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imagej-elphel
Commit 9d5dd318 authored by Andrey Filippov's avatar Andrey Filippov
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refactoring + fixing sensor correction for different resolutions in the 

same system
parent 5e90425c
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Showing with 229 additions and 155 deletions
src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java
View file @ 9d5dd318
...@@ -270,7 +270,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene ...@@ -270,7 +270,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene
1.0, // shiftToRadiusContrib; // Center shift (in pixels) addition to the difference relative to radius difference (in pixels) 1.0, // shiftToRadiusContrib; // Center shift (in pixels) addition to the difference relative to radius difference (in pixels)
2.0, // sharpBonusPower; // increase weight of the "sharp" kernels by dividing weight by radius to this power 2.0, // sharpBonusPower; // increase weight of the "sharp" kernels by dividing weight by radius to this power
0.1, // maxFracDiscardWorse=0.1; // discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger) 0.1, // maxFracDiscardWorse=0.1; // discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger)
0.5, // maxFracDiscardAll=0.5; // continue removing outlayers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse) 0.5, // maxFracDiscardAll=0.5; // continue removing outliers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse)
0.8, //, // internalBonus // cell having 8 around will "seem" twice better than having none (radiusDiff* twice higher) 0.8, //, // internalBonus // cell having 8 around will "seem" twice better than having none (radiusDiff* twice higher)
0.75, // validateThreshold - fraction of full PSF "energy" 0.75, // validateThreshold - fraction of full PSF "energy"
false, // validateShowEllipse - show ellipse parameters of partial PSF arrays false, // validateShowEllipse - show ellipse parameters of partial PSF arrays
...@@ -927,7 +927,7 @@ if (MORE_BUTTONS) { ...@@ -927,7 +927,7 @@ if (MORE_BUTTONS) {
addButton("Filter Grids",panelGoniometer,color_bundle); addButton("Filter Grids",panelGoniometer,color_bundle);
addButton("Update Image Set",panelGoniometer); addButton("Update Image Set",panelGoniometer);
addButton("Remove Outlayers",panelGoniometer,color_bundle); addButton("Remove Outliers",panelGoniometer,color_bundle);
addButton("Remove Sets",panelGoniometer,color_bundle); addButton("Remove Sets",panelGoniometer,color_bundle);
addButton("Update Sets Orientation",panelGoniometer); addButton("Update Sets Orientation",panelGoniometer);
...@@ -2516,7 +2516,7 @@ if (MORE_BUTTONS) { ...@@ -2516,7 +2516,7 @@ if (MORE_BUTTONS) {
gd.addNumericField("Tile half size", tileHalfSize, 0 ,4, "pix"); gd.addNumericField("Tile half size", tileHalfSize, 0 ,4, "pix");
gd.addNumericField("Color channel mask", cmask, 0 ,4, "9 - both green colors"); gd.addNumericField("Color channel mask", cmask, 0 ,4, "9 - both green colors");
gd.addNumericField("\"Normal\" pixels variation", binWidth, 3 ,7, ""); gd.addNumericField("\"Normal\" pixels variation", binWidth, 3 ,7, "");
gd.addNumericField("Empty level gap between \"normal\" pixels and outlayers (caused by wrong cable phase)", gapWidth, 3 ,7, ""); gd.addNumericField("Empty level gap between \"normal\" pixels and outliers (caused by wrong cable phase)", gapWidth, 3 ,7, "");
gd.addNumericField("Disregard pixels above this threshold", satLevel, 3 ,5, "pixel value"); gd.addNumericField("Disregard pixels above this threshold", satLevel, 3 ,5, "pixel value");
gd.addNumericField("Fraction of \"normal\" pixels to determing their average", baseFrac, 3 ,5, "fraction"); gd.addNumericField("Fraction of \"normal\" pixels to determing their average", baseFrac, 3 ,5, "fraction");
gd.addNumericField("Minimal number of non-satureted pixels to process in a tile", minPixToProcess, 0 ,4, "pix"); gd.addNumericField("Minimal number of non-satureted pixels to process in a tile", minPixToProcess, 0 ,4, "pix");
...@@ -2548,7 +2548,7 @@ if (MORE_BUTTONS) { ...@@ -2548,7 +2548,7 @@ if (MORE_BUTTONS) {
COMPONENTS, COMPONENTS,
THREADS_MAX, THREADS_MAX,
DEBUG_LEVEL); DEBUG_LEVEL);
System.out.println("Number of phase outlayer pixels:"+stats[0]); System.out.println("Number of phase outlier pixels:"+stats[0]);
System.out.println("Number of processed pixels:"+stats[1]); System.out.println("Number of processed pixels:"+stats[1]);
return; return;
} }
...@@ -2940,7 +2940,6 @@ if (MORE_BUTTONS) { ...@@ -2940,7 +2940,6 @@ if (MORE_BUTTONS) {
IJ.showMessage("Error",msg); IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
// int series=refineParameters.showDialog("Select Lens Distortion Residual Compensation Parameters", 0x1efff, (this.seriesNumber>=0)?this.seriesNumber:0);
int series=LENS_DISTORTIONS.refineParameters.showDialog( int series=LENS_DISTORTIONS.refineParameters.showDialog(
"Select Lens Distortion Residual Compensation Parameters", "Select Lens Distortion Residual Compensation Parameters",
// 0x846f1, // 0x846f1,
...@@ -5870,7 +5869,7 @@ if (MORE_BUTTONS) { ...@@ -5870,7 +5869,7 @@ if (MORE_BUTTONS) {
return; return;
} }
/* ======================================================================== */ /* ======================================================================== */
if (label.equals("Remove Outlayers")) { if (label.equals("Remove Outliers")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (LENS_DISTORTIONS==null) { if (LENS_DISTORTIONS==null) {
IJ.showMessage("LENS_DISTORTION is not set"); IJ.showMessage("LENS_DISTORTION is not set");
...@@ -5885,9 +5884,9 @@ if (MORE_BUTTONS) { ...@@ -5885,9 +5884,9 @@ if (MORE_BUTTONS) {
selectedChannels=ABERRATIONS_PARAMETERS.getChannelSelection(LENS_DISTORTIONS); selectedChannels=ABERRATIONS_PARAMETERS.getChannelSelection(LENS_DISTORTIONS);
} }
LENS_DISTORTIONS.removeOutLayers( LENS_DISTORTIONS.removeOutLiers(
-1, //int series, (<0 - ask) -1, //int series, (<0 - ask)
-1, //int numOutLayers (<0 - ask) -1, //int numOutLiers (<0 - ask)
selectedChannels selectedChannels
); );
return; return;
...@@ -5903,8 +5902,8 @@ if (MORE_BUTTONS) { ...@@ -5903,8 +5902,8 @@ if (MORE_BUTTONS) {
IJ.showMessage("LENS_DISTORTION.fittingStrategy is not set"); IJ.showMessage("LENS_DISTORTION.fittingStrategy is not set");
return; return;
} }
LENS_DISTORTIONS.removeOutLayerSets( LENS_DISTORTIONS.removeOutLierSets(
-1 //int numOutLayers (<0 - ask) -1 //int numOutLiers (<0 - ask)
); );
return; return;
} }
...@@ -6030,7 +6029,7 @@ if (MORE_BUTTONS) { ...@@ -6030,7 +6029,7 @@ if (MORE_BUTTONS) {
boolean useSetsData= true; boolean useSetsData= true;
gd=new GenericDialog ("Image set # "+imageSetNumber+" re-calibration without laser pointers"); gd=new GenericDialog ("Image set # "+imageSetNumber+" re-calibration without laser pointers");
gd.addMessage("Strategy 0 should have all parameters but 2 goniometer axes disabled"); gd.addMessage("Strategy 0 should have all parameters but 2 goniometer axes disabled");
gd.addMessage("Imgages belonging to the set will be selected, possible to check with \"Remove Outlayers\" for strategy 0"); gd.addMessage("Imgages belonging to the set will be selected, possible to check with \"Remove Outliers\" for strategy 0");
gd.addNumericField("Mismatch tolerance of match between the predicted and acquired grid", hintGridTolerance, 1,4,"fraction of grid half-period"); gd.addNumericField("Mismatch tolerance of match between the predicted and acquired grid", hintGridTolerance, 1,4,"fraction of grid half-period");
gd.addCheckbox("Ignore laser pointers", ignoreLaserPointers); gd.addCheckbox("Ignore laser pointers", ignoreLaserPointers);
gd.addNumericField("Image set tilt", tiltCenter, 2,6,"degrees"); gd.addNumericField("Image set tilt", tiltCenter, 2,6,"degrees");
...@@ -10536,17 +10535,17 @@ if (MORE_BUTTONS) { ...@@ -10536,17 +10535,17 @@ if (MORE_BUTTONS) {
gd.addNumericField("Tile clearSize", tileClearSize, 0 ,4, "pix"); gd.addNumericField("Tile clearSize", tileClearSize, 0 ,4, "pix");
gd.addNumericField("Tile margin (extra) width", tileMargins, 0 ,4, "pix"); gd.addNumericField("Tile margin (extra) width", tileMargins, 0 ,4, "pix");
gd.addNumericField("Color channel mask", cmask, 0 ,4, "9 - both green colors"); gd.addNumericField("Color channel mask", cmask, 0 ,4, "9 - both green colors");
gd.addNumericField("Number of \"remove outlayers\" passes", numPasses, 0 ,4, ""); gd.addNumericField("Number of \"remove outliers\" passes", numPasses, 0 ,4, "");
gd.addNumericField("Number of neighbors (of total 8) to base outlayers", numInBase, 0 ,4, "<=8"); gd.addNumericField("Number of neighbors (of total 8) to base outliers", numInBase, 0 ,4, "<=8");
gd.addNumericField("Base low-pass sigma ", sigma, 3 ,7, "double pixels"); gd.addNumericField("Base low-pass sigma ", sigma, 3 ,7, "double pixels");
gd.addCheckbox ("Process tiles with no outlayer replacements", processNoReplace); gd.addCheckbox ("Process tiles with no outlier replacements", processNoReplace);
gd.addNumericField("\"Normal\" pixels variation", binWidth, 3 ,7, ""); gd.addNumericField("\"Normal\" pixels variation", binWidth, 3 ,7, "");
gd.addNumericField("Empty level gap between \"normal\" pixels and outlayers", gapWidth, 3 ,7, ""); gd.addNumericField("Empty level gap between \"normal\" pixels and outliers", gapWidth, 3 ,7, "");
gd.addNumericField("Post-HPF algorithm number", algNum, 0 ,4, "(1 or 2"); gd.addNumericField("Post-HPF algorithm number", algNum, 0 ,4, "(1 or 2");
gd.addNumericField("Number of neighbors (of total 8) to base outlayers (after high-pass), 0 - no filter", numInBase2, 0 ,4, "<=8"); gd.addNumericField("Number of neighbors (of total 8) to base outliers (after high-pass), 0 - no filter", numInBase2, 0 ,4, "<=8");
gd.addNumericField("\"Normal\" pixels variation (after high-pass)", binWidth2, 3 ,7, ""); gd.addNumericField("\"Normal\" pixels variation (after high-pass)", binWidth2, 3 ,7, "");
gd.addNumericField("Empty level gap between \"normal\" pixels and outlayers (after high-pass)", gapWidth2, 3 ,7, ""); gd.addNumericField("Empty level gap between \"normal\" pixels and outliers (after high-pass)", gapWidth2, 3 ,7, "");
gd.showDialog(); gd.showDialog();
...@@ -10570,7 +10569,7 @@ if (MORE_BUTTONS) { ...@@ -10570,7 +10569,7 @@ if (MORE_BUTTONS) {
tileClearSize, tileClearSize,
tileMargins, tileMargins,
