Changeset 7993


Ignore:
Timestamp:
04/23/12 16:45:17 (8 years ago)
Author:
aivar
Message:

SLIM Plugin: Clean up code, comments.

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

Legend:

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

    r7887 r7993  
    3636 
    3737/** 
    38  * TODO 
     38 * Class that handles drawing the image using progressively smaller "chunky" 
     39 * (larger than single pixel) pixels. 
    3940 * 
    4041 * <dl><dt><b>Source code:</b></dt> 
     
    5253    int[] _outputLocation; 
    5354 
    54     @Deprecated 
     55    /** 
     56     * Constructor. 
     57     *  
     58     * @param x 
     59     * @param y 
     60     * @param width 
     61     * @param height  
     62     */ 
    5563    public ChunkyPixel(int x, int y, int width, int height) { 
    5664        _x = x; 
     
    6270    } 
    6371 
     72    /** 
     73     * Gets the x location. 
     74     *  
     75     * @return  
     76     */ 
    6477    public int getX() { 
    6578        return _x; 
    6679    } 
    6780 
     81    /** 
     82     * Gets the y location. 
     83     *  
     84     * @return  
     85     */ 
    6886    public int getY() { 
    6987        return _y; 
    7088    } 
    7189 
     90    /** 
     91     * Gets the width to draw the pixel. 
     92     *  
     93     * @return  
     94     */ 
    7295    public int getWidth() { 
    7396        return _width; 
    7497    } 
    7598 
     99    /** 
     100     * Gets the height to draw the pixel. 
     101     *  
     102     * @return  
     103     */ 
    76104    public int getHeight() { 
    77105        return _height; 
    78106    } 
    79      
     107 
     108    /** 
     109     * Sets the location of the pixel in the input image. 
     110     *  
     111     * @param location  
     112     */ 
    80113    public void setInputLocation(int[] location) { 
    81114        _inputLocation = location; 
    82115    } 
    83116 
     117    /** 
     118     * Gets the location of the pixel in the input image. 
     119     *  
     120     * @return  
     121     */ 
    84122    public int[] getInputLocation() { 
    85123        return _inputLocation; 
    86124    } 
    87      
     125 
     126    /** 
     127     * Sets the location of the pixel in the output image. 
     128     *  
     129     * @param location  
     130     */ 
    88131    public void setOutputLocation(int[] location) { 
    89132        _outputLocation = location; 
    90133    } 
    91      
     134 
     135    /** 
     136     * Gets the location of the pixel in the output image. 
     137     *  
     138     * @return  
     139     */ 
    92140    public int[] getOutputLocation() { 
    93141        return _outputLocation; 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixelEffectIterator.java

    r7887 r7993  
    3535package loci.slim; 
    3636 
    37 import java.lang.UnsupportedOperationException; 
    3837import java.util.Iterator; 
    3938 
    4039/** 
    41  * TODO 
     40 * Iterator that supplies a series of chunky pixels. 
    4241 * 
    4342 * <dl><dt><b>Source code:</b></dt> 
     
    5655    ChunkyPixel _chunkyPixel; 
    5756 
     57    /** 
     58     * Constructor, sets up the chunky pixel iterator with a table of chunky 
     59     * pixels and the width and height of the image being processed. 
     60     *  
     61     * @param table 
     62     * @param width 
     63     * @param height  
     64     */ 
    5865    public ChunkyPixelEffectIterator(IChunkyPixelTable table, int width, int height) { 
    5966        _table = table; 
     
    7077    } 
    7178 
     79    @Override 
    7280    public boolean hasNext() { 
    7381        return _chunkyPixel != null; 
    7482    } 
    7583 
     84    @Override 
    7685    public ChunkyPixel next() { 
    7786        ChunkyPixel chunkyPixel = _chunkyPixel; 
     
    8089    } 
    8190 
     91    @Override 
    8292    public void remove() { 
    8393        throw new UnsupportedOperationException(); 
    8494    } 
    8595 
     96    /* 
     97     * Gets the next chunky pixel from the table. 
     98     *  
     99     */ 
    86100    ChunkyPixel getNextChunkyPixel() { 
    87101        // get the relative chunky pixel from the table 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ChunkyPixelTableImpl.java

    r7875 r7993  
    3636 
    3737/** 
    38  * TODO 
     38 * Table used for the "chunky pixel" effect. 
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
     
