Commit 3c7b2ccc authored by Edward Andò's avatar Edward Andò
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Merge the spamPaper into master... finally

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Dear Editors,
We present a paper for ``spam`` a collaborative project which is flourishing.
There are a large number of authors, however all have contributed in a significant way to this paper.
For clarity the contribution of each author is outlined:
- Olga Stamati : Core Developer
- Edward Andò : Core Developer
- Emmanuel Roubin : Core Developer
- Rémi Cailletaud : Core Developer
- M. Wiebicke : Bulk of "contact" toolkit
- Ryan C. Hurley : Initial versions of grain triangulator, bagiStrain
- Robert Caulk : spam.mesh.triangulate C++ CGAL triangulation interface
- Cyrille-B Couture : Implementation of initial regularStrain calculator
- Alejandro Ortega Laborin: ProjMorpho development
- Denis Caillerie : Validation of strain and DVC implementation
- Takashi Matsushima : spam.label.ellipseAxes function
- Olumide Okubadejo : ITKwatershed shim
- Riccardo Rorato : spam.label.trueSphericity function
- Pierre Bésuelle : Validation of strain implementation
- Félix Bertoni : spam.kalisphera C++ port
- Tom Arnaud : spam-mmr-graphical scripts
- Yue Sun : spam.measures.globalDescriptors curvature C++
- Alessandro Tengattini : histogramFitting development
- Jean-Baptiste Colliat : spam.filters.morphologicalOperations
- Mohammad Saadatfar : valdation of grain-strain computation
- Estefan Garcia : spam.label.feretDiameters function
- Christos Papazoglou : Initial version of histogramFitting
- Gustavo Pinzon : Fixes in spam.label.contacts, implementation of directional erosion
- Sébastien Brisard : Initial version of directional erosion
- Jelke Dijkstra : High-strain experimental data for testing of DVC
- Georgios Birmpilis : High-strain experimental data for testing of DVC
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title={An in-situ study of stress evolution and fracture growth during compression of concrete},
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pages={26--40},
year={2019},
publisher={Elsevier},
doi={10.1016/j.ijsolstr.2019.03.015}
}
@article{imagej2,
title={ImageJ2: ImageJ for the next generation of scientific image data},
author={Rueden, Curtis T and Schindelin, Johannes and Hiner, Mark C and DeZonia, Barry E and Walter, Alison E and Arena, Ellen T and Eliceiri, Kevin W},
journal={BMC bioinformatics},
volume={18},
number={1},
pages={529},
year={2017},
publisher={IOP Publishing}
publisher={Springer},
doi={10.1186/s12859-017-1934-z}
}
@misc{ikeda:2000,
title={Three-dimensional study on the interconnection and shape of crystals in a graphic granite by X-ray CT and image analysis},
author={Ikeda, S and Nakano, T and Nakashima, Y},
year={2000},
publisher={De Gruyter},
doi={10.1180/002646100549760}
}
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author="Landauer, AK
and Patel, M
and Henann, DL
and Franck, C",
title="A q-Factor-Based Digital Image Correlation Algorithm (qDIC) for Resolving Finite Deformations with Degenerate Speckle Patterns",
journal="Experimental Mechanics",
year="2018",
issn="1741-2765",
doi="10.1007/s11340-018-0377-4",
url="https://doi.org/10.1007/s11340-018-0377-4"
}
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}
@article{mendoza2019complete,
title={Complete mechanical regularization applied to digital image and volume correlation},
author={Mendoza, Arturo and Neggers, Jan and Hild, Fran{\c{c}}ois and Roux, St{\'e}phane},
journal={Computer Methods in Applied Mechanics and Engineering},
volume={355},
pages={27--43},
year={2019},
publisher={Elsevier},
doi={10.1016/j.cma.2019.06.005}
}
@Article{matplotlib,
......@@ -21,22 +214,170 @@
year = 2007
}
@misc{meshio,
author = {Nico Schlömer and
Geordie McBain and
Keurfon Luu and
Tianyi Li and
christos and
Vicente Mataix Ferrándiz and
Chris Barnes and
Lisandro Dalcin and
eolianoe and
nilswagner and
Vladimír Lukeš and
Abhinav Gupta and
Sebastian Müller and
Leo Schwarz and
Jan Blechta and
Chris Coutinho and
Darcy Beurle and
Jørgen Schartum Dokken and
s1291 and
Iban Cereijo and
Bhavesh Shrimali and
Antonio Cervone and
Shriramana Sharma and
Matthias Bussonnier and
lgiraldi and
Guillaume Jacquenot and
Ghislain Antony Vaillant and
Cian Wilson},
title = {nschloe/meshio v4.0.10},
month = mar,
year = 2020,
publisher = {Zenodo},
version = {v4.0.10},
doi = {10.5281/zenodo.3714194},
