Changeset 7079

Timestamp:

10/15/10 21:15:59 (9 years ago)

Author:

aivar

Message:

Many changes to SLIMProcessor, mostly for automatic plugin.

File:

• branches/maven/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java (modified) (12 diffs)

branches/maven/projects/slim-plugin/src/main/java/loci/slim/SLIMProcessor.java

@@ -35 +35 @@
 package loci.slim;
 
-//TODO need to add fiji-lib.jar to maven repository:
-//import fiji.util.gui.GenericDialogPlus;
-
 import ij.IJ;
 import ij.ImagePlus;
@@ -49 +46 @@
 import ij.process.ImageProcessor;
 
+import imagej.process.ImageUtils;
+
 import imagej.io.ImageOpener;
 
@@ -58 +57 @@
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.prefs.Preferences;
 
@@ -68 +70 @@
 import loci.slim.ui.IStartStopListener;
 import loci.slim.ui.IUserInterfacePanel;
-import loci.slim.ui.IUserInterfacePanelListener;
 import loci.slim.ui.UserInterfacePanel;
 import loci.common.DataTools;
@@ -84 +85 @@
 import loci.formats.IFormatReader;
 
-import mpicbg.imglib.cursor.Cursor;
 import mpicbg.imglib.cursor.LocalizableByDimCursor;
 import mpicbg.imglib.image.Image;
-//import mpicbg.imglib.Type;
 import mpicbg.imglib.type.numeric.RealType;
+
+import net.java.sezpoz.Index;
+import net.java.sezpoz.IndexItem;
 
 /**
@@ -100 +102 @@
  */
 public class SLIMProcessor <T extends RealType<T>> implements MouseListener {
-//public class SLIMProcessor <T extends Type> {
     private static final String X = "X";
     private static final String Y = "Y";
@@ -156 +157 @@
     private int m_minWave, m_waveStep; //, m_maxWave;
 
-    // fit parameters
-   // private int m_numExp;
-   // private int m_binRadius;
-   // private int m_cutBins;
-   // private int m_maxPeak;
-
-
     public enum FitRegion {
         SUMMED, ROI, POINT, EACH
@@ -194 +188 @@
     private int m_debug = 0;
 
