Catch some bugs when bad mesh files are used in dtocean-wec (#14)

-   Renamed `dtocean_wec.submodule.utils.mesh_util` module as `dtocean_wec.submodule.utils.mesh` and refactored
-   Fixed bugs that occur if opening wrong type of mesh file in dtocean-wec
-   Bump to version 3.2.0

CHANGELOG.md

@@ -5,6 +5,17 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [3.2.0] - 2022-09-12
+
+### Changed
+
+-   Renamed dtocean_wec.submodule.utils.mesh_util module as 
+    dtocean_wec.submodule.utils.mesh and refactored.
+
+### Fixed
+
+-   Fixed bugs that occur if opening wrong type of mesh file in dtocean-wec.
+
 ## [3.1.1] - 2022-07-15
 
 ### Fixed

README.md

@@ -129,7 +129,7 @@ $ conda activate _dtocean_hydro
 Install pytest to the environment (one time only):
 
 ```
-$ conda install -y mock pytest pytest-mock pytest-qt
+$ conda install -y mock pytest pytest-catchlog pytest-mock pytest-qt
 ```
 
 Run the tests:

appveyor.yml

@@ -8,7 +8,7 @@
 #---------------------------------#
 
 # version format
-version: 3.1.1.build{build}
+version: 3.2.0.build{build}
 
 image:
   - Visual Studio 2015
@@ -41,7 +41,7 @@ install:
   - python setup.py bootstrap
   - conda install --file requirements-conda-dev.txt
   - pip install -e .
-  - conda install mock "pytest>=3.6,<4" pytest-cov pytest-mock pytest-qt
+  - conda install mock "pytest>=3.6,<4" pytest-catchlog pytest-cov pytest-mock pytest-qt
 
 build: off
 

dtocean_wec/submodule/nemoh_run.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 #    Copyright (C) 2016 Pau Mercadez Ruiz
-#    Copyright (C) 2017-2018 Mathew Topper
+#    Copyright (C) 2017-2022 Mathew Topper
 #
 #    This program is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
@@ -33,9 +33,10 @@
 import subprocess
 
 import numpy as np
+from numpy import linalg as LA
 
 from hydrostatics import Hydrostatics_Nemohcal
-from utils.mesh_util import MeshBem
+from utils.mesh import MeshBem
 from utils.multibody_analysis import MultiBodyAnalysis
 
 # Start logging
@@ -198,29 +199,13 @@ def __init__(self,
             self.mesh_obj += [msh_obj]
 
         # identify the size of the circumscribing cylinder
-        if self.Cyl_Nzeta == 0 or self.Cyl_Ntheta == 0 or (not self.__get_array_mat):
+        if (self.Cyl_Nzeta == 0 or
+                self.Cyl_Ntheta == 0 or
+                    not self.__get_array_mat):
             self.Cyl_radius = 0
-        else :
-            coord = np.empty((0, 3))
-            for b_mesh in self.mesh_obj:
-                coord = np.vstack((coord, b_mesh.Vertex))
-                area = 0.0
-                for panel in b_mesh.panels:
-                    if panel.area > area:
-                        area = panel.area
-                        d = max([(panel.x[0]-panel.x[s])**2+(panel.y[0]-panel.y[s])**2+
-                                 (panel.z[0]-panel.z[s])**2 for s in [1,-1]])
-
-            centroid = coord.mean(0)
-            if not np.sqrt(np.sum(centroid[:2]**2))/coord.max() < 1e-3:
-                module_logger.warning("WARNING: the centroid of the mesh file is not centered in the"
-                        " origin of the mesh coordinate system. \nConsider to regenerate"
-                        " a mesh that satisfy this condition.")
-
-            self.Cyl_radius = (np.sqrt(coord[:,0]**2+coord[:,1]**2)).max()
-            self.Cyl_radius += np.sqrt(d)
-
-
+        else:
+            self.Cyl_radius = _get_cylinder_radius(self.mesh_obj)
+
     def load_folder_tree(self):
         self.path_prj_hdy = os.path.join(self.prj_folder,'hydrodynamic')
         self.path_prj_dyn_res = os.path.join(self.path_prj_hdy,'results')
@@ -254,14 +239,8 @@ def gen_mesh_files(self, show_norm=False):
         for nb in range(self.n_bodies):
             msh_obj = self.mesh_obj[nb]
             if self._debug: msh_obj.visualise_mesh()
-
-            if self.bodies[nb]['mesh'][-3:].lower()=="gdf":
-                msh_obj.mesh_generation("nemoh", output_path=self.path_prj_dyn_mesh)
-
-            else:
-                msh_obj.mesh_generation("nemoh", output_path=self.path_prj_dyn_mesh)
-
-            if self._debug and self.n_bodies>1: msh_obj.visualise_mesh()
+            msh_obj.mesh_generation("nemoh",
+                                    output_path=self.path_prj_dyn_mesh)
 
     def gen_multibody_structure(self):
         mb_obj = MultiBodyAnalysis(self.bodies, self.shared_dof_binary,  self.point_application)
@@ -376,7 +355,39 @@ def run_nemoh(self, nemoh_folder, start=True):
                             os.path.join(nemoh_folder, 'postprocessor.exe')
                             )
             os.chdir(actual_dir)
+
+
+def _get_cylinder_radius(meshes):
+
+    coord = np.empty((0, 3))
+    d = None
+
+    for mesh in meshes:
 
+        coord = np.vstack((coord, mesh.vertices))
+
+        for panel in mesh.connectivity:
+
+            d_panel = max([LA.norm(mesh.vertices[panel[0]] -
+                                   mesh.vertices[panel[s]]) for s in [1, -1]])
+
+            if d is None or d_panel > d:
+                d = d_panel
+
+    if d is None:
+        raise RuntimeError("Can not determine mesh extents")
+
+    centroid = coord.mean(0)
+
+    if not np.sqrt(np.sum(centroid[:2] ** 2)) / coord.max() < 1e-3:
+        module_logger.warning(
+            "WARNING: the centroid of the mesh file is not centered "
+            "at the origin of the mesh coordinate system.\n"
+            "Consider regenerating a mesh to satisfy this condition.")
+
+    return (np.sqrt(coord[:, 0] ** 2 + coord[:, 1] ** 2)).max() + d
+
+
 def rot_matrix(ang):
     Rz = lambda angle: np.array([[np.cos(angle), -np.sin(angle), 0], [np.sin(angle), np.cos(angle), 0], [0, 0, 1]])
     Ry = lambda angle: np.array([[np.cos(angle), 0, np.sin(angle)], [0, 1, 0], [-np.sin(angle), 0, np.cos(angle)]])