xmaptools / xmaptools_developers

This developer repository contains the latest version of the source code of XMapTools (development version; pre-release candidates; no stable version)

Welcome to the Developer Repository for XMapTools 4

This repository contains the most recent version of the MATLAB source code of XMapTools not released in a public version yet. All changes compared to the current public version are listed in the Changelog.

XMapTools official website: https://xmaptools.ch

Documentation (work in progress): https://resources.xmaptools.ch

Public repository: https://github.com/xmaptools/XMapTools_Public

This work is licensed under a GPL-3.0 license.

How to join the developer team?

Contact [email protected]

How to get started

You can pull the current developer version of XMapTools from this directory using the main branch. As changes are not all pushed at the same time, some functionalities of the git version could not work due to compatibility issues. Check the public repository if you are looking for a stable version of XMapTools.

Requirements

• MATLAB R2020b with the Statistics Toolbox, Image Processing Toolbox, Mapping Toolbox. Compatibility with more recent version of MATLAB is not checked.
• For compatibility reasons, you must use MATLAB R2020b if you wish to share modifications made with the MATLAB App Designer.

Warnings

• Never overwrite the main branch if you're not invited to do so; create your own branch if you want to push changes to the server!
• We recommend you to copy the files to a separate folder and to work there in order to avoid any modification of the main branch.

Installation/Update and first steps

• Pull the current developer version of XMapTools from this directory using one of the active branch
• Copy the files to your XMapTools setup directory (a different folder from the GIT: e.g. Documents/XMapTools4/)
• Install MATLAB 2020b and the required toolboxes (see above); it is recommended to use MATLAB 2020b if you want to change the code of XMapTools via the app designer (older versions won't work, newest versions might cause troubles)
• Open MATLAB and navigate to your setup directory
• Type in the MATLAB Command Window >> install_MATLAB
• Type in the MATLAB Command Window >> RESET_CONFIG
• Change the Current Path in MATLAB to a directory containing data
• To launch XMapTools use the command: >> XMapTools
• To open the app designer, use the command: >> start XMapTools

xmaptools_developers's Issues

Improve Converter Module (LA-ICP-MS)

• Automated zoom in does not work for primary standard or the sample
• Home button is buggy

LAICPMS data handeling

Calibration of phase with internal standard:

• saving the LOD for each calibrated phase into one subfolder. At the moment it is queuing all into the "others" folder. Maybe a LOD folder can come in handy
• auto contrasting in the calibration module can be useful for selecting areas for the variable value calibration

Major compatibility issue on macOS (XMapTools 4 beta 2 and 3 dev)

Several users are currently experiencing some major compatibility issues with the standalone applications of XMapTools 4 beta 2, and 3 dev on Mac probably due to additional security measures implemented in macOS. 

The error occurs after starting the classification, independently of the algorithm selected. The following message is displayed by macOS:

One of the key MATLAB library is no longer running. This problem has been reported to MATLAB and we are waiting for a workaround. Several other Mac users have reported the same issue with other programs (e.g. https://ch.mathworks.com/matlabcentral/answers/1735020-library-not-loaded-rpath-libcudart-10-2-dylib) and we hope to get a solution soon.

At the moment, it is not recommended to use XMapTools standalone on macOS as classification is not possible. Many other functionalities such as the sampling tools are affected by this problem.

Updates will be posted below.

Improve Data Visualization tool

• Binary plot could use a log scale plot option (it is possible when calculating the log of an element for now)

Add function to import data from an other project

Example:

• File > Import > Mask File (from project)

Submasks are not displayed in the secondary menu when loading a project

This issue will be solved in XMapTools 4.3 beta 2.

LAICPMS calibration

dwell times for elements are not automatically read from xml-file (AcqMethod.xml)

Improve data compatibility (LA-ICPMS)

Activate select and crop to merged maps

For SEM data.

Suggested by Cam Davidson.

Add natural logarithm to the Generator module

Submitted by Martin Kutzschbach.

Error while importing quantitative maps expressed in oxide wt%

The problem is that the indices of the elements are not updated.

Temporary fix: use the converter and convert from Oxide Wt% to Element wt% and then from the newly generated Element wt% back to Oxide Wt%.

What should be done:

• Check and correct the input function
• Option 1: Add an indice check in the function for opening a project
• Option 2: Add a check function in the menu for dealing with such complex (and unanticipated) cases

Option 2 sounds better as the element/oxide lists are not going to change in the future.

Error classification function

The classification in XMapTools 4 beta 2 does not check the selected maps. An error occurs if maps have been eliminated after adding them to the input list.

Add drift correction module

A drift correction module with options similar to XMapTools 3.4 should be implemented.