Changeset 7663 for trunk

Timestamp:

03/21/11 20:26:18 (9 years ago)

Author:

aivar

Message:

Export to text working.

Location:

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

Files:

• SLIMProcessor.java (modified) (13 diffs)
• analysis/plugins/ExportToText.java (modified) (4 diffs)

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

@@ -578 +578 @@
      */
     private Image<DoubleType> fitSummed(IUserInterfacePanel uiPanel) {
+        Image<DoubleType> fittedPixels = null;
         double params[] = uiPanel.getParameters(); //TODO go cumulative
         
@@ -626 +627 @@
         yFitted = new double[m_timeBins];
         curveFitData.setYFitted(yFitted);
+        //int nominalChannel = (-1 == m_channel) ? channel : 0;
+        curveFitData.setChannel(0);
+        curveFitData.setX(0);
+        curveFitData.setY(0);
         curveFitDataList.add(curveFitData);
 
@@ -635 +640 @@
         showDecayGraph("Summed ", uiPanel, dataArray, 0);
         uiPanel.setParameters(dataArray[0].getParams());
-        return null;
+
+        // get the results
+        //int channels = (-1 == m_channel) ? m_channels : 1; //TODO s/b summed for each channel, rather than summing all channels together???
+        //fittedPixels = makeImage(channels, 1, 1, uiPanel.getParameterCount()); //TODO ImgLib bug if you use 1, 1, 1, 4; see "imglibBug()" below.
+        fittedPixels = makeImage(2, 2, 2, uiPanel.getParameterCount()); //TODO this is a workaround; unused pixels will remain NaNs
+        LocalizableByDimCursor<DoubleType> resultsCursor = fittedPixels.createLocalizableByDimCursor();
+        setFittedParamsFromData(resultsCursor, dataArray);
+        return fittedPixels;
     }
 
@@ -642 +654 @@
      */
     private Image<DoubleType> fitROIs(IUserInterfacePanel uiPanel) {
+        Image<DoubleType> fittedPixels = null;
         double params[] = uiPanel.getParameters();
         
@@ -651 +664 @@
         
         int roiNumber = 1;
+        int channel = (-1 == m_channel) ? 0 : m_channel; //TODO better than crashing; need a better channel strategy
+        int outputX = 0;
         for (Roi roi: getRois()) {
             curveFitData = new CurveFitData();
@@ -662 +677 @@
                 for (int y = 0; y < bounds.height; ++y) {
                     if (roi.contains(bounds.x + x, bounds.y + y)) {
-                        System.out.println("roi " + roiNumber + " x " + x + " Y " + y);
                         for (int b = 0; b < m_timeBins; ++b) {
-                            yCount[b] += getData(m_cursor, m_channel, x, y, b);
+                            yCount[b] += getData(m_cursor, channel, x, y, b);
                         }
                     }
@@ -672 +686 @@
             yFitted = new double[m_timeBins];
             curveFitData.setYFitted(yFitted);
+            curveFitData.setChannel(0);
+            curveFitData.setX(outputX++);
+            curveFitData.setY(0);
             curveFitDataList.add(curveFitData);
             ++roiNumber;
@@ -722 +739 @@
         // update UI parameters
         uiPanel.setParameters(dataArray[0].getParams()); //TODO, just picked first ROI here!
-        return null;
+
+        // get the results
+        //int channels = (-1 == m_channel) ? m_channels : 1; //TODO need a proper channel strategy
+        //fittedPixels = makeImage(channels, 1, 1, uiPanel.getParameterCount()); //TODO ImgLib bug if you use 1, 1, 1, 4; see "imglibBug()" below.
+        fittedPixels = makeImage(2, getRois().length + 1, 2, uiPanel.getParameterCount()); //TODO this is a workaround; unused pixels will remain NaNs
+        LocalizableByDimCursor<DoubleType> resultsCursor = fittedPixels.createLocalizableByDimCursor();
+        setFittedParamsFromData(resultsCursor, dataArray);
+        return fittedPixels;
     }
 
@@ -736 +760 @@
         // build the data
         ArrayList<ICurveFitData> curveFitDataList = new ArrayList<ICurveFitData>();
-        double params[] = uiPanel.getParameters(); //TODO NO NO NO
+        double params[] = uiPanel.getParameters(); //TODO wrong; params should possibly come from already fitted data
         ICurveFitData curveFitData;
         double yCount[];
@@ -742 +766 @@
         for (int channel : getChannelIndices(m_channel, m_channels)) {
             curveFitData = new CurveFitData();
-            curveFitData.setParams(params); //TODO NO NO NO s/b either from UI or fitted point or fitted whole image
+            curveFitData.setParams(params.clone()); //TODO NO NO NO s/b either from UI or fitted point or fitted whole image
             yCount = new double[m_timeBins];
             for (int b = 0; b < m_timeBins; ++b) {
@@ -750 +774 @@
             yFitted = new double[m_timeBins];
             curveFitData.setYFitted(yFitted);
-            int nominalChannel = (-1 == m_channel) ? channel : 1;
+            int nominalChannel = (-1 == m_channel) ? channel : 0;
             curveFitData.setChannel(nominalChannel);
             curveFitData.setX(0);
@@ -771 +795 @@
         //fittedPixels = makeImage(channels, 1, 1, uiPanel.getParameterCount()); //TODO ImgLib bug if you use 1, 1, 1, 4; see "imglibBug()" below.
         fittedPixels = makeImage(channels + 1, 2, 2, uiPanel.getParameterCount()); //TODO this is a workaround; unused pixels will remain NaNs
-
         LocalizableByDimCursor<DoubleType> resultsCursor = fittedPixels.createLocalizableByDimCursor();               
         setFittedParamsFromData(resultsCursor, dataArray);
@@ -777 +800 @@
     }
 
+    /*
+     * Demonstrates a bug with ImgLib:
+     * //TODO fix it!
+     */
     private void imglibBug() {
         int dim[] = { 1, 1, 1, 4 };

trunk/projects/slim-plugin/src/main/java/loci/slim/analysis/plugins/ExportToText.java

@@ -93 +93 @@
 
                 // write headers
-                if (channels > 1) {
+                if (channels > 2) { //TODO s/b 1; workaround for ImgLib bug -> always get 2 channels
                     writeChannelHeader();
                 }
@@ -138 +138 @@
                             //TODO distinguish between not fitted and error in fit!
                             if (!Double.isNaN(paramArray[0])) {
-                                if (channels > 1) {
+                                if (channels > 2) { //TODO see above; this is a hacky workaround for a bug; s/b " > 1"
                                     writeChannel(c + 1);
                                 }
@@ -150 +150 @@
                                         writeROI(x + 1);
                                         writeParams(function, paramArray);
+                                        break;
                                     case EACH:
                                         writeXY(x, y);
@@ -247 +248 @@
 
     private void writeROI(int roi) throws IOException {
-        m_fileWriter.write(roi + '\t');
+        m_fileWriter.write("" + roi + '\t');
     }