Started refactoring to get rid of default package

src/main/java/BiQuadParameters.java

@@ -24,6 +24,8 @@
 
 import java.util.Properties;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
+
 public class BiQuadParameters {
 	public boolean rig_mode_debug =            true;
 	public boolean no_int_x0 =                 true; // do not offset window to integer maximum for the rig - used when averaging low textures to avoid "jumps" for very wide maximums
@@ -1223,8 +1225,8 @@ public class BiQuadParameters {
 		if (properties.getProperty(prefix+"lt_replace_lone")!=null)         this.lt_replace_lone=Boolean.parseBoolean(properties.getProperty(prefix+"lt_replace_lone"));
 		if (properties.getProperty(prefix+"lt_extend_dist")!=null)          this.lt_extend_dist=Integer.parseInt(properties.getProperty(prefix+"lt_extend_dist"));
 		if (properties.getProperty(prefix+"lt_wsigma")!=null)               this.lt_wsigma=Double.parseDouble(properties.getProperty(prefix+"lt_wsigma"));
-		if (properties.getProperty(prefix+"lt_max_asigma")!=null)           this.lt_max_asigma=Double.parseDouble(properties.getProperty(prefix+"lt_max_sigma"));
-		if (properties.getProperty(prefix+"lt_max_rsigma")!=null)           this.lt_max_rsigma=Double.parseDouble(properties.getProperty(prefix+"lt_max_sigma"));
+		if (properties.getProperty(prefix+"lt_max_asigma")!=null)           this.lt_max_asigma=Double.parseDouble(properties.getProperty(prefix+"lt_max_asigma"));
+		if (properties.getProperty(prefix+"lt_max_rsigma")!=null)           this.lt_max_rsigma=Double.parseDouble(properties.getProperty(prefix+"lt_max_rsigma"));
 
 		if (properties.getProperty(prefix+"lt_repeat")!=null)               this.lt_repeat=Integer.parseInt(properties.getProperty(prefix+"lt_repeat"));
 		if (properties.getProperty(prefix+"lt_min_new")!=null)              this.lt_min_new=Integer.parseInt(properties.getProperty(prefix+"lt_min_new"));

src/main/java/CorrectionColorProc.java

@@ -28,6 +28,8 @@
 import java.util.Properties;
 import java.util.concurrent.atomic.AtomicInteger;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
+
 import ij.ImageStack;
 import ij.gui.GenericDialog;
 

src/main/java/EyesisCorrectionParameters.java

@@ -33,6 +33,8 @@ import java.util.HashMap;
 import java.util.Properties;
 import java.util.Set;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
+
 import ij.IJ;
 import ij.Prefs;
 import ij.gui.GenericDialog;

src/main/java/Eyesis_Correction.java

@@ -70,6 +70,7 @@ import java.util.concurrent.atomic.AtomicInteger;
 import javax.swing.JFileChooser;
 import javax.swing.filechooser.FileFilter;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
 import com.elphel.imagej.lwir.LwirReader;
 
 import ij.CompositeImage;
@@ -159,6 +160,7 @@ private Panel panel1,
    public static QuadCLT          QUAD_CLT_AUX =   null;
    public static TwoQuadCLT       TWO_QUAD_CLT = null;
    public static GPUTileProcessor GPU_TILE_PROCESSOR = null;
+   public static LwirReader       LWIR_READER = null;
 
    public static EyesisCorrectionParameters.DebayerParameters DEBAYER_PARAMETERS = new EyesisCorrectionParameters.DebayerParameters(
 		   64,    // size //128;
@@ -4805,9 +4807,12 @@ private Panel panel1,
 /* ======================================================================== */
     } else if (label.equals("LWIR_ACQUIRE")) {
         DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
-		loci.common.DebugTools.enableLogging("ERROR"); // INFO"); // ERROR");
-        LwirReader lwirReader = new LwirReader();
-        ImagePlus [][] imps = lwirReader.readAllMultiple(
+		loci.common.DebugTools.enableLogging((DEBUG_LEVEL > 1)?"DEBUG":((DEBUG_LEVEL > 0)?"INFO":"ERROR")); // INFO"); // ERROR");
+		//   public static LwirReader       LWIR_READER = null;
+		if (LWIR_READER == null) {
+			LWIR_READER =  new LwirReader();
+		}
+        ImagePlus [][] imps = LWIR_READER.readAllMultiple(
     			10, // final int     num_frames,
     			true, // final boolean show,
     			false); // true); // final boolean scale)
@@ -4816,15 +4821,14 @@ private Panel panel1,
 		}
 