cmask, // bitmask of color channels to process (9 - two greens) cmask, // bitmask of color channels to process (9 - two greens)
numPasses, // number of passes to replace outlayers (will end if none was replaced) numPasses, // number of passes to replace outliers (will end if none was replaced)
numInBase, // number of neighbors (of 8) to use as a base if they all agree numInBase, // number of neighbors (of 8) to use as a base if they all agree
sigma, // for high-pass filtering sigma, // for high-pass filtering
processNoReplace, // calculate differences even if no replacements were made processNoReplace, // calculate differences even if no replacements were made
...@@ -10588,7 +10587,7 @@ if (MORE_BUTTONS) { ...@@ -10588,7 +10587,7 @@ if (MORE_BUTTONS) {
defectsBayer, defectsBayer,
imp_sel.getWidth(), imp_sel.getWidth(),
imp_sel.getHeight(), imp_sel.getHeight(),
"Outlayer pixels"); "Outlier pixels");
int numDefects=0; int numDefects=0;
for (double d:defectsBayer) if (d!=0.0) numDefects++; for (double d:defectsBayer) if (d!=0.0) numDefects++;
if (numDefects>0) System.out.println("Number of pixel (or phase) defects detected: "+numDefects); if (numDefects>0) System.out.println("Number of pixel (or phase) defects detected: "+numDefects);
...@@ -10614,17 +10613,17 @@ if (MORE_BUTTONS) { ...@@ -10614,17 +10613,17 @@ if (MORE_BUTTONS) {
gd.addNumericField("Tile clearSize", tileClearSize, 0 ,4, "pix"); gd.addNumericField("Tile clearSize", tileClearSize, 0 ,4, "pix");
gd.addNumericField("Tile margin (extra) width", tileMargins, 0 ,4, "pix"); gd.addNumericField("Tile margin (extra) width", tileMargins, 0 ,4, "pix");
gd.addNumericField("Color channel mask", cmask, 0 ,4, "9 - both green colors"); gd.addNumericField("Color channel mask", cmask, 0 ,4, "9 - both green colors");
gd.addNumericField("Number of \"remove outlayers\" passes", numPasses, 0 ,4, ""); gd.addNumericField("Number of \"remove outliers\" passes", numPasses, 0 ,4, "");
gd.addNumericField("Number of neighbors (of total 8) to base outlayers", numInBase, 0 ,4, "<=8"); gd.addNumericField("Number of neighbors (of total 8) to base outliers", numInBase, 0 ,4, "<=8");
gd.addNumericField("Base low-pass sigma ", sigma, 3 ,7, "double pixels"); gd.addNumericField("Base low-pass sigma ", sigma, 3 ,7, "double pixels");
gd.addCheckbox ("Process tiles with no outlayer replacements", processNoReplace); gd.addCheckbox ("Process tiles with no outlier replacements", processNoReplace);
gd.addNumericField("\"Normal\" pixels variation", binWidth, 3 ,7, ""); gd.addNumericField("\"Normal\" pixels variation", binWidth, 3 ,7, "");
gd.addNumericField("Empty level gap between \"normal\" pixels and outlayers", gapWidth, 3 ,7, ""); gd.addNumericField("Empty level gap between \"normal\" pixels and outliers", gapWidth, 3 ,7, "");
gd.addNumericField("Post-HPF algorithm number", algNum, 0 ,4, "(1 or 2"); gd.addNumericField("Post-HPF algorithm number", algNum, 0 ,4, "(1 or 2");
gd.addNumericField("Number of neighbors (of total 8) to base outlayers (after high-pass), 0 - no filter", numInBase2, 0 ,4, "<=8"); gd.addNumericField("Number of neighbors (of total 8) to base outliers (after high-pass), 0 - no filter", numInBase2, 0 ,4, "<=8");
gd.addNumericField("\"Normal\" pixels variation (after high-pass)", binWidth2, 3 ,7, ""); gd.addNumericField("\"Normal\" pixels variation (after high-pass)", binWidth2, 3 ,7, "");
gd.addNumericField("Empty level gap between \"normal\" pixels and outlayers (after high-pass)", gapWidth2, 3 ,7, ""); gd.addNumericField("Empty level gap between \"normal\" pixels and outliers (after high-pass)", gapWidth2, 3 ,7, "");
gd.showDialog(); gd.showDialog();
...@@ -10649,7 +10648,7 @@ if (MORE_BUTTONS) { ...@@ -10649,7 +10648,7 @@ if (MORE_BUTTONS) {
tileClearSize, tileClearSize,
tileMargins, tileMargins,
cmask, // bitmask of color channels to process (9 - two greens) cmask, // bitmask of color channels to process (9 - two greens)
numPasses, // number of passes to replace outlayers (will end if none was replaced) numPasses, // number of passes to replace outliers (will end if none was replaced)
numInBase, // number of neighbors (of 8) to use as a base if they all agree numInBase, // number of neighbors (of 8) to use as a base if they all agree
sigma, // for high-pass filtering sigma, // for high-pass filtering
processNoReplace, // calculate differences even if no replacements were made processNoReplace, // calculate differences even if no replacements were made
...@@ -10731,7 +10730,7 @@ if (MORE_BUTTONS) { ...@@ -10731,7 +10730,7 @@ if (MORE_BUTTONS) {
128, // tileClearSize, 128, // tileClearSize,
16, // tileMargins, 16, // tileMargins,
15, // cmask, // bitmask of color channels to process (9 - two greens) 15, // cmask, // bitmask of color channels to process (9 - two greens)
1000, // numPasses, // number of passes to replace outlayers (will end if none was replaced) 1000, // numPasses, // number of passes to replace outliers (will end if none was replaced)
5, // numInBase, // number of neighbors (of 8) to use as a base if they all agree 5, // numInBase, // number of neighbors (of 8) to use as a base if they all agree
1.5, // sigma, // for high-pass filtering 1.5, // sigma, // for high-pass filtering
true, // processNoReplace, // calculate differences even if no replacements were made true, // processNoReplace, // calculate differences even if no replacements were made
...@@ -20537,7 +20536,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica ...@@ -20537,7 +20536,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
gd.addNumericField("Increase weight of the \"sharp\" kernels by dividing weights by the radius to this power",multiFilePSF.sharpBonusPower,3); // 1.0; // Center shift (in pixels) addition to the difference relative to radius difference (in pixels) gd.addNumericField("Increase weight of the \"sharp\" kernels by dividing weights by the radius to this power",multiFilePSF.sharpBonusPower,3); // 1.0; // Center shift (in pixels) addition to the difference relative to radius difference (in pixels)
gd.addNumericField("Discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger)",100.0*multiFilePSF.maxFracDiscardWorse,1,5,"%"); // 0.1, discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger) gd.addNumericField("Discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger)",100.0*multiFilePSF.maxFracDiscardWorse,1,5,"%"); // 0.1, discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger)
gd.addNumericField("Continue removing outlayers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse)",100.0*multiFilePSF.maxFracDiscardAll,1,5,"%"); // 0.5, continue removing outlayers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse) gd.addNumericField("Continue removing outliers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse)",100.0*multiFilePSF.maxFracDiscardAll,1,5,"%"); // 0.5, continue removing outliers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse)
gd.addNumericField("Cell having 8 around will have thresholds above twice higher than having none when this is set to 1.0, 0.0 - all same thresholds",multiFilePSF.internalBonus,3); gd.addNumericField("Cell having 8 around will have thresholds above twice higher than having none when this is set to 1.0, 0.0 - all same thresholds",multiFilePSF.internalBonus,3);
src/main/java/com/elphel/imagej/calibration/DistortionCalibrationData.java
View file @ 9d5dd318
...@@ -1555,6 +1555,16 @@ import ij.text.TextWindow; ...@@ -1555,6 +1555,16 @@ import ij.text.TextWindow;
sb.append("Lens Distortion Model\t"); sb.append("Lens Distortion Model\t");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]); for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);
sb.append("\n"); sb.append("\n");
sb.append("Sensor width\t");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorWidth(i));
sb.append("\n");
sb.append("Sensor height\t");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorHeight(i));
sb.append("\n");
double [][] cameraPars=new double [numSubCameras][]; double [][] cameraPars=new double [numSubCameras][];
for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i); for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i);
...@@ -1626,6 +1636,15 @@ import ij.text.TextWindow; ...@@ -1626,6 +1636,15 @@ import ij.text.TextWindow;
// sb.append("Lens Distortion Model\t"); // sb.append("Lens Distortion Model\t");
// for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]); // for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);
// sb.append("\n"); // sb.append("\n");
sb.append("Sensor width\t");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorWidth(i));
sb.append("\n");
sb.append("Sensor height\t");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorHeight(i));
sb.append("\n");
double [][] cameraPars=new double [numSubCameras][]; double [][] cameraPars=new double [numSubCameras][];
for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i); for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i);
...@@ -2396,7 +2415,7 @@ import ij.text.TextWindow; ...@@ -2396,7 +2415,7 @@ import ij.text.TextWindow;
IJ.showMessage(msg); IJ.showMessage(msg);
} }
for (int i=0; i<this.gIS.length;i++){ for (int i=0; i<this.gIS.length;i++){
if (selectedImages==null){ // if all selected - remove orientation if there are no enabled images (i.e. after removeOutlayers) if (selectedImages==null){ // if all selected - remove orientation if there are no enabled images (i.e. after removeOutliers)
this.gIS[i].goniometerAxial=Double.NaN; this.gIS[i].goniometerAxial=Double.NaN;
this.gIS[i].goniometerTilt= Double.NaN; this.gIS[i].goniometerTilt= Double.NaN;
this.gIS[i].orientationEstimated=true; this.gIS[i].orientationEstimated=true;
...@@ -3379,7 +3398,7 @@ import ij.text.TextWindow; ...@@ -3379,7 +3398,7 @@ import ij.text.TextWindow;
return true; return true;
} }
/** /**
* Sometimes "Process grid files" generates outlayers (by 0.1..5 pixels) TODO: find the bug * Sometimes "Process grid files" generates outliers (by 0.1..5 pixels) TODO: find the bug
* This program replaces the "bad" ones with predicted by 8 neighbors using 2-nd order interpolation * This program replaces the "bad" ones with predicted by 8 neighbors using 2-nd order interpolation
* @param fPixels stack of pX,pY,target-U,target-V,contrast (some bad pixels have low contrast), red,green,blue * @param fPixels stack of pX,pY,target-U,target-V,contrast (some bad pixels have low contrast), red,green,blue
* @param width grid width * @param width grid width
......
