Commit 77c78973 authored by Andrey Filippov's avatar Andrey Filippov

addedsome of the most used parameters to batch dialog

parent 75d7b5e2
......@@ -557,7 +557,9 @@ public class EyesisCorrectionParameters {
gd.addNumericField("Maximal disparity to try", clt_parameters.grow_disp_max, 6);
gd.addCheckbox ("Equalize green channel gain of the individual cnannels (bug fix for exposure)", clt_parameters.gain_equalize);
gd.addNumericField("Inverse distance to infinity (misalignment correction)", clt_parameters.z_correction, 6);
gd.addNumericField("Number of clusters to keep", clt_parameters.tsNumClust, 0);
gd.addNumericField("Maximal number of output meshes to generate", clt_parameters.max_clusters, 0);
}
WindowTools.addScrollBars(gd);
gd.showDialog();
......@@ -593,7 +595,9 @@ public class EyesisCorrectionParameters {
if (clt_parameters != null) {
clt_parameters.grow_disp_max = gd.getNextNumber();
clt_parameters.gain_equalize = gd.getNextBoolean();
clt_parameters.z_correction = gd.getNextNumber();
clt_parameters.z_correction = gd.getNextNumber();
clt_parameters.tsNumClust = (int) gd.getNextNumber();
clt_parameters.max_clusters = (int) gd.getNextNumber();
}
return true;
}
......@@ -2399,7 +2403,7 @@ public class EyesisCorrectionParameters {
// New for initial growing
public boolean gr_new_expand = true;
public int gr_max_expand = 500; // 150; // 30;
// public int gr_max_expand = 500; // 150; // 30;
public double gr_ovrbg_cmb = 0.3; // 0.3;
public double gr_ovrbg_cmb_hor = 0.3; // 0.3;
public double gr_ovrbg_cmb_vert = 0.3; // 0.3;
......@@ -2520,7 +2524,7 @@ public class EyesisCorrectionParameters {
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 plDiscrVariants = 500; // 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)
......@@ -3031,7 +3035,7 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"grow_retry_inf", this.grow_retry_inf+"");
properties.setProperty(prefix+"gr_new_expand", this.gr_new_expand+"");
properties.setProperty(prefix+"gr_max_expand", this.gr_max_expand+"");
// properties.setProperty(prefix+"gr_max_expand", this.gr_max_expand+"");
properties.setProperty(prefix+"fds_str_floor", this.fds_str_floor +"");
properties.setProperty(prefix+"gr_ovrbg_cmb", this.gr_ovrbg_cmb +"");
properties.setProperty(prefix+"gr_ovrbg_cmb_hor", this.gr_ovrbg_cmb_hor +"");
......@@ -3145,7 +3149,7 @@ public class EyesisCorrectionParameters {
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+"plDiscrVariants", this.plDiscrVariants+"");
properties.setProperty(prefix+"plDiscrMode", this.plDiscrMode+"");
properties.setProperty(prefix+"plDiscrVarFloor", this.plDiscrVarFloor +"");
properties.setProperty(prefix+"plDiscrSigma", this.plDiscrSigma +"");
......@@ -3632,7 +3636,7 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"grow_retry_inf")!=null) this.grow_retry_inf=Boolean.parseBoolean(properties.getProperty(prefix+"grow_retry_inf"));
if (properties.getProperty(prefix+"gr_new_expand")!=null) this.gr_new_expand=Boolean.parseBoolean(properties.getProperty(prefix+"gr_new_expand"));
if (properties.getProperty(prefix+"gr_max_expand")!=null) this.gr_max_expand=Integer.parseInt(properties.getProperty(prefix+"gr_max_expand"));
// if (properties.getProperty(prefix+"gr_max_expand")!=null) this.gr_max_expand=Integer.parseInt(properties.getProperty(prefix+"gr_max_expand"));
if (properties.getProperty(prefix+"fds_str_floor")!=null) this.fds_str_floor=Double.parseDouble(properties.getProperty(prefix+"fds_str_floor"));
if (properties.getProperty(prefix+"gr_ovrbg_cmb")!=null) this.gr_ovrbg_cmb=Double.parseDouble(properties.getProperty(prefix+"gr_ovrbg_cmb"));
if (properties.getProperty(prefix+"gr_ovrbg_cmb_hor")!=null) this.gr_ovrbg_cmb_hor=Double.parseDouble(properties.getProperty(prefix+"gr_ovrbg_cmb_hor"));
......@@ -3745,7 +3749,7 @@ public class EyesisCorrectionParameters {
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+"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"));
......@@ -4173,7 +4177,7 @@ public class EyesisCorrectionParameters {
