Ignore:
Timestamp:
03/22/11 17:06:13 (9 years ago)
Author:
curtis
Message:

Clean up headers, and add a script to check them.

Location:
trunk/projects/slim-plugin/src/main/java/loci/slim
Files:
46 edited

Legend:

Unmodified
Added
Removed
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixel.java

    r7059 r7668  
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/ChunkyPixel.java">Trac</a>, 
    42  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/ChunkyPixel.java">SVN</a></dd></dl> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixel.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixel.java">SVN</a></dd></dl> 
    4343 * 
    4444 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixelEffectIterator.java

    r7059 r7668  
    4242 * 
    4343 * <dl><dt><b>Source code:</b></dt> 
    44  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/ChunkyPixelEffectIterator.java">Trac</a>, 
    45  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/ChunkyPixelEffectIterator.java">SVN</a></dd></dl> 
     44 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixelEffectIterator.java">Trac</a>, 
     45 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixelEffectIterator.java">SVN</a></dd></dl> 
    4646 * 
    4747 * @author Aivar Grislis grislis at wisc.edu 
     
    5555    IChunkyPixelTable m_table; 
    5656    ChunkyPixel m_chunkyPixel; 
    57      
     57 
    5858    public ChunkyPixelEffectIterator(IChunkyPixelTable table, int width, int height) { 
    5959        m_table = table; 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixelTableImpl.java

    r7059 r7668  
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/ChunkyPixelTableImpl.java">Trac</a>, 
    42  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/ChunkyPixelTableImpl.java">SVN</a></dd></dl> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixelTableImpl.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixelTableImpl.java">SVN</a></dd></dl> 
    4343 * 
    4444 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/CursorHelper.java

    r7643 r7668  
     1// 
     2// CursorHelper.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim; 
     
    1140 
    1241/** 
     42 * Based on TRI2 TRCursors.c.  Comments in quotes are from that source file. 
    1343 * 
    14  * Based on TRI2 TRCursors.c.  Comments in quotes are from that source file. 
     44 * <dl><dt><b>Source code:</b></dt> 
     45 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/CursorHelper.java">Trac</a>, 
     46 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/CursorHelper.java">SVN</a></dd></dl> 
    1547 * 
    1648 * @author aivar 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/DecayGraph.java

    r7649 r7668  
    6767 * 
    6868 * <dl><dt><b>Source code:</b></dt> 
    69  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/DecayGraph.java">Trac</a>, 
    70  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/DecayGraph.java">SVN</a></dd></dl> 
     69 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/DecayGraph.java">Trac</a>, 
     70 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/DecayGraph.java">SVN</a></dd></dl> 
    7171 * 
    7272 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/Excitation.java

    r7644 r7668  
     1// 
     2// Excitation.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim; 
    736 
    837/** 
     38 * TODO 
    939 * 
    10  * @author aivar 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/Excitation.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/Excitation.java">SVN</a></dd></dl> 
     43 * 
     44 * @author Aivar Grislis 
    1145 */ 
    1246public class Excitation { 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ExcitationFileHandler.java

    r7645 r7668  
     1// 
     2// ExcitationFileHandler.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim; 
     
    2857 
    2958/** 
     59 * TODO 
     60 * 
     61 * <dl><dt><b>Source code:</b></dt> 
     62 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ExcitationFileHandler.java">Trac</a>, 
     63 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ExcitationFileHandler.java">SVN</a></dd></dl> 
    3064 * 
    3165 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/GrayScaleImage.java

    r7604 r7668  
    5353 * also allows the user to look at all the channels and pick a channel for the 
    5454 * fit. 
     55 * 
     56 * <dl><dt><b>Source code:</b></dt> 
     57 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/GrayScaleImage.java">Trac</a>, 
     58 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/GrayScaleImage.java">SVN</a></dd></dl> 
    5559 * 
    5660 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/IChunkyPixelTable.java

    r7059 r7668  
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/IChunkyPixelTable.java">Trac</a>, 
    42  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/IChunkyPixelTable.java">SVN</a></dd></dl> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/IChunkyPixelTable.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/IChunkyPixelTable.java">SVN</a></dd></dl> 
    4343 * 
    4444 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/IGrayScaleImage.java

