fix macro mode running in EDT

Author: ekatrukha

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>nl.uu.science.cellbiology</groupId>
 	<artifactId>bigtrace</artifactId>
-	<version>0.8.3</version>
+	<version>0.8.3-SNAPSHOT</version>
 
 	<name>BigTrace</name>
 	<description>Tracing of curvilinear structures in 3D</description>

src/main/java/bigtrace/BigTrace.java

@@ -115,8 +115,8 @@ public class BigTrace < T extends RealType< T > & NativeType< T > > implements P
 	public VolumeViewerFrame bvvFrame;
 
 	/** flag to check if user interface is frozen.
-	 * It should be modified only in the main thread (or in done() of SwingWorker,
-	 * since when running in macro mode main thread becomes EDT => problems! **/
+	 * It should be modified only in the main thread (or in done method of SwingWorker,
+	 * since when running in macro mode main thread becomes EDT = problems! **/
 	public volatile boolean bInputLock = false;
 
 	/** visualization of coordinates origin axes **/
@@ -173,8 +173,7 @@ public void run(String arg)
 
 		btData = new BigTraceData<>(this);
 		btLoad = new BigTraceLoad<>(this);
-		
-		
+			
 		if(arg.equals(""))
 		{
 			btData.sFileNameFullImg = IJ.getFilePath("Open TIF/BDV/Bioformats file (3D, composite, time)...");
@@ -228,25 +227,31 @@ public void run(String arg)
 
 		roiManager = new RoiManager3D<>(this);
 
-		initSourcesCanvas(0.25*Math.min(btData.nDimIni[1][0], Math.min(btData.nDimIni[1][1],btData.nDimIni[1][2])));
+		initSourcesCanvas(0.25 * Math.min(btData.nDimIni[1][0], Math.min(btData.nDimIni[1][1],btData.nDimIni[1][2])));
+		if(!btMacro.bMacroMode)
+		{
+			//not sure we really need it, but anyway
+	        javax.swing.SwingUtilities.invokeLater(new Runnable() {
+	            @Override
+				public void run() {
+	                createAndShowGUI();
+	            }
+	        });
+		}
+		else
+		{
+			createAndShowGUI();
+		}
 
-		//not sure we really need it, but anyway
-        javax.swing.SwingUtilities.invokeLater(new Runnable() {
-            @Override
-			public void run() {
-                createAndShowGUI();
-            }
-        });
-        
 
 	}
 
 	public void initOriginAndBox(double axis_length)
 	{
 		int i;
 		//basis vectors 
-		RealPoint basis = new RealPoint(-0.1*axis_length, -0.1*axis_length,-0.1*axis_length);				
-		for(i=0;i<3;i++)
+		RealPoint basis = new RealPoint(-0.1 * axis_length, -0.1 * axis_length,-0.1 * axis_length);				
+		for(i = 0; i < 3; i++)
 		{		
 			ArrayList< RealPoint > point_coords = new ArrayList< >();
 			point_coords.add(new RealPoint(basis));
@@ -262,7 +267,7 @@ public void initOriginAndBox(double axis_length)
 
 		float [][] nDimBox = new float [2][3];
 
-		for(i=0;i<3;i++)
+		for(i = 0; i < 3; i++)
 		{
 			//why is this shift?! I don't know,
 			// but looks better like this

src/main/java/bigtrace/BigTraceMacro.java

@@ -152,8 +152,7 @@ public void macroRunFullAutoTrace(final double dMinIntensity, final int nMinNumP
 		{
 			Thread.sleep(1000);
 		}
-		bt.bInputLock = true;
-		
+				
 		int nFirstTP = 0;
 		int nLastTP = 0;
 
@@ -298,9 +297,7 @@ public void macroLoadROIs(String sFileName, String input) throws InterruptedExce
 		{
 			Thread.sleep(1000);
 		}
-		
-		bt.bInputLock = true;
-		
+			
         if(input == null)
         	return;
         int nLoadMode = 0;
@@ -326,7 +323,7 @@ public void macroSaveROIs(String sFileName, String output) throws InterruptedExc
 		{
 			Thread.sleep(1000);
 		}
-		bt.bInputLock = true;
+		
 		String out = "";
         if(output == null)
         {
@@ -361,13 +358,13 @@ void macroStraighten(final int nStraightenAxis, String sSaveDir, String sShape)
 	{
 		while(bt.bInputLock)
 		{
-			Thread.sleep(100);
+			Thread.sleep(1000);
 		}
 
