next snapshot for dual camera

src/main/java/EyesisCorrectionParameters.java

@@ -228,7 +228,7 @@ public class EyesisCorrectionParameters {
   			cp.x3dDirectory=    		this.x3dDirectory;
   			cp.use_x3d_subdirs=    		this.use_x3d_subdirs;
   			cp.x3dSubdirPrefix=    		this.x3dSubdirPrefix;
-  			cp.x3dSubdirSuffix=    		this.x3dSubdirSuffix;
+// 			cp.x3dSubdirSuffix=    		this.x3dSubdirSuffix;
   			cp.x3dModelVersion=    		this.x3dModelVersion;
   			cp.clt_batch_apply_man=		this.clt_batch_apply_man;
   			cp.clt_batch_extrinsic=		this.clt_batch_extrinsic;
@@ -254,6 +254,8 @@ public class EyesisCorrectionParameters {
   			cp.sensorSuffix=      	    this.sensorSuffix;
   			cp.cltKernelPrefix=    		this.cltKernelPrefix;
   			cp.cltSuffix=               this.cltSuffix;
+  			cp.x3dSubdirSuffix=    		this.x3dSubdirSuffix+"-aux";
+
     	}
 
 		public void auxFromExternal(CorrectionParameters ecp) { // from master to aux
@@ -266,6 +268,7 @@ public class EyesisCorrectionParameters {
 			this.aux_camera.sensorSuffix=      	ecp.sensorSuffix;
 			this.aux_camera.cltKernelPrefix=    ecp.cltKernelPrefix;
 			this.aux_camera.cltSuffix=          ecp.cltSuffix;
+			this.aux_camera.x3dSubdirSuffix=    ecp.x3dSubdirSuffix + "-aux";
     	}
 
 
@@ -387,6 +390,7 @@ public class EyesisCorrectionParameters {
         		properties.setProperty(aux_prefix+"sensorSuffix",       this.aux_camera.sensorSuffix);
         		properties.setProperty(aux_prefix+"cltKernelPrefix",    this.aux_camera.cltKernelPrefix);
         		properties.setProperty(aux_prefix+"cltSuffix",          this.aux_camera.cltSuffix);
+        		properties.setProperty(aux_prefix+"x3dSubdirSuffix",    this.aux_camera.x3dSubdirSuffix);
     		}
 
     	}
@@ -512,6 +516,7 @@ public class EyesisCorrectionParameters {
 			if (properties.getProperty(aux_prefix+"sensorSuffix")!=       null) this.aux_camera.sensorSuffix=properties.getProperty(aux_prefix+"sensorSuffix");
 			if (properties.getProperty(aux_prefix+"cltKernelPrefix")!=    null) this.aux_camera.cltKernelPrefix=properties.getProperty(aux_prefix+"cltKernelPrefix");
 			if (properties.getProperty(aux_prefix+"cltSuffix")!=          null) this.aux_camera.cltSuffix=properties.getProperty(aux_prefix+"cltSuffix");
+			if (properties.getProperty(aux_prefix+"x3dSubdirSuffix")!=    null) this.aux_camera.x3dSubdirSuffix=properties.getProperty(aux_prefix+"x3dSubdirSuffix");
 		}
 
     	public boolean showJDialog(String title) {
@@ -741,6 +746,9 @@ public class EyesisCorrectionParameters {
     		gd.addStringField ("Source files prefix",                              this.sourcePrefix, 60);       // 13
     		gd.addStringField ("Source files suffix",                              this.sourceSuffix, 60);       // 14
 
+    		gd.addStringField ("x3d subdirectory prefix",                          this.x3dSubdirPrefix, 10,    // 14a
+    				"When using timestamp as a subdirectory, add this prefix");
+
 
 			gd.addMessage     ("============ Main camera============");
 
@@ -757,6 +765,9 @@ public class EyesisCorrectionParameters {
 
     		gd.addStringField ("CLT kernel files prefix",                          this.cltKernelPrefix, 40);    // 19
     		gd.addStringField ("CLT kernel files suffix",                          this.cltSuffix, 40);          // 20
+    		gd.addStringField ("x3d subdirectory suffix",                          this.x3dSubdirSuffix, 10,     // 20a
+    				"When using timestamp as a subdirectory, add this suffix");
+
 
 			gd.addMessage     ("============ Auxiliary camera============");
     		gd.addStringField ("Aux sensor calibration directory",                     this.aux_camera.sensorDirectory, 60);    // 4b
@@ -772,6 +783,8 @@ public class EyesisCorrectionParameters {
 
     		gd.addStringField ("Aux CLT kernel files prefix",                          this.aux_camera.cltKernelPrefix, 40);    // 19b
     		gd.addStringField ("Aux CLT kernel files suffix",                          this.aux_camera.cltSuffix, 40);          // 20b
+    		gd.addStringField ("Aux x3d subdirectory suffix",                          this.aux_camera.x3dSubdirSuffix, 10,     // 20ba
+    				"When using timestamp as a subdirectory, add this suffix");
 
