Commit d78d6fde authored by Edward Andò's avatar Edward Andò
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finishing touches on paper

parent 0642a356
Pipeline #46728 canceled with stages
......@@ -106,15 +106,15 @@
publisher={Elsevier}
}
@article{hurley2019situ,
title={An in-situ study of stress evolution and fracture growth during compression of concrete},
author={Hurley, RC and Pagan, DC},
journal={International Journal of Solids and Structures},
volume={168},
pages={26--40},
year={2019},
publisher={Elsevier},
doi={10.1016/j.ijsolstr.2019.03.015}
@article{hall2010discrete,
title={Discrete and continuum analysis of localised deformation in sand using X-ray $\mu$CT and volumetric digital image correlation},
author={Hall, Stephen A and Bornert, Michel and Desrues, Jacques and Pannier, Yannick and Lenoir, Nicolas and Viggiani, Gioacchino and B{\'e}suelle, Pierre},
journal={G{\'e}otechnique},
volume={60},
number={5},
pages={315--322},
year={2010},
publisher={Thomas Telford Ltd}
}
@article{hild2008correliq4,
......@@ -126,6 +126,17 @@
year={2008}
}
@article{hurley2019situ,
title={An in-situ study of stress evolution and fracture growth during compression of concrete},
author={Hurley, RC and Pagan, DC},
journal={International Journal of Solids and Structures},
volume={168},
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},
......
......@@ -155,7 +155,8 @@ It includes functions that give the analytical predictions of the global descrip
The `excursions` toolkit is illustrated in the [examples gallery](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/spam_examples/index.html#random-fields-and-excursion-sets)
- `filters`: toolkit of 3D filters that provide some functionality missing in `scipy.ndimage.filters` such as the computation of a local hessian, or functions which are slow (such as the computation of a local variance).
- `filters`: toolkit of 3D filters that provide some functionality missing in `scipy.ndimage.filters` such as the computation of a local hessian, or functions which are slow.
For example, for the computation of a local variance, the spam-provided function is more than 100 times faster than using the generic filter with variance in `scipy.ndimage`.
The `filters` toolkit is used in the [projection tutorial](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-06-projection.html), and illustrated [examples gallery](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/spam_examples/index.html#image-operations)
- `helpers`: toolkit of internal helper functions such as the parsers for the scripts, as well as tools for reading and writing TSV and VTK files.
......@@ -164,7 +165,8 @@ The latter partially uses `meshio` [@meshio]
- `kalisphera`: wrapper for C++ version of `kalisphera` [@tengattini2015kalisphera] which generates analytically-correct partial-volume spheres which are useful for testing discrete analysis code (see `label` below).
The `kalisphera` toolkit is presented in the [introduction](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/intro.html#kalisphera), is used in the [contacts tutorial](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-08-contacts.html), and is illustrated in the [examples gallery](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/spam_examples/index.html#kalisphera-sphere-generation)
- `label`: toolkit to measure and manipulate "labelled" images, where discrete particles are labelled with integer voxel patches. The computation of standard quantities such as the volume, barycentre and moment of inertia tensor of each particle can be done very rapidly.
- `label`: toolkit to measure and manipulate "labelled" images, where discrete particles are labelled with integer voxel patches.
The computation of standard quantities such as the volume, centre of mass, and moment of inertia tensor of each particle can be done very conveniently and somewhat faster and with a smaller memory footprint than what is available in `scipy.ndimage`.
An estimation of an ellipse fitting of each particle is implemented with the algorithm from @ikeda:2000.
Tools for characterising inter-particle contacts based on the work of @wiebicke2017.
A wrapper for ITK's morphological watershed [@schroeder2003itk; @beare2006watershed] is also provided.
......@@ -190,7 +192,7 @@ Currently, the most-used scripts are related to image correlation:
`spam-ldic` is presented in the [scripts page](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/scripts.html#regular-grid-local-dic-script-spam-ldic) and is the subject of the [DIC practice](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-02b-DIC-practice.html).
`spam-regularStrain` is presented in the [scripts page](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/scripts.html#regular-strain-script-spam-regularstrain) and is used in the [strain tutorial](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-07-strain.html)
- `spam-ddic` and `spam-discreteStrain`: A "discrete" image correlation script, working on greyscale 3D images plus a "labelled" image of the reference configuration. This script also has its own strain calculation based on a triangulation of grain centres.
- `spam-ddic` and `spam-discreteStrain`: A "discrete" image correlation script [@hall2010discrete], working on greyscale 3D images plus a "labelled" image of the reference configuration. This script also has its own strain calculation based on a triangulation of grain centres.
`spam-ddic` is presented in the [scripts page](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/scripts.html#discrete-local-dic-script-spam-ddic) and is the subject of the [discrete DIC tutorial](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-04-discreteDIC.html)
- `spam-gdic` (in beta test): A "global" image correlation script, where the displacement field between two 3D images is computed as a global problem expressed on a tetrahedral mesh.
......@@ -245,7 +247,7 @@ The `spam.DIC.register` correlation engine uses a well-known mathematical framew
The discrete and multimodal image correlation are much more unique.
A number of other image correlation codes exist (this is by far not an exhaustive list):
- CMV and CMV\_3D: Developed at Laboratoire Navier [@bornert2004mesure]
- CMV and CMV\_3D: Developed at Laboratoire Navier [@bornert2004mesure], local and non-rigid code allowing discrete DVC used in @hall2010discrete.
- 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
- 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
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