 		//it should be later unlocked by StraightenCurve,
 		//if we call it 
 		bt.bInputLock = true;
-		
+		bt.setLockMode(true);
 		//build list of ROIs
 		final ArrayList<AbstractCurve3D> curvesOut = new ArrayList<>();
 		IJ.log( "Total " + Integer.toString(bt.roiManager.rois.size()) +" ROIs" );
@@ -400,15 +397,15 @@ void macroStraighten(final int nStraightenAxis, String sSaveDir, String sShape)
 		{	
 			StraightenCurve<T> straightBG = new StraightenCurve<>(curvesOut, bt, -1.0f, nAxis, nShape, 0, 1, sSaveDir);
 			straightBG.addPropertyChangeListener(bt.btPanel);
-			straightBG.execute();
+			straightBG.runStraightenCurve();
 		}
 		else
 		{
 			IJ.log("Cannot find proper curve ROIs to straighten.");
 			bt.btPanel.progressBar.setString("curve straightening aborted.");
-			bt.bInputLock = false;
 		}
-		
+		bt.setLockMode(false);
+		bt.bInputLock = false;
 	}
 
 	public void macroShapeInterpolation(String sShapeInterpol, int nSmoothWindow) throws InterruptedException
@@ -446,7 +443,7 @@ void macroIntensityInterpolation(String sInterpol) throws InterruptedException
 	{
 		while(bt.bInputLock)
 		{
-			Thread.sleep(100);
+			Thread.sleep(1000);
 		}
 		bt.bInputLock = true;
 		switch (sInterpol)
@@ -476,7 +473,7 @@ void macroCloseBT() throws InterruptedException
 	{
 		while(bt.bInputLock)
 		{
-			Thread.sleep(100);
+			Thread.sleep(1000);
 		}
 		bt.closeWindows();
 		IJ.log("BigTrace closed.");

src/main/java/bigtrace/gui/PanelFullAutoTrace.java

@@ -198,7 +198,17 @@ public void launchFullAutoTrace(final double dAutoMinStartTrace, final int nAuto
 		butAuto.setToolTipText( "Stop auto trace" );
 		fullAutoTrace.butAuto = butAuto;
 		fullAutoTrace.tabIconRestore = tabIconAuto;
-		fullAutoTrace.execute();
+		if( !bt.btMacro.bMacroMode )
+		{
+			fullAutoTrace.execute();
+		}
+		else
+		{
+			fullAutoTrace.runFullAutoTrace();			
+			bt.setLockMode(true);
+			bt.bInputLock = true;
+			
+		}
 	}
 
 	@Override

src/main/java/bigtrace/io/ROIsExportCSV.java

@@ -34,12 +34,18 @@ public String getProgressState()
 	@Override
 	public void setProgressState(String state_)
 	{
-		progressState=state_;
+		progressState = state_;
 	}
-
+	
 	@Override
-	protected Void doInBackground() throws Exception {
-
+	protected Void doInBackground() throws Exception 
+	{
+		runROIsExportCSV();
+		return null;
+	}	
+	
+	public void runROIsExportCSV()
+	{
 		int nRoi, nRoiN;		
 