gd.addNumericField("Set new pole segment strength to max of horizontal correlation and this value", this.poles_min_strength, 3);
gd.addCheckbox ("Set disparity to that of the bottom of existing segment (false - use hor. disparity)",this.poles_force_disp);
gd.addNumericField("Maximal number of clusters to generate for one run", this.max_clusters, 0);
gd.addNumericField("Maximal number of output meshes to generate", this.max_clusters, 0);
gd.addCheckbox ("Remove all unneeded scans when generating x3d output to save memory", this.remove_scans);
gd.addCheckbox ("Generate x3d output", this.output_x3d);
gd.addCheckbox ("Generate Wavefront obj output", this.output_obj);
......@@ -4273,7 +4277,7 @@ public class EyesisCorrectionParameters {
gd.addMessage ("--- more growing parameters ---");
gd.addCheckbox ("New expansion mode", this.gr_new_expand);
gd.addNumericField("Expansion steps limit", this.gr_max_expand, 0);
// gd.addNumericField("Expansion steps limit", this.gr_max_expand, 0);
gd.addNumericField("Strength floor for multi-tile (now 5x5) samples (normally < combine_min_strength) ", this.fds_str_floor, 6);
gd.addNumericField("Over background extra reliable strength", this.gr_ovrbg_cmb, 6);
gd.addNumericField("Over background extra reliable strength horizontal", this.gr_ovrbg_cmb_hor, 6);
......@@ -4397,7 +4401,7 @@ public class EyesisCorrectionParameters {
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("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);
......@@ -4898,7 +4902,7 @@ public class EyesisCorrectionParameters {
this.grow_retry_inf= gd.getNextBoolean();
this.gr_new_expand= gd.getNextBoolean();
this.gr_max_expand= (int) gd.getNextNumber();
// this.gr_max_expand= (int) gd.getNextNumber();
this.fds_str_floor= gd.getNextNumber();
this.gr_ovrbg_cmb= gd.getNextNumber();
this.gr_ovrbg_cmb_hor= gd.getNextNumber();
......@@ -5012,7 +5016,7 @@ public class EyesisCorrectionParameters {
this.plDiscrTolerance= gd.getNextNumber();
this.plDiscrDispRange= gd.getNextNumber();
this.plDiscrSteps= (int) gd.getNextNumber();
this.plDiscrVariants= (int) gd.getNextNumber();
// this.plDiscrVariants= (int) gd.getNextNumber();
this.plDiscrMode= (int) gd.getNextNumber();
this.plDiscrVarFloor= gd.getNextNumber();
this.plDiscrSigma= gd.getNextNumber();
......
......@@ -6284,15 +6284,6 @@ public class QuadCLT {
final int disp_index = ImageDtt.DISPARITY_INDEX_CM;
final int str_index = ImageDtt.DISPARITY_STRENGTH_INDEX;
final double strength_floor = clt_parameters.fds_str_floor; // 0.6* clt_parameters.combine_min_strength;
// final double strength_floor = 0.8* clt_parameters.combine_min_strength;
// TODO: define, make parameters
// final double comboMinStrength = clt_parameters.gr_ovrbg_cmb; // 0.3; // 0.3;
// final double comboMinStrengthHor = clt_parameters.gr_ovrbg_cmb_hor ; // 0.3; // 0.3;
// final double comboMinStrengthVert =clt_parameters.gr_ovrbg_cmb_vert ; // 0.3; // 0.3;
// final double filterMinStrength = clt_parameters.gr_ovrbg_filtered ; // 0.3; // 0.3;
// TODO: make parameters
final double strength_pow = clt_parameters.fds_str_pow ; // 1.0;
......@@ -6308,13 +6299,7 @@ public class QuadCLT {
final int dbg_x = 155;
final int dbg_y = 207;
// TEMPORARY EXIT
// if (tp.clt_3d_passes.size() > 0) return null; // just to fool compiler
// above - multiple refinements (reduce, make conditional?)
int num_extended = -1;
// int [] numLeftRemoved;
// process once more to try combining of processed
boolean last_pass = false;
// for (int num_expand = 0; (num_expand < 4) && (num_extended != 0); num_expand++) {
......@@ -8379,7 +8364,7 @@ public class QuadCLT {
int nSet = 0;
for (nSet = 0; nSet < setNames.size(); nSet++){
if ((nSet > 0) &&(debugLevel > -2)) {
System.out.println("Processing set "+(nSet+1)+" (of "+setNames.size()+") finished at "+
System.out.println("Processing set "+(nSet+0)+" (of "+setNames.size()+") finished at "+
IJ.d2s(0.000000001*(System.nanoTime()-this.startSetTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
}
this.startSetTime = System.nanoTime();
......
