# StratigraPy
StratigraPy is a Python package for stratigraphic modeling based on [Landlab](https://github.com/landlab/landlab). Similarly to Landlab, StratigraPy favors flexibility for prototyping and teaching rather than speed.
StratigraPy is still experimental and under heavy development.
[](https://www.youtube.com/watch?v=THp7vKp5ha4)
## Installation
You can directly install StratigraPy from pip:
pip install stratigrapy
Or from GitHub using pip:
pip install git+https://github.com/grongier/stratigrapy.git
To run the Jupyter notebook in [examples](examples) you will also need tqdm, cmocean, pyvista, trame, trame-vtk, trame-vuetify, and jupyter, which you can install from pip too:
pip install tqdm cmocean pyvista trame trame-vtk trame-vuetify jupyter
You can also install everything using conda and the `environment.yml` file included in this repository:
conda env create -f environment.yml
## Usage
StratigraPy follows Landlab's API and you can check [Landlab's extensive documentation](https://landlab.csdms.io) to get an idea of its features. Here's a very basic example of setting up and running a model:
```
import numpy as np
import matplotlib.pyplot as plt
from stratigrapy import RasterModelGrid
from stratigrapy.components import GravityDrivenRouter
# Create the grid with two sediment classes
grid = RasterModelGrid((50, 50),
xy_spacing=(500., 500.),
number_of_classes=2,
initial_allocation=1020,
number_of_layers_to_fuse=20,
number_of_top_layers=20)
grid.set_closed_boundaries_at_grid_edges(True, True, True, False)
# Define the initial topography
elevation = grid.add_zeros('topographic__elevation', at='node', clobber=True)
elevation[grid.y_of_node > 15000.] = 100.
# Define the bathymetry
bathymetry = grid.add_zeros('bathymetric__depth', at='node', clobber=True)
# Define a diffusion component
gdr = GravityDrivenRouter(grid, diffusivity_cont=[2e-1, 2e-2])
# Run the simulation
for i in range(1000):
gdr.run_one_step(100.)
grid.stacked_layers.fuse(time=np.mean)
grid.stacked_layers.fuse(finalize=True, time=np.mean)
# Plot a slice through the domain with sediments and bedrock
fig, ax = plt.subplots(figsize=(8, 4))
pc = grid.plot_layers(ax, 'composition', i_class=1, mask_wedges=True, cmap='pink', zorder=2)
fig.colorbar(pc[0], ax=ax, label='Fraction of the second sediment class')
raster_y = grid.y_of_node[grid.core_nodes].reshape(grid.cell_grid_shape)[:, 24]
raster_z = grid.at_node['topographic__elevation'][grid.core_nodes].reshape(grid.cell_grid_shape)[:, 24]
ymin, ymax = ax.get_ylim()
ax.fill_between(raster_y, raster_z, ymin, color='#d9d9d9', zorder=1)
ax.set(xlabel='y (m)', ylabel='z (m)', ylim=(ymin, ymax));
```
You can find more complete examples in the folder [examples](examples).
## Citation
If you use StratigraPy in your research, please cite the original article(s) describing the method(s) you used (see the docstrings for the references). An acknowledgment of StratigraPy's use is always appreciated.
## Credits
This software was written by:
| [Guillaume Rongier](https://github.com/grongier) <br>[](https://orcid.org/0000-0002-5910-6868)</br> |
| :---: |
## License
Copyright notice: Technische Universiteit Delft hereby disclaims all copyright interest in the program StratigraPy written by the Author(s). Prof.dr.ir. S.G.J. Aarninkhof, Dean of the Faculty of Civil Engineering and Geosciences
© 2025, Guillaume Rongier
This work is licensed under a MIT OSS licence, see [LICENSE](LICENSE) for more information.
