reorganize io

src/main/java/bigtrace/BigTraceControlPanel.java

@@ -40,6 +40,7 @@
 import bigtrace.gui.RangeSliderTF;
 import bigtrace.gui.RenderMethodPanel;
 import bigtrace.gui.VoxelSizePanel;
+import bigtrace.io.ViewsIO;
 import bigtrace.measure.RoiMeasure3D;
 import bigtrace.rois.Box3D;
 import bigtrace.rois.ColorUserSettings;
@@ -48,6 +49,8 @@
 import bigtrace.volume.ExtractClip;
 import bvvpg.vistools.BvvStackSource;
 import ij.Prefs;
+import ij.io.SaveDialog;
+
 import net.imglib2.FinalInterval;
 import net.imglib2.FinalRealInterval;
 import net.imglib2.realtransform.AffineTransform3D;
@@ -57,8 +60,7 @@
 
 
 public class BigTraceControlPanel< T extends RealType< T > & NativeType< T > > extends JPanel
-//public class BigTraceControlPanel extends JFrame
-								implements ActionListener, 
+									implements ActionListener, 
 									PropertyChangeListener {
 
 
@@ -84,6 +86,9 @@ public class BigTraceControlPanel< T extends RealType< T > & NativeType< T > > e
 
 	public JFrame finFrame;
 	public JProgressBar progressBar;
+
+	JButton butSaveView;
+	JButton butLoadView;
 	JButton butSettings;
 
 	public ColorUserSettings selectColors = new ColorUserSettings();
@@ -308,17 +313,20 @@ public void itemStateChanged(ItemEvent e) {
 		//SAVE AND LOAD BUTTONS
 		icon_path = bigtrace.BigTrace.class.getResource("/icons/save.png");
 	    tabIcon = new ImageIcon(icon_path);
-	    JButton butSave = new JButton(tabIcon);
-	    butSave.setToolTipText( "Save image view" );
-	    c.gridx++;
-		panView.add(butSave,c);	
+	    butSaveView = new JButton(tabIcon);
+	    butSaveView.setToolTipText( "Save image view" );
+		butSaveView.addActionListener(this);
+		c.gridx++;
+		panView.add(butSaveView,c);	
 
 		icon_path = bigtrace.BigTrace.class.getResource("/icons/load.png");
 	    tabIcon = new ImageIcon(icon_path);
-	    JButton butLoad = new JButton(tabIcon);
-	    butLoad.setToolTipText( "Load image view" );
+	    butLoadView = new JButton(tabIcon);
+	    butLoadView.setToolTipText( "Load image view" );
+		butLoadView.addActionListener(this);
+
 	    c.gridx++;
-		panView.add(butLoad,c);	
+		panView.add(butLoadView,c);	
 
 		//SETTINGS
 		icon_path = bigtrace.BigTrace.class.getResource("/icons/settings.png");
@@ -408,6 +416,21 @@ public void itemStateChanged(ItemEvent e) {
 		return panNavigation;
 
 	}
+
+	public void dialSaveView()
+	{
+		String filename;
+
+		filename = bt.btData.sFileNameFullImg + "_btview";
+		SaveDialog sd = new SaveDialog("Save ROIs ", filename, ".csv");
+        String path = sd.getDirectory();
+        if (path == null)
+        	return;
+        filename = path + sd.getFileName();	
+        ViewsIO.saveView( bt, filename );
+	}
+
+
 	public void dialSettings()
 	{
 		JPanel pViewSettings = new JPanel();
@@ -583,6 +606,7 @@ public void dialSettings()
 			bt.repaintBVV();
 		}
 	}
+
 	public void extractClippedView()
 	{
 
@@ -867,6 +891,12 @@ public void setRenderMethod(int nRenderType)
 	@Override
 	public void actionPerformed(ActionEvent e) {
 
