Xmipp
v3.23.11-Nereus
|
Classes | |
struct | mdBuffer |
struct | mdBlock |
class | ObjectDoesNotExist |
class | NotImplemented |
class | ColumnDoesNotExist |
class | MetaData |
class | MDLabelData |
class | MDSql |
class | MDCache |
class | MDSqlStaticInit |
Macros | |
#define | BAD_OBJID 0 |
#define | BAD_INDEX -1 |
#define | FILENAME_XMIPP_STAR "# XMIPP_STAR_1" |
#define | FILENAME_XMIPP_SQLITE "SQLite format 3" |
#define | DEFAULT_BLOCK_NAME "noname" |
#define | FOR_ALL_OBJECTS_IN_METADATA(__md) for (size_t objId : __md.ids()) |
#define | FOR_ALL_ROWS_IN_METADATA(__md) for (auto& row : __md) |
#define | END_OF_LINE() ((char*) memchr (iter, '\n', end-iter)) |
#define | BUFFER_CREATE(b) mdBuffer b; b.begin = nullptr; b.size = 0 |
Some macros to use the buffer. More... | |
#define | BUFFER_COPY(b1, b2) mdBuffer b2; b2.begin = b1.begin; b2.size = b1.size |
#define | BUFFER_MOVE(b, n) b.begin += n; b.size -= n |
#define | BUFFER_FIND(b, str, n) (char*) _memmem(b.begin, b.size, str, n) |
#define | BLOCK_CREATE(b) mdBlock b; b.begin = b.end = b.loop = nullptr; b.nameSize = 0 |
Some macros to use the block pointers. More... | |
#define | BLOCK_INIT(b) b.begin = b.end = b.loop = nullptr; b.nameSize = 0 |
#define | BLOCK_NAME(b, s) s.assign(b.begin, b.nameSize) |
#define | FOR_ALL_LABELS() for (int _label = MDL_FIRST_LABEL; _label < MDL_LAST_LABEL; ++_label) |
Typedefs | |
typedef std::vector< MDLabel > | MDLabelVector |
Functions | |
void | getBlocksInMetaDataFile (const FileName &inFile, StringVector &blockList) |
bool | existsBlockInMetaDataFile (const FileName &inFile, const String &inBlock) |
bool | existsBlockInMetaDataFile (const FileName &inFileWithBlock) |
std::ostream & | operator<< (std::ostream &o, const MetaData &mD) |
bool | vectorContainsLabel (const std::vector< MDLabel > &labelsVector, const MDLabel label) |
MDLabelData::MDLabelData () | |
MDLabelData::MDLabelData (MDLabelType t, const String &s, int tags) | |
int | getBlocksInMetaDataFileDB (const FileName &inFile, StringVector &blockList) |
void | sqlite_regexp (sqlite3_context *context, int argc, sqlite3_value **values) |
static void | MDSql::dumpToFile (const FileName &fileName) |
static void | MDSql::sqlTimeOut (int miliSeconds) |
static bool | MDSql::activateMathExtensions (void) |
static bool | MDSql::activateRegExtensions (void) |
bool | MDSql::deactivateThreadMuting (void) |
bool | MDSql::activateThreadMuting (void) |
MDCache::MDCache () | |
MDCache::~MDCache () | |
void | MDCache::clear () |
Variables | |
MDLabelType | MDLabelData::type |
String | MDLabelData::str |
int | MDLabelData::tags |
sqlite3_stmt * | MDCache::iterStmt |
std::map< MDLabel, sqlite3_stmt * > | MDCache::getValueCache |
std::map< MDLabel, sqlite3_stmt * > | MDCache::setValueCache |
sqlite3_stmt * | MDCache::addRowStmt |
Friends | |
class | MDSql::MDSqlStaticInit |
class | MDSql::MetaDataDb |
class | MDSql::MDIterator |
class | MDSqlStaticInit::MDSql |
This file defines abstract class MetaData which defines an API for all MetaData implementations.
#define BAD_INDEX -1 |
Definition at line 56 of file metadata_base.h.
#define BAD_OBJID 0 |
Definition at line 55 of file metadata_base.h.
Some macros to use the block pointers.
Definition at line 101 of file metadata_base.h.
#define BLOCK_INIT | ( | b | ) | b.begin = b.end = b.loop = nullptr; b.nameSize = 0 |
Definition at line 102 of file metadata_base.h.
#define BLOCK_NAME | ( | b, | |
s | |||
) | s.assign(b.begin, b.nameSize) |
Definition at line 103 of file metadata_base.h.
#define BUFFER_COPY | ( | b1, | |
b2 | |||
) | mdBuffer b2; b2.begin = b1.begin; b2.size = b1.size |
Definition at line 89 of file metadata_base.h.
Some macros to use the buffer.
Definition at line 88 of file metadata_base.h.
Definition at line 91 of file metadata_base.h.
Definition at line 90 of file metadata_base.h.
#define DEFAULT_BLOCK_NAME "noname" |
Definition at line 60 of file metadata_base.h.
Definition at line 69 of file metadata_base.h.
#define FILENAME_XMIPP_SQLITE "SQLite format 3" |
Definition at line 59 of file metadata_base.h.
#define FILENAME_XMIPP_STAR "# XMIPP_STAR_1" |
Definition at line 58 of file metadata_base.h.
#define FOR_ALL_LABELS | ( | ) | for (int _label = MDL_FIRST_LABEL; _label < MDL_LAST_LABEL; ++_label) |
Macro for iterate over all labels
Definition at line 944 of file metadata_label.h.
#define FOR_ALL_OBJECTS_IN_METADATA | ( | __md | ) | for (size_t objId : __md.ids()) |
Definition at line 64 of file metadata_base.h.
#define FOR_ALL_ROWS_IN_METADATA | ( | __md | ) | for (auto& row : __md) |
Definition at line 67 of file metadata_base.h.
typedef std::vector<MDLabel> MDLabelVector |
Definition at line 941 of file metadata_label.h.
enum MDLabel |
Enumerate all posible labels to use in MetaData.
