ShollTreeCmd: Improvements to bulk saving of files

Author: tferr

src/main/java/sc/fiji/snt/SNTUtils.java

@@ -233,6 +233,13 @@ public static String stripExtension(final String filename) {
 		return (lastDot > 0) ? filename.substring(0, lastDot) : filename;
 	}
 
+	public static File getUniquelySuffixedTifFile(final File referenceFile) {
+		if (referenceFile != null && !referenceFile.isDirectory() && !referenceFile.getName().endsWith(".tif")) {
+			return getUniquelySuffixedFile(new File(referenceFile.getAbsolutePath() + ".tif"));
+		}
+		return getUniquelySuffixedFile(referenceFile);
+	}
+
 	public static File getUniquelySuffixedFile(final File referenceFile) {
 		if (referenceFile.exists()) {
 			final String extension = "." + FileUtils.getExtension(referenceFile);

src/main/java/sc/fiji/snt/analysis/sholl/gui/ShollPlot.java

@@ -492,7 +492,7 @@ public boolean save(String filepath) {
 	public boolean save(final File file) {
 		if (file == null) return false;
 		final File outFile = (file.isDirectory())
-				? SNTUtils.getUniquelySuffixedFile(new File(file, getImagePlus().getTitle()))
+				? SNTUtils.getUniquelySuffixedTifFile(new File(file, getImagePlus().getTitle()))
 				: file;
 		return IJ.saveAsTiff(getImagePlus(), outFile.getAbsolutePath());
 	}

src/main/java/sc/fiji/snt/analysis/sholl/gui/ShollTable.java

@@ -348,7 +348,7 @@ public boolean saveSilently(final File file) { // csv extension appended as need
 		if (file.isDirectory()) {
 			String fName = getTitle();
 			if (fName == null || fName.trim().isEmpty())
-				fName = "Sholl_Table.csv";
+				fName = "Sholl_Table-1.csv";
 			savedFile = SNTUtils.getUniquelySuffixedFile(new File(file, fName));
 		} else {
 			savedFile = file;

src/main/java/sc/fiji/snt/plugin/ShollAnalysisTreeCmd.java

@@ -836,7 +836,7 @@ else if (output instanceof ShollTable) {
 					}
 					else if (output instanceof ImagePlus) {
 						final ImagePlus imp = (ImagePlus)output;
-						final File outFile = SNTUtils.getUniquelySuffixedFile(new File(saveDir, imp.getTitle()));
+						final File outFile = SNTUtils.getUniquelySuffixedTifFile(new File(saveDir, imp.getTitle()));
 						if (!IJ.saveAsTiff(imp, outFile.getAbsolutePath())) ++failures;
 					}
 				}
@@ -853,10 +853,11 @@ private ShollPlot showOrRebuildPlot(ShollPlot plot,
 			final ShollStats stats)
 		{
 			if (plot != null && plot.isVisible() && !plot.isFrozen()) {
-				plot.rebuild(stats);
-				showStatus("Plot updated...");
+				// TODO: Check why plot#rebuild keeps reference to old plot#ImagePlus
+//				plot.rebuild(stats); showStatus("Plot updated..."); 
+				plot.getImagePlus().close(); // Dispose image for now, until plot#rebuild is not patched
 			}
-			else {
+			{
 				plot = new ShollPlot(stats, false);
 				plot.show();
 			}