Changeset 3177

Timestamp:

09/19/07 10:55:41 (12 years ago)

Author:

melissa

Message:

Added option to reorder stack.

Location:

trunk/loci

Files:

• formats/FormatTools.java (modified) (1 diff)
• plugins/Importer.java (modified) (10 diffs)
• plugins/ImporterOptions.java (modified) (12 diffs)

trunk/loci/formats/FormatTools.java

@@ -326 +326 @@
     for (int i=0; i<lengths.length; i++) len *= lengths[i];
     return len;
+  }
+
+  public static int getReorderedIndex(IFormatReader r, String order, int no)
+    throws FormatException
+  {
+    int[] zct = getZCTCoords(order, r.getSizeZ(), r.getSizeC(), r.getSizeT(),
+      r.getImageCount(), no);
+    return getIndex(r.getDimensionOrder(), r.getSizeZ(), r.getSizeC(),
+      r.getSizeT(), r.getImageCount(), zct[0], zct[1], zct[2]);
   }
 

trunk/loci/plugins/Importer.java

@@ -62 +62 @@
 
   private Vector imps = new Vector();
+  private String stackOrder = null;
 
   // -- Constructor --
@@ -381 +382 @@
 
           int q = 0;
+          stackOrder = options.getStackOrder();
+          if (stackOrder.equals(ImporterOptions.ORDER_DEFAULT)) {
+            stackOrder = r.getDimensionOrder();
+          }
+          if (options.isViewView5D()) {
+            stackOrder = ImporterOptions.ORDER_XYZCT;
+          }
+          if (options.isViewImage5D()) {
+            stackOrder = ImporterOptions.ORDER_XYCZT;
+          }
+
           for (int j=0; j<num[i]; j++) {
             if (!load[j]) continue;
@@ -394 +406 @@
             IJ.showProgress((double) q++ / total);
 
+            int ndx = FormatTools.getReorderedIndex(r, stackOrder, j);
+
             // construct label for this slice
-            int[] zct = r.getZCTCoords(j);
+            int[] zct = r.getZCTCoords(ndx);
             StringBuffer sb = new StringBuffer();
             if (certain[i]) {
@@ -439 +453 @@
 
             // get image processor for jth plane
-            ImageProcessor ip = Util.openProcessor(r, j);
+            ImageProcessor ip = Util.openProcessor(r, ndx);
             if (ip == null) {
               plugin.canceled = true;
@@ -626 +640 @@
     }
 
