idx int64 0 165k | question stringlengths 73 4.15k | target stringlengths 5 918 | len_question int64 21 890 | len_target int64 3 255 |
|---|---|---|---|---|
157,200 | public int totalInstances ( ) { int total = 0 ; for ( int i = 0 ; i < confusion . length ; i ++ ) { for ( int j = 0 ; j < confusion [ i ] . length ; j ++ ) { total += confusion [ i ] [ j ] ; } } return total ; } | The total number of instances covered by this confusion matrix . | 66 | 11 |
157,201 | protected static < A > double [ ] computeDistances ( NumberArrayAdapter < ? , A > adapter , A data ) { final int size = adapter . size ( data ) ; double [ ] dMatrix = new double [ ( size * ( size + 1 ) ) >> 1 ] ; for ( int i = 0 , c = 0 ; i < size ; i ++ ) { for ( int j = 0 ; j < i ; j ++ ) { double dx = adapter . getDouble ( data , i ) - adapter . getDouble ( data , j ) ; dMatrix [ c ++ ] = ( dx < 0 ) ? - dx : dx ; // Absolute difference. } c ++ ; // Diagonal entry: zero } doubleCenterMatrix ( dMatrix , size ) ; return dMatrix ; } | Compute the double - centered delta matrix . | 164 | 9 |
157,202 | public static void doubleCenterMatrix ( double [ ] dMatrix , int size ) { double [ ] rowMean = new double [ size ] ; // row sum for ( int i = 0 , c = 0 ; i < size ; i ++ ) { for ( int j = 0 ; j < i ; j ++ ) { double v = dMatrix [ c ++ ] ; rowMean [ i ] += v ; rowMean [ j ] += v ; } assert ( dMatrix [ c ] == 0. ) ; c ++ ; // Diagonal entry. Must be zero! } // Normalize averages: double matrixMean = 0. ; for ( int i = 0 ; i < size ; i ++ ) { matrixMean += rowMean [ i ] ; rowMean [ i ] /= size ; } matrixMean /= size * size ; for ( int o = 0 , c = 0 ; o < size ; o ++ ) { // Including row mean! for ( int p = 0 ; p <= o ; p ++ ) { dMatrix [ c ++ ] -= rowMean [ o ] + rowMean [ p ] - matrixMean ; } } } | Computes the distance variance matrix of one axis . | 247 | 10 |
157,203 | public HyperBoundingBox determineAlphaMinMax ( HyperBoundingBox interval ) { final int dim = vec . getDimensionality ( ) ; if ( interval . getDimensionality ( ) != dim - 1 ) { throw new IllegalArgumentException ( "Interval needs to have dimensionality d=" + ( dim - 1 ) + ", read: " + interval . getDimensionality ( ) ) ; } if ( extremumType . equals ( ExtremumType . CONSTANT ) ) { double [ ] centroid = SpatialUtil . centroid ( interval ) ; return new HyperBoundingBox ( centroid , centroid ) ; } double [ ] alpha_min = new double [ dim - 1 ] ; double [ ] alpha_max = new double [ dim - 1 ] ; if ( SpatialUtil . contains ( interval , alphaExtremum ) ) { if ( extremumType . equals ( ExtremumType . MINIMUM ) ) { alpha_min = alphaExtremum ; for ( int d = dim - 2 ; d >= 0 ; d -- ) { alpha_max [ d ] = determineAlphaMax ( d , alpha_max , interval ) ; } } else { alpha_max = alphaExtremum ; for ( int d = dim - 2 ; d >= 0 ; d -- ) { alpha_min [ d ] = determineAlphaMin ( d , alpha_min , interval ) ; } } } else { for ( int d = dim - 2 ; d >= 0 ; d -- ) { alpha_min [ d ] = determineAlphaMin ( d , alpha_min , interval ) ; alpha_max [ d ] = determineAlphaMax ( d , alpha_max , interval ) ; } } return new HyperBoundingBox ( alpha_min , alpha_max ) ; } | Determines the alpha values where this function has a minumum and maximum value in the given interval . | 379 | 22 |
157,204 | private ExtremumType extremumType ( int n , double [ ] alpha_extreme , HyperBoundingBox interval ) { // return the type of the global extremum if ( n == alpha_extreme . length - 1 ) { return extremumType ; } // create random alpha values double [ ] alpha_extreme_l = new double [ alpha_extreme . length ] ; double [ ] alpha_extreme_r = new double [ alpha_extreme . length ] ; double [ ] alpha_extreme_c = new double [ alpha_extreme . length ] ; System . arraycopy ( alpha_extreme , 0 , alpha_extreme_l , 0 , alpha_extreme . length ) ; System . arraycopy ( alpha_extreme , 0 , alpha_extreme_r , 0 , alpha_extreme . length ) ; System . arraycopy ( alpha_extreme , 0 , alpha_extreme_c , 0 , alpha_extreme . length ) ; double [ ] centroid = SpatialUtil . centroid ( interval ) ; for ( int i = 0 ; i < n ; i ++ ) { alpha_extreme_l [ i ] = centroid [ i ] ; alpha_extreme_r [ i ] = centroid [ i ] ; alpha_extreme_c [ i ] = centroid [ i ] ; } double intervalLength = interval . getMax ( n ) - interval . getMin ( n ) ; alpha_extreme_l [ n ] = Math . random ( ) * intervalLength + interval . getMin ( n ) ; alpha_extreme_r [ n ] = Math . random ( ) * intervalLength + interval . getMin ( n ) ; double f_c = function ( alpha_extreme_c ) ; double f_l = function ( alpha_extreme_l ) ; double f_r = function ( alpha_extreme_r ) ; if ( f_l < f_c ) { if ( f_r < f_c || Math . abs ( f_r - f_c ) < DELTA ) { return ExtremumType . MAXIMUM ; } } if ( f_r < f_c ) { if ( f_l < f_c || Math . abs ( f_l - f_c ) < DELTA ) { return ExtremumType . MAXIMUM ; } } if ( f_l > f_c ) { if ( f_r > f_c || Math . abs ( f_r - f_c ) < DELTA ) { return ExtremumType . MINIMUM ; } } if ( f_r > f_c ) { if ( f_l > f_c || Math . abs ( f_l - f_c ) < DELTA ) { return ExtremumType . MINIMUM ; } } if ( Math . abs ( f_l - f_c ) < DELTA && Math . abs ( f_r - f_c ) < DELTA ) { return ExtremumType . CONSTANT ; } throw new IllegalArgumentException ( "Houston, we have a problem!\n" + this + // "\nf_l " + f_l + "\nf_c " + f_c + "\nf_r " + f_r + "\np " + vec + // "\nalpha " + FormatUtil . format ( alpha_extreme_c ) + // "\nalpha_l " + FormatUtil . format ( alpha_extreme_l ) + // "\nalpha_r " + FormatUtil . format ( alpha_extreme_r ) + "\nn " + n ) ; // + "box min " + FormatUtil.format(interval.getMin()) + "\n" // + "box max " + FormatUtil.format(interval.getMax()) + "\n" } | Returns the type of the extremum at the specified alpha values . | 802 | 13 |
157,205 | private double determineAlphaMin ( int n , double [ ] alpha_min , HyperBoundingBox interval ) { double alpha_n = extremum_alpha_n ( n , alpha_min ) ; double lower = interval . getMin ( n ) ; double upper = interval . getMax ( n ) ; double [ ] alpha_extreme = new double [ alpha_min . length ] ; System . arraycopy ( alpha_min , n , alpha_extreme , n , alpha_extreme . length - n ) ; alpha_extreme [ n ] = alpha_n ; ExtremumType type = extremumType ( n , alpha_extreme , interval ) ; if ( type . equals ( ExtremumType . MINIMUM ) || type . equals ( ExtremumType . CONSTANT ) ) { // A) lower <= alpha_n <= upper if ( lower <= alpha_n && alpha_n <= upper ) { return alpha_n ; } // B) alpha_n < upper else if ( alpha_n < lower ) { return lower ; } // C) alpha_n > max else { if ( alpha_n <= upper ) { throw new IllegalStateException ( "Should never happen!" ) ; } return upper ; } } // extremum is maximum else { if ( lower <= alpha_n && alpha_n <= upper ) { // A1) min <= alpha_n <= max && alpha_n - min <= max - alpha_n if ( alpha_n - lower <= upper - alpha_n ) { return upper ; } // A2) min <= alpha_n <= max && alpha_n - min > max - alpha_n else { return lower ; } } // B) alpha_n < min else if ( alpha_n < lower ) { return upper ; } // C) alpha_n > max else { if ( alpha_n <= upper ) { throw new IllegalStateException ( "Should never happen!" ) ; } return lower ; } } } | Determines the n - th alpha value where this function has a minimum in the specified interval . | 411 | 20 |