    r7203 r7668  
    4040 * set the current channel selection.  Used for thresholding. 
    4141 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/IGrayScaleImage.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/IGrayScaleImage.java">SVN</a></dd></dl> 
     45 * 
    4246 * @author Aivar Grislis 
    4347 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ISelectListener.java

    r7204 r7668  
    3939 * select a pixel. 
    4040 * 
     41 * <dl><dt><b>Source code:</b></dt> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ISelectListener.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ISelectListener.java">SVN</a></dd></dl> 
     44 * 
    4145 * @author Aivar Grislis 
    4246 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/MyStackWindow.java

    r7205 r7668  
    4646 * A kludge because StackWindow has issues. 
    4747 * 
     48 * <dl><dt><b>Source code:</b></dt> 
     49 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/MyStackWindow.java">Trac</a>, 
     50 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/MyStackWindow.java">SVN</a></dd></dl> 
     51 * 
    4852 * @author Aivar Grislis 
    4953 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java

    r7663 r7668  
    8686//TODO tidy up SLIMProcessor 
    8787/** 
    88  * SLIMProcessor is the main class of the SLIM Plugin.  It was originally just thrown 
    89  * together to get something working, with some code/techniques borrowed from SLIM Plotter. 
    90  * Parts of this code are ugly & experimental. 
     88 * SLIMProcessor is the main class of the SLIM Plugin. It was originally just 
     89 * thrown together to get something working, with some code/techniques borrowed 
     90 * from SLIM Plotter. Parts of this code are ugly and experimental. 
     91 * 
     92 * <dl><dt><b>Source code:</b></dt> 
     93 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java">Trac</a>, 
     94 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java">SVN</a></dd></dl> 
    9195 * 
    9296 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/SLIM_PlugIn.java

    r7391 r7668  
     1// 
     2// SLIM_PlugIn.java 
     3// 
     4 
    15/* 
    26SLIMPlugin for combined spectral-lifetime image analysis. 
     
    3337import ij.ImageJ; 
    3438import ij.plugin.PlugIn; 
     39 
    3540/** 
     41 * TODO 
    3642 * 
    37  * @author aivar 
     43 * <dl><dt><b>Source code:</b></dt> 
     44 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/SLIM_PlugIn.java">Trac</a>, 
     45 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/SLIM_PlugIn.java">SVN</a></dd></dl> 
     46 * 
     47 * @author Aivar Grislis 
    3848 */ 
    3949public class SLIM_PlugIn implements PlugIn { 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/ISLIMAnalyzer.java

    r7295 r7668  
     1// 
     2// ISLIMAnalyzer.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim.analysis; 
     
    1443/** 
    1544 * An interface for analyzing the results of a SLIM Plugin fit. 
    16  *  
     45 * 
     46 * <dl><dt><b>Source code:</b></dt> 
     47 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/ISLIMAnalyzer.java">Trac</a>, 
     48 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/ISLIMAnalyzer.java">SVN</a></dd></dl> 
     49 * 
    1750 * @author Aivar Grislis 
    1851 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/SLIMAnalysis.java

    r7658 r7668  
     1// 
     2// SLIMAnalysis.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim.analysis; 
     
    2251 
    2352/** 
     53 * TODO 
     54 * 
     55 * <dl><dt><b>Source code:</b></dt> 
     56 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/SLIMAnalysis.java">Trac</a>, 
     57 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/SLIMAnalysis.java">SVN</a></dd></dl> 
    2458 * 
    2559 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/SLIMAnalyzer.java

    r7199 r7668  
     1// 
     2// SLIMAnalyzer.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim.analysis; 
     
    2049 *  @Name("Analyzer") 
    2150 * 
     51 * <dl><dt><b>Source code:</b></dt> 
     52 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/SLIMAnalyzer.java">Trac</a>, 
     53 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/SLIMAnalyzer.java">SVN</a></dd></dl> 
     54 * 
    2255 * @author Aivar Grislis 
    2356 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/Display.java

    r7658 r7668  
    6262/** 
    6363 * A plugin within a plugin, this is used to display the fit results. 
     64 * 
     65 * <dl><dt><b>Source code:</b></dt> 
     66 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/Display.java">Trac</a>, 
     67 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/Display.java">SVN</a></dd></dl> 
    6468 * 
    6569 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/ExportToText.java

    r7663 r7668  
     1// 
     2// ExportToText.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim.analysis.plugins; 
     