Enumerator | |
---|---|
MDL_UNDEFINED | |
MDL_FIRST_LABEL | The label MDL_OBJID is special and should not be used. |
MDL_OBJID | object id (int), NOTE: This label is special and shouldn't be used |
MDL_GATHER_ID | |
MDL_ANGLE_PSI | Special label to be used when gathering MDs in MpiMetadataPrograms. Psi angle of an image (double,degrees) |
MDL_ANGLE_PSI2 | Psi angle of an image (double,degrees) |
MDL_ANGLE_PSI3 | Psi angle of an image (double,degrees) |
MDL_ANGLE_PSI_DIFF | difference between psi angles (double,degrees) |
MDL_ANGLE_ROT | Rotation angle of an image (double,degrees) |
MDL_ANGLE_ROT2 | Rotation angle of an image (double,degrees) |
MDL_ANGLE_ROT3 | Rotation angle of an image (double,degrees) |
MDL_ANGLE_ROT_DIFF | difference between rot angles (double,degrees) |
MDL_ANGLE_TILT | Tilting angle of an image (double,degrees) |
MDL_ANGLE_TILT2 | Tilting angle of an image (double,degrees) |
MDL_ANGLE_TILT3 | Tilting angle of an image (double,degrees) |
MDL_ANGLE_TILT_DIFF | difference between tilt angles (double,degrees) |
MDL_ANGLE_DIFF0 | difference between two angles (double,degrees) |
MDL_ANGLE_DIFF | difference between two angles (double,degrees) |
MDL_ANGLE_DIFF2 | difference between two angles (double,degrees) |
MDL_ANGLE_Y | Angle between y-axis and tilt-axis (double, degrees) for untilted micrographs. |
MDL_ANGLE_Y2 | Angle between y-axis and tilt-axis (double, degrees) for tilted micrographs. |
MDL_ANGLE_TEMPERATURE | Angular temperature (double,degrees) |
MDL_APPLY_SHIFT | Apply shift when project the volume ,. |
MDL_AVG | average value (double) |
MDL_AVG_CHANGES_ORIENTATIONS | |
MDL_AVG_CHANGES_OFFSETS | Average change in angular orientation (double degrees) |
MDL_AVG_CHANGES_CLASSES | Average change in offset (double pixels) |
MDL_AVGPMAX | Average change in class assignment(double dimensionaless) Average (per class) of the maximum value of normalized probability function) (double) |
MDL_BFACTOR | |
MDL_BGMEAN | <Bfactor of a map, or even a local bfactor Mean background value for an image |
MDL_BLOCK_NUMBER | Current block number (for incremental EM) |
MDL_CL2D_CHANGES | Number of changes between iterations. |
MDL_CL2D_SIMILARITY | Average cross-correlation for the image (double) |
MDL_CLASS_COUNT | Number of images assigned to the same class as this image. |
MDL_CLASS_PERCENTAGE | Percentage of images assigned to the same class as this image. |
MDL_CLASSIFICATION_DATA | Data vector for classification (vector double) |
MDL_CLASSIFICATION_DATA_SIZE | Size of data vectors for classification (int) |
MDL_CLASSIFICATION_DPR_05 | Differential Phase Residual evaluated at FRC=0.5. |
MDL_CLASSIFICATION_INTRACLASS_DISTANCE | Average intraclass distance (double) |
MDL_CLASSIFICATION_FRC_05 | Digital frequency at which the FRC drops below 0.5 (double) |
MDL_COMMENT | Serve to make annotations on the metadata row. |
MDL_COORD_CONSENSUS_SCORE | Store a score for the coords. consensus (it will change the behavoir of the viewer) |
MDL_COST | Cost for the image (double) |
MDL_COST_PERCENTILE | Cost percentile for the image (double) |
MDL_COUNT | Number of elements of a type (int) [this is a genereic type do not use to transfer information to another program]. |
MDL_COUNT2 | Number of elements of a type (int) [this is a genereic type do not use to transfer information to another program]. |
MDL_CORR_DENOISED_PROJECTION | Correlation between the denoised image and the projection proposed. |
MDL_CORR_DENOISED_NOISY | Correlation between the denoised image and the noisy version. |
MDL_CLASS_INTERSECTION_SIZE_PVALUE | P-value (1-percentile) of the class size compared to a random distribution (double in [0, 1]) |
MDL_CLASS_INTERSECTION_RELATIVE_SIZE_PVALUE | P-value (1-percentile) of the relative class size (size/max(original_classes)) compared to a random distribution (double in [0, 1]) |
MDL_CRYSTAL_CELLX | Cell location for crystals. |
MDL_CRYSTAL_CELLY | Cell location for crystals. |
MDL_CRYSTAL_LATTICE_A | |
MDL_CRYSTAL_LATTICE_B | < Lattice vector for projection (vector double) |
MDL_CRYSTAL_DISAPPEAR_THRE | < Lattice vector for projection (vector double) |
MDL_CRYSTAL_SHFILE | < Disappearing threshold (double) |
MDL_CRYSTAL_ORTHO_PRJ | < Shift file for crystal projection |
MDL_CRYSTAL_PROJ | <Orthogonal projection or not (bool) |
MDL_CRYSTAL_SHIFTX | < Have a crystal projection (bool) Shift for the image in the X axis (double) for crystals |
MDL_CRYSTAL_SHIFTY | Shift for the image in the Y axis (double) for crystals. |
MDL_CRYSTAL_SHIFTZ | Shift for the image in the Z axis (double) for crystals. |
MDL_CRYSTAL_NOISE_SHIFT | noise if center of unit cell (vector double) |
MDL_CONTINUOUS_X | X shift of continuous assignment. |
MDL_CONTINUOUS_Y | Y shift of continuous assignment. |
MDL_CONTINUOUS_FLIP | Flip of continuous assignment. |
MDL_CONTINUOUS_GRAY_A | a value of continuous assignment |
MDL_CONTINUOUS_GRAY_B | b value of continuous assignment |
MDL_CONTINUOUS_SCALE_ANGLE | scale angle of continuous assignment |
MDL_CONTINUOUS_SCALE_X | scale x of continuous assignment |
MDL_CONTINUOUS_SCALE_Y | scale y of continuous assignment |
MDL_CORRELATION_IDX | correlation value between a particle and its assigned projection |
MDL_CORRELATION_MASK | masked correlation value between a particle and its assigned projection inside the region with pixel values higher than the standard deviation |
MDL_CORRELATION_WEIGHT | weighted correlation value between a particle and its assigned projection taking into the difference between both images |
MDL_CTF_DATA_PHASE_FLIPPED | |
MDL_CTF_CORRECTED | |
MDL_CTF_INPUTPARAMS | Parameters file for the CTF Model (std::string) |
MDL_CTF_MODEL | Name for the CTF Model (std::string) |
MDL_CTF_MODEL2 | Name for another CTF model (std::string) |
MDL_CTF_SAMPLING_RATE | Sampling rate. |
MDL_CTF_SAMPLING_RATE_Z | Sampling rate in Z direction. |
MDL_CTF_VOLTAGE | Microscope voltage (kV) |
MDL_CTF_DEFOCUSA | average defocus (Angtroms) |
MDL_CTF_DEFOCUSU | Defocus U (Angstroms) |
MDL_CTF_DEFOCUSV | Defocus V (Angstroms) |
MDL_CTF_DEFOCUS_CHANGE | Defocus change with respect to previous defoucs (Angstroms) |
MDL_CTF_DEFOCUS_R2 | Defocus coefficient of determination. |