 		System.out.println("LWIR_ACQUIRE: got "+imps.length+" image sets");
-		ImagePlus [][] imps_sync =  lwirReader.matchSets(imps, 0.001, 3); // double max_mismatch)
+		ImagePlus [][] imps_sync =  LWIR_READER.matchSets(imps, 0.001, 3); // double max_mismatch)
 		if (imps_sync != null) {
-			ImagePlus [] imps_avg = lwirReader.averageMultiFrames(imps_sync);
+			ImagePlus [] imps_avg = LWIR_READER.averageMultiFrames(imps_sync);
 			for (ImagePlus imp: imps_avg) {
 				imp.show();
 			}
 		}
 
-
 //JTabbedTest
 // End of buttons code
     }

src/main/java/GeometryCorrection.java

 import java.util.ArrayList;
 import java.util.Properties;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
+
 import Jama.Matrix;
 import ij.IJ;
 

src/main/java/ImageDttParameters.java

@@ -24,6 +24,8 @@
 
 import java.util.Properties;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
+
 public class ImageDttParameters {
 	public boolean corr_mode_debug =        true;
 	public boolean mix_corr_poly =          true;

src/main/java/PoleProcessorParameters.java

 import java.util.Properties;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
+
 /**
  **
  ** PoleProcessorParameters - parameters for PoleProcessor class that identifies

src/main/java/TwoQuadCLT.java

@@ -39,6 +39,8 @@ import java.util.ArrayList;
 import java.util.Properties;
 import java.util.Random;
 
+import com.elphel.imagej.common.GenericJTabbedDialog;
+
 import ij.IJ;
 import ij.ImagePlus;
 import ij.ImageStack;

src/main/java/GenericJTabbedDialog.java → src/main/java/com/elphel/imagej/common/GenericJTabbedDialog.java

+package com.elphel.imagej.common;
 /*
  * TabbedPaneDemo.java requires one additional file:
  *   images/middle.gif.

src/main/java/com/elphel/imagej/common/package-info.java

+/**
+ *
+ */
+/**
+ * @author Andrey Filippov
+ *
+ */
+package com.elphel.imagej.common;
\ No newline at end of file

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

@@ -32,7 +32,6 @@ import java.util.Properties;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.elphel.imagej.readers.ElphelTiffReader;
 import com.elphel.imagej.readers.ImagejJp4TiffMulti;
 
 import ij.ImagePlus;
@@ -51,10 +50,6 @@ public class LwirReader {
 			"http://192.168.0.38:2325/bchn4",
 			"http://192.168.0.38:2326/bchn4",
 			};
-//	public static String IMAGE_URL_FIRST="/towp/wait/img/next/save";
-//	public static String IMAGE_URL_NEXT= "/torp/wait/img/next/save";
-//	public static String IMAGE_URL_FIRST="/towp/wait/img/save"; // next image name, same image number/time
-//	public static String IMAGE_URL_NEXT= "/torp/wait/img/save"; // same image name, same image number/time
 
 	public static String IMAGE_URL_FIRST="/towp/wait/img/save";     // next image name, same image number/time
 	public static String IMAGE_URL_NEXT= "/torp/next/wait/img/save"; // same image name, same image number/time
@@ -64,10 +59,14 @@ public class LwirReader {
 
 	/** Logger for this class. */
 	private static final Logger LOGGER =
-			LoggerFactory.getLogger(ElphelTiffReader.class);
+			LoggerFactory.getLogger(LwirReader.class);
 
 	private ImagejJp4TiffMulti imagejJp4TiffMulti;
 
+
+
+
+
 	public LwirReader() {
 		imagejJp4TiffMulti = null;
 	}
@@ -103,7 +102,7 @@ public class LwirReader {
 				} catch (FormatException e) {
 					LOGGER.error("readAllMultiple0:FormatException, priming");
 				}
-				LOGGER.error("priming..."+(i+1));
+				LOGGER.info("priming..."+(i+1));
 				try {
 					Thread.sleep(1000);
 				} catch (InterruptedException e) {
@@ -113,7 +112,7 @@ public class LwirReader {
 			}
 		}
 		for (int n = 0; n < num_frames; n++) {
-			LOGGER.error("---- Acquiring frame set "+n);
+			LOGGER.info("---- Acquiring frame set "+n);
 			try {
 				imagejJp4TiffMulti.getMultiImages( (n==0)? urls0:urls1, imps[n],  scale,  std);
 			} catch (IOException e) {
@@ -141,7 +140,7 @@ public class LwirReader {
 					img_numbers[n][i] = -1;
 				}
 				img_names[n][i] = (String) imps[n][i].getProperty("CONTENT_FILENAME");
-				LOGGER.error("Seconds for" + n+":"+i+" - "+img_seconds[n][i]+", number"+img_numbers[n][i]+", name "+img_names[n][i]);
+				LOGGER.info("Seconds for" + n+":"+i+" - "+img_seconds[n][i]+", number"+img_numbers[n][i]+", name "+img_names[n][i]);
 			}
 		}
 
