Xmipp
v3.23.11-Nereus
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Public Member Functions | |
void | defineParams () |
void | readParams () |
void | read (int argc, char **argv, bool reportErrors=true) |
void | showProgress () |
void | preProcess () |
void | startProcessing () |
virtual bool | getImageToProcess (size_t &objId, size_t &objIndex) override |
void | finishProcessing () |
void | checkPoint () |
For very long programs, it may be needed to write checkpoints. More... | |
void | wait () |
Wait for the distributor to finish. More... | |
Public Member Functions inherited from ProgForwardZernikeImagesPriors | |
ProgForwardZernikeImagesPriors () | |
Empty constructor. More... | |
~ProgForwardZernikeImagesPriors () | |
Destructor. More... | |
void | readParams () |
Read argument from command line. More... | |
void | show () |
Show. More... | |
void | defineParams () |
Define parameters. More... | |
void | preProcess () |
void | processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut) |
void | numCoefficients (int l1, int l2, int &vecSize) |
Length of coefficients vector. More... | |
void | minimizepos (Matrix1D< double > &steps) |
Determine the positions to be minimize of a vector containing spherical harmonic coefficients. More... | |
void | fillVectorTerms (int l1, int l2, Matrix1D< int > &vL1, Matrix1D< int > &vN, Matrix1D< int > &vL2, Matrix1D< int > &vM) |
Zernike and SPH coefficients allocation. More... | |
void | deformVol (MultidimArray< double > &mVD, const MultidimArray< double > &mV, double &def, double rot, double tilt, double psi) |
Deform a volumen using Zernike-Spherical harmonic basis. More... | |
void | updateCTFImage (double defocusU, double defocusV, double angle) |
double | transformImageSph (double *pc_priors) |
virtual void | writeImageParameters (MDRow &row) |
Matrix1D< double > | weightsInterpolation3D (double x, double y, double z) |
void | splattingAtPos (std::array< double, 3 > r, double weight, MultidimArray< double > &mP, const MultidimArray< double > &mV) |
std::vector< double > | string2vector (std::string const &s) const |
void | linearCombinationClnm () |
void | optimalPowellOrder () |
double | bspline1 (double x) |
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 | 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 |
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 ¶m, int verb=2) |
int | version () const |
virtual void | read (int argc, const char **argv, bool reportErrors=true) |
void | read (const String &argumentsLine) |
XmippProgram () | |
XmippProgram (int argc, const char **argv) | |
virtual | ~XmippProgram () |
Public Member Functions inherited from MpiMetadataProgram | |
MpiMetadataProgram () | |
MpiMetadataProgram (const MpiMetadataProgram &)=delete | |
MpiMetadataProgram (const MpiMetadataProgram &&)=delete | |
~MpiMetadataProgram () | |
MpiMetadataProgram & | operator= (const MpiMetadataProgram &)=delete |
MpiMetadataProgram & | operator= (const MpiMetadataProgram &&)=delete |
void | read (int argc, char **argv) |
void | defineParams () |
void | readParams () |
void | createTaskDistributor (MetaData &mdIn, size_t blockSize=0) |
bool | getTaskToProcess (size_t &objId, size_t &objIndex) |
Public Member Functions inherited from XmippMpiProgram | |
void | read (int argc, char **argv) |
virtual int | tryRun () |
Additional Inherited Members | |
Public Types inherited from ProgForwardZernikeImagesPriors | |
enum | Direction { Direction::ROTATE, Direction::UNROTATE } |
Public Attributes inherited from ProgForwardZernikeImagesPriors | |
FileName | fnVolR |
FileName | fnMaskR |
FileName | fnPriors |
FileName | fnOutDir |
Output directory. More... | |
int | L1 |
int | L2 |
Matrix1D< int > | vL1 |
Matrix1D< int > | vN |
Matrix1D< int > | vL2 |
Matrix1D< int > | vM |
double | maxShift |
double | maxAngularChange |
double | maxResol |
double | Ts |
int | Rmax |
bool | optimizeAlignment |
bool | optimizeDefocus |
bool | ignoreCTF |
bool | optimizeRadius |
bool | phaseFlipped |
double | lambda |
int | RmaxDef |
int | num_images |
int | algn_params |
int | ctf_params |
Matrix1D< double > | p |
int | flagEnabled |
int | image_mode |
bool | useCTF |
bool | resume |
MultidimArray< int > | mask2D |
