simple mesh generator (#10)

* 2D mesh generator based on DistMesh algorithm which calls CGAL Delaunay triangulation.

Author: keith roberts

.circleci/config.yml

@@ -15,8 +15,12 @@ jobs:
       - image: circleci/python:3
     steps:
       - checkout
-      - run: pip install . --user
-      - run: pip install -U pytest pytest-cov --user
+      - run: sudo apt install -y cmake python-pybind11
+      - run: sudo apt-get install libmpfr-dev
+      - run: sudo apt-get install libboost-all-dev
+      - run: git clone https://github.com/CGAL/cgal.git && cd cgal/ && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release .. && sudo make install
+      - run: pip install -e .
+      - run: pip install -U pytest pytest-cov
       - run:
           command: pytest --cov oceanmesh
       - run: bash <(curl -s https://codecov.io/bash)

.gitignore

@@ -1,2 +1,15 @@
-__pycache__
 *.nc
+*.pyc
+*.swp
+*.prof
+dist/
+build/
+.coverage
+.cache/
+*.egg-info/
+.pytest_cache/
+*.segy
+*.vtk
+*.hdf5
+*.msh
+*.so

CMakeLists.txt

@@ -0,0 +1,35 @@
+cmake_minimum_required(VERSION 2.8.12)
+
+project(oceanmesh)
+
+##############################################################################
+
+# Add custom CMake modules
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake ${CMAKE_MODULE_PATH})
+
+# Some screen output
+message(STATUS "OS detected: ${CMAKE_SYSTEM_NAME}")
+message(STATUS "CXX Compiler detected: ${CMAKE_CXX_COMPILER_ID}")
+message(STATUS "CMake additional search path for libraries: ${CMAKE_LIBRARY_PATH}")
+
+# CGAL and its components
+find_package(CGAL)
+message(STATUS "CGAL version: ${CGAL_VERSION}")
+
+if( CGAL_VERSION  VERSION_LESS 5.0)
+    message(FATAL_ERROR "This project requires at least CGAL 5.0 library and will not be compiled.")
+endif()
+
+
+# include helper file
+include( ${CGAL_USE_FILE})
+
+set (SRC "oceanmesh/cpp")
+
+include_directories (${SRC})
+
+find_package(pybind11)
+message(STATUS "Found pybind11 v${pybind11_VERSION}: ${pybind11_INCLUDE_DIRS}")
+
+#add_subdirectory(pybind11)
+pybind11_add_module(delaunay_class ${SOURCES} "${SRC}/delaunay_class.cpp")

LICENSE LICENSE.txtLICENSE renamed to LICENSE.txt

@@ -0,0 +1,5 @@
+include oceanmesh/cpp/*.cpp
+include tests/*
+
+include README.md LICENSE.txt
+global-include CMakeLists.txt

MANIFEST.in

@@ -6,10 +6,10 @@ default:
 clean:
 	@find . | grep -E "(__pycache__|\.pyc|\.pyo$\)" | xargs rm -rf
 	@rm -rf build/*
-	@rm -rf pyOceanMesh.egg-info/
+	@rm -rf oceanmesh.egg-info/
 	@rm -rf dist/
 
 format:
-	isort -rc pyOceanMesh/ tests/*.py
-	black pyOceanMesh/ tests/*.py
+	isort -rc oceanmesh/ tests/*.py
+	black oceanmesh/ tests/*.py
 	blacken-docs README.md

Makefile

@@ -1,23 +1,89 @@
 oceanmesh: Automatic coastal ocean mesh generation
 =====================================================
+:ocean: :cyclone:
 
 [![CircleCI](https://circleci.com/gh/circleci/circleci-docs.svg?style=svg)](https://circleci.com/gh/CHLNDDEV/oceanmesh)
 [![CodeCov](https://codecov.io/gh/CHLNDDEV/oceanmesh/branch/master/graph/badge.svg)](https://codecov.io/gh/CHLNDDEV/oceanmesh)
 
 
 
-Coastal ocean mesh generation from ESRI Shapefiles and digitial elevation models. 
+Coastal ocean mesh generation from ESRI Shapefiles and digitial elevation models.
 