url = {https://doi.org/10.5281/zenodo.3714194}
}
@article{muDIC,
title = "μDIC: An open-source toolkit for digital image correlation",
journal = "SoftwareX",
volume = "11",
pages = "100391",
year = "2020",
issn = "2352-7110",
doi = "https://doi.org/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},
journal = {Computing in Science \& Engineering},
volume = {13},
number = {2},
pages = {22-30},
year = {2011},
doi = {10.1109/MCSE.2011.37},
URL = {https://aip.scitation.org/doi/abs/10.1109/MCSE.2011.37},
eprint = {https://aip.scitation.org/doi/pdf/10.1109/MCSE.2011.37}
}
@misc{pybind11,
author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan},
year = {2017},
note = {https://github.com/pybind/pybind11},
title = {pybind11 -- Seamless operability between C++11 and Python}
}
@Manual{Ritself,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2018},
url = {https://www.R-project.org/},
}
@article{roubin2015meso,
TITLE = {{Meso-scale modeling of concrete: A morphological description based on excursion sets of Random Fields}},
AUTHOR = {Roubin, Emmanuel and Colliat, Jean-Baptiste and Benkemoun, Nathan},
URL = {https://hal.archives-ouvertes.fr/hal-01130430},
JOURNAL = {{Computational Materials Science}},
HAL_LOCAL_REFERENCE = {ER4 : Couplages thermo-hydrom{\'e}caniques et chimiques},
PUBLISHER = {{Elsevier}},
VOLUME = {102},
PAGES = {183-196},
YEAR = {2015},
MONTH = May,
DOI = {10.1016/j.commatsci.2015.02.039},
KEYWORDS = {Cementitious material ; Morphological modeling ; Correlated Random Fields ; Excursion sets},
HAL_ID = {hal-01130430},
HAL_VERSION = {v1},
}
@article{roubin2015multi,
title = "Multi-scale failure of heterogeneous materials: A double kinematics enhancement for Embedded Finite Element Method",
journal = "International Journal of Solids and Structures",
volume = "52",
pages = "180 - 196",
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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",
}
@article{roubin2016perco,
TITLE = {{Critical probability of percolation over bounded region in N-dimensional Euclidean space}},
AUTHOR = {Roubin, Emmanuel and Colliat, Jean-Baptiste},
URL = {https://hal.archives-ouvertes.fr/hal-01305745},
JOURNAL = {{Journal of Statistical Mechanics: Theory and Experiment}},
HAL_LOCAL_REFERENCE = {ER4 : Couplages thermo-hydrom{\'e}caniques et chimiques},
PUBLISHER = {{IOP Publishing}},
VOLUME = {2016},
PAGES = {033306},
YEAR = {2016},
MONTH = Mar,
DOI = {10.1088/1742-5468/2016/03/033306},
HAL_ID = {hal-01305745},
HAL_VERSION = {v1},
}
@article{roubin2019colours,
title={The colours of concrete as seen by X-rays and neutrons},
author={Roubin, Emmanuel and Ando, Edward and Roux, St{\'e}phane},
journal={Cement and Concrete Composites},
volume={104},
pages={103336},
year={2019},
publisher={Elsevier},
doi={10.1016/j.cemconcomp.2019.103336}
}
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author = "Gautier, Laurent",
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title={The ITK software guide},
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}
@article{beare2006watershed,
title={The watershed transform in ITK-discussion and new developments},
author={Beare, Richard and Lehmann, Ga{\"e}tan},
journal={Insight J},
volume={92},
pages={1--24},
year={2006}
}
@article{scikitimage,
title={scikit-image: image processing in Python},
author={Van der Walt, Stefan and Sch{\"o}nberger, Johannes L and Nunez-Iglesias, Juan and Boulogne, Fran{\c{c}}ois and Warner, Joshua D and Yager, Neil and Gouillart, Emmanuelle and Yu, Tony},
......@@ -44,70 +385,33 @@
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pages={e453},
year={2014},
publisher={PeerJ Inc.}
publisher={PeerJ Inc.},
doi={10.7717/peerj.453}
}
@ARTICLE{SciPy2020,
author = {{Virtanen}, Pauli and {Gommers}, Ralf and {Oliphant},
Travis E. and {Haberland}, Matt and {Reddy}, Tyler and
{Cournapeau}, David and {Burovski}, Evgeni and {Peterson}, Pearu
and {Weckesser}, Warren and {Bright}, Jonathan and {van der Walt},
St{\'e}fan J. and {Brett}, Matthew and {Wilson}, Joshua and
{Jarrod Millman}, K. and {Mayorov}, Nikolay and {Nelson}, Andrew
R.~J. and {Jones}, Eric and {Kern}, Robert and {Larson}, Eric and
{Carey}, CJ and {Polat}, {\.I}lhan and {Feng}, Yu and {Moore},
Eric W. and {Vand erPlas}, Jake and {Laxalde}, Denis and
{Perktold}, Josef and {Cimrman}, Robert and {Henriksen}, Ian and
{Quintero}, E.~A. and {Harris}, Charles R and {Archibald}, Anne M.