 
 
@@ -809,6 +822,7 @@ public class EyesisCorrectionParameters {
     		this.use_x3d_subdirs=        gd.getNextBoolean(); // 10
     		this.sourcePrefix=           gd.getNextString();  // 13
     		this.sourceSuffix=           gd.getNextString();  // 14
+    		this.x3dSubdirPrefix=        gd.getNextString();  // 14a
 
 // main camera
     		this.sensorDirectory=        gd.getNextString(); if (gd.getNextBoolean()) selectSensorDirectory(false, false);   // 5
@@ -820,6 +834,7 @@ public class EyesisCorrectionParameters {
     		this.sensorSuffix=           gd.getNextString();  // 18
     		this.cltKernelPrefix=        gd.getNextString();  // 19
     		this.cltSuffix=              gd.getNextString();  // 20
+    		this.x3dSubdirSuffix=        gd.getNextString();  // 20a
 
 // aux camera
     		this.aux_camera.sensorDirectory=        gd.getNextString(); if (gd.getNextBoolean()) aux_camera.selectSensorDirectory(false, false);   // 5b
@@ -831,6 +846,7 @@ public class EyesisCorrectionParameters {
     		this.aux_camera.sensorSuffix=           gd.getNextString();  // 18b
     		this.aux_camera.cltKernelPrefix=        gd.getNextString();  // 19b
     		this.aux_camera.cltSuffix=              gd.getNextString();  // 20b
+    		this.aux_camera.x3dSubdirSuffix=        gd.getNextString();  // 20ba
 
     		this.clt_batch_apply_man=    gd.getNextBoolean(); // 21
     		this.clt_batch_extrinsic=    gd.getNextBoolean(); // 22

