Changeset 6229


Ignore:
Timestamp:
05/04/10 17:23:02 (10 years ago)
Author:
curtis
Message:

Minor progress on Bio-Formats plugins refactoring.

  • Reorganize some packages.
  • Simplify custom color panel logic.
Location:
trunk/components/loci-plugins
Files:
1 added
1 deleted
29 edited
5 moved

Legend:

Unmodified
Added
Removed
  • trunk/components/loci-plugins/build.properties

    r6045 r6229  
    2121component.resources-text = plugins.config \ 
    2222                           loci/plugins/config/*.txt \ 
    23                            loci/plugins/importer/*.txt 
     23                           loci/plugins/in/*.txt 
    2424 
    2525component.main-class     = loci.plugins.About 
  • trunk/components/loci-plugins/src/loci/plugins/LociExporter.java

    r6007 r6229  
    3232import java.util.HashSet; 
    3333 
    34 import loci.plugins.exporter.Exporter; 
     34import loci.plugins.out.Exporter; 
    3535import loci.plugins.util.LibraryChecker; 
    3636 
    3737/** 
    3838 * ImageJ plugin for writing files using the LOCI Bio-Formats package. 
    39  * Wraps core logic in {@link loci.plugins.exporter.Exporter}, to avoid 
     39 * Wraps core logic in {@link loci.plugins.out.Exporter}, to avoid 
    4040 * direct references to classes in the external Bio-Formats library. 
    4141 * 
  • trunk/components/loci-plugins/src/loci/plugins/LociImporter.java

    r6007 r6229  
    3030import java.util.HashSet; 
    3131 
    32 import loci.plugins.importer.Importer; 
     32import loci.plugins.in.Importer; 
    3333import loci.plugins.util.LibraryChecker; 
    3434 
    3535/** 
    3636 * ImageJ plugin for reading files using the LOCI Bio-Formats package. 
    37  * Wraps core logic in {@link loci.plugins.importer.Importer}, to avoid 
     37 * Wraps core logic in {@link loci.plugins.in.Importer}, to avoid 
    3838 * direct references to classes in the external Bio-Formats library. 
    3939 * 
  • trunk/components/loci-plugins/src/loci/plugins/Slicer.java

    r6220 r6229  
    3636import ij.process.ImageProcessor; 
    3737import ij.process.LUT; 
     38 
    3839import loci.formats.FormatTools; 
    3940import loci.plugins.util.ImagePlusTools; 
  • trunk/components/loci-plugins/src/loci/plugins/colorize/Colorizer.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins; 
     26package loci.plugins.colorize; 
    2727 
    2828import ij.CompositeImage; 
     
    4343 
    4444import loci.formats.FormatTools; 
    45 import loci.plugins.importer.ImporterOptions; 
    46 import loci.plugins.importer.MergeDialog; 
     45import loci.plugins.in.ImporterOptions; 
    4746import loci.plugins.prefs.OptionsDialog; 
    4847import loci.plugins.util.ImagePlusTools; 
     
    8382    if (!LibraryChecker.checkJava() || !LibraryChecker.checkImageJ()) return; 
    8483 
     84    ImageStack stack = imp.getImageStack(); 
     85 
     86    if (stack.isVirtual()) { 
     87      IJ.error("Colorizer plugin cannot be used with virtual stacks.\n" + 
     88        "Please convert the virtual stack using Image>Duplicate."); 
     89      return; 
     90    } 
     91 
    8592    String stackOrder = "XYCZT"; 
    8693    boolean color = false; 
     
    98105      gd.addChoice("Stack order", new String[] {"XYCZT", "XYCTZ", "XYZCT", 
    99106        "XYZTC", "XYTCZ", "XYTZC"}, "XYCZT"); 
    100       gd.addCheckbox("Open as HyperStack", false); 
     107      gd.addCheckbox("Open as hyperstack", true); 
    101108      gd.showDialog(); 
    102109 
     
    122129    } 
    123130 
    124     ImageStack stack = imp.getImageStack(); 
    125  
    126     if (stack.isVirtual()) { 
    127       IJ.error("Colorizer plugin cannot be used with virtual stacks.\n" + 
    128         "Please convert the virtual stack using Image>Duplicate."); 
    129       return; 
    130     } 
    131      
    132131    ImagePlus newImp = Colorizer.colorize(imp, color, stackOrder, lut, series, mergeOption, hyperstack); 
    133132 
     
