diff --git a/README.md b/README.md index b462440..f485dac 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,8 @@ Processing schemes to mirror and reorder these points are provided to address further symmetry issues. By: -- Fidji Berio ([GitHub](https://github.com/fberio)) from [ISEM](http://www.isem.univ-montp2.fr/en/) and [IGFL](http://igfl.ens-lyon.fr/igfl/annuaire/berio-fidji)), -- Yann Bayle ([Website](http://yannbayle.fr/english/index.php), [GitHub](https://github.com/ybayle)) from [LaBRI](http://www.labri.fr/), [Univ. Bordeaux](https://www.u-bordeaux.fr/), [CNRS](http://www.cnrs.fr/), and [SCRIME](https://scrime.u-bordeaux.fr/)) +- Fidji Berio ([GitHub](https://github.com/fberio)) from [ISEM](http://www.isem.univ-montp2.fr/en/) and [IGFL](http://igfl.ens-lyon.fr/igfl/annuaire/berio-fidji), +- Yann Bayle ([Website](http://yannbayle.fr/english/index.php), [GitHub](https://github.com/ybayle)) from [LaBRI](http://www.labri.fr/), [Univ. Bordeaux](https://www.u-bordeaux.fr/), [CNRS](http://www.cnrs.fr/), and [SCRIME](https://scrime.u-bordeaux.fr/). ## Installation @@ -35,26 +35,26 @@ We provide 7 landmark and 31 semilandmark coordinates for 2 upper teeth and for The function `pts2csv()` is the core of **Scyland3D** and takes the following arguments: -- indir (required) +- *indir* (required) - A string containing the input directory where the files are stored. You can use any number of sub-directories. Folder and file names can specify the feature modalities separated by `_` (e.g. speciesA_ageX_sex1.pts). - Example: `Scyland3D.pts2csv("example/")` -- mirror_factor (optional) +- *mirror_factor* (optional) - A string containing the keyword for items to be mirrored in the 3D space. - Default: None - Example: `Scyland3D.pts2csv("example/", mirror_factor="upper")` will mirror in 3D the files containing the keyword `upper` before processing them with the remaining `lower` items. -- order (optional) +- *order* (optional) - A list of integer indicating the new order to apply to the landmarks. - Default: None - Example: `Scyland3D.pts2csv("example/", order_factor="upper", order=[36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, 37])` -- order_factor (optional) +- *order_factor* (optional) - A string containing the keyword for items that need their landmarks and semilandmarks to be reordered. - Default: None - Example: `Scyland3D.pts2csv("example/", order_factor="upper", order=[36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, 37])` -- feature_names (optional) +- *feature_names* (optional) - A list of string containing the feature names. - Default: None - Example: `Scyland3D.pts2csv("example/", feature_names=["identifier", "species", "location", "length", "sex", "stage", "jaw", "position", "generation"])` -- verbose (optional) +- *verbose* (optional) - A boolean indicating if information should be printed on the console by the process. - Default: True - Example: `Scyland3D.pts2csv("example/", verbose=False)` for removing the display of information to the console. @@ -74,8 +74,8 @@ Please refer to the [CONTRIBUTING.md](CONTRIBUTING.md) file. ``` @article{Berio2019, author = {Berio, Fidji and Bayle, Yann}, - title = {Scyland3D: Processing 3D landmarks}, - journal = {The Journal of Open Source Software}, + title = {{Scyland3D: Processing 3D landmarks}}, + journal = {{The Journal of Open Source Software}}, page = {1--3}, note = {Review pending} }