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Commit e5d30e06 authored by Andrey Filippov's avatar Andrey Filippov
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working on re-discriminating, some bug fixes

parent 0ab422e2
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Showing with 1376 additions and 274 deletions
src/main/java/EyesisCorrectionParameters.java
View file @ e5d30e06
......@@ -2188,7 +2188,20 @@ public class EyesisCorrectionParameters {
public double plMaxZRatio = 2.0; // Maximal ratio of Z to allow plane merging
public double plMaxDisp = 0.6; // Maximal disparity of one of the planes to apply maximal ratio
public double plCutTail = 1.4; // When merging with neighbors cut the tail that is worse than scaled best
public double plMinTail = 0.015;// Set cutoff value livel not less than
public double plMinTail = 0.015;// Set cutoff value level not less than
// parameters to recreate planes from tiles disparity/strengths using determined plane connections to neighbors
public double plDiscrTolerance = 0.4; // Maximal disparity difference from the plane to consider tile
public double plDiscrDispRange = 1.0; // Parallel move known planes around original know value for the best overall fit
public int plDiscrSteps = 10; // Number of steps (each direction) for each plane to search for the best fit (0 - single, 1 - 1 each side)
public int plDiscrVariants = 100; // total number of variants to try (protect from too many planes)
public int plDiscrMode = 3; // 0 - weighted, 1 - equalized, 2 - best, 3 - combined
public double plDiscrVarFloor = 0.03; // Squared add to variance to calculate reverse flatness (used mostly for single-cell clusters)
public double plDiscrSigma = 0.05; // Gaussian sigma to compare how measured data is attracted to planes
public double plDiscrBlur = 0.05; // Sigma to blur histograms while re-discriminating
public double plDiscrExclusivity = 1.5; // Tile exclusivity: 1.0 - tile belongs to one plane only, 0.0 - regardless of others
public double plDiscrExclus2 = 0.8; // For second pass if exclusivity > 1.0 - will assign only around strong neighbors
public boolean plDiscrStrict = false; // When growing selection do not allow any offenders around (false - more these than others)
// comparing merge quality for plane pairs
public double plCostKrq = 0.8; // cost of merge quality weighted in disparity space
......@@ -2578,6 +2591,18 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"plCutTail", this.plCutTail +"");
properties.setProperty(prefix+"plMinTail", this.plMinTail +"");
properties.setProperty(prefix+"plDiscrTolerance", this.plDiscrTolerance +"");
properties.setProperty(prefix+"plDiscrDispRange", this.plDiscrDispRange +"");
properties.setProperty(prefix+"plDiscrSteps", this.plDiscrSteps+"");
properties.setProperty(prefix+"plDiscrVariants", this.plDiscrVariants+"");
properties.setProperty(prefix+"plDiscrMode", this.plDiscrMode+"");
properties.setProperty(prefix+"plDiscrVarFloor", this.plDiscrVarFloor +"");
properties.setProperty(prefix+"plDiscrSigma", this.plDiscrSigma +"");
properties.setProperty(prefix+"plDiscrBlur", this.plDiscrBlur +"");
properties.setProperty(prefix+"plDiscrExclusivity",this.plDiscrExclusivity +"");
properties.setProperty(prefix+"plDiscrExclus2", this.plDiscrExclus2 +"");
properties.setProperty(prefix+"plDiscrStrict", this.plDiscrStrict+"");
properties.setProperty(prefix+"plCostKrq", this.plCostKrq +"");
