refactored, continue grid import

src/main/java/com/elphel/imagej/calibration/CalibrationFileManagement.java

@@ -248,5 +248,104 @@ public class CalibrationFileManagement {
 			  return description;
 		  }
 	  }
+	  // select directory that contains matching MultipleExtensionsFileFilter in specified min/max quantities
+//https://stackoverflow.com/questions/22302199/java-filefilter-to-select-certain-directories
+//	  public static class DirectoryContentsFilter extends FileFilter implements FilenameFilter {
+	  public static class DirectoryChoser extends javax.swing.JFileChooser {
+		  private static final long serialVersionUID = 390855361964415146L;
+		  protected MultipleExtensionsFileFilter multipleExtensionsFileFilter;
+		  protected int    min_files;
+		  protected int    max_files;
+		  protected String description;
+
+		  public DirectoryChoser (
+				  MultipleExtensionsFileFilter multipleExtensionsFileFilter,
+				  int                          min_files,
+				  int                          max_files,
+				  String                       description) // may be null;
+		  {
+			  this.multipleExtensionsFileFilter=   multipleExtensionsFileFilter;
+			  this.min_files = min_files;
+			  this.max_files = max_files;
+			  this.description = description;
+		  }
+		  @Override
+		  public boolean isDirectorySelectionEnabled() {
+//			  setOpenButtonState(this, false);
+			  File file = getSelectedFile();
+//			  File [] files = getSelectedFiles();
+			  if(file == null){
+//				  setOpenButtonState(this, true);
+				  return  true; // false;
+			  }
+//			  setOpenButtonState(this, false);
+			  if (!file.isDirectory()) return false;
+/*
+	// Can not make it work correctly with multiple selection, giving up for now
+			  // get a list of all matching files
+
+			  int num_match = file.list(multipleExtensionsFileFilter).length;
+			  if (num_match < min_files) return false;
+			  if ((max_files > 0) && (num_match > max_files)) {
+				  return false;
+			  }
+*/
+			  setOpenButtonState(this, true);
+			  return true;
+		  }
+
+		    private void setOpenButtonState(java.awt.Container c, boolean flag) {
+		        int len = c.getComponentCount();
+		        for (int i = 0; i < len; i++) {
+		            java.awt.Component comp = c.getComponent(i);
+
+		            if (comp instanceof javax.swing.JButton) {
+		                javax.swing.JButton b = (javax.swing.JButton)comp;
+
+		                if ( b != null && b.getText() != null && b.getText().equals("Select") ) {
+		                    b.setEnabled(flag);
+		                }
+
+		            } else if (comp instanceof java.awt.Container) {
+		                setOpenButtonState((java.awt.Container) comp, flag);
+		            }
+		        }
+		    }
+
+
+/*
+		  @Override
+		  public boolean accept (File file) {
+			  if (!file.isDirectory()) return false;
+			  // get a list of all matching files
+			  int num_match = file.list(multipleExtensionsFileFilter).length;
+			  if (num_match < min_files) return false;
+			  if ((max_files > 0) && (num_match > max_files)) return false;
+			  return true;
+		  }
+		  @Override
+		  public boolean accept (File dir, String name) {
+			  // No name filter, need to resolve
+			  //			  Path dir_path = dir.toPath();
+			  File target = Paths.get(dir.toString(),name).toFile();
+			  return accept(target);
+		  }
+
+		  @Override
+		  public String getDescription() { // if description is null - generate it
+			  if (description == null) {
+				  description = "Directories containing";
+				  if (min_files > 0)  description +=" not less than "+min_files;
+				  if (max_files > 0)  description +=" not more than "+max_files;
+				  description += " "+multipleExtensionsFileFilter.description;
+
+			  }
+			  return description;
+		  }
+*/
+	  }
+
+
+
 
