Commit ad47d01e authored by Olga Stamati's avatar Olga Stamati
Browse files

[skip-ci] updates to paper according to editor

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......@@ -21,7 +21,8 @@
number={3},
pages={107--112},
year={2012},
publisher={Thomas Telford Ltd}
publisher={Thomas Telford Ltd},
doi={10.1680/geolett.12.00027}
}
@article{ando2019peek,
......@@ -44,7 +45,8 @@
number={3},
pages={165--178},
year={1996},
publisher={Amsterdam: North-Holland, 1982-}
publisher={Amsterdam: North-Holland, 1982-},
doi={10.1016/0167-6636(95)00044-5}
}
@article{bar2014fast,
......@@ -102,7 +104,8 @@
number={11},
pages={1309--1331},
year={2009},
publisher={Wiley Online Library}
publisher={Wiley Online Library},
doi={10.1002/nme.2579}
}
......@@ -114,7 +117,8 @@
number={29},
pages={4293--4307},
year={1996},
publisher={Elsevier}
publisher={Elsevier},
doi={10.1016/0020-7683(95)00240-5}
}
@article{hall2010discrete,
......@@ -125,7 +129,8 @@
number={5},
pages={315--322},
year={2010},
publisher={Thomas Telford Ltd}
publisher={Thomas Telford Ltd},
doi={10.1680/geot.2010.60.5.315}
}
@article{hild2008correliq4,
......@@ -259,10 +264,11 @@ volume = "11",
pages = "100391",
year = "2020",
issn = "2352-7110",
doi = "https://doi.org/10.1016/j.softx.2019.100391",
doi = {10.1016/j.softx.2019.100391},
url = "http://www.sciencedirect.com/science/article/pii/S2352711019301967",
author = "Sindre Nordmark Olufsen and Marius Endre Andersen and Egil Fagerholt"
}
@article{numpy,
author = {Van der Walt, Stefan and Colbert,S. Chris and Varoquaux,Gaël },
title = {The NumPy Array: A Structure for Efficient Numerical Computation},
......@@ -317,7 +323,7 @@ author = "Sindre Nordmark Olufsen and Marius Endre Andersen and Egil Fagerholt"
pages = "180 - 196",
year = "2015",
issn = "0020-7683",
doi = "https://doi.org/10.1016/j.ijsolstr.2014.10.001",
doi = {10.1016/j.ijsolstr.2014.10.001},
url = "http://www.sciencedirect.com/science/article/pii/S0020768314003710",
author = "Emmanuel Roubin and Alexis Vallade and Nathan Benkemoun and Jean-Baptiste Colliat",
keywords = "Heterogeneous quasi-brittle material, Strong discontinuity approach, E-FEM method, EAS method",
......@@ -406,9 +412,9 @@ author = "Sindre Nordmark Olufsen and Marius Endre Andersen and Egil Fagerholt"
title = "{SciPy 1.0: Fundamental Algorithms for Scientific
Computing in Python}",
journal = {Nature Methods},
year = "2020",
year = "2020",
adsurl = {https://rdcu.be/b08Wh},
doi = {https://doi.org/10.1038/s41592-019-0686-2},
doi = {10.1038/s41592-019-0686-2},
}
@article{stamati2018phase,
......@@ -543,7 +549,8 @@ author = "Sindre Nordmark Olufsen and Marius Endre Andersen and Egil Fagerholt"
number={1},
pages={79--93},
year={2020},
publisher={Springer}
publisher={Springer},
doi={10.1007/s11440-019-00869-9}
}
@article{zhang2015large,
......
......@@ -205,11 +205,11 @@ Currently, the most-used scripts are related to image correlation:
Spam is based on simple Python data types, avoiding complex data structures, and all functions have a reasonable and safe set of default parameters, with required parameters kept to a minimum.
Spam has a number of different use cases:
- Use in a highly interactive manner in iPython or Jupyter. Many outputs from 3D analysis in materials science are highly sensitive to the parameters used, encouraging a "live" exploration of optimal settings
- Interactive use, such as in iPython or Jupyter. Many outputs from 3D analysis in materials science are highly sensitive to the parameters used, encouraging a "live" exploration of optimal settings
- To be imported and used within user-written Python scripts
- Embedded use, such as importing in user-written Python scripts
- Standalone use of more complex `spam-` scripts. These chain together a number of functions and are intended to be called from a command line, and produce output as live plots, or files saved to disk
- Standalone use, particularly of the more complex `spam-` scripts. These chain together a number of functions and are intended to be called from a command line, and produce output as live plots, or files saved to disk
Given the large data volumes often encountered in 3D analysis, critical parts of the code are written in C/C++ wrapped with appropriate Python calling functions which are responsible for checking input sanity.
The current wrapping method is with pybind11 [@pybind11].
......@@ -238,8 +238,8 @@ There are three main components to the documentation:
<!-- # Other software available -->
# State of the field
Other software packages exist for material science analysis, such as the popular commercial software Avizo whose closedness makes it unsuitable inspection and therefore trust.
Other open-source packages could be ITK [@schroeder2003itk] which remains quite a complex ecosystem, or ImageJ/Fiji [@imagej2] which is not fully 3D and not perfectly suited to scripting or running remotely.
Other software packages exist for material science analysis, such as the popular commercial software Avizo, which is closed-source, cannot be inspected, and therefore has limited trust.
Other open-source packages include ITK [@schroeder2003itk], which is a quite complex ecosystem, and ImageJ/Fiji [@imagej2], which is not fully 3D and not well-suited to scripting or running remotely.
All of the above have some version of the `label` toolkit which allows discrete objects to be characterised as well as some parts of the `measurements` toolkit.
On the specific topic of Digital Image/Volume Correlation, many pieces of software are available for 2D, surface and 3D image correlation.
......@@ -251,7 +251,7 @@ A number of other image correlation codes exist (this is by far not an exhaustiv
- Correlli: Developed by LMT Cachan, shared with colleagues but not open source [@hild2008correliq4]. Contains a cutting edge integrated DVC global approach
- FIDVC and qDIC: Open source code 2D running on Matlab [@bar2014fast, @Landauer2018] from The Franck Lab which is suitable for measuring large transformations
- FIDVC and qDIC: Open source code 2D running on Matlab [@bar2014fast; @Landauer2018] from The Franck Lab which is suitable for measuring large transformations
- TomoWarp2: Developed by some of the co-authors [@tudisco2017tomowarp2]. This software has a graphical interface for facilitating correlation but is technically limited to displacements/rotations, and has a slow line-search in rotation space
......@@ -266,11 +266,11 @@ A number of other image correlation codes exist (this is by far not an exhaustiv
# Getting `spam`
`spam` is available to Linux users on Python 3 through a `pip` on PyPI package.
`spam` is available for Linux users with Python 3 as a PyPI package installed via `pip`.
Developers or curious users are encouraged to clone the [Git repository](https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam).
Solid build instructions exist for Debian-based environments (in principle any GNU/Linux distribution should work) and for some versions of OSX.
Compilation for Windows has not been attempted given the large number of dependencies, but the availability of Ubuntu through WSL has been sufficient for users.
Compilation for Windows has not been attempted given the large number of dependencies.
However, users have been able to get it `spam` to work using Ubuntu in the Windows Subsystem for Linux (WSL).
# Use in existing work
......
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