Merge branch 'master' of https://github.com/hpgem/nanomesh into master

nanomesh/mesh.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from types import MappingProxyType
 from typing import TYPE_CHECKING, Dict, List, Sequence
 
 import matplotlib.pyplot as plt
@@ -45,6 +46,7 @@ class BaseMesh:
     def __init__(self,
                  points: np.ndarray,
                  cells: np.ndarray,
+                 fields: Dict[str, int] = None,
                  region_markers: List[RegionMarker] = None,
                  **cell_data):
         """Base class for meshes.
@@ -55,6 +57,8 @@ def __init__(self,
             Array with points.
         cells : (i, j) np.ndarray[int]
             Index array describing the cells of the mesh.
+        fields : Dict[str, int]:
+            Mapping from field names to labels
         region_markers : List[RegionMarker], optional
             List of region markers used for assigning labels to regions.
             Defaults to an empty list.
@@ -68,11 +72,22 @@ def __init__(self,
         else:
             self.default_key = list(cell_data.keys())[0]
 
+        if not fields:
+            fields = {}
+
         self.points = points
         self.cells = cells
+        self.field_to_number = fields
         self.region_markers = [] if region_markers is None else region_markers
         self.cell_data = cell_data
 
+    @property
+    def number_to_field(self):
+        """Mapping from numbers to fields, proxy to `.field_to_number`."""
+        return MappingProxyType(
+            {v: k
+             for k, v in self.field_to_number.items()})
+
     def add_region_marker(self, region_marker: RegionMarkerLike):
         """Add marker to list of region markers.
 
@@ -240,7 +255,6 @@ class LineMesh(BaseMesh):
     def plot_mpl(self,
                  ax: plt.Axes = None,
                  key: str = None,
-                 fields: Dict[int, str] = None,
                  **kwargs) -> plt.Axes:
         """Simple line mesh plot using `matplotlib`.
 
@@ -262,9 +276,6 @@ def plot_mpl(self,
         if not ax:
             fig, ax = plt.subplots()
 
-        if fields is None:
-            fields = {}
-
         if key is None:
             try:
                 key = tuple(self.cell_data.keys())[0]
@@ -277,7 +288,7 @@ def plot_mpl(self,
         for cell_data_val in np.unique(cell_data):
             vert_x, vert_y = self.points.T
 
-            name = fields.get(cell_data_val, cell_data_val)
+            name = self.number_to_field.get(cell_data_val, cell_data_val)
 
             lineplot(
                 ax,
@@ -330,7 +341,6 @@ def plot(self, **kwargs):
     def plot_mpl(self,
                  ax: plt.Axes = None,
                  key: str = None,
-                 fields: Dict[int, str] = None,
                  **kwargs) -> plt.Axes:
         """Simple mesh plot using `matplotlib`.
 
@@ -353,9 +363,6 @@ def plot_mpl(self,
         if not ax:
             fig, ax = plt.subplots()
 
-        if fields is None:
-            fields = {}
-
         if key is None:
             try:
                 key = tuple(self.cell_data.keys())[0]
@@ -368,7 +375,7 @@ def plot_mpl(self,
         for cell_data_val in np.unique(cell_data):
             vert_x, vert_y = self.points.T
 
-            name = fields.get(cell_data_val, cell_data_val)
+            name = self.number_to_field.get(cell_data_val, cell_data_val)
 
             ax.triplot(vert_y,
                        vert_x,

nanomesh/mesh2d/helpers.py

@@ -86,11 +86,14 @@ def simple_triangulate(points: np.ndarray,
     return mesh
 
 
-def pad(mesh: LineMesh,
-        *,
-        side: str,
-        width: int,
-        label: int = None) -> LineMesh:
+def pad(
+    mesh: LineMesh,
+    *,
+    side: str,
+    width: int,
+    label: int = None,
+    name: str = None,
+) -> LineMesh:
     """Pad a triangle mesh (2D).
 
     Parameters
@@ -104,6 +107,9 @@ def pad(mesh: LineMesh,
     label : int, optional
         The label to assign to the padded area. If not defined, generates the
         next unique label based on the existing ones.
+    name : str, optional
+        Name of the added region. Note that in case of conflicts, the `label`
+        takes presedence over the `name`.
 
