgOut.write(fnImgOut);
         rowOut.resetGeo(false);
     }
     else
     {
         transformationMatrix2Geo(T, rowOut);
         if (fnImg != fnImgOut )
             img.write(fnImgOut);
     }
 }

◆ readParams()

void ProgTransformGeometry::readParams ( )

protectedvirtual

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

In most cases output "-o" is a metadata with the new geometry keeping the names of input images so we set the flags to keep the same image names in the output metadata

If "-o" is a metadata but we are writing output images, -o can only be a stack if –oroot is no passed, and then MD is generated automatically

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgTransformGeometry >.

Definition at line 97 of file transform_geometry.cpp.

 {
     XmippMetadataProgram::readParams();
     applyTransform = checkParam("--apply_transform");
     inverse = checkParam("--inverse");
     wrap = ! checkParam("--dont_wrap");
     String degree = getParam("--interp");
     if (degree == "spline")
         splineDegree = xmipp_transformation::BSPLINE3;
     else if (degree == "linear")
         splineDegree = xmipp_transformation::LINEAR;
     flip = checkParam("--flip");
 
     if ( !checkParam("--oroot") && fn_out.hasMetadataExtension())
     {
         if ( input_is_metadata && !applyTransform )
             each_image_produces_an_output = !(produces_a_metadata = true);
         else 
             fn_out = fn_out.replaceExtension("stk");
     }
     else if ( !checkParam("--oroot") && !checkParam("-o") )
         produces_a_metadata = true;
 }

Member Data Documentation

◆ A

Matrix2D<double> ProgTransformGeometry::A

protected

Definition at line 48 of file transform_geometry.h.

◆ applyTransform

bool ProgTransformGeometry::applyTransform

protected

Definition at line 47 of file transform_geometry.h.

◆ B

Matrix2D<double> ProgTransformGeometry::B

protected

Definition at line 48 of file transform_geometry.h.

◆ dim

int ProgTransformGeometry::dim

protected

Definition at line 46 of file transform_geometry.h.

◆ flip

bool ProgTransformGeometry::flip

protected

Definition at line 47 of file transform_geometry.h.

◆ img

ImageGeneric ProgTransformGeometry::img

protected

Definition at line 49 of file transform_geometry.h.

◆ imgOut

ImageGeneric ProgTransformGeometry::imgOut

protected

Definition at line 49 of file transform_geometry.h.

◆ inverse

bool ProgTransformGeometry::inverse

protected

Definition at line 47 of file transform_geometry.h.

◆ isVol

bool ProgTransformGeometry::isVol

protected

Definition at line 47 of file transform_geometry.h.

◆ matrixStr

String ProgTransformGeometry::matrixStr

protected

Definition at line 50 of file transform_geometry.h.

◆ mdVol

bool ProgTransformGeometry::mdVol

protected

Definition at line 47 of file transform_geometry.h.

◆ R

Matrix2D<double> ProgTransformGeometry::R

protected

Definition at line 48 of file transform_geometry.h.

◆ splineDegree

int ProgTransformGeometry::splineDegree

protected

Definition at line 46 of file transform_geometry.h.

◆ T

Matrix2D<double> ProgTransformGeometry::T

protected

Definition at line 48 of file transform_geometry.h.

◆ wrap

bool ProgTransformGeometry::wrap

protected

Definition at line 47 of file transform_geometry.h.

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

xmipp/libraries/data/transform_geometry.h
xmipp/libraries/data/transform_geometry.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgTransformGeometry()

◆ ~ProgTransformGeometry()

Member Function Documentation

◆ calculateRotationMatrix()

◆ defineParams()

◆ preProcess()

◆ processImage()

◆ readParams()

Member Data Documentation

◆ A

◆ applyTransform

◆ B

◆ dim

◆ flip

◆ img

◆ imgOut

◆ inverse

◆ isVol

◆ matrixStr

◆ mdVol

◆ R

◆ splineDegree

◆ T

◆ wrap