Changeset 3196

Timestamp:

09/27/07 11:29:18 (12 years ago)

Author:

melissa

Message:

Added option to turn off autoscaling.

Location:

trunk/loci/plugins

Files:

• CustomImage.java (modified) (3 diffs)
• Importer.java (modified) (8 diffs)
• ImporterOptions.java (modified) (12 diffs)

trunk/loci/plugins/CustomImage.java

@@ -35 +35 @@
   protected String order;
   protected int z, t, channels;
-
-        public CustomImage(ImagePlus imp, String order, int z, int t, int channels) {
+  boolean autoscale;
+
+        public CustomImage(ImagePlus imp, String order, int z, int t, int channels,
+    boolean autoscale)
+  {
     this.z = z;
     this.t = t;
     this.channels = channels;
     this.order = order;
+    this.autoscale = autoscale;
     ImageStack stack2;
                 boolean isRGB = imp.getBitDepth() == 24;
@@ -117 +121 @@
                 if (slice > nChannels) slice = nChannels;
 
-                if (slice - 1 != currentChannel) {
+                if (slice - 1 != currentChannel && autoscale) {
                         currentChannel = slice - 1;
                         getProcessor().setMinAndMax(cip[currentChannel].getMin(),
@@ -136 +140 @@
 
                 ImageProcessor iip = getProcessor();
-                cip[currentChannel].setMinAndMax(iip.getMin(), iip.getMax());
+                if (autoscale) cip[currentChannel].setMinAndMax(iip.getMin(), iip.getMax());
                 if (singleChannel) {
                         PixelGrabber pg = new PixelGrabber(cip[currentChannel].createImage(),

trunk/loci/plugins/Importer.java

@@ -30 +30 @@
 import ij.measure.Calibration;
 import ij.process.*;
-import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.event.*;
 import java.awt.image.*;
 import java.io.*;
@@ -131 +128 @@
     boolean concatenate = options.isConcatenate();
     boolean specifyRanges = options.isSpecifyRanges();
+    boolean autoscale = options.isAutoscale();
 
     boolean viewNone = options.isViewNone();
@@ -713 +711 @@
     boolean mergeChannels = options.isMergeChannels();
     boolean concatenate = options.isConcatenate();
-
-    Util.adjustColorRange(imp);
+    if (options.isAutoscale()) Util.adjustColorRange(imp);
 
     // convert to RGB if needed
@@ -722 +719 @@
       !r.isIndexed())
     {
-      makeRGB(imp, r, r.getSizeC());
+      makeRGB(imp, r, r.getSizeC(), options.isAutoscale());
     }
     else if (mergeChannels && r.getSizeC() > 1 && r.getSizeC() < 4 &&
@@ -743 +740 @@
         catch (ReflectException exc) {
           imp = new CustomImage(imp, stackOrder, r.getSizeZ(),
-            r.getSizeT(), r.getSizeC());
+            r.getSizeT(), r.getSizeC(), options.isAutoscale());
         }
       }
       else {
         imp = new CustomImage(imp, stackOrder, r.getSizeZ(),
-          r.getSizeT(), r.getSizeC());
+          r.getSizeT(), r.getSizeC(), options.isAutoscale());
       }
     }
@@ -766 +763 @@
       {
         String option = options.getMergeOption();
-        if (option.indexOf("2 channels") != -1) makeRGB(imp, r, 2);
-        else if (option.indexOf("3 channels") != -1) makeRGB(imp, r, 3);
+        if (option.indexOf("2 channels") != -1) {
+          makeRGB(imp, r, 2, options.isAutoscale());
+        }
+        else if (option.indexOf("3 channels") != -1) {
+          makeRGB(imp, r, 3, options.isAutoscale());
+        }
       }
     }
@@ -832 +833 @@
   }
 