 }

src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java

@@ -4562,6 +4562,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
     	public String partialKernelDirectory="";
     	public String psfKernelDirectory="";
     	public String aberrationsKernelDirectory="";
+    	public String calibrationDirectory="";
     	public boolean autoRestore;
     	public String calibrationPath="";
     	public String strategyPath="";
@@ -4598,6 +4599,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
 			properties.setProperty(prefix+"partialKernelDirectory",this.partialKernelDirectory);
 			properties.setProperty(prefix+"psfKernelDirectory",this.psfKernelDirectory);
 			properties.setProperty(prefix+"aberrationsKernelDirectory",this.aberrationsKernelDirectory);
+			properties.setProperty(prefix+"calibrationDirectory",this.calibrationDirectory);
 
 			properties.setProperty(prefix+"autoRestore",this.autoRestore+"");
 			properties.setProperty(prefix+"calibrationPath",this.calibrationPath);
@@ -4642,6 +4644,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
 			if (properties.getProperty(prefix+"partialKernelDirectory")!=null)     this.partialKernelDirectory=properties.getProperty(prefix+"partialKernelDirectory");
 			if (properties.getProperty(prefix+"psfKernelDirectory")!=null)         this.psfKernelDirectory=properties.getProperty(prefix+"psfKernelDirectory");
 			if (properties.getProperty(prefix+"aberrationsKernelDirectory")!=null) this.aberrationsKernelDirectory=properties.getProperty(prefix+"aberrationsKernelDirectory");
+			if (properties.getProperty(prefix+"calibrationDirectory")!=null)       this.calibrationDirectory=properties.getProperty(prefix+"calibrationDirectory");
 
 			if (properties.getProperty(prefix+"autoRestore")!=null)                this.autoRestore=Boolean.parseBoolean(properties.getProperty(prefix+"autoRestore"));
 			if (properties.getProperty(prefix+"calibrationPath")!=null)            this.calibrationPath=properties.getProperty(prefix+"calibrationPath");
@@ -4792,6 +4795,8 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
     		gd.addCheckbox("Select combined kernsls directory", false);
     		gd.addStringField("Aberrations kernels directory", this.aberrationsKernelDirectory, 60);
     		gd.addCheckbox("Select aberrations kernels directory", false);
+    		gd.addStringField("Calibration directory (sensor, grid, strategy...)", this.calibrationDirectory, 60);
+    		gd.addCheckbox("Select calibration directory", false);
     		gd.addCheckbox("Supress non-essential message boxes", this.noMessageBoxes);
     		gd.addCheckbox("Overwrite result files if they exist", this.overwriteResultFiles);
     		gd.addCheckbox("Use reprojected grids for partial kernel calculation (false - extracted grids)", this.partialToReprojected);
@@ -4843,6 +4848,8 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
     		if (gd.getNextBoolean()) selectPSFKernelDirectory(false, this.psfKernelDirectory, false);
     		this.aberrationsKernelDirectory=gd.getNextString();
     		if (gd.getNextBoolean()) selectAberrationsKernelDirectory(false, this.aberrationsKernelDirectory, false);
+    		this.calibrationDirectory=gd.getNextString();
+    		if (gd.getNextBoolean()) selectCalibrationDirectory(false, this.calibrationDirectory, false);
     		this.noMessageBoxes=        gd.getNextBoolean();
     		this.overwriteResultFiles=  gd.getNextBoolean();
     		this.partialToReprojected=  gd.getNextBoolean();
@@ -4921,7 +4928,18 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
     		if (dir!=null) this.aberrationsKernelDirectory=dir;
     		return dir;
     	}
-
+    	public String selectCalibrationDirectory(boolean smart, String defaultPath, boolean newAllowed) {
+    		String dir= CalibrationFileManagement.selectDirectory(
+    				smart,
+    				newAllowed, // save
+    				"Calibration directory", // title
+    				"Select calibration directory", // button
+    				null, // filter
+    				defaultPath); //this.sourceDirectory);
+    		if (dir!=null) this.calibrationDirectory=dir;
+    		return dir;
+    	}
+//
 
     }
 

src/main/java/com/elphel/imagej/calibration/Goniometer.java

@@ -29,6 +29,8 @@ package com.elphel.imagej.calibration;
 import java.util.Properties;
 import java.util.concurrent.atomic.AtomicInteger;
 
