Added restructured Python code to new branch

.gitignore

@@ -67,3 +67,5 @@ examples/global-lunar-bombardment/scale.ipynb
 
 *.m4
 *.code-workspace
+
+*.png

python/ctem/ctem/__init__.py

@@ -0,0 +1,3 @@
+# from ctem.ctem_io_readers import *
+# from ctem.ctem_io_writers import *
+# from ctem.ctem_driver import *

python/ctem/ctem/ctem_viewer_3d.py

@@ -0,0 +1,101 @@
+import numpy as np
+import open3d as o3d
+import trimesh
+
+class surf:
+    """A model of a self-gravitating small body"""
+    def __init__(self):
+        self.polyfile = ""
+        self.mesh = trimesh.Trimesh()
+        #used for Open3d module
+        self.o3d_mesh = o3d.geometry.TriangleMesh()
+        self.nface = 0
+        self.nvert = 0
+        return
+
+    def io_read_ply(self,filename):
+        """Reads in PLY file into Open3d triangular mesh object and computes normals"""
+        self.polyfile = filename
+        self.mesh = trimesh.load(f"{self.polyfile}")
+        trimesh.repair.fix_normals(self.mesh)
+        self.mesh.vertex_colors = np.full((self.nvert,4),1.0)
+        self.nvert = len(self.mesh.vertices)
+        self.nface = len(self.mesh.faces)
+        self.convert_trimesh_to_o3d()
+        return
+
+    def render(self):
+        """Renders output"""
+        self.convert_trimesh_to_o3d()
+        o3d.visualization.draw_geometries([self.o3d_mesh])
+        return
+
+    def convert_trimesh_to_o3d(self):
+        """Update Open3D mesh with new vertices and faces, and recompute all normals"""
+        self.o3d_mesh.vertices  = o3d.utility.Vector3dVector(self.mesh.vertices)
+        self.o3d_mesh.triangles = o3d.utility.Vector3iVector(self.mesh.faces)
+        self.o3d_mesh.compute_vertex_normals()
+        self.o3d_mesh.compute_triangle_normals()
+        self.o3d_mesh.vertex_colors = o3d.utility.Vector3dVector(self.mesh.vertex_colors[:,0:3])
+        return
+
+if __name__ == '__main__':
+    import os
+    import ctem_io_readers
+    import open3d
+
+    #Create and initialize data dictionaries for parameters and options from CTEM.in
+    notset = '-NOTSET-'
+    currentdir = os.getcwd() + os.sep
+
+    parameters={'restart': notset,
+                'runtype': notset,
+                'popupconsole': notset,
+                'saveshaded': notset,
+                'saverego': notset,
+                'savepres': notset,
+                'savetruelist': notset,
+                'seedn': 1,
+                'totalimpacts': 0,
+                'ncount': 0,
+                'curyear': 0.0,
+                'fracdone': 1.0,
+                'masstot': 0.0,
+                'interval': 0.0,
+                'numintervals': 0,
+                'pix': -1.0,
+                'gridsize': -1,
+                'seed': 0,
+                'maxcrat': 1.0,
+                'shadedminhdefault': 1,
+                'shadedmaxhdefault': 1,
+                'shadedminh': 0.0,
+                'shadedmaxh': 0.0,
+                'workingdir': currentdir,
+                'ctemfile': 'ctem.in',
+                'datfile': 'ctem.dat',
+                'impfile': notset,
+                'sfdcompare': notset,
+                'sfdfile': notset}
+
+    #Read ctem.in to initialize parameter values based on user input
+    ctem_io_readers.read_ctemin(parameters,notset)
+    #Read surface dem(shaded relief) and ejecta data files
+    dem_file = parameters['workingdir'] + 'surface_dem.dat'
+    surface_dem = ctem_io_readers.read_unformatted_binary(dem_file, parameters['gridsize'])
+    # Build mesh grid
+    gridsize = parameters['gridsize']
+    pix = parameters['pix']
+    ygrid, xgrid = np.mgrid[-gridsize / 2:gridsize / 2,
+                             -gridsize / 2:gridsize / 2] * pix
+
+    xvals = xgrid.flatten()
+    yvals = ygrid.flatten()
+    zvals = surface_dem.flatten()
+    dem_vec = np.array((xvals, yvals, zvals*10)).T
+    pcd = open3d.geometry.PointCloud()
+    pcd.points = open3d.utility.Vector3dVector(dem_vec)
+
+    o3d.visualization.draw_geometries([pcd])
+
+