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imagej-elphel
Commit 24b642b0 authored by Andrey Filippov's avatar Andrey Filippov
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Updating batch mode of the 3d scene processing

parent 91409a1a
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Showing with 823 additions and 776 deletions
src/main/java/CorrectionColorProc.java
View file @ 24b642b0
......@@ -3,12 +3,12 @@
** CorrectionColorProc.java
**
** Color conversion methods used in aberration correction for Eyesis4pi
**
**
**
** Copyright (C) 2012 Elphel, Inc.
**
** -----------------------------------------------------------------------------**
**
**
** CorrectionColorProc.java is free software: you can redistribute it and/or modify
** it under the terms of the GNU General Public License as published by
** the Free Software Foundation, either version 3 of the License, or
......@@ -25,12 +25,12 @@
**
*/
import ij.ImageStack;
import ij.gui.GenericDialog;
import java.util.Properties;
import java.util.concurrent.atomic.AtomicInteger;
import ij.ImageStack;
import ij.gui.GenericDialog;
public class CorrectionColorProc {
showDoubleFloatArrays SDFA_INSTANCE= new showDoubleFloatArrays();
......@@ -46,7 +46,7 @@ public class CorrectionColorProc {
int getDenoiseMaskChromaWidth() {return this.denoiseMaskChromaWidth;}
void setDebug(int debugLevel){this.debugLevel=debugLevel;}
public void processColorsWeights(ImageStack stack, // does not like NaN (in GaussianBlur
double scale, // initial maximal pixel value (16))
EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
......@@ -108,9 +108,9 @@ public class CorrectionColorProc {
for (i=0;i<length;i++) {
double Y=Ar*fpixels_r[i]+Ag*fpixels_g[i]+Ab*fpixels_b[i];
Y= (Y !=0.0) ? (linGamma(colorProcParameters.gamma, gamma_a, gamma_linK, colorProcParameters.minLin, Y)/Y): 0.0;
fpixels_r[i]*=Y*gain_red;
fpixels_g[i]*=Y*gain_green;
fpixels_b[i]*=Y*gain_blue;
fpixels_r[i]*=Y*gain_red;
fpixels_g[i]*=Y*gain_green;
fpixels_b[i]*=Y*gain_blue;
}
if (colorProcParameters.corrBlueLeak && blueProc) {
......@@ -222,11 +222,11 @@ public class CorrectionColorProc {
gb.blurDouble(dpixels_pr_dark, width, height, colorProcParameters.chromaDarkSigma, colorProcParameters.chromaDarkSigma, 0.01);
gb.blurDouble(dpixels_pb_dark, width, height, colorProcParameters.chromaDarkSigma, colorProcParameters.chromaDarkSigma, 0.01);
if (debugLevel> 2) {
SDFA_INSTANCE.showArrays(dmask, width, height,"dmask");
SDFA_INSTANCE.showArrays(dpixels_pr, width, height,"dpixels_pr");
SDFA_INSTANCE.showArrays(dpixels_pb, width, height,"dpixels_pb");
SDFA_INSTANCE.showArrays(dpixels_pr_dark, width, height,"dpixels_pr_dark");
SDFA_INSTANCE.showArrays(dpixels_pb_dark, width, height,"dpixels_pb_dark");
SDFA_INSTANCE.showArrays(dmask, width, height,"dmask");
SDFA_INSTANCE.showArrays(dpixels_pr, width, height,"dpixels_pr");
SDFA_INSTANCE.showArrays(dpixels_pb, width, height,"dpixels_pb");
SDFA_INSTANCE.showArrays(dpixels_pr_dark, width, height,"dpixels_pr_dark");
SDFA_INSTANCE.showArrays(dpixels_pb_dark, width, height,"dpixels_pb_dark");
}
double mp;
double k =1.0/(colorProcParameters.maskMax-colorProcParameters.maskMin);
......@@ -241,7 +241,7 @@ public class CorrectionColorProc {
//TODO: null DENOISE_MASK if it is not calculated
if (colorProcParameters.combineWithSharpnessMask) {
if (denoiseMask==null) {
System.out.println ( "Can not combine masks as denoiseMask is null (i.e. no denoise was performed)");
System.out.println ( "Can not combine masks as denoiseMask is null (i.e. no denoise was performed)"); // here
} else if (denoiseMask.length!=dmask.length) {
System.out.println ( "Can not combine masks as denoiseMask length is different from that of dmask");
} else {
......@@ -324,7 +324,7 @@ public class CorrectionColorProc {
fpixels_g[i]=(float) linGamma(colorProcParameters.gamma, gamma_a, gamma_linK, colorProcParameters.minLin, fpixels_g[i]*gain_green);
fpixels_b[i]=(float) linGamma(colorProcParameters.gamma, gamma_a, gamma_linK, colorProcParameters.minLin, fpixels_b[i]*gain_blue);
}
/* Convert to YPbPr */
double Y,Pb,Pr;
double Kg=1.0-colorProcParameters.kr-colorProcParameters.kb;
......@@ -411,11 +411,11 @@ public class CorrectionColorProc {