+    int[][] indices = new int[c][is.getSize() / c];
+    int[] pt = new int[c];
+    Arrays.fill(pt, 0);
+
+    for (int i=0; i<is.getSize(); i++) {
+      int[] zct = FormatTools.getZCTCoords(stackOrder, r.getSizeZ(),
+        r.getSizeC(), r.getSizeT(), r.getImageCount(), i);
+      int cndx = zct[1];
+      indices[cndx][pt[cndx]++] = i;
+    }
+
     for (int i=0; i<c; i++) {
       if (range) {
@@ -636 +661 @@
       }
       else {
-        for (int j=0; j<z; j++) {
-          for (int k=0; k<t; k++) {
-            int s = r.getIndex(j, i, k) + 1;
-            newStacks[i].addSlice(is.getSliceLabel(s), is.getProcessor(s));
-          }
+        for (int j=0; j<indices[i].length; j++) {
+          newStacks[i].addSlice(is.getSliceLabel(indices[i][j] + 1),
+            is.getProcessor(indices[i][j] + 1));
         }
       }
@@ -719 +742 @@
         }
         catch (ReflectException exc) {
-          imp = new CustomImage(imp, r.getDimensionOrder(), r.getSizeZ(),
+          imp = new CustomImage(imp, stackOrder, r.getSizeZ(),
             r.getSizeT(), r.getSizeC());
         }
       }
       else {
-        imp = new CustomImage(imp, r.getDimensionOrder(), r.getSizeZ(),
+        imp = new CustomImage(imp, stackOrder, r.getSizeZ(),
           r.getSizeT(), r.getSizeC());
       }
@@ -753 +776 @@
     if (options.isViewBrowser()) { }
     else if (options.isViewImage5D()) {
-      int sizeZ = r.getSizeZ();
-      int sizeT = r.getSizeT();
-      int sizeC = r.getSizeC();
-      if (imp.getStackSize() == sizeZ * sizeT) sizeC = 1;
-
-      // reorder stack to Image5D's preferred order: XYCZT
-      ImageStack is;
-      ImageStack stack = imp.getStack();
-      if (r.getDimensionOrder().equals("XYCZT")) is = stack;
-      else {
-        is = new ImageStack(r.getSizeX(), r.getSizeY());
-        for (int t=0; t<sizeT; t++) {
-          for (int z=0; z<sizeZ; z++) {
-            for (int c=0; c<sizeC; c++) {
-              int ndx = r.getIndex(z, c, t) + 1;
-              is.addSlice(stack.getSliceLabel(ndx), stack.getProcessor(ndx));
-            }
-          }
-        }
-      }
-
       ReflectedUniverse ru = new ReflectedUniverse();
       try {
         ru.exec("import i5d.Image5D");
         ru.setVar("title", imp.getTitle());
-        ru.setVar("stack", is);
-        ru.setVar("sizeC", sizeC);
-        ru.setVar("sizeZ", sizeZ);
-        ru.setVar("sizeT", sizeT);
+        ru.setVar("stack", imp.getStack());
+        ru.setVar("sizeC", r.getSizeC());
+        ru.setVar("sizeZ", r.getSizeZ());
+        ru.setVar("sizeT", r.getSizeT());
         ru.exec("i5d = new Image5D(title, stack, sizeC, sizeZ, sizeT)");
         ru.setVar("cal", imp.getCalibration());
@@ -797 +799 @@
     }
     else if (options.isViewView5D()) {
-      int sizeZ = r.getSizeZ();
-      int sizeC = r.getSizeC();
-      int sizeT = r.getSizeT();
-      if (imp.getStackSize() == sizeZ * sizeT) sizeC = 1;
-      ChannelMerger ndxReader = new ChannelMerger(r);
-
-      // reorder stack to View5D's preferred order: XYZCT
-      if (!r.getDimensionOrder().equals("XYZCT")) {
-        ImageStack is = new ImageStack(r.getSizeX(), r.getSizeY());
-        ImageStack stack = imp.getStack();
-        for (int t=0; t<sizeT; t++) {
-          for (int c=0; c<sizeC; c++) {
-            for (int z=0; z<sizeZ; z++) {
-              int ndx = mergeChannels ? ndxReader.getIndex(z, c, t) + 1 :
-                r.getIndex(z, c, t) + 1;
-              is.addSlice(stack.getSliceLabel(ndx), stack.getProcessor(ndx));
-            }
-          }
-        }
-        imp.setStack(imp.getTitle(), is);
-      }
       WindowManager.setTempCurrentImage(imp);
       IJ.run("View5D ", "");
@@ -867 +848 @@
     int sizeT = r.getSizeT();
 
-    for (int z=0; z<sizeZ; z++) {
-      for (int t=0; t<sizeT; t++) {
-        byte[][] bytes = new byte[c][];
-        for (int ch=0; ch<r.getSizeC()/c; ch++) {
-          for (int ch1=0; ch1<c; ch1++) {
-            int ndx = r.getIndex(z, ch*c + ch1, t) + 1;
-            bytes[ch1] = (byte[]) s.getProcessor(ndx).getPixels();
-          }
-          ColorProcessor cp = new ColorProcessor(s.getWidth(), s.getHeight());
-          cp.setRGB(bytes[0], bytes[1], bytes.length == 3 ? bytes[2] :
-            new byte[s.getWidth() * s.getHeight()]);
-          int ndx = r.getIndex(z, ch*c, t) + 1;
-          newStack.addSlice(s.getSliceLabel(ndx), cp);
-        }
-      }
-    }
+    int[][] indices = new int[c][s.getSize() / c];
+    int[] pt = new int[c];
+    Arrays.fill(pt, 0);
+
+    for (int i=0; i<s.getSize(); i++) {
+      int[] zct = FormatTools.getZCTCoords(stackOrder, sizeZ, r.getSizeC(),
+        sizeT, r.getImageCount(), i);
+      int cndx = zct[1];
+      indices[cndx][pt[cndx]++] = i;
+    }
+
+    for (int i=0; i<indices[0].length; i++) {
+      ColorProcessor cp = new ColorProcessor(s.getWidth(), s.getHeight());
+      byte[][] bytes = new byte[indices.length][];
+      for (int j=0; j<indices.length; j++) {
+        bytes[j] = (byte[]) s.getProcessor(indices[j][i] + 1).getPixels();
+      }
+      cp.setRGB(bytes[0], bytes[1], bytes.length == 3 ? bytes[2] :
+        new byte[s.getWidth() * s.getHeight()]);
+      newStack.addSlice(s.getSliceLabel(
+        indices[indices.length - 1][i] + 1), cp);
+    }
+
     imp.setStack(imp.getTitle(), newStack);
   }

trunk/loci/plugins/ImporterOptions.java

@@ -64 +64 @@
   public static final String VIEW_VIEW_5D = "View5D";
 