    3059/** 
    3160 * Exports to text for further analysis of SLIMPlugin results. 
     61 * 
     62 * <dl><dt><b>Source code:</b></dt> 
     63 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/ExportToText.java">Trac</a>, 
     64 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/ExportToText.java">SVN</a></dd></dl> 
    3265 * 
    3366 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/VisADAnalysisPlugin.java

    r7616 r7668  
     1// 
     2// VisADAnalysisPlugin.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim.analysis.plugins; 
     
    2554 * This will run on a separate thread, control returns to the caller right away. 
    2655 * 
     56 * <dl><dt><b>Source code:</b></dt> 
     57 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/VisADAnalysisPlugin.java">Trac</a>, 
     58 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/VisADAnalysisPlugin.java">SVN</a></dd></dl> 
     59 * 
    2760 * @author Aivar Grislis 
    2861 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/binning/ISLIMBinner.java

    r7300 r7668  
    4141 * An interface for binning SLIM Plugin data before the fit. 
    4242 * 
     43 * <dl><dt><b>Source code:</b></dt> 
     44 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/ISLIMBinner.java">Trac</a>, 
     45 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/ISLIMBinner.java">SVN</a></dd></dl> 
     46 * 
    4347 * @author Aivar Grislis 
    4448 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/binning/SLIMBinner.java

    r7301 r7668  
    4949 *  @SLIMBinner("Binner") 
    5050 * 
     51 * <dl><dt><b>Source code:</b></dt> 
     52 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/SLIMBinner.java">Trac</a>, 
     53 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/SLIMBinner.java">SVN</a></dd></dl> 
     54 * 
    5155 * @author Aivar Grislis 
    5256 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/binning/SLIMBinning.java

    r7302 r7668  
    4747 
    4848/** 
     49 * TODO 
     50 * 
     51 * <dl><dt><b>Source code:</b></dt> 
     52 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/SLIMBinning.java">Trac</a>, 
     53 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/SLIMBinning.java">SVN</a></dd></dl> 
    4954 * 
    5055 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin3x3.java

    r7303 r7668  
    4444 * A plugin within a plugin, this is used to bin the fit input. 
    4545 * 
     46 * <dl><dt><b>Source code:</b></dt> 
     47 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin3x3.java">Trac</a>, 
     48 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin3x3.java">SVN</a></dd></dl> 
     49 * 
    4650 * @author Aivar Grislis 
    4751 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin5x5.java

    r7304 r7668  
    4444 * A plugin within a plugin, this is used to bin the fit input. 
    4545 * 
     46 * <dl><dt><b>Source code:</b></dt> 
     47 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin5x5.java">Trac</a>, 
     48 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin5x5.java">SVN</a></dd></dl> 
     49 * 
    4650 * @author Aivar Grislis 
    4751 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin7x7.java

    r7600 r7668  
    11// 
    2 // Bin5x5.java 
     2// Bin7x7.java 
    33// 
    44 
     
    4444 * A plugin within a plugin, this is used to bin the fit input. 
    4545 * 
     46 * <dl><dt><b>Source code:</b></dt> 
     47 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin7x7.java">Trac</a>, 
     48 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/Bin7x7.java">SVN</a></dd></dl> 
     49 * 
    4650 * @author Aivar Grislis 
    4751 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/BinNxN.java

    r7601 r7668  
    4545/** 
    4646 * Helper class, this is used by plugins to bin the fit input data. 
     47 * 
     48 * <dl><dt><b>Source code:</b></dt> 
     49 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/BinNxN.java">Trac</a>, 
     50 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/binning/plugins/BinNxN.java">SVN</a></dd></dl> 
    4751 * 
    4852 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/ColorBar.java

    r7403 r7668  
    4343 * Displays a color bar with the current colorization scheme.  Live, 
    4444 * reflects ongoing changes. 
     45 * 
     46 * <dl><dt><b>Source code:</b></dt> 
     47 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/ColorBar.java">Trac</a>, 
     48 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/ColorBar.java">SVN</a></dd></dl> 
    4549 * 
    4650 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizer.java