src/main/java/com/elphel/imagej/calibration/Distortions.java
View file @ 9d5dd318
...@@ -4102,16 +4102,16 @@ List calibration ...@@ -4102,16 +4102,16 @@ List calibration
return true; return true;
} }
public boolean removeOutLayers( public boolean removeOutLiers(
int series, int series,
int numOutLayers, int numOutLiers,
boolean [] selectedChannels){ boolean [] selectedChannels){
int numSeries=fittingStrategy.getNumSeries(); int numSeries=fittingStrategy.getNumSeries();
boolean removeEmpty=false; boolean removeEmpty=false;
boolean recalculate=false; boolean recalculate=false;
boolean applyChannelFilter=false; boolean applyChannelFilter=false;
int filter=filterForAll; int filter=filterForAll;
if ((series<0) || (numOutLayers<0)) { if ((series<0) || (numOutLiers<0)) {
GenericDialog gd = new GenericDialog("Select series to process"); GenericDialog gd = new GenericDialog("Select series to process");
gd.addNumericField("Iteration number to start (0.."+(numSeries-1)+")", this.seriesNumber, 0); gd.addNumericField("Iteration number to start (0.."+(numSeries-1)+")", this.seriesNumber, 0);
if (selectedChannels != null) { if (selectedChannels != null) {
...@@ -4120,7 +4120,7 @@ List calibration ...@@ -4120,7 +4120,7 @@ List calibration
gd.addCheckbox("Filter by channel selection ("+s+")", applyChannelFilter); gd.addCheckbox("Filter by channel selection ("+s+")", applyChannelFilter);
} }
gd.addCheckbox("Recalculate parameters vector from selected strategy",recalculate); gd.addCheckbox("Recalculate parameters vector from selected strategy",recalculate);
gd.addNumericField("Number of outlayers to show", 10, 0); gd.addNumericField("Number of outliers to show", 10, 0);
gd.addCheckbox("Remove empty (rms==NaN) images", removeEmpty); gd.addCheckbox("Remove empty (rms==NaN) images", removeEmpty);
gd.addCheckbox("Ask filter (current filter="+filter+")", this.askFilter); gd.addCheckbox("Ask filter (current filter="+filter+")", this.askFilter);
gd.showDialog(); gd.showDialog();
...@@ -4128,7 +4128,7 @@ List calibration ...@@ -4128,7 +4128,7 @@ List calibration
this.seriesNumber= (int) gd.getNextNumber(); this.seriesNumber= (int) gd.getNextNumber();
if (selectedChannels != null) applyChannelFilter= gd.getNextBoolean(); if (selectedChannels != null) applyChannelFilter= gd.getNextBoolean();
recalculate= gd.getNextBoolean(); recalculate= gd.getNextBoolean();
numOutLayers= (int) gd.getNextNumber(); numOutLiers= (int) gd.getNextNumber();
removeEmpty= gd.getNextBoolean(); removeEmpty= gd.getNextBoolean();
this.askFilter= gd.getNextBoolean(); this.askFilter= gd.getNextBoolean();
if (this.askFilter) filter= selectFilter(filter); if (this.askFilter) filter= selectFilter(filter);
...@@ -4162,14 +4162,14 @@ List calibration ...@@ -4162,14 +4162,14 @@ List calibration
int index=0; int index=0;
for (int i=0;i<selectedImages.length;i++) if ( selectedImages[i] && !Double.isNaN(errors[i])) imgIndices[index++]=i; // OOB 2389 for (int i=0;i<selectedImages.length;i++) if ( selectedImages[i] && !Double.isNaN(errors[i])) imgIndices[index++]=i; // OOB 2389
if (numOutLayers>numSelectedNotNaNImages) numOutLayers=numSelectedNotNaNImages; if (numOutLiers>numSelectedNotNaNImages) numOutLiers=numSelectedNotNaNImages;
int [] indices=new int [numOutLayers]; int [] indices=new int [numOutLiers];
boolean [] availableImages=selectedImages.clone(); boolean [] availableImages=selectedImages.clone();
for (int i=0;i<selectedImages.length;i++) if (selectedImages[i] && Double.isNaN(errors[i])) availableImages[i]=false; for (int i=0;i<selectedImages.length;i++) if (selectedImages[i] && Double.isNaN(errors[i])) availableImages[i]=false;
if ((this.debugLevel>0) && (numNaN>0)){ if ((this.debugLevel>0) && (numNaN>0)){
System.out.println("removeOutLayers(): Number of empty (rms=NaN) images="+numNaN+":"); System.out.println("removeOutLiers(): Number of empty (rms=NaN) images="+numNaN+":");
int n=0; int n=0;
for (int i=0;i<selectedImages.length;i++) if (selectedImages[i] && Double.isNaN(errors[i])){ for (int i=0;i<selectedImages.length;i++) if (selectedImages[i] && Double.isNaN(errors[i])){
n++; n++;
...@@ -4187,8 +4187,8 @@ List calibration ...@@ -4187,8 +4187,8 @@ List calibration
} }
System.out.println("removeOutLayers(): availableImages.length="+availableImages.length+" numSelectedNotNaNImages="+numSelectedNotNaNImages); System.out.println("removeOutLiers(): availableImages.length="+availableImages.length+" numSelectedNotNaNImages="+numSelectedNotNaNImages);
for (int n=0;n<numOutLayers;n++){ for (int n=0;n<numOutLiers;n++){
double maxRMS=-1.0; double maxRMS=-1.0;
indices[n]=-1; indices[n]=-1;
for (int i=0;i<availableImages.length;i++)if (availableImages[i] && (Double.isNaN(errors[i]) || (errors[i]>maxRMS))){ // Double.NaN will be greater for (int i=0;i<availableImages.length;i++)if (availableImages[i] && (Double.isNaN(errors[i]) || (errors[i]>maxRMS))){ // Double.NaN will be greater
...@@ -4196,14 +4196,14 @@ List calibration ...@@ -4196,14 +4196,14 @@ List calibration
indices[n]=i; indices[n]=i;
} }
if (indices[n]<0){ if (indices[n]<0){
System.out.println("removeOutLayers(): indices["+n+"]="+indices[n]); System.out.println("removeOutLiers(): indices["+n+"]="+indices[n]);
continue; continue;
} }
availableImages[indices[n]]=false; // java.lang.ArrayIndexOutOfBoundsException: -1 availableImages[indices[n]]=false; // java.lang.ArrayIndexOutOfBoundsException: -1
} }
GenericDialog gd = new GenericDialog("Select images to remove (RMS="+IJ.d2s(rms,3)+")"); GenericDialog gd = new GenericDialog("Select images to remove (RMS="+IJ.d2s(rms,3)+")");
if (this.debugLevel>0) System.out.println("Listing "+numOutLayers+" worst images:"); if (this.debugLevel>0) System.out.println("Listing "+numOutLiers+" worst images:");
for (int n=0;n<indices.length;n++){ for (int n=0;n<indices.length;n++){
String msg=n+" ("+indices[n]+" / "+ this.fittingStrategy.distortionCalibrationData.gIP[indices[n]].getSetNumber()+"): "+ String msg=n+" ("+indices[n]+" / "+ this.fittingStrategy.distortionCalibrationData.gIP[indices[n]].getSetNumber()+"): "+
IJ.d2s(errors[indices[n]],3)+" "+ IJ.d2s(errors[indices[n]],3)+" "+
...@@ -4218,7 +4218,7 @@ List calibration ...@@ -4218,7 +4218,7 @@ List calibration
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
if (this.debugLevel>0) System.out.println("Removing outlayers:"); if (this.debugLevel>0) System.out.println("Removing outliers:");
for (int n=0;n<indices.length;n++){ for (int n=0;n<indices.length;n++){
if (gd.getNextBoolean()) { if (gd.getNextBoolean()) {
if (this.debugLevel>0) System.out.println(n+" :"+IJ.d2s(errors[indices[n]],3)+" "+this.fittingStrategy.distortionCalibrationData.gIP[indices[n]].path); if (this.debugLevel>0) System.out.println(n+" :"+IJ.d2s(errors[indices[n]],3)+" "+this.fittingStrategy.distortionCalibrationData.gIP[indices[n]].path);
...@@ -4230,18 +4230,18 @@ List calibration ...@@ -4230,18 +4230,18 @@ List calibration
return true; return true;
} }
public boolean removeOutLayerSets(int numOutLayers){ public boolean removeOutLierSets(int numOutLiers){
boolean removeEmptySets=false; boolean removeEmptySets=false;
if (numOutLayers<0) { if (numOutLiers<0) {
GenericDialog gd = new GenericDialog("Select sets to process"); GenericDialog gd = new GenericDialog("Select sets to process");
gd.addNumericField("Series number (<0 - all images)", -1, 0); gd.addNumericField("Series number (<0 - all images)", -1, 0);
gd.addNumericField("Number of outlayers to show", 5, 0); gd.addNumericField("Number of outliers to show", 5, 0);
gd.addCheckbox("Remove empty sets", removeEmptySets); gd.addCheckbox("Remove empty sets", removeEmptySets);
gd.addCheckbox("Ask for weight function filter", this.askFilter); gd.addCheckbox("Ask for weight function filter", this.askFilter);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
this.seriesNumber= (int) gd.getNextNumber(); this.seriesNumber= (int) gd.getNextNumber();
numOutLayers= (int) gd.getNextNumber(); numOutLiers= (int) gd.getNextNumber();
removeEmptySets= gd.getNextBoolean(); removeEmptySets= gd.getNextBoolean();
this.askFilter= gd.getNextBoolean(); this.askFilter= gd.getNextBoolean();
} }
...@@ -4291,12 +4291,12 @@ List calibration ...@@ -4291,12 +4291,12 @@ List calibration
// int index=0; // int index=0;
// for (int i=0;i<imageSets.length;i++) if ( selectedImages[i]) imgIndices[index++]=i; // for (int i=0;i<imageSets.length;i++) if ( selectedImages[i]) imgIndices[index++]=i;
if (numOutLayers>numSelectedSets) numOutLayers=numSelectedSets; if (numOutLiers>numSelectedSets) numOutLiers=numSelectedSets;
int [] indices=new int [numOutLayers]; int [] indices=new int [numOutLiers];
boolean [] availableSets= new boolean [imageSets.length]; boolean [] availableSets= new boolean [imageSets.length];
for (int i=0;i<imageSets.length;i++) availableSets[i]= !allNaNInSet[i]; //!Double.isNaN(rmsPerSet[i]); for (int i=0;i<imageSets.length;i++) availableSets[i]= !allNaNInSet[i]; //!Double.isNaN(rmsPerSet[i]);
if (removeEmptySets && (numNaN>0)){ //(this.debugLevel>0) if (removeEmptySets && (numNaN>0)){ //(this.debugLevel>0)
if (this.debugLevel>0) System.out.println("removeOutLayerSets(): Number of empty (rms=NaN) sets="+numNaN+":"); if (this.debugLevel>0) System.out.println("removeOutLierSets(): Number of empty (rms=NaN) sets="+numNaN+":");
// int n=0; // int n=0;
for (int setNum=0;setNum<imageSets.length;setNum++) if (!availableSets[setNum]){ for (int setNum=0;setNum<imageSets.length;setNum++) if (!availableSets[setNum]){
// n++; // n++;
...@@ -4311,8 +4311,8 @@ List calibration ...@@ -4311,8 +4311,8 @@ List calibration
} }
} }
System.out.println("removeOutLayerSets(): availableSets.length="+availableSets.length+" numSelectedSets="+numSelectedSets); System.out.println("removeOutLierSets(): availableSets.length="+availableSets.length+" numSelectedSets="+numSelectedSets);
for (int n=0;n<numOutLayers;n++){ for (int n=0;n<numOutLiers;n++){
double maxRMS=-1.0; double maxRMS=-1.0;
indices[n]=-1; indices[n]=-1;
for (int i=0;i<availableSets.length;i++)if (availableSets[i] && (rmsPerSet[i]>maxRMS)){ // NaN are already skipped for (int i=0;i<availableSets.length;i++)if (availableSets[i] && (rmsPerSet[i]>maxRMS)){ // NaN are already skipped
...@@ -4320,14 +4320,14 @@ List calibration ...@@ -4320,14 +4320,14 @@ List calibration
indices[n]=i; indices[n]=i;
} }
if (indices[n]<0){ if (indices[n]<0){
System.out.println("removeOutLayerSets(): indices["+n+"]="+indices[n]); System.out.println("removeOutLierSets(): indices["+n+"]="+indices[n]);
continue; continue;
} }
availableSets[indices[n]]=false; // java.lang.ArrayIndexOutOfBoundsException: -1 availableSets[indices[n]]=false; // java.lang.ArrayIndexOutOfBoundsException: -1
} }
GenericDialog gd = new GenericDialog("Select image Sets to remove (RMS="+IJ.d2s(rms,3)+")"); GenericDialog gd = new GenericDialog("Select image Sets to remove (RMS="+IJ.d2s(rms,3)+")");
if (this.debugLevel>0) System.out.println("Listing "+numOutLayers+" worst image sets"); if (this.debugLevel>0) System.out.println("Listing "+numOutLiers+" worst image sets");
for (int n=0;n<indices.length;n++){ for (int n=0;n<indices.length;n++){
int numSet=indices[n]; int numSet=indices[n];
double setWeight=this.fittingStrategy.distortionCalibrationData.gIS[numSet].setWeight; double setWeight=this.fittingStrategy.distortionCalibrationData.gIS[numSet].setWeight;
...@@ -4351,7 +4351,7 @@ List calibration ...@@ -4351,7 +4351,7 @@ List calibration
// this.fittingStrategy.setImageSelection(0, oldSelection); // restore original selection in series 0 // this.fittingStrategy.setImageSelection(0, oldSelection); // restore original selection in series 0
return false; return false;
} }
if (this.debugLevel>0) System.out.println("Removing outlayers:"); if (this.debugLevel>0) System.out.println("Removing outliers:");
for (int n=0;n<indices.length;n++){ for (int n=0;n<indices.length;n++){
if (gd.getNextBoolean()) { if (gd.getNextBoolean()) {
int numSet=indices[n]; int numSet=indices[n];
...@@ -4371,16 +4371,16 @@ List calibration ...@@ -4371,16 +4371,16 @@ List calibration
return true; return true;
} }
public boolean removeOutLayersJunk(int series, int numOutLayers){ public boolean removeOutLiersJunk(int series, int numOutLiers){
int numSeries=fittingStrategy.getNumSeries(); int numSeries=fittingStrategy.getNumSeries();
if ((series<0) || (numOutLayers<0)) { if ((series<0) || (numOutLiers<0)) {
GenericDialog gd = new GenericDialog("Select series to process"); GenericDialog gd = new GenericDialog("Select series to process");
gd.addNumericField("Iteration number to start (0.."+(numSeries-1)+")", this.seriesNumber, 0); gd.addNumericField("Iteration number to start (0.."+(numSeries-1)+")", this.seriesNumber, 0);
gd.addNumericField("Number of outlayers to show", 10, 0); gd.addNumericField("Number of outliers to show", 10, 0);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
this.seriesNumber= (int) gd.getNextNumber(); this.seriesNumber= (int) gd.getNextNumber();
numOutLayers= (int) gd.getNextNumber(); numOutLiers= (int) gd.getNextNumber();
} else { } else {
this.seriesNumber=series; this.seriesNumber=series;
} }
...@@ -4395,12 +4395,12 @@ List calibration ...@@ -4395,12 +4395,12 @@ List calibration
int index=0; int index=0;
for (int i=0;i<selectedImages.length;i++) if ( selectedImages[i]) imgIndices[index++]=i; for (int i=0;i<selectedImages.length;i++) if ( selectedImages[i]) imgIndices[index++]=i;
if (numOutLayers>numSelectedImages) numOutLayers=numSelectedImages; if (numOutLiers>numSelectedImages) numOutLiers=numSelectedImages;
int [] indices=new int [numOutLayers]; int [] indices=new int [numOutLiers];
int [] indicesSelected=new int [numOutLayers]; int [] indicesSelected=new int [numOutLiers];
boolean [] availableImages=new boolean[numSelectedImages]; boolean [] availableImages=new boolean[numSelectedImages];
for (int i=0;i<availableImages.length;i++)availableImages[i]=true; for (int i=0;i<availableImages.length;i++)availableImages[i]=true;
for (int n=0;n<numOutLayers;n++){ for (int n=0;n<numOutLiers;n++){
double maxRMS=0; double maxRMS=0;
indices[n]=-1; indices[n]=-1;
indicesSelected[n]=-1; indicesSelected[n]=-1;
......