    4242 * <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 * 
    44  * @author Aivar Grislis grislis at wisc.edu 
     44 * @author Aivar Grislis grislis at wisc dot edu 
    4545 */ 
    4646public class ChunkyPixelTableImpl implements IChunkyPixelTable { 
    4747   static final int WIDTH  = 16; 
    4848   static final int HEIGHT = 16; 
    49    static final ChunkyPixel[] m_table = { 
     49   static final ChunkyPixel[] _table = { 
    5050        
    5151       // divide 16x16 square into 4 8x8 parts 
     
    406406   }; 
    407407 
     408   @Override 
    408409   public int size() { 
    409410       return WIDTH * HEIGHT; 
    410411   } 
    411412 
     413   @Override 
    412414   public int getWidth() { 
    413415       return WIDTH; 
    414416   } 
    415417 
     418   @Override 
    416419   public int getHeight() { 
    417420       return HEIGHT; 
    418421   } 
    419422 
     423   @Override 
    420424   public ChunkyPixel getChunkyPixel(int index) { 
    421425       ChunkyPixel chunkyPixel = null; 
    422        if (index < m_table.length) { 
    423            chunkyPixel = m_table[index]; 
     426       if (index < _table.length) { 
     427           chunkyPixel = _table[index]; 
    424428       } 
    425429       return chunkyPixel; 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/DecayImageWrapper.java

    r7990 r7993  
    88import loci.slim.process.IProcessor; 
    99 
    10 import mpicbg.imglib.container.planar.PlanarContainerFactory; 
    11 import mpicbg.imglib.cursor.Cursor; 
    1210import mpicbg.imglib.cursor.LocalizableByDimCursor; 
    1311import mpicbg.imglib.image.Image; 
    14 import mpicbg.imglib.image.ImageFactory; 
    15 import mpicbg.imglib.io.ImageOpener; 
    16 import mpicbg.imglib.outofbounds.OutOfBoundsStrategyMirrorFactory; 
    1712import mpicbg.imglib.type.numeric.RealType; 
    18 import mpicbg.imglib.type.numeric.real.DoubleType; 
    1913 
    2014/** 
     
    4135        _binIndex = binIndex; 
    4236 
    43 //        OutOfBoundsStrategyMirrorFactory strategyFactory = new OutOfBoundsStrategyMirrorFactory<T>(); 
    44 //        _cursor = image.createLocalizableByDimCursor(strategyFactory); 
    4537        _cursor = image.createLocalizableByDimCursor(); 
    4638    } 
     
    122114    } 
    123115 
     116    /** 
     117     * Gets underlying image. 
     118     */ 
    124119    @Override 
    125120    public Image<T> getImage() { 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/Excitation.java

    r7892 r7993  
    3939 * aka excitation, aka prompt, aka lamp function. 
    4040 * 
    41  * @author Aivar Grislis 
     41 * @author Aivar Grislis grislis at wisc dot edu 
    4242 */ 
    4343public class Excitation { 
    44     private final String m_fileName; 
    45     private final double[] m_values; 
    46     private final double m_timeInc; 
    47     private int m_start; 
    48     private int m_stop; 
    49     private double m_base; 
     44    private final String _fileName; 
     45    private final double[] _values; 
     46    private final double _timeInc; 
     47    private int _start; 
     48    private int _stop; 
     49    private double _base; 
    5050 
    5151    /** 
     
    5656     */ 
    5757    public Excitation(String fileName, double[] values, double timeInc) { 
    58         m_fileName = fileName; 
    59         m_values = values; 
    60         m_timeInc = timeInc; 
     58        _fileName = fileName; 
     59        _values = values; 
     60        _timeInc = timeInc; 
    6161    } 
    6262 
     
    6767     */ 
    6868    public String getFileName() { 
    69         return m_fileName; 
     69        return _fileName; 
    7070    } 
    7171 
     
    7676     */ 
    7777    public double[] getValues() { 
    78         return m_values; 
     78        return _values; 
    7979    } 
    8080 
     
    8585     */ 
    8686    public double getTimeInc() { 
    87         return m_timeInc; 
     87        return _timeInc; 
    8888    } 
    8989 
     
    9494     */ 
    9595    public void setStart(int start) { 
    96         m_start = start; 
     96        _start = start; 
    9797    } 
    9898 
     
