From 785f0a439cf914655b1ff0c4161a8bcee5081520 Mon Sep 17 00:00:00 2001
From: Eugene Katrukha <katpyxa@gmail.com>
Date: Mon, 30 Dec 2024 13:44:33 +0100
Subject: [PATCH] traces csv and swc export

---
 src/main/java/bigtrace/io/ROIsExportCSV.java  | 115 +++++++++++++++++
 src/main/java/bigtrace/io/ROIsExportSWC.java  | 120 ++++++++++++++++++
 src/main/java/bigtrace/io/ROIsSaveBG.java     |   3 +-
 .../bigtrace/rois/RoiManager3DDialogs.java    | 102 ++++++++++++---
 4 files changed, 318 insertions(+), 22 deletions(-)
 create mode 100644 src/main/java/bigtrace/io/ROIsExportCSV.java
 create mode 100644 src/main/java/bigtrace/io/ROIsExportSWC.java

diff --git a/src/main/java/bigtrace/io/ROIsExportCSV.java b/src/main/java/bigtrace/io/ROIsExportCSV.java
new file mode 100644
index 0000000..e8a1367
--- /dev/null
+++ b/src/main/java/bigtrace/io/ROIsExportCSV.java
@@ -0,0 +1,115 @@
+package bigtrace.io;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.text.DecimalFormat;
+import java.text.DecimalFormatSymbols;
+import java.util.ArrayList;
+
+import javax.swing.SwingWorker;
+
+import net.imglib2.RealPoint;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+
+import bigtrace.BigTrace;
+import bigtrace.BigTraceBGWorker;
+import bigtrace.rois.AbstractCurve3D;
+import bigtrace.rois.Roi3D;
+
+import ij.IJ;
+
+public class ROIsExportCSV < T extends RealType< T > & NativeType< T > > extends SwingWorker<Void, String> implements BigTraceBGWorker
+{
+	private String progressState;
+	public BigTrace<T> bt;
+	public String sFilename;
+	
+	@Override
+	public String getProgressState()
+	{
+		return progressState;
+	}
+	@Override
+	public void setProgressState(String state_)
+	{
+		progressState=state_;
+	}
+
+	@Override
+	protected Void doInBackground() throws Exception {
+		int nRoi, nRoiN;		
+
+		bt.bInputLock = true;
+    	bt.setLockMode(true);
+    	
+        try {
+			final File file = new File(sFilename);
+			
+			try (FileWriter writer = new FileWriter(file))
+			{
+				//column titles
+				
+				writer.write("ROI_Number,X_coord,Y_coord,Z_coord,ROI_Name,ROI_Type,ROI_Group,ROI_TimePoint\n");
+				DecimalFormatSymbols symbols = new DecimalFormatSymbols();
+				symbols.setDecimalSeparator('.');
+				DecimalFormat df3 = new DecimalFormat ("#.#####", symbols);
+				nRoiN = bt.roiManager.rois.size();
+				String sRoiName;
+				String sRoiGroup;
+				String sRoiType;
+				String sRoiTP;
+				int nRoiCurrN = 0;
+				//writer.write("ROIsNumber," + Integer.toString(nRoiN)+"\n");
+				for(nRoi=0; nRoi<nRoiN; nRoi++)
+				{
+					  //Sleep for up to one second.
+					try {
+						Thread.sleep(1);
+					} catch (InterruptedException ignore) {}
+					setProgress(nRoi*100/nRoiN);
+					if(bt.roiManager.rois.get( nRoi ) instanceof AbstractCurve3D)
+					{
+						nRoiCurrN++;
+						AbstractCurve3D currRoi = ((AbstractCurve3D)bt.roiManager.rois.get( nRoi ));
+						sRoiTP = Integer.toString( currRoi.getTimePoint() );
+						sRoiName = currRoi.getName();
+						sRoiType = Roi3D.intTypeToString( currRoi.getType());
+						sRoiGroup = bt.roiManager.groups.get(currRoi.getGroupInd()).getName();
+						ArrayList< RealPoint > points = currRoi.getJointSegmentResampled();
+						for(int nP=0; nP<points.size(); nP++)
+						{
+							writer.write( Integer.toString( nRoiCurrN ) +"," );
+							for (int d=0;d<3;d++)
+							{
+								writer.write( df3.format(points.get( nP ).getDoublePosition( d ) ) +"," );								
+							}
+							writer.write( sRoiName + "," + sRoiType + "," + sRoiGroup + "," + sRoiTP + "\n");
+						}
+					}
+
+				}
+				writer.close();
+			}
+			setProgress(100);
+			setProgressState("exporting ROIs done.");
+		} catch (IOException e) {	
+			IJ.log(e.getMessage());
+			//e.printStackTrace();
+		}
+		return null;
+	}
+    /*
+     * Executed in event dispatching thread
+     */
+    @Override
+    public void done() 
+    {
+		//unlock user interaction
+    	bt.bInputLock = false;
+    	bt.setLockMode(false);
