Merge pull request #161 from noaa-ocs-modeling/bugfix/meshplot

Fix index vs ID core bug
oceanmodeling · Mar 2, 2023 · 811b1b9 · 811b1b9
2 parents 244ae8a + bbca5ae
commit 811b1b9
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Showing 20 changed files with 275 additions and 196 deletions.
diff --git a/.github/workflows/quick_test.yml b/.github/workflows/quick_test.yml
@@ -50,6 +50,9 @@ jobs:
           path: ${{ env.pythonLocation }}
           key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
       - name: install dependencies
-        run: pip install ".[testing]"
+        run: |
+          sudo apt install libhdf5-dev
+          sudo apt install libnetcdf-dev
+          pip install ".[testing]"
       - name: run tests
         run: pytest --numprocesses auto
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -61,7 +61,17 @@ jobs:
         with:
           path: ${{ env.pythonLocation }}
           key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
-      - name: install dependencies
+      - name: install linux dependencies
+        run: |
+          sudo apt install libhdf5-dev
+          sudo apt install libnetcdf-dev
+        if: runner.os == 'Linux'
+      - name: install macos dependencies
+        run: |
+          brew install hdf5
+          brew install netcdf
+        if: runner.os == 'macOS'
+      - name: install repo
         run: pip install ".[testing]"
       - name: run tests
         run: pytest --numprocesses auto
@@ -80,7 +90,17 @@ jobs:
         with:
           path: ${{ env.pythonLocation }}
           key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
-      - name: install dependencies
+      - name: install linux dependencies
+        run: |
+          sudo apt install libhdf5-dev
+          sudo apt install libnetcdf-dev
+        if: runner.os == 'Linux'
+      - name: install macos dependencies
+        run: |
+          brew install hdf5
+          brew install netcdf
+        if: runner.os == 'macOS'
+      - name: install repo
         run: pip install ".[testing]"
       - name: run tests with coverage
         run: pytest --numprocesses auto --cov . --cov-report xml:coverage.xml

diff --git a/adcircpy/fort15.py b/adcircpy/fort15.py
@@ -609,7 +609,7 @@ def get_tidal_forcing(self) -> str:
             for index, row in self.mesh.boundaries.ocean.gdf.iterrows():
                 for constituent in self.mesh.forcings.tides.get_active_constituents():
                     f.append(fort15_line(constituent))
-                    vertices = self.mesh.get_xy(crs='EPSG:4326').loc[row.indexes, :].values
+                    vertices = self.mesh.get_xy(crs='EPSG:4326').iloc[row.indexes, :].values
                     amp, phase = self.mesh.forcings.tides.tidal_dataset(constituent, vertices)
                     f.extend(
                         fort15_line(f'{amp[i]:.8e} {phase[i]:.8e}')

diff --git a/adcircpy/mesh/base.py b/adcircpy/mesh/base.py
@@ -460,15 +460,35 @@ def open(cls, file: Union[str, os.PathLike], crs: Union[str, CRS] = None):
     @figure
     def tricontourf(self, axes=None, show=True, figsize=None, cbar=False, **kwargs):
         if len(self.triangles) > 0:
-            ax = axes.tricontourf(self.x, self.y, self.triangles, self.values, **kwargs)
+            values = self.values.values  # this is a numpy array
+            if values.shape[1] > 1:
+                values = np.linalg.norm(values, ord=2, axis=1)
+            get_idx = self.nodes.index.get_loc
+            ax = axes.tricontourf(
+                self.x,
+                self.y,
+                [[get_idx(n_id) for n_id in tri] for tri in self.triangles.values],
+                values.squeeze(),
+                **kwargs,
+            )
             if cbar is True:
                 plt.colorbar(ax)
         return axes
 