gb.blurDouble(dpixels_pr_dark, width, height, colorProcParameters.chromaDarkSigma, colorProcParameters.chromaDarkSigma, 0.01);
gb.blurDouble(dpixels_pb_dark, width, height, colorProcParameters.chromaDarkSigma, colorProcParameters.chromaDarkSigma, 0.01);
if (debugLevel>2) {
SDFA_INSTANCE.showArrays(dmask, width, height,"dmask");
SDFA_INSTANCE.showArrays(dpixels_pr, width, height,"dpixels_pr");
SDFA_INSTANCE.showArrays(dpixels_pb, width, height,"dpixels_pb");
SDFA_INSTANCE.showArrays(dpixels_pr_dark, width, height,"dpixels_pr_dark");
SDFA_INSTANCE.showArrays(dpixels_pb_dark, width, height,"dpixels_pb_dark");
SDFA_INSTANCE.showArrays(dmask, width, height,"dmask");
SDFA_INSTANCE.showArrays(dpixels_pr, width, height,"dpixels_pr");
SDFA_INSTANCE.showArrays(dpixels_pb, width, height,"dpixels_pb");
SDFA_INSTANCE.showArrays(dpixels_pr_dark, width, height,"dpixels_pr_dark");
SDFA_INSTANCE.showArrays(dpixels_pb_dark, width, height,"dpixels_pb_dark");
}
double mp;
double k =1.0/(colorProcParameters.maskMax-colorProcParameters.maskMin);
......@@ -439,7 +439,7 @@ public class CorrectionColorProc {
if (dmask[i]>1.0) dmask[i]=1.0;
}
}
}
for (i=0;i<dmask.length;i++) {
mp=dmask[i];
......@@ -469,7 +469,7 @@ public class CorrectionColorProc {
}
/* ======================================================================== */
public double linGamma(double gamma, double a, double k, double x0, double x) {
if (x<0) return 0.0;
......@@ -518,25 +518,25 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
}
public static class ColorGainsParameters {
public double[] gain={
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0};
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0};
public double[] balanceRed={
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0};
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0};
public double[] balanceBlue={
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0};
1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0};
public ColorGainsParameters(){
}
......@@ -561,7 +561,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
}
}
}
public void modifyNumChannels(int numChannels){
if ((numChannels>0) && (numChannels!=this.gain.length)) {
double [] gain1=this.gain;
......@@ -579,7 +579,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
}
}
}
public boolean showDialog() {
GenericDialog gd = new GenericDialog("Individual channels colors/gains");
for (int i =0; i<this.gain.length;i++){
......
src/main/java/EyesisCorrectionParameters.java
View file @ 24b642b0
......@@ -3004,6 +3004,9 @@ public class EyesisCorrectionParameters {
public HashMap<String,Double> z_corr_map = new HashMap<String,Double>();
public static String Z_CORR_PREFIX = "z_corr.";
public boolean batch_run = false; // turned on only while running in batch mode
public CLTParameters(){}
public void setProperties(String prefix,Properties properties){
......
src/main/java/EyesisDCT.java
View file @ 24b642b0
This diff is collapsed.
src/main/java/Eyesis_Correction.java
View file @ 24b642b0
......@@ -776,7 +776,7 @@ private Panel panel1,
Runtime runtime = Runtime.getRuntime();
runtime.gc();
if (DEBUG_LEVEL>0) System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
CLT_PARAMETERS.batch_run = false;
if (label==null) return;
/* ======================================================================== */
if (label.equals("Configure spilt")) {
......@@ -5051,7 +5051,6 @@ private Panel panel1,
RGB_PARAMETERS, // EyesisCorrectionParameters.RGBParameters rgbParameters,
THREADS_MAX, // final int threadsMax, // maximal number of threads to launch
UPDATE_STATUS, // final boolean updateStatus,
false, // final boolean batch_mode,
DEBUG_LEVEL); //final int debugLevel);
if (!OK) {
String msg="Image data not initialized, run 'CLT 3D' command first";
......@@ -5059,18 +5058,9 @@ private Panel panel1,
IJ.showMessage("Error",msg);
}
/*
if (configPath!=null) {
saveTimestampedProperties( // save config again
configPath, // full path or null
null, // use as default directory if path==null
true,
PROPERTIES);
}
*/
} else if (label.equals("CLT batch process")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
CLT_PARAMETERS.batch_run = true;
EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
if (QUAD_CLT == null){
QUAD_CLT = new QuadCLT (
......