157,206 | public static double sinusProduct ( int start , int end , double [ ] alpha ) { double result = 1 ; for ( int j = start ; j < end ; j ++ ) { result *= FastMath . sin ( alpha [ j ] ) ; } return result ; } | Computes the product of all sinus values of the specified angles from start to end index . | 58 | 19 |
157,207 | private void determineGlobalExtremum ( ) { alphaExtremum = new double [ vec . getDimensionality ( ) - 1 ] ; for ( int n = alphaExtremum . length - 1 ; n >= 0 ; n -- ) { alphaExtremum [ n ] = extremum_alpha_n ( n , alphaExtremum ) ; if ( Double . isNaN ( alphaExtremum [ n ] ) ) { throw new IllegalStateException ( "Houston, we have a problem!\n" + this + "\n" + vec + "\n" + FormatUtil . format ( alphaExtremum ) ) ; } } determineGlobalExtremumType ( ) ; } | Determines the global extremum of this parameterization function . | 148 | 13 |
157,208 | private void determineGlobalExtremumType ( ) { final double f = function ( alphaExtremum ) ; // create random alpha values double [ ] alpha_1 = new double [ alphaExtremum . length ] ; double [ ] alpha_2 = new double [ alphaExtremum . length ] ; for ( int i = 0 ; i < alphaExtremum . length ; i ++ ) { alpha_1 [ i ] = Math . random ( ) * Math . PI ; alpha_2 [ i ] = Math . random ( ) * Math . PI ; } // look if f1 and f2 are less, greater or equal to f double f1 = function ( alpha_1 ) ; double f2 = function ( alpha_2 ) ; if ( f1 < f && f2 < f ) { extremumType = ExtremumType . MAXIMUM ; } else if ( f1 > f && f2 > f ) { extremumType = ExtremumType . MINIMUM ; } else if ( Math . abs ( f1 - f ) < DELTA && Math . abs ( f2 - f ) < DELTA ) { extremumType = ExtremumType . CONSTANT ; } else { throw new IllegalStateException ( "Houston, we have a problem:" + "\n" + this + "\nextremum at " + FormatUtil . format ( alphaExtremum ) + "\nf " + f + "\nf1 " + f1 + "\nf2 " + f2 ) ; } } | Determines the type of the global extremum . | 323 | 11 |
157,209 | public void setParameters ( Parameterization config ) { TrackParameters track = new TrackParameters ( config ) ; configureStep ( track ) ; // update parameter table { parameterTable . setEnabled ( false ) ; parameterTable . clear ( ) ; for ( TrackedParameter pair : track . getAllParameters ( ) ) { parameterTable . addParameter ( pair . getOwner ( ) , pair . getParameter ( ) , track ) ; } // parameters.updateFromTrackParameters(track); parameterTable . revalidate ( ) ; parameterTable . setEnabled ( true ) ; } // Update status and notify observers updateStatus ( ) ; firePanelUpdated ( ) ; } | Do the actual setParameters invocation . | 136 | 7 |
157,210 | protected void reportErrors ( Parameterization config ) { StringBuilder buf = new StringBuilder ( ) ; for ( ParameterException e : config . getErrors ( ) ) { if ( e instanceof UnspecifiedParameterException ) { continue ; } buf . append ( e . getMessage ( ) ) . append ( FormatUtil . NEWLINE ) ; } if ( buf . length ( ) > 0 ) { LOG . warning ( "Configuration errors:" + FormatUtil . NEWLINE + FormatUtil . NEWLINE + buf . toString ( ) ) ; } // config.clearErrors(); } | Report errors in a single error log record . | 126 | 9 |
157,211 | public boolean canRun ( ) { Status status = getStatus ( ) ; return Status . STATUS_READY . equals ( status ) || Status . STATUS_COMPLETE . equals ( status ) ; } | Test if this tab is ready - to - run | 43 | 10 |
157,212 | public SVGPath lineTo ( double x , double y ) { return append ( PATH_LINE_TO ) . append ( x ) . append ( y ) ; } | Draw a line to the given coordinates . | 34 | 8 |
157,213 | public SVGPath relativeLineTo ( double x , double y ) { return append ( PATH_LINE_TO_RELATIVE ) . append ( x ) . append ( y ) ; } | Draw a line to the given relative coordinates . | 38 | 9 |
157,214 | public SVGPath moveTo ( double x , double y ) { return append ( PATH_MOVE ) . append ( x ) . append ( y ) ; } | Move to the given coordinates . | 33 | 6 |
157,215 | public SVGPath relativeMoveTo ( double x , double y ) { return append ( PATH_MOVE_RELATIVE ) . append ( x ) . append ( y ) ; } | Move to the given relative coordinates . | 37 | 7 |
157,216 | public SVGPath smoothQuadTo ( double x , double y ) { return append ( PATH_SMOOTH_QUAD_TO ) . append ( x ) . append ( y ) ; } | Smooth quadratic Bezier line to the given coordinates . | 41 | 14 |
157,217 | public SVGPath relativeSmoothQuadTo ( double x , double y ) { return append ( PATH_SMOOTH_QUAD_TO_RELATIVE ) . append ( x ) . append ( y ) ; } | Smooth quadratic Bezier line to the given relative coordinates . | 46 | 15 |
157,218 | private SVGPath append ( char action ) { assert lastaction != 0 || action == PATH_MOVE : "Paths must begin with a move to the initial position!" ; if ( lastaction != action ) { buf . append ( action ) ; lastaction = action ; } return this ; } | Append an action to the current path . | 61 | 9 |
157,219 | private SVGPath append ( double x ) { if ( ! Double . isFinite ( x ) ) { throw new IllegalArgumentException ( "Cannot draw an infinite/NaN position." ) ; } if ( x >= 0 ) { final int l = buf . length ( ) ; if ( l > 0 ) { char c = buf . charAt ( l - 1 ) ; assert c != ' ' && c != ' ' : "Invalid exponential in path" ; if ( c >= ' ' && c <= ' ' ) buf . append ( ' ' ) ; } } buf . append ( SVGUtil . FMT . format ( x ) ) ; return this ; } | Append a value to the current path . | 141 | 9 |
157,220 | public SVGPath close ( ) { assert lastaction != 0 : "Paths must begin with a move to the initial position!" ; if ( lastaction != PATH_CLOSE ) { buf . append ( ' ' ) . append ( PATH_CLOSE ) ; lastaction = PATH_CLOSE ; } return this ; } | Close the path . | 64 | 4 |
157,221 | public Element makeElement ( SVGPlot plot ) { Element elem = plot . svgElement ( SVGConstants . SVG_PATH_TAG ) ; elem . setAttribute ( SVGConstants . SVG_D_ATTRIBUTE , buf . toString ( ) ) ; return elem ; } | Turn the path buffer into an SVG element . | 63 | 9 |
157,222 | public void setParameters ( Parameterization config ) { // Clear errors after each step, so they don't consider themselves failed // because of earlier errors. logTab . setParameters ( config ) ; // config.clearErrors(); inputTab . setParameters ( config ) ; // config.clearErrors(); algTab . setParameters ( config ) ; // config.clearErrors(); evalTab . setParameters ( config ) ; // config.clearErrors(); outTab . setParameters ( config ) ; // config.clearErrors(); } | Set the parameters . | 113 | 4 |
157,223 | public ArrayList < String > serializeParameters ( ) { ListParameterization params = new ListParameterization ( ) ; logTab . appendParameters ( params ) ; inputTab . appendParameters ( params ) ; algTab . appendParameters ( params ) ; evalTab . appendParameters ( params ) ; outTab . appendParameters ( params ) ; return params . serialize ( ) ; } | Get the serialized parameters | 79 | 5 |
