ProgNmaAlignmentVol Class Reference

#include <nma_alignment_vol.h>

Inheritance diagram for ProgNmaAlignmentVol:

Collaboration diagram for ProgNmaAlignmentVol:

Public Member Functions
	ProgNmaAlignmentVol ()
	Empty constructor. More...
	~ProgNmaAlignmentVol ()
	Destructor. More...
void	defineParams ()
	Define params. More...
void	readParams ()
	Read arguments from command line. More...
void	show ()
	Show. More...
FileName	createDeformedPDB () const
double	computeFitness (Matrix1D< double > &trial) const
bool	updateBestFit (double fitness)
virtual void	preProcess ()
virtual void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)
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	MPIversion
bool	resume
FileName	fnPDB
	Reference atomic or pseudo-atomic structure in PDB format. More...
FileName	fnOutPDB
	Output PDB. More...
FileName	fnOutDir
	Output directory. More...
FileName	fnModeList
	File with a list of mode filenames. More...
double	sampling_rate
	Pixel size in Angstroms. More...
FileName	fnmask
	Mask file for 2D masking of the projections of the deformed volume. More...
bool	do_centerPDB
	Center the PDB structure. More...
bool	do_FilterPDBVol
	Low-pass filter the volume from PDB. More...
double	cutoff_LPfilter
	Low-pass cut-off frequency. More...
bool	useFixedGaussian
	Use pseudo-atoms instead of atoms. More...
double	sigmaGaussian
	Gaussian standard deviation for pseudo-atoms. More...
bool	alignVolumes
	Align volumes. More...
double	trustradius_scale
	Parameters required from the CONDOR optimization. More...
double	rhoStartBase
double	rhoEndBase
int	niter
int	tilt0
int	tiltF
double	frm_freq
int	frm_shift
int	rangen
Matrix1D< double >	parameters
Matrix1D< double >	trial
Matrix1D< double >	trial_best
double	fitness_min
int	numberOfModes
int	imgSize
FileName	currentVolName
char	nameTemplate [256]
ProgPdbConverter *	progVolumeFromPDB
Image< double >	V
Image< double >	Vdeformed
MultidimArray< int >	mask
FILE *	AnglesShiftsAndScore
float	Best_Angles_Shifts [6]
float	fit_value
bool	flip = false
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

NMA Alignment Parameters.

Definition at line 39 of file nma_alignment_vol.h.

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

• xmipp/libraries/reconstruction/nma_alignment_vol.h
• xmipp/libraries/reconstruction/nma_alignment_vol.cpp