Xmipp
v3.23.11-Nereus
|
#include <resolution_localfilter.h>
Public Member Functions | |
void | defineParams () |
void | readParams () |
void | produceSideInfo () |
void | amplitudeMonogenicSignal3D (MultidimArray< std::complex< double > > &myfftV, double freq, double freqH, double freqL, MultidimArray< double > &litude, int count, FileName fnDebug) |
void | postProcessingLocalResolutions (MultidimArray< double > &resolutionVol, std::vector< double > &list, MultidimArray< double > &resolutionChimera, double &cut_value, MultidimArray< int > &pMask, double &resolutionThreshold) |
void | resolution2eval (int &count_res, double step, double &resolution, double &last_resolution, double &freq, double &freqL, int &last_fourier_idx, bool &continueIter, bool &breakIter, bool &doNextIteration) |
void | run () |
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) |
virtual void | initComments () |
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 ¶m, int verb=2) |
int | version () const |
virtual void | show () 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 | fnOut |
FileName | fnVol |
FileName | fnRes |
FileName | fnMask |
FileName | fnchim |
FileName | fnSpatial |
FileName | fnMeanVol |
FileName | fnMaskOut |
FileName | fnMd |
FileName | fnFilt |
double | sampling |
double | minRes |
double | maxRes |
double | R |
int | NVoxelsOriginalMask |
int | Nvoxels |
int | nthrs |
double | freq_step |
double | trimBound |
double | significance |
bool | noiseOnlyInHalves |
bool | automaticMode |
MultidimArray< double > | iu |
MultidimArray< std::complex< double > > | fftV |
FourierTransformer | transformer_inv |
Image< double > | Vfiltered |
Image< double > | VresolutionFiltered |
Image< double > | resVol |
Matrix1D< double > | freq_fourier |
double | sigma |
Public Attributes inherited from XmippProgram | |
bool | doRun |
bool | runWithoutArgs |
int | verbose |
Verbosity level. More... | |
int | debug |
Additional Inherited Members | |
Protected Member Functions inherited from XmippProgram | |
void | defineCommons () |
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 |
SSNR parameters.
Definition at line 48 of file resolution_localfilter.h.
void ProgResLocalFilter::amplitudeMonogenicSignal3D | ( | MultidimArray< std::complex< double > > & | myfftV, |
double | freq, | ||
double | freqH, | ||
double | freqL, | ||
MultidimArray< double > & | amplitude, | ||
int | count, | ||
FileName | fnDebug | ||
) |
|
virtual |
Function in which the param of each Program are defined.
Reimplemented from XmippProgram.
Definition at line 44 of file resolution_localfilter.cpp.
void ProgResLocalFilter::postProcessingLocalResolutions | ( | MultidimArray< double > & | resolutionVol, |
std::vector< double > & | list, | ||
MultidimArray< double > & | resolutionChimera, | ||
double & | cut_value, | ||
MultidimArray< int > & | pMask, | ||
double & | resolutionThreshold | ||
) |
void ProgResLocalFilter::produceSideInfo | ( | ) |
Definition at line 58 of file resolution_localfilter.cpp.
|
virtual |
Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.
Reimplemented from XmippProgram.
Definition at line 31 of file resolution_localfilter.cpp.
void ProgResLocalFilter::resolution2eval | ( | int & | count_res, |
double | step, | ||
double & | resolution, | ||
double & | last_resolution, | ||
double & | freq, | ||
double & | freqL, | ||
int & | last_fourier_idx, | ||
bool & | continueIter, | ||
bool & | breakIter, | ||
bool & | doNextIteration | ||
) |
|
virtual |
This function will be start running the program. it also should be implemented by derived classes.
Reimplemented from XmippProgram.
Definition at line 207 of file resolution_localfilter.cpp.
bool ProgResLocalFilter::automaticMode |
Definition at line 65 of file resolution_localfilter.h.
MultidimArray< std::complex<double> > ProgResLocalFilter::fftV |
Definition at line 94 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnchim |
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnFilt |
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnMask |
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnMaskOut |
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnMd |
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnMeanVol |
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnOut |
Filenames
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnRes |
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnSpatial |
Definition at line 52 of file resolution_localfilter.h.
FileName ProgResLocalFilter::fnVol |
Definition at line 52 of file resolution_localfilter.h.
Matrix1D<double> ProgResLocalFilter::freq_fourier |
Definition at line 97 of file resolution_localfilter.h.
double ProgResLocalFilter::freq_step |
Step in digital frequency
Definition at line 62 of file resolution_localfilter.h.
MultidimArray<double> ProgResLocalFilter::iu |
Definition at line 93 of file resolution_localfilter.h.
double ProgResLocalFilter::maxRes |
Definition at line 56 of file resolution_localfilter.h.
double ProgResLocalFilter::minRes |
Definition at line 56 of file resolution_localfilter.h.
bool ProgResLocalFilter::noiseOnlyInHalves |
The search for resolutions is linear or inverse
Definition at line 65 of file resolution_localfilter.h.
int ProgResLocalFilter::nthrs |
Definition at line 59 of file resolution_localfilter.h.
int ProgResLocalFilter::Nvoxels |
Definition at line 59 of file resolution_localfilter.h.
int ProgResLocalFilter::NVoxelsOriginalMask |
Is the volume previously masked?
Definition at line 59 of file resolution_localfilter.h.
double ProgResLocalFilter::R |
Definition at line 56 of file resolution_localfilter.h.
Image<double> ProgResLocalFilter::resVol |
Definition at line 96 of file resolution_localfilter.h.
double ProgResLocalFilter::sampling |
sampling rate, minimum resolution, and maximum resolution
Definition at line 56 of file resolution_localfilter.h.
double ProgResLocalFilter::sigma |
Definition at line 98 of file resolution_localfilter.h.
double ProgResLocalFilter::significance |
Definition at line 62 of file resolution_localfilter.h.
FourierTransformer ProgResLocalFilter::transformer_inv |
Definition at line 95 of file resolution_localfilter.h.
double ProgResLocalFilter::trimBound |
Definition at line 62 of file resolution_localfilter.h.
Image<double> ProgResLocalFilter::Vfiltered |
Definition at line 96 of file resolution_localfilter.h.
Image<double> ProgResLocalFilter::VresolutionFiltered |
Definition at line 96 of file resolution_localfilter.h.