Changeset 7997

Timestamp:

05/07/12 15:41:25 (8 years ago)

Author:

avivekan

Message:

trial ratio method added

Location:

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

Files:

• Find_Particle_Areas.java (modified) (3 diffs)
• FlowCyto.java (modified) (3 diffs)

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

@@ -21 +21 @@
         private int stackSize, curSlice, sizeMin;
         private Duplicator duplicator;
-        private TextWindow twindow;
+        private static TextWindow twindow;
         
 
@@ -212 +212 @@
                         for(int i=0; i<totalParticleValues.size(); i++)
                                 particleValue+=totalParticleValues.get(i);
-                        //make custom entry for average and median
-                        twindow.append("Average pixel area over    \t"+ numEntries + "\t    slices is    \t"+(particleValue/numEntries));
-                        twindow.append("Median pixel area from    \t"+ numEntries + "\t    slices is    \t"+(totalParticleValues.get(numEntries/2)));
+                        //make custom entry for average median min and max
+                        twindow.append("Average particle pixel area over    \t"+ numEntries + "\t    slices is    \t"+(particleValue/numEntries));
+                        twindow.append("Median particle pixel area from    \t"+ numEntries + "\t    slices is    \t"+(totalParticleValues.get(numEntries/2)));
+                        twindow.append("MIN particle pixel area over    \t"+ numEntries + "\t    slices is    \t"+(totalParticleValues.get(0)));
+                        twindow.append("MAX particle pixel area over    \t"+ numEntries + "\t    slices is    \t"+(totalParticleValues.get(totalParticleValues.size()-1)));
                         
                         imageToAnalyze.flush();
@@ -224 +226 @@
                         IJ.log(e.getMessage());
                 }
+        }
+        
+        public static TextWindow getTextWindow(){
+                return twindow;
         }
         

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

@@ -12 +12 @@
 import ij.plugin.frame.RoiManager;
 import ij.process.ByteProcessor;
+import ij.text.TextWindow;
 
 import java.awt.image.ColorModel;
@@ -148 +149 @@
                         if (pixelsPerMicron > 0){ 
                                 pixelMicronSquared = pixelsPerMicron*pixelsPerMicron;
-                                IJ.run("Set Scale...", "distance="+width+" known="+((double)width/pixelsPerMicron) +" pixel=1 unit=microns");
+//                              IJ.run("Set Scale...", "distance="+width+" known="+((double)width/pixelsPerMicron) +" pixel=1 unit=microns");
                                 //-----------------------FOR DEBUG PURPOSES--------------------//
                                 IJ.log("ImageJ started for "+mode+" mode in "+ ((System.nanoTime() - initialTime)/1000) +"us");
@@ -296 +297 @@
                 return false;
         }
+        
+        @SuppressWarnings("static-access")
+        public static void calcTrialRatio(){
+                ImagePlus impIN2=new ImagePlus(), tempimp=new ImagePlus();
+                ImageStack stackIN2 = new ImageStack();
+                float[] summedPixelAreasArray, foundInSliceArray;
+                float avgBF, medBF, minBF, maxBF, avgIN, medIN, minIN, maxIN;           
+
+                impBF.setSlice(1);
+                IJ.run(impBF, "Find Particle Areas", "channel=Brightfield threshold_minimum=170 size_minimum=100 run_plugin_over_entire_stack");
+
+                ResultsTable rtab = Find_Particle_Areas.getTextWindow().getTextPanel().getResultsTable();
+                summedPixelAreasArray = rtab.getColumn(rtab.getColumnIndex("Area"));
+                maxBF = summedPixelAreasArray[summedPixelAreasArray.length-1];
+                minBF = summedPixelAreasArray[summedPixelAreasArray.length-2];
+                medBF = summedPixelAreasArray[summedPixelAreasArray.length-3];
+                avgBF = summedPixelAreasArray[summedPixelAreasArray.length-4];
+                
+                foundInSliceArray = rtab.getColumn(rtab.getColumnIndex("Slice"));
+                for(int i=0; i<foundInSliceArray.length; i++){
+                        int index = (int)foundInSliceArray[i];
+                        tempimp = dup.run(impIN, index, index);
+                        stackIN2.addSlice(tempimp.getProcessor());
+                        impIN2.setStack(stackIN2);
+                        imp.unlock();
+                }
+                
+                impIN2.setSlice(1);
+                IJ.run(impIN2, "Find Particle Areas", "channel=Intensity threshold_minimum=20 size_minimum=0 run_plugin_over_entire_stack");
+                rtab = Find_Particle_Areas.getTextWindow().getTextPanel().getResultsTable();
+                summedPixelAreasArray = rtab.getColumn(rtab.getColumnIndex("Area"));
+                maxIN = summedPixelAreasArray[summedPixelAreasArray.length-1];
+                minIN = summedPixelAreasArray[summedPixelAreasArray.length-2];
+                medIN = summedPixelAreasArray[summedPixelAreasArray.length-3];
+                avgIN = summedPixelAreasArray[summedPixelAreasArray.length-4];
+                
+                IJ.log("Average pixel ratio: "+avgIN/avgBF);
+                IJ.log("Median pixel ratio: "+medIN/medBF);             
+                IJ.log("Minimum pixel ratio: "+minIN/minBF);
+                IJ.log("Maximum pixel ratio: "+maxIN/maxBF);
+                
+                impIN2.flush();
+                impIN2.close();
+                tempimp.flush();
+                tempimp.close();
+                stackIN2=null;
+        }
 
         @SuppressWarnings("static-access")