     @figure
     def tripcolor(self, axes=None, show=True, figsize=None, **kwargs):
         if len(self.triangles) > 0:
-            axes.tripcolor(self.x, self.y, self.triangles, self.values, **kwargs)
+            values = self.values.values  # this is a numpy array
+            if values.shape[1] > 1:
+                values = np.linalg.norm(values, ord=2, axis=1)
+            get_idx = self.nodes.index.get_loc
+            axes.tripcolor(
+                self.x,
+                self.y,
+                [[get_idx(n_id) for n_id in tri] for tri in self.triangles.values],
+                values.squeeze(),
+                **kwargs,
+            )
         return axes
 
     @figure
@@ -478,7 +498,13 @@ def triplot(
         if len(self.triangles) > 0:
             kwargs.update({'linewidth': linewidth})
             kwargs.update({'color': color})
-            axes.triplot(self.x, self.y, self.triangles, **kwargs)
+            get_idx = self.nodes.index.get_loc
+            axes.triplot(
+                self.x,
+                self.y,
+                [[get_idx(n_id) for n_id in tri] for tri in self.triangles.values],
+                **kwargs,
+            )
         return axes
 
     @figure

diff --git a/adcircpy/mesh/fort14.py b/adcircpy/mesh/fort14.py
@@ -26,28 +26,31 @@ def ids(self):
     @property
     def indexes(self):
         if not hasattr(self, '_indexes'):
-            self._indexes = [self._mesh.nodes.index[data['node_id']] for data in self._data]
-        return np.array(self._indexes)
+            self._indexes = [
+                [self._mesh.nodes.index.get_loc(int(node_id)) for node_id in data['node_id']]
+                for data in self._data.values()
+            ]
+        return self._indexes
 
     @property
     def node_id(self):
         if not hasattr(self, '_node_id'):
             self._node_id = list()
-            for data in self._data:
+            for data in self._data.values():
                 self._node_id.append(data['node_id'])
         return self._node_id
 
     @property
     def gdf(self):
         if not hasattr(self, '_gdf'):
             data = []
-            for i, boundary in enumerate(self._data):
+            for i, (bnd_id, boundary) in enumerate(self._data.items()):
                 data.append(
                     {
                         'geometry': LineString(
-                            self._mesh.coords.loc[self.indexes[i], :].values
+                            self._mesh.coords.iloc[self.indexes[i], :].values
                         ),
-                        'key': f'{boundary.get("ibtype")}:{id}',
+                        'key': f'{boundary.get("ibtype")}:{bnd_id}',
                         'indexes': self.indexes[i],
                         **boundary,
                     }
@@ -141,7 +144,9 @@ def plot(
     @property
     def ocean(self):
         if not hasattr(self, '_ocean'):
-            self._ocean = OceanBoundaries(self._mesh, self._data.get(None, {}))
+            self._ocean = OceanBoundaries(
+                self._mesh, {en: bdry for en, bdry in enumerate(self._data.get(None, []))}
+            )
         return self._ocean
 
     @property
@@ -182,11 +187,12 @@ def culvert(self):
 
     def _aggregate_boundaries(self, endswith):
         boundaries = {}
+
         for ibtype, _boundaries in self._data.items():
             if ibtype is None:
                 continue
             if ibtype.endswith(endswith):
-                for bdata in list(_boundaries.values()):
+                for bdata in _boundaries:
                     boundaries.update({len(boundaries) + 1: {'ibtype': ibtype, **bdata,}})
         return boundaries
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -35,6 +35,7 @@ requests = '*'
 scipy = '*'
 shapely = '*'
 stormevents = '^1.4.0'
+typepigeon = '<2' # newer versions require code update
 utm = '*'
 isort = { version = '*', optional = true }
 oitnb = { version = '*', optional = true }

