Changeset 7868 for trunk

Timestamp:

01/19/12 12:54:08 (8 years ago)

Author:

avivekan

Message:

 

File:

• trunk/projects/flow-cytometry/src/main/java/loci/apps/flow/FlowCytometry.java (modified) (4 diffs)

trunk/projects/flow-cytometry/src/main/java/loci/apps/flow/FlowCytometry.java

@@ -39 +39 @@
 import ij.ImagePlus;
 import ij.ImageStack;
+import ij.WindowManager;
 import ij.gui.ImageWindow;
+import ij.measure.Measurements;
 import ij.measure.ResultsTable;
 import ij.plugin.filter.Analyzer;
+import ij.plugin.filter.GaussianBlur;
+import ij.plugin.filter.ParticleAnalyzer;
 import ij.plugin.frame.RoiManager;
+import ij.process.AutoThresholder;
 import ij.process.ByteProcessor;
 import ij.process.ImageProcessor;
@@ -194 +199 @@
                 nSlices++;
         }
-        
-        
+
+
         /*
         public static void showImageForBrightfield(int width, int height, byte[] imageData) {
@@ -253 +258 @@
                 }
         }
-*/
+         */
         public static void showImage(int width, int height, byte[] imageData) {
                 //bp = new ByteProcessor(width,height,imageData,
@@ -633 +638 @@
                 return micronAreas;
         }
-        
+
         //ajeet
-                public static int[] getBFParticleAreas(){
-                        IJ.runPlugIn("flow bfParticleAreas", null);
-
-                        RoiManager rm = RoiManager.getInstance();
-                        int lenghtOfRoiTable =rm.getRoisAsArray().length;
+        public static int[] getBFParticleAreas(){
+                ImagePlus img = WindowManager.getCurrentImage();
+                //      IJ.runPlugIn("bf ParticleAreasPlugin", null);
+                ImageProcessor imgProc = img.getProcessor();
+
+                imgProc.findEdges();
+                imgProc.findEdges();
+
+                GaussianBlur gb = new GaussianBlur();
+                gb.blur(imgProc, 5);
+
+                AutoThresholder thresh = new AutoThresholder();
+                thresh.getThreshold(AutoThresholder.Method.valueOf("Minimum"), imgProc.getHistogram());
+
+                RoiManager rm = new RoiManager(true);
+                ResultsTable rt = new ResultsTable();
+                img = new ImagePlus("thresholdedImage", imgProc);
+                ParticleAnalyzer pa = new ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER | ParticleAnalyzer.CLEAR_WORKSHEET | ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES | ParticleAnalyzer.INCLUDE_HOLES, Measurements.AREA, rt, 0, Double.POSITIVE_INFINITY, 0, 1);
+                int lenghtOfRoiTable = 0;
+
+                if (pa.analyze(img)){
+                        lenghtOfRoiTable = rm.getRoisAsArray().length;
+
                         int[] retVal = new int[lenghtOfRoiTable];
+                        double[] temp = rt.getColumnAsDoubles(0);
 
                         for (int i = 0; i < lenghtOfRoiTable; i++){
-                                retVal[i] = Integer.parseInt(IJ.runMacro("getResults(\"Area\", i)", null));
+                                retVal[i]=(int)temp[i];
                         }
 
+                        rm.dispose();
+                        rt.reset();
+                        img.flush();
+                        img.close();
+
                         return retVal;
                 }
-                
+
+                rm.dispose();
+                rt.reset();
+                img.flush();
+                img.close();
+
+                return null;
+
+
+        }
+
 
         private static boolean addParticle(Particle particle) {