157,224 | public static void main ( final String [ ] args ) { GUIUtil . logUncaughtExceptions ( LOG ) ; GUIUtil . setLookAndFeel ( ) ; OutputStep . setDefaultHandlerVisualizer ( ) ; javax . swing . SwingUtilities . invokeLater ( new Runnable ( ) { @ Override public void run ( ) { try { final MultiStepGUI gui = new MultiStepGUI ( ) ; gui . run ( ) ; if ( args != null && args . length > 0 ) { gui . setParameters ( new SerializedParameterization ( args ) ) ; } else { gui . setParameters ( new SerializedParameterization ( ) ) ; } } catch ( Exception | Error e ) { // Restore error handler, as the GUI is likely broken. LoggingConfiguration . replaceDefaultHandler ( new CLISmartHandler ( ) ) ; LOG . exception ( e ) ; } } } ) ; } | Main method that just spawns the UI . | 195 | 8 |
157,225 | protected static boolean match ( Object ref , Object test ) { if ( ref == null ) { return false ; } // Cheap and fast, may hold for class labels! if ( ref == test ) { return true ; } if ( ref instanceof LabelList && test instanceof LabelList ) { final LabelList lref = ( LabelList ) ref ; final LabelList ltest = ( LabelList ) test ; final int s1 = lref . size ( ) , s2 = ltest . size ( ) ; if ( s1 == 0 || s2 == 0 ) { return false ; } for ( int i = 0 ; i < s1 ; i ++ ) { String l1 = lref . get ( i ) ; if ( l1 == null ) { continue ; } for ( int j = 0 ; j < s2 ; j ++ ) { if ( l1 . equals ( ltest . get ( j ) ) ) { return true ; } } } } // Fallback to equality, e.g. on class labels return ref . equals ( test ) ; } | Test whether two relation agree . | 224 | 6 |
157,226 | private void findMatches ( ModifiableDBIDs posn , Relation < ? > lrelation , Object label ) { posn . clear ( ) ; for ( DBIDIter ri = lrelation . iterDBIDs ( ) ; ri . valid ( ) ; ri . advance ( ) ) { if ( match ( label , lrelation . get ( ri ) ) ) { posn . add ( ri ) ; } } } | Find all matching objects . | 93 | 5 |
157,227 | private void computeDistances ( ModifiableDoubleDBIDList nlist , DBIDIter query , final DistanceQuery < O > distQuery , Relation < O > relation ) { nlist . clear ( ) ; O qo = relation . get ( query ) ; for ( DBIDIter ri = relation . iterDBIDs ( ) ; ri . valid ( ) ; ri . advance ( ) ) { if ( ! includeSelf && DBIDUtil . equal ( ri , query ) ) { continue ; } double dist = distQuery . distance ( qo , ri ) ; if ( dist != dist ) { /* NaN */ dist = Double . POSITIVE_INFINITY ; } nlist . add ( dist , ri ) ; } nlist . sort ( ) ; } | Compute the distances to the neighbor objects . | 168 | 9 |
157,228 | private PrintStream newStream ( String name ) throws IOException { if ( LOG . isDebuggingFiner ( ) ) { LOG . debugFiner ( "Requested stream: " + name ) ; } // Ensure the directory exists: if ( ! basename . exists ( ) ) { basename . mkdirs ( ) ; } String fn = basename . getAbsolutePath ( ) + File . separator + name + EXTENSION ; fn = usegzip ? fn + GZIP_EXTENSION : fn ; OutputStream os = new FileOutputStream ( fn ) ; if ( usegzip ) { // wrap into gzip stream. os = new GZIPOutputStream ( os ) ; } PrintStream res = new PrintStream ( os ) ; if ( LOG . isDebuggingFiner ( ) ) { LOG . debugFiner ( "Opened new output stream:" + fn ) ; } // cache. return res ; } | Open a new stream of the given name | 200 | 8 |
157,229 | protected < N extends Page & Externalizable > PageFile < N > makePageFile ( Class < N > cls ) { @ SuppressWarnings ( "unchecked" ) final PageFileFactory < N > castFactory = ( PageFileFactory < N > ) pageFileFactory ; return castFactory . newPageFile ( cls ) ; } | Make the page file for this index . | 73 | 8 |
157,230 | public static boolean isAngularDistance ( AbstractMaterializeKNNPreprocessor < ? > kNN ) { DistanceFunction < ? > distanceFunction = kNN . getDistanceQuery ( ) . getDistanceFunction ( ) ; return CosineDistanceFunction . class . isInstance ( distanceFunction ) // || ArcCosineDistanceFunction . class . isInstance ( distanceFunction ) ; } | Test whether the given preprocessor used an angular distance function | 77 | 11 |
157,231 | public static Element drawCosine ( SVGPlot svgp , Projection2D proj , NumberVector mid , double angle ) { // Project origin double [ ] pointOfOrigin = proj . fastProjectDataToRenderSpace ( new double [ proj . getInputDimensionality ( ) ] ) ; // direction of the selected Point double [ ] selPoint = proj . fastProjectDataToRenderSpace ( mid ) ; double [ ] range1 , range2 ; { // Rotation plane: double [ ] pm = mid . toArray ( ) ; // Compute relative vectors double [ ] p1 = minusEquals ( proj . fastProjectRenderToDataSpace ( selPoint [ 0 ] + 10 , selPoint [ 1 ] ) , pm ) ; double [ ] p2 = minusEquals ( proj . fastProjectRenderToDataSpace ( selPoint [ 0 ] , selPoint [ 1 ] + 10 ) , pm ) ; // Scale p1 and p2 to unit length: timesEquals ( p1 , 1. / euclideanLength ( p1 ) ) ; timesEquals ( p2 , 1. / euclideanLength ( p2 ) ) ; if ( Math . abs ( scalarProduct ( p1 , p2 ) ) > 1E-10 ) { LoggingUtil . warning ( "Projection does not seem to be orthogonal?" ) ; } // Project onto p1, p2: double l1 = scalarProduct ( pm , p1 ) , l2 = scalarProduct ( pm , p2 ) ; // Rotate projection by + and - angle // Using sin(-x) = -sin(x) and cos(-x)=cos(x) final DoubleWrapper tmp = new DoubleWrapper ( ) ; // To return cosine final double sangle = FastMath . sinAndCos ( angle , tmp ) , cangle = tmp . value ; double r11 = + cangle * l1 - sangle * l2 , r12 = + sangle * l1 + cangle * l2 ; double r21 = + cangle * l1 + sangle * l2 , r22 = - sangle * l1 + cangle * l2 ; // Build rotated vectors - remove projected component, add rotated // component: double [ ] r1 = plusTimesEquals ( plusTimes ( pm , p1 , - l1 + r11 ) , p2 , - l2 + r12 ) ; double [ ] r2 = plusTimesEquals ( plusTimes ( pm , p1 , - l1 + r21 ) , p2 , - l2 + r22 ) ; // Project to render space: range1 = proj . fastProjectDataToRenderSpace ( r1 ) ; range2 = proj . fastProjectDataToRenderSpace ( r2 ) ; } // Continue lines to viewport. { CanvasSize viewport = proj . estimateViewport ( ) ; minusEquals ( range1 , pointOfOrigin ) ; plusEquals ( timesEquals ( range1 , viewport . continueToMargin ( pointOfOrigin , range1 ) ) , pointOfOrigin ) ; minusEquals ( range2 , pointOfOrigin ) ; plusEquals ( timesEquals ( range2 , viewport . continueToMargin ( pointOfOrigin , range2 ) ) , pointOfOrigin ) ; // Go backwards into the other direction - the origin might not be in the // viewport! double [ ] start1 = minus ( pointOfOrigin , range1 ) ; plusEquals ( timesEquals ( start1 , viewport . continueToMargin ( range1 , start1 ) ) , range1 ) ; double [ ] start2 = minus ( pointOfOrigin , range2 ) ; plusEquals ( timesEquals ( start2 , viewport . continueToMargin ( range2 , start2 ) ) , range2 ) ; // TODO: add filled variant? return new SVGPath ( ) . moveTo ( start1 ) . lineTo ( range1 ) . moveTo ( start2 ) . lineTo ( range2 ) . makeElement ( svgp ) ; } } | Visualizes Cosine and ArcCosine distance functions | 888 | 10 |
