From 6f6e828b3453fbfd59d4fd65731b5117e3d941d5 Mon Sep 17 00:00:00 2001
From: Wayne Rasband <rasband@gmail.com>
Date: Fri, 24 May 2024 22:33:46 -0400
Subject: [PATCH] 2024.05.24 (1.54j22; ROI Manager saving)

---
 functions.html                  | 12 +++++++++---
 ij/IJ.java                      |  1 +
 ij/ImageJ.java                  |  2 +-
 ij/Prefs.java                   |  2 ++
 ij/gui/GenericDialog.java       |  6 +++++-
 ij/gui/StackWindow.java         |  2 ++
 ij/macro/Functions.java         |  6 ++++--
 ij/plugin/ZProjector.java       | 29 +++++++++++++++--------------
 ij/plugin/frame/RoiManager.java |  4 ++--
 release-notes.html              | 18 +++++++++++++++++-
 10 files changed, 58 insertions(+), 24 deletions(-)

diff --git a/functions.html b/functions.html
index aa3b1bcf7..2eea6f68d 100644
--- a/functions.html
+++ b/functions.html
@@ -4542,6 +4542,13 @@ <h1>Built-in Macro Functions</h1>
 Enables/disables monospaced text in the "Log" window.
 Requires 1.54c.
 <br>
+
+<a name="setOption_MouseWheelStackScrolling"></a>
+<b>setOption("MouseWheelStackScrolling", boolean)</b><br>
+Enables/disables mouse wheel stack scrolling.
+Requires 1.54j.
+<br>
+
 <a name="setOption_OpenGrayscaleJpegsAsRGB"></a>
 <b>setOption("OpenGrayscaleJpegsAsRGB", boolean)</b><br>
 Enable to open grayscale RGB JPEGs as RGB images.
@@ -5431,8 +5438,7 @@ <h1>Built-in Macro Functions</h1>
 To display a multi-line
 message, add newline characters ("\n") to <i>string</i>. 
 This function is based on 
-Michael Schmid's
-<a href="https://imagejdocu.tudor.lu/imagej-documentation-wiki/plugins/wait_for_user">Wait_For_User</a> plugin.
+Michael Schmid's "Wait For User" plugin.
 Example:
 <a href="../../macros/WaitForUserDemo.txt">WaitForUserDemo</a>.
 <p>
@@ -5453,7 +5459,7 @@ <h1>Built-in Macro Functions</h1>
 
 <p class=navbar> <a href="#Top">top</a> | <a href="https://imagej.nih.gov/ij/index.html">home</a></p>
 
-<small>Last updated 2024/03/13</small>
+<small>Last updated 2024/05/15</small>
 
 </body>
 </html>
diff --git a/ij/IJ.java b/ij/IJ.java
index 03202c1ef..8e05de270 100644
--- a/ij/IJ.java
+++ b/ij/IJ.java
@@ -812,6 +812,7 @@ public static void showMessage(String title, String msg) {
 				if (isMacro() && md.escapePressed())
 					throw new RuntimeException(Macro.MACRO_CANCELED);
 			}
+			IJ.wait(25); // fix GenericDialog non-editable text field
 		} else
 			System.out.println(msg);
 	}
diff --git a/ij/ImageJ.java b/ij/ImageJ.java
index 51ec2a8ac..bca69cbf9 100644
--- a/ij/ImageJ.java
+++ b/ij/ImageJ.java
@@ -79,7 +79,7 @@ public class ImageJ extends Frame implements ActionListener,
 
 	/** Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string. */
 	public static final String VERSION = "1.54j";
-	public static final String BUILD = "15";
+	public static final String BUILD = "22";
 	public static Color backgroundColor = new Color(237,237,237);
 	/** SansSerif, 12-point, plain font. */
 	public static final Font SansSerif12 = new Font("SansSerif", Font.PLAIN, 12);
diff --git a/ij/Prefs.java b/ij/Prefs.java
index 95dd78ba1..79a6eee62 100644
--- a/ij/Prefs.java
+++ b/ij/Prefs.java
@@ -197,6 +197,8 @@ public class Prefs {
 	public static boolean calibrateConversions;
 	/** Open grayscale RGB JPEGs as RGB */
 	public static boolean openGrayscaleJpegsAsRGB;
+	/** Scroll stacks using mouse wheel */
+	public static boolean mouseWheelStackScrolling = true;
 