MultidimArray< int > | V_mask |
std::vector< std::vector< double > > | priors |
size_t | Xdim |
std::vector< FileName > | fnImage |
Image< double > | V |
Image< double > | Vdeformed |
std::vector< Image< double > > | I |
std::vector< Image< double > > | Ifiltered |
std::vector< Image< double > > | Ifilteredp |
std::vector< Image< double > > | P |
FourierFilter | filter |
Matrix2D< double > | A1 |
Matrix2D< double > | A2 |
Matrix2D< double > | A3 |
std::vector< double > | old_rot |
std::vector< double > | old_tilt |
std::vector< double > | old_psi |
std::vector< double > | deltaRot |
std::vector< double > | deltaTilt |
std::vector< double > | deltaPsi |
std::vector< double > | old_shiftX |
std::vector< double > | old_shiftY |
std::vector< double > | deltaX |
std::vector< double > | deltaY |
bool | old_flip |
bool | hasCTF |
std::vector< double > | old_defocusU |
std::vector< double > | old_defocusV |
std::vector< double > | old_defocusAngle |
std::vector< double > | deltaDefocusU |
std::vector< double > | deltaDefocusV |
std::vector< double > | deltaDefocusAngle |
std::vector< double > | currentDefocusU |
std::vector< double > | currentDefocusV |
std::vector< double > | currentAngle |
FourierFilter | FilterCTF1 |
FourierFilter | FilterCTF2 |
FourierFilter | FilterCTF3 |
int | vecSize |
Matrix1D< double > | c_priors |
Matrix1D< double > | clnm |
Matrix1D< double > | steps_cp |
double | totalDeformation |
double | prior_deformation |
std::vector< double > | prior_deformations |
bool | showOptimization |
double | correlation |
int | loop_step |
struct blobtype | blob |
double | blob_r |
bool | do_not_init |
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 inherited from ProgForwardZernikeImagesPriors | |
void | createWorkFiles () |
Protected Member Functions inherited from XmippMetadataProgram | |
virtual void | initComments () |
virtual void | postProcess () |
void | show () const override |
virtual void | writeOutput () |
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) |
Protected Member Functions inherited from XmippMpiProgram | |
void | setNode (const std::shared_ptr< MpiNode > &node) |
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 |
Protected Attributes inherited from MpiMetadataProgram | |
int | blockSize |
std::vector< size_t > | imgsId |
MpiTaskDistributor * | distributor =nullptr |
size_t | first |
size_t | last |
Protected Attributes inherited from XmippMpiProgram | |
std::shared_ptr< MpiNode > | node |
size_t | nProcs |
size_t | numberOfJobs |
MPI_Status | status |
Definition at line 31 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
For very long programs, it may be needed to write checkpoints.
Reimplemented from ProgForwardZernikeImagesPriors.
Definition at line 117 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
Function in which the param of each Program are defined.
Reimplemented from XmippMetadataProgram.
Definition at line 40 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
finishProcessing
Reimplemented from MpiMetadataProgram.
Definition at line 106 of file mpi_forward_zernike_images_priors.cpp.
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inlineoverridevirtual |
Reimplemented from XmippMetadataProgram.
Definition at line 88 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
Preprocess
Reimplemented from MpiMetadataProgram.
Definition at line 65 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
Read the command line arguments A convenience wrapper
Reimplemented from XmippProgram.
Definition at line 50 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.
Reimplemented from XmippMetadataProgram.
Definition at line 45 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
Reimplemented from XmippMetadataProgram.
Definition at line 57 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
Do some stuff before starting processing in a parallel environment usually this only be executed by master.
Reimplemented from XmippMetadataProgram.
Definition at line 79 of file mpi_forward_zernike_images_priors.cpp.
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inlinevirtual |
Wait for the distributor to finish.
Reimplemented from XmippMetadataProgram.
Definition at line 124 of file mpi_forward_zernike_images_priors.cpp.