......@@ -2263,7 +2263,7 @@ public class SuperTiles{
final double plDiscrTolerance, // = 0.4; // Maximal disparity difference from the plane to consider tile
final double plDiscrDispRange, // = 0.6; // Parallel move known planes around original know value for the best overall fit
final int plDiscrSteps, // = 3; // Number of steps (each direction) for each plane to search for the best fit (0 - single, 1 - 1 each side)
final int plDiscrVariants, // = 100; // Total number of variants to try (protect from too many planes)
// final int plDiscrVariants, // = 100; // Total number of variants to try (protect from too many planes)
final int plDiscrMode, // = 3; // What plane to use as a hint: 0 - weighted, 1 - equalized, 2 - best, 3 - combined
final double plDiscrVarFloor, // = 0.03; // Squared add to variance to calculate reverse flatness (used mostly for single-cell clusters)
......@@ -2785,7 +2785,7 @@ public class SuperTiles{
final double plDiscrTolerance, // = 0.4; // Maximal disparity difference from the plane to consider tile
final double plDiscrDispRange, // = 0.6; // Parallel move known planes around original know value for the best overall fit
final int plDiscrSteps, // = 3; // Number of steps (each direction) for each plane to search for the best fit (0 - single, 1 - 1 each side)
final int plDiscrVariants, // = 100; // Total number of variants to try (protect from too many planes)
// final int plDiscrVariants, // = 100; // Total number of variants to try (protect from too many planes)
final int plDiscrMode, // = 3; // What plane to use as a hint: 0 - weighted, 1 - equalized, 2 - best, 3 - combined
final double plDiscrVarFloor, // = 0.03; // Squared add to variance to calculate reverse flatness (used mostly for single-cell clusters)
......@@ -2827,7 +2827,7 @@ public class SuperTiles{
plDiscrTolerance, //final double plDiscrTolerance, // = 0.4; // Maximal disparity difference from the plane to consider tile
plDiscrDispRange, // final double plDiscrDispRange, // = 0.6; // Parallel move known planes around original know value for the best overall fit
plDiscrSteps, // final int plDiscrSteps, // = 3; // Number of steps (each direction) for each plane to search for the best fit (0 - single, 1 - 1 each side)
plDiscrVariants, // final int plDiscrVariants, // = 100; // Total number of variants to try (protect from too many planes)
// plDiscrVariants, // final int plDiscrVariants, // = 100; // Total number of variants to try (protect from too many planes)
plDiscrMode, // final int plDiscrMode, // = 3; // What plane to use as a hint: 0 - weighted, 1 - equalized, 2 - best, 3 - combined
plDiscrVarFloor, // final double plDiscrVarFloor, // = 0.03; // Squared add to variance to calculate reverse flatness (used mostly for single-cell clusters)
......
......@@ -1562,7 +1562,7 @@ public class TileProcessor {
// scan.restoreKeepTileOpDisparity();// it is not used from this scan, but from last_scan
continue;
}
if (debugLevel > -1){
if (debugLevel > -2){
System.out.println("prepareExpandVariants(): remaining "+num_left+" tiles to be processed, used variant "+num_var+" ("+num_left+")");
}
int [] rslt = {num_left, num_var};
......@@ -5261,7 +5261,7 @@ public class TileProcessor {
clt_parameters.plDiscrTolerance, // final double plDiscrTolerance, // = 0.4; // Maximal disparity difference from the plane to consider tile
clt_parameters.plDiscrDispRange, // final double plDiscrDispRange, // = 0.6; // Parallel move known planes around original know value for the best overall fit
clt_parameters.plDiscrSteps, // final int plDiscrSteps, // = 3; // Number of steps (each direction) for each plane to search for the best fit (0 - single, 1 - 1 each side)
clt_parameters.plDiscrVariants, // final int plDiscrVariants, // = 100; // Total number of variants to try (protect from too many planes)
// clt_parameters.plDiscrVariants, // final int plDiscrVariants, // = 100; // Total number of variants to try (protect from too many planes)
clt_parameters.plDiscrMode, // final int plDiscrMode, // = 3; // What plane to use as a hint: 0 - weighted, 1 - equalized, 2 - best, 3 - combined
clt_parameters.plDiscrVarFloor, // final double plDiscrVarFloor, // = 0.03; // Squared add to variance to calculate reverse flatness (used mostly for single-cell clusters)
......
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