Add raster mesh (#45)

addresses (#44)

Author: kip-hart

CHANGELOG.rst

@@ -6,6 +6,12 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog`_,
 and this project adheres to `Semantic Versioning`_.
 
+`1.5.0`_ - 2021-09-08
+--------------------------
+Added
+'''''
+- RasterMesh class, to create pixel/voxel meshes. (addresses `#44`_)
+
 `1.4.10`_ - 2021-06-08
 --------------------------
 Fixed
@@ -237,7 +243,8 @@ Added
 
 .. LINKS
 
-.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.4.10...HEAD
+.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.5.0...HEAD
+.. _`1.5.0`: https://github.com/kip-hart/MicroStructPy/compare/v1.4.10...v1.5.0
 .. _`1.4.10`: https://github.com/kip-hart/MicroStructPy/compare/v1.4.9...v1.4.10
 .. _`1.4.9`: https://github.com/kip-hart/MicroStructPy/compare/v1.4.8...v1.4.9
 .. _`1.4.8`: https://github.com/kip-hart/MicroStructPy/compare/v1.4.7...v1.4.8
@@ -270,3 +277,4 @@ Added
 
 .. _`#14`: https://github.com/kip-hart/MicroStructPy/issues/14
 .. _`#16`: https://github.com/kip-hart/MicroStructPy/issues/16
+.. _`#44`: https://github.com/kip-hart/MicroStructPy/issues/44

docs/source/cli/settings.rst

@@ -43,7 +43,7 @@ quality, among other things. The default settings are:
             <edge_opt> False </edge_opt>
             <edge_opt_n_iter> 100 </edge_opt_n_iter>
 
-            <mesher>  Triangle/TetGen </mesher>
+            <mesher> Triangle/TetGen </mesher>
 
             <mesh_size> inf </mesh_size> <!-- used with gmsh -->
             <mesh_max_volume> inf </mesh_max_volume> <!-- used with Triangle and TetGen -->
@@ -286,6 +286,18 @@ The default is ``<edge_opt_n_iter> 100 </edge_opt_n_iter>``, which limits the
 optimizer to 100 attempts per edge.
 This field is ignored if ``edge_opt`` is set to ``False``.
 
+mesher
+------
+
+This field specifies how to mesh the PolyMesh. If set to ``raster``, the output
+mesh will contain pixels/voxels of the PolyMesh.
+Other options include ``Triangle/Tetgen`` and ``gmsh``.
+
+mesh_size
+---------
+
+This field specifies a target element size if using the ``gmsh`` mesher.
+
 mesh_max_volume
 ---------------
 

src/microstructpy/__init__.py

@@ -4,4 +4,4 @@
 import microstructpy.seeding
 import microstructpy.verification
 
-__version__ = '1.4.10'
+__version__ = '1.5.0'

src/microstructpy/cli.py

@@ -29,6 +29,7 @@
 from microstructpy import seeding
 from microstructpy import verification
 from microstructpy.meshing import PolyMesh
+from microstructpy.meshing import RasterMesh
 from microstructpy.meshing import TriMesh
 from microstructpy.meshing.trimesh import facet_check
 
@@ -301,7 +302,8 @@ def run(phases, domain, verbose=False, restart=True, directory='.',
         edge_opt_n_iter (int): *(optional)* Maximum number of iterations per
             edge during optimization. Ignored if `edge_opt` set to False.
             Defaults to 100.
-        mesher (str): {'Triangle/TetGen' | 'Triangle'  | 'TetGen' | 'gmsh'}
+        mesher (str): {'raster' | 'Triangle/TetGen' | 'Triangle'  | 'TetGen' |
+            'gmsh'}
             specify the mesh generator. Default is 'Triangle/TetGen'.
         mesh_max_volume (float): *(optional)* The maximum volume (area in 2D)
             of a mesh cell in the triangular mesh. Default is infinity,
@@ -491,28 +493,41 @@ def run(phases, domain, verbose=False, restart=True, directory='.',
     # ----------------------------------------------------------------------- #
     # Create Triangular Mesh                                                  #
     # ----------------------------------------------------------------------- #
-    tri_basename = 'trimesh.txt'
+    raster = mesher == 'raster'
+    if raster:
+        tri_basename = 'rastermesh.txt'
+    else:
+        tri_basename = 'trimesh.txt'
     tri_filename = os.path.join(directory, tri_basename)
     exts = {'abaqus': '.inp', 'txt': '.txt', 'str': '.txt', 'tet/tri': '',
             'vtk': '.vtk'}
 
     if restart and os.path.exists(tri_filename) and not poly_created:
         # Read triangle mesh
         if verbose:
-            print('Reading triangular mesh.')
-            print('Triangular mesh filename: ' + tri_filename)
+            if raster:
+                print('Reading raster mesh.')
+            else:
+                print('Reading triangular mesh.')
+            print('Mesh filename: ' + tri_filename)
 
         tmesh = TriMesh.from_file(tri_filename)
         tri_created = False
     else:
         tri_created = True
         # Create triangular mesh
         if verbose:
-            print('Creating triangular mesh.')
+            if raster:
+                print('Creating raster mesh.')
+            else:
+                print('Creating triangular mesh.')
 
-        tmesh = TriMesh.from_polymesh(pmesh, phases, mesher, mesh_min_angle,
-                                      mesh_max_volume, mesh_max_edge_length,
-                                      mesh_size)
+        if raster:
+            tmesh = RasterMesh.from_polymesh(pmesh, mesh_size, phases)
+        else:
+            tmesh = TriMesh.from_polymesh(pmesh, phases, mesher,
+                                          mesh_min_angle, mesh_max_volume,
+                                          mesh_max_edge_length, mesh_size)
 
     # Write triangular mesh
     tri_types = filetypes.get('tri', [])
@@ -535,12 +550,19 @@ def run(phases, domain, verbose=False, restart=True, directory='.',
 
     plot_files = []
     for ext in plot_types:
-        fname = os.path.join(directory, 'trimesh.' + str(ext))
+        if raster:
+            bname = 'rastermesh'
+        else:
+            bname = 'trimesh'
+        fname = os.path.join(directory, bname + '.' + str(ext))
         if tri_created or not os.path.exists(fname):
             plot_files.append(fname)
 
     if plot_files and verbose:
-        print('Plotting triangular mesh.')
+        if raster:
+            print('Plotting raster mesh.')
+        else:
+            print('Plotting triangular mesh.')
 
     if plot_files:
         plot_tri(tmesh, phases, seeds, pmesh, plot_files, plot_axes, color_by,

src/microstructpy/meshing/__init__.py

@@ -1,4 +1,5 @@
 from microstructpy.meshing.polymesh import PolyMesh
+from microstructpy.meshing.trimesh import RasterMesh
 from microstructpy.meshing.trimesh import TriMesh
 
-__all__ = ['PolyMesh', 'TriMesh']
+__all__ = ['PolyMesh', 'RasterMesh', 'TriMesh']