and {Ribeiro}, Ant{\^o}nio H. and {Pedregosa}, Fabian and
{van Mulbregt}, Paul and {Contributors}, SciPy 1. 0},
title = "{SciPy 1.0: Fundamental Algorithms for Scientific
Computing in Python}",
journal = {Nature Methods},
year = "2020",
adsurl = {https://rdcu.be/b08Wh},
doi = {https://doi.org/10.1038/s41592-019-0686-2},
}
@article{numpy,
author = {Walt,Stéfan van der and Colbert,S. Chris and Varoquaux,Gaël },
title = {The NumPy Array: A Structure for Efficient Numerical Computation},
journal = {Computing in Science \& Engineering},
volume = {13},
number = {2},
pages = {22-30},
year = {2011},
doi = {10.1109/MCSE.2011.37},
URL = {https://aip.scitation.org/doi/abs/10.1109/MCSE.2011.37},
eprint = {https://aip.scitation.org/doi/pdf/10.1109/MCSE.2011.37}
}
@misc{pybind11,
author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan},
year = {2017},
note = {https://github.com/pybind/pybind11},
title = {pybind11 -- Seamless operability between C++11 and Python}
author = {{Virtanen}, Pauli and {Gommers}, Ralf and {Oliphant},
Travis E. and {Haberland}, Matt and {Reddy}, Tyler and
{Cournapeau}, David and {Burovski}, Evgeni and {Peterson}, Pearu
and {Weckesser}, Warren and {Bright}, Jonathan and {van der Walt},
St{\'e}fan J. and {Brett}, Matthew and {Wilson}, Joshua and
{Jarrod Millman}, K. and {Mayorov}, Nikolay and {Nelson}, Andrew
R.~J. and {Jones}, Eric and {Kern}, Robert and {Larson}, Eric and
{Carey}, CJ and {Polat}, {\.I}lhan and {Feng}, Yu and {Moore},
Eric W. and {Vand erPlas}, Jake and {Laxalde}, Denis and
{Perktold}, Josef and {Cimrman}, Robert and {Henriksen}, Ian and
{Quintero}, E.~A. and {Harris}, Charles R and {Archibald}, Anne M.
and {Ribeiro}, Ant{\^o}nio H. and {Pedregosa}, Fabian and
{van Mulbregt}, Paul and {Contributors}, SciPy 1. 0},
title = "{SciPy 1.0: Fundamental Algorithms for Scientific
Computing in Python}",
journal = {Nature Methods},
year = "2020",
adsurl = {https://rdcu.be/b08Wh},
doi = {https://doi.org/10.1038/s41592-019-0686-2},
}
@article{imagej2,
title={ImageJ2: ImageJ for the next generation of scientific image data},
author={Rueden, Curtis T and Schindelin, Johannes and Hiner, Mark C and DeZonia, Barry E and Walter, Alison E and Arena, Ellen T and Eliceiri, Kevin W},
journal={BMC bioinformatics},
volume={18},
number={1},
pages={529},
year={2017},
publisher={Springer}
}
@misc{ikeda:2000,
title={Three-dimensional study on the interconnection and shape of crystals in a graphic granite by X-ray CT and image analysis},
author={Ikeda, S and Nakano, T and Nakashima, Y},
year={2000},
publisher={De Gruyter}
}
@article{stamati:2018phase,
@article{stamati2018phase,
TITLE = {{Phase segmentation of concrete x-ray tomographic images at meso-scale: Validation with neutron tomography}},
AUTHOR = {Stamati, Olga and Roubin, Emmanuel and And{\`o}, Edward and Malecot, Yann},
URL = {http://hal.univ-grenoble-alpes.fr/hal-01876110},
......@@ -121,7 +425,7 @@ eprint = {https://aip.scitation.org/doi/pdf/10.1109/MCSE.2011.37}
HAL_VERSION = {v1},
}
@article{stamati:2018tensile,
@article{stamati2018tensile,
TITLE = {{Tensile failure of micro-concrete: from mechanical tests to FE meso-model with the help of X-ray tomography}},
AUTHOR = {Stamati, Olga and Roubin, Emmanuel and And{\`o}, Edward and Malecot, Yann},
URL = {https://hal.archives-ouvertes.fr/hal-01920221},
......@@ -133,20 +437,19 @@ eprint = {https://aip.scitation.org/doi/pdf/10.1109/MCSE.2011.37}
HAL_VERSION = {v1},
}
@article{stavropoulou:2018,
TITLE = {{Liquid water uptake in unconfined Callovo Oxfordian clay-rock studied with neutron and x-ray imaging}},