MDL_CTF_DEFOCUS_COEFS | Coefficients of the defocus adjustment plane. |
MDL_CTF_DEFOCUS_RESIDUAL | Difference between the observed defocus value and the estimated defocus value. |
MDL_CTF_X0 | The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates. |
MDL_CTF_Y0 | The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates. |
MDL_CTF_XF | The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates. |
MDL_CTF_YF | The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates. |
MDL_CTF_DEFOCUS_PLANEUA | Defocus = A*x+B*y+C. |
MDL_CTF_DEFOCUS_PLANEUB | Defocus = A*x+B*y+C. |
MDL_CTF_DEFOCUS_PLANEUC | Defocus = A*x+B*y+C. |
MDL_CTF_DEFOCUS_PLANEVA | Defocus = A*x+B*y+C. |
MDL_CTF_DEFOCUS_PLANEVB | Defocus = A*x+B*y+C. |
MDL_CTF_DEFOCUS_PLANEVC | Defocus = A*x+B*y+C. |
MDL_CTF_DEFOCUS_ANGLE | Defocus angle (degrees) |
MDL_CTF_CS | Spherical aberration. |
MDL_CTF_CA | Chromatic aberration. |
MDL_CTF_GROUP | group images by defocus |
MDL_CTF_ENERGY_LOSS | Energy loss. |
MDL_CTF_ENVELOPE | |
MDL_CTF_ENVELOPE_PLOT | |
MDL_CTF_LENS_STABILITY | Lens stability. |
MDL_CTF_CONVERGENCE_CONE | Convergence cone. |
MDL_CTF_LONGITUDINAL_DISPLACEMENT | Longitudinal displacement. |
MDL_CTF_TRANSVERSAL_DISPLACEMENT | Transversal displacemente. |
MDL_CTF_Q0 | Inelastic absorption. |
MDL_CTF_K | CTF gain. |
MDL_CTF_ENV_R0 | CTF Envelope polynomial parameter. |
MDL_CTF_ENV_R1 | CTF Envelope polynomial parameter. |
MDL_CTF_ENV_R2 | CTF Envelope polynomial parameter. |
MDL_CTF_BG_GAUSSIAN_K | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN_SIGMAU | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN_SIGMAV | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN_CU | CTF_ CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN_CV | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN_ANGLE | CTF Background parameter. |
MDL_CTF_BG_SQRT_K | CTF Background parameter. |
MDL_CTF_BG_SQRT_U | CTF Background parameter. |
MDL_CTF_BG_SQRT_V | CTF Background parameter. |
MDL_CTF_BG_SQRT_ANGLE | CTF Background parameter. |
MDL_CTF_BG_BASELINE | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN2_K | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN2_SIGMAU | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN2_SIGMAV | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN2_CU | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN2_CV | CTF Background parameter. |
MDL_CTF_BG_GAUSSIAN2_ANGLE | CTF Background parameter. |
MDL_CTF_BG_R1 | CTF Background polynomial parameter. |
MDL_CTF_BG_R2 | CTF Background polynomial parameter. |
MDL_CTF_BG_R3 | CTF Background polynomial parameter. |
MDL_CTF_CRIT_NONASTIGMATICVALIDITY | Maximum frequency (in Angstroms) at which non-astigmatic CTF correction is valid. |
MDL_CTF_CRIT_PSDCORRELATION90 | PSD correlation at 90 degrees. |
MDL_CTF_CRIT_FIRSTZERORATIO | First zero ratio. |
MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_RATIO | Ratio sigma(firstMinimum)/sigma(firstZero) |
MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_DIFF_RATIO | Ratio sigma(firstMinimum-firstZero)/sigma(firstZero) |
MDL_CTF_CRIT_FIRSTZEROAVG | First zero average (in Angstroms) |
MDL_CTF_CRIT_FIRSTZERODISAGREEMENT | First zero disagreement with second model (in Angstroms) |
MDL_CTF_CRIT_MAXFREQ | Maximum frequency at which the envelope drops below 0.1 (in Angstroms) |
MDL_CTF_CRIT_DAMPING | Minimum damping at border. |
MDL_CTF_CRIT_PSDRADIALINTEGRAL | Integral of the radial PSD. |
MDL_CTF_CRIT_FITTINGSCORE | Score of the fitting. |
MDL_CTF_CRIT_FITTINGCORR13 | Correlation between the 1st and 3rd ring of the CTF. |
MDL_CTF_CRIT_PSDVARIANCE | PSD variance. |
MDL_CTF_CRIT_PSDPCA1VARIANCE | Variance in the first principal component of the PSDs. |
MDL_CTF_CRIT_PSDPCARUNSTEST | Runs test on the projection of the PSD on the first principal component. |
MDL_CTF_CRIT_NORMALITY | Normality test between histogram of micrography and gaussian distribution. |
MDL_CTF_CRIT_ICENESS | Iceness of the micrograph. |
MDL_CTF_DOWNSAMPLE_PERFORMED | Downsampling performed to estimate the CTF. |
MDL_CTF_DIMENSIONS | |
MDL_CTF_LAMBDA | |
MDL_CTF_XRAY_LENS_TYPE | Wavelength (nm) |
MDL_CTF_XRAY_OUTER_ZONE_WIDTH | Algorithm used to generate Xray PSF. |
MDL_CTF_XRAY_ZONES_NUMBER | Outermost zone width of the X-ray Fresnel lens (nm) |
MDL_CTF_PHASE_SHIFT | |
MDL_CTF_VPP_RADIUS | |
MDL_CUMULATIVE_SSNR | Cumulative SSNR (double) |
MDL_DATATYPE | if read from file original image datatype, this is an struct defined in image |
MDL_DEFGROUP | Defocus group. |
MDL_DIMRED | Projection onto a reduced manifold (vector double) |
MDL_DIRECTION | Direction in 3D. |
MDL_DM3_IDTAG | |
MDL_DM3_NODEID | |
MDL_DM3_NUMBER_TYPE | |
MDL_DM3_PARENTID | |
MDL_DM3_TAGCLASS | |
MDL_DM3_TAGNAME | |
MDL_DM3_SIZE | |
MDL_DM3_VALUE | |
MDL_DOSE | Dose e/A^2 (double) |
MDL_ENABLED | Is this image enabled? (int [-1 or 1]) |
MDL_DATE | |
MDL_TIME | |
MDL_FLIP | Flip the image? (bool) |
MDL_FOM | Figure of Merit in 0-1 range (double) |
MDL_FRAME_ID | Unique id of frame inside a Movie. |
MDL_GRAPH_DISTANCE2MAX | Distance to graph filtered max. |
MDL_GRAPH_DISTANCE2MAX_PREVIOUS | when previous assignment validation |
MDL_GRAPH_CC | Correlation between assigned direction and graph filtered maximum. |
MDL_GRAPH_CC_PREVIOUS | when previous assignment validation |
MDL_HALF1 | Half map/image 1 file name (string) |
MDL_HALF2 | Half map/image file name (string) |
MDL_IDX | Index within a list (size_t) |
MDL_IMAGE | Name of an image (std::string) |
MDL_IMAGE_COVARIANCE | Name of the covariance imagee associated to this image. |
MDL_IMAGE_IDX | Index of an image within a list (size_t) |
MDL_IMAGE_ORIGINAL | Name of an image from which MDL_IMAGE is coming from. |
MDL_IMAGE_REF | Name of of the class image from which MDL_IMAGE is coming from. |
MDL_IMAGE_RESIDUAL | Name of a residual image associated to this image. |
MDL_IMAGE_TILTED | Name of the tilted images associated to MDL_IMAGE. |
MDL_IMED | imed value between a particle and its assigned projection |
MDL_IMGMD | Name of Metadata file for all images (string) |
MDL_IMAGE1 | Image associated to this object (std::string) |
MDL_IMAGE2 | Image associated to this object (std::string) |
MDL_IMAGE3 | Image associated to this object (std::string) |