src/main/java/TwoQuadCLT.java

+import ij.IJ;
+import ij.ImagePlus;
+
+/**
+ ** TwoQuadCLT - Process images from a pair of Quad/Octal cameras
+ **
+ ** Copyright (C) 2018 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  TwoQuadCLT.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
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+
+public class TwoQuadCLT {
+	public long                                            startTime;     // start of batch processing
+	public long                                            startSetTime;  // start of set processing
+	public long                                            startStepTime; // start of step processing
+
+/*
+	public QuadCLT quadCLT_main;
+	public QuadCLT quadCLT_aux;
+	public TwoQuadCLT (
+			QuadCLT quadCLT_main,
+			QuadCLT quadCLT_aux
+			) {
+		this.quadCLT_main = quadCLT_main;
+		this.quadCLT_aux =  quadCLT_aux;
+	}
+*/
+
+	  public void processCLTQuadCorrs(
+			  QuadCLT quadCLT_main,
+			  QuadCLT quadCLT_aux,
+			  EyesisCorrectionParameters.CLTParameters       clt_parameters,
+			  EyesisCorrectionParameters.DebayerParameters   debayerParameters,
+			  EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
+			  CorrectionColorProc.ColorGainsParameters       channelGainParameters_main,
+			  CorrectionColorProc.ColorGainsParameters       channelGainParameters_aux,
+			  EyesisCorrectionParameters.RGBParameters       rgbParameters,
+			  final int                                      threadsMax,  // maximal number of threads to launch
+			  final boolean                                  updateStatus,
+			  final int                                      debugLevel) throws Exception
+	  {
+
+		  this.startTime=System.nanoTime();
+		  String [] sourceFiles=quadCLT_main.correctionsParameters.getSourcePaths();
+		  QuadCLT.SetChannels [] set_channels_main = quadCLT_main.setChannels(debugLevel);
+		  QuadCLT.SetChannels [] set_channels_aux =  quadCLT_aux.setChannels(debugLevel);
+		  if ((set_channels_main == null) || (set_channels_main.length==0) || (set_channels_aux == null) || (set_channels_aux.length==0)) {
+			  System.out.println("No files to process (of "+sourceFiles.length+")");
+			  return;
+		  }
+		  double [] referenceExposures_main = quadCLT_main.eyesisCorrections.calcReferenceExposures(debugLevel); // multiply each image by this and divide by individual (if not NaN)
+		  double [] referenceExposures_aux =  quadCLT_aux.eyesisCorrections.calcReferenceExposures(debugLevel); // multiply each image by this and divide by individual (if not NaN)
+		  for (int nSet = 0; nSet < set_channels_main.length; nSet++){
+			  // check it is the same set for both cameras
+			  if (set_channels_aux.length <= nSet ) {
+				  throw new Exception ("Set naims for cameras do not match: main camera: '"+set_channels_main[nSet].name()+"', aux. camera: nothing");
+			  }
+			  if (!set_channels_main[nSet].name().equals(set_channels_aux[nSet].name())) {
+				  throw new Exception ("Set naims for cameras do not match: main camera: '"+set_channels_main[nSet].name()+"', aux. camera: '"+set_channels_main[nSet].name()+"'");
+			  }
+
+			  int [] channelFiles_main = set_channels_main[nSet].fileNumber();
+			  int [] channelFiles_aux =  set_channels_aux[nSet].fileNumber();
+			  boolean [][] saturation_imp_main = (clt_parameters.sat_level > 0.0)? new boolean[channelFiles_main.length][] : null;
+			  boolean [][] saturation_imp_aux =  (clt_parameters.sat_level > 0.0)? new boolean[channelFiles_main.length][] : null;
+			  double [] scaleExposures_main = new double[channelFiles_main.length];
+			  double [] scaleExposures_aux =  new double[channelFiles_main.length];
+
+			  ImagePlus [] imp_srcs_main = quadCLT_main.conditionImageSet(
+					  clt_parameters,                 // EyesisCorrectionParameters.CLTParameters  clt_parameters,
+					  sourceFiles,                    // String []                                 sourceFiles,
+					  set_channels_main[nSet].name(), // String                                    set_name,
+					  referenceExposures_main,        // double []                                 referenceExposures,
+					  channelFiles_main,              // int []                                    channelFiles,
+					  scaleExposures_main,            //output  // double [] scaleExposures
+					  saturation_imp_main,            //output  // boolean [][]                              saturation_imp,
+					  debugLevel); // int                                       debugLevel);
+
+			  ImagePlus [] imp_srcs_aux = quadCLT_aux.conditionImageSet(
+					  clt_parameters,                 // EyesisCorrectionParameters.CLTParameters  clt_parameters,
+					  sourceFiles,                    // String []                                 sourceFiles,
+					  set_channels_aux[nSet].name(), // String                                    set_name,
+					  referenceExposures_aux,        // double []                                 referenceExposures,
+					  channelFiles_aux,              // int []                                    channelFiles,
+					  scaleExposures_aux,            //output  // double [] scaleExposures
+					  saturation_imp_aux,            //output  // boolean [][]                              saturation_imp,
+					  debugLevel); // int                                       debugLevel);
+
+			  // Tempporarily processing individaully with the old code
+			  quadCLT_main.processCLTQuadCorr( // returns ImagePlus, but it already should be saved/shown
+					  imp_srcs_main, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
+					  saturation_imp_main, // boolean [][] saturation_imp, // (near) saturated pixels or null
+					  clt_parameters,
+					  debayerParameters,
+					  colorProcParameters,
+					  channelGainParameters_main,
+					  rgbParameters,
+					  scaleExposures_main,
+					  false, // apply_corr, // calculate and apply additional fine geometry correction
+					  false, // infinity_corr, // calculate and apply geometry correction at infinity
+					  threadsMax,  // maximal number of threads to launch
+					  updateStatus,
+					  debugLevel);
+
+			  Runtime.getRuntime().gc();
+			  if (debugLevel >-1) System.out.println("Processing set "+(nSet+1)+" (of "+set_channels_main.length+") finished at "+
+					  IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
+
+			  quadCLT_aux.processCLTQuadCorr( // returns ImagePlus, but it already should be saved/shown
+					  imp_srcs_aux, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
+					  saturation_imp_aux, // boolean [][] saturation_imp, // (near) saturated pixels or null
+					  clt_parameters,
+					  debayerParameters,
+					  colorProcParameters,
+					  channelGainParameters_aux,
+					  rgbParameters,
+					  scaleExposures_aux,
+					  false, // apply_corr, // calculate and apply additional fine geometry correction
+					  false, // infinity_corr, // calculate and apply geometry correction at infinity
+					  threadsMax,  // maximal number of threads to launch
+					  updateStatus,
+					  debugLevel);
+
+			  Runtime.getRuntime().gc();
+			  if (debugLevel >-1) System.out.println("Processing set "+(nSet+1)+" (of "+set_channels_aux.length+") finished at "+
+					  IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
+
+			  if (quadCLT_aux.eyesisCorrections.stopRequested.get()>0) {
+				  System.out.println("User requested stop");
+				  System.out.println("Processing "+(nSet + 1)+" file sets (of "+set_channels_main.length+") finished at "+
+						  IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
+				  return;
+			  }
+		  }
+		  System.out.println("processCLTQuadCorrs(): processing "+(quadCLT_main.getTotalFiles(set_channels_main)+quadCLT_aux.getTotalFiles(set_channels_aux))+" files ("+set_channels_main.length+" file sets) finished at "+
+				  IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
+
+	  }
+
+}