Changeset 7996

Timestamp:

05/03/12 19:10:47 (8 years ago)

Author:

aivar

Message:

SLIM Plugin: Fixes Trac #686 log and linear scales and #687 show photon count. Also #689 masking is partially working.

Location:

trunk/projects/slim-plugin/src/main/java/loci/slim

Files:

• SLIMProcessor.java (modified) (12 diffs)
• fitting/images/AbstractBaseFittedImage.java (modified) (3 diffs)
• fitting/images/IFittedImage.java (modified) (2 diffs)
• histogram/HistogramDataNode.java (modified) (5 diffs)
• mask/MaskGroup.java (modified) (1 diff)
• ui/DecayGraph.java (modified) (4 diffs)
• ui/IDecayGraph.java (modified) (1 diff)

trunk/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java

@@ -68 +68 @@
 import loci.slim.process.IProcessor;
 import loci.slim.process.Threshold;
+import loci.slim.ui.DecayGraph;
 import loci.slim.ui.ExcitationPanel;
+import loci.slim.ui.IDecayGraph;
 import loci.slim.ui.IUserInterfacePanel;
 import loci.slim.ui.IUserInterfacePanelListener;
@@ -1081 +1083 @@
         double yCount[];
         double yFitted[];
+        int photons = 0;
 
         // loop over all channels or just the current one
@@ -1092 +1095 @@
 
             // count photons and pixels
-            int photons = 0;
             int pixels = 0;
 
@@ -1132 +1134 @@
             title += " Channel " + (_channel + 1);
         }
-        showDecayGraph(title, uiPanel, _fittingCursor, dataArray[visibleChannel]);
+        showDecayGraph(title, uiPanel, _fittingCursor,
+                dataArray[visibleChannel], photons);
         uiPanel.setParameters(dataArray[visibleChannel].getParams());
 
@@ -1156 +1159 @@
         double yCount[];
         double yFitted[];
+        int[] photons = new int[getRois().length];
+        for (int i = 0; i < photons.length; ++i) {
+            photons[i] = 0;
+        }
 
         // loop over all channels or just the current one
@@ -1174 +1181 @@
                             ++pixels;
                             for (int b = 0; b < _bins; ++b) {
-                                yCount[b] += getData(_cursor, channel, x, y, b);
+                                double count = getData(_cursor, channel, x, y, b);
+                                yCount[b] += count;
+                                photons[roiNumber - 1] += count;
                             }
                         }
@@ -1215 +1224 @@
                 title += " Channel " + (_channel + 1);
             }
-            showDecayGraph(title, uiPanel, _fittingCursor, dataArray[dataIndex]);
+            showDecayGraph(title, uiPanel, _fittingCursor,
+                    dataArray[dataIndex], photons[roiNumber - 1]);
             double lifetime = dataArray[dataIndex].getParams()[3];
             if (lifetime < min) {
@@ -1305 +1315 @@
         double yCount[];
         double yFitted[];
+        int photons = 0;
 
         // loop over all channels or just the current one
@@ -1313 +1324 @@
             location[2] = channel;
             yCount = processor.getPixel(location);
-            int photons = 0;
             for (int c = 0; c < _bins; ++c) {
                 photons += yCount[c];
@@ -1354 +1364 @@
             visibleChannel = _channel;
         }
-        showDecayGraph(title, uiPanel, _fittingCursor, dataArray[visibleChannel]);
+        showDecayGraph(title, uiPanel, _fittingCursor,
+                dataArray[visibleChannel], photons);
 
         // update UI parameters
@@ -1749 +1760 @@
             final IUserInterfacePanel uiPanel,
             final FittingCursor fittingCursor,
-            final ICurveFitData data)
+            final ICurveFitData data,
+            int photons)
     {
-        loci.slim.ui.IDecayGraph decayGraph = loci.slim.ui.DecayGraph.getInstance();
+        IDecayGraph decayGraph = DecayGraph.getInstance();
         JFrame frame = decayGraph.init(uiPanel.getFrame(), _bins, _timeRange);
         decayGraph.setTitle(title);
@@ -1760 +1772 @@
         decayGraph.setStartStop(transStart, dataStart, transStop);
         decayGraph.setData(data);
+        decayGraph.setPhotons(photons);
     }
     

trunk/projects/slim-plugin/src/main/java/loci/slim/fitting/images/AbstractBaseFittedImage.java

@@ -77 +77 @@
     private HistogramDataGroup _histogramData;
     private IColorizedFittedImage _fittedImage;
+    private Mask _mask;
     
     public AbstractBaseFittedImage(
@@ -108 +109 @@
             clear(_values);
             HistogramDataNode histogramDataChannel
-                    = new HistogramDataNode(_values);
+                    = new HistogramDataNode(this, _values);
             dataChannelList.add(histogramDataChannel);
             
