Merge pull request #66 from nschloe/dmsh-adaptations

Dmsh adaptations

.circleci/config.yml

@@ -28,7 +28,8 @@ jobs:
       - run: apt-get install -y git python3-pip python3-vtk7
       - run: pip3 install -U pytest pytest-cov excode
       - checkout
-      # install
+      # install; need a new pip
+      - run: pip3 install pip -U --force
       - run: pip3 install -r test_requirements.txt
       - run: pip3 install .[all]
       # The tests

Makefile

@@ -11,11 +11,12 @@ tag:
 	# git push --tags
 	curl -H "Authorization: token `cat $(HOME)/.github-access-token`" -d '{"tag_name": "v$(VERSION)"}' https://api.github.com/repos/nschloe/meshplex/releases
 
-upload: setup.py
+upload:
 	@if [ "$(shell git rev-parse --abbrev-ref HEAD)" != "master" ]; then exit 1; fi
 	rm -f dist/*
-	python3 setup.py sdist
-	python3 setup.py bdist_wheel
+	# python3 setup.py sdist bdist_wheel
+	# https://stackoverflow.com/a/58756491/353337
+	python3 -m pep517.build --source --binary .
 	twine upload dist/*
 
 publish: tag upload

README.md

@@ -138,5 +138,4 @@ pytest
 ```
 
 ### License
-
-meshplex is published under the [MIT license](https://en.wikipedia.org/wiki/MIT_License).
+This software is published under the [GPLv3 license](https://www.gnu.org/licenses/gpl-3.0.en.html).

meshplex/base.py

@@ -8,11 +8,16 @@
 
 
 def compute_tri_areas(ei_dot_ej):
-    return 0.5 * numpy.sqrt(
+    vol2 = 0.25 * (
         ei_dot_ej[2] * ei_dot_ej[0]
         + ei_dot_ej[0] * ei_dot_ej[1]
         + ei_dot_ej[1] * ei_dot_ej[2]
     )
+    # vol2 is the squared volume, but can be slightly negative if it comes to round-off
+    # errors. Corrrect those.
+    assert numpy.all(vol2 > -1.0e-14)
+    vol2[vol2 < 0] = 0.0
+    return numpy.sqrt(vol2)
 
 
 def compute_ce_ratios(ei_dot_ej, tri_areas):

meshplex/mesh_tri.py

@@ -141,6 +141,22 @@ def __repr__(self):
     #     self.update_values()
     #     return
 
+    @property
+    def euler_characteristic(self):
+        # number of vertices - number of edges + number of faces
+        if "edges" not in self.cells:
+            self.create_edges()
+        return (
+            self.node_coords.shape[0]
+            - self.edges["nodes"].shape[0]
+            + self.cells["nodes"].shape[0]
+        )
+
+    @property
+    def genus(self):
+        # https://math.stackexchange.com/a/85164/36678
+        return 1 - self.euler_characteristic / 2
+
     @property
     def ce_ratios(self):
         if self._ce_ratios is None:
@@ -171,8 +187,8 @@ def update_values(self):
 
         if self.cell_volumes is not None or self.ce_ratios is not None:
             self.cell_volumes = compute_tri_areas(self.ei_dot_ej)
-            self._ce_ratios = compute_ce_ratios(self.ei_dot_ej, self.cell_volumes)
 
+        self._ce_ratios = None
         self._interior_edge_lengths = None
         self._cell_circumcenters = None
         self._interior_ce_ratios = None
@@ -185,6 +201,51 @@ def update_values(self):
         self._cell_centroids = None
         return
 
+    def remove_degenerate_cells(self, threshold):
+        is_okay = self.cell_volumes > threshold
+
+        self.cell_volumes = self.cell_volumes[is_okay]
+        self.cells["nodes"] = self.cells["nodes"][is_okay]
+        self.idx_hierarchy = self.idx_hierarchy[..., is_okay]
+
+        if "edges" in self.cells:
+            self.cells["edges"] = self.cells["edges"][is_okay]
+
+        if self._ce_ratios is not None:
+            self._ce_ratios = self._ce_ratios[is_okay]
+
+        if self.half_edge_coords is not None:
+            self.half_edge_coords = self.half_edge_coords[:, is_okay]
+
+        if self.ei_dot_ej is not None:
+            self.ei_dot_ej = self.ei_dot_ej[:, is_okay]
+
+        if self.ei_dot_ei is not None:
+            self.ei_dot_ei = self.ei_dot_ei[:, is_okay]
+
+        if self._cell_centroids is not None:
+            self._cell_centroids = self._cell_centroids[is_okay]
+
+        if self._cell_circumcenters is not None:
+            self._cell_circumcenters = self._cell_circumcenters[is_okay]
+
+        if self._cell_partitions is not None:
+            self._cell_partitions = self._cell_partitions[is_okay]
+
+        self._interior_edge_lengths = None
+        self._interior_ce_ratios = None
+        self._control_volumes = None
+        self._cv_centroids = None
+        self._cvc_cell_mask = None
+        self._surface_areas = None
+        self._signed_cell_areas = None
+        self._is_boundary_node = None
+        self.is_boundary_edge = None
+
+        self.create_edges()
+
+        return numpy.sum(~is_okay)
+
     @property
     def ce_ratios_per_interior_edge(self):
         """
@@ -757,7 +818,7 @@ def save(self, filename, *args, **kwargs):
         """Save the mesh to a file.
         """
         _, file_extension = os.path.splitext(filename)
-        if file_extension in ".png":
+        if file_extension in [".png", ".svg"]:
             import matplotlib.pyplot as plt
 
             self.plot(*args, **kwargs)

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = meshplex
-version = 0.12.3
+version = 0.13.0
 author = Nico Schlömer
 email = nico.schloemer@gmail.com
 description = Fast tools for simplex meshes,
@@ -10,12 +10,12 @@ project_urls =
     Issues=https://github.com/nschloe/meshplex/issues
 long_description = file: README.md
 long_description_content_type = text/markdown
-license = MIT
+license = GPLv3
 platforms = any
 classifiers =
     Development Status :: 4 - Beta
     Intended Audience :: Science/Research
-    License :: OSI Approved :: MIT License
+    License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
     Operating System :: OS Independent
     Programming Language :: Python
     Programming Language :: Python :: 3