src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java
View file @ 9d5dd318
...@@ -1585,7 +1585,7 @@ public class EyesisAberrations { ...@@ -1585,7 +1585,7 @@ public class EyesisAberrations {
if (thisDebugLevel>1) sdfa_instance.showArrays(weightsMasked, kWidth, kHeight, true, "weightsMasked"); if (thisDebugLevel>1) sdfa_instance.showArrays(weightsMasked, kWidth, kHeight, true, "weightsMasked");
double [][][] psfRadius=c[5]; // later may remove all other calculations for c[i]? double [][][] psfRadius=c[5]; // later may remove all other calculations for c[i]?
double [][][] pxfCenterX=c[0]; // some outlayer kernels have large x/y shift with normal radius - remove them too double [][][] pxfCenterX=c[0]; // some outlier kernels have large x/y shift with normal radius - remove them too
double [][][] pxfCenterY=c[1]; double [][][] pxfCenterY=c[1];
if (thisDebugLevel>1) { if (thisDebugLevel>1) {
for (int color=0;color<nChn;color++) sdfa_instance.showArrays(psfRadius[color], kWidth, kHeight, true, "psfRadius-"+color); for (int color=0;color<nChn;color++) sdfa_instance.showArrays(psfRadius[color], kWidth, kHeight, true, "psfRadius-"+color);
...@@ -1610,11 +1610,11 @@ public class EyesisAberrations { ...@@ -1610,11 +1610,11 @@ public class EyesisAberrations {
pxfCenterY[color][0][index]=0.0; pxfCenterY[color][0][index]=0.0;
} }
double sumWeights=0.0; double sumWeights=0.0;
for (int nFile=0;nFile<nFiles;nFile++) if ((weightsMasked[nFile+1][index]>0.0) && (weights[nFile+1][index]>0.0)){ // both, with outlayers removed for (int nFile=0;nFile<nFiles;nFile++) if ((weightsMasked[nFile+1][index]>0.0) && (weights[nFile+1][index]>0.0)){ // both, with outliers removed
for (int i=0;i<dirs.length;i++) { for (int i=0;i<dirs.length;i++) {
int yn=tileY+dirs[i][1]; int yn=tileY+dirs[i][1];
int xn=tileX+dirs[i][0]; int xn=tileX+dirs[i][0];
if ((yn>=0) && (yn<kHeight) && (xn>=0) && (xn<kWidth) && (weightsNotMasked[nFile+1][yn*kWidth+xn]>0.0)){ // including removed outlayers if ((yn>=0) && (yn<kHeight) && (xn>=0) && (xn<kWidth) && (weightsNotMasked[nFile+1][yn*kWidth+xn]>0.0)){ // including removed outliers
int indexNeib=xn+ kWidth*yn; int indexNeib=xn+ kWidth*yn;
double weight=weightsMasked[nFile+1][indexNeib]; double weight=weightsMasked[nFile+1][indexNeib];
if (multiFilePSF.sharpBonusPower>0) { if (multiFilePSF.sharpBonusPower>0) {
...@@ -1643,7 +1643,7 @@ public class EyesisAberrations { ...@@ -1643,7 +1643,7 @@ public class EyesisAberrations {
double [] diffs=new double[nFiles]; double [] diffs=new double[nFiles];
double [] diffsXY2=new double[nFiles]; double [] diffsXY2=new double[nFiles];
// for (int nFile=0;nFile<nFiles;nFile++) if ( weights[nFile+1][index]>0.0){ // here all , not just masked - why? // for (int nFile=0;nFile<nFiles;nFile++) if ( weights[nFile+1][index]>0.0){ // here all , not just masked - why?
for (int nFile=0;nFile<nFiles;nFile++) if ((weights[nFile+1][index]>0.0) && (weightsMasked[nFile+1][index]>0.0)){ //no outlayers, no masked - find worst for (int nFile=0;nFile<nFiles;nFile++) if ((weights[nFile+1][index]>0.0) && (weightsMasked[nFile+1][index]>0.0)){ //no outliers, no masked - find worst
diffs[nFile]=0; diffs[nFile]=0;
diffsXY2[nFile]=0; diffsXY2[nFile]=0;
for (int color=0;color<nChn;color++) { for (int color=0;color<nChn;color++) {
...@@ -1658,11 +1658,11 @@ public class EyesisAberrations { ...@@ -1658,11 +1658,11 @@ public class EyesisAberrations {
diffs[nFile]+=multiFilePSF.shiftToRadiusContrib*(Math.sqrt(diffXY2)/radiusRatio[color][0][index]); // now difference combines size and position diffs[nFile]+=multiFilePSF.shiftToRadiusContrib*(Math.sqrt(diffXY2)/radiusRatio[color][0][index]); // now difference combines size and position
} }
} }
// mask out outlayers // mask out outliers
//weightsMasked[0] //weightsMasked[0]
// TODO: when averaging, divide by r^2 to some power to give bonus low-radius samples. // TODO: when averaging, divide by r^2 to some power to give bonus low-radius samples.
// also - combine dX^2+dY2+dR^2 when selecting outlayers // also - combine dX^2+dY2+dR^2 when selecting outliers
if (thisDebugLevel>1) { if (thisDebugLevel>1) {
System.out.print("\n === "+tileY+":"+tileX); System.out.print("\n === "+tileY+":"+tileX);
for (int nFile=0;nFile<nFiles;nFile++) if ( weights[nFile+1][index]>0.0){ for (int nFile=0;nFile<nFiles;nFile++) if ( weights[nFile+1][index]>0.0){
...@@ -1740,7 +1740,7 @@ public class EyesisAberrations { ...@@ -1740,7 +1740,7 @@ public class EyesisAberrations {
// for each channel, each cell - compare radius calculated for neighbors (use masked weights) and the cell // for each channel, each cell - compare radius calculated for neighbors (use masked weights) and the cell
// TODO: Filter out outlayers: Add bonus to cells surrounded by others? // TODO: Filter out outliers: Add bonus to cells surrounded by others?
// double [][][][] c= new double[numResults][nChn][nFiles+1][kLength]; // double [][][][] c= new double[numResults][nChn][nFiles+1][kLength];
...@@ -4466,7 +4466,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -4466,7 +4466,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
public double shiftToRadiusContrib=1.0; // Center shift (in pixels) addition to the difference relative to radius difference (in pixels) public double shiftToRadiusContrib=1.0; // Center shift (in pixels) addition to the difference relative to radius difference (in pixels)
public double sharpBonusPower=2.0; // increase weight of the "sharp" kernels by dividing weight by radius to this power public double sharpBonusPower=2.0; // increase weight of the "sharp" kernels by dividing weight by radius to this power
public double maxFracDiscardWorse=0.1; // discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger) public double maxFracDiscardWorse=0.1; // discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger)
public double maxFracDiscardAll=0.5; // continue removing outlayers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse) public double maxFracDiscardAll=0.5; // continue removing outliers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse)
public double internalBonus=1.0; // cell having 8 around will "seem" twice better than having none (radiusDiff* twice higher) public double internalBonus=1.0; // cell having 8 around will "seem" twice better than having none (radiusDiff* twice higher)
public double validateThreshold; // fraction of full PSF "energy" public double validateThreshold; // fraction of full PSF "energy"
public boolean validateShowEllipse; // show ellipse parameters of partial PSF arrays public boolean validateShowEllipse; // show ellipse parameters of partial PSF arrays
...@@ -4480,7 +4480,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -4480,7 +4480,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
double shiftToRadiusContrib, // Center shift (in pixels) addition to the difference relative to radius difference (in pixels) double shiftToRadiusContrib, // Center shift (in pixels) addition to the difference relative to radius difference (in pixels)
double sharpBonusPower, // increase weight of the "sharp" kernels by dividing weight by radius to this power double sharpBonusPower, // increase weight of the "sharp" kernels by dividing weight by radius to this power
double maxFracDiscardWorse, // discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger) double maxFracDiscardWorse, // discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger)
double maxFracDiscardAll, // continue removing outlayers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse) double maxFracDiscardAll, // continue removing outliers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse)
double internalBonus, double internalBonus,
double validateThreshold, double validateThreshold,
boolean validateShowEllipse, boolean validateShowEllipse,
...@@ -4494,7 +4494,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //*********************************** ...@@ -4494,7 +4494,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
this.shiftToRadiusContrib=shiftToRadiusContrib; // Center shift (in pixels) addition to the difference relative to radius difference (in pixels) this.shiftToRadiusContrib=shiftToRadiusContrib; // Center shift (in pixels) addition to the difference relative to radius difference (in pixels)
this.sharpBonusPower=sharpBonusPower; // increase weight of the "sharp" kernels by dividing weight by radius to this power this.sharpBonusPower=sharpBonusPower; // increase weight of the "sharp" kernels by dividing weight by radius to this power
this.maxFracDiscardWorse=maxFracDiscardWorse; // discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger) this.maxFracDiscardWorse=maxFracDiscardWorse; // discard up to this fraction of samples that have larger radius (i.e. falling on the target seam that may only make PSF larger)
this.maxFracDiscardAll=maxFracDiscardAll; // continue removing outlayers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse) this.maxFracDiscardAll=maxFracDiscardAll; // continue removing outliers (combined radius and shift), removing not more that this fraction (including maxFracDiscardWorse)
this.internalBonus=internalBonus; this.internalBonus=internalBonus;
this.validateThreshold=validateThreshold; this.validateThreshold=validateThreshold;
this.validateShowEllipse=validateShowEllipse; this.validateShowEllipse=validateShowEllipse;
......