+		setProgress(100);
+		setProgressState("export ROIs to CSV done.");
+    }
+}
diff --git a/src/main/java/bigtrace/io/ROIsExportSWC.java b/src/main/java/bigtrace/io/ROIsExportSWC.java
new file mode 100644
index 0000000..3bd12fc
--- /dev/null
+++ b/src/main/java/bigtrace/io/ROIsExportSWC.java
@@ -0,0 +1,120 @@
+package bigtrace.io;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.text.DecimalFormat;
+import java.text.DecimalFormatSymbols;
+import java.util.ArrayList;
+
+import javax.swing.SwingWorker;
+
+import net.imglib2.RealPoint;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+
+import bigtrace.BigTrace;
+import bigtrace.BigTraceBGWorker;
+import bigtrace.BigTraceData;
+import bigtrace.rois.AbstractCurve3D;
+
+import ij.IJ;
+
+public class ROIsExportSWC< T extends RealType< T > & NativeType< T > > extends SwingWorker<Void, String> implements BigTraceBGWorker
+{
+	private String progressState;
+	public BigTrace<T> bt;
+	public String sFilename;
+	
+	@Override
+	public String getProgressState()
+	{
+		return progressState;
+	}
+	@Override
+	public void setProgressState(String state_)
+	{
+		progressState=state_;
+	}
+
+	@Override
+	protected Void doInBackground() throws Exception {
+		int nRoi, nRoiN;		
+
+		bt.bInputLock = true;
+    	bt.setLockMode(true);
+    	
+        try {
+			final File file = new File(sFilename);
+			
+			try (FileWriter writer = new FileWriter(file))
+			{
+				DecimalFormatSymbols symbols = new DecimalFormatSymbols();
+				symbols.setDecimalSeparator('.');
+				DecimalFormat df3 = new DecimalFormat ("#.#####", symbols);
+				nRoiN = bt.roiManager.rois.size();
+				long nPointCount = 1;
+				//int nCurrActivePoint;
+				String sRadius;
+				writer.write("#raw "+ bt.btData.sFileNameFullImg+"\n");
+				writer.write("#original_source BigTrace_ver_" +BigTraceData.sVersion+"\n");
+				for(nRoi=0; nRoi<nRoiN; nRoi++)
+				{
+					
+					  //Sleep for up to one second.
+					try {
+						Thread.sleep(1);
+					} catch (InterruptedException ignore) {}
+					setProgress(nRoi*100/nRoiN);
+					if(bt.roiManager.rois.get( nRoi ) instanceof AbstractCurve3D)
+					{						
+						AbstractCurve3D currRoi = ((AbstractCurve3D)bt.roiManager.rois.get( nRoi ));
+						sRadius = df3.format( currRoi.getLineThickness()*0.5*BigTraceData.dMinVoxelSize);
+						ArrayList< RealPoint > points = currRoi.getJointSegmentResampled();
+						for(int nP=0; nP<points.size(); nP++)
+						{
+							writer.write( Long.toString( nPointCount ) +" 0 " );
+							for (int d=0;d<3;d++)
+							{
+								writer.write( df3.format(points.get( nP ).getDoublePosition( d ) ) +" " );								
+							}
+							writer.write( sRadius + " ");
+							if(nP == 0)
+							{
+								writer.write( "-1 \n");
+								
+							}
+							else
+							{
+								writer.write( Long.toString( nPointCount-1 ) + " \n");
+							}							
+							nPointCount++;
+						}
+					}
+
+				}
+				writer.close();
+			}
+			setProgress(100);
+			setProgressState("exporting curve ROIs done.");
+		} catch (IOException e) {	
+			IJ.log(e.getMessage());
+			//e.printStackTrace();
+		}
+		return null;
+	}
+    /*
+     * Executed in event dispatching thread
+     */
+    @Override
+    public void done() 
+    {
+		//unlock user interaction
+    	bt.bInputLock = false;
+    	bt.setLockMode(false);
+		setProgress(100);
+		setProgressState("export traces to SWC done.");
+    }
+
+
+}
diff --git a/src/main/java/bigtrace/io/ROIsSaveBG.java b/src/main/java/bigtrace/io/ROIsSaveBG.java
index d377ff5..2c31c98 100644
--- a/src/main/java/bigtrace/io/ROIsSaveBG.java
+++ b/src/main/java/bigtrace/io/ROIsSaveBG.java
@@ -16,7 +16,8 @@
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 
-public class ROIsSaveBG < T extends RealType< T > & NativeType< T > > extends SwingWorker<Void, String> implements BigTraceBGWorker{
+public class ROIsSaveBG < T extends RealType< T > & NativeType< T > > extends SwingWorker<Void, String> implements BigTraceBGWorker
+{
 