diff --git a/tests/data/reference/example_3/fort.15.coldstart b/tests/data/reference/example_3/fort.15.coldstart
@@ -1,4 +1,4 @@
-created on 2022-04-20 15:31                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2023-02-23 16:47                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER
@@ -63,7 +63,6 @@ S2
 K2
 0.000145842 0.864095 256.729
 Q1
-1.17940985e-02 1.73069764e+02
 1.13893401e-02 1.83698935e+02
 1.21085823e-02 1.73352953e+02
 1.20789492e-02 1.73360490e+02
@@ -138,8 +137,8 @@ Q1
 1.17568855e-02 1.72204623e+02
 1.17685268e-02 1.72637761e+02
 1.17802916e-02 1.73069629e+02
+1.17922348e-02 1.73499568e+02
 O1
-4.78577634e-02 1.95367552e+02
 3.79374677e-02 1.78529759e+02
 4.03967701e-02 1.78123913e+02
 4.28200109e-02 1.77731749e+02
@@ -214,8 +213,8 @@ O1
 4.81119864e-02 1.93069508e+02
 4.80269313e-02 1.94273959e+02
 4.79411731e-02 1.95473663e+02
+4.78544025e-02 1.96666224e+02
 P1
-2.77636120e-02 1.97069071e+02
 2.39791106e-02 2.20627560e+02
 2.55117562e-02 2.13441513e+02
 2.70220036e-02 2.06350152e+02
@@ -290,8 +289,8 @@ P1
 2.83762520e-02 1.93784200e+02
 2.80685313e-02 1.95423100e+02
 2.77617353e-02 1.97057324e+02
+2.74563430e-02 1.98684434e+02
 K1
-7.24141814e-02 1.79513779e+02
 6.39327411e-02 1.75237072e+02
 6.80804771e-02 1.74586196e+02
 7.21663730e-02 1.73945369e+02
@@ -366,8 +365,8 @@ K1
 7.34069773e-02 1.77609524e+02
 7.28725542e-02 1.78581902e+02
 7.23405409e-02 1.79551002e+02
+7.18121397e-02 1.80515143e+02
 N2
-1.21859723e-01 2.04783594e+02
 1.00892997e-01 2.72404213e+02
 1.07287245e-01 2.84727230e+02
 1.13581222e-01 2.96886645e+02
@@ -442,8 +441,8 @@ N2
 1.20482261e-01 2.56015198e+02
 1.21125964e-01 2.30890590e+02
 1.21768816e-01 2.05827798e+02
+1.22410314e-01 1.80859639e+02
 M2
-4.83605669e-01 2.20112655e+02
 4.17823412e-01 3.11130902e+02
 4.44913133e-01 3.18628023e+02
 4.71558150e-01 3.26026894e+02
@@ -518,8 +517,8 @@ M2
 4.77395433e-01 2.72630955e+02
 4.80228035e-01 2.46897948e+02
 4.83058572e-01 2.21227733e+02
+4.85885604e-01 1.95653681e+02
 S2
-1.17248923e-01 2.27815587e+01
 9.55332752e-02 5.27716328e+01
 1.01727604e-01 4.33217911e+01
 1.07823677e-01 3.39973551e+01
@@ -594,8 +593,8 @@ S2
 1.14840665e-01 1.79486568e+01
 1.15964353e-01 2.03622746e+01
 1.17086597e-01 2.27689523e+01
+1.18206537e-01 2.51650756e+01
 K2
-2.70764097e-02 2.04341770e+01
 2.64366106e-02 3.18940471e+01
 2.79369274e-02 2.11382069e+01
 2.94414143e-02 1.03221912e+01
@@ -670,6 +669,7 @@ K2
 2.68472571e-02 1.58475451e+01
 2.69465780e-02 1.81354841e+01
 2.70459553e-02 2.04169051e+01
+2.71453977e-02 2.26884102e+01
 110                                                             ! ANGINN                              - INNER ANGLE THRESHOLD
 0 0 0 0                                                         ! NOUTE TOUTSE TOUTFE NSPOOLE         - ELEV STATION OUTPUT INFO (UNIT 61)
 0                                                               ! NSTAE                               - TOTAL NUMBER OF ELEVATION RECORDING STATIONS