src/main/java/com/elphel/imagej/cameras/EyesisCameraParameters.java
View file @ 9d5dd318
...@@ -960,8 +960,12 @@ import ij.gui.GenericDialog; ...@@ -960,8 +960,12 @@ import ij.gui.GenericDialog;
gd.addNumericField("Channel "+numSubCam+" default weight", subCam.channelWeightDefault, 5,8,""); gd.addNumericField("Channel "+numSubCam+" default weight", subCam.channelWeightDefault, 5,8,"");
} }
if (this.numStations>1) gd.addMessage("--- Station number "+numStation+" ---"); if (this.numStations>1) gd.addMessage("--- Station number "+numStation+" ---");
gd.addNumericField("Subcamera lens distortion model", subCam.lensDistortionModel, 5,0,""); gd.addNumericField("Subcamera lens distortion model", subCam.lensDistortionModel, 8,0,"");
gd.addCheckbox ("Enable matching w/o laser pointers", subCam.enableNoLaser); gd.addCheckbox ("Enable matching w/o laser pointers", subCam.enableNoLaser);
if (numStation == 0) {
gd.addNumericField("Image sensor width", this.getSensorWidth (numSubCam), 0,4,"pix");
gd.addNumericField("Image sensor height", this.getSensorHeight(numSubCam), 0,4,"pix");
}
if (subCam.cartesian) { if (subCam.cartesian) {
gd.addNumericField("Subcamera right from the axis", subCam.right, 5,9,"mm"); gd.addNumericField("Subcamera right from the axis", subCam.right, 5,9,"mm");
gd.addNumericField("Subcamera forward from the rotation axis", subCam.forward, 5,9,"mm"); gd.addNumericField("Subcamera forward from the rotation axis", subCam.forward, 5,9,"mm");
...@@ -1044,6 +1048,10 @@ import ij.gui.GenericDialog; ...@@ -1044,6 +1048,10 @@ import ij.gui.GenericDialog;
subCam.channelWeightDefault= channelWeightDefault; // assign to all stations subCam.channelWeightDefault= channelWeightDefault; // assign to all stations
subCam.lensDistortionModel= (int) gd.getNextNumber(); subCam.lensDistortionModel= (int) gd.getNextNumber();
subCam.enableNoLaser = gd.getNextBoolean(); subCam.enableNoLaser = gd.getNextBoolean();
if (numStation == 0) {
this.setSensorWidth (numSubCam,(int) gd.getNextNumber());
this.setSensorHeight(numSubCam,(int) gd.getNextNumber());
}
if (subCam.cartesian) { if (subCam.cartesian) {
subCam.right= gd.getNextNumber(); subCam.right= gd.getNextNumber();
subCam.forward= gd.getNextNumber(); subCam.forward= gd.getNextNumber();
...@@ -1106,6 +1114,9 @@ import ij.gui.GenericDialog; ...@@ -1106,6 +1114,9 @@ import ij.gui.GenericDialog;
for (int numStation=1;numStation<this.numStations;numStation++) { for (int numStation=1;numStation<this.numStations;numStation++) {
EyesisSubCameraParameters subCam=this.eyesisSubCameras[numStation][numSubCam]; EyesisSubCameraParameters subCam=this.eyesisSubCameras[numStation][numSubCam];
if (subCam!=null) { if (subCam!=null) {
this.setSensorWidth (numSubCam,first.getSensorWidth ());
this.setSensorHeight(numSubCam,first.getSensorHeight ());
if (subCam.cartesian) { if (subCam.cartesian) {
subCam.right= first.right; subCam.right= first.right;
subCam.forward= first.forward; subCam.forward= first.forward;
...@@ -1298,22 +1309,39 @@ import ij.gui.GenericDialog; ...@@ -1298,22 +1309,39 @@ import ij.gui.GenericDialog;
public int getGoniometerHorizontalIndex(){return 6;} public int getGoniometerHorizontalIndex(){return 6;}
public int getGoniometerAxialIndex(){return 7;} public int getGoniometerAxialIndex(){return 7;}
public int getInterAxisAngleIndex(){return 9;} public int getInterAxisAngleIndex(){return 9;}
@Deprecated
public int getSensorWidth() { return this.defaultSensorWidth;} public int getSensorWidth() { return this.defaultSensorWidth;}
@Deprecated
public int getSensorHeight() { return this.defaultSensorHeight;} public int getSensorHeight() { return this.defaultSensorHeight;}
@Deprecated
public int getDecimateMasks() { return this.defaultDecimateMasks;} public int getDecimateMasks() { return this.defaultDecimateMasks;}
@Deprecated
public void setSensorWidth(int v) { this.defaultSensorWidth = v;} public void setSensorWidth(int v) { this.defaultSensorWidth = v;}
@Deprecated
public void setSensorHeight(int v) { this.defaultSensorHeight = v;} public void setSensorHeight(int v) { this.defaultSensorHeight = v;}
@Deprecated
public void setDecimateMasks(int v) { this.defaultDecimateMasks = v;} public void setDecimateMasks(int v) { this.defaultDecimateMasks = v;}
public int getSensorWidth(int subCam) { return this.eyesisSubCameras[0][subCam].sensorWidth;} // for the future? different sensors public int getSensorWidth(int subCam) { return this.eyesisSubCameras[0][subCam].getSensorWidth();} // for the future? different sensors
public int getSensorHeight(int subCam) { return this.eyesisSubCameras[0][subCam].sensorHeight;}// for the future? different sensors public int getSensorHeight(int subCam) { return this.eyesisSubCameras[0][subCam].getSensorHeight();}// for the future? different sensors
public int getDecimateMasks(int subCam) { return this.eyesisSubCameras[0][subCam].decimateMasks;}// for the future? different sensors public int getDecimateMasks(int subCam) { return this.eyesisSubCameras[0][subCam].getDecimateMasks();}// for the future? different sensors
public void setSensorWidth(int subCam, int v) { this.eyesisSubCameras[0][subCam].sensorWidth = v;} public void setSensorWidth(int subCam, int v) {
public void setSensorHeight(int subCam, int v) { this.eyesisSubCameras[0][subCam].sensorHeight = v;} for (int station = 0; station < this.eyesisSubCameras.length; station++) {
public void setDecimateMasks(int subCam, int v) { this.eyesisSubCameras[0][subCam].decimateMasks = v;} this.eyesisSubCameras[station][subCam].setSensorWidth(v);
}
}
public void setSensorHeight(int subCam, int v) {
for (int station = 0; station < this.eyesisSubCameras.length; station++) {
this.eyesisSubCameras[station][subCam].setSensorHeight(v);
}
}
public void setDecimateMasks(int subCam, int v) {
for (int station = 0; station < this.eyesisSubCameras.length; station++) {
this.eyesisSubCameras[station][subCam].setDecimateMasks(v);
}
}
public int [] getSensorWidths() { public int [] getSensorWidths() {
int [] v = new int [eyesisSubCameras[0].length]; int [] v = new int [eyesisSubCameras[0].length];
......
src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java
View file @ 9d5dd318
...@@ -2863,10 +2863,10 @@ public class EyesisCorrectionParameters { ...@@ -2863,10 +2863,10 @@ public class EyesisCorrectionParameters {
public double stHighMix = 0.4; // Consider merging initial planes if jumps between ratio above public double stHighMix = 0.4; // Consider merging initial planes if jumps between ratio above
public double outlayerStrength = 0.3; // Outlayer tiles weaker than this may be replaced from neighbors public double outlierStrength = 0.3; // Outlier tiles weaker than this may be replaced from neighbors
public double outlayerDiff = 0.4; // Replace weak outlayer tiles that do not have neighbors within this disparity difference public double outlierDiff = 0.4; // Replace weak outlier tiles that do not have neighbors within this disparity difference
public double outlayerDiffPos = 1.0; // Replace weak outlayer tiles that have higher disparity than weighted average public double outlierDiffPos = 1.0; // Replace weak outlier tiles that have higher disparity than weighted average
public double outlayerDiffNeg = 0.4; // Replace weak outlayer tiles that have lower disparity than weighted average public double outlierDiffNeg = 0.4; // Replace weak outlier tiles that have lower disparity than weighted average
// TODO: Make refine skip if already good? // TODO: Make refine skip if already good?
public boolean combine_refine = true; // combine with all previous after refine pass public boolean combine_refine = true; // combine with all previous after refine pass
...@@ -3582,10 +3582,10 @@ public class EyesisCorrectionParameters { ...@@ -3582,10 +3582,10 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"stHighMix", this.stHighMix +""); properties.setProperty(prefix+"stHighMix", this.stHighMix +"");
properties.setProperty(prefix+"outlayerStrength", this.outlayerStrength +""); properties.setProperty(prefix+"outlierStrength", this.outlierStrength +"");
properties.setProperty(prefix+"outlayerDiff", this.outlayerDiff +""); properties.setProperty(prefix+"outlierDiff", this.outlierDiff +"");
properties.setProperty(prefix+"outlayerDiffPos", this.outlayerDiffPos +""); properties.setProperty(prefix+"outlierDiffPos", this.outlierDiffPos +"");
properties.setProperty(prefix+"outlayerDiffNeg", this.outlayerDiffNeg +""); properties.setProperty(prefix+"outlierDiffNeg", this.outlierDiffNeg +"");
properties.setProperty(prefix+"combine_refine", this.combine_refine+""); properties.setProperty(prefix+"combine_refine", this.combine_refine+"");
...@@ -4282,10 +4282,17 @@ public class EyesisCorrectionParameters { ...@@ -4282,10 +4282,17 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"stSmallDiff")!=null) this.stSmallDiff=Double.parseDouble(properties.getProperty(prefix+"stSmallDiff")); if (properties.getProperty(prefix+"stSmallDiff")!=null) this.stSmallDiff=Double.parseDouble(properties.getProperty(prefix+"stSmallDiff"));
if (properties.getProperty(prefix+"stHighMix")!=null) this.stHighMix=Double.parseDouble(properties.getProperty(prefix+"stHighMix")); if (properties.getProperty(prefix+"stHighMix")!=null) this.stHighMix=Double.parseDouble(properties.getProperty(prefix+"stHighMix"));
if (properties.getProperty(prefix+"outlayerStrength")!=null) this.outlayerStrength=Double.parseDouble(properties.getProperty(prefix+"outlayerStrength")); // old wrong spelling
if (properties.getProperty(prefix+"outlayerDiff")!=null) this.outlayerDiff=Double.parseDouble(properties.getProperty(prefix+"outlayerDiff")); if (properties.getProperty(prefix+"outlayerStrength")!=null) this.outlierStrength=Double.parseDouble(properties.getProperty(prefix+"outlayerStrength"));
if (properties.getProperty(prefix+"outlayerDiffPos")!=null) this.outlayerDiffPos=Double.parseDouble(properties.getProperty(prefix+"outlayerDiffPos")); if (properties.getProperty(prefix+"outlayerDiff")!=null) this.outlierDiff=Double.parseDouble(properties.getProperty(prefix+"outlayerDiff"));
if (properties.getProperty(prefix+"outlayerDiffNeg")!=null) this.outlayerDiffNeg=Double.parseDouble(properties.getProperty(prefix+"outlayerDiffNeg")); if (properties.getProperty(prefix+"outlayerDiffPos")!=null) this.outlierDiffPos=Double.parseDouble(properties.getProperty(prefix+"outlayerDiffPos"));
if (properties.getProperty(prefix+"outlayerDiffNeg")!=null) this.outlierDiffNeg=Double.parseDouble(properties.getProperty(prefix+"outlayerDiffNeg"));
if (properties.getProperty(prefix+"outlierStrength")!=null) this.outlierStrength=Double.parseDouble(properties.getProperty(prefix+"outlierStrength"));
if (properties.getProperty(prefix+"outlierDiff")!=null) this.outlierDiff=Double.parseDouble(properties.getProperty(prefix+"outlierDiff"));
if (properties.getProperty(prefix+"outlierDiffPos")!=null) this.outlierDiffPos=Double.parseDouble(properties.getProperty(prefix+"outlierDiffPos"));
if (properties.getProperty(prefix+"outlierDiffNeg")!=null) this.outlierDiffNeg=Double.parseDouble(properties.getProperty(prefix+"outlierDiffNeg"));
if (properties.getProperty(prefix+"combine_refine")!=null) this.combine_refine=Boolean.parseBoolean(properties.getProperty(prefix+"combine_refine")); if (properties.getProperty(prefix+"combine_refine")!=null) this.combine_refine=Boolean.parseBoolean(properties.getProperty(prefix+"combine_refine"));
...@@ -5030,10 +5037,10 @@ public class EyesisCorrectionParameters { ...@@ -5030,10 +5037,10 @@ public class EyesisCorrectionParameters {
gd.addNumericField("Consider merging initial planes if disparity difference below", this.stSmallDiff, 6); gd.addNumericField("Consider merging initial planes if disparity difference below", this.stSmallDiff, 6);
gd.addNumericField("Consider merging initial planes if jumps between ratio above", this.stHighMix, 6); gd.addNumericField("Consider merging initial planes if jumps between ratio above", this.stHighMix, 6);
gd.addNumericField("Outlier tiles weaker than this may be replaced from neighbors", this.outlayerStrength, 6); gd.addNumericField("Outlier tiles weaker than this may be replaced from neighbors", this.outlierStrength, 6);
gd.addNumericField("Replace weak outlier tiles that do not have neighbors within this disparity difference", this.outlayerDiff, 6); gd.addNumericField("Replace weak outlier tiles that do not have neighbors within this disparity difference", this.outlierDiff, 6);
gd.addNumericField("Replace weak outlier tiles that have higher disparity than weighted average", this.outlayerDiffPos, 6); gd.addNumericField("Replace weak outlier tiles that have higher disparity than weighted average", this.outlierDiffPos, 6);
gd.addNumericField("Replace weak outlier tiles that have lower disparity than weighted average", this.outlayerDiffNeg, 6); gd.addNumericField("Replace weak outlier tiles that have lower disparity than weighted average", this.outlierDiffNeg, 6);
gd.addCheckbox ("Combine with all previous after refine pass", this.combine_refine); gd.addCheckbox ("Combine with all previous after refine pass", this.combine_refine);
gd.addNumericField("Disregard weaker tiles when combining scans", this.combine_min_strength, 6); gd.addNumericField("Disregard weaker tiles when combining scans", this.combine_min_strength, 6);
...@@ -5792,10 +5799,10 @@ public class EyesisCorrectionParameters { ...@@ -5792,10 +5799,10 @@ public class EyesisCorrectionParameters {
this.stSmallDiff= gd.getNextNumber(); this.stSmallDiff= gd.getNextNumber();
this.stHighMix= gd.getNextNumber(); this.stHighMix= gd.getNextNumber();
this.outlayerStrength= gd.getNextNumber(); this.outlierStrength= gd.getNextNumber();
this.outlayerDiff= gd.getNextNumber(); this.outlierDiff= gd.getNextNumber();
this.outlayerDiffPos= gd.getNextNumber(); this.outlierDiffPos= gd.getNextNumber();
this.outlayerDiffNeg= gd.getNextNumber(); this.outlierDiffNeg= gd.getNextNumber();
this.combine_refine= gd.getNextBoolean(); this.combine_refine= gd.getNextBoolean();
......