157,232 | public void splitupNoSort ( ArrayModifiableDBIDs ind , int begin , int end , int dim , Random rand ) { final int nele = end - begin ; dim = dim % projectedPoints . length ; // choose a projection of points DoubleDataStore tpro = projectedPoints [ dim ] ; // save set such that used for density or neighborhood computation // sets should be roughly minSplitSize if ( nele > minSplitSize * ( 1 - sizeTolerance ) && nele < minSplitSize * ( 1 + sizeTolerance ) ) { // sort set, since need median element later ind . sort ( begin , end , new DataStoreUtil . AscendingByDoubleDataStore ( tpro ) ) ; splitsets . add ( DBIDUtil . newArray ( ind . slice ( begin , end ) ) ) ; } // compute splitting element // do not store set or even sort set, since it is too large if ( nele > minSplitSize ) { // splits can be performed either by distance (between min,maxCoord) or by // picking a point randomly(picking index of point) // outcome is similar // int minInd splitByDistance(ind, nele, tpro); int minInd = splitRandomly ( ind , begin , end , tpro , rand ) ; // split set recursively // position used for splitting the projected points into two // sets used for recursive splitting int splitpos = minInd + 1 ; splitupNoSort ( ind , begin , splitpos , dim + 1 , rand ) ; splitupNoSort ( ind , splitpos , end , dim + 1 , rand ) ; } } | Recursively splits entire point set until the set is below a threshold | 344 | 14 |
157,233 | public int splitRandomly ( ArrayModifiableDBIDs ind , int begin , int end , DoubleDataStore tpro , Random rand ) { final int nele = end - begin ; DBIDArrayIter it = ind . iter ( ) ; // pick random splitting element based on position double rs = tpro . doubleValue ( it . seek ( begin + rand . nextInt ( nele ) ) ) ; int minInd = begin , maxInd = end - 1 ; // permute elements such that all points smaller than the splitting // element are on the right and the others on the left in the array while ( minInd < maxInd ) { double currEle = tpro . doubleValue ( it . seek ( minInd ) ) ; if ( currEle > rs ) { while ( minInd < maxInd && tpro . doubleValue ( it . seek ( maxInd ) ) > rs ) { maxInd -- ; } if ( minInd == maxInd ) { break ; } ind . swap ( minInd , maxInd ) ; maxInd -- ; } minInd ++ ; } // if all elements are the same split in the middle if ( minInd == end - 1 ) { minInd = ( begin + end ) >>> 1 ; } return minInd ; } | Split the data set randomly . | 264 | 6 |
157,234 | public int splitByDistance ( ArrayModifiableDBIDs ind , int begin , int end , DoubleDataStore tpro , Random rand ) { DBIDArrayIter it = ind . iter ( ) ; // pick random splitting point based on distance double rmin = Double . MAX_VALUE * .5 , rmax = - Double . MAX_VALUE * .5 ; int minInd = begin , maxInd = end - 1 ; for ( it . seek ( begin ) ; it . getOffset ( ) < end ; it . advance ( ) ) { double currEle = tpro . doubleValue ( it ) ; rmin = Math . min ( currEle , rmin ) ; rmax = Math . max ( currEle , rmax ) ; } if ( rmin != rmax ) { // if not all elements are the same double rs = rmin + rand . nextDouble ( ) * ( rmax - rmin ) ; // permute elements such that all points smaller than the splitting // element are on the right and the others on the left in the array while ( minInd < maxInd ) { double currEle = tpro . doubleValue ( it . seek ( minInd ) ) ; if ( currEle > rs ) { while ( minInd < maxInd && tpro . doubleValue ( it . seek ( maxInd ) ) > rs ) { maxInd -- ; } if ( minInd == maxInd ) { break ; } ind . swap ( minInd , maxInd ) ; maxInd -- ; } minInd ++ ; } } else { // if all elements are the same split in the middle minInd = ( begin + end ) >>> 1 ; } return minInd ; } | Split the data set by distances . | 356 | 7 |
157,235 | public DataStore < ? extends DBIDs > getNeighs ( ) { final DBIDs ids = points . getDBIDs ( ) ; // init lists WritableDataStore < ModifiableDBIDs > neighs = DataStoreUtil . makeStorage ( ids , DataStoreFactory . HINT_HOT , ModifiableDBIDs . class ) ; for ( DBIDIter it = ids . iter ( ) ; it . valid ( ) ; it . advance ( ) ) { neighs . put ( it , DBIDUtil . newHashSet ( ) ) ; } FiniteProgress splitp = LOG . isVerbose ( ) ? new FiniteProgress ( "Processing splits for neighborhoods" , splitsets . size ( ) , LOG ) : null ; // go through all sets Iterator < ArrayDBIDs > it1 = splitsets . iterator ( ) ; DBIDVar v = DBIDUtil . newVar ( ) ; while ( it1 . hasNext ( ) ) { ArrayDBIDs pinSet = it1 . next ( ) ; final int indoff = pinSet . size ( ) >> 1 ; // middle point of projection pinSet . assignVar ( indoff , v ) ; // add all points as neighbors to middle point neighs . get ( v ) . addDBIDs ( pinSet ) ; // and the the middle point to all other points in set for ( DBIDIter it = pinSet . iter ( ) ; it . valid ( ) ; it . advance ( ) ) { neighs . get ( it ) . add ( v ) ; } LOG . incrementProcessed ( splitp ) ; } LOG . ensureCompleted ( splitp ) ; return neighs ; } | Compute list of neighbors for each point from sets resulting from projection | 356 | 13 |
157,236 | public DoubleDataStore computeAverageDistInSet ( ) { WritableDoubleDataStore davg = DataStoreUtil . makeDoubleStorage ( points . getDBIDs ( ) , DataStoreFactory . HINT_HOT ) ; WritableIntegerDataStore nDists = DataStoreUtil . makeIntegerStorage ( points . getDBIDs ( ) , DataStoreFactory . HINT_HOT | DataStoreFactory . HINT_TEMP ) ; FiniteProgress splitp = LOG . isVerbose ( ) ? new FiniteProgress ( "Processing splits for density estimation" , splitsets . size ( ) , LOG ) : null ; DBIDVar v = DBIDUtil . newVar ( ) ; for ( Iterator < ArrayDBIDs > it1 = splitsets . iterator ( ) ; it1 . hasNext ( ) ; ) { ArrayDBIDs pinSet = it1 . next ( ) ; final int len = pinSet . size ( ) ; final int indoff = len >> 1 ; pinSet . assignVar ( indoff , v ) ; V midpoint = points . get ( v ) ; for ( DBIDArrayIter it = pinSet . iter ( ) ; it . getOffset ( ) < len ; it . advance ( ) ) { if ( DBIDUtil . equal ( it , v ) ) { continue ; } double dist = EuclideanDistanceFunction . STATIC . distance ( points . get ( it ) , midpoint ) ; ++ distanceComputations ; davg . increment ( v , dist ) ; nDists . increment ( v , 1 ) ; davg . increment ( it , dist ) ; nDists . increment ( it , 1 ) ; } LOG . incrementProcessed ( splitp ) ; } LOG . ensureCompleted ( splitp ) ; for ( DBIDIter it = points . getDBIDs ( ) . iter ( ) ; it . valid ( ) ; it . advance ( ) ) { // it might be that a point does not occur for a certain size of a // projection (likely if do few projections, in this case there is no avg // distance) int count = nDists . intValue ( it ) ; double val = ( count == 0 ) ? FastOPTICS . UNDEFINED_DISTANCE : ( davg . doubleValue ( it ) / count ) ; davg . put ( it , val ) ; } nDists . destroy ( ) ; // No longer needed after normalization return davg ; } | Compute for each point a density estimate as inverse of average distance to a point in a projected set | 532 | 20 |