diff --git a/tests/data/reference/example_3/fort.15.hotstart b/tests/data/reference/example_3/fort.15.hotstart
@@ -1,4 +1,4 @@
-created on 2022-04-20 15:31                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2023-02-23 16:47                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER
@@ -64,7 +64,6 @@ S2
 K2
 0.000145842 0.864095 256.729
 Q1
-1.17940985e-02 1.73069764e+02
 1.13893401e-02 1.83698935e+02
 1.21085823e-02 1.73352953e+02
 1.20789492e-02 1.73360490e+02
@@ -139,8 +138,8 @@ Q1
 1.17568855e-02 1.72204623e+02
 1.17685268e-02 1.72637761e+02
 1.17802916e-02 1.73069629e+02
+1.17922348e-02 1.73499568e+02
 O1
-4.78577634e-02 1.95367552e+02
 3.79374677e-02 1.78529759e+02
 4.03967701e-02 1.78123913e+02
 4.28200109e-02 1.77731749e+02
@@ -215,8 +214,8 @@ O1
 4.81119864e-02 1.93069508e+02
 4.80269313e-02 1.94273959e+02
 4.79411731e-02 1.95473663e+02
+4.78544025e-02 1.96666224e+02
 P1
-2.77636120e-02 1.97069071e+02
 2.39791106e-02 2.20627560e+02
 2.55117562e-02 2.13441513e+02
 2.70220036e-02 2.06350152e+02
@@ -291,8 +290,8 @@ P1
 2.83762520e-02 1.93784200e+02
 2.80685313e-02 1.95423100e+02
 2.77617353e-02 1.97057324e+02
+2.74563430e-02 1.98684434e+02
 K1
-7.24141814e-02 1.79513779e+02
 6.39327411e-02 1.75237072e+02
 6.80804771e-02 1.74586196e+02
 7.21663730e-02 1.73945369e+02
@@ -367,8 +366,8 @@ K1
 7.34069773e-02 1.77609524e+02
 7.28725542e-02 1.78581902e+02
 7.23405409e-02 1.79551002e+02
+7.18121397e-02 1.80515143e+02
 N2
-1.21859723e-01 2.04783594e+02
 1.00892997e-01 2.72404213e+02
 1.07287245e-01 2.84727230e+02
 1.13581222e-01 2.96886645e+02
@@ -443,8 +442,8 @@ N2
 1.20482261e-01 2.56015198e+02
 1.21125964e-01 2.30890590e+02
 1.21768816e-01 2.05827798e+02
+1.22410314e-01 1.80859639e+02
 M2
-4.83605669e-01 2.20112655e+02
 4.17823412e-01 3.11130902e+02
 4.44913133e-01 3.18628023e+02
 4.71558150e-01 3.26026894e+02
@@ -519,8 +518,8 @@ M2
 4.77395433e-01 2.72630955e+02
 4.80228035e-01 2.46897948e+02
 4.83058572e-01 2.21227733e+02
+4.85885604e-01 1.95653681e+02
 S2
-1.17248923e-01 2.27815587e+01
 9.55332752e-02 5.27716328e+01
 1.01727604e-01 4.33217911e+01
 1.07823677e-01 3.39973551e+01
@@ -595,8 +594,8 @@ S2
 1.14840665e-01 1.79486568e+01
 1.15964353e-01 2.03622746e+01
 1.17086597e-01 2.27689523e+01
+1.18206537e-01 2.51650756e+01
 K2
-2.70764097e-02 2.04341770e+01
 2.64366106e-02 3.18940471e+01
 2.79369274e-02 2.11382069e+01
 2.94414143e-02 1.03221912e+01
@@ -671,6 +670,7 @@ K2
 2.68472571e-02 1.58475451e+01
 2.69465780e-02 1.81354841e+01
 2.70459553e-02 2.04169051e+01
+2.71453977e-02 2.26884102e+01
 110                                                             ! ANGINN                              - INNER ANGLE THRESHOLD
 0 0 0 0                                                         ! NOUTE TOUTSE TOUTFE NSPOOLE         - ELEV STATION OUTPUT INFO (UNIT 61)
 0                                                               ! NSTAE                               - TOTAL NUMBER OF ELEVATION RECORDING STATIONS