    103103     */ 
    104104    public int getStart() { 
    105         return m_start; 
     105        return _start; 
    106106    } 
    107107 
     
    112112     */ 
    113113    public void setStop(int stop) { 
    114         m_stop = stop; 
     114        _stop = stop; 
    115115    } 
    116116 
     
    121121     */ 
    122122    public int getStop() { 
    123         return m_stop; 
     123        return _stop; 
    124124    } 
    125125 
     
    130130     */ 
    131131    public void setBase(double base) { 
    132         m_base = base; 
     132        _base = base; 
    133133    } 
    134134 
     
    139139     */ 
    140140    public double getBase() { 
    141         return m_base; 
     141        return _base; 
    142142    } 
    143143 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ExcitationFileHandler.java

    r7892 r7993  
    4444import loci.formats.in.ICSReader; 
    4545import loci.formats.meta.MetadataRetrieve; 
    46 import loci.formats.meta.MetadataStore; 
    4746import loci.formats.out.ICSWriter; 
    4847 
    49 import mpicbg.imglib.container.planar.PlanarContainerFactory; 
    50 import mpicbg.imglib.cursor.Cursor; 
    51 import mpicbg.imglib.cursor.LocalizableByDimCursor; 
    52 import mpicbg.imglib.image.Image; 
    53 import mpicbg.imglib.image.ImageFactory; 
    54 import mpicbg.imglib.io.ImageOpener; 
    5548import mpicbg.imglib.type.numeric.RealType; 
    56 import mpicbg.imglib.type.numeric.real.DoubleType; 
    5749 
    5850/** 
    59  * TODO 
     51 * Loads and saves excitation files. 
    6052 * 
    6153 * <dl><dt><b>Source code:</b></dt> 
     
    6355 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ExcitationFileHandler.java">SVN</a></dd></dl> 
    6456 * 
    65  * @author Aivar Grislis 
     57 * @author Aivar Grislis grislis at wisc dot edu 
    6658 */ 
    6759public class ExcitationFileHandler <T extends RealType<T>> { 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/GrayScaleImage.java

    r7922 r7993  
    5656 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/GrayScaleImage.java">SVN</a></dd></dl> 
    5757 * 
    58  * @author Aivar Grislis 
     58 * @author Aivar Grislis grislis at wisc dot edu 
    5959 */ 
    6060public class GrayScaleImage<T extends RealType<T>> implements IGrayScaleImage { 
    61     private int m_width; 
    62     private int m_height; 
    63     private ImageStack m_imageStack; 
    64     private MyStackWindow m_stackWindow; 
    65     private ISelectListener m_listener; 
    66     private byte[] m_saveOutPixels[]; 
    67     private double m_minNonZeroPhotonCount; 
    68     private int[] m_brightestPoint; 
     61    private int _width; 
     62    private int _height; 
     63    private ImageStack _imageStack; 
     64    private MyStackWindow _stackWindow; 
     65    private ISelectListener _listener; 
     66    private byte[] _saveOutPixels[]; 
     67    private double _minNonZeroPhotonCount; 
     68    private int[] _brightestPoint; 
    6969 
    7070    public GrayScaleImage(Image<T> image) { 
     
    7878        //    System.out.println("dim[" + i + "] " + dimensions[i]); 
    7979        //} 
    80         m_width = dimensions[0]; 
    81         m_height = dimensions[1]; 
     80        _width = dimensions[0]; 
     81        _height = dimensions[1]; 
    8282        int bins = dimensions[2]; 
    8383        int channels = 1; 
     
    8787 
    8888        // building an image stack 
    89         m_imageStack = new ImageStack(m_width, m_height); 
    90         m_saveOutPixels = new byte[channels][]; 
     89        _imageStack = new ImageStack(_width, _height); 
     90        _saveOutPixels = new byte[channels][]; 
    9191 
    9292        LocalizableByDimCursor cursor = image.createLocalizableByDimCursor(); 
    93         double[][] pixels = new double[m_width][m_height]; 
     93        double[][] pixels = new double[_width][_height]; 
    9494        int[] position = (channels > 1) ? new int[4] : new int[3]; 
    9595 
    96         m_minNonZeroPhotonCount = Double.MAX_VALUE; 
     96        _minNonZeroPhotonCount = Double.MAX_VALUE; 
    9797        for (int c = 0; c < channels; ++c) { 
    9898            if (channels > 1) { 
    9999                position[3] = c; 
    100100            } 
    101             byte[] outPixels = new byte[m_width * m_height]; 
     101            byte[] outPixels = new byte[_width * _height]; 
    102102 
    103103            // sum photon counts 
    104104            double maxPixel = 0.0; 
    105             for (int x = 0; x < m_width; ++x) { 
     105            for (int x = 0; x < _width; ++x) { 
    106106                position[0] = x; 
    107                 for (int y = 0; y < m_height; ++y) { 
     107                for (int y = 0; y < _height; ++y) { 
    108108                    position[1] = y; 
    109109                    pixels[x][y] = 0.0; 
     