    293292    return lut; 
    294293  } 
    295    
     294 
    296295  // -- Helper methods -- 
    297296 
     
    343342    return channelLut; 
    344343  } 
    345    
     344 
    346345  private static byte[][][] promptForColors(int nChannels, int series) { 
    347346    byte[][][] lut = new byte[nChannels][][]; 
  • trunk/components/loci-plugins/src/loci/plugins/colorize/CustomColorChooser.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins; 
     26package loci.plugins.colorize; 
    2727 
    2828import ij.gui.GenericDialog; 
     
    5656public class CustomColorChooser implements TextListener { 
    5757  Vector<TextField> colors; 
    58   CustomColorPanel panel; 
     58  Panel panel; 
    5959  Color initialColor; 
    6060  int red, green, blue; 
     
    8787    gd.addSlider(makeLabel("Green:"), 0, 255, green); 
    8888    gd.addSlider(makeLabel("Blue:"), 0, 255, blue); 
    89     panel = new CustomColorPanel(initialColor); 
     89 
     90    panel = new Panel(); 
     91    Dimension prefSize = new Dimension(100, 50); 
     92    panel.setPreferredSize(prefSize); 
     93    panel.setMinimumSize(prefSize); 
     94    panel.setBackground(initialColor); 
    9095    gd.addPanel(panel, GridBagConstraints.CENTER, new Insets(10, 0, 0, 0)); 
     96 
    9197    colors = WindowTools.getNumericFields(gd); 
    9298    for (int i=0; i<colors.size(); i++) { 
     
    105111    int green = getColorValue(1); 
    106112    int blue = getColorValue(2); 
    107     panel.setColor(new Color(red, green, blue)); 
     113    panel.setBackground(new Color(red, green, blue)); 
    108114    panel.repaint(); 
    109115  } 
     
    121127    return "Series_" + series + "_Channel_" + channel + "_" + baseLabel; 
    122128  } 
    123    
    124   // -- Helper classes -- 
    125129 
    126         static class CustomColorPanel extends Panel { 
    127           private static final int WIDTH = 100, HEIGHT = 50; 
    128           private Color c; 
    129          
    130           public CustomColorPanel(Color c) { 
    131             this.c = c; 
    132           } 
    133          
    134           public Dimension getPreferredSize() { 
    135             return new Dimension(WIDTH, HEIGHT); 
    136           } 
    137          
    138           void setColor(Color c) { this.c = c; } 
    139          
    140           public Dimension getMinimumSize() { 
    141             return new Dimension(WIDTH, HEIGHT); 
    142           } 
    143          
    144           public void paint(Graphics g) { 
    145             g.setColor(c); 
    146             g.fillRect(0, 0, WIDTH, HEIGHT); 
    147             g.setColor(Color.black); 
    148             g.drawRect(0, 0, WIDTH-1, HEIGHT-1); 
    149           } 
    150         } 
    151          
    152130} 
  • trunk/components/loci-plugins/src/loci/plugins/colorize/MergeDialog.java

    r5138 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.colorize; 
    2727 
    2828import ij.gui.GenericDialog; 
     29 
    2930import loci.plugins.prefs.OptionsDialog; 
     31import loci.plugins.in.ImporterOptions; 
    3032 
    3133/** 
  • trunk/components/loci-plugins/src/loci/plugins/config/ConfigWindow.java

    r6128 r6229  
    6262import javax.swing.event.ListSelectionListener; 
    6363 
    64 import loci.plugins.importer.ImporterOptions; 
     64import loci.plugins.in.ImporterOptions; 
    6565import loci.plugins.util.WindowTools; 
    6666 
  • trunk/components/loci-plugins/src/loci/plugins/config/FlexWidgets.java

    r6026 r6229  
    6868      throw new RuntimeException(e); 
    6969    } 
    70      
     70 
    7171    // get license code from ImageJ preferences 
    7272    String prefCode = Prefs.get(LuraWaveServiceImpl.LICENSE_PROPERTY, null); 
  • trunk/components/loci-plugins/src/loci/plugins/in/Concatenator.java

    r6223 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.ImagePlus; 
     