 	//Save location of moved image windows */	
 	//public static boolean saveImageLocation = true;
diff --git a/ij/gui/GenericDialog.java b/ij/gui/GenericDialog.java
index 47ec38c6f..a67f5ad72 100644
--- a/ij/gui/GenericDialog.java
+++ b/ij/gui/GenericDialog.java
@@ -2005,7 +2005,11 @@ public TextDropTarget(TextField text) {
 		@Override
 		public void drop(DropTargetDropEvent event) {
 			try {
-				text.setText(getString(event));
+				String path = getString(event);
+				path = Recorder.fixPath(path);
+				if (!path.endsWith("/")&& (new File(path)).isDirectory())
+					path = path + "/";
+				text.setText(path);
 			} catch (Exception e) { e.printStackTrace(); }
 		}
 	}
diff --git a/ij/gui/StackWindow.java b/ij/gui/StackWindow.java
index 8fe40b0bd..df1b48ff9 100644
--- a/ij/gui/StackWindow.java
+++ b/ij/gui/StackWindow.java
@@ -184,6 +184,8 @@ else if (rotation>0)
 					ic.zoomOut(x,y);
 				return;
 			}
+			if (!Prefs.mouseWheelStackScrolling)
+				return;
 			if (hyperStack) {
 				if (rotation>0)
 					IJ.run(imp, "Next Slice [>]", "");
diff --git a/ij/macro/Functions.java b/ij/macro/Functions.java
index 14aa72b2d..bd9a19f45 100644
--- a/ij/macro/Functions.java
+++ b/ij/macro/Functions.java
@@ -4796,7 +4796,9 @@ else if (arg1.startsWith("opengrayscale"))
 		else if (arg1.startsWith("calibrate")) {
 			Prefs.calibrateConversions = state;
 			ImageConverter.setDoScaling(true);
-		} else
+		} else if (arg1.startsWith("mousewheel"))
+			Prefs.mouseWheelStackScrolling = state;
+		else
 			interp.error("Invalid option");
 	}
 
@@ -7149,7 +7151,7 @@ void addDrawingToOverlay(ImagePlus imp) {
 
 	void addRoi(ImagePlus imp, Roi roi){
 		Overlay overlay = imp.getOverlay();
-		if (overlay==null || overlay.size()==0) {
+		if (overlay==null) {
 			if (offscreenOverlay==null)
 				offscreenOverlay = new Overlay();
 			overlay = offscreenOverlay;
diff --git a/ij/plugin/ZProjector.java b/ij/plugin/ZProjector.java
index 550d4f6c0..e357b7f89 100644
--- a/ij/plugin/ZProjector.java
+++ b/ij/plugin/ZProjector.java
@@ -659,20 +659,23 @@ private ImagePlus doAverageFloatProjection(ImagePlus imp) {
 		int d = stack.getSize();
 		ImagePlus projection = IJ.createImage(makeTitle(), "32-bit Black", w, h, 1);
 		ImageProcessor ip = projection.getProcessor();
-		for (int x=0; x<w; x++) {
-			for (int y=0; y<h; y++) {
-				double sum = 0.0;
-				int count = 0;
-				for (int z=startSlice-1; z<stopSlice; z+=increment) {
-					double value = stack.getVoxel(x, y, z);
-					if (!Double.isNaN(value)) {
-						sum += value;
-						count++;
-					}
-				}
-				ip.setf(x, y, (float)(sum/count));
+		double[] sum = new double[w*h];
+		int[] count = new int[w*h];
+		for (int z=startSlice; z<=stopSlice; z+=increment) {
+		    ImageProcessor stackIp = stack.getProcessor(z);
+		    for (int y=0, p=0; y<h; y++) {
+			for (int x=0; x<w; x++, p++) {				
+			    float value = stackIp.getPixelValue(x, y);
+			    if (!Double.isNaN(value)) {
+				sum[p] += value;
+				count[p]++;
+			    }
 			}
+		    }
 		}
+		for (int y=0, p=0; y<h; y++)
+		    for (int x=0; x<w; x++, p++)
+				ip.setf(x, y, (float)(sum[p]/count[p]));
 		ip.resetMinAndMax();
 		return projection;
 	}
@@ -864,5 +867,3 @@ public void postProcess() {
     } // end StandardDeviation
 