    116116                         
    117117                        // keep track of minimum 
    118                         if (0.0 < photonCount && photonCount < m_minNonZeroPhotonCount) { 
    119                             m_minNonZeroPhotonCount = photonCount; 
     118                        if (0.0 < photonCount && photonCount < _minNonZeroPhotonCount) { 
     119                            _minNonZeroPhotonCount = photonCount; 
    120120                        } 
    121121                    } 
     
    123123                    if (pixels[x][y] > maxPixel) { 
    124124                        maxPixel = pixels[x][y]; 
    125                         m_brightestPoint = new int[] { x , y }; 
     125                        _brightestPoint = new int[] { x , y }; 
    126126                    } 
    127127                } 
     
    129129 
    130130            // convert to grayscale 
    131             for (int x = 0; x < m_width; ++x) { 
    132                 for (int y = 0; y < m_height; ++y) { 
    133                     outPixels[y * m_width + x] = (byte) (pixels[x][y] * 255 / maxPixel); 
     131            for (int x = 0; x < _width; ++x) { 
     132                for (int y = 0; y < _height; ++y) { 
     133                    outPixels[y * _width + x] = (byte) (pixels[x][y] * 255 / maxPixel); 
    134134                } 
    135135            } 
    136136 
    137137            // add a slice 
    138            // m_imageStack.addSlice("" + c, true, outPixels); // stopped working 12/1/10 
    139             m_imageStack.addSlice("" + c, outPixels); 
    140             m_saveOutPixels[c] = outPixels; 
     138           // _imageStack.addSlice("" + c, true, outPixels); // stopped working 12/1/10 
     139            _imageStack.addSlice("" + c, outPixels); 
     140            _saveOutPixels[c] = outPixels; 
    141141        } 
    142         ImagePlus imagePlus = new ImagePlus(title, m_imageStack); 
    143         m_stackWindow = new MyStackWindow(imagePlus); 
    144         m_stackWindow.setVisible(true); 
     142        ImagePlus imagePlus = new ImagePlus(title, _imageStack); 
     143        _stackWindow = new MyStackWindow(imagePlus); 
     144        _stackWindow.setVisible(true); 
    145145         
    146         System.out.println("minNonZeroPhotonCount is " + m_minNonZeroPhotonCount); 
    147  
    148         //System.out.println("Channel selector " + m_stackWindow.getChannelSelector()); 
    149         //System.out.println("Slice selector " + m_stackWindow.getSliceSelector()); 
    150         //System.out.println("Frame selector " + m_stackWindow.getFrameSelector()); 
     146        System.out.println("minNonZeroPhotonCount is " + _minNonZeroPhotonCount); 
     147 
     148        //System.out.println("Channel selector " + _stackWindow.getChannelSelector()); 
     149        //System.out.println("Slice selector " + _stackWindow.getSliceSelector()); 
     150        //System.out.println("Frame selector " + _stackWindow.getFrameSelector()); 
    151151 
    152152        // hook up mouse listener 
    153         ImageCanvas canvas = m_stackWindow.getCanvas(); 
     153        ImageCanvas canvas = _stackWindow.getCanvas(); 
    154154        canvas.addMouseListener( 
    155155            new MouseListener() { 
     
    164164                @Override 
    165165                public void mouseReleased(MouseEvent e) { 
    166                     if (null != m_listener) { 
    167                         m_listener.selected(getChannel(), e.getX(), e.getY()); 
     166                    if (null != _listener) { 
     167                        _listener.selected(getChannel(), e.getX(), e.getY()); 
    168168                    } 
    169169                } 
     
    179179    @Override 
    180180    public void setListener(ISelectListener listener) { 
    181         m_listener = listener; 
     181        _listener = listener; 
    182182    } 
    183183 
     