properties.setProperty(prefix+"plCostKrqEq", this.plCostKrqEq +"");
properties.setProperty(prefix+"plCostWrq", this.plCostWrq +"");
......@@ -2943,6 +2968,18 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"plCutTail")!=null) this.plCutTail=Double.parseDouble(properties.getProperty(prefix+"plCutTail"));
if (properties.getProperty(prefix+"plMinTail")!=null) this.plMinTail=Double.parseDouble(properties.getProperty(prefix+"plMinTail"));
if (properties.getProperty(prefix+"plDiscrTolerance")!=null) this.plDiscrTolerance=Double.parseDouble(properties.getProperty(prefix+"plDiscrTolerance"));
if (properties.getProperty(prefix+"plDiscrDispRange")!=null) this.plDiscrDispRange=Double.parseDouble(properties.getProperty(prefix+"plDiscrDispRange"));
if (properties.getProperty(prefix+"plDiscrSteps")!=null) this.plDiscrSteps=Integer.parseInt(properties.getProperty(prefix+"plDiscrSteps"));
if (properties.getProperty(prefix+"plDiscrVariants")!=null) this.plDiscrVariants=Integer.parseInt(properties.getProperty(prefix+"plDiscrVariants"));
if (properties.getProperty(prefix+"plDiscrMode")!=null) this.plDiscrMode=Integer.parseInt(properties.getProperty(prefix+"plDiscrMode"));
if (properties.getProperty(prefix+"plDiscrVarFloor")!=null) this.plDiscrVarFloor=Double.parseDouble(properties.getProperty(prefix+"plDiscrVarFloor"));
if (properties.getProperty(prefix+"plDiscrSigma")!=null) this.plDiscrSigma=Double.parseDouble(properties.getProperty(prefix+"plDiscrSigma"));
if (properties.getProperty(prefix+"plDiscrBlur")!=null) this.plDiscrBlur=Double.parseDouble(properties.getProperty(prefix+"plDiscrBlur"));
if (properties.getProperty(prefix+"plDiscrExclusivity")!=null)this.plDiscrExclusivity=Double.parseDouble(properties.getProperty(prefix+"plDiscrExclusivity"));
if (properties.getProperty(prefix+"plDiscrExclus2")!=null) this.plDiscrExclus2=Double.parseDouble(properties.getProperty(prefix+"plDiscrExclus2"));
if (properties.getProperty(prefix+"plDiscrStrict")!=null) this.plDiscrStrict=Boolean.parseBoolean(properties.getProperty(prefix+"plDiscrStrict"));
if (properties.getProperty(prefix+"plCostKrq")!=null) this.plCostKrq=Double.parseDouble(properties.getProperty(prefix+"plCostKrq"));
if (properties.getProperty(prefix+"plCostKrqEq")!=null) this.plCostKrqEq=Double.parseDouble(properties.getProperty(prefix+"plCostKrqEq"));
if (properties.getProperty(prefix+"plCostWrq")!=null) this.plCostWrq=Double.parseDouble(properties.getProperty(prefix+"plCostWrq"));
......@@ -3338,6 +3375,19 @@ public class EyesisCorrectionParameters {
gd.addNumericField("When merging with neighbors cut the tail that is worse than scaled best", this.plCutTail, 6);
gd.addNumericField("Set cutoff value livel not less than this", this.plMinTail, 6);
gd.addMessage ("--- Parameters to regenerate planes using preliminary tile connections ---");
gd.addNumericField("Maximal disparity difference from the plane to consider tile", this.plDiscrTolerance, 6);
gd.addNumericField("Parallel move known planes around original know value for the best overall fit",this.plDiscrDispRange, 6);
gd.addNumericField("Number of steps (each direction) for each plane to search for the best fit (0 - single, 1 - 1 each side)",this.plDiscrSteps, 0);
gd.addNumericField("Total number of variants to try (protect from too many planes)", this.plDiscrVariants, 0);
gd.addNumericField("What plane to use as a hint: 0 - weighted, 1 - equalized, 2 - best, 3 - combined", this.plDiscrMode, 0);
