Bug fixes, new tests and increased coverage

pvelissariou1 · Jan 15, 2020 · d016f57 · d016f57
1 parent 5f64bcb
commit d016f57
Show file tree

Hide file tree

Showing 11 changed files with 212 additions and 17 deletions.
diff --git a/pyschism/mesh/__init__.py b/pyschism/mesh/__init__.py
@@ -11,6 +11,5 @@
     "Gmesh",
     "Hgrid",
     "Vgrid",
-    # "Fgrid",
     "Mesh"
 ]
diff --git a/pyschism/mesh/friction/fgrid.py b/pyschism/mesh/friction/fgrid.py
@@ -5,3 +5,13 @@ class Fgrid(Gmesh):
     """
     Base class for all friction types (e.g. manning.gr3, drag.gr3, etc...)
     """
+
+    def __init__(
+        self,
+        nodes,
+        elements,
+        values=None,
+        crs=None,
+        description=None,
+    ):
+        super().__init__(*self._gr3_to_mesh(nodes, elements), crs, description)
diff --git a/pyschism/mesh/friction/manning.py b/pyschism/mesh/friction/manning.py
@@ -7,10 +7,8 @@ class ManningsN(Fgrid):
     @classmethod
     def constant(cls, mesh, value):
         return cls(
-            mesh._coords,
-            mesh._triangles,
-            mesh._quads,
-            values=len(mesh.coords)*[value],
+            mesh.nodes,
+            mesh.elements,
             crs=mesh.crs,
             description=mesh.description + "_mannings"
             )
diff --git a/pyschism/mesh/gmesh.py b/pyschism/mesh/gmesh.py
@@ -15,14 +15,14 @@ class Geomesh:
     def __init__(
         self,
         coords,
-        triang=None,
+        triangles=None,
         quads=None,
         values=None,
         crs=None,
         description=None,
     ):
         self._coords = coords
-        self._triangles = triang
+        self._triangles = triangles
         self._quads = quads
         self._values = values
         self._crs = crs
@@ -39,6 +39,10 @@ def transform_to(self, dst_crs):
     def get_index(self, id):
         return self.node_indexes[id]
 
+    @classmethod
+    def from_gr3(cls, nodes, elements):
+        return cls(*cls._gr3_to_mesh(nodes, elements))
+
     @_figure
     def tricontourf(self, axes=None, show=True, figsize=None, **kwargs):
         if len(self.triangles) > 0:
@@ -190,6 +194,17 @@ def _crs(self):
     def _description(self):
         return self.__description
 
+    @staticmethod
+    def _gr3_to_mesh(nodes, elements):
+        # cast gr3 inputs into a geomesh structure format
+        coords = {id: (x, y) for id, ((x, y), value) in nodes.items()}
+        triangles = {id: geom for id, geom in elements.items()
+                     if len(geom) == 3}
+        quads = {id: geom for id, geom in elements.items()
+                 if len(geom) == 4}
+        values = [value for coord, value in nodes.values()]
+        return coords, triangles, quads, values
+
     @_coords.setter
     def _coords(self, coords):
         msg = "coords argument must be a dictionary of the form "

diff --git a/pyschism/mesh/hgrid.py b/pyschism/mesh/hgrid.py
@@ -26,13 +26,9 @@ def __init__(
         description=None,
     ):
         # cast gr3 inputs into a geomesh structure format
-        coords = {id: (x, y) for id, ((x, y), value) in nodes.items()}
-        values = [-value for coord, value in nodes.values()]
-        triangles = {id: geom for id, geom in elements.items()
-                     if len(geom) == 3}
-        quads = {id: geom for id, geom in elements.items()
-                 if len(geom) == 4}
-        super().__init__(coords, triangles, quads, values, crs, description)
+        msh = list(self._gr3_to_mesh(nodes, elements))
+        msh[3] = [-value for coord, value in nodes.values()]
+        super().__init__(*msh, crs, description)
         self._boundaries = boundaries
 
     @classmethod

diff --git a/pyschism/mesh/vgrid.py b/pyschism/mesh/vgrid.py
@@ -4,7 +4,11 @@
 
 class Vgrid:
 
-    def dump(self, path, overwrite=False):
+    @classmethod
+    def open(cls, path):
+        pass
+
+    def write(self, path, overwrite=False):
         path = pathlib.Path(path)
         if path.is_file() and not overwrite:
             msg = 'File exists, pass overwrite=True to allow overwrite.'

diff --git a/tests/coverage.svg b/tests/coverage.svg
diff --git a/tests/mesh/test_fgrid.py b/tests/mesh/test_fgrid.py
@@ -0,0 +1,44 @@
+#! /usr/bin/env python
+import tempfile
+import pathlib
+from pyschism.mesh.friction import Fgrid
+import unittest
+
+
+class FgridTestCase(unittest.TestCase):
+
+    def setUp(self):
+        self.nodes = {
+            '1': ((0., 0.), -5.),
+            '2': ((.5, 0.), -4.),
+            '3': ((0., 1.), -3.),
+            '4': ((1., 1.), -2.),
+            '5': ((0., 1.), -1.),
+            '6': ((.5, 1.5), 0.),
+            '7': ((.33, .33), 1.),
+            '8': ((.66, .33), 2.),
+            '9': ((.5, .66), 3.),
+            '10': ((-1., 1.), 4.),
+            '11': ((-1., 0.), 5.),
+            }
+        self.elements = {
+            '1': ['5', '7', '9'],
+            '2': ['1', '2', '7'],
+            '3': ['2', '3', '8'],
+            '4': ['8', '7', '2'],
+            '5': ['3', '4', '8'],
+            '6': ['4', '9', '8'],
+            '7': ['4', '6', '5'],
+            '8': ['5', '10', '11', '1'],
+            '9': ['9', '4', '5'],
+            '10': ['5', '1', '7']
+            }
+
+        self.fgrid = {
+            'nodes': self.nodes,
+            'elements': self.elements,
+        }
+
+    # def test_open(self):
+    #     f = Fgrid.open()
+
diff --git a/tests/mesh/test_gmesh.py b/tests/mesh/test_gmesh.py
@@ -116,6 +116,13 @@ def test_default_description(self):
         gmsh.description = 'test'
         self.assertEqual(gmsh.description, 'test')
 