-    /**
-     * Run thread for the plugin.
-     *
-     * @param arg
-     */
-    public void run(String arg) {
+    public SLIMProcessor() {
         m_fitInProgress = false;
         m_fitted = false;
-
-        IUserInterfacePanel uiPanel = new UserInterfacePanel(true);
-        JPanel panel = uiPanel.getPanel();
-        
-        m_channel = 0; //TODO s/b a JSlider that controls current channel
-        
+    }
+
+    public void processImage(Image<T> image) {
         boolean success = false;
-        if (showFileDialog(getFileFromPreferences())) {
-            if (m_fakeData) {
-                fakeData();
-                success = true;
-            }
-            else {
-                if (newLoadData(m_file)) {
-                    saveFileInPreferences(m_file);
-                    success = true;
-                }
-            }
-        }
-        
-        if (success) {
+System.out.println("processImage " + image);
+        if (newLoadData(image)) {
             // create a grayscale image from the data
             createGlobalGrayScale();
@@ -237 +211 @@
             }
         }
-
-        // ask for which file to load
-       /* if (showFileDialog(getFileFromPreferences())) {
-            // load the file
-            if (loadFile(m_file)) {
-                if (m_fakeData) {
-                    fakeData();
-                }
-                else {
-                    saveFileInPreferences(m_file);
-                }
-                // show parameters from file
-                if (showParamsDialog()) {
-                    if (!m_fakeData) {
-                        loadData();
-                    }
-                    // create a grayscale image from the data
-                    createGlobalGrayScale();
-                    while (true) {
-                        // ask what kind of fit
-                        if (!showFitDialog()) {
-                            break;
-                        }
-                        // ask for fit parameters
-                        if (!showFitParamsDialog()) {
-                            break;
-                        }
-                        fitData();
-                    }
-                }
-            }
-            else {
-                //TODO shouldn't UI be separate?
-                IJ.error("File Error", "Unable to load file.");
-            }
-        }*/
-    }
-
-    /**
-     * Prompts for a .sdt file.
-     *
-     * @param defaultFile
-     * @return
-     */
-    private boolean showFileDialog(String defaultFile) {
-        //TODO shouldn't UI be in separate class?
-        //TODO need to include fiji-lib.jar in repository:
-        //GenericDialogPlus dialog = new GenericDialogPlus("Load Data");
-        GenericDialog dialog = new GenericDialog("Load Data");
-        //TODO works with GenericDialogPlus, dialog.addFileField("File:", defaultFile, 24);
-        dialog.addStringField("File", defaultFile);
-        dialog.addCheckbox("Fake data", m_fakeData);
-        dialog.showDialog();
-        if (dialog.wasCanceled()) {
-            return false;
-        }
-
-        m_file = dialog.getNextString();
-        m_fakeData = dialog.getNextBoolean();
-
-        return true;
-    }
-
-    private boolean newLoadData(String file) {
-        ImageOpener imageOpener = new ImageOpener();
-        Image<T> image = null;
-        try {
-            image = imageOpener.openImage(file);
-        }
-        catch (Exception e) {
-            System.out.println("Error " + e.getMessage());
-        }
-
-        int[] dimensions = image.getDimensions();
-        Map map = dimensionMap(image.getName());
-        Integer xIndex, yIndex, lifetimeIndex, channelIndex;
-        xIndex = (Integer) map.get(X);
-        yIndex = (Integer) map.get(Y);
-        lifetimeIndex = (Integer) map.get(LIFETIME);
-        if (null != xIndex && null != yIndex && null != lifetimeIndex) {
-            m_width = dimensions[xIndex];
-            m_height = dimensions[yIndex];
-            m_timeBins = dimensions[lifetimeIndex];
-        }
-        else {
-            System.out.println("Can't find dimensions of .sdt Image " + image.getName());
-            return false;
-        }
-        m_channels = 1;
-        channelIndex = (Integer) map.get(CHANNELS);
-        if (null != channelIndex) {
-            m_channels = dimensions[channelIndex];
-        }
-
-        System.out.println("width " + m_width + " height " + m_height + " timeBins " + m_timeBins + " channels " + m_channels);
+        /*
+        m_width = ImageUtils.getWidth(image);
+        m_height = ImageUtils.getHeight(image);
+        m_timeBins = ImageUtils.getDimSize(image, FormatTools.LIFETIME, 0);
+        
         m_data = new int[m_channels][m_height][m_width][m_timeBins];
-        final LocalizableByDimCursor<T> cursor = image.createLocalizableByDimCursor();
+        final LocalizableByDimCursor<?> cursor = image.createLocalizableByDimCursor();
         int x, y, bin, channel;
         for (channel = 0; channel < m_channels; ++channel) {
@@ -354 +238 @@
             }
         }
+
+        // patch things up
+        m_timeRange = 10.0f;
+        m_minWave = 400;
+        m_waveStep = 10;
+        */
+    }
+
+    /**
+     * Run method for the plugin.  Throws up a file dialog.
+     *
+     * @param arg
+     */
+    public void process(String arg) {
+        //IUserInterfacePanel uiPanel = new UserInterfacePanel(true);
+        //JPanel panel = uiPanel.getPanel();
+        
+        m_channel = 0; //TODO s/b a JSlider that controls current channel
+        
+        boolean success = false;