+import com.elphel.imagej.calibration.hardware.CamerasInterface;
+import com.elphel.imagej.calibration.hardware.GoniometerMotors;
 import com.elphel.imagej.cameras.EyesisCameraParameters;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.common.WindowTools;
@@ -50,7 +52,7 @@ horizontal axis:
 	private ShowDoubleFloatArrays sdfaInstance = new ShowDoubleFloatArrays(); // just
 																				// for
 																				// debugging
-	public CalibrationHardwareInterface.CamerasInterface cameras = null;
+	public CamerasInterface cameras = null;
 	public LwirReader lwirReader = null;
 	// public CalibrationHardwareInterface.LaserPointers lasers = null;
 	// public static CalibrationHardwareInterface.FocusingMotors motorsS=null;
@@ -67,7 +69,7 @@ horizontal axis:
 
 	public MatchSimulatedPattern[] matchSimulatedPatterns = null; // =new
 																	// MatchSimulatedPattern();
-	public MatchSimulatedPattern.LaserPointer laserPointers = null;
+	public LaserPointer laserPointers = null;
 	MatchSimulatedPattern.PatternDetectParameters patternDetectParameters=null;
 	public SimulationPattern.SimulParameters simulParametersDefault=null;
 	public Goniometer.GoniometerParameters goniometerParameters = null;
@@ -78,11 +80,11 @@ horizontal axis:
 	public double bottomRollersClearance=36.0; // angular clearance between the two bottom rollers
 
 
-	public Goniometer(CalibrationHardwareInterface.CamerasInterface cameras,
+	public Goniometer(CamerasInterface cameras,
 			MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
 			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
 			EyesisCameraParameters eyesisCameraParameters,
-			MatchSimulatedPattern.LaserPointer laserPointers,
+			LaserPointer laserPointers,
 			SimulationPattern.SimulParameters simulParametersDefault,
 			Goniometer.GoniometerParameters goniometerParameters,
 			DistortionProcessConfiguration distortionProcessConfiguration
@@ -104,7 +106,7 @@ horizontal axis:
 			MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
 			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
 			EyesisCameraParameters eyesisCameraParameters,
-			MatchSimulatedPattern.LaserPointer laserPointers,
+			LaserPointer laserPointers,
 			SimulationPattern.SimulParameters simulParametersDefault,
 			Goniometer.GoniometerParameters goniometerParameters,
 			DistortionProcessConfiguration distortionProcessConfiguration
@@ -754,15 +756,10 @@ horizontal axis:
 	public double[] estimateOrientation(
 			ImagePlus[] images, // last acquire images with number of pointers
 								// detected>0
-//			MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
-//			LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
-//			Goniometer.GoniometerParameters goniometerParameters,
-//			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
-//			MatchSimulatedPattern.LaserPointer laserPointer, // null OK
-//			SimulationPattern.SimulParameters simulParametersDefault,
 			DistortionCalibrationData distortionCalibrationData,
 			PatternParameters patternParameters, // should not be  null
 			Distortions lensDistortions, // should not be null
+			LaserPointer laserPointers, // as a back up measure
 			boolean equalizeGreens,
 			int threadsMax,
 			boolean updateStatus,
@@ -815,8 +812,7 @@ horizontal axis:
 				// used alternatively if keeping it
 				this.matchSimulatedPatterns[numSensor].invalidateFlatFieldForGrid(); // Reset Flat Filed calibration - different image.
 				this.matchSimulatedPatterns[numSensor].invalidateFocusMask();
-				if (matchSimulatedPatterns[numSensor].getPointersXY(images[numSensor],
-								this.laserPointers.laserUVMap.length) == null) { // no pointers in this image
+				if (MatchSimulatedPattern.getPointersXYUV(images[numSensor],this.laserPointers) == null) { // no pointers in this image
 					String msg = "No laser pointers detected for "+ images[numSensor].getTitle()+ " - they are needed for absolute grid positioning";
 					if (debug_level > 0) System.out.println("Warning: " + msg);
 					IJ.showMessage("Warning", msg);
@@ -933,8 +929,9 @@ horizontal axis:
 		 * //PatternParameters patternParameters, eyesisCameraParameters
 		 * //EyesisCameraParameters eyesisCameraParameters );
 		 */
-		distortionCalibrationData.setImages(imp_calibrated, // ImagePlus [] images, // imagesin the memory
-				patternParameters); // PatternParameters patternParameters);
+		distortionCalibrationData.setImages(imp_calibrated, // ImagePlus [] images, // images in the memory
+				patternParameters, // PatternParameters patternParameters);
+				laserPointers);
 		distortionCalibrationData.initImageSet(eyesisCameraParameters);
 