@@ -251,7 +250,7 @@ public class LwirReader {
 		}
 		for (int i = 0; i < num_channels; i++) {
 			// change to info later:
-			LOGGER.error("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
+			LOGGER.info("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
 		}
 		ImagePlus [][] imps_synced = new ImagePlus [num_frames - fr_max + fr_min][num_channels];
 		for (int n = 0; n < imps_synced.length; n++) {

src/main/java/com/elphel/imagej/readers/services.properties.forelphel

+###
+# #%L
+# Common package for I/O and related utilities
+# %%
+# Copyright (C) 2005 - 2016 Open Microscopy Environment:
+#   - Board of Regents of the University of Wisconsin-Madison
+#   - Glencoe Software, Inc.
+#   - University of Dundee
+# %%
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+# #L%
+###
+
+#
+# NOTE: All service classes must be fully qualified
+#
+## ClassNotFoundException: loci.formats.services.JPEGXRService
+## ClassNotFoundException: loci.formats.services.JHDFService
+# OME-XML service (interface and implementation in bio-formats component)
+loci.formats.services.OMEXMLService=loci.formats.services.OMEXMLServiceImpl
+# POI service (interface and implementation in bio-formats component)
+###loci.formats.services.POIService=loci.formats.services.POIServiceImpl
+# NetCDF service (interface and implementation in bio-formats component)
+###loci.formats.services.NetCDFService=loci.formats.services.NetCDFServiceImpl
+# JHDF service (interface and implementation in bio-formats component)
+## loci.formats.services.JHDFService=loci.formats.services.JHDFServiceImpl # ClassNotFoundException
+# MDB Tools service (interface and implementation in bio-formats component)
+###loci.formats.services.MDBService=loci.formats.services.MDBServiceImpl
+# JAI Image I/O service (interface and implementation in bio-formats component)
+###loci.formats.services.JAIIIOService=loci.formats.services.JAIIIOServiceImpl
+# LuraWave decoder service (interface and implementation in bio-formats
+# component; depends on stubs.jar for compilation)
+###loci.formats.services.LuraWaveService=loci.formats.services.LuraWaveServiceImpl
+# Metakit reader service (interface and implementation in bio-formats component;
+# depends upon metakit.jar for compilation)
+###loci.formats.services.MetakitService=loci.formats.services.MetakitServiceImpl
+# libjpeg-turbo service
+###loci.formats.services.JPEGTurboService=loci.formats.services.JPEGTurboServiceImpl
+# Woolz service (interface and implementation in bio-formats)
+###loci.formats.services.WlzService=loci.formats.services.WlzServiceImpl
+
+loci.formats.services.EXIFService=loci.formats.services.EXIFServiceImpl
+
+## loci.formats.services.JPEGXRService=loci.formats.services.JPEGXRServiceImpl # ClassNotFoundException
+# Minio S3 client service
+###loci.common.services.S3ClientService=loci.common.services.S3ClientServiceImpl
+# OME Codecs JAI Image I/O service
+###ome.codecs.services.JAIIIOService=ome.codecs.services.JAIIIOServiceImpl
+# OME Codecs LuraWave decoder service (depends on stubs.jar for compilation)
+###ome.codecs.services.LuraWaveService=ome.codecs.services.LuraWaveServiceImpl