@@ -227 +228 @@
         redisplay(minMaxLUT);
     }
+    
+    public void redraw(Mask mask) {
+        if (mask != _mask) {
+            _mask = mask;
+            
+            if (_histogramData.getAutoRange()) {
+                double[] minMaxLUT = _histogramData.getMinMaxLUT(); //TODO too much repeated code from "redisplay()"
+                minMaxLUT = PaletteFix.adjustMinMax(minMaxLUT[0], minMaxLUT[1]);
+                if (_colorizeGrayScale) {
+                    // redraw all images with new LUT
+                    for (IColorizedFittedImage fittedImage : _fittedImages) {
+                        fittedImage.setMinAndMax(minMaxLUT[0], minMaxLUT[1]); //TODO we are redrawing all images anyway, then the current one again below...
+                    }
+                }
+                else {
+                    // when using a FloatProcessor the LUT belongs to entire stack
+                    _fittedImage.setMinAndMax(minMaxLUT[0], minMaxLUT[1]);
+                }
+            }
+
+            for (int y = 0; y < _values[0].length; ++y) {
+                for (int x = 0; x < _values.length; ++x) {
+                    double value = Double.NaN;
+                    if (null == mask || mask.test(x, y)) {
+                        value = _values[x][y];
+                    }
+                    _fittedImage.draw(x, y, value);
+                }
+            }
+
+            //TODO
+            System.out.println("imagePlus.setProcessor etc.");
+            _imagePlus.setProcessor(_fittedImage.getImageProcessor().duplicate()); 
+        }
+    }
 
     //TODO MASK

trunk/projects/slim-plugin/src/main/java/loci/slim/fitting/images/IFittedImage.java

@@ -38 +38 @@
 
 import loci.slim.histogram.HistogramDataGroup;
+import loci.slim.mask.Mask;
 
 /**
@@ -106 +107 @@
 
     /**
-     * Redisplays the image.
+     * Redisplays the image after a LUT change.
      */
     public void redisplay();
+    
+    /**
+     * Redisplays the image after masking.
+     * 
+     * @param mask
+     */
+    public void redraw(Mask mask);
 
     /**

trunk/projects/slim-plugin/src/main/java/loci/slim/histogram/HistogramDataNode.java

@@ -35 +35 @@
 package loci.slim.histogram;
 
+import loci.slim.fitting.images.IFittedImage;
 import loci.slim.mask.IMaskGroup;
 import loci.slim.mask.IMaskNode;
@@ -49 +50 @@
  */
 public class HistogramDataNode {
+    private IFittedImage _fittedImage;
     private double[][] _values;
     private IMaskNode _maskNode;
@@ -65 +67 @@
      * will be incorrect.
      * 
+     * @param fittedImage
      * @param values 
      */
-    public HistogramDataNode(double[][] values) {
+    public HistogramDataNode(IFittedImage fittedImage, double[][] values) {
+        _fittedImage = fittedImage;
         _values = values;
     }
-    
+
+    /**
+     * Assigns a mask group.
+     * 
+     * @param maskGroup 
+     */
     public void setMaskGroup(IMaskGroup maskGroup) {
+        // create a new mask node that listens to the group
         _maskNode = new MaskNode(maskGroup, new IMaskNodeListener () {
             public void updateMask(Mask mask) {
                 System.out.println("HistogramDataNode.setMaskGroup IMaskNodeListener.updateMask " + mask);
+                if (null != mask) {
+                    boolean[][] bits = mask.getBits();
+                    if (null != bits) {
+                        System.out.println("mask excludes " + countBits(bits));
+                    }
+                }
                 setOtherMask(mask);
                 //TODO redraw, here or in setOtherMask()
+                _fittedImage.redraw(mask);
             }
         });
@@ -111 +128 @@
         _otherMask = mask;
         if (null == _selfMask) {
+            // no self, so total mask is just other
             _totalMask = mask;
         }
         else {
+            // total mask is self plus other
             _totalMask = _selfMask.add(mask);
         }
@@ -145 +164 @@
         }
 
-        System.out.println("I am " + this + " setSelfMask, total mask excludes " + countBits(_totalMask.getBits()));
+        System.out.print("I am " + this);
+        if (null != _totalMask) System.out.print(" setSelfMask, total mask excludes " + countBits(_totalMask.getBits()));
+        System.out.println();
     }
     

trunk/projects/slim-plugin/src/main/java/loci/slim/mask/MaskGroup.java

@@ -68 +68 @@
     @Override
     public void updateMask(IMaskNode node, Mask mask) {
+        checkMask("incoming", mask);
         // update map with given mask
         _maskMap.put(node, mask);
 