+    def test_from_gr3(self):
+        nodes = {id: (coord, -99999.) for id, coord in self.coords.items()}
+        elements = {id: index for id, index in self.triangles.items()}
+        elements.update({id: index for id, index in self.quads.items()})
+        gmsh = Gmesh.from_gr3(nodes, elements)
+        self.assertIsInstance(gmsh, Gmesh)
+
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/tests/mesh/test_mesh.py b/tests/mesh/test_mesh.py
@@ -0,0 +1,94 @@
+#! /usr/bin/env python
+import tempfile
+import pathlib
+from pyschism.mesh import Mesh, Vgrid
+import unittest
+
+
+class MeshTestCase(unittest.TestCase):
+
+    def setUp(self):
+        self.nodes = {
+            '1': ((0., 0.), -5.),
+            '2': ((.5, 0.), -4.),
+            '3': ((0., 1.), -3.),
+            '4': ((1., 1.), -2.),
+            '5': ((0., 1.), -1.),
+            '6': ((.5, 1.5), 0.),
+            '7': ((.33, .33), 1.),
+            '8': ((.66, .33), 2.),
+            '9': ((.5, .66), 3.),
+            '10': ((-1., 1.), 4.),
+            '11': ((-1., 0.), 5.),
+            }
+        self.elements = {
+            '1': ['5', '7', '9'],
+            '2': ['1', '2', '7'],
+            '3': ['2', '3', '8'],
+            '4': ['8', '7', '2'],
+            '5': ['3', '4', '8'],
+            '6': ['4', '9', '8'],
+            '7': ['4', '6', '5'],
+            '8': ['5', '10', '11', '1'],
+            '9': ['9', '4', '5'],
+            '10': ['5', '1', '7']
+            }
+
+        self.boundaries = dict()
+
+        self.boundaries[None] = {  # "open" boundaries
+                0: ['10', '11', '1', '2'],
+                1: ['2', '3', '4']
+        }
+
+        self.boundaries[0] = {  # "land" boundaries
+            0: ['4', '6'],
+            1: ['6',  '5', '10']
+        }
+
+        self.boundaries[1] = {0: ['7', '8', '9']}  # "interior" boundary
+
+        self.grd = {
+            'nodes': self.nodes,
+            'elements': self.elements,
+            'boundaries': self.boundaries,
+            'description': 'gr3_unittest'
+        }
+
+    def test_open(self):
+        # write hgrid
+        tmpdir = tempfile.TemporaryDirectory()
+        hgrid = pathlib.Path(tmpdir.name) / 'hgrid.gr3'
+        with open(hgrid, 'w') as f:
+            f.write('\n')
+            f.write(f'{len(self.elements):d} ')
+            f.write(f'{len(self.nodes):d}\n')
+            for id, ((x, y), z) in self.nodes.items():
+                f.write(f"{id} ")
+                f.write(f"{x} ")
+                f.write(f"{y} ")
+                f.write(f"{z}\n")
+            for id, geom in self.elements.items():
+                f.write(f"{id} ")
+                f.write(f"{len(geom)} ")
+                for idx in geom:
+                    f.write(f"{idx} ")
+                f.write(f"\n")
+        vgrid = pathlib.Path(tmpdir.name) / 'vgrid.gr3'
+        with open(vgrid, 'w') as f:
+            f.write("2 !ivcor\n")
+            f.write("2 1 1.e6 !nvrt, kz (# of Z-levels); h_s (transition depth between S and Z)\n")
+            f.write("Z levels\n")
+            f.write("1  -1.e6\n")
+            f.write("S levels\n")
+            f.write("40. 1. 1.e-4  !h_c, theta_b, theta_f\n")
+            f.write("   1    -1.\n")
+            f.write("   2     0.\n")
+
+        self.assertIsInstance(
+            Mesh.open(
+                hgrid,
+                vgrid
+                ),
+            Mesh
+        )
diff --git a/tests/mesh/test_vgrid.py b/tests/mesh/test_vgrid.py
@@ -0,0 +1,28 @@
+#! /usr/bin/env python
+import tempfile
+import pathlib
+import unittest
+from pyschism.mesh import Vgrid
+
+
+class VgridTestCase(unittest.TestCase):
+
+    def test_init(self):
+        v = Vgrid()
+        v.boilerplate_2D
+        self.assertIsInstance(v, Vgrid)
+
+    def test_write(self):
+        tmpdir = tempfile.TemporaryDirectory()
+        v = Vgrid()
+        v.write(pathlib.Path(tmpdir.name) / 'vgrid.in')
+        self.assertIsInstance(v, Vgrid)
+
+    def test_write_overwrite_raises(self):
+        tmpfile = tempfile.NamedTemporaryFile()
+        v = Vgrid()
+        self.assertRaises(
+            Exception,
+            v.write,
+            pathlib.Path(tmpfile.name)
+        )