MDL_IMAGE4 | Image associated to this object (std::string) |
MDL_IMAGE5 | Image associated to this object (std::string) |
MDL_INTSCALE | Intensity scale for an image. |
MDL_ITEM_ID | Unique identifier for items inside a list or set (std::size_t) |
MDL_ITER | Current iteration number (int) |
MDL_KERDENSOM_FUNCTIONAL | Functional value (double) |
MDL_KERDENSOM_REGULARIZATION | Regularization value (double) |
MDL_KERDENSOM_SIGMA | Sigma value (double) |
MDL_KEYWORDS | Keywords associated to this line, should be a single string block (do not use spaces as separators) |
MDL_KMEANS2D_CENTROID | Centroid of a cluster for the KMEANS2D classification. |
MDL_KSTEST | KS-test statistics. |
MDL_LL | contribution of an image to log-likelihood value |
MDL_LOCAL_ALIGNMENT_PATCHES | Two values representing number of patches used for local alignment (X, Y) |
MDL_LOCAL_ALIGNMENT_COEFFS_X | BSpline coefficient in X dim. |
MDL_LOCAL_ALIGNMENT_COEFFS_Y | BSpline coefficient in Y dim. |
MDL_LOCAL_ALIGNMENT_CONF_2_5_PERC | A shift amount at confidence level of 2.5%. |
MDL_LOCAL_ALIGNMENT_CONF_97_5_PERC | A shift amount at confidence level of 95.5%. |
MDL_LOCAL_ALIGNMENT_CONTROL_POINTS | Three values representing number of control points used for local alignment (X, Y, N) |
MDL_MAGNIFICATION | |
MDL_MAPTOPOLOGY | Magnification of microscope. Map topology (KerDenSOM, ...) |
MDL_MASK | Name of a mask associated to image. |
MDL_MAXCC | Maximum cross-correlation for the image (double) |
MDL_MAXCC_PERCENTILE | Percentile of the maximum cross-correlation for the image (double) |
MDL_MAX | Maximum value (double) |
MDL_MAXCC_PREVIOUS | Correlation from previous alignment. |
MDL_MICROGRAPH | Name of a micrograph (std::string) |
MDL_MICROGRAPH_ID | Micrograph unique id for reference (MDL_ITEM_ID should be used for Micrographs list) |
MDL_MICROGRAPH_MOVIE | Name of a movie (std::string) |
MDL_MICROGRAPH_MOVIE_ID | Unique identifier of a movie. |
MDL_MICROGRAPH_PARTICLES | Name of a position file (std::string) |
MDL_MICROGRAPH_ORIGINAL | Name of the original micrograph, MDL_MICROGRAPH is probably a downsampled version of this one (std::string) |
MDL_MICROGRAPH_TILTED | Name of the corresponding tilted micrograph (std::string) |
MDL_MICROGRAPH_TILTED_ORIGINAL | Name of the corresponding original, tilted micrograph (std::string) |
MDL_MIN | Minimum value (double) |
MDL_MIRRORFRAC | Mirror fraction for a Maximum Likelihood model. |
MDL_MISSINGREGION_NR | Number of missing region in subtomogram. |
MDL_MISSINGREGION_TYPE | Type of missing region in subtomogram. |
MDL_MISSINGREGION_THY0 | Initial tilt angle in Y for missing region in subtomogram. |
MDL_MISSINGREGION_THYF | Final tilt angle in Y for missing region in subtomogram. |
MDL_MISSINGREGION_THX0 | Initial tilt angle in X for missing region in subtomogram. |
MDL_MISSINGREGION_THXF | Final tilt angle in X for missing region in subtomogram. |
MDL_MLF_CTF | MLF CTF estimated value (double) |
MDL_MLF_WIENER | MLF Wiener filter (double) |
MDL_MLF_SIGNAL | MLF signal (double) |
MDL_MLF_NOISE | MLF Wiener filter (double) |
MDL_MODELFRAC | Model fraction (alpha_k) for a Maximum Likelihood model. |
MDL_NEIGHBORS | Vector of indexes to points some "neighbors". |
MDL_NEIGHBOR | Particular neighbor (pointed myNEIGHBORS) |
MDL_NEIGHBORHOOD_RADIUS | Radius of the neighborhood (radians) |
MDL_NMA | Normal mode displacements (vector double) |
MDL_NMA_COLLECTIVITY | NMA Collectivity of a given mode. |
MDL_NMA_ATOMSHIFT | NMA Atom shift in Angstroms. |
MDL_NMA_ENERGY | NMA energy contained in the NMA displacement vector. |
MDL_NMA_MINRANGE | Minimum value observed for a given NMA mode. |
MDL_NMA_MAXRANGE | Maximum value observed for a given NMA mode. |
MDL_NMA_MODEFILE | File with an NMA mode. |
MDL_NMA_SCORE | NMA Score of a given mode. |
MDL_NMA_EIGENVAL | NMA Eigenvalue of a given mode. |
MDL_NOISE_ANGLES | Noise description for projected angles. |
MDL_NOISE_PARTICLE_COORD | Noise description for particle's center coordenates (when projecting) |
MDL_NOISE_COORD | |
MDL_NOISE_PIXEL_LEVEL | Noise description for pixels' gray level (when projecting) |
MDL_ORDER | |
MDL_ORIGIN_X | auxiliary label to be used as an index (long) Origin for the image in the X axis (double) |
MDL_ORIGIN_Y | Origin for the image in the Y axis (double) |
MDL_ORIGIN_Z | Origin for the image in the Z axis (double) |
MDL_OPTICALFLOW_MEANX | Mean of the movement in x direction of the motion map> (double) |
MDL_OPTICALFLOW_MEANY | Mean of the movement in y direction of the motion map> (double) |
MDL_OPTICALFLOW_STDX | Standatd deviation of the movement in x direction of the motion map> (double) |
MDL_OPTICALFLOW_STDY | Standard deviation of the movement in y direction of the motion map> (double) |
MDL_PARTICLE_ID | Particle unique identifier for reference. (The MDL_ITEM_ID should be used when particle list) |
MDL_PHANTOM_BGDENSITY | Phantom background density (double) |
MDL_PHANTOM_FEATURE_CENTER | Center of the feature (vector double) |
MDL_PHANTOM_FEATURE_DENSITY | The density of the feature (double) |
MDL_PHANTOM_FEATURE_OPERATION | Operation in case of overlapping features (+,-) |
MDL_PHANTOM_FEATURE_SPECIFIC | Specific parameters for a feature (vector double) |
MDL_PHANTOM_FEATURE_TYPE | |
MDL_PHANTOM_SCALE | Number which will multiply all features (double) |
MDL_MACRO_CMD | |
MDL_MACRO_CMD_ARGS | |
MDL_COLOR | Color for particle picking. |
MDL_PICKING_TEMPLATES | Number of templates. |
MDL_PICKING_STATE | State for particle picking. |
MDL_PICKING_MICROGRAPH_STATE | Micrograph state for particle picking. |
MDL_PICKING_AUTOPICKPERCENT | |
MDL_PICKING_PARTICLE_SIZE | Particle size for particle picking. |
MDL_PICKING_AUTOPARTICLES_SIZE | Number of automatic particles picked. |
MDL_PICKING_MANUALPARTICLES_SIZE | Number of manual particles picked. |
MDL_PMAX | Maximum value of normalized probability function (now called "Pmax/sumP") (double) |
MDL_POINTSASYMETRICUNIT | |
MDL_PRJ_DIMENSIONS | < Number of non-redundant projections directions (size_t) |
MDL_PRJ_ANGFILE | File for generated angles. |
MDL_PRJ_PSI_NOISE | |
MDL_PRJ_PSI_RANDSTR | < Psi angle dev and mean noise (vector double) |
