class javadoc + copyright comments

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/extract/ImageSettingsExtractor.java

@@ -1,3 +1,28 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.extract;
 
 import org.w3c.dom.Node;
@@ -6,6 +31,11 @@
 import loci.formats.in.LeicaMicrosystemsMetadata.helpers.LMSMainXmlNodes;
 import loci.formats.in.LeicaMicrosystemsMetadata.model.ImageDetails;
 
+/**
+ * Helper class for extracting image details from LMS XML
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class ImageSettingsExtractor {
 
   /**

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/extract/confocal/ConfocalSettingRecordsExtractor.java

@@ -1,3 +1,28 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.extract.confocal;
 
 import java.util.regex.Matcher;
@@ -15,6 +40,11 @@
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.LaserSetting;
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.Multiband;
 
+/**
+ * Helper class for translating confocal scanner and filter setting records to more easily accessible data structures
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class ConfocalSettingRecordsExtractor extends Extractor {
   public static void extractSettingRecords(LMSMainXmlNodes xmlNodes){
 

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/extract/confocal/ConfocalSettingsFromAtlSettingsExtractor.java

@@ -1,3 +1,28 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.extract.confocal;
 
 import java.util.ArrayList;
@@ -16,6 +41,11 @@
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.LaserSetting;
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.Multiband;
 
+/**
+ * Helper class for extracting confocal acquisition settings from ATLConfocalSettings nodes 
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class ConfocalSettingsFromAtlSettingsExtractor extends Extractor {
 
   public static void extractChannelSettings(LMSMainXmlNodes xmlNodes, ConfocalAcquisitionSettings acquisitionSettings){

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/extract/confocal/ConfocalSettingsFromSettingRecordsExtractor.java

@@ -1,3 +1,28 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.extract.confocal;
 
 import java.util.ArrayList;
@@ -14,6 +39,11 @@
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.LaserSetting;
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.Multiband;
 
+/**
+ * Helper class for extracting confocal acquisition settings from filter and scanner setting records
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class ConfocalSettingsFromSettingRecordsExtractor extends Extractor {
 
   public static void extractChannelSettings(LMSMainXmlNodes xmlNodes, ConfocalAcquisitionSettings acquisitionSettings){

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/extract/confocal/DetectorExtractor.java

@@ -1,3 +1,28 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.extract.confocal;
 
 import java.util.ArrayList;
@@ -13,6 +38,11 @@
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.DetectorSetting;
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.Multiband;
 
+/**
+ * DetectorExtractor is a helper class for extracting detector information from LMS XML files.
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class DetectorExtractor extends Extractor {
 
   /**

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/extract/confocal/LaserExtractor.java

@@ -1,3 +1,28 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.extract.confocal;
 
 import java.util.ArrayList;
@@ -14,6 +39,11 @@
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.Laser.LmsLightSourceQualifier;
 import loci.formats.in.LeicaMicrosystemsMetadata.model.confocal.Laser.LmsLightSourceType;
 
+/**
+ * LaserExtractor is a helper class for extracting laser information from LMS XML files.
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class LaserExtractor extends Extractor {
 
   /**

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/model/Dye.java

@@ -1,5 +1,36 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.model;
 
+
+/**
+ * Data structure for dye information extracted from LMS XML
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class Dye {
     public String name; //e.g. Nuclei, ALEXA 488
     public String fluochromeName; //e.g. Hoechst 33342, ALEXA 488

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/model/ImageDetails.java

@@ -1,8 +1,38 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.model;
 
 import java.util.ArrayList;
 import java.util.List;
 
+/**
+ * Data structure for different image names and descriptions extracted from LMS XML
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class ImageDetails {
   public String originalImageName;
   public String targetImageName; // differs for tiles which are treated as separate series

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/model/MicroscopeDetails.java

@@ -1,7 +1,37 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.model;
 
 import ome.xml.model.enums.MicroscopeType;
 
+/**
+ * Data structure for microscope stand and objective details extracted from LMS XML
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class MicroscopeDetails {
   public String microscopeModel;
   public MicroscopeType microscopeType;

components/formats-gpl/src/loci/formats/in/LeicaMicrosystemsMetadata/model/Objective.java

@@ -1,9 +1,39 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program 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 2 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/gpl-2.0.html>.
+ * #L%
+ */
+
 package loci.formats.in.LeicaMicrosystemsMetadata.model;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+/**
+ * Data structure for objective information extracted from LMS XML
+ * 
+ * @author Constanze Wendlandt constanze.wendlandt at leica-microsystems.com
+ */
 public class Objective {
   public String model;
   public double numericalAperture;