Changeset 7672

Timestamp:

03/24/11 22:04:01 (9 years ago)

Author:

aivar

Message:

Loading/using IRFs. Estimate decay cursors.

Location:

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

Files:

• CursorHelper.java (modified) (4 diffs)
• DecayGraph.java (modified) (5 diffs)
• SLIMProcessor.java (modified) (12 diffs)
• ui/ExcitationPanel.java (modified) (1 diff)

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

@@ -120 +120 @@
         returnValue[2] = baseline;
         return returnValue;
+    }
+
+    public static int[] estimateDecayCursors(float xInc, double[] decay) {
+        int maxIndex = findMax(decay);
+        double[] diffed = new double[maxIndex];
+        // "Differentiate"
+        for (int i = 0; i < maxIndex - 1; ++i) {
+            diffed[i] = decay[i + 1] - decay[i];
+        }
+        int steepIndex = findMax(diffed);
+
+        int startIndex = 2 * maxIndex - steepIndex;
+        int stopIndex = 9 * decay.length / 10;
+
+        // sanity check
+        if (startIndex > stopIndex) {
+            startIndex = stopIndex - 1;
+        }
+        if (startIndex < 0) {
+            startIndex = 0;
+        }
+
+        return new int[] { startIndex, stopIndex };
     }
 
@@ -216 +239 @@
         }
 
-            // save estimates //TODO not in original
+        System.out.println("steepest prompt " + steepp + " steepest transient " + steept);
+        System.out.println("startt is " + startt);
+        System.out.println("   startp " + startp + " endp " + endp + " baseline " + baseline);
+
+        // "Now we've got estimates we can do some Marquardt fitting to fine-tune
+        // the estimates"
+
+        transStartIndex = startt - ATTEMPTS;
+        if (transStartIndex < 0) {
+            transStartIndex = 0;
+        }
+        transEndIndex = 9 * decay.length / 10; // "90% of transient"
+        if (transEndIndex <= transStartIndex + 2 * ATTEMPTS) { // "oops"
             returnValue[0] = startp;
             returnValue[1] = endp;
             returnValue[2] = baseline;
             returnValue[3] = startt;
-            returnValue[4] = endt; //TODO ITS JUST ZERO HERE!!
-
-        // "Now we've got estimates we can do some Marquardt fitting to fine-tune
-        // the estimates"
-
-        transStartIndex = startt - ATTEMPTS;
-        if (transStartIndex < 0) {
-            transStartIndex = 0;
-        }
-        transEndIndex = 9 * decay.length / 10; // "90% of transient"
-        if (transEndIndex <= transStartIndex + 2 * ATTEMPTS) { // "oops"
-            System.out.println("oops return");
+            returnValue[4] = transEndIndex;
             return returnValue; //TODO "do_estimate_resets; do_estimate_frees; "
         }
 
+        System.out.println("prompt " + prompt.length + " decay " + decay.length);
+
+        //TODO convert everything to float, not double
+        double[] response = new double[decay.length];
+        for (int n = 0; n < decay.length; ++n) {
+            response[n] = decay[index];
+        }
+
         for (i = 0; i < 2 * ATTEMPTS + 1; ++i, ++transStartIndex) {
 
             transFitStartIndex = transStartIndex;
+            System.out.println("transStartIndex " + transStartIndex + " transFitStartIndex " + transFitStartIndex + " transEndIndex " + transEndIndex);
 
             int fitStart = transFitStartIndex - transStartIndex;
             int fitStop = transEndIndex - transStartIndex;
             int nData = transEndIndex - transStartIndex;
-            System.out.println("fitStart " + fitStart + " fitStop " + fitStop + " nData " + nData);
+            System.out.println("  fitStart " + fitStart + " fitStop " + fitStop + " nData " + nData);
 
             CurveFitData curveFitData = new CurveFitData();
@@ -255 +288 @@
             curveFitter.setXInc(xInc);
             curveFitter.setFree(free);
+            curveFitter.setInstrumentResponse(response);
 
             int ret = curveFitter.fitData(data, fitStart, fitStop);
@@ -276 +310 @@
             }
             System.out.println("index is " + index);
-            return null; //TODO do estimate resets/frees???
+            returnValue[0] = startp;
+            returnValue[1] = endp;
+            returnValue[2] = baseline;
+            returnValue[3] = startt;
+            returnValue[4] = transEndIndex;
+            return returnValue; //TODO do estimate resets/frees???
         }
 