src/main/resources/services.properties

+###
+# #%L
+# Common package for I/O and related utilities
+# %%
+# Copyright (C) 2005 - 2016 Open Microscopy Environment:
+#   - Board of Regents of the University of Wisconsin-Madison
+#   - Glencoe Software, Inc.
+#   - University of Dundee
+# %%
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+# #L%
+###
+
+#
+# NOTE: All service classes must be fully qualified
+#
+## ClassNotFoundException: loci.formats.services.JPEGXRService
+## ClassNotFoundException: loci.formats.services.JHDFService
+# OME-XML service (interface and implementation in bio-formats component)
+loci.formats.services.OMEXMLService=loci.formats.services.OMEXMLServiceImpl
+# POI service (interface and implementation in bio-formats component)
+loci.formats.services.POIService=loci.formats.services.POIServiceImpl
+# NetCDF service (interface and implementation in bio-formats component)
+loci.formats.services.NetCDFService=loci.formats.services.NetCDFServiceImpl
+# JHDF service (interface and implementation in bio-formats component)
+## loci.formats.services.JHDFService=loci.formats.services.JHDFServiceImpl # ClassNotFoundException
+# MDB Tools service (interface and implementation in bio-formats component)
+loci.formats.services.MDBService=loci.formats.services.MDBServiceImpl
+# JAI Image I/O service (interface and implementation in bio-formats component)
+loci.formats.services.JAIIIOService=loci.formats.services.JAIIIOServiceImpl
+# LuraWave decoder service (interface and implementation in bio-formats
+# component; depends on stubs.jar for compilation)
+loci.formats.services.LuraWaveService=loci.formats.services.LuraWaveServiceImpl
+# Metakit reader service (interface and implementation in bio-formats component;
+# depends upon metakit.jar for compilation)
+loci.formats.services.MetakitService=loci.formats.services.MetakitServiceImpl
+# libjpeg-turbo service
+loci.formats.services.JPEGTurboService=loci.formats.services.JPEGTurboServiceImpl
+# Woolz service (interface and implementation in bio-formats)
+loci.formats.services.WlzService=loci.formats.services.WlzServiceImpl
+loci.formats.services.EXIFService=loci.formats.services.EXIFServiceImpl
+## loci.formats.services.JPEGXRService=loci.formats.services.JPEGXRServiceImpl # ClassNotFoundException
+# Minio S3 client service
+loci.common.services.S3ClientService=loci.common.services.S3ClientServiceImpl
+# OME Codecs JAI Image I/O service
+ome.codecs.services.JAIIIOService=ome.codecs.services.JAIIIOServiceImpl
+# OME Codecs LuraWave decoder service (depends on stubs.jar for compilation)
+ome.codecs.services.LuraWaveService=ome.codecs.services.LuraWaveServiceImpl

src/main/resources/services.properties.forelphel

+###
+# #%L
+# Common package for I/O and related utilities
+# %%
+# Copyright (C) 2005 - 2016 Open Microscopy Environment:
+#   - Board of Regents of the University of Wisconsin-Madison
+#   - Glencoe Software, Inc.
+#   - University of Dundee
+# %%
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+# #L%
+###
+
+#
+# NOTE: All service classes must be fully qualified
+#
+## ClassNotFoundException: loci.formats.services.JPEGXRService
+## ClassNotFoundException: loci.formats.services.JHDFService
+# OME-XML service (interface and implementation in bio-formats component)
+loci.formats.services.OMEXMLService=loci.formats.services.OMEXMLServiceImpl
+# POI service (interface and implementation in bio-formats component)
+###loci.formats.services.POIService=loci.formats.services.POIServiceImpl
+# NetCDF service (interface and implementation in bio-formats component)
+###loci.formats.services.NetCDFService=loci.formats.services.NetCDFServiceImpl
+# JHDF service (interface and implementation in bio-formats component)
+## loci.formats.services.JHDFService=loci.formats.services.JHDFServiceImpl # ClassNotFoundException
+# MDB Tools service (interface and implementation in bio-formats component)
+###loci.formats.services.MDBService=loci.formats.services.MDBServiceImpl
+# JAI Image I/O service (interface and implementation in bio-formats component)
+###loci.formats.services.JAIIIOService=loci.formats.services.JAIIIOServiceImpl
+# LuraWave decoder service (interface and implementation in bio-formats
+# component; depends on stubs.jar for compilation)
+###loci.formats.services.LuraWaveService=loci.formats.services.LuraWaveServiceImpl
+# Metakit reader service (interface and implementation in bio-formats component;
+# depends upon metakit.jar for compilation)
+###loci.formats.services.MetakitService=loci.formats.services.MetakitServiceImpl
+# libjpeg-turbo service
+###loci.formats.services.JPEGTurboService=loci.formats.services.JPEGTurboServiceImpl
+# Woolz service (interface and implementation in bio-formats)
+###loci.formats.services.WlzService=loci.formats.services.WlzServiceImpl
+
+loci.formats.services.EXIFService=loci.formats.services.EXIFServiceImpl
+
+## loci.formats.services.JPEGXRService=loci.formats.services.JPEGXRServiceImpl # ClassNotFoundException
+# Minio S3 client service
+###loci.common.services.S3ClientService=loci.common.services.S3ClientServiceImpl
+# OME Codecs JAI Image I/O service
+###ome.codecs.services.JAIIIOService=ome.codecs.services.JAIIIOServiceImpl
+# OME Codecs LuraWave decoder service (depends on stubs.jar for compilation)
+###ome.codecs.services.LuraWaveService=ome.codecs.services.LuraWaveServiceImpl