    3333 
    3434import loci.formats.IFormatReader; 
    35 import loci.plugins.Colorizer; 
    36 import loci.plugins.Slicer; 
     35import loci.plugins.colorize.Colorizer; 
    3736 
    3837/** 
     
    4039 * 
    4140 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/Slicer.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/Slicer.java">SVN</a></dd></dl> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Concatenator.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Concatenator.java">SVN</a></dd></dl> 
    4443 * 
    4544 * @author Melissa Linkert linkert at wisc.edu 
    4645 */ 
    4746public class Concatenator { 
    48    
     47 
    4948  protected ImporterOptions options; 
    50    
     49 
    5150  public Concatenator(ImporterOptions options) { 
    5251    this.options = options; 
  • trunk/components/loci-plugins/src/loci/plugins/in/CropDialog.java

    r5144 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.gui.GenericDialog; 
     
    3838 * 
    3939 * <dl><dt><b>Source code:</b></dt> 
    40  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/CropDialog.java">Trac</a>, 
    41  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/CropDialog.java">SVN</a></dd></dl> 
     40 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/CropDialog.java">Trac</a>, 
     41 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/CropDialog.java">SVN</a></dd></dl> 
    4242 */ 
    4343public class CropDialog extends OptionsDialog { 
  • trunk/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java

    r6223 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    4646import loci.formats.gui.XMLWindow; 
    4747import loci.formats.services.OMEXMLService; 
    48 import loci.plugins.Colorizer; 
    49 import loci.plugins.Slicer; 
     48import loci.plugins.colorize.Colorizer; 
    5049import loci.plugins.util.ROIHandler; 
    5150import loci.plugins.util.SearchableWindow; 
     
    5857 * 
    5958 * <dl><dt><b>Source code:</b></dt> 
    60  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/DisplayHandler.java">Trac</a>, 
    61  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/DisplayHandler.java">SVN</a></dd></dl> 
     59 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java">Trac</a>, 
     60 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java">SVN</a></dd></dl> 
    6261 * 
    6362 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java

    r5138 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    3636 * 
    3737 * <dl><dt><b>Source code:</b></dt> 
    38  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/FilePatternDialog.java">Trac</a>, 
    39  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/FilePatternDialog.java">SVN</a></dd></dl> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">SVN</a></dd></dl> 
    4040 */ 
    4141public class FilePatternDialog extends OptionsDialog { 
  • trunk/components/loci-plugins/src/loci/plugins/in/IdDialog.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    3636 * 
    3737 * <dl><dt><b>Source code:</b></dt> 
    38  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/IdDialog.java">Trac</a>, 
    39  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/IdDialog.java">SVN</a></dd></dl> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/IdDialog.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/IdDialog.java">SVN</a></dd></dl> 
    4040 */ 
    4141public class IdDialog extends OptionsDialog { 
  • trunk/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.ImagePlus; 
     
    6767 * 
    6868 * <dl><dt><b>Source code:</b></dt> 
    69  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/ImagePlusReader.java">Trac</a>, 
    70  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/ImagePlusReader.java">SVN</a></dd></dl> 
     69 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java">Trac</a>, 
     70 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java">SVN</a></dd></dl> 
    7171 */ 
    7272public class ImagePlusReader implements StatusReporter { 
     
    8181  public String stackOrder;//TEMP! 
    8282  public IndexColorModel[] colorModels;//TEMP! 
    83    
     83 
    8484  // -- Constructors -- 
    8585 
     
    397397    if (used.length > 1 && groupFiles) { 
    398398      FilePattern fp = new FilePattern(new Location(file)); 
    399             title = fp.getPattern(); 
    400             if (title == null) { 
    401               title = file; 
    402               if (title.indexOf(".") != -1) { 
    403                 title = title.substring(0, title.lastIndexOf(".")); 
    404               } 
    405             } 
    406             title = title.substring(title.lastIndexOf(File.separator) + 1); 
     399      title = fp.getPattern(); 
     400      if (title == null) { 
     401        title = file; 
     402        if (title.indexOf(".") != -1) { 
     403          title = title.substring(0, title.lastIndexOf(".")); 
     404        } 
     405      } 
     406      title = title.substring(title.lastIndexOf(File.separator) + 1); 
    407407    } 
    408408    if (seriesName != null && !file.endsWith(seriesName) && 
  • trunk/components/loci-plugins/src/loci/plugins/in/Importer.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.ImageJ; 
     