157,237 | public boolean containedIn ( SparseNumberVector bv ) { int i1 = this . iter ( ) , i2 = bv . iter ( ) ; while ( this . iterValid ( i1 ) ) { if ( ! bv . iterValid ( i2 ) ) { return false ; } int d1 = this . iterDim ( i1 ) , d2 = bv . iterDim ( i2 ) ; if ( d1 < d2 ) { return false ; // Missing } if ( d1 == d2 ) { if ( bv . iterDoubleValue ( i2 ) == 0. ) { return false ; } i1 = this . iterAdvance ( i1 ) ; } i2 = bv . iterAdvance ( i2 ) ; } return true ; } | Test whether the itemset is contained in a bit vector . | 167 | 12 |
157,238 | public static long [ ] toBitset ( Itemset i , long [ ] bits ) { for ( int it = i . iter ( ) ; i . iterValid ( it ) ; it = i . iterAdvance ( it ) ) { BitsUtil . setI ( bits , i . iterDim ( it ) ) ; } return bits ; } | Get the items . | 74 | 4 |
157,239 | protected static int compareLexicographical ( Itemset a , Itemset o ) { int i1 = a . iter ( ) , i2 = o . iter ( ) ; while ( a . iterValid ( i1 ) && o . iterValid ( i2 ) ) { int v1 = a . iterDim ( i1 ) , v2 = o . iterDim ( i2 ) ; if ( v1 < v2 ) { return - 1 ; } if ( v2 < v1 ) { return + 1 ; } i1 = a . iterAdvance ( i1 ) ; i2 = o . iterAdvance ( i2 ) ; } return a . iterValid ( i1 ) ? 1 : o . iterValid ( i2 ) ? - 1 : 0 ; } | Robust compare using the iterators lexicographical only! | 164 | 12 |
157,240 | public final StringBuilder appendTo ( StringBuilder buf , VectorFieldTypeInformation < BitVector > meta ) { appendItemsTo ( buf , meta ) ; return buf . append ( ": " ) . append ( support ) ; } | Append items and support to a string buffer . | 47 | 10 |
157,241 | public StringBuilder appendItemsTo ( StringBuilder buf , VectorFieldTypeInformation < BitVector > meta ) { int it = this . iter ( ) ; if ( this . iterValid ( it ) ) { while ( true ) { int v = this . iterDim ( it ) ; String lbl = ( meta != null ) ? meta . getLabel ( v ) : null ; if ( lbl == null ) { buf . append ( v ) ; } else { buf . append ( lbl ) ; } it = this . iterAdvance ( it ) ; if ( ! this . iterValid ( it ) ) { break ; } buf . append ( ", " ) ; } } return buf ; } | Only append the items to a string buffer . | 145 | 9 |
157,242 | @ Override public double getWeight ( double distance , double max , double stddev ) { if ( max <= 0 ) { return 1.0 ; } double relativedistance = distance / max ; // -2.303 is log(.1) to suit the intended range of 1.0-0.1 return FastMath . exp ( - 2.3025850929940455 * relativedistance * relativedistance ) ; } | Get Gaussian weight . stddev is not used scaled using max . | 92 | 15 |
157,243 | @ Override public void writePage ( int pageID , P page ) { if ( page . isDirty ( ) ) { try { countWrite ( ) ; byte [ ] array = pageToByteArray ( page ) ; file . getRecordBuffer ( pageID ) . put ( array ) ; page . setDirty ( false ) ; } catch ( IOException e ) { throw new RuntimeException ( e ) ; } } } | Write page to disk . | 90 | 5 |
157,244 | private byte [ ] pageToByteArray ( P page ) { try { if ( page == null ) { ByteArrayOutputStream baos = new ByteArrayOutputStream ( ) ; ObjectOutputStream oos = new ObjectOutputStream ( baos ) ; oos . writeInt ( EMPTY_PAGE ) ; oos . close ( ) ; baos . close ( ) ; byte [ ] array = baos . toByteArray ( ) ; byte [ ] result = new byte [ pageSize ] ; System . arraycopy ( array , 0 , result , 0 , array . length ) ; return result ; } else { ByteArrayOutputStream baos = new ByteArrayOutputStream ( ) ; ObjectOutputStream oos = new ObjectOutputStream ( baos ) ; oos . writeInt ( FILLED_PAGE ) ; oos . writeObject ( page ) ; oos . close ( ) ; baos . close ( ) ; byte [ ] array = baos . toByteArray ( ) ; if ( array . length > this . pageSize ) { throw new IllegalArgumentException ( "Size of page " + page + " is greater than specified" + " pagesize: " + array . length + " > " + pageSize ) ; } else if ( array . length == this . pageSize ) { return array ; } else { byte [ ] result = new byte [ pageSize ] ; System . arraycopy ( array , 0 , result , 0 , array . length ) ; return result ; } } } catch ( IOException e ) { throw new RuntimeException ( "IOException occurred! " , e ) ; } } | Serializes an object into a byte array . | 342 | 9 |
157,245 | public static SinCosTable make ( int steps ) { if ( ( steps & 0x3 ) == 0 ) { return new QuarterTable ( steps ) ; } if ( ( steps & 0x1 ) == 0 ) { return new HalfTable ( steps ) ; } return new FullTable ( steps ) ; } | Make a table for the given number of steps . | 64 | 10 |
157,246 | @ Override protected void process ( DBIDRef id , ArrayDBIDs ids , DBIDArrayIter it , int n , WritableDBIDDataStore pi , WritableDoubleDataStore lambda , WritableDoubleDataStore m ) { clinkstep3 ( id , it , n , pi , lambda , m ) ; clinkstep4567 ( id , ids , it , n , pi , lambda , m ) ; clinkstep8 ( id , it , n , pi , lambda , m ) ; } | CLINK main loop based on the SLINK main loop . | 109 | 12 |
157,247 | private void clinkstep8 ( DBIDRef id , DBIDArrayIter it , int n , WritableDBIDDataStore pi , WritableDoubleDataStore lambda , WritableDoubleDataStore m ) { DBIDVar p_i = DBIDUtil . newVar ( ) , pp_i = DBIDUtil . newVar ( ) ; for ( it . seek ( 0 ) ; it . getOffset ( ) < n ; it . advance ( ) ) { p_i . from ( pi , it ) ; // p_i = pi[i] pp_i . from ( pi , p_i ) ; // pp_i = pi[pi[i]] if ( DBIDUtil . equal ( pp_i , id ) && lambda . doubleValue ( it ) >= lambda . doubleValue ( p_i ) ) { pi . putDBID ( it , id ) ; } } } | Update hierarchy . | 193 | 3 |
157,248 | public static int levenshteinDistance ( String o1 , String o2 ) { // Let o1 be the shorter one: if ( o1 . length ( ) > o2 . length ( ) ) { return levenshteinDistance ( o2 , o1 ) ; } final int l1 = o1 . length ( ) , l2 = o2 . length ( ) ; // Exploit that Java caches the hash code of strings: if ( l1 == l2 && o1 . hashCode ( ) == o2 . hashCode ( ) && o1 . equals ( o2 ) ) { return 0 ; } // Determine prefix and postfix lengths: final int prefix = prefixLen ( o1 , o2 ) ; if ( prefix == l1 || prefix == l2 ) { return Math . abs ( l1 - l2 ) ; } final int postfix = postfixLen ( o1 , o2 , prefix ) ; return // Prefix and postfix are a complete object: ( prefix + postfix == l1 || prefix + postfix == l2 ) ? Math . abs ( l1 - l2 ) : // // Exactly one char difference optimization: ( l1 == l2 && prefix + postfix + 1 == l1 ) ? 1 : // // Default case, compute levenshteinDistance ( o1 , o2 , prefix , postfix ) ; } | Levenshtein distance for two strings . | 292 | 9 |
157,249 | private static int prefixLen ( String o1 , String o2 ) { final int l1 = o1 . length ( ) , l2 = o2 . length ( ) , l = l1 < l2 ? l1 : l2 ; int prefix = 0 ; while ( prefix < l && ( o1 . charAt ( prefix ) == o2 . charAt ( prefix ) ) ) { prefix ++ ; } return prefix ; } | Compute the length of the prefix . | 91 | 8 |
157,250 | private static int postfixLen ( String o1 , String o2 , int prefix ) { int postfix = 0 ; int p1 = o1 . length ( ) , p2 = o2 . length ( ) ; while ( p1 > prefix && p2 > prefix && ( o1 . charAt ( -- p1 ) == o2 . charAt ( -- p2 ) ) ) { ++ postfix ; } return postfix ; } | Compute the postfix length . | 93 | 7 |