src/main/java/LinkPlanes.java
View file @ 24b642b0
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src/main/java/MacroCorrelation.java
View file @ 24b642b0
......@@ -269,7 +269,7 @@ public class MacroCorrelation {
clt_parameters.corr_magic_scale, // still not understood coefficient that reduces reported disparity value. Seems to be around 0.85
clt_parameters.shift_x, // final int shiftX, // shift image horizontally (positive - right) - just for testing
clt_parameters.shift_y, // final int shiftY, // shift image vertically (positive - down)
31, // clt_parameters.tileX, // final int debug_tileX,
clt_parameters.batch_run? -1: 31, // clt_parameters.tileX, // final int debug_tileX,
10, // clt_parameters.tileY, // final int debug_tileY,
(clt_parameters.dbg_mode & 64) != 0, // no fract shift
true, // no convolve
......
src/main/java/MeasuredLayers.java
View file @ 24b642b0
......@@ -732,7 +732,7 @@ public class MeasuredLayers {
int st2 = 2 * superTileSize;
int st_half = superTileSize/2;
double [][] ds = new double [2][st2*st2];
final int dbg_tile = ((stX == 22) && (stY == 19)) ? (5 + 7*16) : -1;// 50397;
final int dbg_tile = -1; // = ((stX == 22) && (stY == 19)) ? (5 + 7*16) : -1;// 50397;
int num_selected = 0;
int smpl_center = mlfp.smplSide /2;
......@@ -1023,7 +1023,7 @@ public class MeasuredLayers {
int st2 = 2 * superTileSize;
int st_half = superTileSize/2;
double [][] ds = new double [2][st2*st2];
final int dbg_tile = ((stX == 22) && (stY == 19)) ? (5 + 7*16) : -1;// 50397;
final int dbg_tile =-1; // ((stX == 22) && (stY == 19)) ? (5 + 7*16) : -1;// 50397;
int num_selected = 0;
int smpl_center = mlfp.smplSide /2;
......
src/main/java/QuadCLT.java
View file @ 24b642b0
This diff is collapsed.
src/main/java/SuperTiles.java
View file @ 24b642b0
......@@ -663,9 +663,9 @@ public class SuperTiles{
int numMax = 0;
int lo = 0;
int hi = 1;
if ((globalDebugLevel > -1 ) && (nsTile == 795)) {
System.out.println(nsTile);
}
// if ((globalDebugLevel > -1 ) && (nsTile == 795)) {
// System.out.println("getMaxMinMax(): nsTile="+nsTile);
// }
while (hi < numBins) {
// looking for next max
while ((hi < numBins) && (dh[hi] >= dh[hi - 1])) hi++; // flat or higher - continue
......@@ -949,9 +949,9 @@ public class SuperTiles{
}
}
for (int nsTile = 0; nsTile < sTiles; nsTile++){
if (nsTile == 795){
System.out.println("showMaxMinMax(), nsTile="+nsTile);
}
// if (nsTile == 795){
// System.out.println("showMaxMinMax(), nsTile="+nsTile);
// }
int stileY = nsTile / sTilesX;
int stileX = nsTile % sTilesX;
int x0 = stileX * (numBins + 1);
......@@ -1580,6 +1580,9 @@ public class SuperTiles{
final double [][][][] plane_disp_strength = new double [nStiles][][][];
// DEBUG feature:
final double [][] zero_tilts = {{0.0,0.0}}; // set to null for float
if (debugLevel > -1) {
System.out.println("getPlaneDispStrengthsST(x): debugLevel == "+debugLevel);
}
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
......
src/main/java/TileAssignment.java
View file @ 24b642b0
This diff is collapsed.
src/main/java/TilePlanes.java
View file @ 24b642b0
......@@ -3504,12 +3504,14 @@ public class TilePlanes {
System.out.println("mergePlaneToThisWorld()");
}
if (wvalues == null ) {
System.out.println("mergePlaneToThisWorld(): wvalues=null:\n"+toString());
if (debugLevel > -2) {
System.out.println("mergePlaneToThisWorld(): wvalues=null:\n"+toString());
}
return null;
}
if (otherPd.wvalues == null ) {
System.out.println("mergePlaneToThisWorld(): otherPd.wvalues=null:\n"+otherPd.toString());
if (debugLevel > -1) System.out.println("mergePlaneToThisWorld(): otherPd.wvalues=null:\n"+otherPd.toString());
return null;
}
double [][] this_eig_avals = {
......@@ -4036,6 +4038,9 @@ public class TilePlanes {
if (debugLevel > 2) {
debugLevel += 0; // +=1 // no show all eigen stuff (debugLevel > 3)
}
if (debugLevel > 0) {
System.out.println("Debug debugLevel"); // +=1 // no show all eigen stuff (debugLevel > 3)
}
// first make a plane from all tiles
ArrayList<PlaneData> st_planes = new ArrayList<PlaneData>();
......