MDL_PRJ_PSI_RANGE | < Type of randomness for Psi (std::string) |
MDL_PRJ_ROT_NOISE | < Psi angle range (vector double) |
MDL_PRJ_ROT_RANDSTR | < Rotational angle dev and mean noise (vector double) |
MDL_PRJ_ROT_RANGE | < Type of randomness for Rotational (std::string) |
MDL_PRJ_TILT_NOISE | |
MDL_PRJ_TILT_RANDSTR | < Tilt angle dev and mean noise (vector double) |
MDL_PRJ_TILT_RANGE | < Type of randomness for Tilt (std::string) |
MDL_PRJ_VOL | |
MDL_PROGRAM | |
MDL_USER | |
MDL_DIMENSIONS_3D | |
MDL_DIMENSIONS_2D | |
MDL_PSD | A Power Spectrum Density file name (std::string) |
MDL_PSD_ENHANCED | A enhanced Power Spectrum Density file name (std::string) |
MDL_RANDOMSEED | Seed for random number generator. |
MDL_REF3D | 3D Class to which the image belongs (int) |
MDL_REF | Class to which the image belongs (int) |
MDL_REF2 | Store a second class (int) |
MDL_REFMD | Name of Metadata file for all references(string) |
MDL_ASSIGNED_DIR_REF_CC | correlation of references assigned by two methods |
MDL_RESIDUE | |
MDL_RESOLUTION_ANISOTROPY | Resolution anisotropy used to store the significance of the Bingham Test (double) |
MDL_RESOLUTION_DPR | differential phase residual (double) |
MDL_RESOLUTION_ERRORL2 | Error in l2 (double) |
MDL_RESOLUTION_FRC | Fourier shell correlation (double) |
MDL_RESOLUTION_FRCRANDOMNOISE | Fourier shell correlation noise (double) |
MDL_RESOLUTION_FREQ | Frequency in 1/A (double) |
MDL_RESOLUTION_FREQ2 | Frequency in 1/A squared (double) |
MDL_RESOLUTION_FREQREAL | Frequency in A (double) |
MDL_RESOLUTION_FSO | Fourier shell occupancy (double) |
MDL_RESOLUTION_LOCAL_RESIDUE | Frequency in A of the local resolution of a residue (double) |
MDL_RESOLUTION_LOG_STRUCTURE_FACTOR | Logarithm of the structure factor. |
MDL_RESOLUTION_SSNR | Fourier shell correlation (double) |
MDL_RESOLUTION_STRUCTURE_FACTOR | Structure factor. |
MDL_RESOLUTION_RFACTOR | |
MDL_SAMPLINGRATE | rfactor sampling rate in A/pixel (double) |
MDL_SAMPLINGRATE_ORIGINAL | original sampling rate in A/pixel (double) |
MDL_SAMPLINGRATE_X | sampling rate in A/pixel (double) |
MDL_SAMPLINGRATE_Y | sampling rate in A/pixel (double) |
MDL_SAMPLINGRATE_Z | sampling rate in A/pixel (double) |
MDL_SCALE | scaling factor for an image or volume (double) |
MDL_SCORE_BY_PCA_RESIDUAL_PROJ | |
MDL_SCORE_BY_PCA_RESIDUAL_EXP | |
MDL_SCORE_BY_PCA_RESIDUAL | |
MDL_SCORE_BY_ALIGNABILITY | score by alignability (double) |
MDL_SCORE_BY_ALIGNABILITY_PRECISION | score by alignability (double) |
MDL_SCORE_BY_ALIGNABILITY_ACCURACY | score by alignability (double) |
MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXP | score by alignability experimental particles (double) |
MDL_SCORE_BY_ALIGNABILITY_PRECISION_REF | score by alignability references (double) |
MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXP | score by alignability experimental particles (double) |
MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REF | score by alignability references (double) |
MDL_SCORE_BY_ALIGNABILITY_NOISE | score by alignability noise (double) |
MDL_SCORE_BY_EMPTINESS | Small values represent worse particles. Much larger than 1 for good particles. |
MDL_SCORE_BY_ENTROPY | Feature vectors used to classify particles (vector double) |
MDL_SCORE_BY_GRANULO | Feature vectors used to classify particles (vector double) |
MDL_SCORE_BY_HISTDIST | Feature vectors used to classify particles (vector double) |
MDL_SCORE_BY_LBP | Feature vectors used to classify particles (vector double) |
MDL_SCORE_BY_MIRROR | score by mirror (double) |
MDL_SCORE_BY_RAMP | Feature vectors used to classify particles (vector double) |
MDL_SCORE_BY_SCREENING | Feature vectors used to classify particles (vector double) |
MDL_SCORE_BY_VARIANCE | Feature vectors used to classify particles (vector double) |
MDL_SCORE_BY_VAR | |
MDL_SCORE_BY_GINI | < Particle variance (double) |
MDL_SCORE_BY_ZERNIKE | < Micrographs Gini Coeff. (double) Feature vectors used to classify particles (vector double) |
MDL_SCORE_BY_ZSCORE | |
MDL_SELFILE | Name of an image (std::string) |
MDL_SERIE | A collection of micrographs, e.g. a tilt serie (std::string) |
MDL_SHIFT_X | Shift for the image in the X axis (double) |
MDL_SHIFT_X2 | Shift for the image in the X axis (double) |
MDL_SHIFT_X3 | Shift for the image in the X axis (double) |
MDL_SHIFT_X_DIFF | difference in Shift along X axis (double) |
MDL_SHIFT_Y | Shift for the image in the Y axis (double) |
MDL_SHIFT_Y2 | Shift for the image in the Y axis (double) |
MDL_SHIFT_Y3 | Shift for the image in the Y axis (double) |
MDL_SHIFT_Y_DIFF | difference in Shift along Y axis (double) |
MDL_SHIFT_Z | Shift for the image in the Z axis (double) |
MDL_SHIFT_Z2 | Shift for the image in the Z axis (double) |
MDL_SHIFT_Z3 | Shift for the image in the Z axis (double) |
MDL_SHIFT_DIFF0 | shift difference (double) |
MDL_SHIFT_DIFF | shift difference (double) |
MDL_SHIFT_DIFF2 | shift difference (double) |
MDL_SIGMANOISE | Standard deviation of the noise in ML model. |
MDL_SIGMAOFFSET | Standard deviation of the offsets in ML model. |
MDL_SIGNALCHANGE | Signal change for an image. |
MDL_SPH_COEFFICIENTS | Deformation coefficients. |
MDL_SPH_DEFORMATION | Deformation in voxels. |
MDL_SPH_TSNE_COEFF1D | |
MDL_SPH_TSNE_COEFF2D | tsne coefficicient in 1D |
MDL_STDDEV | tsne coefficients in 2D stdandard deviation value (double) |
MDL_STAR_COMMENT | A comment for this object /*** NOTE THIS IS A SPECIAL CASE AND SO IS TREATED ***/. |
MDL_SUBTRACTION_R2 | R2 coefficient of subtracted particle. |
MDL_SUBTRACTION_BETA0 | Beta 0 coefficient of adjusted model for subtract particle. |
MDL_SUBTRACTION_BETA1 | Beta 1 coefficient of adjusted model for subtract particle. |
MDL_SUM | Sum of elements of a given type (double) [this is a genereic type do not use to transfer information to another program]. |
MDL_SUMWEIGHT | Sum of all weights in ML model. |
MDL_SYMNO | Symmetry number for a projection (used in ART) |
MDL_TOMOGRAM_VOLUME | Name for the reconstructed tomogram volume (std::string) |
MDL_TOMOGRAMMD | Name for a Metadata file (std::string) |
MDL_TRANSFORM_MATRIX | transformation matrix in numpy string format or space separated (std::string) |
MDL_TSID | Tilt series id (std::string) |