 
 Functionality
 =============
 
-* WIP
+* A toolkit for the development of meshes and their auxiliary files that are used in the simulation of coastal ocean circulation. The software integrates mesh generation with geophysical datasets such as topobathymetric rasters/digital elevation models and shapefiles representing coastal features. It provides some necessary pre- and post-processing tools to inevitably perform a succesful numerical simulations with the developed model.
+    * Automatically deal with arbitrarily complex shoreline vector datasets that represent complex coastal boundaries and incorporate the data in an automatic-sense into the mesh generation process.
+    * A variety of commonly used mesh size functions to distribute element sizes that can easily be controlled via a simple scripting application interface.
+    * Mesh checking and clean-up methods to avoid simulation problems.
+    
+Questions?
+============
+
+Besides posting issues with the code on Github, you can also ask questions via our Slack channel [here](https://join.slack.com/t/oceanmesh2d/shared_invite/zt-hcu2nag7-NUBw52cxxlYupLrc1hqvhw).
+
+Otherwise please reach out to either Dr. William Pringle (wpringle@nd.edu) or Dr. Keith Roberts (krober@usp.br) with questions or concerns!
+
+Installation
+============
+
+For installation, oceanmesh needs [CGAL](https://www.cgal.org/) and
+[pybind11](https://github.com/pybind/pybind11):
+
+    sudo apt install libcgal-dev python3-pybind11
+
+After that, clone the repo and oceanmesh can be updated/installed using pip.
+
+    pip install -U -e .
+
+:warning:
+
+**WARNING: THIS PROGRAM IS IN ACTIVE DEVELOPMENT. INSTALLATION IS ONLY RECOMMENDED FOR DEVELOPERS AT THIS TIME. WHEN A STABLE API IS REACHED, THE PROGRAM WILL BE AVAILABLE VIA pypi**
 
 Examples
 ==========
 
-* WIP 
+Build a simple mesh around New York witha minimum element size of 1 km expanding linear from the shoreline to a maximum size of 5 km.
+
+
+**Here we use the GSHHS shoreline [here](http://www.soest.hawaii.edu/pwessel/gshhg/gshhg-shp-2.3.7.zip) and the Python package `meshio` to write the mesh to a VTK file for visualization in ParaView.**
+
+![NewYorkMesh](https://user-images.githubusercontent.com/18619644/94013474-8196b400-fd80-11ea-8471-21fa8853f264.png)
+
+```
+ import meshio
+ 
+ from oceanmesh import (
+     Shoreline,
+     distance_sizing_function,
+     signed_distance_function,
+     generate_mesh,
+ )
+ 
+ 
+ fname = "datasets/gshhg-shp-2.3.7/GSHHS_shp/f/GSHHS_f_L1.shp"
+ 
+ bbox, h0 = (-75.000, -70.001, 40.0001, 41.9000), 1e3
+ 
+ shore = Shoreline(fname, bbox, h0)
+ 
+ cell_size = distance_sizing_function(shore, max_size=5e3/ 111e3)
+ 
+ domain = signed_distance_function(shore)
+ 
+ points, cells = generate_mesh(
+     domain=domain, cell_size=cell_size, h0=1e3 / 111e3
+ )
+ 
+ meshio.write_points_cells(
+     "simple_new_york.vtk",
+     points,
+     [("triangle", cells)],
+     file_format="vtk",
+ )
+~           
+```
 
 Testing
 ============
@@ -32,4 +98,3 @@ License
 =======
 
 This software is published under the [GPLv3 license](https://www.gnu.org/licenses/gpl-3.0.en.html)
-

README.md

@@ -1,19 +1,28 @@
+from oceanmesh.edgefx import distance_sizing_function
+from oceanmesh.edges import draw_edges, get_poly_edges
 from oceanmesh.geodata import DEM, Geodata, Shoreline
 from oceanmesh.grid import Grid
-from oceanmesh.edgefx import distance_sizing_function
-from oceanmesh.signed_distance_function import signed_distance_function
-from oceanmesh.edges import get_poly_edges, draw_edges
+from oceanmesh.signed_distance_function import signed_distance_function, Domain
+
+from .cpp.delaunay_class import DelaunayTriangulation
+from .fix_mesh import fix_mesh, simp_vol
 from .inpoly import inpoly
+from .mesh_generator import generate_mesh
 
 __all__ = [
     "SizeFunction",
     "Grid",
     "Geodata",
     "DEM",
+    "Domain",
     "Shoreline",
     "distance_sizing_function",
     "signed_distance_function",
     "get_poly_edges",
     "draw_edges",
     "inpoly",
+    "DelaunayTriangulation",
+    "generate_mesh",
+    "fix_mesh",
+    "simp_vol",
 ]