@@ -148,7 +148,7 @@ The `DIC` toolkit is presented in the [introduction](https://ttk.gricad-pages.un

Tools are also provided to compute fields of $F$ from a displacement field measured on a regular grid (coming from a "local" correlation for example), either using square/cubic finite element shape functions, or the method proposed in @geers1996computing.

For a displacement field on an irregular grid (for example defined at particle centres coming from a "discrete" correlation), a Delaunay triangulation based method [@bagi1996stress; @zhang2015large; @catalano2014] is implemented.

Both finite (large) strain and infinitesimal (small) strain frameworks are implemented for both regular and irregular grids.

The `deformation` toolkit is presented (together with `DIC`) in the [introduction](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/intro.html#image-correlation-deformation-toolkit), discussed in detail in the [continuum mechanics refresher](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-00-refreshments.html) the start of [DIC theory](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-02a-DIC-theory.html) and [strain tutorial](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-07-strain.html), and is used throughout the DIC examples (see above)

The `deformation` toolkit is presented (together with `DIC`) in the [introduction](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/intro.html#image-correlation-deformation-toolkit), discussed in detail in the [continuum mechanics refresher](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-00-refreshments.html), the start of [DIC theory](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-02a-DIC-theory.html) and [strain tutorial](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-07-strain.html), and is used throughout the DIC examples (see above)

-`excursions`: toolkit for the excursion set of correlated random fields theory [@adler2008new].

It includes functions that give the analytical predictions of the global descriptors (or Lipschitz-Killing curvatures) of excursions in spaces of arbitrary dimensions [@roubin2015meso; @roubin2016perco] along with the generation of correlated random fields using `RandomFields` in R through `rpy2` [@Ritself; @rpy2; @schlather2015randomfields].

...

...

@@ -171,7 +171,7 @@ A wrapper for ITK's morphological watershed [@schroeder2003itk; @beare2006waters

The `label` toolkit is presented in the [introduction](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/intro.html#label-toolkit), discussed in detail in tutorials covering [the base toolkit](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-03-labelToolkit.html) and [contacts](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/tutorial-08-contacts.html), and illustrated in the [examples gallery](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/spam_examples/index.html#labeltoolkit-examples)

-`measurements`: toolkit implementing the measurement of covariance, porosity and global descriptors (volume, perimeter, surface area, and Euler characteristic).

The `measurements` toolkit is used [in the examples](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/spam_examples/index.html#random-fields-and-excursion-sets)

The `measurements` toolkit is used in the [examples gallery](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/spam_examples/index.html#random-fields-and-excursion-sets)

-`mesh`: toolkit for the creation or manipulation of meshes -- in `spam` tetrahedral meshes are principally used. Meshers based on Gmsh [@geuzaine2009gmsh] are used through `pygmsh` and weighted Delaunay triangulation (Laguerre triangulation) is provided through an interface with CGAL [@cgal] -- alpha-shapes are also implemented to help clean up badly-shaped tetrahedra.

In addition, a set of projection functions creates meshes able to represent heterogeneities (phases and interfaces of a given meso/micro structure) based on binary or trinary images or continuous fields (level set) with outputs easily convertible to any FE software [@roubin2015multi; @stamati2018tensile].

...

...

@@ -180,14 +180,18 @@ The `mesh` toolkit is presented in the [introduction](https://ttk.gricad-pages.u

-`plotting`: toolkit of plotting tools based on `matplotlib` [@matplotlib] for creating complex plots such as a 3D orientation plot.

The `plotting` toolkit is presented in the [introduction](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/intro.html#plotting-tools) and used throughout tutorials and examples

-`visual`: toolkit of graphical helper functions for scripts.

-`visual`: toolkit of graphical helper functions for scripts

A number of scripts are available to be called from the command line, at the moment the most-used scripts are related to image correlation:

A number of scripts are available to be called from the command line.

Currently, the most-used scripts are related to image correlation:

-`spam-ldic` and `spam-regularStrain`: A "local" image correlation script, working for series of greyscale 2D or 3D images where kinematics are measured on independent points spread on a regular grid, accompanied by a strain computation script.

`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` 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.