MDL_TEST_SIZE | |
MDL_TILT_ANALYSIS_MEAN | |
MDL_TILT_ANALYSIS_STD | |
MDL_TILT_ANALYSIS_MIN | |
MDL_TILT_ANALYSIS_MAX | |
MDL_TILT_ANALYSIS_PSDs | |
MDL_VOLUME_SCORE_SUM | |
MDL_VOLUME_SCORE_SUM_TH | < Score corresponding to the sum of cc with cc>threshold Score corresponding to the sum of cc-threshold with cc>threshold |
MDL_VOLUME_SCORE_MEAN | Score corresponding to the mean of cc with cc>threshold. |
MDL_VOLUME_SCORE_MIN | Score corresponding to the min of cc with cc>threshold. |
MDL_VOLUME_SCORE1 | |
MDL_VOLUME_SCORE2 | < Score 1 for volumes |
MDL_VOLUME_SCORE3 | < Score 2 for volumes |
MDL_VOLUME_SCORE4 | < Score 3 for volumes |
MDL_WEIGHT | < Score 4 for volumes Weight assigned to the image (double) |
MDL_WEIGHT_P | Weight assigned to the image accordint to its clusterability with a significance with respect noise (double) |
MDL_WEIGHT_CONTINUOUS2 | Weight due to angular continuous assignment. |
MDL_WEIGHT_JUMPER0 | Weight due to angular jumping. |
MDL_WEIGHT_JUMPER | Weight due to angular jumping. |
MDL_WEIGHT_JUMPER2 | Weight due to angular jumping. |
MDL_WEIGHT_REALCORR | Weight due correlation between two images/subtomos. |
MDL_WEIGHT_PHASECORR | Weight due phase correlation between two images/subtomos. |
MDL_WEIGHT_SIGNIFICANT | Weight due to Angular significance. |
MDL_WEIGHT_SSNR | Weight due to SSNR. |
MDL_WEIGHT_PRECISION_ALIGNABILITY | Weight due to Alignability Precision. |
MDL_WEIGHT_ALIGNABILITY | Weight due to Alignability Precision and Accuracy. |
MDL_WEIGHT_ACCURACY_ALIGNABILITY | Weight due to Alignability Accuracy. |
MDL_WEIGHT_PRECISION_MIRROR | Weight due to Mirror Precision. |
MDL_WROBUST | Weight of t-student distribution in robust Maximum likelihood. |
MDL_X | X component (double) |
MDL_XCOOR | X component (int) |
MDL_XCOOR_TILT | X component in tilted micrograph (int) |
MDL_XSIZE | X size (int) |
MDL_Y | Y component (double) |
MDL_YCOOR | Y component (int) |
MDL_YCOOR_TILT | Y component in tilted micrograph (int) |
MDL_YSIZE | Y size (int) |
MDL_Z | Z component (double) |
MDL_ZCOOR | Z component (int) |
MDL_ZSCORE | Global Z Score (double) |
MDL_ZSCORE_DEEPLEARNING1 | Z Score (double) |
MDL_GOOD_REGION_SCORE | Z Score (double) |
MDL_ZSCORE_HISTOGRAM | Z Score (double) |
MDL_ZSCORE_RESMEAN | Z Score of the mean of the residuals (double) |
MDL_ZSCORE_RESVAR | Z Score of the stddev of the residuals (double) |
MDL_ZSCORE_RESCOV | Z Score of the covariance matrix of the residuals (double) |
MDL_ZSCORE_SHAPE1 | Z Score (double) |
MDL_ZSCORE_SHAPE2 | Z Score (double) |
MDL_ZSCORE_SNR1 | Z Score (double) |
MDL_ZSCORE_SNR2 | Z Score (double) |
MDL_ZSIZE | Z size (int) |
RLN_AREA_ID | ID for the area (or field of view). If one does not use (tilt) series, area would be the same as micrograph... RELION labels |
RLN_AREA_NAME | Name for the area (or field of view). If one does not use (tilt) series, area would be the same as micrograph... |
RLN_COMMENT | |
RLN_CTF_BFACTOR | B-factor. |
RLN_CTF_SCALEFACTOR | linear scale-factor |
RLN_CTF_SAMPLING_RATE | Sampling rate. |
RLN_CTF_VOLTAGE | Microscope voltage (kV) |
RLN_CTF_DEFOCUSU | Defocus U (Angstroms) |
RLN_CTF_DEFOCUSV | Defocus V (Angstroms) |
RLN_CTF_DEFOCUS_ANGLE | Defocus angle (degrees) |
RLN_CTF_CS | Spherical aberration. |
RLN_CTF_CA | Chromatic aberration. |
RLN_CTF_DETECTOR_PIXEL_SIZE | Pixel size for detector as used in CTF-determination. |
RLN_CTF_ENERGY_LOSS | Energy loss. |
RLN_CTF_FOM | ctffind3 FOM (CC) for quality of CTF-fit |
RLN_CTF_IMAGE | name of an image describing the CTF model |
RLN_CTF_LENS_STABILITY | Lens stability. |
RLN_CTF_MAGNIFICATION | Magnification used for CTF-determination. |
RLN_CTF_MAXRES | Maximum resolution with Thon rings. |
RLN_CTF_CONVERGENCE_CONE | Convergence cone. |
RLN_CTF_LONGITUDINAL_DISPLACEMENT | Longitudinal displacement. |
RLN_CTF_TRANSVERSAL_DISPLACEMENT | Transversal displacemente. |
RLN_CTF_Q0 | Amplitude contrast. |
RLN_CTF_K | CTF gain. |
RLN_CTF_VALUE | CTF value. |
RLN_CTF_VALIDATIONSCORE | Gctf-based validation score for CTF fit. |
RLN_CTF_PHASESHIFT | Phase-shift from a phase-plate (in degrees) |
RLN_IMAGE_NAME | |
RLN_IMAGE_RECONSTRUCT_NAME | |
RLN_IMAGE_ID | |
RLN_IMAGE_ENABLED | |
RLN_IMAGE_DATATYPE | |
RLN_IMAGE_DIMENSIONALITY | |
RLN_IMAGE_BEAMTILT_X | |
RLN_IMAGE_BEAMTILT_Y | |
RLN_IMAGE_BEAMTILT_GROUP | |
RLN_IMAGE_COORD_X | |
RLN_IMAGE_COORD_Y | |
RLN_IMAGE_COORD_Z | |
RLN_IMAGE_FRAME_NR | |
RLN_IMAGE_MAGNIFICATION_CORRECTION | |
RLN_IMAGE_NORM_CORRECTION | |
RLN_IMAGE_ORI_NAME | |
RLN_IMAGE_SAMPLINGRATE | |
RLN_IMAGE_SAMPLINGRATE_X | |
RLN_IMAGE_SAMPLINGRATE_Y | |
RLN_IMAGE_SAMPLINGRATE_Z | |
RLN_IMAGE_SIZE | |
RLN_IMAGE_SIZEX | |
RLN_IMAGE_SIZEY | |
RLN_IMAGE_SIZEZ | |
RLN_IMAGE_STATS_MIN | |
RLN_IMAGE_STATS_MAX | |
RLN_IMAGE_STATS_AVG | |
RLN_IMAGE_STATS_STDDEV | |
RLN_IMAGE_STATS_SKEW | |
RLN_IMAGE_STATS_KURT | |
RLN_IMAGE_WEIGHT | |
RLN_MASK_NAME | |
RLN_MATRIX_1_1 | |
RLN_MATRIX_1_2 | |
RLN_MATRIX_1_3 | |
RLN_MATRIX_2_1 | |
RLN_MATRIX_2_2 | |
RLN_MATRIX_2_3 | |
RLN_MATRIX_3_1 | |
RLN_MATRIX_3_2 | |
RLN_MATRIX_3_3 | |
RLN_MICROGRAPH_ID | |
RLN_MICROGRAPH_MOVIE_NAME | |
RLN_MICROGRAPH_NAME | |
RLN_MICROGRAPH_NAME_WODOSE | |
RLN_MICROGRAPH_TILT_ANGLE | |
RLN_MICROGRAPH_TILT_AXIS_DIRECTION | |
RLN_MICROGRAPH_TILT_AXIS_OUTOFPLANE | |
RLN_MLMODEL_ACCURACY_ROT | |
RLN_MLMODEL_ACCURACY_TRANS | |
RLN_MLMODEL_AVE_PMAX | |
RLN_MLMODEL_CURRENT_RESOLUTION | |
RLN_MLMODEL_CURRENT_SIZE | |
RLN_MLMODEL_DATA_VS_PRIOR_REF | |
RLN_MLMODEL_DIMENSIONALITY | |
RLN_MLMODEL_DIMENSIONALITY_DATA | |
RLN_MLMODEL_DIFF2_HALVES_REF | |
RLN_MLMODEL_ESTIM_RESOL_REF | |
RLN_MLMODEL_FOURIER_COVERAGE_REF | |
RLN_MLMODEL_FOURIER_COVERAGE_TOTAL_REF | |
RLN_MLMODEL_FSC_HALVES_REF | |
RLN_MLMODEL_GROUP_NAME | |
RLN_MLMODEL_GROUP_NO | |
RLN_MLMODEL_GROUP_NR_PARTICLES | |
RLN_MLMODEL_GROUP_SCALE_CORRECTION | |
RLN_MLMODEL_HELICAL_NR_ASU | |
RLN_MLMODEL_HELICAL_TWIST | |
RLN_MLMODEL_HELICAL_TWIST_MIN | |
RLN_MLMODEL_HELICAL_TWIST_MAX | |
RLN_MLMODEL_HELICAL_TWIST_INITIAL_STEP | |
RLN_MLMODEL_HELICAL_RISE | |
RLN_MLMODEL_HELICAL_RISE_MIN | |
RLN_MLMODEL_HELICAL_RISE_MAX | |
RLN_MLMODEL_HELICAL_RISE_INITIAL_STEP | |
RLN_MLMODEL_IS_HELIX | |
RLN_MLMODEL_INTERPOLATOR | |
RLN_MLMODEL_LL | |