     Returns
     -------
@@ -115,8 +121,17 @@ def pad(mesh: LineMesh,
     ValueError
         When the value of `side` is invalid.
     """
+    labels = [m.label for m in mesh.region_markers]
+    names = [m.name for m in mesh.region_markers]
+
+    if (label in labels) and (name is None):
+        name = [m.name for m in mesh.region_markers if m.label == label][0]
+
+    if name and (name in names) and (label is None):
+        label = [m.label for m in mesh.region_markers if m.name == name][0]
+
     if label is None:
-        label = mesh.labels.max() + 1
+        label = max(max(labels) + 1, 2)
 
     if width == 0:
         return mesh
@@ -171,7 +186,7 @@ def pad(mesh: LineMesh,
     cells = np.vstack([mesh.cells, additional_segments])
 
     center = corners.mean(axis=0)
-    region_markers = mesh.region_markers + [RegionMarker(label, center)]
+    region_markers = mesh.region_markers + [RegionMarker(label, center, name)]
 
     new_mesh = mesh.__class__(
         points=all_points,

nanomesh/mesh2d/mesher.py

@@ -80,7 +80,7 @@ def generate_regions(polygons: List[Polygon]) -> List[Tuple[int, np.ndarray]]:
         point = polygon.find_point()
 
         # in LineMesh format
-        regions.append((label + 1, point))
+        regions.append((1, point))
 
     return regions
 
@@ -223,6 +223,12 @@ def triangulate(self,
         mesh.set_field_data('triangle', {0: 'background', 1: 'feature'})
         mesh.set_field_data('line', {0: 'body', 1: 'external', 2: 'internal'})
 
+        fields = {
+            m.label: m.name
+            for m in self.contour.region_markers if m.name
+        }
+        mesh.set_field_data('triangle', fields)
+
         return mesh
 
     def generate_domain_mask_from_contours(

nanomesh/mesh_container.py

@@ -28,7 +28,9 @@ def number_to_field(self):
             dim_name = CellType(dimension).name.lower()
             number_to_field[dim_name][number] = field
 
-        return MappingProxyType(dict(number_to_field))
+        return MappingProxyType(
+            {k: MappingProxyType(v)
+             for k, v in number_to_field.items()})
 
     @property
     def field_to_number(self):
@@ -39,22 +41,24 @@ def field_to_number(self):
             dim_name = CellType(dimension).name.lower()
             field_to_number[dim_name][field] = number
 
-        return MappingProxyType(dict(field_to_number))
+        return MappingProxyType(
+            {k: MappingProxyType(v)
+             for k, v in field_to_number.items()})
 
     def set_field_data(self, cell_type: str, field_data: Dict[int, str]):
         """Update the values in `.field_data`.
 
         Parameters
         ----------
         cell_type : str
-            Cell type to update the values ofr.
+            Cell type to update the values for.
         field_data : dict
             Dictionary with key-to-number mapping, i.e.
             `field_data={0: 'green', 1: 'blue', 2: 'red'}`
             maps `0` to `green`, etc.
         """
         try:
-            input_field_data = dict(self.number_to_field)[cell_type]
+            input_field_data = dict(self.number_to_field[cell_type])
         except KeyError:
             input_field_data = {}
 
@@ -144,7 +148,12 @@ def get(self, cell_type: str = None) -> BaseMesh:
 
         cell_data = self.get_all_cell_data(cell_type)
 
-        return BaseMesh.create(cells=cells, points=points, **cell_data)
+        fields = self.field_to_number.get(cell_type, None)
+
+        return BaseMesh.create(cells=cells,
+                               points=points,
+                               fields=fields,
+                               **cell_data)
 
     def get_all_cell_data(self, cell_type: str = None) -> dict:
         """Get all cell data for given `cell_type`.

nanomesh/region_markers.py

@@ -1,5 +1,5 @@
 from dataclasses import dataclass
-from typing import Tuple, Union
+from typing import Optional, Tuple, Union
 
 import numpy.typing as npt
 
@@ -8,6 +8,7 @@
 class RegionMarker:
     label: int
     coordinates: npt.NDArray
+    name: Optional[str] = None
 
 
 RegionMarkerLike = Union[RegionMarker, Tuple[int, npt.NDArray]]