    r7602 r7668  
    4242 
    4343/** 
    44  * Displays a colorized lifetime image and a UI that shows the lifetime histogram 
    45  * and controls the colorization. 
     44 * Displays a colorized lifetime image and a UI that shows the lifetime 
     45 * histogram and controls the colorization. 
     46 * 
     47 * <dl><dt><b>Source code:</b></dt> 
     48 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizer.java">Trac</a>, 
     49 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizer.java">SVN</a></dd></dl> 
    4650 * 
    4751 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizerUI.java

    r7597 r7668  
    4343 * used to colorize the lifetime data, and an input panel that allows the user 
    4444 * to control the colorization. 
     45 * 
     46 * <dl><dt><b>Source code:</b></dt> 
     47 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizerUI.java">Trac</a>, 
     48 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/DataColorizerUI.java">SVN</a></dd></dl> 
    4549 * 
    4650 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/FiveColorColorize.java

    r7212 r7668  
    3939/** 
    4040 * Colorizes data based on a sequence of five colors. 
     41 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/FiveColorColorize.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/FiveColorColorize.java">SVN</a></dd></dl> 
    4145 * 
    4246 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/Histogram.java

    r7403 r7668  
    4848 * 
    4949 * <dl><dt><b>Source code:</b></dt> 
    50  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/colorizer/Histogram.java">Trac</a>, 
    51  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/colorizer/Histogram.java">SVN</a></dd></dl> 
     50 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/Histogram.java">Trac</a>, 
     51 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/Histogram.java">SVN</a></dd></dl> 
    5252 * 
    5353 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/IColorize.java

    r7403 r7668  
    4141 * 
    4242 * <dl><dt><b>Source code:</b></dt> 
    43  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/colorizer/IColorize.java">Trac</a>, 
    44  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/colorizer/IColorize.java">SVN</a></dd></dl> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/IColorize.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/IColorize.java">SVN</a></dd></dl> 
    4545 * 
    4646 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/IColorizeRangeListener.java

    r7403 r7668  
    3838 * Passes around settings changes. 
    3939 * 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/IColorizeRangeListener.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/IColorizeRangeListener.java">SVN</a></dd></dl> 
     43 * 
    4044 * @author Aivar Grislis grislis at wisc.edu 
    4145 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/InputPanel.java

    r7403 r7668  
    5353 * range selection.  When automatic mode is off it allows the user to enter 
    5454 * minimum and maximum values. 
     55 * 
     56 * <dl><dt><b>Source code:</b></dt> 
     57 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/InputPanel.java">Trac</a>, 
     58 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/InputPanel.java">SVN</a></dd></dl> 
    5559 * 
    5660 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/LifetimeHistogram.java

    r7403 r7668  
    7878 * 
    7979 * <dl><dt><b>Source code:</b></dt> 
    80  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/colorizer/LifetimeHistogram.java">Trac</a>, 
    81  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/colorizer/LifetimeHistogram.java">SVN</a></dd></dl> 
     80 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/LifetimeHistogram.java">Trac</a>, 
     81 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/LifetimeHistogram.java">SVN</a></dd></dl> 
    8282 * 
    8383 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/MultiColorColorize.java

    r7215 r7668  
    3939/** 
    4040 * Abstract base class for colorizers that interpolate between colors. 
     41 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/MultiColorColorize.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/MultiColorColorize.java">SVN</a></dd></dl> 
    4145 * 
    4246 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/ThreeColorColorize.java

    r7403 r7668  
    3939/** 
    4040 * Colorizes data based on a sequence of three colors. 
     41 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/ThreeColorColorize.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/colorizer/ThreeColorColorize.java">SVN</a></dd></dl> 
    4145 * 
    4246 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ui/ExcitationGraph.java

    r7646 r7668  
     1// 
     2// ExcitationGraph.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim.ui; 
     
    3665 
    3766/** 
     67 * TODO 
     68 * 
     69 * <dl><dt><b>Source code:</b></dt> 
     70 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/ExcitationGraph.java">Trac</a>, 
     71 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/ExcitationGraph.java">SVN</a></dd></dl> 
    3872 * 
    3973 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ui/ExcitationPanel.java

    r7647 r7668  
     1// 
     2// ExcitationPanel.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim.ui; 
     