 }  // end ZProjection
-
-
diff --git a/ij/plugin/frame/RoiManager.java b/ij/plugin/frame/RoiManager.java
index fbf46e745..52069d388 100644
--- a/ij/plugin/frame/RoiManager.java
+++ b/ij/plugin/frame/RoiManager.java
@@ -980,8 +980,8 @@ boolean saveMultiple(int[] indexes, String path) {
 			RoiEncoder re = new RoiEncoder(out);
 			for (int i=0; i<indexes.length; i++) {
 				IJ.showProgress(i, indexes.length);
-				String label = (String)listModel.getElementAt(i);
 				Roi roi = (Roi)rois.get(indexes[i]);
+				String label = (String)listModel.getElementAt(indexes[i]);
 				if (IJ.debugMode) IJ.log("saveMultiple: "+i+"  "+label+"  "+roi);
 				if (roi==null) continue;
 				if (!label.endsWith(".roi")) label += ".roi";
@@ -1491,7 +1491,7 @@ boolean drawOrFill(int mode) {
 			if (roi==null) continue;
 			if (mode==FILL&&(type==Roi.POLYLINE||type==Roi.FREELINE||type==Roi.ANGLE))
 				mode = DRAW;
-			String name = (String) listModel.getElementAt(indexes[i]);
+			String name = (String)listModel.getElementAt(indexes[i]);
 			int slice2 = getSliceNumber(roi, name);
 			if (slice2>=1 && slice2<=imp.getStackSize()) {
 				imp.setSlice(slice2);
diff --git a/release-notes.html b/release-notes.html
index e0e577bbc..9dcf5542a 100644
--- a/release-notes.html
+++ b/release-notes.html
@@ -5,7 +5,7 @@
 </head>
 <body>
 
-<li> <u>1.54j15  15 April 2024</u>
+<li> <u>1.54j22  24 May 2024</u>
 <ul>
 <li> Thanks to 'ramnoob', added a number of official tags 
 to the DICOM reader.
@@ -15,6 +15,9 @@
 <li> Thanks to Gabriel Landini, ImageJ adds an "*" next to
 the Mode value in the Histogram window if the histogram is
 multi-modal.
+<li> Thanks to Norbert Vischer, added the
+setOption("MouseWheelStackScrolling",boolean) macro
+function.
 <li> Thanks to Albert Cardona and Curtis Rueden, added
 public setEqualize() and setSaturated() methods to the
 ContrastEnhancer class.
@@ -27,6 +30,19 @@
 <li> Thanks to Stein Rorvik, fixed a bug where the
 Table.getColumn() macro function did not work with
 columns containing empty strings.
+<li> Thanks to Norbert Vischer, fixed bug where
+text fields in GenericDialogs opened after a showMessage()
+were non-editable.
+<li> Thanks to Jan Brocher, fixed bug where drag-and-drop of
+directories onto GenericDialog directory fields did not
+work as expected.
+<li> Thanks to Norbert Vischer, fixed an Overlay.clear macro
+function bug.
+<Li> Thanks to Alexander Bender, fixed bug with ROI Manager
+ignoring selection when saving.
+<li> Thanks to Michael Schmid, fixed 1.53t regression
+where Image&gt;Stacks&gt;Z Project</i> failed when doing
+"Average" projection of 32-bit float stacks
 </ul>
 
 <li> <u>1.54i  03 March 2024</u>