    190190    public int getChannel(){ 
    191191        // covert 1...n to 0...n-1 
    192         return m_stackWindow.getSlice() - 1; 
     192        return _stackWindow.getSlice() - 1; 
    193193    } 
    194194 
     
    200200    @Override 
    201201    public void enable(boolean enable) { 
    202         m_stackWindow.setEnabled(enable); 
     202        _stackWindow.setEnabled(enable); 
    203203    } 
    204204 
    205205    @Override 
    206206    public float getZoomFactor() { 
    207         return m_stackWindow.getZoomFactor(); 
     207        return _stackWindow.getZoomFactor(); 
    208208    } 
    209209 
     
    221221        //TODO this consistently results in "OutOfMemoryError: Java heap space" 
    222222        // getPixels calls getProcessor. 
    223         // byte pixels[] = (byte [])m_imageStack.getPixels(channel + 1); 
    224         byte pixels[] = m_saveOutPixels[channel]; 
    225         returnValue |= pixels[y * m_width + x] & 0xff; 
     223        // byte pixels[] = (byte [])_imageStack.getPixels(channel + 1); 
     224        byte pixels[] = _saveOutPixels[channel]; 
     225        returnValue |= pixels[y * _width + x] & 0xff; 
    226226        return returnValue; 
    227227    } 
     
    229229    @Override 
    230230    public double getMinNonZeroPhotonCount() { 
    231         return m_minNonZeroPhotonCount; 
     231        return _minNonZeroPhotonCount; 
    232232    } 
    233233     
    234234    @Override 
    235235    public int[] getBrightestPoint() { 
    236         return m_brightestPoint; 
     236        return _brightestPoint; 
    237237    } 
    238238} 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/IChunkyPixelTable.java

    r7668 r7993  
    3636 
    3737/** 
    38  * TODO 
     38 * Interface for a table of chunky pixels. 
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/IGrayScalePixelValue.java

    r7970 r7993  
     1// 
     2// IGrayScalePixelValue.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*/ 
     34 
    535package loci.slim; 
    636 
    737/** 
    8  * 
    9  * @author aivar 
     38 * Interface for a grayscale pixel value. 
     39 *  
     40 * @author Aivar Grislis grislis at wisc dot edu 
    1041 */ 
    1142public interface IGrayScalePixelValue { 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ISelectListener.java

    r7668 r7993  
    4343 * <a href="http://dev.loci.wisc.edu/svn/software/trunk/projects/slim-plugin/src/main/java/loci/slim/ISelectListener.java">SVN</a></dd></dl> 
    4444 * 
    45  * @author Aivar Grislis 
     45 * @author Aivar Grislis grislis at wisc dot edu 
    4646 */ 
    4747public interface ISelectListener { 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/ImageUtils.java

    r7676 r7993  
    3838 
    3939/** 
    40  * TODO 
     40 * Utility class for accessing Image dimensions. 
    4141 * 
    4242 * @author Barry DeZonia 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/MyStackWindow.java

    r7837 r7993  
    4343 
    4444/** 
    45  * A kludge because StackWindow has issues. 
     45 * A kludge needed because StackWindow has issues. 
    4646 * 
    4747 * <dl><dt><b>Source code:</b></dt> 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/OutputImageWrapper.java

    r7957 r7993  
     1// 
     2// OutputImageWrapper.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*/ 
     34 
    535package loci.slim; 
    636 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java

    r7992 r7993  
    6868import loci.slim.process.IProcessor; 
    6969import loci.slim.process.Threshold; 
    70 import loci.slim.ui.DecayGraph; 
    7170import loci.slim.ui.ExcitationPanel; 
    7271import loci.slim.ui.IUserInterfacePanel; 
     
    108107import loci.curvefitter.ICurveFitter.FitRegion; 
    109108 
    110  
    111 //TODO tidy up SLIMProcessor 
    112109/** 
    113110 * SLIMProcessor is the main class of the SLIM Plugin. It was originally just 
  • trunk/projects/slim-plugin/src/main/java/loci/slim/SLIM_PlugIn.java

    r7668 r7993  
    4545 * <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> 
    4646 * 
    47  * @author Aivar Grislis 
     47 * @author Aivar Grislis grislis at wisc dot edu 
    4848 */ 
    4949public class SLIM_PlugIn implements PlugIn { 
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