         try {
@@ -61,13 +67,13 @@ protected Void doInBackground() throws Exception {
 				String sRadius;
 				int nRoiCurrN = 0;
 				//writer.write("ROIsNumber," + Integer.toString(nRoiN)+"\n");
-				for(nRoi=0; nRoi<nRoiN; nRoi++)
+				for(nRoi = 0; nRoi < nRoiN; nRoi++)
 				{
-					  //Sleep for up to one second.
+					//Sleep for up to one second.
 					try {
 						Thread.sleep(1);
 					} catch (InterruptedException ignore) {}
-					setProgress(nRoi*100/nRoiN);
+					setProgress(nRoi * 100 / nRoiN);
 					if(bt.roiManager.rois.get( nRoi ) instanceof AbstractCurve3D)
 					{
 						nRoiCurrN++;
@@ -78,10 +84,10 @@ protected Void doInBackground() throws Exception {
 						sRoiGroup = bt.roiManager.groups.get(currRoi.getGroupInd()).getName();
 						sRadius = df3.format( currRoi.getLineThickness() * 0.5 * bt.btData.dMinVoxelSize);
 						ArrayList< RealPoint > points = currRoi.getJointSegmentResampled();
-						for(int nP=0; nP<points.size(); nP++)
+						for(int nP = 0; nP < points.size(); nP++)
 						{
 							writer.write( Integer.toString( nRoiCurrN ) +"," );
-							for (int d=0;d<3;d++)
+							for (int d = 0; d < 3; d++)
 							{
 								writer.write( df3.format(points.get( nP ).getDoublePosition( d ) ) +"," );								
 							}
@@ -98,8 +104,10 @@ protected Void doInBackground() throws Exception {
 			IJ.log(e.getMessage());
 			//e.printStackTrace();
 		}
-		return null;
+		return;
+		
 	}
+
     /*
      * Executed in event dispatching thread
      */

src/main/java/bigtrace/io/ROIsExportSWC.java

@@ -39,6 +39,12 @@ public void setProgressState(String state_)
 
 	@Override
 	protected Void doInBackground() throws Exception 
+	{
+		runROIsExportSWC();
+		return null;
+	}
+
+	public void runROIsExportSWC()
 	{
 		int nRoi, nRoiN;		
 
@@ -114,8 +120,10 @@ protected Void doInBackground() throws Exception
 			IJ.log(e.getMessage());
 			//e.printStackTrace();
 		}
-		return null;
+		return;
+		
 	}
+	
     /*
      * Executed in event dispatching thread
      */

src/main/java/bigtrace/io/ROIsIO.java

@@ -27,7 +27,18 @@ public static <T extends RealType< T > & NativeType< T > > void loadROIs(String
         loadTask.nLoadMode = nLoadMode;
         loadTask.bt = bt;
         loadTask.addPropertyChangeListener(bt.btPanel);
-        loadTask.execute();	
+        
+        if(!bt.btMacro.bMacroMode)
+        {
+        	loadTask.execute();
+        }
+        else
+        {
+        	loadTask.runROIsload();            
+        	bt.setLockMode(false);
+        	bt.bInputLock = false;
+            
+        }
 	}
 
 	public static <T extends RealType< T > & NativeType< T > > void saveROIs(String fullFilename, final int nSaveMode, final BigTrace<T> bt)
@@ -43,22 +54,49 @@ public static <T extends RealType< T > & NativeType< T > > void saveROIs(String
 			saveTask.sFilename = fullFilename;
 			saveTask.bt = bt;
 			saveTask.addPropertyChangeListener(bt.btPanel);
-			saveTask.execute();
+			if( !bt.btMacro.bMacroMode )
+			{
+				saveTask.execute();
+			}
+			else
+			{
+				saveTask.runROIsSave();
+			}
 			break;
 		case 1: 	
 			ROIsExportCSV<T> exportTask = new ROIsExportCSV<>();
 			exportTask.sFilename = fullFilename;
 			exportTask.bt = bt;
 			exportTask.addPropertyChangeListener(bt.btPanel);
-			exportTask.execute();
+			if( !bt.btMacro.bMacroMode )
+			{
+				exportTask.execute();
+			}
+			else
+			{
+				exportTask.runROIsExportCSV();
+			}			
 			break;
 		case 2: 
 			ROIsExportSWC<T> exportSWCTask = new ROIsExportSWC<>();
 			exportSWCTask.sFilename = fullFilename;
 			exportSWCTask.bt = bt;
 			exportSWCTask.addPropertyChangeListener(bt.btPanel);
-			exportSWCTask.execute();
+			if( !bt.btMacro.bMacroMode )
+			{
+				exportSWCTask.execute();
+			}
+			else
+			{
+				exportSWCTask.runROIsExportSWC();
+			}
 			break;
 		}
+		
+		if( bt.btMacro.bMacroMode )
+		{
+			bt.setLockMode(false);
+			bt.bInputLock = false;
+		}
 	}
 }