+        if (showFileDialog(getFileFromPreferences())) {
+            if (m_fakeData) {
+                fakeData();
+                success = true;
+            }
+            else {
+                if (newLoadData(loadImage(m_file))) {
+                    saveFileInPreferences(m_file);
+                    success = true;
+                }
+            }
+        }
+        
+        if (success) {
+            // create a grayscale image from the data
+            createGlobalGrayScale();
+            while (true) {
+                // ask what kind fo fit
+                if (!showFitDialog()) {
+                    break;
+                }
+                // ask for fit parameters
+                if (!showFitParamsDialog()) {
+                    break;
+                }
+                fitData();
+            }
+        }
+    }
+
+    /**
+     * Prompts for a .sdt file.
+     *
+     * @param defaultFile
+     * @return
+     */
+    private boolean showFileDialog(String defaultFile) {
+        //TODO shouldn't UI be in separate class?
+        //TODO need to include fiji-lib.jar in repository:
+        //GenericDialogPlus dialog = new GenericDialogPlus("Load Data");
+        GenericDialog dialog = new GenericDialog("Load Data");
+        //TODO works with GenericDialogPlus, dialog.addFileField("File:", defaultFile, 24);
+        dialog.addStringField("File", defaultFile);
+        dialog.addCheckbox("Fake data", m_fakeData);
+        dialog.showDialog();
+        if (dialog.wasCanceled()) {
+            return false;
+        }
+
+        m_file = dialog.getNextString();
+        m_fakeData = dialog.getNextBoolean();
+
+        return true;
+    }
+
+    private Image<T> loadImage(String file) {
+        ImageOpener imageOpener = new ImageOpener();
+        Image<T> image = null;
+        try {
+            image = imageOpener.openImage(file);
+        }
+        catch (Exception e) {
+            System.out.println("Error " + e.getMessage());
+        }
+        return image;
+    }
+   
+    private boolean newLoadData(Image<T> image) {
+        int[] dimensions = image.getDimensions();
+        System.out.println("dimensions size is " + dimensions.length);
+        /*
+        Map map = dimensionMap(image.getName());
+        Integer xIndex, yIndex, lifetimeIndex, channelIndex;
+        xIndex = (Integer) map.get(X);
+        yIndex = (Integer) map.get(Y);
+        lifetimeIndex = (Integer) map.get(LIFETIME);
+        if (null != xIndex && null != yIndex && null != lifetimeIndex) {
+            m_width = dimensions[xIndex];
+            m_height = dimensions[yIndex];
+            m_timeBins = dimensions[lifetimeIndex];
+        }
+        else {
+            System.out.println("Can't find dimensions of .sdt Image " + image.getName());
+            return false;
+        }
+        m_channels = 1;
+        channelIndex = (Integer) map.get(CHANNELS);
+        if (null != channelIndex) {
+            System.out.println("Do have channel dimension");
+            m_channels = dimensions[channelIndex];
+        }
+        else System.out.println("Don't have channel dimension");
+        */
+        Integer xIndex, yIndex, lifetimeIndex, channelIndex;
+        m_width = ImageUtils.getWidth(image);
+        m_height = ImageUtils.getHeight(image);
+        m_channels = ImageUtils.getNChannels(image);
+        m_timeBins = ImageUtils.getDimSize(image, FormatTools.LIFETIME);
+        System.out.println("timeBins is " + m_timeBins);
+        int index = 0;
+        xIndex = index++;
+        yIndex = index++;
+        if (m_channels > 1) {
+            channelIndex = index++;
+        }
+        else {
+            channelIndex = null;
+        }
+        lifetimeIndex = index;
+
+        System.out.println("width " + m_width + " height " + m_height + " timeBins " + m_timeBins + " channels " + m_channels);
+        m_data = new int[m_channels][m_height][m_width][m_timeBins];
+        final LocalizableByDimCursor<T> cursor = image.createLocalizableByDimCursor();
+        int x, y, bin, channel;
+        for (channel = 0; channel < m_channels; ++channel) {
+            if (null != channelIndex) {
+                dimensions[channelIndex] = channel;
+            }
+            for (y = 0; y < m_height; ++y) {
+                dimensions[yIndex] = y;
+                for (x = 0; x < m_width; ++x) {
+                    dimensions[xIndex] = x;
+                    for (bin = 0; bin < m_timeBins; ++bin) {
+                        dimensions[lifetimeIndex] = bin;
+                        cursor.moveTo(dimensions);
+                        m_data[channel][y][x][bin] = (int) cursor.getType().getRealFloat();
+                    }
+                }
+            }
+        }
         cursor.close();
         // print out some useful information about the image
@@ -364 +398 @@
         // patch things up
         m_timeRange = 10.0f;
+        m_minWave = 400;
+        m_waveStep = 10;
 
         return true;
@@ -371 +407 @@
      * This method parses a string of the format:
      * "Name [X Y Timebins]" and builds a map with
-     * the dimensions 'X', 'Y', and 'Timebins'.
+     * the dimensions 'X', 'Y', and 'Timebins' mapped
+     * to the dimension indices.
      *
      * Temporary kludge.
      */
-    private Map dimensionMap(String name) {
-        Map map = new HashMap<String, Integer>();
+    private Map<String, Integer> dimensionMap(String name) {
+        System.out.println("name is " + name);
+        Map<String, Integer> map = new HashMap<String, Integer>();
         int startIndex = name.indexOf('[') + 1;
         int endIndex = name.indexOf(']');