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

@@ -105 +105 @@
      * @param data fitted data
      */
-    DecayGraph(final String title, final int start, final int stop, final int bins, final double timeInc, ICurveFitData data) {
+    DecayGraph(final String title, final int start, final int stop, final int bins, final double timeInc, final double[] irf, ICurveFitData data) {
         m_start = start;
         m_stop = stop;
@@ -111 +111 @@
 
         // create the combined chart
-        JFreeChart chart = createCombinedChart(start, stop, bins, timeInc, data); //TODO got ugly; rethink params, globals etc
+        JFreeChart chart = createCombinedChart(start, stop, bins, timeInc, irf, data); //TODO got ugly; rethink params, globals etc
         m_panel = new ChartPanel(chart, true, true, true, false, true);
         m_panel.setDomainZoomable(false);
@@ -184 +184 @@
      * @return the chart
      */
-    JFreeChart createCombinedChart(int start, int stop, int bins, double timeInc, ICurveFitData data) {
+    JFreeChart createCombinedChart(int start, int stop, int bins, double timeInc, double[] irf, ICurveFitData data) {
 
         // create chart data
-        createDatasets(start, stop, bins, timeInc, data);
+        createDatasets(start, stop, bins, timeInc, irf, data);
 
         // make a common horizontal axis for both sub-plots
@@ -253 +253 @@
      * @param data from the fit
      */
-    private void createDatasets(int start, int stop, int bins, double timeInc, ICurveFitData data) {
-        //TODO lamp function; comes from where?
+    private void createDatasets(int start, int stop, int bins, double timeInc, double[] irf, ICurveFitData data) {
+
         XYSeries series1 = new XYSeries("IRF");
-   /*     series1.add(1.0, 1.0);
-        series1.add(2.0, 4.0);
-        series1.add(3.0, 3.0);
-        series1.add(4.0, 5.0);
-        series1.add(5.0, 5.0);
-        series1.add(6.0, 7.0);
-        series1.add(7.0, 7.0);
-        series1.add(8.0, 8.0); */
+        double xCurrent = 0;
+        if (null != irf) {
+            for (int i = 0; i < bins; ++i) {
+                if (irf[i] > 0.0) {
+                    series1.add(xCurrent, irf[i]);
+                }
+                xCurrent += timeInc;
+            }
+        }
 
         XYSeries series2 = new XYSeries("Fitted");
@@ -269 +270 @@
         XYSeries series4 = new XYSeries("Residuals");
 
-
         double yData, yFitted;
-        double xCurrent = 0;
+        xCurrent = 0;
         for (int i = 0; i < bins; ++i) {
             yData = data.getYCount()[i];

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

@@ -343 +343 @@
         );
 
+        // set start and stop for now; will be updated if we load an excitation curvce
+        updateDecayCursors(uiPanel);
+
         // processing loop; waits for UI panel input
         while (!m_quit) {
@@ -373 +376 @@
     }
 
+    private void updateDecayCursors(IUserInterfacePanel uiPanel) {
+        // sum selected channel
+        double[] decay = new double[m_timeBins];
+        for (int i = 0; i < decay.length; ++i) {
+            decay[i] = 0.0;
+        }
+        for (int y = 0; y < m_height; ++y) {
+            for (int x = 0; x < m_width; ++x) {
+                for (int b = 0; b < m_timeBins; ++b) {
+                    decay[b] += getData(m_cursor, m_channel, x, y, b);
+                }
+            }
+        }
+
+        int[] results = CursorHelper.estimateDecayCursors(m_timeRange, decay);
+        uiPanel.setStart(results[0]);
+        uiPanel.setStop(results[1]);
+    }
+
     private boolean updateExcitation(IUserInterfacePanel uiPanel, Excitation excitation) {
         boolean success = false;
@@ -398 +420 @@
             excitation.setBase(results[2]);
 
-            uiPanel.setStart(22);
-            uiPanel.setStop(33);
+            uiPanel.setStart((int) results[3]);
+            uiPanel.setStop((int) results[4]);
 
             m_excitationPanel = new ExcitationPanel(excitation);
@@ -660 +682 @@
         double yFitted[];
         