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"description": "# StratigraPy\n\nStratigraPy is a Python package for stratigraphic modeling based on [Landlab](https://github.com/landlab/landlab). Similarly to Landlab, StratigraPy favors flexibility for prototyping and teaching rather than speed.\n\nStratigraPy is still experimental and under heavy development.\n\n[](https://www.youtube.com/watch?v=THp7vKp5ha4)\n\n## Installation\n\nYou can directly install StratigraPy from pip:\n\n pip install stratigrapy\n\nOr from GitHub using pip:\n\n pip install git+https://github.com/grongier/stratigrapy.git\n\nTo run the Jupyter notebook in [examples](examples) you will also need tqdm, cmocean, pyvista, trame, trame-vtk, trame-vuetify, and jupyter, which you can install from pip too:\n\n pip install tqdm cmocean pyvista trame trame-vtk trame-vuetify jupyter\n\nYou can also install everything using conda and the `environment.yml` file included in this repository:\n\n conda env create -f environment.yml\n\n## Usage\n\nStratigraPy follows Landlab's API and you can check [Landlab's extensive documentation](https://landlab.csdms.io) to get an idea of its features. Here's a very basic example of setting up and running a model:\n\n```\nimport numpy as np\nimport matplotlib.pyplot as plt\nfrom stratigrapy import RasterModelGrid\nfrom stratigrapy.components import GravityDrivenRouter\n\n# Create the grid with two sediment classes\ngrid = RasterModelGrid((50, 50),\n xy_spacing=(500., 500.),\n number_of_classes=2,\n initial_allocation=1020,\n number_of_layers_to_fuse=20,\n number_of_top_layers=20)\ngrid.set_closed_boundaries_at_grid_edges(True, True, True, False)\n\n# Define the initial topography\nelevation = grid.add_zeros('topographic__elevation', at='node', clobber=True)\nelevation[grid.y_of_node > 15000.] = 100.\n\n# Define the bathymetry\nbathymetry = grid.add_zeros('bathymetric__depth', at='node', clobber=True)\n\n# Define a diffusion component\ngdr = GravityDrivenRouter(grid, diffusivity_cont=[2e-1, 2e-2])\n\n# Run the simulation\nfor i in range(1000):\n gdr.run_one_step(100.)\n grid.stacked_layers.fuse(time=np.mean)\ngrid.stacked_layers.fuse(finalize=True, time=np.mean)\n\n# Plot a slice through the domain with sediments and bedrock\nfig, ax = plt.subplots(figsize=(8, 4))\npc = grid.plot_layers(ax, 'composition', i_class=1, mask_wedges=True, cmap='pink', zorder=2)\nfig.colorbar(pc[0], ax=ax, label='Fraction of the second sediment class')\nraster_y = grid.y_of_node[grid.core_nodes].reshape(grid.cell_grid_shape)[:, 24]\nraster_z = grid.at_node['topographic__elevation'][grid.core_nodes].reshape(grid.cell_grid_shape)[:, 24]\nymin, ymax = ax.get_ylim()\nax.fill_between(raster_y, raster_z, ymin, color='#d9d9d9', zorder=1)\nax.set(xlabel='y (m)', ylabel='z (m)', ylim=(ymin, ymax));\n```\n\nYou can find more complete examples in the folder [examples](examples).\n\n## Citation\n\nIf you use StratigraPy in your research, please cite the original article(s) describing the method(s) you used (see the docstrings for the references). An acknowledgment of StratigraPy's use is always appreciated.\n\n## Credits\n\nThis software was written by:\n\n| [Guillaume Rongier](https://github.com/grongier) <br>[](https://orcid.org/0000-0002-5910-6868)</br> |\n| :---: |\n\n## License\n\nCopyright notice: Technische Universiteit Delft hereby disclaims all copyright interest in the program StratigraPy written by the Author(s). Prof.dr.ir. S.G.J. Aarninkhof, Dean of the Faculty of Civil Engineering and Geosciences\n\n© 2025, Guillaume Rongier\n\nThis work is licensed under a MIT OSS licence, see [LICENSE](LICENSE) for more information.\n",
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