progress on h5py method

README.md

@@ -57,7 +57,7 @@ material tag mat1.
 from vertices_to_h5m import vertices_to_h5m
 import numpy as np
 
-# these are the x,y,z coordinates of each vertex. Entries should be floats 
+# these are the x,y,z coordinates of each vertex. Entries should be floats
 vertices = np.array(
     [
         [0.0, 0.0, 0.0],
@@ -69,15 +69,15 @@ vertices = np.array(
 
 
 # These are the triangle that connect individual vertices together to form a continious surface and also a closed volume. Entries should be ints
-triangles = [
+triangle_groups = [
     np.array([[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]]),
 ]
 
 
 # This will produce a h5m file called one_volume.h5m ready for use with DAGMC enabled codes.
 vertices_to_h5m(
     vertices=vertices,
-    triangles=triangles,
+    triangle_groups=triangle_groups,
     material_tags=["mat1"],
     h5m_filename="one_volume.h5m",
 )
@@ -99,19 +99,18 @@ vertices = np.array(
 )
 
 # These are the two sets triangle that connect individual vertices together to form a continious surfaces and also two closed volume.
-triangles = [
+triangle_groups = [
     np.array([[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]]),
     np.array([[4, 5, 1], [4, 5, 2], [4, 1, 2], [5, 1, 2]]),
 ]
 
