fix: read physical groups from msh file

opstool/pre/_read_gmsh.py

@@ -1,3 +1,4 @@
+import re
 import gmsh
 import numpy as np
 import openseespy.opensees as ops
@@ -35,12 +36,14 @@ def __init__(self, ndm: int = 3, ndf: int = 3):
         self.out_file = None
         self.out_type = None
 
-    def set_output_file(self, filename: str = "src.tcl"):
+    def set_output_file(self, filename: str = "src.tcl", encoding: str = "utf-8"):
         """
         Parameters:
         ------------
         filename: str, default = "src.tcl".
             The output file-path-name must end with ``.tcl`` or ``.py``.
+        encoding: str, default = "utf-8".
+            The file encoding.
         """
         self.out_file = filename
         if filename.endswith(".tcl"):
@@ -49,7 +52,7 @@ def set_output_file(self, filename: str = "src.tcl"):
             self.out_type = "py"
         else:
             raise ValueError("output_filename must end with .tcl or .py!")
-        with open(self.out_file, "w+") as outf:
+        with open(self.out_file, "w+", encoding=encoding) as outf:
             outf.write(f"# This file was created by {self.__class__.__name__}\n\n")
             if self.out_type == "py":
                 outf.write("import openseespy.opensees as ops\n\n")
@@ -61,7 +64,12 @@ def set_output_file(self, filename: str = "src.tcl"):
                 outf.write("wipe\n")
                 outf.write(f"model basic -ndm {self.ndm} -ndf {self.ndf}\n\n")
 
-    def read_gmsh_file(self, file_path: str, print_info: bool = True):
+    def read_gmsh_file(
+            self,
+            file_path: str,
+            encoding: str = "utf-8",
+            print_info: bool = True
+    ):
         """
         Read an ``.msh`` file generated by ``GMSH``.
 
@@ -74,10 +82,12 @@ def read_gmsh_file(self, file_path: str, print_info: bool = True):
         -----------
         file_path: str
             the file path.
+        encoding: str, default='utf-8'
+            The file encoding.
         print_info: bool, default=True
             Print info.
         """
-        with open(file_path) as inf:
+        with open(file_path, encoding=encoding) as inf:
             lines = [ln.strip() for ln in inf.readlines()]
         # Remove comments
         lines = [ln for ln in lines if not ln.startswith("**")]
@@ -92,7 +102,7 @@ def read_gmsh_file(self, file_path: str, print_info: bool = True):
             physical_idx.append(lines.index("$PhysicalNames"))
             physical_idx.append(lines.index("$EndPhysicalNames"))
 
-        # key: physical_tag, value: physical_name
+        # key: (dim, physical_tag), value: physical_name
         physical_tag_name_map = _retrieve_physical_groups(lines, physical_idx)
         self.gmsh_entities, self.gmsh_physical_groups = _retrieve_entities(
             lines, entities_idx, physical_tag_name_map
@@ -668,21 +678,32 @@ def _get_boundary_dim_tags(boundary_dimtags, dim_entity_tags, entites):
 #             if eetag[0] > 0:
 #                 _get_boundary_dim_tags(boundary_dimtags, [eetag])
 def _retrieve_physical_groups(lines, physical_idx):
+    pattern = r'(\d+)\s+(\d+)\s+"(.*)"'
     tag_name_map = dict()
     if len(physical_idx) > 0:
         idx = physical_idx[0] + 1
-        num = int(lines(idx))
-        print(f"Info:: {num} Physical Groups.")
+        num = int(lines[idx])
+        print(f"Info:: {num} Physical Names.")
         for i in range(num):
-            idx += i + 1
-            contents = [int(data) for data in lines[idx].split(" ")]
-            # dim = contents[0]
-            tag = contents[1]
-            name = contents[2]
-            tag_name_map[tag] = name
+            idx += 1
+            match = re.match(pattern, lines[idx])
+            if match:
+                dim = int(match.group(1))
+                tag = int(match.group(2))
+                name = match.group(3)
+            else:
+                raise RuntimeError("Not all physical groups have names set!")
+            tag_name_map[(dim, tag)] = name
     return tag_name_map
 
 
+def _check_physical_tag_name_map(key, physical_tag_name_map):
+    if key not in physical_tag_name_map.keys():
+        raise KeyError(
+            f"(dim={key[0]}, physical tag={key[1]}) has no physical name set!"
+        )
+
+
 def _retrieve_entities(lines, entities_idx, physical_tag_name_map):
     entities = defaultdict(dict)
     gmsh_physical_groups = defaultdict(list)
@@ -698,7 +719,8 @@ def _retrieve_entities(lines, entities_idx, physical_tag_name_map):
             entities[(0, tag)]["numPhysicalTags"] = int(contents[4])
             physical_tags = [int(contents[5 + iii]) for iii in range(int(contents[4]))]
             for ptag in physical_tags:
-                pname = physical_tag_name_map[ptag]
+                _check_physical_tag_name_map((0, ptag), physical_tag_name_map)
+                pname = physical_tag_name_map[(0, ptag)]
                 gmsh_physical_groups[pname].append((0, tag))
             entities[(0, tag)]["physicalTags"] = physical_tags
             entities[(0, tag)]["numBound"] = 0
@@ -713,7 +735,8 @@ def _retrieve_entities(lines, entities_idx, physical_tag_name_map):
             entities[(1, tag)]["numPhysicalTags"] = int(contents[7])
             physical_tags = [int(contents[8 + iii]) for iii in range(int(contents[7]))]
             for ptag in physical_tags:
-                pname = physical_tag_name_map[ptag]
+                _check_physical_tag_name_map((1, ptag), physical_tag_name_map)
+                pname = physical_tag_name_map[(1, ptag)]
                 gmsh_physical_groups[pname].append((1, tag))
             entities[(1, tag)]["physicalTags"] = physical_tags
             numBounds = int(contents[8 + int(contents[7])])
@@ -732,7 +755,8 @@ def _retrieve_entities(lines, entities_idx, physical_tag_name_map):
             entities[(2, tag)]["numPhysicalTags"] = int(contents[7])
             physical_tags = [int(contents[8 + iii]) for iii in range(int(contents[7]))]
             for ptag in physical_tags:
-                pname = physical_tag_name_map[ptag]
+                _check_physical_tag_name_map((2, ptag), physical_tag_name_map)
+                pname = physical_tag_name_map[(2, ptag)]
                 gmsh_physical_groups[pname].append((2, tag))
             entities[(2, tag)]["physicalTags"] = physical_tags
             numBounds = int(contents[8 + int(contents[7])])
@@ -751,7 +775,8 @@ def _retrieve_entities(lines, entities_idx, physical_tag_name_map):
             entities[(3, tag)]["numPhysicalTags"] = int(contents[7])
             physical_tags = [int(contents[8 + iii]) for iii in range(int(contents[7]))]
             for ptag in physical_tags:
-                pname = physical_tag_name_map[ptag]
+                _check_physical_tag_name_map((3, ptag), physical_tag_name_map)
+                pname = physical_tag_name_map[(3, ptag)]
                 gmsh_physical_groups[pname].append((3, tag))
             entities[(3, tag)]["physicalTags"] = physical_tags
             numBounds = int(contents[8 + int(contents[7])])