 		// Set initial azimuth and elevation
@@ -1075,7 +1072,7 @@ horizontal axis:
         5682.48889 per degree
         	 */
         // motors rotate positive - look down, positive - CCW
-        CalibrationHardwareInterface.GoniometerMotors goniometerMotors=null;
+        GoniometerMotors goniometerMotors=null;
 //        public double stepsPerDegreeTilt=-5682.48889; // minus that positive steps make negative elevation
 //        public double stepsPerDegreeAxial=-36.0; // minus that positive steps make rotate CCW when looking from Eyesis top
 //        public double scanStepTilt=20.0;   // degrees (equal steps not larger than
@@ -1098,11 +1095,11 @@ horizontal axis:
 
 
 
-    	public GoniometerParameters(CalibrationHardwareInterface.GoniometerMotors goniometerMotors){
+    	public GoniometerParameters(GoniometerMotors goniometerMotors){
     		    		this.goniometerMotors=goniometerMotors;
     	}
     	public GoniometerParameters(
-    			CalibrationHardwareInterface.GoniometerMotors goniometerMotors,
+    			GoniometerMotors goniometerMotors,
     	    	String gridGeometryFile,
     	    	String initialCalibrationFile, // not needed
     	    	String strategyFile,

src/main/java/com/elphel/imagej/calibration/LensAdjustment.java

@@ -45,7 +45,7 @@ public class LensAdjustment {
 			MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
 			LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
 			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
-			MatchSimulatedPattern.LaserPointer laserPointer, // null OK
+			LaserPointer laserPointer, // null OK
 			SimulationPattern.SimulParameters  simulParametersDefault,
 			boolean maskNonPSF, // mask out areas not needed for focusing PSF measurements
 			boolean equalizeGreens,

src/main/java/com/elphel/imagej/calibration/hardware/package-info.java

+/**
+ * 
+ */
+/**
+ * @author eyesis
+ *
+ */
+package com.elphel.imagej.calibration.hardware;
\ No newline at end of file

src/main/java/com/elphel/imagej/lwir/LwirReaderParameters.java

@@ -56,7 +56,6 @@ public class LwirReaderParameters {
 	protected double  vnir_gain_bg =          2.401;  // 1.476;
 	protected boolean [] selected_channels =  {true, true, true, true, true, true, true, true};
 	protected int     max_lwir_width =        1024; //
-
 /*
 	protected double [] vnir_exp_corr = {1.0, 1.0, 1.0, 1.0};
 	protected double [] vnir_gcorr_rbgb = {
@@ -64,7 +63,6 @@ public class LwirReaderParameters {
 			1.0,    1.0,    1.0,
 			1.0,    1.0,    1.0,
 			1.0,    1.0,    1.0};
-
  */
 	protected double [] vnir_exp_corr =	{
 			1.0, 1.0026, 0.9868, 1.0211};
@@ -80,7 +78,19 @@ public class LwirReaderParameters {
 	protected int     debug_level =           0;//-3: OFF, -2:Fatal, -1:ERROR, 0:WARN, 1:INFO,2:DEBUG
 	protected boolean show_images = false;
 
+	protected int     lwir_chn0 =             0; // not configurable
+	protected int     vnir_chn0 =             4; // not configurable
+
+
 	// --- interface methods
+	public int getLwirChn0 () {
+		return lwir_chn0;
+	}
+
+	public int getVnirChn0 () {
+		return vnir_chn0;
+	}
+
 	public boolean is_LWIR(int width) {
 		return width <= max_lwir_width;
 	}