#include <volumeset_align.h>

Inheritance diagram for ProgVolumeSetAlign:

Collaboration diagram for ProgVolumeSetAlign:

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

void	defineParams ()
	Define params. More...

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

virtual void	preProcess ()

void	processImage (const FileName &fnImg, const FileName &, const MDRow &, MDRow &)

virtual void	finishProcessing ()

virtual void	writeVolumeParameters (const FileName &fnImg)

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
bool	resume = false

FileName	fnREF
	Reference volume structure. More...

FileName	fnOutDir
	Output directory. More...

bool	alignVolumes
	Align volumes. More...

int	tilt0

int	tiltF

double	frm_freq

int	frm_shift

FileName	fnMask

FILE *	fnAnglesAndShifts

float	Matrix_Angles_Shifts [6]

float	fitness

bool	flipped = false

int	rangen = 0

Matrix1D< double >	parameters

FileName	currentVolName = ""

char	nameTemplate [256]

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

Protected Member Functions
virtual void	createWorkFiles ()

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	writeOutput ()

virtual void	showProgress ()

virtual void	defineLabelParam ()

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Member Functions inherited from Rerunable
	Rerunable (const FileName &fn)

virtual void	createWorkFiles (bool resume, MetaData *md)

const FileName &	getFileName () const

void	setFileName (const FileName &fn)

Additional Inherited Members
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

Definition at line 35 of file volumeset_align.h.

Constructor & Destructor Documentation

◆ ProgVolumeSetAlign()

ProgVolumeSetAlign::ProgVolumeSetAlign ( )

Empty constructor.

Definition at line 31 of file volumeset_align.cpp.

                                        : Rerunable("") {
     each_image_produces_an_output = false;
     produces_an_output = true;
 }

Member Function Documentation

◆ createWorkFiles()

virtual void ProgVolumeSetAlign::createWorkFiles ( )

inlineprotectedvirtual

Definition at line 105 of file volumeset_align.h.

                                    {
       return Rerunable::createWorkFiles(resume, getInputMd());
     }

◆ defineParams()

void ProgVolumeSetAlign::defineParams ( )

virtual

Define params.

Reimplemented from XmippMetadataProgram.

Definition at line 37 of file volumeset_align.cpp.

                                       {
     addUsageLine("Align a set of volumes with a reference volume");
     defaultComments["-i"].clear();
     defaultComments["-i"].addComment("Metadata with volume filenames");
     defaultComments["-o"].clear();
     defaultComments["-o"].addComment("Metadata with output Euler angles and shifts");
     XmippMetadataProgram::defineParams();
     addParamsLine("   --ref <VOL_filename>                : Reference volume");
     addParamsLine("  [--odir <outputDir=\".\">]           : Output directory");
     addParamsLine("  [--resume]                           : Resume processing");
     addParamsLine("  [--frm_parameters <frm_freq=0.25> <frm_shift=10>]  : This is using frm method for volume alignment with frm_freq and frm_shift as parameters");
     addParamsLine("  [--tilt_values <tilt0=-90> <tiltF=90>]  : Optional compensation for the missing wedge. Tested extensively with tilt between [-60 60]");
     addParamsLine("  [--mask <mask_filename=\"\">]        : Optional mask during the alignment");
     addExampleLine("xmipp_volumeset_align -i volumes.xmd --ref reference.vol -o output.xmd --resume");
 }

◆ finishProcessing()

void ProgVolumeSetAlign::finishProcessing ( )

virtual

Write the final parameters.

Reimplemented from XmippMetadataProgram.

Definition at line 74 of file volumeset_align.cpp.

                                           {
     XmippMetadataProgram::finishProcessing();
     const char* aligneddata = "/AlignedSoFar.xmd";
     rename((fnOutDir+aligneddata).c_str(), fn_out.c_str());
 }

◆ preProcess()

void ProgVolumeSetAlign::preProcess ( )

virtual

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

Reimplemented from XmippMetadataProgram.

Definition at line 69 of file volumeset_align.cpp.

                                     {
     // Set the pointer of the program to this object
     createWorkFiles();
 }

◆ processImage()

void ProgVolumeSetAlign::processImage	(	const FileName &	fnImg,
		const FileName &	,
		const MDRow &	,
		MDRow &
	)

virtual

Assign NMA and Alignment parameters to a volume

Implements XmippMetadataProgram.

Definition at line 132 of file volumeset_align.cpp.

                                                   {
     static size_t imageCounter = 0;
     ++imageCounter;
     currentVolName = fnImg;
     snprintf(nameTemplate, 255 ,"_node%d_img%lu_XXXXXX", rangen, (long unsigned int)imageCounter);
     computeFitness();
     writeVolumeParameters(fnImg);
 }

◆ readParams()

void ProgVolumeSetAlign::readParams ( )

virtual

Read arguments from command line.

Reimplemented from XmippMetadataProgram.

Definition at line 54 of file volumeset_align.cpp.

