Merge pull request #41 from xmaptools/dev-b1-lanari

Merge for final deployment of 4.5 beta 1

Author: lanari

Changelog.md

@@ -2,14 +2,18 @@
 
 ## XMapTools 4.5 (no build yet)
 
-This version is highly recommended for all users as it includes new features, compatibility enhancements, bug fixes and stability improvements to the software.
-
-- Compatibility information for MacOS users:
-Note that the public compiled version of XMapTools 4.5 runs natively on Apple Silicon Macs using MATLAB Runtime 24.3, resulting in a significant performance gain. However, the version of XMapTools 4.5 compatible with the M-Series chip is limited to MacOS Ventura (13), Sonoma (14), Sequoia (15) and more recent. The previous MATLAB runtime version v912 can be removed after upgrading to XMapTools 4.5 final release.
+This release is highly recommended for all users as it includes new features, performance and compatibility enhancements, bug fixes and stability improvements to the software.
 
+- Major update and compatibility notes:
+  - MacOS compatibility: XMapTools 4.5 runs natively on Apple Silicon Macs using MATLAB Runtime 25.1, resulting in a significant performance gain. However, the version of XMapTools 4.5 compatible with the M-Series chip is limited to MacOS Ventura (13), Sonoma (14), Sequoia (15) and newer. The previous MATLAB runtime version v912 can be removed after installing this version.
+  - Windows compatibility: XMapTools 4.5 is only compatible with Windows 10 and Windows 11. The previous MATLAB runtime version v912 can be removed after installing this version.
+  - MacOS Installation and Update: The initial installation of XMapTools 4.5 and MATLAB Runtime 25.1 can be performed using the terminal command "curl -fsSL https://xmaptools.ch/install.sh | bash". In the future, XMapTools updates on MacOS will be distributed using the terminal command "curl -fsSL https://xmaptools.ch/update.sh | bash".
+  - Windows installation and Update: ...
+  
 - General:
   - Add an image converter module (in Add-ons) to convert images into numerical values stored in text files that can be imported into XMapTools. The converter module has additional tools to set the minimum and maximum value and to crop the image.
   - Enhance the Data Export module with a new mode that randomly selects n pixels to export. This can be combined with other export formats in the same file.
+  - Add an option to display the "bulk value (average)" of plotted pixels in binary and ternary plots in the Data Visualisation module, improving the statistical output of the plots.
   - Add an option to change the colour of the ROI drawn in the main windows and modules. The default colour is selected when the program starts, but the user's choice is saved for each project.
 
 - LA-ICP-MS: 
@@ -18,7 +22,6 @@ Note that the public compiled version of XMapTools 4.5 runs natively on Apple Si
   - Add a new compatible format for automatic identification of the analysis ID. The list of compatible formats is "Name - ID", "Name-ID", "Name_ID".
   - Add a check to detect if the wrong format of the name has been selected and the analysis ID cannot be retrieved.
 
-
 - Other:
   - Add the creation of colormap data on opening to allow modules to use the default colormap before the first map is displayed.
   - Correction of an error in the data converter for the LA-ICP-MS module that prevented the manual adjustment of the integration sweep for the primary and secondary standards.
@@ -242,7 +245,7 @@ Release 4.1 includes new functionalities and updates to XMapTools and improvemen
 
 
 
-## XMapTools 4 beta 4 Developer (no public release yet)
+## XMapTools 4.0 beta 4 Developer (no public release yet)
 - Release notes:
   - Add tools for single-mask classification and the creation of sub-masks. At the moment, it is recommended to use the Random Algorithm forest for creating sub-masks. 
   - Add a point counting tool to evaluate pseudo-modes; XMapTools selects randomly 300 pixels on the map and estimates the modal abundances (in %). A version with uncertainty estimation using Monte-Carlo can be activated in the developer version.
@@ -260,7 +263,7 @@ Release 4.1 includes new functionalities and updates to XMapTools and improvemen
   - Add a mask file signature to ensure data compatibility throughout XMapTools and add-ons  
 
 
-## XMapTools 4 beta 3 Developer (no public release yet)
+## XMapTools 4.0 beta 3 Developer (no public release yet)
 - Release notes:
   - Add the old function to run XMapTools and open immediately a project in the MATLAB version using the command: _XMapTools open ProjectName_
   - ...

Compilation_2025.md

@@ -9,6 +9,7 @@ __Last update 09.05.2025 (Pierre Lanari)__
 - Open the App Designer (open XMapTools or start XMapTools); the code will automatically be updated to the MATLAB version.
 
 - Change the hardcoded version in the startup function.
+- Change the version in the Sharing Details of the main XMapTools object. 
 - Save the project to update the version and code.
 
 - Click "Share" > "Standalone Desktop App". 
@@ -17,7 +18,7 @@ __Last update 09.05.2025 (Pierre Lanari)__
 - Select "Share using a project" in "Manage App Sharing with a MATLAB Project".
 - Edit the name to "XMapTools" and click Ok.
 
-- In the the main MATLAB window and the Project tab, click on "Compiler Task Manager" and select the task. 
+- In the the main MATLAB window and the Project tab, click on "Compiler Task Manager" and select the task by clicking in XMapTools Standalone Application. 
 - Add the following folders manually (important): 
   - Program/Addons/BingoAntidote/Databases/
   - Program/Addons/BingoAntidote/Dev/
@@ -26,25 +27,26 @@ __Last update 09.05.2025 (Pierre Lanari)__
   - Program/Dev/help
   - Program/Dev/help/img
 
-- Select "Fetch MATLAB Runtime" option and change the name to XMapToolsInstaller_macOS_Intel or XMapToolsInstaller_macOS_AppleSilicon_2025 or XMapToolsInstaller_WIN.  
+- Select "Fetch MATLAB Runtime" option and change the name to XMapToolsInstaller_macOS or XMapToolsInstaller_Windows.  
 
