Changeset 7893 for trunk/projects/flow-cytometry

Timestamp:

02/18/12 02:11:40 (8 years ago)

Author:

avivekan

Message:

small bugfix

Location:

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

Files:

• FlowCytometry.java (modified) (6 diffs)
• bf_ParticleAreasPlugin.java (modified) (2 diffs)

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

@@ -51 +51 @@
 import ij.process.ImageProcessor;
 import java.awt.BorderLayout;
+import java.awt.Component;
 import java.awt.Scrollbar;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
@@ -166 +169 @@
         private static FunctionType fn;
         private static DataReferenceImpl data_ref;
-        private static Scrollbar scroll;
+        private static Component scroll;
         private static DisplayImpl display;
         private static ResultsTable rt;
@@ -274 +277 @@
                 else if (nSlices == 2) {
                         ImageWindow stackwin = imp.getWindow();
-                        scroll = (Scrollbar) stackwin.getComponent(1);
-
-                        AdjustmentListener l = new AdjustmentListener() {
+                        scroll = stackwin.getComponent(1);
+
+                        ComponentListener l = new ComponentListener() {
                                 @SuppressWarnings("synthetic-access")
-                                @Override
                                 public void adjustmentValueChanged(AdjustmentEvent arg0) {
                                         try {
@@ -311 +313 @@
                                         }
                                 }
+
+                                @Override
+                                public void componentHidden(ComponentEvent e) {
+                                        // TODO Auto-generated method stub
+                                        
+                                }
+
+                                @Override
+                                public void componentMoved(ComponentEvent e) {
+                                        // TODO Auto-generated method stub
+                                        
+                                }
+
+                                @Override
+                                public void componentResized(ComponentEvent e) {
+                                        // TODO Auto-generated method stub
+                                        
+                                }
+
+                                @Override
+                                public void componentShown(ComponentEvent e) {
+                                        // TODO Auto-generated method stub
+                                        
+                                }
                         };
-                        scroll.addAdjustmentListener(l);
+                        scroll.addComponentListener((ComponentListener) l);
                 }
         }
@@ -648 +674 @@
                         IJ.run("bf ParticleAreasPlugin");
 //                      IJ.runPlugIn("bf ParticleAreasPlugin", null);
-                        RoiManager rm = RoiManager.getInstance();
-                        ResultsTable rt = ResultsTable.getResultsTable();
-
-                        int lengthOfRoiTable = rm.getCount();
-                        rm.runCommand("Deselect");
-                        rm.runCommand("Delete");
-                        
+                        RoiManager rman = RoiManager.getInstance();
+                        ResultsTable rtab = ResultsTable.getResultsTable();
+
+                        int lengthOfRoiTable = rman.getCount();
+
                         if (lengthOfRoiTable!=0){
+                                rman.runCommand("Deselect");
+                                rman.runCommand("Delete");
 
                                 retVal = new int[lengthOfRoiTable];
-                                float[] temp = rt.getColumn(rt.getColumnIndex("Area"));
-
-                                if(temp!=null && retVal!=null){
+                                float[] temp = rtab.getColumn(rtab.getColumnIndex("Area"));
+
+                                if(temp!=null){
                                         for (int i = 0; i < lengthOfRoiTable; i++){
                                                 retVal[i]=(int)temp[i];
@@ -1218 +1244 @@
                         //fall through
                 }
+                ResultsTable.getResultsTable().reset();
+                WindowManager.closeAllWindows();
                 ij.quit();
         }

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

@@ -1 +1 @@
 package loci.apps.flow;
-// DELETE the package script above, and place in WiscScan/plugins
+
+
 import ij.*;
 import ij.plugin.*;
@@ -25 +26 @@
                 try{
                         Interpreter.batchMode=true;
-                        Duplicator dup = new Duplicator();
-                        ImagePlus duplicate = dup.run(image);
+
+                        //Duplicator dup = new Duplicator();
+                        //ImagePlus duplicate = dup.run(image);
                         //TODO use duplicate image in all "run"s, 
-                        IJ.run("Duplicate...", "title=Duplicate");
-                        IJ.run("Find Edges");
-                        IJ.run("Find Edges");
-                        IJ.run("Gaussian Blur...", "sigma=5");
-                        IJ.run("Auto Threshold", "method=Minimum white");
-                        IJ.run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Masks exclude clear add");
-                        IJ.runMacro("roiManager(\"Measure\")",null);
+                        IJ.log("Started scan");//TEMP                   
+                        ImageProcessor duplicatedArg0 = arg0.duplicate();
+                        ImagePlus imp = new ImagePlus("duplicate", duplicatedArg0); // has only one slice
+                        IJ.log("Duplicate ImageProcessor and ImagePlus successfully created");//TEMP
+                        
+                        //IJ.run(imp, "Duplicate...", "title=Duplicate");
+                        IJ.run(imp, "Find Edges", null);
+                        IJ.run(imp, "Find Edges", null);
+                        IJ.log("Ran Find Edges twice...");//TEMP
+                        
+                        IJ.run(imp, "Gaussian Blur...", "sigma=5");
+                        IJ.log("Gaussian Blur with sigma 5");//TEMP
+                        
+                        IJ.run(imp, "Auto Threshold", "method=Minimum white");
+                        IJ.log("thresholded ImagePlus duplicate with Auto Threshold Minimum");//TEMP
+                        
+                        IJ.run(imp, "Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Masks exclude clear add");
+                        IJ.log("Analyzed particles, loaded to ROI Manager");//TEMP
+                        
+                        IJ.log("ROI count = " + RoiManager.getInstance().getCount());//TEMP
+                        if(RoiManager.getInstance().getCount()>0)
+                                IJ.runMacro("roiManager(\"Measure\")",null);
+                        
+                        IJ.log("Successfully measured, finished all calculations");//TEMP
+
+                        //IJ.selectWindow("Duplicate");
+                        //WindowManager.removeWindow(WindowManager.getFrontWindow());
+                        imp.close();
+                        IJ.log("Closed ImagePlus duplicate.");//TEMP
+                        IJ.log("Done.");//TEMP
+                        
+                        Interpreter.batchMode=false;
+
                 } catch(Exception e){
-
+                        e.printStackTrace();
+                        //String stackTrace = DebugTools.printStackTrace(e);
+                        //IJ.handleException(e);
                 }
                 Interpreter.batchMode=false;
-
+//REPLACE SIZE IN ANALYZE PARTICLE TO ACCOMODATE MIN AND MAX
 
         }