Merge pull request #8 from tferr/asa-snt

Implement the ShollAnalysisPlugin
fiji · Oct 25, 2016 · 73ff077 · 73ff077
2 parents 4e0185f + 9e898fb
commit 73ff077
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Showing 7 changed files with 559 additions and 23 deletions.
diff --git a/pom.xml b/pom.xml
@@ -144,12 +144,6 @@
 		<dependency>
 			<groupId>ca.mcgill</groupId>
 			<artifactId>Sholl_Analysis</artifactId>
-			<exclusions>
-				<exclusion>
-					<groupId>*</groupId>
-					<artifactId>*</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -172,6 +166,6 @@
 		</dependency>
 	</dependencies>
 	<properties>
-		<Sholl_Analysis.version>3.6.7</Sholl_Analysis.version>
+		<Sholl_Analysis.version>3.6.8</Sholl_Analysis.version>
 	</properties>
 </project>
diff --git a/src/main/java/tracing/NeuriteTracerResultsDialog.java b/src/main/java/tracing/NeuriteTracerResultsDialog.java
@@ -34,6 +34,7 @@
 import ij.ImagePlus;
 import ij.WindowManager;
 import ij.gui.GenericDialog;
+import ij.gui.WaitForUserDialog;
 import ij.gui.YesNoCancelDialog;
 import ij.io.FileInfo;
 import ij.io.OpenDialog;
@@ -101,7 +102,6 @@ public class NeuriteTracerResultsDialog
 	protected JMenuItem makeLineStackMenuItem;
 	protected JMenuItem exportCSVMenuItemAgain;
 	protected JMenuItem sendToTrakEM2;
-	protected JMenuItem shollAnalysiHelpMenuItem;
 
 	protected JCheckBoxMenuItem mipOverlayMenuItem;
 	protected JCheckBoxMenuItem drawDiametersXYMenuItem;
@@ -714,6 +714,8 @@ public NeuriteTracerResultsDialog( String title,
 		viewMenu = new JMenu("View");
 		menuBar.add(viewMenu);
 
+		menuBar.add(helpMenu());
+
 		loadMenuItem = new JMenuItem("Load traces / SWC file...");
 		loadMenuItem.addActionListener(this);
 		fileMenu.add(loadMenuItem);
@@ -754,10 +756,6 @@ public NeuriteTracerResultsDialog( String title,
 		exportCSVMenuItemAgain.addActionListener(this);
 		analysisMenu.add(exportCSVMenuItemAgain);
 
-		shollAnalysiHelpMenuItem = new JMenuItem("Sholl Analysis help...");
-		shollAnalysiHelpMenuItem.addActionListener(this);
-		analysisMenu.add(shollAnalysiHelpMenuItem);
-
 		String opacityLabel = "Show MIP overlay(s) at "+
 			SimpleNeuriteTracer.OVERLAY_OPACITY_PERCENT+
 			"% opacity";
@@ -1287,10 +1285,6 @@ public void actionPerformed( ActionEvent e ) {
 				imagePlus.show();
 			}
 
-		} else if( source == shollAnalysiHelpMenuItem ) {
-
-			IJ.runPlugIn("ij.plugin.BrowserLauncher", "http://fiji.sc/wiki/index.php/Simple_Neurite_Tracer:_Sholl_analysis");
-
 		} else if( source == cancelSearch ) {
 
 			if( currentState == SEARCHING ) {
@@ -1522,4 +1516,65 @@ public void textValueChanged( TextEvent e ) {
 		plugin.justDisplayNearSlices(nearbySlices(),getEitherSide());
 	}
 