 - Update the Installer Notes: 
 ```
 #### THIS IS A BETA VERSION OF XMAPTOOLS: Some features will only be available in the public release ####
 
 Find out more at https://github.com/xmaptools/XMapTools_Developers/blob/main/Changelog.md
 ```
-```
---
-  
-Remember that you need to update permissions on macOS before to run XMapTools: https://resources.xmaptools.ch/installation-macos/
-Open a terminal and type in: chmod -R 755 /Applications/XMapTools/
-```  
 
 - Select the splash screen
 - Select the icon
 - Select the Sidebar Image
 
 - Click "Build and Package"
 
+- Zip the installer for macOS using: 
+```
+ditto -c -k --sequesterRsrc --keepParent "XMapToolsInstaller_macOS.app" "XMapToolsInstaller_macOS.zip"
+```
+```
+ditto -c -k --sequesterRsrc --keepParent "XMapTools.app" "XMapTools_macOS.zip"
+```
 - If this is a public version, update the version online!  

Program/Dev/help/AddPath_help.m

@@ -0,0 +1,3 @@
+% attemp to help for the compilation on Windows.
+function AppPath_help()
+end

Program/Dev/help/XMT_help_DataVizualizationTools.html

@@ -13,7 +13,7 @@
 
 <BODY>
 <h1> Help > Data Visualization Tools </h1>    	
-<p><i>Help file version 13.01.2024 by M. Tedeschi & P. Lanari</i></p>
+<p><i>Help file version 09.05.2025 by M. Tedeschi & P. Lanari</i></p>
 <br \>
 <hr>
 <p><b>Table of content</b><br \><br \>
@@ -131,11 +131,40 @@ <h4>Low ressource mode</h4>
 
 
 
-<h4>Statistics</h4>
+<h4>Plot "Bulk Value" (Average)</h4>
+
+<p> The "Bulk Value" (Average) is calculated from the data plotted in the figure, e.g. 20% when Low Resource Mode is enabled. There is <u>no</u> density correction applied, so deviations from the true bulk composition are expected if phases have different densities.</p>
+
+
+<h4>Statistics and plotting report</h4>
 
 <p>Statistics are reported in the Statistics section and are updated each time the plot is changed.</p>
 
-<p>A detailed description will be added in the future.</p>
+<p>The statistics section can contain the following information:</p>
+<ul>
+  <li>Bulk Value (average of plotted pixels) in binary & ternary plots if the "Plot "Bulk Value" (Average)" option is enabled.</li>
+  <li>Bulk Value (std of plotted pixels) in binary & ternary plots if the "Plot "Bulk Value" (Average)" option is enabled.</li>
+  <li>Bulk Value (relative fraction of <i>X</i>, <i>Y</i> and <i>Z</i>) in ternary plots if the "Plot "Bulk Value" (Average)" option is enabled.</li>
+  <li>Correlation coefficient between <i>X</i> and <i>Y</i> in binary plots.</li>
+</ul>
+
+<p>The plotting report section can contain the following information:</p>
+
+<ul>
+  <li>Plot type and Low Resource Mode status.</li>
+  <li>Size of dataset: number of pixels and fraction displayed. </li>
+  <li>Various plotting times that can be reported to the developers in case of problems with the module (see example below).</li>
+</ul>
+
+<code>Plotting binary data [low ressource mode: ON]</code> <br /><br />
+
+<code>Size of dataset: 687718 data points (20% plotted)</code><br />
+<code>Extracting & Plotting data: 0.10176s</code><br />
+<code>Adjusting plot; force plotting: 0.089678s</code><br />
+<code>Calculating and plotting the density map : 0.34156s</code><br />
+<code>Final update of plots & interface : 0.00819s</code><br />
+<code>Drawnow : 0.073919s</code><br />
+
 
 
 

Program/Dev/help/img/AddPath_help_img.m

@@ -0,0 +1,3 @@
+% attemp to help for the compilation on Windows.
+function AppPath_help_img()
+end

Program/Dev/icons/113-server.png

@@ -93,7 +93,7 @@ function createComponents(app)
             app.Information.FontSize = 11;
             app.Information.Layout.Row = [7 10];
             app.Information.Layout.Column = [2 7];
-            app.Information.Text = {'XMapTools is a free software solution for the analysis of chemical maps developed by Prof. Pierre Lanari at the University of Lausanne, Switzerland.

'; ''; 'Main contributors: Pierre Lanari, Philip Hartmeir, Thorsten Markmann, Joshua Laughton, and Mahyra Tedeschi

'; ''; 'License: GNU General Public License v3.0'; ''; '

Website: https://xmaptools.ch
'; 'Resources: https://resources.xmaptools.ch'; '
Github: https://github.com/xmaptools '; 'PTtoolbox (by J. Laughton): https://github.com/JoshuaLaughton/PTtoolbox '};
+            app.Information.Text = {'XMapTools is a free software solution for the analysis of chemical maps currently developed by Prof. Pierre Lanari at the University of Lausanne, Switzerland.
 and previously at the University of Bern.'; ''; 'Main contributors: Pierre Lanari, Thorsten Markmann, Renée Tamblyn, Joshua Laughton, Philip Hartmeir, and Mahyra Tedeschi

'; ''; 'License: GNU General Public License v3.0'; ''; '

Website: https://xmaptools.ch
'; 'Resources: https://resources.xmaptools.ch'; '
Github: https://github.com/xmaptools '; 'PTtoolbox (by J. Laughton): https://github.com/JoshuaLaughton/PTtoolbox '};
 
             % Show the figure after all components are created
             app.XMapTools_Info.Visible = 'on';