add to swap axis if only one time point and several Z

src/main/java/fiji/plugin/trackmate/LoadTrackMatePlugIn.java

@@ -136,7 +136,8 @@ public void run( final String filePath )
 		ImagePlus imp = reader.readImage();
 		if ( null == imp )
 			imp = ViewUtils.makeEmpytImagePlus( model );
-
+
+
 		/*
 		 * Read settings.
 		 */
@@ -151,6 +152,11 @@ public void run( final String filePath )
 					+ "The file did not contain a settings element. Using default values." );
 			settings = new Settings( imp );
 		}
+
+                /**
+                 * Check if settings and image dimensions don't match in Z and T dimensions
+                 */
+                GuiUtils.checkDimensionsImpAndSettings( imp, settings );
 
 		/*
 		 * Declare the analyzers that are in the settings to the model. This is

src/main/java/fiji/plugin/trackmate/gui/GuiUtils.java

@@ -21,6 +21,7 @@
  */
 package fiji.plugin.trackmate.gui;
 
+
 import java.awt.Color;
 import java.awt.Component;
 import java.awt.Desktop;
@@ -62,6 +63,7 @@
 import org.scijava.prefs.PrefService;
 
 import fiji.plugin.trackmate.util.TMUtils;
+import fiji.plugin.trackmate.Settings;
 import ij.IJ;
 import ij.ImagePlus;
 import ij.measure.Calibration;
@@ -255,6 +257,44 @@ public static final void userCheckImpDimensions( final ImagePlus imp )
 			}
 		}
 	}
+
+        /**
+         * Check if the image dimensions and the dimensions in the settings match
+         * @param imp movie to check Z and T dimensions
+         * @param settings settings loaded from TrackMate file
+         */
+        public static final void checkDimensionsImpAndSettings( final ImagePlus imp, final Settings settings )
+	{
+		final int[] dims = imp.getDimensions();
+                // dimension of image and .xml metadata match, don't do anything
+                if ( ( settings.nslices == dims[3] ) && ( settings.nframes == dims[4] ) )
+                    return;
+
+		if ( dims[ 4 ] == 1 && dims[ 3 ] > 1 )
+		{
+                    	switch ( JOptionPane.showConfirmDialog( null,
+					"It appears this image has 1 timepoint but "
+							+ dims[ 3 ]
+							+ " slices, while the TrackMate file has "+settings.nframes+" timepoint and "+settings.nslices+" slices.\n"
+							+ "Do you want to swap Z and T?",
+					"Z/T swapped?", JOptionPane.YES_NO_CANCEL_OPTION ) )
+			{
+			case JOptionPane.YES_OPTION:
+				imp.setDimensions( dims[ 2 ], dims[ 4 ], dims[ 3 ] );
+				final Calibration calibration = imp.getCalibration();
+				if ( 0. == calibration.frameInterval )
+				{
+					calibration.frameInterval = 1;
+					calibration.setTimeUnit( "frame" );
+				}
+				break;
+
+			case JOptionPane.CANCEL_OPTION:
+				return;
+			}
+		}
+	}
+
 
 	public static void setSystemLookAndFeel()
 	{