+  // enumeration for stackOrder
+  public static final String ORDER_DEFAULT = "Default";
+  public static final String ORDER_XYZCT = "XYZCT";
+  public static final String ORDER_XYZTC = "XYZTC";
+  public static final String ORDER_XYCZT = "XYCZT";
+  public static final String ORDER_XYTCZ = "XYTCZ";
+  public static final String ORDER_XYCTZ = "XYCTZ";
+  public static final String ORDER_XYTZC = "XYTZC";
+
   public static final String MERGE_DEFAULT = "Do not merge";
 
@@ -82 +91 @@
   // keys for use in IJ_Prefs.txt
   public static final String PREF_STACK = "bioformats.stackFormat";
+  public static final String PREF_ORDER = "bioformats.stackOrder";
   public static final String PREF_MERGE = "bioformats.mergeChannels";
   public static final String PREF_COLORIZE = "bioformats.colorize";
@@ -94 +104 @@
   // labels for user dialog; when trimmed these double as argument & macro keys
   public static final String LABEL_STACK = "View stack with: ";
+  public static final String LABEL_ORDER = "Stack order: ";
   public static final String LABEL_MERGE = "Merge channels to RGB";
   public static final String LABEL_COLORIZE = "Colorize channels";
@@ -111 +122 @@
 
   private Choice stackChoice;
+  private Choice orderChoice;
   private Checkbox mergeBox;
   private Checkbox colorizeBox;
@@ -123 +135 @@
 
   private String stackFormat;
+  private String stackOrder;
   private boolean mergeChannels;
   private boolean colorize;
@@ -144 +157 @@
 
   public String getStackFormat() { return stackFormat; }
+  public String getStackOrder() { return stackOrder; }
   public boolean isMergeChannels() { return mergeChannels; }
   public boolean isColorize() { return colorize; }
@@ -175 +189 @@
 
   public void setStackFormat(String s) { stackFormat = s; }
+  public void setStackOrder(String s) { stackOrder = s; }
   public void setMergeChannels(boolean b) { mergeChannels = b; }
   public void setColorize(boolean b) { colorize = b; }
@@ -187 +202 @@
   public void loadPreferences() {
     stackFormat = Prefs.get(PREF_STACK, VIEW_STANDARD);
+    stackOrder = Prefs.get(PREF_ORDER, ORDER_DEFAULT);
     mergeChannels = Prefs.get(PREF_MERGE, false);
     colorize = Prefs.get(PREF_COLORIZE, false);
@@ -201 +217 @@
   public void savePreferences() {
     Prefs.set(PREF_STACK, stackFormat);
+    Prefs.set(PREF_ORDER, stackOrder);
     Prefs.set(PREF_MERGE, mergeChannels);
     Prefs.set(PREF_COLORIZE, colorize);
@@ -390 +407 @@
     stackTypes.copyInto(stackFormats);
 
+    String[] stackOrders = new String[] {
+      ORDER_DEFAULT, ORDER_XYZCT, ORDER_XYZTC, ORDER_XYCZT, ORDER_XYCTZ,
+      ORDER_XYTZC, ORDER_XYTCZ
+    };
+
     // prompt user for parameters (or grab from macro options)
     GenericDialog gd = new GenericDialog("Bio-Formats Import Options");
     gd.addChoice(LABEL_STACK, stackFormats, stackFormat);
+    gd.addChoice(LABEL_ORDER, stackOrders, stackOrder);
     gd.addCheckbox(LABEL_MERGE, mergeChannels);
     gd.addCheckbox(LABEL_COLORIZE, colorize);
@@ -405 +428 @@
     if (choices != null) {
       stackChoice = (Choice) choices.get(0);
+      orderChoice = (Choice) choices.get(1);
       for (int i=0; i<choices.size(); i++) {
         ((Choice) choices.get(i)).addItemListener(this);
@@ -427 +451 @@
 
     stackFormat = stackFormats[gd.getNextChoiceIndex()];
+    stackOrder = stackOrders[gd.getNextChoiceIndex()];
     mergeChannels = gd.getNextBoolean();
     colorize = gd.getNextBoolean();