157,251 | public static int levenshteinDistance ( String o1 , String o2 , int prefix , int postfix ) { final int l1 = o1 . length ( ) , l2 = o2 . length ( ) ; // Buffer, interleaved. Even and odd values are our rows. int [ ] buf = new int [ ( l2 + 1 - ( prefix + postfix ) ) << 1 ] ; // Initial "row", on even positions for ( int j = 0 ; j < buf . length ; j += 2 ) { buf [ j ] = j >> 1 ; } int inter = 1 ; // Interleaving offset for ( int i = prefix , e1 = l1 - postfix ; i < e1 ; i ++ , inter ^= 1 ) { final char chr = o1 . charAt ( i ) ; buf [ inter ] = i + 1 - prefix ; // First entry for ( int c = 2 + inter , p = 3 - inter , j = prefix ; c < buf . length ; c += 2 , p += 2 ) { buf [ c ] = min ( buf [ p ] + 1 , buf [ c - 2 ] + 1 , buf [ p - 2 ] + ( ( chr == o2 . charAt ( j ++ ) ) ? 0 : 1 ) ) ; } } return buf [ buf . length - 2 + ( inter ^ 1 ) ] ; } | Compute the Levenshtein distance except for prefix and postfix . | 296 | 15 |
157,252 | private static int nextSep ( String str , int start ) { int next = str . indexOf ( ' ' , start ) ; return next == - 1 ? str . length ( ) : next ; } | Find the next separator . | 42 | 6 |
157,253 | public static double [ ] [ ] computeWeightMatrix ( final int quanth , final int quants , final int quantb ) { final int dim = quanth * quants * quantb ; final DoubleWrapper tmp = new DoubleWrapper ( ) ; // To return cosine assert ( dim > 0 ) ; final double [ ] [ ] m = new double [ dim ] [ dim ] ; for ( int x = 0 ; x < dim ; x ++ ) { final int hx = x / ( quantb * quants ) ; final int sx = ( x / quantb ) % quants ; final int bx = x % quantb ; for ( int y = x ; y < dim ; y ++ ) { final int hy = y / ( quantb * quants ) ; final int sy = ( y / quantb ) % quants ; final int by = y % quantb ; final double shx = FastMath . sinAndCos ( ( hx + .5 ) / quanth * MathUtil . TWOPI , tmp ) ; final double chx = tmp . value ; final double shy = FastMath . sinAndCos ( ( hy + .5 ) / quanth * MathUtil . TWOPI , tmp ) ; final double chy = tmp . value ; final double cos = chx * ( sx + .5 ) / quants - chy * ( sy + .5 ) / quants ; final double sin = shx * ( sx + .5 ) / quants - shy * ( sy + .5 ) / quants ; final double db = ( bx - by ) / ( double ) quantb ; final double val = 1. - FastMath . sqrt ( ( db * db + sin * sin + cos * cos ) / 5 ) ; m [ x ] [ y ] = m [ y ] [ x ] = val ; } } return m ; } | Compute the weight matrix for HSB similarity . | 405 | 10 |
157,254 | public static double [ ] plus ( final double [ ] v1 , final double [ ] v2 ) { assert v1 . length == v2 . length : ERR_VEC_DIMENSIONS ; final double [ ] result = new double [ v1 . length ] ; for ( int i = 0 ; i < result . length ; i ++ ) { result [ i ] = v1 [ i ] + v2 [ i ] ; } return result ; } | Computes component - wise v1 + v2 for vectors . | 98 | 13 |
157,255 | public static double [ ] plusEquals ( final double [ ] v1 , final double [ ] v2 ) { assert v1 . length == v2 . length : ERR_VEC_DIMENSIONS ; for ( int i = 0 ; i < v1 . length ; i ++ ) { v1 [ i ] += v2 [ i ] ; } return v1 ; } | Computes component - wise v1 = v1 + v2 overwriting the vector v1 . | 82 | 21 |
157,256 | public static double [ ] plus ( final double [ ] v1 , final double s1 ) { final double [ ] result = new double [ v1 . length ] ; for ( int i = 0 ; i < result . length ; i ++ ) { result [ i ] = v1 [ i ] + s1 ; } return result ; } | Computes component - wise v1 + s1 . | 71 | 11 |
157,257 | public static double [ ] plusEquals ( final double [ ] v1 , final double s1 ) { for ( int i = 0 ; i < v1 . length ; i ++ ) { v1 [ i ] += s1 ; } return v1 ; } | Computes component - wise v1 = v1 + s1 overwriting the vector v1 . | 55 | 21 |
157,258 | public static double [ ] minus ( final double [ ] v1 , final double [ ] v2 ) { assert v1 . length == v2 . length : ERR_VEC_DIMENSIONS ; final double [ ] sub = new double [ v1 . length ] ; for ( int i = 0 ; i < v1 . length ; i ++ ) { sub [ i ] = v1 [ i ] - v2 [ i ] ; } return sub ; } | Computes component - wise v1 - v2 . | 99 | 11 |
157,259 | public static double [ ] minusEquals ( final double [ ] v1 , final double [ ] v2 ) { assert v1 . length == v2 . length : ERR_VEC_DIMENSIONS ; for ( int i = 0 ; i < v1 . length ; i ++ ) { v1 [ i ] -= v2 [ i ] ; } return v1 ; } | Computes component - wise v1 = v1 - v2 overwriting the vector v1 . | 82 | 21 |
157,260 | public static double [ ] minus ( final double [ ] v1 , final double s1 ) { final double [ ] result = new double [ v1 . length ] ; for ( int i = 0 ; i < v1 . length ; i ++ ) { result [ i ] = v1 [ i ] - s1 ; } return result ; } | Subtract component - wise v1 - s1 . | 72 | 12 |
157,261 | public static double [ ] minusEquals ( final double [ ] v1 , final double s1 ) { for ( int i = 0 ; i < v1 . length ; i ++ ) { v1 [ i ] -= s1 ; } return v1 ; } | Subtract component - wise in - place v1 = v1 - s1 overwriting the vector v1 . | 55 | 25 |
157,262 | public static double sum ( final double [ ] v1 ) { double acc = 0. ; for ( int row = 0 ; row < v1 . length ; row ++ ) { acc += v1 [ row ] ; } return acc ; } | Sum of the vector components . | 50 | 6 |
157,263 | public static int argmax ( double [ ] v ) { assert ( v . length > 0 ) ; int maxIndex = 0 ; double currentMax = v [ 0 ] ; for ( int i = 1 ; i < v . length ; i ++ ) { final double x = v [ i ] ; if ( x > currentMax ) { maxIndex = i ; currentMax = x ; } } return maxIndex ; } | Find the maximum value . | 87 | 5 |
157,264 | public static double [ ] normalize ( final double [ ] v1 ) { final double norm = 1. / euclideanLength ( v1 ) ; double [ ] re = new double [ v1 . length ] ; if ( norm < Double . POSITIVE_INFINITY ) { for ( int row = 0 ; row < v1 . length ; row ++ ) { re [ row ] = v1 [ row ] * norm ; } } return re ; } | Normalizes v1 to the length of 1 . 0 . | 99 | 12 |
157,265 | public static double [ ] normalizeEquals ( final double [ ] v1 ) { final double norm = 1. / euclideanLength ( v1 ) ; if ( norm < Double . POSITIVE_INFINITY ) { for ( int row = 0 ; row < v1 . length ; row ++ ) { v1 [ row ] *= norm ; } } return v1 ; } | Normalizes v1 to the length of 1 . 0 in place . | 84 | 14 |
157,266 | public static void clear ( final double [ ] [ ] m ) { for ( int i = 0 ; i < m . length ; i ++ ) { Arrays . fill ( m [ i ] , 0.0 ) ; } } | Reset the matrix to 0 . | 48 | 7 |
157,267 | public static double [ ] rotate90Equals ( final double [ ] v1 ) { assert v1 . length == 2 : "rotate90Equals is only valid for 2d vectors." ; final double temp = v1 [ 0 ] ; v1 [ 0 ] = v1 [ 1 ] ; v1 [ 1 ] = - temp ; return v1 ; } | Rotate the two - dimensional vector by 90 degrees . | 77 | 11 |
157,268 | public static double [ ] [ ] diagonal ( final double [ ] v1 ) { final int dim = v1 . length ; final double [ ] [ ] result = new double [ dim ] [ dim ] ; for ( int i = 0 ; i < dim ; i ++ ) { result [ i ] [ i ] = v1 [ i ] ; } return result ; } | Returns a quadratic matrix consisting of zeros and of the given values on the diagonal . | 77 | 19 |