    3564 
    3665/** 
     66 * TODO 
     67 * 
     68 * <dl><dt><b>Source code:</b></dt> 
     69 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/ExcitationPanel.java">Trac</a>, 
     70 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/ExcitationPanel.java">SVN</a></dd></dl> 
    3771 * 
    3872 * @author Aivar Grislis 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IStartStopBaseListener.java

    r7648 r7668  
     1// 
     2// IStartStopBaseListener.java 
     3// 
     4 
    15/* 
    2  * To change this template, choose Tools | Templates 
    3  * and open the template in the editor. 
    4  */ 
     6SLIMPlugin for combined spectral-lifetime image analysis. 
     7 
     8Copyright (c) 2010, UW-Madison LOCI 
     9All rights reserved. 
     10 
     11Redistribution and use in source and binary forms, with or without 
     12modification, are permitted provided that the following conditions are met: 
     13    * Redistributions of source code must retain the above copyright 
     14      notice, this list of conditions and the following disclaimer. 
     15    * Redistributions in binary form must reproduce the above copyright 
     16      notice, this list of conditions and the following disclaimer in the 
     17      documentation and/or other materials provided with the distribution. 
     18    * Neither the name of the UW-Madison LOCI nor the 
     19      names of its contributors may be used to endorse or promote products 
     20      derived from this software without specific prior written permission. 
     21 
     22THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
     23AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
     24IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
     25ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE 
     26LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
     27CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
     28SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
     29INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
     30CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
     31ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
     32POSSIBILITY OF SUCH DAMAGE. 
     33*/ 
    534 
    635package loci.slim.ui; 
    736 
    837/** 
     38 * TODO 
    939 * 
    10  * @author aivar 
     40 * <dl><dt><b>Source code:</b></dt> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IStartStopBaseListener.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IStartStopBaseListener.java">SVN</a></dd></dl> 
     43 * 
     44 * @author Aivar Grislis 
    1145 */ 
    1246public interface IStartStopBaseListener { 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IStartStopListener.java

    r7061 r7668  
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/IStartStopListener.java">Trac</a>, 
    42  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/IStartStopListener.java">SVN</a></dd></dl> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IStartStopListener.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IStartStopListener.java">SVN</a></dd></dl> 
    4343 * 
    4444 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanel.java

    r7658 r7668  
    4040 * Interface to the User Interface Panel 
    4141 * 
     42 * <dl><dt><b>Source code:</b></dt> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanel.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanel.java">SVN</a></dd></dl> 
     45 * 
    4246 * @author Aivar Grislis 
    4347 */ 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanelListener.java

    r7115 r7668  
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanelListener.java">Trac</a>, 
    42  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanelListener.java">SVN</a></dd></dl> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanelListener.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IUserInterfacePanelListener.java">SVN</a></dd></dl> 
    4343 * 
    4444 * @author Aivar Grislis grislis at wisc.edu 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ui/SpringUtilities.java

    r7080 r7668  
    6969 * 
    7070 * <dl><dt><b>Source code:</b></dt> 
    71  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/slim-plotter/src/loci/slim/SpringUtilities.java">Trac</a>, 
    72  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/slim-plotter/src/loci/slim/SpringUtilities.java">SVN</a></dd></dl> 
     71 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/SpringUtilities.java">Trac</a>, 
     72 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/SpringUtilities.java">SVN</a></dd></dl> 
    7373 */ 
    7474public class SpringUtilities { 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java

    r7658 r7668  
    7676 * 
    7777 * <dl><dt><b>Source code:</b></dt> 
    78  * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java">Trac</a>, 
    79  * <a href="http://dev.loci.wisc.edu/svn/java/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java">SVN</a></dd></dl> 
     78 * <dd><a href="http://dev.loci.wisc.edu/trac/software/browser/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java">Trac</a>, 
     79 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ui/UserInterfacePanel.java">SVN</a></dd></dl> 
    8080 * 
    8181 * @author Aivar Grislis grislis at wisc.edu 
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