src/main/java/com/elphel/imagej/cameras/EyesisSubCameraParameters.java
View file @ 9d5dd318
...@@ -370,4 +370,25 @@ import java.util.Properties; ...@@ -370,4 +370,25 @@ import java.util.Properties;
return this.distortionRadius; return this.distortionRadius;
} }
public void setSensorWidth(int v) {
this.sensorWidth = v;
}
public void setSensorHeight(int v) {
this.sensorHeight = v;
}
public void setDecimateMasks(int v) {
this.decimateMasks = v;
}
public int getSensorWidth() {
return this.sensorWidth;
}
public int getSensorHeight() {
return this.sensorHeight;
}
public int getDecimateMasks() {
return this.decimateMasks;
}
} }
src/main/java/com/elphel/imagej/cameras/SFEPhases.java
View file @ 9d5dd318
...@@ -113,7 +113,7 @@ public class SFEPhases { ...@@ -113,7 +113,7 @@ public class SFEPhases {
} }
final AtomicInteger aNumTile=new AtomicInteger(0); final AtomicInteger aNumTile=new AtomicInteger(0);
final AtomicInteger numOutlayers=new AtomicInteger(0); final AtomicInteger numOutliers=new AtomicInteger(0);
final AtomicInteger numPix=new AtomicInteger(0); final AtomicInteger numPix=new AtomicInteger(0);
final Thread[] threads = newThreadArray(threadsMax); final Thread[] threads = newThreadArray(threadsMax);
for (int ithread = 0; ithread < threads.length; ithread++) { for (int ithread = 0; ithread < threads.length; ithread++) {
...@@ -138,7 +138,7 @@ public class SFEPhases { ...@@ -138,7 +138,7 @@ public class SFEPhases {
colorComponents, colorComponents,
debugLevel); debugLevel);
if (tilePhaseStats[0]>0){ if (tilePhaseStats[0]>0){
numOutlayers.getAndAdd(tilePhaseStats[0]); numOutliers.getAndAdd(tilePhaseStats[0]);
numPix.getAndAdd(tilePhaseStats[1]); numPix.getAndAdd(tilePhaseStats[1]);
if (debugLevel>debugThreshold){ if (debugLevel>debugThreshold){
System.out.println("x0="+tileList[nTile][0]+" y0="+tileList[nTile][1]+" tilePhaseStats[0]="+tilePhaseStats[0]+" tilePhaseStats[1]"+tilePhaseStats[1]); System.out.println("x0="+tileList[nTile][0]+" y0="+tileList[nTile][1]+" tilePhaseStats[0]="+tilePhaseStats[0]+" tilePhaseStats[1]"+tilePhaseStats[1]);
...@@ -149,7 +149,7 @@ public class SFEPhases { ...@@ -149,7 +149,7 @@ public class SFEPhases {
}; };
} }
startAndJoin(threads); startAndJoin(threads);
int [] result = {numOutlayers.get(),numPix.get()}; int [] result = {numOutliers.get(),numPix.get()};
return result; return result;
} }
...@@ -265,7 +265,7 @@ public class SFEPhases { ...@@ -265,7 +265,7 @@ public class SFEPhases {
if ((polyCoeff==null) || (polyCoeff.length==0) || (polyCoeff[0]==null)) continue; if ((polyCoeff==null) || (polyCoeff.length==0) || (polyCoeff[0]==null)) continue;
nPix=0; nPix=0;
int nOutlayers=0; int nOutliers=0;
double halfBinWidth=binWidth/2; double halfBinWidth=binWidth/2;
int nGap=0; // should be 0 to count int nGap=0; // should be 0 to count
for (int i=0;i<input_bayer[chn].length;i++){ for (int i=0;i<input_bayer[chn].length;i++){
...@@ -291,7 +291,7 @@ public class SFEPhases { ...@@ -291,7 +291,7 @@ public class SFEPhases {
double diff=Math.abs(d-f); double diff=Math.abs(d-f);
if (diff >= halfBinWidth) { if (diff >= halfBinWidth) {
if (diff >= (halfBinWidth+gapWidth)){ if (diff >= (halfBinWidth+gapWidth)){
nOutlayers++; nOutliers++;
} else { } else {
nGap++; // do not need to continue, only if for debug nGap++; // do not need to continue, only if for debug
break; break;
...@@ -302,7 +302,7 @@ public class SFEPhases { ...@@ -302,7 +302,7 @@ public class SFEPhases {
} }
} }
if (nGap>0) continue; // gap is not empty, can not tell if the phase is wrong if (nGap>0) continue; // gap is not empty, can not tell if the phase is wrong
result[0]+=nOutlayers; result[0]+=nOutliers;
result[1]+=nPix; result[1]+=nPix;
} }
return result; return result;
...@@ -313,7 +313,7 @@ public class SFEPhases { ...@@ -313,7 +313,7 @@ public class SFEPhases {
final int tileClearSize0, final int tileClearSize0,
final int tileMargins0, final int tileMargins0,
final int cmask, // bitmask of color channels to process (9 - two greens) final int cmask, // bitmask of color channels to process (9 - two greens)
final int numPasses, // number of passes to replace outlayers (will end if none was replaced) final int numPasses, // number of passes to replace outliers (will end if none was replaced)
final int numInBase, // number of neighbors (of 8) to use as a base if they all agree final int numInBase, // number of neighbors (of 8) to use as a base if they all agree
final double sigma, // for high-pass filtering final double sigma, // for high-pass filtering
final boolean processNoReplace, // calculate differences even if no replacements were made final boolean processNoReplace, // calculate differences even if no replacements were made
...@@ -332,7 +332,7 @@ public class SFEPhases { ...@@ -332,7 +332,7 @@ public class SFEPhases {
tileClearSize0, tileClearSize0,
tileMargins0, tileMargins0,
cmask, // bitmask of color channels to process (9 - two greens) cmask, // bitmask of color channels to process (9 - two greens)
numPasses, // number of passes to replace outlayers (will end if none was replaced) numPasses, // number of passes to replace outliers (will end if none was replaced)
numInBase, // number of neighbors (of 8) to use as a base if they all agree numInBase, // number of neighbors (of 8) to use as a base if they all agree
sigma, // for high-pass filtering sigma, // for high-pass filtering
processNoReplace, // calculate differences even if no replacements were made processNoReplace, // calculate differences even if no replacements were made
...@@ -366,7 +366,7 @@ public class SFEPhases { ...@@ -366,7 +366,7 @@ public class SFEPhases {
final int tileClearSize0, final int tileClearSize0,
final int tileMargins0, final int tileMargins0,
final int cmask, // bitmask of color channels to process (9 - two greens) final int cmask, // bitmask of color channels to process (9 - two greens)
final int numPasses, // number of passes to replace outlayers (will end if none was replaced) final int numPasses, // number of passes to replace outliers (will end if none was replaced)
final int numInBase, // number of neighbors (of 8) to use as a base if they all agree final int numInBase, // number of neighbors (of 8) to use as a base if they all agree
final double sigma, // for high-pass filtering final double sigma, // for high-pass filtering
final boolean processNoReplace, // calculate differences even if no replacements were made final boolean processNoReplace, // calculate differences even if no replacements were made
...@@ -427,7 +427,7 @@ public class SFEPhases { ...@@ -427,7 +427,7 @@ public class SFEPhases {
imp, imp,
tileHalfSize, tileHalfSize,
cmask, // bitmask of color channels to process (9 - two greens) cmask, // bitmask of color channels to process (9 - two greens)
numPasses, // number of passes to replace outlayers (will end if none was replaced) numPasses, // number of passes to replace outliers (will end if none was replaced)
numInBase, // number of neighbors (of 8) to use as a base if they all agree numInBase, // number of neighbors (of 8) to use as a base if they all agree
sigma, // for high-pass filtering sigma, // for high-pass filtering
processNoReplace, // calculate differences even if no replacements were made processNoReplace, // calculate differences even if no replacements were made
...@@ -477,7 +477,7 @@ public class SFEPhases { ...@@ -477,7 +477,7 @@ public class SFEPhases {
ImagePlus imp, ImagePlus imp,
int tileHalfSize, int tileHalfSize,
int cmask, // bitmask of color channels to process (9 - two greens) int cmask, // bitmask of color channels to process (9 - two greens)
int numPasses, // number of passes to replace outlayers (will end if none was replaced) int numPasses, // number of passes to replace outliers (will end if none was replaced)
int numInBase, // number of neighbors (of 8) to use as a base if they all agree int numInBase, // number of neighbors (of 8) to use as a base if they all agree
double sigma, // for high-pass filtering double sigma, // for high-pass filtering
boolean processNoReplace, // calculate differences even if no replacements were made boolean processNoReplace, // calculate differences even if no replacements were made
...@@ -551,7 +551,7 @@ public class SFEPhases { ...@@ -551,7 +551,7 @@ public class SFEPhases {
} }
} }
if ((numReplacements==0) && !processNoReplace) continue; if ((numReplacements==0) && !processNoReplace) continue;
// run low pass filter on the tile with outlayers replaced with the averages // run low pass filter on the tile with outliers replaced with the averages
if (doubleGaussianBlur==null) doubleGaussianBlur=new DoubleGaussianBlur(); if (doubleGaussianBlur==null) doubleGaussianBlur=new DoubleGaussianBlur();
doubleGaussianBlur.blurDouble(tilePix,tileHalfSize,tileHalfSize,sigma,sigma, 0.01); doubleGaussianBlur.blurDouble(tilePix,tileHalfSize,tileHalfSize,sigma,sigma, 0.01);
for (int i=0;i<tilePix.length;i++) tilePix[i]=input_bayer[chn][i]-tilePix[i]; for (int i=0;i<tilePix.length;i++) tilePix[i]=input_bayer[chn][i]-tilePix[i];
...@@ -863,7 +863,7 @@ public class SFEPhases { ...@@ -863,7 +863,7 @@ public class SFEPhases {
int tileClearSize, int tileClearSize,
int tileMargins, int tileMargins,
int cmask, // bitmask of color channels to process (9 - two greens) int cmask, // bitmask of color channels to process (9 - two greens)
int numPasses, // number of passes to replace outlayers (will end if none was replaced) int numPasses, // number of passes to replace outliers (will end if none was replaced)
int numInBase, // number of neighbors (of 8) to use as a base if they all agree int numInBase, // number of neighbors (of 8) to use as a base if they all agree
double sigma, // for high-pass filtering double sigma, // for high-pass filtering
boolean processNoReplace, // calculate differences even if no replacements were made boolean processNoReplace, // calculate differences even if no replacements were made
...@@ -885,17 +885,17 @@ public class SFEPhases { ...@@ -885,17 +885,17 @@ public class SFEPhases {
gd.addNumericField("Tile clearSize", tileClearSize, 0 ,4, "pix"); gd.addNumericField("Tile clearSize", tileClearSize, 0 ,4, "pix");
gd.addNumericField("Tile margin (extra) width", tileMargins, 0 ,4, "pix"); gd.addNumericField("Tile margin (extra) width", tileMargins, 0 ,4, "pix");
gd.addNumericField("Color channel mask", cmask, 0 ,4, "9 - both green colors"); gd.addNumericField("Color channel mask", cmask, 0 ,4, "9 - both green colors");
gd.addNumericField("Number of \"remove outlayers\" passes", numPasses, 0 ,4, ""); gd.addNumericField("Number of \"remove outliers\" passes", numPasses, 0 ,4, "");
gd.addNumericField("Number of neighbors (of total 8) to base outlayers", numInBase, 0 ,4, "<=8"); gd.addNumericField("Number of neighbors (of total 8) to base outliers", numInBase, 0 ,4, "<=8");
gd.addNumericField("Base low-pass sigma ", sigma, 3 ,7, "double pixels"); gd.addNumericField("Base low-pass sigma ", sigma, 3 ,7, "double pixels");
gd.addCheckbox ("Process tiles with no outlayer replacements", processNoReplace); gd.addCheckbox ("Process tiles with no outlier replacements", processNoReplace);
gd.addNumericField("\"Normal\" pixels variation", binWidth, 3 ,7, ""); gd.addNumericField("\"Normal\" pixels variation", binWidth, 3 ,7, "");
gd.addNumericField("Empty level gap between \"normal\" pixels and outlayers", gapWidth, 3 ,7, ""); gd.addNumericField("Empty level gap between \"normal\" pixels and outliers", gapWidth, 3 ,7, "");