-        // combine maska and notify other nodes
-        for (IMaskNode otherNode : _nodeList) {
-            System.out.println("MaskGroup.updateMask, consider " + otherNode);
+        // combine masks and notify other nodes
+        for (IMaskNode peerNode : _nodeList) {
+            System.out.println("MaskGroup.updateMask, consider " + peerNode);
             // don't notify the caller
-            if (otherNode != node) {
+            if (peerNode != node) {
                 // don't combine the recipients mask
-                Mask combinedMask = Mask.addOtherMasks(mask, _maskMap.values());
+                Mask peerMask = _maskMap.get(peerNode);
+                Mask combinedMask = Mask.addOtherMasks(peerMask, _maskMap.values());
+                checkMask("combined", combinedMask);
                 System.out.println("MaskGroup.updateMask, notify " + combinedMask);
-                otherNode.updateOtherMask(combinedMask);
+                peerNode.updateOtherMask(combinedMask);
             }
+            else System.out.println("MaskGroup.updateMask, originating node " + node + " skipped");
         }
 
 
     }
+    
+    private void checkMask(String title, Mask mask) {
+        int trues = 0;
+        int falses = 0;
+        if (null == mask) {
+            System.out.println("Mask is null");
+            return;
+        }
+        boolean[][] bits = mask.getBits();
+        if (null == bits) {
+            System.out.println("mask has null bits");
+            return;
+        }
+        for (int y = 0; y < bits[0].length; ++y) {
+            for (int x = 0; x < bits.length; ++x) {
+                if (bits[x][y]) {
+                    ++trues;
+                }
+                else {
+                    ++falses;
+                }
+            }
+        }
+        System.out.println(title + " mask has " + trues + " trues " + falses + " falses");
+    }
 }

trunk/projects/slim-plugin/src/main/java/loci/slim/ui/DecayGraph.java

@@ -38 +38 @@
 import java.awt.BasicStroke;
 import java.awt.Color;
+import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.Graphics2D;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 import java.awt.event.MouseEvent;
 import java.awt.geom.Ellipse2D;
 import java.awt.geom.Rectangle2D;
-
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import javax.swing.BoxLayout;
+
+
+import javax.swing.JCheckBox;
 import javax.swing.JComponent;
 import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
 import javax.swing.SwingUtilities;
 
@@ -114 +125 @@
     XYSeriesCollection _residualDataset;
 
-    JFreeChart m_decayChart;
-    JFreeChart m_residualsChart;
+    JTextField _photonTextField;
+    JCheckBox _logCheckBox;
 
     /**
@@ -179 +190 @@
             // create a frame for the chart
             _frame = new JFrame();
-            _frame.getContentPane().add(layer);
+            Container container = _frame.getContentPane();
+            container.setLayout(new BoxLayout(container, BoxLayout.PAGE_AXIS));
+            container.add(layer);
+            
+            JPanel miscPane = new JPanel();
+            miscPane.setLayout(new FlowLayout());
+            JLabel label = new JLabel("Photon count:");
+            miscPane.add(label);
+            _photonTextField = new JTextField(7);
+            _photonTextField.setEditable(false);
+            miscPane.add(_photonTextField);
+            _logCheckBox = new JCheckBox("Logarithmic");
+            _logCheckBox.setSelected(_logarithmic);
+            _logCheckBox.addItemListener(new ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    _logarithmic = _logCheckBox.isSelected();
+                    NumberAxis photonAxis;
+                    if (_logarithmic) {
+                        photonAxis = new LogarithmicAxis(PHOTON_AXIS_LABEL);
+                    }
+                    else {
+                        photonAxis = new NumberAxis(PHOTON_AXIS_LABEL);
+                    }
+                    _decaySubPlot.setRangeAxis(photonAxis);
+                }
+            });
+            miscPane.add(_logCheckBox);
+            container.add(miscPane);
+
             _frame.setSize(FRAME_SIZE);
             _frame.pack();
@@ -223 +262 @@
         createDatasets(_bins, _timeInc, data);
 
+    }
+
+    /**
+     * Sets the displayed photon count.
+     * 
+     * @param photons 
+     */
+    public void setPhotons(int photons) {
+        _photonTextField.setText("" + photons);
+    }
+
+    /*
+     * Sets whether vertical axis should be logarithmic.
+     * 
+     * @param logarithmic
+     */
+    public void setLogarithmic(boolean logarithmic) {
+        _logarithmic = logarithmic;
     }
 

trunk/projects/slim-plugin/src/main/java/loci/slim/ui/IDecayGraph.java

@@ -75 +75 @@
     
     /**
+     * Sets number of photons in fit.
+     * 
+     * @param photons
+     */
+    public void setPhotons(int photons);
+    
+    /**
      * Changes (or initializes) the start and stop vertical bars.
      *