SPIERS Software

Coded by:

• Mark Sutton ([email protected])
• Russell J. Garwood ([email protected])
• Alan R.T. Spencer ([email protected])

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Relevant references:

Sutton, M.D., Garwood, R.J., Siveter, D.J. & Siveter, D.J. 2012. Spiers and VAXML; A software toolkit for tomographic visualisation, and a format for virtual specimen interchange. Palaeontologia Electronica 15(2): 15.2.5T

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CONTENTS:

1. Copyright and Licence
2. Introduction
3. Installation
4. Minimum Requirements
5. Documentation
6. Contributing to the code
7. Bug reporting and feature requests

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1. Copyright and Licence

All SPIERS code is released under the GNU General Public License. See LICENSE.md files in the programme directories.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but without any warranty.

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2. Introduction

SPIERS (Serial Palaeontological Image Editing and Rendering System) is a package of three programs for the reconstruction and analysis of tomographic (serial image) datasets, such as those obtained from serial-grinding of specimens, or from CT scanning. More details are available in the documentation for each program.

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3. Installation

SPIERS may be compiled using QT from the source code or installed from the binary releases on our GitHub.

Compiling from source

Windows 64-bit - QT Creator + QT v5.x and VTK v8.1 using MSYS2 (64-bit) and MinGW (64-bit)

We recommend you install and use MSYS2 (64-bit) a Windows package manager, based on modern Cygwin (POSIX compatibility layer) and MinGW-w64, that allows easy installation of QT v5.x 64-bit and VTK v8.1.

1. Download and run the latest version of MSYS2 https://www.msys2.org/ for 64-bit Windows. This will be name "mysys2-x86_64-..." for the 64-bit installer.
2. Follow the install instructions. We have used the default install location of "C:\mysys64" and it is here that includes required in the .pro files point. If you install MSYS2 to another location the .pro files will need to be updated to your install location.
3. Once installed open up MSYS2 shell and run the pacman update command: pacman -Syu Note that as this will almost certainly update pacman itself you may have to close down and restart the MYSYS2 shell before re-running the command to finish.
4. Once MSYS2 and pacman are fully updated run the following command to install QT 5.x and its dependencies: pacman -S mingw-w64-x86_64-qt-creator mingw-w64-x86_64-qt5
5. (OPTIONAL) If you intend on debugging the software in QT and wish to use GDB then run the following to install the matching GBD debugger: pacman -S mingw-w64-x86_64-gdb
6. At this stage you should have the following under the MYSYS2 install location:

• {install location}/mingw64 (Main ming64 folder)
• {install location}/mingw64/bin/qmake.exe (QMake for QT version)
• {install location}/mingw64/bin/g++.exe (C++ complier)
• {install location}/mingw64/bin/gcc.exe (C complier)
• {install location}/mingw64/bin/gdb.exe (Debugger | OPTIONAL)

7. We now want to install the VTK v8.1 package. To do this run the following command: pacman -S mingw-w64-x86_64-vtk
8. You should now be able to find the required libraries under "{install location}/mingw64/bin" and the required header (.h) files for QT v5.x and VTK v8.1 under "{install location}/mingw64/include".
9. Use the information above to setup a new 64-bit ming64 kit under QT creator and follow standard QT Creator debug/release procedure.

Ubuntu 22.04/24.04 64-bit - QT v6.x and OpenCV 4.10.0 using GCC (64-bit)

1. Install GCC and QT6.X on your system. You can do this two ways, by using system packages:

sudo apt-get install build-essential libgl1-mesa-dev cmake

sudo apt install qt6-base-dev libqt6core5compat6-dev

Or by downloading and running the installer from Qt: https://download.qt.io/official_releases/qt/

2. SPIERSview requires OpenCV: The Linux version of SPIERSview uses a packaged version, that can also be installed from the Ubuntu packages:

sudo apt-get install libopencv-dev

3. Download source code, or clone using Git:

git clone https://github.com/palaeoware/SPIERS.git

You can then compile SPIERS by opening the .pro file in QT creator and following standard debug/release procedure (or see alternative below). The resulting executables will be placed in their individual bin folders. SPIERS is set up to work with this directory structure. Copy the build folders to your required location if this differs from the build location.

4. Alternatively you can build using the following commands - navigate into the SPIERS source folder in a terminal window:

cd SPIERS

Create a makefile:

qmake6 ./SPIERS.pro

Build by running the make command:

make

You can then copy the build folders to your desired location.

6. Should you wish to create desktop icons or for SPIERS to appear in your launcher, we provide exemplar desktop entries in the SPIERS/examples folder of the repository, coupled with icons for these. Place the icons in the same folder alongside the executable files, and place this folder wherever you would like it to live on your system. The edit the paths to the executables and icons by replacing XXXXX in the example files with your path. Double clicking on the desktop entry will ask you to trust and launch the program. Placing the entry on your desktop will create an icon that launches the software. Additionally, if you open a terminal at the location where the desktop entry is stored, and copy it from there to /usr/share/applications/ using this command:

sudo cp SPIERSalign.desktop /usr/share/applications/

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