    4141 * 
    4242 * <dl><dt><b>Source code:</b></dt> 
    43  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/Importer.java">Trac</a>, 
    44  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/Importer.java">SVN</a></dd></dl> 
     43 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Importer.java">Trac</a>, 
     44 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Importer.java">SVN</a></dd></dl> 
    4545 * 
    4646 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/components/loci-plugins/src/loci/plugins/in/ImporterDialog.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.gui.GenericDialog; 
     
    5757 * 
    5858 * <dl><dt><b>Source code:</b></dt> 
    59  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/ImporterDialog.java">Trac</a>, 
    60  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/ImporterDialog.java">SVN</a></dd></dl> 
     59 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterDialog.java">Trac</a>, 
     60 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterDialog.java">SVN</a></dd></dl> 
    6161 */ 
    6262public class ImporterDialog extends OptionsDialog 
  • trunk/components/loci-plugins/src/loci/plugins/in/ImporterMetadata.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import java.util.ArrayList; 
     
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/ImporterMetadata.java">Trac</a>, 
    42  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/ImporterMetadata.java">SVN</a></dd></dl> 
     41 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterMetadata.java">Trac</a>, 
     42 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterMetadata.java">SVN</a></dd></dl> 
    4343 */ 
    4444public class ImporterMetadata extends HashMap<String, Object> { 
  • trunk/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    5050 * 
    5151 * <dl><dt><b>Source code:</b></dt> 
    52  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/ImporterOptions.java">Trac</a>, 
    53  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/ImporterOptions.java">SVN</a></dd></dl> 
     52 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java">Trac</a>, 
     53 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java">SVN</a></dd></dl> 
    5454 */ 
    5555public class ImporterOptions extends OptionsList { 
  • trunk/components/loci-plugins/src/loci/plugins/in/ImporterReader.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    5757 * 
    5858 * <dl><dt><b>Source code:</b></dt> 
    59  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/ImporterReader.java">Trac</a>, 
    60  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/ImporterReader.java">SVN</a></dd></dl> 
     59 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterReader.java">Trac</a>, 
     60 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterReader.java">SVN</a></dd></dl> 
    6161 */ 
    6262public class ImporterReader { 
  • trunk/components/loci-plugins/src/loci/plugins/in/LocationDialog.java

    r5138 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.gui.GenericDialog; 
     
    3333 * 
    3434 * <dl><dt><b>Source code:</b></dt> 
    35  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/LocationDialog.java">Trac</a>, 
    36  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/LocationDialog.java">SVN</a></dd></dl> 
     35 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/LocationDialog.java">Trac</a>, 
     36 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/LocationDialog.java">SVN</a></dd></dl> 
    3737 */ 
    3838public class LocationDialog extends OptionsDialog { 
  • trunk/components/loci-plugins/src/loci/plugins/in/RangeDialog.java

    r5138 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.gui.GenericDialog; 
     
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/RangeDialog.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/RangeDialog.java">SVN</a></dd></dl> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/RangeDialog.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/RangeDialog.java">SVN</a></dd></dl> 
    3939 */ 
    4040public class RangeDialog extends OptionsDialog { 
  • trunk/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java

    r6155 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    5959 * 
    6060 * <dl><dt><b>Source code:</b></dt> 
    61  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/SeriesDialog.java">Trac</a>, 
    62  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/SeriesDialog.java">SVN</a></dd></dl> 
     61 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java">Trac</a>, 
     62 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java">SVN</a></dd></dl> 
    6363 */ 
    6464public class SeriesDialog extends OptionsDialog implements ActionListener { 
  • trunk/components/loci-plugins/src/loci/plugins/in/SwapDialog.java

    r6132 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    3636 * 
    3737 * <dl><dt><b>Source code:</b></dt> 
    38  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/SwapDialog.java">Trac</a>, 
    39  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/SwapDialog.java">SVN</a></dd></dl> 
     38 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/SwapDialog.java">Trac</a>, 
     39 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/SwapDialog.java">SVN</a></dd></dl> 
    4040 */ 
    4141public class SwapDialog extends OptionsDialog { 
  • trunk/components/loci-plugins/src/loci/plugins/in/ThumbLoader.java