157,269 | public static double [ ] [ ] copy ( final double [ ] [ ] m1 ) { final int rowdim = m1 . length , coldim = getColumnDimensionality ( m1 ) ; final double [ ] [ ] X = new double [ rowdim ] [ coldim ] ; for ( int i = 0 ; i < rowdim ; i ++ ) { System . arraycopy ( m1 [ i ] , 0 , X [ i ] , 0 , coldim ) ; } return X ; } | Make a deep copy of a matrix . | 106 | 8 |
157,270 | public static double [ ] getCol ( double [ ] [ ] m1 , int col ) { double [ ] ret = new double [ m1 . length ] ; for ( int i = 0 ; i < ret . length ; i ++ ) { ret [ i ] = m1 [ i ] [ col ] ; } return ret ; } | Get a column from a matrix as vector . | 70 | 9 |
157,271 | public static double [ ] getDiagonal ( final double [ ] [ ] m1 ) { final int dim = Math . min ( getColumnDimensionality ( m1 ) , m1 . length ) ; final double [ ] diagonal = new double [ dim ] ; for ( int i = 0 ; i < dim ; i ++ ) { diagonal [ i ] = m1 [ i ] [ i ] ; } return diagonal ; } | getDiagonal returns array of diagonal - elements . | 89 | 10 |
157,272 | public static void normalizeColumns ( final double [ ] [ ] m1 ) { final int columndimension = getColumnDimensionality ( m1 ) ; for ( int col = 0 ; col < columndimension ; col ++ ) { double norm = 0.0 ; for ( int row = 0 ; row < m1 . length ; row ++ ) { final double v = m1 [ row ] [ col ] ; norm += v * v ; } if ( norm > 0 ) { norm = FastMath . sqrt ( norm ) ; for ( int row = 0 ; row < m1 . length ; row ++ ) { m1 [ row ] [ col ] /= norm ; } } } } | Normalizes the columns of this matrix to length of 1 . 0 . | 152 | 14 |
157,273 | public static double [ ] [ ] appendColumns ( final double [ ] [ ] m1 , final double [ ] [ ] m2 ) { final int columndimension = getColumnDimensionality ( m1 ) ; final int ccolumndimension = getColumnDimensionality ( m2 ) ; assert m1 . length == m2 . length : "m.getRowDimension() != column.getRowDimension()" ; final int rcolumndimension = columndimension + ccolumndimension ; final double [ ] [ ] result = new double [ m1 . length ] [ rcolumndimension ] ; for ( int i = 0 ; i < rcolumndimension ; i ++ ) { // FIXME: optimize - excess copying! if ( i < columndimension ) { setCol ( result , i , getCol ( m1 , i ) ) ; } else { setCol ( result , i , getCol ( m2 , i - columndimension ) ) ; } } return result ; } | Returns a matrix which consists of this matrix and the specified columns . | 232 | 13 |
157,274 | public static double [ ] [ ] orthonormalize ( final double [ ] [ ] m1 ) { final int columndimension = getColumnDimensionality ( m1 ) ; final double [ ] [ ] v = copy ( m1 ) ; // FIXME: optimize - excess copying! for ( int i = 1 ; i < columndimension ; i ++ ) { final double [ ] u_i = getCol ( m1 , i ) ; final double [ ] sum = new double [ m1 . length ] ; for ( int j = 0 ; j < i ; j ++ ) { final double [ ] v_j = getCol ( v , j ) ; final double scalar = scalarProduct ( u_i , v_j ) / scalarProduct ( v_j , v_j ) ; plusEquals ( sum , times ( v_j , scalar ) ) ; } final double [ ] v_i = minus ( u_i , sum ) ; setCol ( v , i , v_i ) ; } normalizeColumns ( v ) ; return v ; } | Returns an orthonormalization of this matrix . | 236 | 10 |
157,275 | public static double [ ] [ ] inverse ( double [ ] [ ] A ) { final int rows = A . length , cols = A [ 0 ] . length ; return rows == cols // ? ( new LUDecomposition ( A , rows , cols ) ) . inverse ( ) // : ( new QRDecomposition ( A , rows , cols ) ) . inverse ( ) ; } | Matrix inverse or pseudoinverse | 85 | 6 |
157,276 | public static boolean almostEquals ( final double [ ] m1 , final double [ ] m2 , final double maxdelta ) { if ( m1 == m2 ) { return true ; } if ( m1 == null || m2 == null ) { return false ; } final int rowdim = m1 . length ; if ( rowdim != m2 . length ) { return false ; } for ( int i = 0 ; i < rowdim ; i ++ ) { if ( Math . abs ( m1 [ i ] - m2 [ i ] ) > maxdelta ) { return false ; } } return true ; } | Compare two matrices with a delta parameter to take numerical errors into account . | 132 | 15 |
157,277 | public static double angle ( double [ ] v1 , double [ ] v2 ) { final int mindim = ( v1 . length <= v2 . length ) ? v1 . length : v2 . length ; // Essentially, we want to compute this: // v1.transposeTimes(v2) / (v1.euclideanLength() * v2.euclideanLength()); // We can just compute all three in parallel. double s = 0 , e1 = 0 , e2 = 0 ; for ( int k = 0 ; k < mindim ; k ++ ) { final double r1 = v1 [ k ] , r2 = v2 [ k ] ; s += r1 * r2 ; e1 += r1 * r1 ; e2 += r2 * r2 ; } for ( int k = mindim ; k < v1 . length ; k ++ ) { final double r1 = v1 [ k ] ; e1 += r1 * r1 ; } for ( int k = mindim ; k < v2 . length ; k ++ ) { final double r2 = v2 [ k ] ; e2 += r2 * r2 ; } double a = FastMath . sqrt ( ( s / e1 ) * ( s / e2 ) ) ; return ( a < 1. ) ? a : 1. ; } | Compute the cosine of the angle between two vectors where the smaller angle between those vectors is viewed . | 292 | 21 |
157,278 | protected void updateFromSelection ( ) { DBIDSelection sel = context . getSelection ( ) ; if ( sel != null ) { this . dbids = DBIDUtil . newArray ( sel . getSelectedIds ( ) ) ; this . dbids . sort ( ) ; } else { this . dbids = DBIDUtil . newArray ( ) ; } } | Update our selection | 86 | 3 |
157,279 | public static DataStoreEvent insertionEvent ( DBIDs inserts ) { return new DataStoreEvent ( inserts , DBIDUtil . EMPTYDBIDS , DBIDUtil . EMPTYDBIDS ) ; } | Insertion event . | 43 | 4 |
157,280 | public static DataStoreEvent removalEvent ( DBIDs removals ) { return new DataStoreEvent ( DBIDUtil . EMPTYDBIDS , removals , DBIDUtil . EMPTYDBIDS ) ; } | Removal event . | 47 | 4 |
157,281 | public static DataStoreEvent updateEvent ( DBIDs updates ) { return new DataStoreEvent ( DBIDUtil . EMPTYDBIDS , DBIDUtil . EMPTYDBIDS , updates ) ; } | Update event . | 43 | 3 |
157,282 | private Visualization instantiateVisualization ( VisualizationTask task ) { try { Visualization v = task . getFactory ( ) . makeVisualization ( context , task , this , width , height , item . proj ) ; if ( task . has ( RenderFlag . NO_EXPORT ) ) { v . getLayer ( ) . setAttribute ( NO_EXPORT_ATTRIBUTE , NO_EXPORT_ATTRIBUTE ) ; } return v ; } catch ( Exception e ) { if ( LOG . isDebugging ( ) ) { LOG . warning ( "Visualizer " + task . getFactory ( ) . getClass ( ) . getName ( ) + " failed." , e ) ; } else { LOG . warning ( "Visualizer " + task . getFactory ( ) . getClass ( ) . getName ( ) + " failed - enable debugging to see details: " + e . toString ( ) ) ; } } return null ; } | Instantiate a visualization . | 203 | 5 |
157,283 | public void destroy ( ) { context . removeVisualizationListener ( this ) ; context . removeResultListener ( this ) ; for ( Entry < VisualizationTask , Visualization > v : taskmap . entrySet ( ) ) { Visualization vis = v . getValue ( ) ; if ( vis != null ) { vis . destroy ( ) ; } } taskmap . clear ( ) ; } | Cleanup function . To remove listeners . | 81 | 8 |