gd.addNumericField("Squared add to variance to calculate reverse flatness (used mostly for single-cell clusters)",this.plDiscrVarFloor, 6);
gd.addNumericField("Gaussian sigma to compare how measured data is attracted to planes", this.plDiscrSigma, 6);
gd.addNumericField("Sigma to blur histograms while re-discriminating", this.plDiscrBlur, 6);
gd.addNumericField("Tile exclusivity: 1.0 - tile belongs to one plane only, 0.0 - regardless of others",this.plDiscrExclusivity, 6);
gd.addNumericField("For second pass if exclusivity > 1.0 - will assign only around strong neighbors",this.plDiscrExclus2, 6);
gd.addCheckbox ("When growing selection do not allow any offenders around (false - more these than others)", this.plDiscrStrict);
gd.addMessage ("--- Planes merge costs ---");
gd.addNumericField("Cost of merge quality weighted in disparity space", this.plCostKrq, 6);
gd.addNumericField("Cost of merge quality equal weight in disparity space", this.plCostKrqEq, 6);
......@@ -3717,6 +3767,18 @@ public class EyesisCorrectionParameters {
this.plCutTail= gd.getNextNumber();
this.plMinTail= gd.getNextNumber();
this.plDiscrTolerance= gd.getNextNumber();
this.plDiscrDispRange= gd.getNextNumber();
this.plDiscrSteps= (int) gd.getNextNumber();
this.plDiscrVariants= (int) gd.getNextNumber();
this.plDiscrMode= (int) gd.getNextNumber();
this.plDiscrVarFloor= gd.getNextNumber();
this.plDiscrSigma= gd.getNextNumber();
this.plDiscrBlur= gd.getNextNumber();
this.plDiscrExclusivity= gd.getNextNumber();
this.plDiscrExclus2= gd.getNextNumber();
this.plDiscrStrict= gd.getNextBoolean();
this.plCostKrq= gd.getNextNumber();
this.plCostKrqEq= gd.getNextNumber();
this.plCostWrq= gd.getNextNumber();
......
src/main/java/LinkPlanes.java
View file @ e5d30e06
......@@ -282,7 +282,7 @@ public class LinkPlanes {
w2, // double w2)
0.0);// double eigen_floor)
double this_wrq_norm = this_rq;
double this_wrq_norm = this_wrq;
if ((w1 + w2) < plWeakWorsening) this_wrq_norm *= (w1 + w2) / plWeakWorsening; // forgive more for weak planes
double this_wrq_eq = mergeRQuality(
......@@ -293,7 +293,7 @@ public class LinkPlanes {
1.0, // double w2)
0.0);// double eigen_floor)
this_wrq_eq /= (w1 + w2); // for comparison reduce this value for stronger planes
double this_wrq_eq_norm = this_rq_eq;
double this_wrq_eq_norm = this_wrq_eq;
if ((w1 + w2) < plWeakWorsening) this_wrq_eq_norm *= (w1 + w2) / plWeakWorsening; // forgive more for weak planes
boolean OK_to_merge = false;
......@@ -395,9 +395,13 @@ public class LinkPlanes {
if (debugLevel > 1){
System.out.println(prefix+" (do not fit) this_rq="+this_rq+
", this_rq_eq="+this_rq_eq+
" this_wrq=" + (this_wrq) +
" this_wrq_eq=" + (this_wrq_eq) +
" w1="+w1+" w2="+w2+
" L1="+plane1.getValue()+" L2="+plane2.getValue()+
" L="+merged_ev+" L_eq="+merged_ev_eq);
" L="+merged_ev+" L_eq="+merged_ev_eq+
" L1W="+plane1.getWValue()+" L2W="+plane2.getWValue()+" LW="+merged_wev+
" L_eqW="+merged_wev_eq);
System.out.println(prefix+" (do not fit) world sin2 ="+
plane1.getWorldSin2(plane2));
System.out.println(prefix+" (do not fit)"+
......
src/main/java/SuperTiles.java
View file @ e5d30e06
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src/main/java/TilePlanes.java
View file @ e5d30e06
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src/main/java/TileProcessor.java
View file @ e5d30e06
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