gd.addNumericField("Post-HPF algorithm number", algorithmNumber, 0 ,4, "(1 or 2"); gd.addNumericField("Post-HPF algorithm number", algorithmNumber, 0 ,4, "(1 or 2");
gd.addNumericField("Number of neighbors (of total 8) to base outlayers (after high-pass), 0 - no filter", numInBase2, 0 ,4, "<=8"); gd.addNumericField("Number of neighbors (of total 8) to base outliers (after high-pass), 0 - no filter", numInBase2, 0 ,4, "<=8");
gd.addNumericField("\"Normal\" pixels variation (after high-pass)", binWidth2, 3 ,7, ""); gd.addNumericField("\"Normal\" pixels variation (after high-pass)", binWidth2, 3 ,7, "");
gd.addNumericField("Empty level gap between \"normal\" pixels and outlayers (after high-pass)", gapWidth2, 3 ,7, ""); gd.addNumericField("Empty level gap between \"normal\" pixels and outliers (after high-pass)", gapWidth2, 3 ,7, "");
gd.addCheckbox ("Update sensor calibration files with defects data", updateSensorCalibrationFiles); gd.addCheckbox ("Update sensor calibration files with defects data", updateSensorCalibrationFiles);
gd.addCheckbox ("Clear defects in sensor calibration files if none new detected", clearDefects); gd.addCheckbox ("Clear defects in sensor calibration files if none new detected", clearDefects);
...@@ -922,7 +922,7 @@ public class SFEPhases { ...@@ -922,7 +922,7 @@ public class SFEPhases {
tileClearSize, tileClearSize,
tileMargins, tileMargins,
cmask, // bitmask of color channels to process (9 - two greens) cmask, // bitmask of color channels to process (9 - two greens)
numPasses, // number of passes to replace outlayers (will end if none was replaced) numPasses, // number of passes to replace outliers (will end if none was replaced)
numInBase, // number of neighbors (of 8) to use as a base if they all agree numInBase, // number of neighbors (of 8) to use as a base if they all agree
sigma, // for high-pass filtering sigma, // for high-pass filtering
processNoReplace, // calculate differences even if no replacements were made processNoReplace, // calculate differences even if no replacements were made
...@@ -964,7 +964,7 @@ public class SFEPhases { ...@@ -964,7 +964,7 @@ public class SFEPhases {
int tileClearSize, int tileClearSize,
int tileMargins, int tileMargins,
int cmask, // bitmask of color channels to process (9 - two greens) int cmask, // bitmask of color channels to process (9 - two greens)
int numPasses, // number of passes to replace outlayers (will end if none was replaced) int numPasses, // number of passes to replace outliers (will end if none was replaced)
int numInBase, // number of neighbors (of 8) to use as a base if they all agree int numInBase, // number of neighbors (of 8) to use as a base if they all agree
double sigma, // for high-pass filtering double sigma, // for high-pass filtering
boolean processNoReplace, // calculate differences even if no replacements were made boolean processNoReplace, // calculate differences even if no replacements were made
...@@ -991,7 +991,7 @@ public class SFEPhases { ...@@ -991,7 +991,7 @@ public class SFEPhases {
tileClearSize, tileClearSize,
tileMargins, tileMargins,
cmask, // bitmask of color channels to process (9 - two greens) cmask, // bitmask of color channels to process (9 - two greens)
numPasses, // number of passes to replace outlayers (will end if none was replaced) numPasses, // number of passes to replace outliers (will end if none was replaced)
numInBase, // number of neighbors (of 8) to use as a base if they all agree numInBase, // number of neighbors (of 8) to use as a base if they all agree
sigma, // for high-pass filtering sigma, // for high-pass filtering
processNoReplace, // calculate differences even if no replacements were made processNoReplace, // calculate differences even if no replacements were made
...@@ -1212,7 +1212,7 @@ public class SFEPhases { ...@@ -1212,7 +1212,7 @@ public class SFEPhases {
int tileClearSize, int tileClearSize,
int tileMargins, int tileMargins,
int cmask, // bitmask of color channels to process (9 - two greens) int cmask, // bitmask of color channels to process (9 - two greens)
int numPasses, // number of passes to replace outlayers (will end if none was replaced) int numPasses, // number of passes to replace outliers (will end if none was replaced)
int numInBase, // number of neighbors (of 8) to use as a base if they all agree int numInBase, // number of neighbors (of 8) to use as a base if they all agree
double sigma, // for high-pass filtering double sigma, // for high-pass filtering
boolean processNoReplace, // calculate differences even if no replacements were made boolean processNoReplace, // calculate differences even if no replacements were made
...@@ -1249,7 +1249,7 @@ public class SFEPhases { ...@@ -1249,7 +1249,7 @@ public class SFEPhases {
tileClearSize, tileClearSize,
tileMargins, tileMargins,
cmask, // bitmask of color channels to process (9 - two greens) cmask, // bitmask of color channels to process (9 - two greens)
numPasses, // number of passes to replace outlayers (will end if none was replaced) numPasses, // number of passes to replace outliers (will end if none was replaced)
numInBase, // number of neighbors (of 8) to use as a base if they all agree numInBase, // number of neighbors (of 8) to use as a base if they all agree
sigma, // for high-pass filtering sigma, // for high-pass filtering
processNoReplace, // calculate differences even if no replacements were made processNoReplace, // calculate differences even if no replacements were made
......
src/main/java/com/elphel/imagej/correction/EyesisCorrections.java
View file @ 9d5dd318
...@@ -510,7 +510,7 @@ public class EyesisCorrections { ...@@ -510,7 +510,7 @@ public class EyesisCorrections {
if (this.defectsXY[srcChannel]==null){ if (this.defectsXY[srcChannel]==null){
System.out.println("No pixel defects info is available for channel "+srcChannel); System.out.println("No pixel defects info is available for channel "+srcChannel);
} else { } else {
System.out.println("Extracted "+this.defectsXY[srcChannel].length+" pixel outlayers for channel "+srcChannel+ System.out.println("Extracted "+this.defectsXY[srcChannel].length+" pixel outliers for channel "+srcChannel+
" (x:y:difference"); " (x:y:difference");
int numInLine=8; int numInLine=8;
for (int i=0;i<this.defectsXY[srcChannel].length;i++){ for (int i=0;i<this.defectsXY[srcChannel].length;i++){
......
src/main/java/com/elphel/imagej/tileprocessor/BiScan.java
View file @ 9d5dd318
...@@ -1919,7 +1919,7 @@ public class BiScan { ...@@ -1919,7 +1919,7 @@ public class BiScan {
double rms = Double.NaN; double rms = Double.NaN;
if (smpl_p == null) smpl_p = new double [smpl_len]; if (smpl_p == null) smpl_p = new double [smpl_len];
while (num_in_sample >= fin_samples) { while (num_in_sample >= fin_samples) {
// fit plane to the selected and remove outlayers after each iteration // fit plane to the selected and remove outliers after each iteration
disp_tilts = fitPlane( disp_tilts = fitPlane(
smpl_radius, //int smpl_radius, smpl_radius, //int smpl_radius,
max_tilt, //double max_tilt, max_tilt, //double max_tilt,
......
src/main/java/com/elphel/imagej/tileprocessor/CLTPass3d.java
View file @ 9d5dd318
...@@ -528,7 +528,7 @@ public class CLTPass3d{ ...@@ -528,7 +528,7 @@ public class CLTPass3d{
final int tilesY = tileProcessor.getTilesY(); final int tilesY = tileProcessor.getTilesY();
final int nTiles = tilesX*tilesY; final int nTiles = tilesX*tilesY;
final boolean [] weakOutlayers = new boolean [nTiles]; final boolean [] weakOutliers = new boolean [nTiles];
int [] dirs8 = {-tilesX, -tilesX + 1, 1, tilesX +1, tilesX, tilesX - 1, -1, -tilesX - 1}; int [] dirs8 = {-tilesX, -tilesX + 1, 1, tilesX +1, tilesX, tilesX - 1, -1, -tilesX - 1};
final int [] dirs = dirs8; final int [] dirs = dirs8;
final double [] disparity = getDisparity(0); final double [] disparity = getDisparity(0);
...@@ -554,11 +554,11 @@ public class CLTPass3d{ ...@@ -554,11 +554,11 @@ public class CLTPass3d{
double dbg_disparity_nTile = disparity[nTile]; double dbg_disparity_nTile = disparity[nTile];
double dbg_disparityFar = disparityFar; double dbg_disparityFar = disparityFar;
double dbg_disparityNear = disparityNear; double dbg_disparityNear = disparityNear;
boolean [] dbg_weakOutlayers = weakOutlayers; boolean [] dbg_weakOutliers = weakOutliers;
int tileY = nTile / tilesX; int tileY = nTile / tilesX;
int tileX = nTile % tilesX; int tileX = nTile % tilesX;
if ((tileY > 0) && (tileY < (tilesY -1)) &&(tileX > 0) && (tileX < (tilesX -1))){ // disregard outer row/cols if ((tileY > 0) && (tileY < (tilesY -1)) &&(tileX > 0) && (tileX < (tilesX -1))){ // disregard outer row/cols
weakOutlayers[nTile] = true; weakOutliers[nTile] = true;
boolean hasNeighbors = false; boolean hasNeighbors = false;
double sd = 0.0, sw = 0.0; double sd = 0.0, sw = 0.0;
for (int dir = 0; dir< dirs.length; dir++){ for (int dir = 0; dir< dirs.length; dir++){
...@@ -572,20 +572,20 @@ public class CLTPass3d{ ...@@ -572,20 +572,20 @@ public class CLTPass3d{
sd += w * disparity[nTile1]; sd += w * disparity[nTile1];
hasNeighbors = true; hasNeighbors = true;
if (Math.abs(disparity[nTile]-disparity[nTile1]) <= maxDiff){ // any outlier - will be false if (Math.abs(disparity[nTile]-disparity[nTile1]) <= maxDiff){ // any outlier - will be false
weakOutlayers[nTile] = false; weakOutliers[nTile] = false;
// break; // break;
} }
} }
} }
if (sw >= 0.0) { if (sw >= 0.0) {
sd /= sw; sd /= sw;
if (disparity[nTile] < (sd - maxDiffNeg)) weakOutlayers[nTile] = true; if (disparity[nTile] < (sd - maxDiffNeg)) weakOutliers[nTile] = true;
else if (disparity[nTile] > (sd + maxDiffPos)) weakOutlayers[nTile] = true; else if (disparity[nTile] > (sd + maxDiffPos)) weakOutliers[nTile] = true;
} }
if (disparity[nTile] < disparityFar) weakOutlayers[nTile] = true; if (disparity[nTile] < disparityFar) weakOutliers[nTile] = true;
if (disparity[nTile] > disparityNear) weakOutlayers[nTile] = true; if (disparity[nTile] > disparityNear) weakOutliers[nTile] = true;
if (!hasNeighbors) { if (!hasNeighbors) {
weakOutlayers[nTile] = false; // lone tile or NaN among NaNs weakOutliers[nTile] = false; // lone tile or NaN among NaNs
} }
} }
} }
...@@ -606,11 +606,11 @@ public class CLTPass3d{ ...@@ -606,11 +606,11 @@ public class CLTPass3d{
if (nTile == dbg_nTile){ if (nTile == dbg_nTile){
System.out.println("replaceWeakOutliers():2 nTile="+nTile); System.out.println("replaceWeakOutliers():2 nTile="+nTile);
} }
if (weakOutlayers[nTile]) { if (weakOutliers[nTile]) {
double sw = 0.0, sd = 0.0; double sw = 0.0, sd = 0.0;
for (int dir = 0; dir< dirs.length; dir++){ for (int dir = 0; dir< dirs.length; dir++){
int nTile1 = nTile + dirs[dir]; int nTile1 = nTile + dirs[dir];
if (!weakOutlayers[nTile1] && ((selection == null) || selection[nTile1 ]) ) { if (!weakOutliers[nTile1] && ((selection == null) || selection[nTile1 ]) ) {
double w = strength[nTile1]; double w = strength[nTile1];
sw += w; sw += w;
sd += w * src_disparity[nTile1]; sd += w * src_disparity[nTile1];
...@@ -642,7 +642,7 @@ public class CLTPass3d{ ...@@ -642,7 +642,7 @@ public class CLTPass3d{
}; };
} }
ImageDtt.startAndJoin(threads); ImageDtt.startAndJoin(threads);
return weakOutlayers; return weakOutliers;
} }
public boolean [] getUntestedBackgroundBorder ( public boolean [] getUntestedBackgroundBorder (
......
