add support for .stl, arrays of points (teeths), stop if nodes are not identified

models/boneload.py

@@ -143,11 +143,10 @@ def identify_nodes(coords, all_no, all_coords, eps=1e-3):
             ntags.append(no)
             break
         if not found:
-            notfound.append(no)
+            notfound.append(n)
 
     if(len(notfound)!=0):
-        Exception(f'ERROR: {len(notfound)} nodes have not been found!')
-
+        raise Exception(f'ERROR: {len(notfound)} nodes have not been found!')
     return ntags
 
 

models/dolicorhynchops_10k.py

@@ -3,18 +3,21 @@
 # Dolicorhynchops osborni FHSM VP404
 #   10k faces on the mandible surface
 
+
 def parms(d={}):
     p = {}
     path = 'dolicorhynchops/10k'
-    p['mandible'] = f'{path}/mandible.ply'
-    p['teeth'] = f'{path}/teeth.off'
+    p['mandible'] = f'{path}/mandible.stl'
+    p['teeth'] = [[-10.20362, -17.46838, -229.9061],
+                  [-11.92466, 26.3042, -229.5354]]
     p['LTMJ'] = f'{path}/LTMJ.off'
-    p['RTMJ'] = f'{path}/RTMJ.off'
+    p['RTMJ'] = [ -8.716309, 79.13171, 233.8385 ]
     p['muscles'] = [
         {
             'file': f'{path}/Lmuscle.ply',
             'force': 100.,
-            'focalpt': [-100.1458893, -173.13895, 227.3909], #f'{path}/LmuscleF.off',
+            # f'{path}/LmuscleF.off',
+            'focalpt': [-100.1458893, -173.13895, 227.3909],
             'method': 'U'                              # 'U', 'T', 'T+N'
         },
         {
@@ -24,10 +27,10 @@ def parms(d={}):
             'method': 'T'
         }
     ]
-    p['fixations'] = {  
+    p['fixations'] = {
         'teeth': ['x'],
-        'LTMJ': ['x','y','z'],
-        'RTMJ': ['x','z']
+        'LTMJ': ['x', 'y', 'z'],
+        'RTMJ': ['x', 'z']
     }
 
     # material properties

models/mandiblemodel.py

@@ -236,7 +236,7 @@ def import_mesh(domain, filename):
         raise Exception(f'{mandible_gmsh} not found!')
     # extract extension
     noext,ext = os.path.splitext(mandible_gmsh)
-    if ext=='.ply':
+    if ext in ['.ply', '.stl']:
         plyfile = mandible_gmsh
         # create 2 workspace files
         basename = os.path.join(os.getcwd(), os.path.basename(noext))
@@ -257,6 +257,10 @@ def import_mesh(domain, filename):
             f.write('Mesh.MshFileVersion = 2.2;\n')
             f.close()
             mandible_gmsh=geofile
+    elif ext in ['.geo', '.msh']:
+        pass
+    else:
+        raise Exception(f'Unknown extension: {ext}, please use .ply, .stl, .msh, .geo')
 
     print(f'importing {mandible_gmsh}')
     from toolbox.gmsh import GmshImport
@@ -283,17 +287,30 @@ def create_group(mesh_file_or_coord, all_no, all_coords, domain, groups, gname=N
     """loads the mesh file "mesh_file_or_coord" and identify vertices among vertices
     stored in all_coords. 
     Then, the routine creates a group named "gname" (built from mesh_file_or_coord if None)
-    """
-    # load mesh file
-    if isinstance(mesh_file_or_coord, str): 
+
+    mesh_file_or_coord can be either:
+      a filename
+      an array of points: [ [x1,y1,z1], [x2,y2,z2], ... ]
+      one single point: [x1,y1,z1]
+    """  
+    if isinstance(mesh_file_or_coord, str):
+        # load mesh file
+        print(f'\n* create_group {mesh_file_or_coord}...')
         fullpath = os.path.join(os.path.dirname(__file__), mesh_file_or_coord) 
         nodes, tris = boneload.load_msh(fullpath)
-    else: 
-        nodes = [ mesh_file_or_coord ]
+    elif type(mesh_file_or_coord) in [list, tuple]:
+        print(f'\n* create_group {gname}...')
+        if type(mesh_file_or_coord[0]) in [list, tuple]:
+            # array of points
+            nodes = mesh_file_or_coord
+        else:
+            # one single point
+            nodes = [ mesh_file_or_coord ]
         print(f'nodes={nodes}')
         print(f'mesh_file_or_coord={mesh_file_or_coord}')
         tris = []
-
+    else:
+        raise Exception(f'Data is not understood: {mesh_file_or_coord}')
     # identify nodes of the mesh among the given vertices of the main mesh
     ntags = boneload.identify_nodes(nodes, all_no, all_coords)