    r6132 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    4848 * 
    4949 * <dl><dt><b>Source code:</b></dt> 
    50  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/ThumbLoader.java">Trac</a>, 
    51  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/ThumbLoader.java">SVN</a></dd></dl> 
     50 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ThumbLoader.java">Trac</a>, 
     51 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ThumbLoader.java">SVN</a></dd></dl> 
    5252 */ 
    5353public class ThumbLoader implements Runnable { 
  • trunk/components/loci-plugins/src/loci/plugins/in/UpgradeDialog.java

    r5139 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.importer; 
     26package loci.plugins.in; 
    2727 
    2828import ij.IJ; 
     
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/importer/UpgradeDialog.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/importer/UpgradeDialog.java">SVN</a></dd></dl> 
     37 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/UpgradeDialog.java">Trac</a>, 
     38 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/UpgradeDialog.java">SVN</a></dd></dl> 
    3939 */ 
    4040public class UpgradeDialog extends OptionsDialog { 
  • trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java

    r6128 r6229  
    2424*/ 
    2525 
    26 package loci.plugins.exporter; 
     26package loci.plugins.out; 
    2727 
    2828import ij.IJ; 
     
    7171 * 
    7272 * <dl><dt><b>Source code:</b></dt> 
    73  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/exporter/Exporter.java">Trac</a>, 
    74  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/exporter/Exporter.java">SVN</a></dd></dl> 
     73 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java">Trac</a>, 
     74 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java">SVN</a></dd></dl> 
    7575 * 
    7676 * @author Melissa Linkert linkert at wisc.edu 
  • trunk/components/loci-plugins/src/loci/plugins/util/BF.java

    r6155 r6229  
    4646    if (IJ.debugMode) IJ.log("LOCI: " + msg); 
    4747  } 
    48    
     48 
    4949} 
  • trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorReader.java

    r6155 r6229  
    4545 * A low-level reader for {@link ij.process.ImageProcessor} objects. 
    4646 * For a higher-level reader that returns {@link ij.ImagePlus} objects, 
    47  * see {@link loci.plugins.importer.ImagePlusReader} instead. 
     47 * see {@link loci.plugins.in.ImagePlusReader} instead. 
    4848 * 
    4949 * <dl><dt><b>Source code:</b></dt> 
     
    219219    return ip; 
    220220  } 
    221    
     221 
    222222  // -- IFormatReader methods -- 
    223    
    224   /** @Override */ 
     223 
     224  @Override 
    225225  public Class<?> getNativeDataType() { 
    226226    return ImageProcessor[].class; 
    227227  } 
    228    
    229   /** @Override */ 
     228 
     229  @Override 
    230230  public Object openPlane(int no, int x, int y, int w, int h) 
    231     throws FormatException, IOException  
     231    throws FormatException, IOException 
    232232  { 
    233233    return openProcessors(no, new Rectangle(x, y, w, h)); 
  • trunk/components/loci-plugins/src/loci/plugins/util/RecordedImageProcessor.java

    r6128 r6229  
    11111111    record(method, (Object[]) null, (Class<?>) null); 
    11121112  } 
    1113    
     1113 
    11141114  private void record(String method, Object v, Class<?> c) { 
    11151115    record(method, v == null ? null : new Object[] {v}, 
  • trunk/components/loci-plugins/src/loci/plugins/util/WindowTools.java

    r6155 r6229  
    198198    return gd.getNumericFields(); 
    199199  } 
    200    
     200 
    201201  @SuppressWarnings("unchecked") 
    202202  public static Vector<Checkbox> getCheckboxes(GenericDialog gd) { 
    203203    return gd.getCheckboxes(); 
    204204  } 
    205    
     205 
    206206} 
  • trunk/components/loci-plugins/src/plugins.config

    r5108 r6229  
    3535Plugins>LOCI, "-" 
    3636Plugins>LOCI, "Stack Slicer", loci.plugins.Slicer("") 
    37 Plugins>LOCI, "Stack Colorizer", loci.plugins.Colorizer("") 
     37Plugins>LOCI, "Stack Colorizer", loci.plugins.colorize.Colorizer("") 
    3838 
    3939Plugins>LOCI, "-" 
Note: See TracChangeset for help on using the changeset viewer.