src/main/java/com/elphel/imagej/tileprocessor/TilePlanes.java
View file @ 9d5dd318
...@@ -829,7 +829,7 @@ public class TilePlanes { ...@@ -829,7 +829,7 @@ public class TilePlanes {
for (int nl = 0; nl < measuredLayers.getNumLayers(); nl ++){ for (int nl = 0; nl < measuredLayers.getNumLayers(); nl ++){
if ((measuredSelection[nl] != null) && ((measSel & (1 << nl)) !=0)) { if ((measuredSelection[nl] != null) && ((measSel & (1 << nl)) !=0)) {
if (smplMode) { if (smplMode) {
disp_strength[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_strength[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
nl, // int num_layer, nl, // int num_layer,
getSTileXY()[0], // int stX, getSTileXY()[0], // int stX,
getSTileXY()[1], // int stY, getSTileXY()[1], // int stY,
...@@ -964,7 +964,7 @@ public class TilePlanes { ...@@ -964,7 +964,7 @@ public class TilePlanes {
if ((measuredSelection[nl] != null) && ((measSel & (1 << nl)) !=0)) { if ((measuredSelection[nl] != null) && ((measSel & (1 << nl)) !=0)) {
// recalculate for all measure tiles, not just selected in the original PD // recalculate for all measure tiles, not just selected in the original PD
if (smplMode) { if (smplMode) {
disp_strength[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_strength[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
nl, // int num_layer, nl, // int num_layer,
getSTileXY()[0], // int stX, getSTileXY()[0], // int stX,
getSTileXY()[1], // int stY, getSTileXY()[1], // int stY,
...@@ -1222,7 +1222,7 @@ public class TilePlanes { ...@@ -1222,7 +1222,7 @@ public class TilePlanes {
for (int nl = 0; nl < measuredSelection.length; nl++){ for (int nl = 0; nl < measuredSelection.length; nl++){
if (measuredSelection[nl] != null){ if (measuredSelection[nl] != null){
if (smplMode) { if (smplMode) {
disp_str[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_str[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
nl, // int num_layer, nl, // int num_layer,
sTileXY[0], // int stX, sTileXY[0], // int stX,
sTileXY[1], // int stY, sTileXY[1], // int stY,
...@@ -1373,7 +1373,7 @@ public class TilePlanes { ...@@ -1373,7 +1373,7 @@ public class TilePlanes {
if (measuredSelection[nl] != null){ if (measuredSelection[nl] != null){
if (smplMode) { if (smplMode) {
// if (need_disp_str) { // if (need_disp_str) {
disp_str[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_str[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
nl, // int num_layer, nl, // int num_layer,
sTileXY[0], // int stX, sTileXY[0], // int stX,
sTileXY[1], // int stY, sTileXY[1], // int stY,
...@@ -1652,7 +1652,7 @@ public class TilePlanes { ...@@ -1652,7 +1652,7 @@ public class TilePlanes {
if (tile_sel[nl] != null){ if (tile_sel[nl] != null){
if (smplMode) { if (smplMode) {
if (need_disp_str) { if (need_disp_str) {
disp_str[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_str[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
nl, // int num_layer, nl, // int num_layer,
sTileXY[0], // int stX, sTileXY[0], // int stX,
sTileXY[1], // int stY, sTileXY[1], // int stY,
...@@ -2067,7 +2067,7 @@ public class TilePlanes { ...@@ -2067,7 +2067,7 @@ public class TilePlanes {
if (tile_sel[nl] != null){ if (tile_sel[nl] != null){
if (smplMode) { if (smplMode) {
if (need_disp_str) { if (need_disp_str) {
disp_str[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_str[nl] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
nl, // int num_layer, nl, // int num_layer,
sTileXY[0], // int stX, sTileXY[0], // int stX,
sTileXY[1], // int stY, sTileXY[1], // int stY,
...@@ -4597,7 +4597,7 @@ public class TilePlanes { ...@@ -4597,7 +4597,7 @@ public class TilePlanes {
double [][][] disp_strength = new double[measuredLayers.getNumLayers()][][]; double [][][] disp_strength = new double[measuredLayers.getNumLayers()][][];
for (int ml = 0; ml < disp_strength.length; ml++) if ((stMeasSel & ( 1 << ml)) != 0){ for (int ml = 0; ml < disp_strength.length; ml++) if ((stMeasSel & ( 1 << ml)) != 0){
if (smplMode) { if (smplMode) {
disp_strength[ml] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_strength[ml] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
ml, // int num_layer, ml, // int num_layer,
getSTileXY()[0], // int stX, getSTileXY()[0], // int stX,
getSTileXY()[1], // int stY, getSTileXY()[1], // int stY,
...@@ -5042,7 +5042,7 @@ public class TilePlanes { ...@@ -5042,7 +5042,7 @@ public class TilePlanes {
double [][][] disp_strength = new double[measuredLayers.getNumLayers()][][]; double [][][] disp_strength = new double[measuredLayers.getNumLayers()][][];
for (int ml = 0; ml < disp_strength.length; ml++) if ((stMeasSel & ( 1 << ml)) != 0){ for (int ml = 0; ml < disp_strength.length; ml++) if ((stMeasSel & ( 1 << ml)) != 0){
if (smplMode) { if (smplMode) {
disp_strength[ml] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_strength[ml] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
ml, // int num_layer, ml, // int num_layer,
getSTileXY()[0], // int stX, getSTileXY()[0], // int stX,
getSTileXY()[1], // int stY, getSTileXY()[1], // int stY,
...@@ -5822,12 +5822,12 @@ public class TilePlanes { ...@@ -5822,12 +5822,12 @@ public class TilePlanes {
} }
} }
// it is foreground, now get measured data and find maximal strength (remove outlayers? // it is foreground, now get measured data and find maximal strength (remove outliers?
double [] lap_weights = measuredLayers.getLapWeights1d(); double [] lap_weights = measuredLayers.getLapWeights1d();
double [][][] disp_strength = new double[measuredLayers.getNumLayers()][][]; double [][][] disp_strength = new double[measuredLayers.getNumLayers()][][];
for (int ml = 0; ml < disp_strength.length; ml++) if (fg_sel[ml] != null){ // if ((stMeasSel & ( 1 << ml)) != 0) { for (int ml = 0; ml < disp_strength.length; ml++) if (fg_sel[ml] != null){ // if ((stMeasSel & ( 1 << ml)) != 0) {
if (this.smplMode) { if (this.smplMode) {
disp_strength[ml] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outlayers disp_strength[ml] = measuredLayers.getDisparityStrengthMLTilted( // expensive to calculate (improve removing outliers
ml, // int num_layer, ml, // int num_layer,
getSTileXY()[0], // int stX, getSTileXY()[0], // int stX,
getSTileXY()[1], // int stY, getSTileXY()[1], // int stY,
......
src/main/java/com/elphel/imagej/tileprocessor/TileProcessor.java
View file @ 9d5dd318
...@@ -5032,10 +5032,10 @@ public class TileProcessor { ...@@ -5032,10 +5032,10 @@ public class TileProcessor {
// replace weak outliers tiles with weighted averages (modifies disparity) // replace weak outliers tiles with weighted averages (modifies disparity)
boolean[] outliers = scan_prev.replaceWeakOutliers( boolean[] outliers = scan_prev.replaceWeakOutliers(
null, // final boolean [] selection, null, // final boolean [] selection,
clt_parameters.outlayerStrength , //final double weakStrength, // strength to be considered weak, subject to this replacement clt_parameters.outlierStrength , //final double weakStrength, // strength to be considered weak, subject to this replacement
clt_parameters.outlayerDiff, // final double maxDiff) clt_parameters.outlierDiff, // final double maxDiff)
clt_parameters.outlayerDiffPos, // final double maxDiff) clt_parameters.outlierDiffPos, // final double maxDiff)
clt_parameters.outlayerDiffNeg, // final double maxDiff) clt_parameters.outlierDiffNeg, // final double maxDiff)
0.5 * disparity_far, 0.5 * disparity_far,
2.0 * disparity_near, 2.0 * disparity_near,
debugLevel); debugLevel);
...@@ -5124,7 +5124,7 @@ public class TileProcessor { ...@@ -5124,7 +5124,7 @@ public class TileProcessor {
} }
if (show_super && (debugLevel > 100)){ // something is broken, java.lang.NullPointerException at TileProcessor.refinePassSetup(TileProcessor.java:4488) if (show_super && (debugLevel > 100)){ // something is broken, java.lang.NullPointerException at TileProcessor.refinePassSetup(TileProcessor.java:4488)
String [] dbg_disp_tiltes={"masked", "filtered", "disp_combo", "disparity","st_disparity", "strength", String [] dbg_disp_tiltes={"masked", "filtered", "disp_combo", "disparity","st_disparity", "strength",
"st_strength","outlayers","these","border","border_tiles"}; // ,"before","after","after1","after2","after3","neib"}; "st_strength","outliers","these","border","border_tiles"}; // ,"before","after","after1","after2","after3","neib"};
double [][] dbg_disp = new double [dbg_disp_tiltes.length][]; double [][] dbg_disp = new double [dbg_disp_tiltes.length][];
dbg_disp[0] = masked_filtered; // + dbg_disp[0] = masked_filtered; // +
dbg_disp[1] = scan_prev.getDisparity(); // + dbg_disp[1] = scan_prev.getDisparity(); // +
...@@ -7165,7 +7165,7 @@ public class TileProcessor { ...@@ -7165,7 +7165,7 @@ public class TileProcessor {
this_disparity[i] = ortho_disparity[i]; this_disparity[i] = ortho_disparity[i];
} }
// average disparity along the runs, if they are close enough (remove outlayers?) // average disparity along the runs, if they are close enough (remove outliers?)
if (clt_parameters.ortho_rms > 0){ if (clt_parameters.ortho_rms > 0){
double ortho_rms2 = clt_parameters.ortho_rms * clt_parameters.ortho_rms; double ortho_rms2 = clt_parameters.ortho_rms * clt_parameters.ortho_rms;
......
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