 # This will produce a h5m file called two_volume_touching_edge.h5m ready for use with DAGMC enabled codes
 vertices_to_h5m(
     vertices=vertices,
-    triangles=triangles,
+    triangle_groups=triangle_groups,
     material_tags=["mat1", "mat2"],
     h5m_filename="two_volume_touching_edge.h5m",
 )
-
 ```
 ![two_volumes](images/two_volumes.png)
 

examples/example_single_volume_h5py.py

@@ -0,0 +1,70 @@
+import h5py
+import numpy as np
+
+vertices = np.array(
+    [
+        [0.0, 0.0, 0.0],
+        [1.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0],
+        [0.0, 0.0, 1.0],
+    ]
+)
+
+
+triangles = np.array([[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]])
+
+
+f = h5py.File("one_volume.h5m", "w")
+
+tstt = f.create_group("tstt")
+
+elements = tstt.create_group("elements")
+
+global_id = (
+    1  # not sure if this is need, appears to count both triangles and coordinates
+)
+mesh_type = "Tri3"
+mesh_name = 2
+
+elem_dt = h5py.special_dtype(
+    enum=(
+        "i",
+        {
+            "Edge": 1,
+            "Tri": 2,
+            "Quad": 3,
+            "Polygon": 4,
+            "Tet": 5,
+            "Pyramid": 6,
+            "Prism": 7,
+            "Knife": 8,
+            "Hex": 9,
+            "Polyhedron": 10,
+        },
+    )
+)
+
+my_group = elements.create_group(mesh_type)
+my_group.attrs.create("element_type", mesh_name, dtype=elem_dt)
+
+# compression="gzip"
+# compression_opts=4 #meshio defaults
+conn = my_group.create_dataset(
+    "connectivity",
+    data=triangles + 1,  # node indices are 1 based in h5m
+    # compression=compression,
+    # compression_opts=compression_opts,
+)
+
+conn.attrs.create("start_id", global_id)
+global_id += len(triangles)
+
+nodes = tstt.create_group("nodes")
+
+coords = nodes.create_dataset("coordinates", data=vertices)
+coords.attrs.create("start_id", global_id)
+global_id += len(vertices)
+
+sets = tstt.create_group("sets")
+
+tags = tstt.create_group("tags")

examples/example_two_volume_h5py.py

@@ -0,0 +1,223 @@
+import h5py
+import numpy as np
+import trimesh
+
+"""
+Creates a DAGMC compatible h5m file based on the H%M file format layout can be
+found here https://sigma.mcs.anl.gov/moab/h5m-file-format/
+"""
+
+print("started")
+
+vertices = np.array(
+    [
+        [0.42, 0.42, 0.42],
+        [1.42, 0.42, 0.42],
+        [0.42, 1.42, 0.42],
+        [0.42, 0.42, 1.42],
+        [1.42, 0.42, 1.42],
+        [0.42, 1.42, 1.42],
+    ]
+)
+
+triangle_groups = [
+    np.array([[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]]),
+    np.array([[1, 2, 3], [1, 3, 4], [3, 5, 2], [1, 2, 4], [2, 4, 5], [3, 5, 4]]),
+]
+
+# commented out for now as this just reorders the nodes in a specific order so they point outwards
+#
+# def fix_normals(vertices, triangles_in_each_volume):
+#     fixed_triangles = []
+#     for triangles in triangles_in_each_volume:
+#         fixed_triangles.append(fix_normal(vertices, triangles))
+#     return fixed_triangles
+#
+# def fix_normal(vertices, triangles):
+
+#     # for triangles in triangles_in_each_volume:
+#     mesh = trimesh.Trimesh(vertices=vertices, faces=triangles, process=False)
+
+#     mesh.fix_normals()
+
+#     return mesh.faces
+#
+# triangles = fix_normals(
+#     vertices=vertices, triangles_in_each_volume=triangle_groups
+# )
+
+f = h5py.File("h5py_two_volumes.h5m", "w")
+
+all_triangles = np.vstack(triangle_groups)
+
+
+tstt_group = f.create_group("tstt")
+
+group_elements = tstt_group.create_group("elements")
+
+global_id = 1  # appears to count both triangles and coordinates
+
+elem_dt = h5py.special_dtype(
+    enum=(
+        "i",
+        {
+            # "Edge": 1,
+            "Tri": 2,
+            # "Quad": 3,
+            # "Polygon": 4,
+            # "Tet": 5,
+            # "Pyramid": 6,
+            # "Prism": 7,
+            # "Knife": 8,
+            # "Hex": 9,
+            # "Polyhedron": 10,
+        },
+    )
+)
+
+# for triangles in triangle_groups:
+
+mesh_name = 2
+tri3_group = group_elements.create_group("Tri3")
+tri3_group.attrs.create("element_type", mesh_name, dtype=elem_dt)
+
+# compression="gzip"
+# compression_opts=4 #meshio defaults
+connectivity_group = tri3_group.create_dataset(
+    "connectivity",
+    data=all_triangles + 1,  # node indices are 1 based in h5m
+    # compression=compression,
+    # compression_opts=compression_opts,
+)
+
+connectivity_group.attrs.create("start_id", global_id)
+global_id += len(all_triangles)
+
+
+tags_tri3_group = tri3_group.create_group("tags")
+tags_tri3_group.create_dataset(
+    "GLOBAL_ID",
+    data=[-1] * len(vertices),
+    # compression=compression,
+    # compression_opts=compression_opts,
+)
+
+
+nodes_group = tstt_group.create_group("nodes")
+tags_nodes_group = nodes_group.create_group("tags")
+tags_nodes_group.create_dataset(
+    "materials",
+    data=[-1] * len(vertices),
+    # compression=compression,
+    # compression_opts=compression_opts,
+)
+
+coordinates_group = nodes_group.create_dataset("coordinates", data=vertices)
+coordinates_group.attrs.create("start_id", global_id)
+global_id += len(vertices)
+
+sets_group = tstt_group.create_group("sets")
+sets_group.create_dataset(
+    "children",
+    data=[
+        [
+            23,
+            26,
+        ]  # TODO not sure where these numbers come from, automate the production of these numbers
+    ],
+)
+sets_group.create_dataset(
+    "contents",
+    data=[
+        [
+            1,
+            6,
+            13,
+            4,
+            24,
+            7,
+            6,
+            17,
+            6,
+            27,
+            1,
+            28,
+        ]  # TODO not sure where these numbers come from
+    ],
+)
+sets_group.create_dataset(
+    "list",
+    data=[
+        # TODO make an entry like this, not sure what these numbers are based on
+        # {
+        # (0,0): 3, -1, 0, 10,
+        # (1,0): 3, 0, 0, 2,
+        # (2,0): 4, 0, 0, 2,
+        # (3,0): 8, 0, 1, 10,
+        # (4,0): 8, 1, 1, 2,
+        # (5,0): 9, 1, 1, 2,
+        # (6,0): 11, 1, 1, 10
+        # }
+    ],
+)
+sets_group.create_dataset(
+    "parents", data=[[24, 27]]  # TODO not sure where these numbers come from
+)
+sets_group.create_dataset(
+    "GLOBAL_ID",
+    data=[[1, 1, -1, 2, 2, -1, -1]],  # TODO not sure where these numbers come from
+)
+
+
+def hex_encode(string_to_encode: str) -> str:
+    """encodes a string in hex format and adds : between characters"""
+    hex_string = string_to_encode.encode("utf-8").hex()
+    deliminated_string = ":".join(
+        hex_string[i : i + 2] for i in range(0, len(hex_string), 2)
+    )
+    # TODO pad the string up to the correct number of characters with 00: entries
+    return deliminated_string
+
+
+tags_tstt_group = tstt_group.create_group("tags")
+cat = tags_tstt_group.create_group("CATEGORY")
+cat.create_dataset(
+    "values",
+    # appears to repeat twice as we have two volumes
+    # these words appear in hex format with padding in the h5m file
+    # for example 53:75:72:66:61:63:65:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00:00
+    data=[
+        hex_encode("Surface"),
+        "Volume",
+        "Group",
+        "Surface",
+        "Volume",
+        "Group",
+    ],
+)
+
+cat = tags_tstt_group.create_group("id_list")
+# TODO populate group
+cat = tags_tstt_group.create_group("values")
+# TODO populate group
+
+# tried these two methods of making a list in the h5m dataset
+# metho 1
+# arr = np.array(['mat:mat1','mat:mat2'])
+# arr=arr.astype(h5py.opaque_dtype(arr.dtype))
+# method 2
+# binary_blob = b"mat:mat1"
+# dset.attrs["attribute_name"] = np.void(binary_blob)
+# out = dset.attrs["attribute_name"]
+
+name_group = tags_tstt_group.create_group("NAME")
+name_group.create_dataset(
+    "values",
+    # TODO needs padding and nesting as pymoab does it
+    data=[np.void(b"mat:mat1"), np.void(b"mat:mat2")],
+)
+
+
+tstt_group.attrs.create("max_id", global_id)
+
+print("finished")

examples/example_two_volume_pymoab.py

@@ -0,0 +1,30 @@
+import os
+
+import numpy as np
+
+from vertices_to_h5m import vertices_to_h5m
+
+vertices = np.array(
+    [
+        [0.42, 0.42, 0.42],
+        [1.42, 0.42, 0.42],
+        [0.42, 1.42, 0.42],
+        [0.42, 0.42, 1.42],
+        [1.42, 0.42, 1.42],
+        [0.42, 1.42, 1.42],
+    ]
+)
+
+triangle_groups = [
+    np.array([[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]]),
+    np.array([[1, 2, 3], [1, 3, 4], [3, 5, 2], [1, 2, 4], [2, 4, 5], [3, 5, 4]]),
+]
+
+vertices_to_h5m(
+    vertices=vertices,
+    triangle_groups=triangle_groups,
+    material_tags=["mat1", "mat2"],
+    h5m_filename="pymoab_two_volumes.h5m",
+)
+
+os.system("mbconvert pymoab_two_volumes.h5m pymoab_two_volumes.vtk")