src/main/java/TileProcessor.java
View file @ 24b642b0
......@@ -4572,9 +4572,10 @@ public class TileProcessor {
GeometryCorrection geometryCorrection,
final int threadsMax, // maximal number of threads to launch
final boolean updateStatus,
final boolean batch_mode,
// final boolean batch_mode,
final int debugLevel)
{
final boolean batch_mode = clt_parameters.batch_run;
final int debugLevelInner = batch_mode ? -5: debugLevel;
trimCLTPasses(); // make possible to run this method multiple times - remove extra passes added by it last time
CLTPass3d scan_prev = clt_3d_passes.get(clt_3d_passes.size() -1); // get last one
......@@ -5140,9 +5141,9 @@ public class TileProcessor {
GeometryCorrection geometryCorrection,
final int threadsMax, // maximal number of threads to launch
final boolean updateStatus,
final boolean batch_mode,
final int debugLevel)
{
final boolean batch_mode = clt_parameters.batch_run; //disable any debug images
trimCLTPasses(); // make possible to run this method multiple time - remove extra passes added by it last time
CLTPass3d scan_prev = clt_3d_passes.get(clt_3d_passes.size() -1); // get last one
......@@ -5311,7 +5312,7 @@ public class TileProcessor {
clt_parameters.stHighMix, // stHighMix = 0.4; // Consider merging initial planes if jumps between ratio above
world_hor, // final double [] world_hor, // horizontal plane normal (default [0.0, 1.0, 0.0])
clt_parameters.show_histograms, // final boolean show_histograms,
1, // -1, // debugLevel, // final int debugLevel)
clt_parameters.batch_run?-1:1, // -1, // debugLevel, // final int debugLevel)
clt_parameters.tileX,
clt_parameters.tileY);
// showDoubleFloatArrays sdfa_instance = null;
......@@ -5334,7 +5335,7 @@ public class TileProcessor {
lp.conditionSuperTiles(
st.planes, // final TilePlanes.PlaneData [][] planes,
10, // final int max_num_merge_try,
0); // 1); // debugLevel); // final int debugLevel);
clt_parameters.batch_run?-2:0); // 1); // debugLevel); // final int debugLevel);
// Used only by conflicts (not processed currently)
lp.calcStarValueStrength(
true, // boolean set_start_planes,
......@@ -5398,7 +5399,7 @@ public class TileProcessor {
clt_parameters.plDiscrXMedian, // final double plDiscrXMedian, // = 1.5; // Remove outliers from the final selection that have distance more than scaled median
debugLevel, // -1, // debugLevel, // final int debugLevel)
clt_parameters.tileX,
clt_parameters.batch_run ? -1 : clt_parameters.tileX, // clt_parameters.tileX,
clt_parameters.tileY);
// condition the redefined planes
......@@ -6064,9 +6065,9 @@ public class TileProcessor {
GeometryCorrection geometryCorrection,
final int threadsMax, // maximal number of threads to launch
final boolean updateStatus,
final boolean batch_mode,
final int debugLevel)
{
final boolean batch_mode = clt_parameters.batch_run; //disable any debug images
int debugLevelInner = batch_mode ? -5: debugLevel;
CLTPass3d scan_bg = clt_3d_passes.get(bg_scan_index); //
CLTPass3d scan_prev = clt_3d_passes.get(clt_3d_passes.size() -1); // get last one
......@@ -6146,7 +6147,7 @@ public class TileProcessor {
true, // final boolean keep_raw_fg, // do not replace raw tiles by the plates, if raw is closer (like poles)
0.0, // final double scale_filtered_strength_pre, // scale plate_ds[1] before comparing to raw strength
0.0,// final double scale_filtered_strength_post,// scale plate_ds[1] when replacing raw (generally plate_ds is more reliable if it exists)
true, // clt_parameters.show_filter_scan,
batch_mode, // true, // clt_parameters.show_filter_scan,
clt_parameters.min_clstr_seed, // clt_parameters.min_clstr_seed
clt_parameters.min_clstr_weight, // double min_weight // minimal total weight of the cluster
clt_parameters.min_clstr_max, // double min_max_weight // minimal value of the maximal strengh in the cluster
......
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