RLN_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION | |
RLN_MLMODEL_NORM_CORRECTION_AVG | |
RLN_MLMODEL_NR_BODIES | |
RLN_MLMODEL_NR_CLASSES | |
RLN_MLMODEL_NR_GROUPS | |
RLN_MLMODEL_ORIGINAL_SIZE | |
RLN_MLMODEL_ORIENTABILITY_CONTRIBUTION | |
RLN_MLMODEL_PADDING_FACTOR | |
RLN_MLMODEL_PDF_CLASS | |
RLN_MLMODEL_PRIOR_OFFX_CLASS | |
RLN_MLMODEL_PRIOR_OFFY_CLASS | |
RLN_MLMODEL_PDF_ORIENT | |
RLN_MLMODEL_PIXEL_SIZE | |
RLN_MLMODEL_POWER_REF | |
RLN_MLMODEL_PRIOR_MODE | |
RLN_MLMODEL_SGD_GRADIENT_IMAGE | |
RLN_MLMODEL_SIGMA_OFFSET | |
RLN_MLMODEL_SIGMA_ROT | |
RLN_MLMODEL_SIGMA_TILT | |
RLN_MLMODEL_SIGMA_PSI | |
RLN_MLMODEL_REF_IMAGE | |
RLN_MLMODEL_SIGMA2_NOISE | |
RLN_MLMODEL_SIGMA2_REF | |
RLN_MLMODEL_SSNR_REF | |
RLN_MLMODEL_TAU2_FUDGE_FACTOR | |
RLN_MLMODEL_TAU2_REF | |
RLN_OPTIMISER_ACCURACY_ROT | |
RLN_OPTIMISER_ACCURACY_TRANS | |
RLN_OPTIMISER_ADAPTIVE_FRACTION | |
RLN_OPTIMISER_ADAPTIVE_OVERSAMPLING | |
RLN_OPTIMISER_AUTO_LOCAL_HP_ORDER | |
RLN_OPTIMISER_AVAILABLE_MEMORY | |
RLN_OPTIMISER_BEST_RESOL_THUS_FAR | |
RLN_OPTIMISER_CHANGES_OPTIMAL_OFFSETS | |
RLN_OPTIMISER_CHANGES_OPTIMAL_ORIENTS | |
RLN_OPTIMISER_CHANGES_OPTIMAL_CLASSES | |
RLN_OPTIMISER_COARSE_SIZE | |
RLN_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED | |
RLN_OPTIMISER_DATA_ARE_CTF_PREMULTIPLIED | |
RLN_OPTIMISER_DATA_STARFILE | |
RLN_OPTIMISER_DO_AUTO_REFINE | |
RLN_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES | |
RLN_OPTIMISER_DO_CORRECT_CTF | |
RLN_OPTIMISER_DO_CORRECT_MAGNIFICATION | |
RLN_OPTIMISER_DO_CORRECT_NORM | |
RLN_OPTIMISER_DO_CORRECT_SCALE | |
RLN_OPTIMISER_DO_HELICAL_REFINE | |
RLN_OPTIMISER_DO_REALIGN_MOVIES | |
RLN_OPTIMISER_DO_MAP | |
RLN_OPTIMISER_DO_SGD | |
RLN_OPTIMISER_DO_SOLVENT_FLATTEN | |
RLN_OPTIMISER_DO_SKIP_ALIGN | |
RLN_OPTIMISER_DO_SKIP_ROTATE | |
RLN_OPTIMISER_DO_SPLIT_RANDOM_HALVES | |
RLN_OPTIMISER_DO_ZERO_MASK | |
RLN_OPTIMISER_FIX_SIGMA_NOISE | |
RLN_OPTIMISER_FIX_SIGMA_OFFSET | |
RLN_OPTIMISER_FIX_TAU | |
RLN_OPTIMISER_HAS_CONVERGED | |
RLN_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT | |
RLN_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO | |
RLN_OPTIMISER_HELICAL_TWIST_INITIAL | |
RLN_OPTIMISER_HELICAL_RISE_INITIAL | |
RLN_OPTIMISER_HELICAL_Z_PERCENTAGE | |
RLN_OPTIMISER_HELICAL_TUBE_INNER_DIAMETER | |
RLN_OPTIMISER_HELICAL_TUBE_OUTER_DIAMETER | |
RLN_OPTIMISER_HELICAL_SYMMETRY_LOCAL_REFINEMENT | |
RLN_OPTIMISER_HELICAL_SIGMA_DISTANCE | |
RLN_OPTIMISER_HIGHRES_LIMIT_SGD | |
RLN_OPTIMISER_IGNORE_HELICAL_SYMMETRY | |
RLN_OPTIMISER_HELICAL_KEEP_TILT_PRIOR_FIXED | |
RLN_OPTIMISER_HIGHRES_LIMIT_EXP | |
RLN_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK | |
RLN_OPTIMISER_INCR_SIZE | |
RLN_OPTIMISER_ITERATION_NO | |
RLN_OPTIMISER_LOCAL_SYMMETRY_FILENAME | |
RLN_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES | |
RLN_OPTIMISER_MAGNIFICATION_RANGE | |
RLN_OPTIMISER_MAGNIFICATION_STEP | |
RLN_OPTIMISER_MAX_COARSE_SIZE | |
RLN_OPTIMISER_MAX_NR_POOL | |
RLN_OPTIMISER_MODEL_STARFILE | |
RLN_OPTIMISER_MODEL_STARFILE2 | |
RLN_OPTIMISER_NR_ITERATIONS | |
RLN_OPTIMISER_NR_ITER_WO_RESOL_GAIN | |
RLN_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES | |
RLN_OPTIMISER_OUTPUT_ROOTNAME | |
RLN_OPTIMISER_PARTICLE_DIAMETER | |
RLN_OPTIMISER_RADIUS_MASK_3D_MAP | |
RLN_OPTIMISER_RADIUS_MASK_EXP_PARTICLES | |
RLN_OPTIMISER_RANDOM_SEED | |
RLN_OPTIMISER_REFS_ARE_CTF_CORRECTED | |
RLN_OPTIMISER_SAMPLING_STARFILE | |
RLN_OPTIMISER_SGD_MU | |
RLN_OPTIMISER_SGD_SIGMA2FUDGE_INI | |
RLN_OPTIMISER_SGD_SIGMA2FUDGE_HALFLIFE | |
RLN_OPTIMISER_SGD_SUBSET_START | |
RLN_OPTIMISER_SGD_SUBSET_SIZE | |
RLN_OPTIMISER_SGD_WRITE_EVERY_SUBSET | |
RLN_OPTIMISER_SGD_MAX_SUBSETS | |
RLN_OPTIMISER_SGD_STEPSIZE | |
RLN_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES | |
RLN_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS | |
RLN_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS | |
RLN_OPTIMISER_SOLVENT_MASK_NAME | |
RLN_OPTIMISER_SOLVENT_MASK2_NAME | |
RLN_OPTIMISER_TAU_SPECTRUM_NAME | |
RLN_OPTIMISER_USE_TOO_COARSE_SAMPLING | |
RLN_OPTIMISER_WIDTH_MASK_EDGE | |
RLN_ORIENT_FLIP | |
RLN_ORIENT_ID | |
RLN_ORIENT_ORIGIN_X | |
RLN_ORIENT_ORIGIN_X_PRIOR | |
RLN_ORIENT_ORIGIN_Y | |
RLN_ORIENT_ORIGIN_Y_PRIOR | |
RLN_ORIENT_ORIGIN_Z | |
RLN_ORIENT_ORIGIN_Z_PRIOR | |
RLN_ORIENT_ROT | |
RLN_ORIENT_ROT_PRIOR | |
RLN_ORIENT_TILT | |
RLN_ORIENT_TILT_PRIOR | |
RLN_ORIENT_PSI | |
RLN_ORIENT_PSI_PRIOR | |
RLN_ORIENT_PSI_PRIOR_FLIP_RATIO | |
RLN_PARTICLE_AUTOPICK_FOM | |
RLN_PARTICLE_CLASS | |
RLN_PARTICLE_DLL | |
RLN_PARTICLE_ID | |
RLN_PARTICLE_FOM | |
RLN_PARTICLE_KL_DIVERGENCE | |
RLN_PARTICLE_MOVIE_RUNNING_AVG | |
RLN_PARTICLE_RANDOM_SUBSET | |
RLN_PARTICLE_NAME | |
RLN_PARTICLE_ORI_NAME | |
RLN_PARTICLE_NR_SIGNIFICANT_SAMPLES | |
RLN_PARTICLE_NR_FRAMES | |
RLN_PARTICLE_NR_FRAMES_AVG | |
RLN_PARTICLE_PMAX | |
RLN_PARTICLE_HELICAL_TUBE_ID | |
RLN_PARTICLE_HELICAL_TUBE_PITCH | |
RLN_PARTICLE_HELICAL_TRACK_LENGTH | |
RLN_PIPELINE_JOB_COUNTER | |
RLN_PIPELINE_NODE_NAME | |
RLN_PIPELINE_NODE_TYPE | |
RLN_PIPELINE_PROCESS_ALIAS | |
RLN_PIPELINE_PROCESS_NAME | |
RLN_PIPELINE_PROCESS_TYPE | |
RLN_PIPELINE_PROCESS_STATUS | |
RLN_PIPELINE_EDGE_FROM | |
RLN_PIPELINE_EDGE_TO | |
RLN_PIPELINE_EDGE_PROCESS | |
RLN_POSTPROCESS_AMPLCORR_MASKED | |
RLN_POSTPROCESS_AMPLCORR_UNMASKED | |
RLN_POSTPROCESS_BFACTOR | |
RLN_POSTPROCESS_DPR_MASKED | |
RLN_POSTPROCESS_DPR_UNMASKED | |
RLN_POSTPROCESS_FINAL_RESOLUTION | |
RLN_POSTPROCESS_FSC_GENERAL | |
RLN_POSTPROCESS_FSC_TRUE | |
RLN_POSTPROCESS_FSC_MASKED | |
RLN_POSTPROCESS_FSC_UNMASKED | |
RLN_POSTPROCESS_FSC_RANDOM_MASKED | |
RLN_POSTPROCESS_GUINIER_FIT_CORRELATION | |
RLN_POSTPROCESS_GUINIER_FIT_INTERCEPT | |
RLN_POSTPROCESS_GUINIER_FIT_SLOPE | |
RLN_POSTPROCESS_GUINIER_VALUE_IN | |
RLN_POSTPROCESS_GUINIER_VALUE_INVMTF | |
RLN_POSTPROCESS_GUINIER_VALUE_WEIGHTED | |
RLN_POSTPROCESS_GUINIER_VALUE_SHARPENED | |
RLN_POSTPROCESS_GUINIER_VALUE_INTERCEPT | |
RLN_POSTPROCESS_GUINIER_RESOL_SQUARED | |
RLN_POSTPROCESS_MTF_VALUE | Detector MTF value. |
RLN_SAMPLING_IS_3D | |
RLN_SAMPLING_IS_3D_TRANS | |
RLN_SAMPLING_HEALPIX_ORDER | |
RLN_SAMPLING_HELICAL_OFFSET_STEP | |
RLN_SAMPLING_LIMIT_TILT | |
RLN_SAMPLING_OFFSET_RANGE | |
RLN_SAMPLING_OFFSET_STEP | |
