TrakEM2_/src/main/java/mpicbg/trakem2/align/AbstractLayerAlignmentParam.java

   1 package mpicbg.trakem2.align;
   2
   3 import ij.gui.GenericDialog;
   4 import mpicbg.ij.SIFT;
   5 import mpicbg.trakem2.align.AlignmentUtils.ParamPointMatch;
   6
   7 public class AbstractLayerAlignmentParam
   8 {
   9         final public ParamPointMatch ppm = new ParamPointMatch();
  10         {
  11                 ppm.sift.fdSize = 8;
  12         }
  13
  14         /**
  15          * Maximal accepted alignment error in px
  16          */
  17         public float maxEpsilon = 200.0f;
  18
  19         /**
  20          * Inlier/candidates ratio
  21          */
  22         public float minInlierRatio = 0.0f;
  23
  24         /**
  25          * Minimal absolute number of inliers
  26          */
  27         public int minNumInliers = 12;
  28
  29         /**
  30          * Transformation models for choice
  31          */
  32         final static public String[] modelStrings = new String[]{ "Translation", "Rigid", "Similarity", "Affine" };
  33         public int expectedModelIndex = 3;
  34         public boolean multipleHypotheses = false;
  35
  36         /**
  37          * Ignore identity transform up to a given tolerance
  38          */
  39         public boolean rejectIdentity = false;
  40         public float identityTolerance = 5.0f;
  41
  42         /**
  43          * Maximal number of consecutive sections to be tested for an alignment model
  44          */
  45         public int maxNumNeighbors = 1;
  46
  47         /**
  48          * Maximal number of consecutive slices for which no model could be found
  49          */
  50         public int maxNumFailures = 3;
  51
  52         public int desiredModelIndex = 1;
  53         public int maxIterationsOptimize = 1000;
  54         public int maxPlateauwidthOptimize = 200;
  55
  56         public boolean visualize = false;
  57
  58         public int maxNumThreads = Runtime.getRuntime().availableProcessors();
  59
  60
  61         public boolean setupSIFT( final String title )
  62         {
  63                 /* SIFT */
  64                 final GenericDialog gdSIFT = new GenericDialog( title + "SIFT parameters" );
  65
  66                 SIFT.addFields( gdSIFT, ppm.sift );
  67
  68                 gdSIFT.addMessage( "Local Descriptor Matching:" );
  69                 gdSIFT.addNumericField( "closest/next_closest_ratio :", ppm.rod, 2 );
  70
  71                 gdSIFT.addMessage( "Miscellaneous:" );
  72                 gdSIFT.addCheckbox( "clear_cache", ppm.clearCache );
  73                 gdSIFT.addNumericField( "feature_extraction_threads :", ppm.maxNumThreadsSift, 0 );
  74
  75                 gdSIFT.showDialog();
  76
  77                 if ( gdSIFT.wasCanceled() )
  78                         return false;
  79
  80                 SIFT.readFields( gdSIFT, ppm.sift );
  81
  82                 ppm.rod = ( float )gdSIFT.getNextNumber();
  83                 ppm.clearCache = gdSIFT.getNextBoolean();
  84                 ppm.maxNumThreadsSift = ( int )gdSIFT.getNextNumber();
  85
  86                 return true;
  87         }
  88
  89         public AbstractLayerAlignmentParam() {}
  90
  91         public AbstractLayerAlignmentParam(
  92                         final int SIFTfdBins,
  93                         final int SIFTfdSize,
  94                         final float SIFTinitialSigma,
  95                         final int SIFTmaxOctaveSize,
  96                         final int SIFTminOctaveSize,
  97                         final int SIFTsteps,
  98
  99                         final boolean clearCache,
 100                         final int maxNumThreadsSift,
 101                         final float rod,
 102
 103                         final int desiredModelIndex,
 104                         final int expectedModelIndex,
 105                         final float identityTolerance,
 106                         final float maxEpsilon,
 107                         final int maxIterationsOptimize,
 108                         final int maxNumFailures,
 109                         final int maxNumNeighbors,
 110                         final int maxNumThreads,
 111                         final int maxPlateauwidthOptimize,
 112                         final float minInlierRatio,
 113                         final int minNumInliers,
 114                         final boolean multipleHypotheses,
 115                         final boolean rejectIdentity,
 116                         final boolean visualize )
 117         {
 118                 ppm.sift.fdBins = SIFTfdBins;
 119                 ppm.sift.fdSize = SIFTfdSize;
 120                 ppm.sift.initialSigma = SIFTinitialSigma;
 121                 ppm.sift.maxOctaveSize = SIFTmaxOctaveSize;
 122                 ppm.sift.minOctaveSize = SIFTminOctaveSize;
 123                 ppm.sift.steps = SIFTsteps;
 124
 125                 ppm.clearCache = clearCache;
 126                 ppm.maxNumThreadsSift = maxNumThreadsSift;
 127                 ppm.rod = rod;
 128
 129                 this.desiredModelIndex = desiredModelIndex;
 130                 this.expectedModelIndex = expectedModelIndex;
 131                 this.identityTolerance = identityTolerance;
 132                 this.maxEpsilon = maxEpsilon;
 133                 this.maxIterationsOptimize = maxIterationsOptimize;
 134                 this.maxNumFailures = maxNumFailures;
 135                 this.maxNumNeighbors = maxNumNeighbors;
 136                 this.maxNumThreads = maxNumThreads;
 137                 this.maxPlateauwidthOptimize = maxPlateauwidthOptimize;
 138                 this.minInlierRatio = minInlierRatio;
 139                 this.minNumInliers = minNumInliers;
 140                 this.multipleHypotheses = multipleHypotheses;
 141                 this.rejectIdentity = rejectIdentity;
 142                 this.visualize = visualize;
 143         }
 144
 145         @Override
 146         public AbstractLayerAlignmentParam clone()
 147         {
 148                 return new AbstractLayerAlignmentParam(
 149                                 ppm.sift.fdBins,
 150                                 ppm.sift.fdSize,
 151                                 ppm.sift.initialSigma,
 152                                 ppm.sift.maxOctaveSize,
 153                                 ppm.sift.minOctaveSize,
 154                                 ppm.sift.steps,
 155
 156                                 ppm.clearCache,
 157                                 ppm.maxNumThreadsSift,
 158                                 ppm.rod,
 159
 160                                 desiredModelIndex,
 161                                 expectedModelIndex,
 162                                 identityTolerance,
 163                                 maxEpsilon,
 164                                 maxIterationsOptimize,
 165                                 maxNumFailures,
 166                                 maxNumNeighbors,
 167                                 maxNumThreads,
 168                                 maxPlateauwidthOptimize,
 169                                 minInlierRatio,
 170                                 minNumInliers,
 171                                 multipleHypotheses,
 172                                 rejectIdentity,
 173                                 visualize );
 174         }
 175 }