 	private String progressState;
 	public BigTrace<T> bt;
diff --git a/src/main/java/bigtrace/rois/RoiManager3DDialogs.java b/src/main/java/bigtrace/rois/RoiManager3DDialogs.java
index 5011d48..03d8ced 100644
--- a/src/main/java/bigtrace/rois/RoiManager3DDialogs.java
+++ b/src/main/java/bigtrace/rois/RoiManager3DDialogs.java
@@ -23,6 +23,8 @@
 import bigtrace.BigTraceData;
 import bigtrace.gui.GBCHelper;
 import bigtrace.gui.NumberField;
+import bigtrace.io.ROIsExportCSV;
+import bigtrace.io.ROIsExportSWC;
 import bigtrace.io.ROIsImportTrackMateBG;
 import bigtrace.io.ROIsSaveBG;
 import ij.Prefs;
@@ -676,23 +678,85 @@ public void dialGroupVisibility()
 	/** Save ROIS dialog and saving **/
 	public void diagSaveROIs()
 	{
-		String filename;
 		
-		filename = bt.btData.sFileNameFullImg + "_btrois";
-		SaveDialog sd = new SaveDialog("Save ROIs ", filename, ".csv");
-        String path = sd.getDirectory();
-        if (path == null)
-        	return;
-        filename = path + sd.getFileName();
-        
-        bt.setLockMode(true);
-        bt.bInputLock = true;
+		String [] sRoiSaveOptions = new String [] {"Save ROIs BigTrace format","Export interpolated traces CSV", "Export neurite SWC"};	
+
+		String output = (String) JOptionPane.showInputDialog(bt.roiManager, "Save/export ROIs",
+				"Load mode:", JOptionPane.QUESTION_MESSAGE, null,
+				sRoiSaveOptions, // Array of choices
+				sRoiSaveOptions[(int)Prefs.get("BigTrace.SaveRoisMode", 0)]);
+		if(output == null)
+			return;
+
+		int nSaveMode = 0;
+
+		for (int i=0;i<3; i++)
+		{
+			if(output.equals( sRoiSaveOptions[i] ))
+			{
+				nSaveMode = i;
+			}
+		}
+        Prefs.set("BigTrace.SaveRoisMode", nSaveMode);
+
         
-        ROIsSaveBG<T> saveTask = new ROIsSaveBG<>();
-        saveTask.sFilename = filename;
-        saveTask.bt = this.bt;
-        saveTask.addPropertyChangeListener(bt.btPanel);
-        saveTask.execute();
+		String filename;
+		SaveDialog sd;
+		String path;
+		switch (nSaveMode)
+		{
+		case 0: 
+			filename = bt.btData.sFileNameFullImg + "_btrois";
+			sd = new SaveDialog("Save ROIs ", filename, ".csv");
+			path = sd.getDirectory();
+			if (path == null)
+				return;
+			filename = path + sd.getFileName();
+
+			bt.setLockMode(true);
+			bt.bInputLock = true;
+
+			ROIsSaveBG<T> saveTask = new ROIsSaveBG<>();
+			saveTask.sFilename = filename;
+			saveTask.bt = this.bt;
+			saveTask.addPropertyChangeListener(bt.btPanel);
+			saveTask.execute();
+			break;
+		case 1: 
+			filename = bt.btData.sFileNameFullImg + "_traces";
+			sd = new SaveDialog("Export ROIs ", filename, ".csv");
+			path = sd.getDirectory();
+			if (path == null)
+				return;
+			filename = path + sd.getFileName();
+
+			bt.setLockMode(true);
+			bt.bInputLock = true;
+
+			ROIsExportCSV<T> exportTask = new ROIsExportCSV<>();
+			exportTask.sFilename = filename;
+			exportTask.bt = this.bt;
+			exportTask.addPropertyChangeListener(bt.btPanel);
+			exportTask.execute();
+			break;
+		case 2: 
+			filename = bt.btData.sFileNameFullImg + "_traces";
+			sd = new SaveDialog("Export ROIs to SWC ", filename, ".swc");
+			path = sd.getDirectory();
+			if (path == null)
+				return;
+			filename = path + sd.getFileName();
+
+			bt.setLockMode(true);
+			bt.bInputLock = true;
+
+			ROIsExportSWC<T> exportSWCTask = new ROIsExportSWC<>();
+			exportSWCTask.sFilename = filename;
+			exportSWCTask.bt = this.bt;
+			exportSWCTask.addPropertyChangeListener(bt.btPanel);
+			exportSWCTask.execute();
+			break;
+		}
 	}
 	
 	
@@ -721,13 +785,9 @@ void diagLoadROIs()
         if(input == null)
         	 return;
         
-        int nLoadMode;
+        int nLoadMode = 0;
         
-        if(input.equals("Clean load ROIs and groups"))
-        {
-        	nLoadMode = 0;
-        }
-        else
+        if(input.equals(sRoiLoadOptions[1]))
         {
         	nLoadMode = 1;
         }