+		//SAVE VIEW
+		if(e.getSource() ==  butSaveView)
+		{
+			dialSaveView();
+		}
+
 		//SETTINGS
 		if(e.getSource() == butSettings)
 		{

src/main/java/bigtrace/animation/AnimationPanel.java

@@ -45,6 +45,8 @@
 import bigtrace.BigTrace;
 import bigtrace.gui.NumberField;
 import bigtrace.gui.PanelTitle;
+import bigtrace.io.StorylineLoad;
+import bigtrace.io.StorylineSave;
 import bigtrace.rois.Roi3D;
 import ij.Prefs;
 import ij.io.OpenDialog;
@@ -82,7 +84,7 @@ public class AnimationPanel < T extends RealType< T > & NativeType< T > > extend
 
 	int nChangeTotalTimeMode = (int)Prefs.get("BigTrace.nChangeTotalTimeMode", ANIMTIME_END);
 
-	final KeyFrameAnimation<T> kfAnim;
+	final public KeyFrameAnimation<T> kfAnim;
 
 	final JToggleButton butUpdateSlider;
 
@@ -731,7 +733,7 @@ int getTickTime()
 	}
 
 	/** updates timeline display **/
-	void updateKeyMarks()
+	public void updateKeyMarks()
 	{
 		ArrayList<Float> keyPoints = new ArrayList<>();
 		for (int i=0;i<listModel.size();i++)
@@ -743,7 +745,7 @@ void updateKeyMarks()
 	}
 
 	/** updates numbering of keyframes **/
-	void updateKeyIndices()
+	public void updateKeyIndices()
 	{
 		for(int i=0;i<listModel.size(); i++)
 		{
@@ -832,7 +834,7 @@ protected void paintComponent(Graphics g)
 	    }
 	}
 
-	void updateScene()
+	public void updateScene()
 	{			
 		if(listModel.size()>1)
 		{

src/main/java/bigtrace/animation/KeyFrame.java

@@ -62,6 +62,11 @@ public void setMovieTimePoint(float fMovieTimePoint_)
 		return;
 	}
 
+	public float getMovieTimePoint()
+	{
+		return fMovieTimePoint;
+	}
+
 	public KeyFrame duplicate()
 	{
 		final KeyFrame out = new KeyFrame(scene, fMovieTimePoint);

src/main/java/bigtrace/animation/KeyFrameAnimation.java

@@ -16,7 +16,7 @@ public class KeyFrameAnimation < T extends RealType< T > & NativeType< T > >
 	final BigTrace<T> bt;
 	int nTotalTime;
 
-	final DefaultListModel<KeyFrame> keyFrames;
+	final public DefaultListModel<KeyFrame> keyFrames;
 	final ArrayList<AnisotropicTransformAnimator3D> viewAnimate  = new ArrayList<>(); 
 	final ArrayList<Float> timeIntervals = new ArrayList<>();
 	final ArrayList<KeyFrame> fullList = new ArrayList<>();
@@ -44,7 +44,7 @@ public int getTotalTime()
 		return nTotalTime;
 	}
 
-	void updateTransitionTimeline()
+	public void updateTransitionTimeline()
 	{
 		timeIntervals.clear();
 		viewAnimate.clear();

src/main/java/bigtrace/animation/UnCoilAnimation.java

@@ -42,6 +42,7 @@
 import bigtrace.BigTraceData;
 import bigtrace.geometry.Pipe3D;
 import bigtrace.geometry.Plane3D;
+import bigtrace.io.UnCoilHDF5Saver;
 import bigtrace.rois.AbstractCurve3D;
 import bigtrace.rois.LineTrace3D;
 import bigtrace.rois.Roi3D;
@@ -65,7 +66,7 @@ public class UnCoilAnimation < T extends RealType< T > & NativeType< T > > exten
 	public int nUnCoilTask = 0;
 
 	/** interval containing all ROIs **/
-	FinalInterval unionInterval;
+	public FinalInterval unionInterval;
 
 	/** plugin instance **/
 	BigTrace<T> bt;
@@ -85,7 +86,7 @@ public class UnCoilAnimation < T extends RealType< T > & NativeType< T > > exten
 	ArrayList <AbstractCurve3D> allRois;
 