-        // sum up all the photons
+        // sum up all the photons for all the pixels
         curveFitData = new CurveFitData();
         curveFitData.setParams(params);
@@ -668 +690 @@
         }
         int photons = 0;
-        
+        int pixels = 0;
         if (-1 == m_channel) {
             // sum all of the channels
@@ -679 +701 @@
                             photons += (int) count;
                         }
+                        ++pixels;
                     }
                 }
@@ -692 +715 @@
                         photons += (int) count;
                     }
+                    ++pixels;
                 }
             }    
         }
-        System.out.println("Summed photons " + photons);
+        System.out.println("Summed photons " + photons + " Summed pixels " + pixels);
 
         curveFitData.setYCount(yCount);
@@ -711 +735 @@
 
         // show decay and update UI parameters
-        showDecayGraph("Summed ", uiPanel, dataArray, 0);
+        double[] irf = null;
+        if (null != m_excitationPanel) {
+            irf = m_excitationPanel.getValues();
+        }
+        showDecayGraph("Summed ", uiPanel, irf, dataArray, 0);
         uiPanel.setParameters(dataArray[0].getParams());
 
@@ -771 +799 @@
 
         // show the decay graphs
+        double[] irf = null;
+        if (null != m_excitationPanel) {
+            irf = m_excitationPanel.getValues();
+        }
         double min = Double.MAX_VALUE;
         double max = Double.MIN_VALUE;
         roiNumber = 1;
         for (Roi roi: getRois()) {
-            showDecayGraph("Roi " + roiNumber, uiPanel, dataArray, roiNumber - 1);
+            showDecayGraph("Roi " + roiNumber, uiPanel, irf, dataArray, roiNumber - 1);
             double lifetime = dataArray[roiNumber - 1].getParams()[3];
             if (lifetime < min) {
@@ -858 +890 @@
         getCurveFitter(uiPanel).fitData(dataArray, m_startBin, m_stopBin);
 
-        // show decay graph for visible channel //TODO need m_visibleChannel or the like        
-        showDecayGraph("Pixel " + x + " " + y, uiPanel, dataArray, 0);
+        // show decay graph for visible channel //TODO need m_visibleChannel or the like
+        double irf[] = null;
+        if (null != m_excitationPanel) {
+            irf = m_excitationPanel.getValues();
+        }
+        showDecayGraph("Pixel " + x + " " + y, uiPanel, irf, dataArray, 0);
 
         // update UI parameters
@@ -1442 +1478 @@
         curveFitter.setXInc(m_timeRange);
         curveFitter.setFree(translateFree(uiPanel.getFunction(), uiPanel.getFree()));
+        if (null != m_excitationPanel) {
+            curveFitter.setInstrumentResponse(m_excitationPanel.getValues());
+        }
         return curveFitter;
     }
@@ -1499 +1538 @@
      * @param index to show
      */
-    private void showDecayGraph(String title, final IUserInterfacePanel uiPanel, ICurveFitData dataArray[], int index) {
+    private void showDecayGraph(String title, final IUserInterfacePanel uiPanel, double irf[], ICurveFitData dataArray[], int index) {
         if (index < dataArray.length) {
-            DecayGraph decayGraph = new DecayGraph(title, m_startBin, m_stopBin, m_timeBins, m_timeRange, dataArray[index]);
+            DecayGraph decayGraph = new DecayGraph(title, m_startBin, m_stopBin, m_timeBins, m_timeRange, irf, dataArray[index]);
             decayGraph.setStartStopListener(
                 new IStartStopListener() {

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

@@ -128 +128 @@
     }
 
+    public double[] getValues() {
+        float floatValues[] = m_excitation.getValues();
+        double[] values = new double[floatValues.length];
+        for (int i = 0; i < values.length; ++i) {
+            if (i < m_start || i >= m_stop) {
+                values[i] = 0.0;
+            }
+            else if (floatValues[i] > m_base) {
+                values[i] = floatValues[i];
+            }
+            else {
+                values[i] = 0.0;
+            }
+        }
+        return values;
+    }
+
     /*
      * Creates a panel with file name.