157,284 | private void lazyRefresh ( ) { Runnable pr = new Runnable ( ) { @ Override public void run ( ) { if ( pendingRefresh . compareAndSet ( this , null ) ) { refresh ( ) ; } } } ; pendingRefresh . set ( pr ) ; scheduleUpdate ( pr ) ; } | Trigger a refresh . | 69 | 4 |
157,285 | public boolean nextLine ( ) throws IOException { while ( reader . readLine ( buf . delete ( 0 , buf . length ( ) ) ) ) { ++ lineNumber ; if ( lengthWithoutLinefeed ( buf ) > 0 ) { return true ; } } return false ; } | Read the next line . | 58 | 5 |
157,286 | public static int lengthWithoutLinefeed ( CharSequence line ) { int length = line . length ( ) ; while ( length > 0 ) { char last = line . charAt ( length - 1 ) ; if ( last != ' ' && last != ' ' ) { break ; } -- length ; } return length ; } | Get the length of the string not taking trailing linefeeds into account . | 67 | 15 |
157,287 | public synchronized void logAndClearReportedErrors ( ) { for ( ParameterException e : getErrors ( ) ) { if ( LOG . isDebugging ( ) ) { LOG . warning ( e . getMessage ( ) , e ) ; } else { LOG . warning ( e . getMessage ( ) ) ; } } clearErrors ( ) ; } | Log any error that has accumulated . | 76 | 7 |
157,288 | public void addParameter ( Object owner , Parameter < ? > param , TrackParameters track ) { this . setBorder ( new SoftBevelBorder ( SoftBevelBorder . LOWERED ) ) ; ParameterConfigurator cfg = null ; { // Find Object cur = owner ; while ( cur != null ) { cfg = childconfig . get ( cur ) ; if ( cfg != null ) { break ; } cur = track . getParent ( cur ) ; } } if ( cfg != null ) { cfg . addParameter ( owner , param , track ) ; return ; } else { cfg = makeConfigurator ( param ) ; cfg . addChangeListener ( this ) ; children . add ( cfg ) ; } } | Add parameter to this panel . | 158 | 6 |
157,289 | protected static < E extends MTreeEntry , N extends AbstractMTreeNode < ? , N , E > > double [ ] [ ] computeDistanceMatrix ( AbstractMTree < ? , N , E , ? > tree , N node ) { final int n = node . getNumEntries ( ) ; double [ ] [ ] distancematrix = new double [ n ] [ n ] ; // Build distance matrix for ( int i = 0 ; i < n ; i ++ ) { E ei = node . getEntry ( i ) ; double [ ] row_i = distancematrix [ i ] ; for ( int j = i + 1 ; j < n ; j ++ ) { row_i [ j ] = distancematrix [ j ] [ i ] = tree . distance ( ei , node . getEntry ( j ) ) ; } } return distancematrix ; } | Compute the pairwise distances in the given node . | 184 | 11 |
157,290 | protected static double sparsity ( final int setsize , final int dbsize , final int k , final double phi ) { // calculate sparsity c final double fK = MathUtil . powi ( 1. / phi , k ) ; return ( setsize - ( dbsize * fK ) ) / FastMath . sqrt ( dbsize * fK * ( 1 - fK ) ) ; } | Method to calculate the sparsity coefficient of . | 90 | 9 |
157,291 | protected DBIDs computeSubspace ( int [ ] subspace , ArrayList < ArrayList < DBIDs > > ranges ) { HashSetModifiableDBIDs ids = DBIDUtil . newHashSet ( ranges . get ( subspace [ 0 ] ) . get ( subspace [ 1 ] ) ) ; // intersect all selected dimensions for ( int i = 2 , e = subspace . length - 1 ; i < e ; i += 2 ) { DBIDs current = ranges . get ( subspace [ i ] ) . get ( subspace [ i + 1 ] - GENE_OFFSET ) ; ids . retainAll ( current ) ; if ( ids . isEmpty ( ) ) { break ; } } return ids ; } | Method to get the ids in the given subspace . | 156 | 12 |
157,292 | protected DBIDs computeSubspaceForGene ( short [ ] gene , ArrayList < ArrayList < DBIDs > > ranges ) { HashSetModifiableDBIDs m = null ; // intersect all present restrictions for ( int i = 0 ; i < gene . length ; i ++ ) { if ( gene [ i ] != DONT_CARE ) { DBIDs current = ranges . get ( i ) . get ( gene [ i ] - GENE_OFFSET ) ; if ( m == null ) { m = DBIDUtil . newHashSet ( current ) ; } else { m . retainAll ( current ) ; } } } assert ( m != null ) : "All genes set to '*', should not happen!" ; return m ; } | Get the DBIDs in the current subspace . | 157 | 10 |
157,293 | private static void updateFilterSDASet ( double mib , List < SteepDownArea > sdaset , double ixi ) { Iterator < SteepDownArea > iter = sdaset . iterator ( ) ; while ( iter . hasNext ( ) ) { SteepDownArea sda = iter . next ( ) ; if ( sda . getMaximum ( ) * ixi <= mib ) { iter . remove ( ) ; } else { // Update if ( mib > sda . getMib ( ) ) { sda . setMib ( mib ) ; } } } } | Update the mib values of SteepDownAreas and remove obsolete areas . | 130 | 16 |
157,294 | private static void sort5 ( double [ ] keys , int [ ] vals , final int m1 , final int m2 , final int m3 , final int m4 , final int m5 ) { if ( keys [ m1 ] > keys [ m2 ] ) { swap ( keys , vals , m1 , m2 ) ; } if ( keys [ m3 ] > keys [ m4 ] ) { swap ( keys , vals , m3 , m4 ) ; } // Merge 1+2 and 3+4 if ( keys [ m2 ] > keys [ m4 ] ) { swap ( keys , vals , m2 , m4 ) ; } if ( keys [ m1 ] > keys [ m3 ] ) { swap ( keys , vals , m1 , m3 ) ; } if ( keys [ m2 ] > keys [ m3 ] ) { swap ( keys , vals , m2 , m3 ) ; } // Insertion sort m5: if ( keys [ m4 ] > keys [ m5 ] ) { swap ( keys , vals , m4 , m5 ) ; if ( keys [ m3 ] > keys [ m4 ] ) { swap ( keys , vals , m3 , m4 ) ; if ( keys [ m2 ] > keys [ m3 ] ) { swap ( keys , vals , m2 , m3 ) ; if ( keys [ m1 ] > keys [ m1 ] ) { swap ( keys , vals , m1 , m2 ) ; } } } } } | An explicit sort for the five pivot candidates . | 330 | 9 |
157,295 | private static void swap ( double [ ] keys , int [ ] vals , int j , int i ) { double td = keys [ j ] ; keys [ j ] = keys [ i ] ; keys [ i ] = td ; int ti = vals [ j ] ; vals [ j ] = vals [ i ] ; vals [ i ] = ti ; } | Swap two entries . | 78 | 5 |
157,296 | public EvaluationResult . MeasurementGroup newGroup ( String string ) { EvaluationResult . MeasurementGroup g = new MeasurementGroup ( string ) ; groups . add ( g ) ; return g ; } | Add a new measurement group . | 41 | 6 |
157,297 | public EvaluationResult . MeasurementGroup findOrCreateGroup ( String label ) { for ( EvaluationResult . MeasurementGroup g : groups ) { if ( label . equals ( g . getName ( ) ) ) { return g ; } } return newGroup ( label ) ; } | Find or add a new measurement group . | 57 | 8 |
157,298 | public int numLines ( ) { int r = header . size ( ) ; for ( MeasurementGroup m : groups ) { r += 1 + m . measurements . size ( ) ; } return r ; } | Number of lines recommended for display . | 44 | 7 |
157,299 | public static EvaluationResult findOrCreate ( ResultHierarchy hierarchy , Result parent , String name , String shortname ) { ArrayList < EvaluationResult > ers = ResultUtil . filterResults ( hierarchy , parent , EvaluationResult . class ) ; EvaluationResult ev = null ; for ( EvaluationResult e : ers ) { if ( shortname . equals ( e . getShortName ( ) ) ) { ev = e ; break ; } } if ( ev == null ) { ev = new EvaluationResult ( name , shortname ) ; hierarchy . add ( parent , ev ) ; } return ev ; } | Find or create an evaluation result . | 125 | 7 |
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