+	private JMenu helpMenu() {
+		final JMenu helpMenu = new JMenu("Help");
+		final String URL = "http://imagej.net/Simple_Neurite_Tracer";
+		JMenuItem mi = menuItemTrigerringURL("Main documentation page", URL);
+		helpMenu.add(mi);
+		helpMenu.addSeparator();
+		mi = menuItemTrigerringURL("Tutorials", URL + "#Tutorials");
+		helpMenu.add(mi);
+		mi = menuItemTrigerringURL("Basic instructions", URL + ":_Basic_Instructions");
+		helpMenu.add(mi);
+		mi = menuItemTrigerringURL("Step-by-step instructions", URL + ":_Step-By-Step_Instructions");
+		helpMenu.add(mi);
+		mi = menuItemTrigerringURL("3D interaction", URL + ":_3D_Interaction");
+		helpMenu.add(mi);
+		helpMenu.addSeparator();
+		mi = menuItemTrigerringURL("List of shortcuts", URL + ":_Key_Shortcuts");
+		helpMenu.add(mi);
+		helpMenu.addSeparator();
+		mi = menuItemTrigerringURL("Sholl analysis: Online help", URL + ":_Sholl_analysis");
+		helpMenu.add(mi);
+		mi = new JMenuItem("Sholl analysis: Offline help");
+		mi.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(final ActionEvent e) {
+				final Thread newThread = new Thread(new Runnable() {
+					@Override
+					public void run() {
+						String modKey = IJ.isMacOSX() ? "Alt" : "Ctrl";
+						modKey += "+Shift";
+						final String instructions = "To manually select the center of analysis:\n"
+								+ "    1. Mouse over the path of interest and press \"G\" to activate it\n"
+								+ "    2. Press \"" + modKey + "\" to select a point along the path\n"
+								+ "    3. Press \"" + modKey + "+A\" to initiate Sholl analysis\n \n"
+								+ "For batch processing run \"Sholl Analysis (Tracings)...\".";
+						final WaitForUserDialog wd = new WaitForUserDialog("Sholl Analysis Cheat Sheet", instructions);
+						wd.show();
+					}
+				});
+				newThread.start();
+			}
+		});
+		helpMenu.add(mi);
+		helpMenu.addSeparator();
+		mi = menuItemTrigerringURL("Ask a question", "http://forum.imagej.net");
+		helpMenu.add(mi);
+		helpMenu.addSeparator();
+		mi = menuItemTrigerringURL("Citing SNT...", URL + "#Citing_Simple_Neurite_Tracer");
+		helpMenu.add(mi);
+		return helpMenu;
+	}
+
+	public static JMenuItem menuItemTrigerringURL(final String label, final String URL) {
+		final JMenuItem mi = new JMenuItem(label);
+		mi.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(final ActionEvent e) {
+				IJ.runPlugIn("ij.plugin.BrowserLauncher", URL);
+			}
+		});
+		return mi;
+	}
 }
diff --git a/src/main/java/tracing/PathAndFillManager.java b/src/main/java/tracing/PathAndFillManager.java
@@ -1719,9 +1719,11 @@ public boolean importSWC( BufferedReader br, boolean assumeCoordinatesIndexVoxel
 				if( previous == -1 )
 					primaryPoints.add( p );
 				else {
-					SWCPoint previousPoint = idToSWCPoint.get( previous );
-					p.previousPoint = previousPoint;
-					previousPoint.addNextPoint( p );
+					SWCPoint previousPoint = idToSWCPoint.get(previous);
+					if (previousPoint != null) {
+						p.previousPoint = previousPoint;
+						previousPoint.addNextPoint(p);
+					}
 				}
 			} catch( NumberFormatException nfe ) {
 				IJ.error( "There was a malformed number in line: "+line );
@@ -1796,7 +1798,8 @@ public boolean importSWC( BufferedReader br, boolean assumeCoordinatesIndexVoxel
 		}
 
 		if( alreadySeen.size() > 0 ) {
-			IJ.error( "Malformed file: there are some misconnected points" );
+			IJ.error("Malformed file: there are some misconnected points.\n"
+					+ "(List will now be shown in ImageJ's Console)");
 			for( int i : alreadySeen ) {
 				SWCPoint p = idToSWCPoint.get( i );
 				System.out.println( "  Misconnected: " + p);

diff --git a/src/main/java/tracing/ShollAnalysisDialog.java b/src/main/java/tracing/ShollAnalysisDialog.java
@@ -545,6 +545,7 @@ public void analyzeWithShollAnalysisPlugin(final String exportDir, final double
 				sa.setCenter(pX, pY, pZ);
 				sa.setUnit(cal.getUnit());
 			}
+			sa.setStepRadius(sphereSeparation);
 			sa.setPrimaryBranches(primaryBranches);
 			sa.setExportPath(exportDir);
 			sa.analyzeProfile(sampled_distances, sampled_counts, !twoDimensional);