                                     {
     XmippMetadataProgram::readParams();
     fnREF = getParam("--ref");
     fnOutDir = getParam("--odir");
     Rerunable::setFileName(fnOutDir+"/AlignedSoFar.xmd");
     resume = checkParam("--resume");
     frm_freq = getDoubleParam("--frm_parameters",0);
     frm_shift= getIntParam("--frm_parameters",1);
     tilt0=getIntParam("--tilt_values",0);
     tiltF=getIntParam("--tilt_values",1);
     fnMask = getParam("--mask");
 }

◆ writeVolumeParameters()

void ProgVolumeSetAlign::writeVolumeParameters ( const FileName & fnImg )

virtual

Write the parameters found for one image

Definition at line 142 of file volumeset_align.cpp.

                                                                     {
     MetaDataVec md;
     size_t objId = md.addObject();
     md.setValue(MDL_IMAGE, fnImg, objId);
     md.setValue(MDL_ENABLED, 1, objId);
     md.setValue(MDL_ANGLE_ROT,  (double)this->Matrix_Angles_Shifts[0], objId);
     md.setValue(MDL_ANGLE_TILT, (double)this->Matrix_Angles_Shifts[1], objId);
     md.setValue(MDL_ANGLE_PSI,  (double)this->Matrix_Angles_Shifts[2], objId);
     md.setValue(MDL_SHIFT_X,    (double)this->Matrix_Angles_Shifts[3], objId);
     md.setValue(MDL_SHIFT_Y,    (double)this->Matrix_Angles_Shifts[4], objId);
     md.setValue(MDL_SHIFT_Z,    (double)this->Matrix_Angles_Shifts[5], objId);
     md.setValue(MDL_MAXCC,     -(double)this->fitness, objId);
     if (this->flipped){
         md.setValue(MDL_ANGLE_Y, 90.0 , objId);
     }
     else{
         md.setValue(MDL_ANGLE_Y, 0.0 , objId);
     }
     md.append(Rerunable::getFileName());
 }

Member Data Documentation

◆ alignVolumes

bool ProgVolumeSetAlign::alignVolumes

Align volumes.

Definition at line 49 of file volumeset_align.h.

◆ currentVolName

FileName ProgVolumeSetAlign::currentVolName = ""

Definition at line 77 of file volumeset_align.h.

◆ fitness

float ProgVolumeSetAlign::fitness

Definition at line 65 of file volumeset_align.h.

◆ flipped

bool ProgVolumeSetAlign::flipped = false

Definition at line 68 of file volumeset_align.h.

◆ fnAnglesAndShifts

FILE* ProgVolumeSetAlign::fnAnglesAndShifts

Definition at line 63 of file volumeset_align.h.

◆ fnMask

FileName ProgVolumeSetAlign::fnMask

Definition at line 60 of file volumeset_align.h.

◆ fnOutDir

FileName ProgVolumeSetAlign::fnOutDir

Output directory.

Definition at line 46 of file volumeset_align.h.

◆ fnREF

FileName ProgVolumeSetAlign::fnREF

Reference volume structure.

Definition at line 43 of file volumeset_align.h.

◆ frm_freq

double ProgVolumeSetAlign::frm_freq

Definition at line 56 of file volumeset_align.h.

◆ frm_shift

int ProgVolumeSetAlign::frm_shift

Definition at line 57 of file volumeset_align.h.

◆ Matrix_Angles_Shifts

float ProgVolumeSetAlign::Matrix_Angles_Shifts[6]

Definition at line 64 of file volumeset_align.h.

◆ nameTemplate

char ProgVolumeSetAlign::nameTemplate[256]

Definition at line 80 of file volumeset_align.h.

◆ parameters

Matrix1D<double> ProgVolumeSetAlign::parameters

Definition at line 74 of file volumeset_align.h.

◆ rangen

int ProgVolumeSetAlign::rangen = 0

Definition at line 71 of file volumeset_align.h.

◆ resume

bool ProgVolumeSetAlign::resume = false

Resume computations

Definition at line 40 of file volumeset_align.h.

◆ tilt0

int ProgVolumeSetAlign::tilt0

Definition at line 52 of file volumeset_align.h.

◆ tiltF

int ProgVolumeSetAlign::tiltF

Definition at line 53 of file volumeset_align.h.

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

xmipp/libraries/reconstruction/volumeset_align.h
xmipp/libraries/reconstruction/volumeset_align.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgVolumeSetAlign()

Member Function Documentation

◆ createWorkFiles()

◆ defineParams()

◆ finishProcessing()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ writeVolumeParameters()

Member Data Documentation

◆ alignVolumes

◆ currentVolName

◆ fitness

◆ flipped

◆ fnAnglesAndShifts

◆ fnMask

◆ fnOutDir

◆ fnREF

◆ frm_freq

◆ frm_shift

◆ Matrix_Angles_Shifts

◆ nameTemplate

◆ parameters

◆ rangen

◆ resume

◆ tilt0

◆ tiltF