 	/** all intervals for all ROIs **/
-	ArrayList <FinalInterval> allIntervals;
+	public ArrayList <FinalInterval> allIntervals;
 
 	double [] finalOrientation = null;
 

src/main/java/bigtrace/rois/ROIsImportTrackMateBG.java → src/main/java/bigtrace/io/ROIsImportTrackMateBG.java

@@ -1,4 +1,4 @@
-package bigtrace.rois;
+package bigtrace.io;
 
 import java.awt.Color;
 import java.io.FileInputStream;
@@ -13,6 +13,8 @@
 import bigtrace.BigTrace;
 import bigtrace.BigTraceBGWorker;
 import bigtrace.BigTraceData;
+import bigtrace.rois.Point3D;
+import bigtrace.rois.Roi3D;
 import ij.IJ;
 import net.imglib2.RealPoint;
 

src/main/java/bigtrace/rois/ROIsLoadBG.java → src/main/java/bigtrace/io/ROIsLoadBG.java

@@ -1,4 +1,4 @@
-package bigtrace.rois;
+package bigtrace.io;
 
 import java.awt.Color;
 import java.io.BufferedReader;
@@ -13,6 +13,13 @@
 import bigtrace.BigTrace;
 import bigtrace.BigTraceBGWorker;
 import bigtrace.BigTraceData;
+import bigtrace.rois.CrossSection3D;
+import bigtrace.rois.LineTrace3D;
+import bigtrace.rois.Point3D;
+import bigtrace.rois.PolyLine3D;
+import bigtrace.rois.Roi3D;
+import bigtrace.rois.Roi3DGroup;
+import bigtrace.rois.Roi3DGroupManager;
 
 import net.imglib2.RealPoint;
 import net.imglib2.type.NativeType;

src/main/java/bigtrace/rois/ROIsSaveBG.java → src/main/java/bigtrace/io/ROIsSaveBG.java

@@ -1,4 +1,4 @@
-package bigtrace.rois;
+package bigtrace.io;
 
 import java.io.File;
 import java.io.FileWriter;
@@ -11,6 +11,7 @@
 import bigtrace.BigTrace;
 import bigtrace.BigTraceBGWorker;
 import bigtrace.BigTraceData;
+import bigtrace.rois.Roi3DGroupManager;
 import ij.IJ;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;

src/main/java/bigtrace/animation/StorylineLoad.java → src/main/java/bigtrace/io/StorylineLoad.java

@@ -1,4 +1,4 @@
-package bigtrace.animation;
+package bigtrace.io;
 
 import java.io.BufferedReader;
 import java.io.FileNotFoundException;
@@ -12,13 +12,17 @@
 
 import bigtrace.BigTrace;
 import bigtrace.BigTraceData;
+import bigtrace.animation.AnimationPanel;
+import bigtrace.animation.KeyFrame;
+import bigtrace.animation.KeyFrameAnimation;
+import bigtrace.animation.Scene;
 
 
 public class StorylineLoad < T extends RealType< T > & NativeType< T > > 
 {
 
 	/** plugin instance **/
-	BigTrace<T> bt;
+	final BigTrace<T> bt;
 
 	final AnimationPanel< T > aPanel;
 

src/main/java/bigtrace/animation/StorylineSave.java → src/main/java/bigtrace/io/StorylineSave.java

@@ -1,4 +1,4 @@
-package bigtrace.animation;
+package bigtrace.io;
 
 import java.io.File;
 import java.io.FileWriter;
@@ -11,13 +11,15 @@
 
 import bigtrace.BigTrace;
 import bigtrace.BigTraceData;
+import bigtrace.animation.AnimationPanel;
+import bigtrace.animation.KeyFrame;
 import ij.IJ;
 
 public class StorylineSave < T extends RealType< T > & NativeType< T > > 
 {
 
 	/** plugin instance **/
-	BigTrace<T> bt;
+	final BigTrace<T> bt;
 	final AnimationPanel< T > aPanel;
 
