sphinx doc

Makefile

 all :
 	python setup.py install --user
+	make -C doc html
+
+html:
+	make -C doc html

doc/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'msea'
+copyright = '2020, Jonathan Lambrechts'
+author = 'Jonathan Lambrechts'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc','sphinx.ext.napoleon']
+
+napoleon_google_docstring = True
+napoleon_numpy_docstring = False
+napoleon_include_special_with_doc = True
+autoclass_content = 'both'
+html_show_sourcelink = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+

doc/index.rst

+Welcome to msea's documentation!
+================================
+
+.. include:: modules.rst
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+* :ref:`genindex`
+
+..
+  * :ref:`modindex`
+  * :ref:`search`

doc/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/modules.rst

+msea
+====
+
+.. toctree::
+   :maxdepth: 4
+
+   msea

doc/msea.Field.rst

+msea.Field module
+=================
+
+.. automodule:: msea.Field
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/msea.rst

+msea package
+============
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   msea.Field
+
+Module contents
+---------------
+
+.. automodule:: msea
+   :members:
+   :undoc-members:
+   :show-inheritance:

msea/Field.py

+from ._private import Domain
+import numpy as np
+from osgeo import osr
+
+class Distance:
+    """Callable evaluating the distance to a set of discretized curves.
+
+    The curves are discretized as sets of points, then the distance to the
+    closest point is computed.
+    """
+
+    def __init__(self, domain:Domain, sampling:float, tags=None):
+        """
+        Args:
+            domain: a Domain object containing the set of curves
+            sampling: the interval between two consecutive sampling points.
+            tags: List of physical tags specifying the curve from the domain.
+                if None, all curves are taken into account (default: None)
+        """
+        points = []
+        for curve in domain._curves:
+            if (tags is None) or (curve.tag in tags):
+                points.append(curve.sample(sampling))
+        points = np.vstack(points)
+        self._tree = cKDTree(points)
+        self._projection = domain._projection
+
+    def __call__(self, x:np.ndarray, projection:osr.SpatialReference
+                 )->np.ndarray:
+        """Compute the distance between each point of x and the curves.
+
+        Args:
+            x: the points [n,2]
+            projection: the coordinate system of the points, should be
+                the same coordinate system as the domain, otherwise no
+                conversion is done and an exception is raised.
+        Returns:
+            The distance expressed in the domain unit. [n]
+        """
+        if not projection.IsSame(self._projection):
+            raise ValueError("incompatible projection")
+        x = x[:, :2]
+        return self._tree.query(x)[0]
+
+
+class Raster:
+    """Callable to evaluate a raster field loaded from a file."""
+
+    def __init__(self, filename:str):
+        """
+        Args:
+            filename: A geotiff file or any other raster file supported by gdal.
+        """
+        src_ds = gdal.Open(filename)
+        self._geo_matrix = src_ds.GetGeoTransform()
+        self._data = src_ds.GetRasterBand(1).ReadAsArray()
+        assert(self._geo_matrix[2] == 0.)
+        assert(self._geo_matrix[4] == 0.)
+        self._projection = src_ds.GetProjection()
+
+    def __call__(self, x:np.ndarray, projection:osr.SpatialReference
+                 )->np.ndarray:
+        """Evaluate the field value on each point of x.
+
+        Keyword arguments:
+            x: the points [n,2]
+            projection: the coordinate system of the points
+        Returns:
+            The field value on points x. [n]
+        """
+        x = _ensure_valid_points(x, projection, self._proection)
+        gm = self._geo_matrix
+        xi = (x[:, 0]-gm[3])/gm[5]
+        eta = (x[:, 1]-gm[0])/gm[1]
+        return self._data[xi.astype(int), eta.astype(int)]
+

msea/__init__.py

+from . import Field
+from ._private import Domain, CurveType, convert_msh_gis
+__all__ = ["Field","Domain","CurveType","convert_msh_gis"]
+

setup.py

@@ -26,7 +26,7 @@ setuptools.setup(
     include_package_data=True,
     url="https://www.migflow.be",
     packages=["msea"],
-    package_dir={"msea":"src"},
+    package_dir={"msea":"msea"},
     #ext_modules=[CMakeExtension("msealib")],
     #ext_modules=[setuptools.Extension("seameshlib",["seamesh.c"])],
     package_data={"msea":["*.so"]},

src/__init__.py

-from .msea import *

testshp.py

@@ -2,9 +2,9 @@ import msea
 import numpy as np
 from osgeo import osr 
 
-def mesh_size(x) :
-    s_coast = np.clip((dist_coast_field(x)-400)*0.5,200,5000)
-    s_porquerolles = np.clip((dist_porquerolles_field(x)-200)*0.5,50,5000)
+def mesh_size(x,projection) :
+    s_coast = np.clip((dist_coast_field(x,projection)-400)*0.5,200,5000)
+    s_porquerolles = np.clip((dist_porquerolles_field(x,projection)-200)*0.5,50,5000)
     return np.minimum(s_coast,s_porquerolles)
 
 domain_srs = osr.SpatialReference()
@@ -16,8 +16,8 @@ domain = msea.Domain(domain_srs)
 domain.add_shapefile("test/data_no_duplicate.shp","physical",curve_type=msea.POLYLINE)
 #domain.add_shapefile("test/interior.shp",None,True,curve_type=msea.POLYLINE)
 #domain.add_interior_points("test/interior.shp")
+bath_field = msea.RasterField("medit.tiff")
 dist_coast_field = msea.DistanceField(domain,100,["coast","island"])
 dist_porquerolles_field = msea.DistanceField(domain,20,["porquerolles"])
 domain.unrefine_boundaries(8e5,4.68e6,20,mesh_size)
-domain.build_topology()
 msea.mesh_gmsh(domain,"test.msh",mesh_size)