RLN_SAMPLING_PERTURB | |
RLN_SAMPLING_PERTURBATION_FACTOR | |
RLN_SAMPLING_PRIOR_MODE | |
RLN_SAMPLING_PSI_STEP | |
RLN_SAMPLING_SIGMA_ROT | |
RLN_SAMPLING_SIGMA_TILT | |
RLN_SAMPLING_SIGMA_PSI | |
RLN_SAMPLING_SYMMETRY | |
RLN_SELECTED | |
RLN_SELECT_PARTICLES_ZSCORE | |
RLN_SORTED_IDX | |
RLN_STARFILE_MOVIE_PARTICLES | |
RLN_PERFRAME_CUMULATIVE_WEIGHT | |
RLN_PERFRAME_RELATIVE_WEIGHT | |
RLN_RESOLUTION | |
RLN_RESOLUTION_ANGSTROM | |
RLN_RESOLUTION_INVPIXEL | |
RLN_SPECTRAL_IDX | |
BUFFER_LABELS_START | Buffer labels to read generic labels |
BUFFER_01 | |
BUFFER_02 | |
BUFFER_03 | |
BUFFER_04 | |
BUFFER_05 | |
BUFFER_06 | |
BUFFER_07 | |
BUFFER_08 | |
BUFFER_09 | |
BUFFER_10 | |
BUFFER_11 | |
BUFFER_12 | |
BUFFER_13 | |
BUFFER_14 | |
BUFFER_15 | |
BUFFER_16 | |
BUFFER_17 | |
BUFFER_18 | |
BUFFER_19 | |
BUFFER_20 | |
BUFFER_21 | |
BUFFER_22 | |
BUFFER_23 | |
BUFFER_24 | |
BUFFER_25 | |
BUFFER_26 | |
BUFFER_27 | |
BUFFER_28 | |
BUFFER_29 | |
BUFFER_30 | |
BUFFER_31 | |
BUFFER_32 | |
BUFFER_33 | |
BUFFER_34 | |
BUFFER_35 | |
BUFFER_36 | |
BUFFER_37 | |
BUFFER_38 | |
BUFFER_39 | |
BUFFER_40 | |
BUFFER_41 | |
BUFFER_42 | |
BUFFER_43 | |
BUFFER_44 | |
BUFFER_45 | |
BUFFER_46 | |
BUFFER_47 | |
BUFFER_48 | |
BUFFER_49 | |
BUFFER_50 | |
BUFFER_51 | |
BUFFER_52 | |
BUFFER_53 | |
BUFFER_54 | |
BUFFER_55 | |
BUFFER_56 | |
BUFFER_57 | |
BUFFER_58 | |
BUFFER_59 | |
BUFFER_60 | |
BUFFER_61 | |
BUFFER_62 | |
BUFFER_63 | |
BUFFER_64 | |
BUFFER_65 | |
BUFFER_66 | |
BUFFER_67 | |
BUFFER_68 | |
BUFFER_69 | |
BUFFER_70 | |
BUFFER_71 | |
BUFFER_72 | |
BUFFER_73 | |
BUFFER_74 | |
BUFFER_75 | |
BUFFER_76 | |
BUFFER_77 | |
BUFFER_78 | |
BUFFER_79 | |
BUFFER_80 | |
BUFFER_81 | |
BUFFER_82 | |
BUFFER_83 | |
BUFFER_84 | |
BUFFER_85 | |
BUFFER_86 | |
BUFFER_87 | |
BUFFER_88 | |
BUFFER_89 | |
BUFFER_90 | |
BUFFER_91 | |
BUFFER_92 | |
BUFFER_93 | |
BUFFER_94 | |
BUFFER_95 | |
BUFFER_96 | |
BUFFER_97 | |
BUFFER_98 | |
BUFFER_99 | |
MDL_LAST_LABEL |
Definition at line 44 of file metadata_label.h.
enum MDLabelTag |
Possible types of the values of labels
Enumerator | |
---|---|
TAGLABEL_NOTAG | |
TAGLABEL_TEXTFILE | |
TAGLABEL_METADATA | |
TAGLABEL_CTFPARAM | |
TAGLABEL_IMAGE | |
TAGLABEL_VOLUME | |
TAGLABEL_STACK | |
TAGLABEL_MICROGRAPH | |
TAGLABEL_PSD |
Definition at line 961 of file metadata_label.h.
enum MDLabelType |
Possible types of the values of labels
Enumerator | |
---|---|
LABEL_NOTYPE | |
LABEL_INT | |
LABEL_BOOL | |
LABEL_DOUBLE | |
LABEL_STRING | |
LABEL_VECTOR_DOUBLE | |
LABEL_SIZET | |
LABEL_VECTOR_SIZET | |
LABEL_VECTOR_FLOAT |
Definition at line 947 of file metadata_label.h.
|
static |
This library will provide common mathematical and string functions in SQL queries using the operating system libraries or provided definitions. It includes the following functions:
Math: acos, asin, atan, atn2, atan2, acosh, asinh, atanh, difference, degrees, radians, cos, sin, tan, cot, cosh, sinh, tanh, coth, exp, log, log10, power, sign, sqrt, square, ceil, floor, pi.
String: replicate, charindex, leftstr, rightstr, ltrim, rtrim, trim, replace, reverse, proper, padl, padr, padc, strfilter.
Aggregate: stdev, variance, mode, median, lower_quartile, upper_quartile.
Definition at line 198 of file metadata_sql.cpp.
|
static |
Definition at line 208 of file metadata_sql.cpp.
bool MDSql::activateThreadMuting | ( | void | ) |
activate SAFED serialized mode mode
Definition at line 221 of file metadata_sql.cpp.
void MDCache::clear | ( | ) |
Definition at line 1579 of file metadata_sql.cpp.
bool MDSql::deactivateThreadMuting | ( | void | ) |
activate UNSAFED Multi-thread mode SQLite support three different threading modes:
Single-thread. In this mode, all mutexes are disabled and SQLite is unsafe to use in more than a single thread at once.
Multi-thread. In this mode, SQLite can be safely used by multiple threads provided that no single database connection is used simultaneously in two or more threads.
Serialized. In serialized mode, SQLite can be safely used by multiple threads with no restriction.
Definition at line 216 of file metadata_sql.cpp.
|
static |
Definition at line 1157 of file metadata_sql.cpp.
Definition at line 78 of file metadata_base.cpp.
bool existsBlockInMetaDataFile | ( | const FileName & | inFileWithBlock | ) |
Definition at line 73 of file metadata_base.cpp.
void getBlocksInMetaDataFile | ( | const FileName & | inFile, |
StringVector & | blockList | ||
) |
Which are the blocks available in a metadata
Definition at line 40 of file metadata_base.cpp.
int getBlocksInMetaDataFileDB | ( | const FileName & | inFile, |
StringVector & | blockList | ||
) |
Definition at line 71 of file metadata_sql.cpp.
MDCache::MDCache | ( | ) |
Definition at line 1568 of file metadata_sql.cpp.
|
inline |
Definition at line 985 of file metadata_label.h.
|
inline |
Definition at line 991 of file metadata_label.h.
std::ostream& operator<< | ( | std::ostream & | o, |
const MetaData & | mD | ||
) |
print metadata
Definition at line 1726 of file metadata_db.cpp.
void sqlite_regexp | ( | sqlite3_context * | context, |
int | argc, | ||
sqlite3_value ** | values | ||
) |
Definition at line 48 of file metadata_sql.cpp.
|
static |
Definition at line 1337 of file metadata_sql.cpp.
Just an utility function
Definition at line 137 of file metadata_base.cpp.
MDCache::~MDCache | ( | ) |
Definition at line 1574 of file metadata_sql.cpp.
sqlite3_stmt* MDCache::addRowStmt |
Definition at line 319 of file metadata_sql.h.
std::map<MDLabel, sqlite3_stmt*> MDCache::getValueCache |
Definition at line 317 of file metadata_sql.h.
sqlite3_stmt* MDCache::iterStmt |
Definition at line 316 of file metadata_sql.h.
std::map<MDLabel, sqlite3_stmt*> MDCache::setValueCache |
Definition at line 318 of file metadata_sql.h.
String MDLabelData::str |
Definition at line 982 of file metadata_label.h.
int MDLabelData::tags |
Definition at line 983 of file metadata_label.h.
MDLabelType MDLabelData::type |
Definition at line 981 of file metadata_label.h.
|
friend |
Definition at line 303 of file metadata_sql.h.
|
friend |
Definition at line 341 of file metadata_sql.h.
|
friend |
Definition at line 301 of file metadata_sql.h.
|
friend |
Definition at line 302 of file metadata_sql.h.