 	public StorylineSave(final BigTrace<T> bt_, AnimationPanel< T > aPanel_)
@@ -36,16 +38,16 @@ public void saveAnimation(String sFilename)
 			symbols.setDecimalSeparator('.');
 			DecimalFormat df3 = new DecimalFormat ("#.#####", symbols);
 			writer.write("BigTrace_StoryLine,version," + BigTraceData.sVersion + "\n");
-			writer.write("TotalTime," + Integer.toString(aPanel.kfAnim.nTotalTime) + "\n");
+			writer.write("TotalTime," + Integer.toString(aPanel.kfAnim.getTotalTime()) + "\n");
 			final int nTotKeyFramesN = aPanel.kfAnim.keyFrames.size();
 			writer.write("KeyFrameNumber," + Integer.toString(nTotKeyFramesN) + "\n");
 			for(int nKF=0; nKF < nTotKeyFramesN; nKF++)
 			{
 				KeyFrame currKF =  aPanel.kfAnim.keyFrames.get( nKF );
 				writer.write("KeyFrame,"+Integer.toString(nKF+1)+"\n");
 				writer.write("KeyFrameName,"+currKF.getName()+"\n");
-				writer.write("KeyFrameTime," + df3.format(currKF.fMovieTimePoint) + "\n");
-				currKF.scene.save( writer );
+				writer.write("KeyFrameTime," + df3.format(currKF.getMovieTimePoint()) + "\n");
+				currKF.getScene().save( writer );
 
 			}
 			writer.write("End of BigTrace Story Line\n");

src/main/java/bigtrace/animation/UnCoilFrameImgLoader.java → src/main/java/bigtrace/io/UnCoilFrameImgLoader.java

@@ -1,4 +1,4 @@
-package bigtrace.animation;
+package bigtrace.io;
 
 import net.imglib2.Dimensions;
 import net.imglib2.FinalDimensions;
@@ -15,6 +15,7 @@
 
 import bigtrace.BigTrace;
 import bigtrace.BigTraceData;
+import bigtrace.animation.UnCoilAnimation;
 import mpicbg.spim.data.generic.sequence.BasicImgLoader;
 import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
 import mpicbg.spim.data.generic.sequence.ImgLoaderHint;

src/main/java/bigtrace/animation/UnCoilHDF5Saver.java → src/main/java/bigtrace/io/UnCoilHDF5Saver.java

@@ -1,4 +1,4 @@
-package bigtrace.animation;
+package bigtrace.io;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -27,6 +27,7 @@
 import bdv.spimdata.XmlIoSpimDataMinimal;
 import bigtrace.BigTrace;
 import bigtrace.BigTraceData;
+import bigtrace.animation.UnCoilAnimation;
 import mpicbg.spim.data.generic.sequence.BasicViewSetup;
 import mpicbg.spim.data.registration.ViewRegistration;
 import mpicbg.spim.data.registration.ViewRegistrations;

src/main/java/bigtrace/io/ViewsIO.java

@@ -0,0 +1,39 @@
+package bigtrace.io;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+
+import bigtrace.BigTrace;
+import bigtrace.BigTraceData;
+import ij.IJ;
+
+public class ViewsIO
+{
+
+	/** saving current view as csv **/
+	public static < T extends RealType< T > & NativeType< T > > void saveView(final BigTrace<T> bt, String sFilename)
+	{		
+		bt.bInputLock = true;
+		bt.setLockMode(true);
+        try {
+			final File file = new File(sFilename);
+
+			try (FileWriter writer = new FileWriter(file))
+			{
+				writer.write("BigTrace_View,version," + BigTraceData.sVersion + "\n");
+				writer.write("End of BigTrace View\n");
+				writer.close();
+			}
+
+			bt.btPanel.progressBar.setString("saving view done.");
+		} catch (IOException e) {	
+			IJ.log(e.getMessage());
+			//e.printStackTrace();
+		}
+	}	
+
+}