-  private void makeRGB(ImagePlus imp, IFormatReader r, int c) {
+  private void makeRGB(ImagePlus imp, IFormatReader r, int c, boolean scale) {
     ImageStack s = imp.getStack();
     ImageStack newStack = new ImageStack(s.getWidth(), s.getHeight());
@@ -840 +841 @@
     }
     imp.setStack(imp.getTitle(), newStack);
-    Util.adjustColorRange(imp);
+    if (scale) Util.adjustColorRange(imp);
 
     s = imp.getStack();

trunk/loci/plugins/ImporterOptions.java

@@ -101 +101 @@
   public static final String PREF_THUMBNAIL = "bioformats.forceThumbnails";
   public static final String PREF_MERGE_OPTION = "bioformats.mergeOption";
+  public static final String PREF_AUTOSCALE = "bioformats.autoscale";
 
   // labels for user dialog; when trimmed these double as argument & macro keys
@@ -114 +115 @@
     "Concatenate compatible series";
   public static final String LABEL_RANGE = "Specify range for each series";
+  public static final String LABEL_AUTOSCALE = "Autoscale images";
 
   public static final String LABEL_LOCATION = "Location: ";
@@ -130 +132 @@
   private Checkbox concatenateBox;
   private Checkbox rangeBox;
+  private Checkbox autoscaleBox;
   private Choice mergeChoice;
 
@@ -143 +146 @@
   private boolean concatenate;
   private boolean specifyRanges;
+  private boolean autoscale;
   private boolean forceThumbnails;
   private String mergeOption;
@@ -166 +170 @@
   public boolean isSpecifyRanges() { return specifyRanges; }
   public boolean isForceThumbnails() { return forceThumbnails; }
+  public boolean isAutoscale() { return autoscale; }
   public String getMergeOption() { return mergeOption; }
 
@@ -198 +203 @@
   public void setSpecifyRanges(boolean b) { specifyRanges = b; }
   public void setForceThumbnails(boolean b) { forceThumbnails = b; }
+  public void setAutoscale(boolean b) { autoscale = b; }
 
   /** Loads default option values from IJ_Prefs.txt. */
@@ -211 +217 @@
     specifyRanges = Prefs.get(PREF_RANGE, false);
     forceThumbnails = Prefs.get(PREF_THUMBNAIL, false);
+    autoscale = Prefs.get(PREF_AUTOSCALE, true);
     mergeOption = Prefs.get(PREF_MERGE_OPTION, MERGE_DEFAULT);
   }
@@ -226 +233 @@
     Prefs.set(PREF_RANGE, specifyRanges);
     Prefs.set(PREF_MERGE_OPTION, mergeOption);
+    Prefs.set(PREF_AUTOSCALE, autoscale);
   }
 
@@ -262 +270 @@
       stackFormat = Macro.getValue(arg, LABEL_STACK, stackFormat);
       mergeOption = Macro.getValue(arg, LABEL_MERGE_OPTION, mergeOption);
+      autoscale = getMacroValue(arg, LABEL_AUTOSCALE, autoscale);
 
       location = Macro.getValue(arg, LABEL_LOCATION, location);
@@ -423 +432 @@
     gd.addCheckbox(LABEL_CONCATENATE, concatenate);
     gd.addCheckbox(LABEL_RANGE, specifyRanges);
+    gd.addCheckbox(LABEL_AUTOSCALE, autoscale);
 
     // extract GUI components from dialog and add listeners
@@ -442 +452 @@
       concatenateBox = (Checkbox) boxes.get(5);
       rangeBox = (Checkbox) boxes.get(6);
+      autoscaleBox = (Checkbox) boxes.get(7);
       for (int i=0; i<boxes.size(); i++) {
         ((Checkbox) boxes.get(i)).addItemListener(this);
@@ -459 +470 @@
     concatenate = gd.getNextBoolean();
     specifyRanges = gd.getNextBoolean();
+    autoscale = gd.getNextBoolean();
 
     return STATUS_OK;