AUTHOR = {Stavropoulou, Eleni and And{\`o}, Edward and Tengattini, Alessandro and Dufour, Fr{\'e}d{\'e}ric and Atkins, Duncan and Armand, Gilles},
URL = {https://hal.archives-ouvertes.fr/hal-02158205},
JOURNAL = {{Acta Geotechnica}},
PUBLISHER = {{Springer Verlag}},
YEAR = {2018},
DOI = {10.1007/s11440-018-0639-4},
PDF = {https://hal.archives-ouvertes.fr/hal-02158205/file/liquid-water-uptake_final_numbered.pdf},
HAL_ID = {hal-02158205},
HAL_VERSION = {v1},
@article{stavropoulou2019liquid,
title={Liquid water uptake in unconfined Callovo Oxfordian clay-rock studied with neutron and X-ray imaging},
author={Stavropoulou, Eleni and And{\`o}, Edward and Tengattini, Alessandro and Briffaut, Matthieu and Dufour, Fr{\'e}d{\'e}ric and Atkins, Duncan and Armand, Gilles},
journal={Acta Geotechnica},
volume={14},
number={1},
pages={19--33},
year={2019},
publisher={Springer},
doi={10.1007/s11440-018-0639-4}
}
@article{stavropoulou:2020,
@article{stavropoulou2020,
TITLE = {{Dynamics of water absorption in Callovo-Oxfordian claystone revealed with multimodal x-ray and neutron tomography}},
AUTHOR = {Stavropoulou, Eleni and And{\`o}, Edward and Roubin, Emmanuel and Lenoir, Nicholas and Tengattini, Alessandro and Briffaut, Matthieu and Bésuelle, Pierre},
JOURNAL = {{Frontiers in Earth Science}},
......@@ -155,7 +458,63 @@ eprint = {https://aip.scitation.org/doi/pdf/10.1109/MCSE.2011.37}
DOI = {10.3389/feart.2020.00006 },
}
@article{wiebicke:2019benchmark,
@article{tengattini2015kalisphera,
title={Kalisphera: an analytical tool to reproduce the partial volume effect of spheres imaged in 3D},
author={Tengattini, Alessandro and And{\`o}, Edward},
journal={Measurement Science and Technology},
volume={26},
number={9},
pages={095606},
year={2015},
publisher={IOP Publishing},
doi={10.1088/0957-0233/26/9/095606}
}
@misc{tifffile,
author = "Gohlke, Christoph",
title = "tifffile",
year = "2020",
url = "https://www.lfd.uci.edu/~gohlke/code/tifffile.py.html"
}
@article{tudisco2017extension,
title={An extension of digital volume correlation for multimodality image registration},
author={Tudisco, Erika and Jailin, Cl{\'e}ment and Mendoza, Arturo and Tengattini, A and And{\`o}, E and Hall, Stephen A and Viggiani, Gioacchino and Hild, Francois and Roux, St{\'e}phane},
journal={Measurement Science and Technology},
volume={28},
number={9},
pages={095401},
year={2017},
publisher={IOP Publishing},
doi={10.1088/1361-6501/aa7b48}
}
@article{tudisco2017tomowarp2,
title={TomoWarp2: A local digital volume correlation code},
author={Tudisco, Erika and And{\`o}, Edward and Cailletaud, R{\'e}mi and Hall, Stephen A},
journal={SoftwareX},
volume={6},
pages={267--270},
year={2017},
publisher={Elsevier},
doi={10.1016/j.softx.2017.10.002}
}
@software{ufreckles,
author = {Julien Rethoré},
title = {UFreckles},
month = oct,
year = 2018,
publisher = {Zenodo},
version = {v 2.0},
doi = {10.5281/zenodo.1433776},
url = {https://doi.org/10.5281/zenodo.1433776}
}
@article{wiebicke2019benchmark,
title={A benchmark strategy for the experimental measurement of contact fabric},
author={Wiebicke, Max and And{\`o}, Edward and {\v{S}}milauer, V{\'a}clav and Herle, Ivo and Viggiani, Gioacchino},
journal={Granular Matter},
......@@ -163,5 +522,37 @@ eprint = {https://aip.scitation.org/doi/pdf/10.1109/MCSE.2011.37}
number={3},
pages={54},
year={2019},
publisher={Springer},
doi={10.1007/s10035-019-0902-x}
}
@article{wiebicke2017,
title={On the metrology of interparticle contacts in sand from x-ray tomography images},
author={Wiebicke, Max and And{\`o}, Edward and Herle, Ivo and Viggiani, Cino},
journal={Measurement Science and Technology},