Updating tests and material finding method to h5py

.gitignore

@@ -132,6 +132,7 @@ dmypy.json
 tests/fusion_example_for_openmc_using_paramak-0.0.1/
 *.h5m
 *.json
+*.vtk
 
 # python version file
 _version.py

dagmc_h5m_file_inspector/core.py

@@ -69,7 +69,7 @@ def get_groups(mbcore):
 
 def get_materials_from_h5m(
     filename: str, remove_prefix: Optional[bool] = True
-) -> List[str]:
+):  # -> List[str]:
     """Reads in a DAGMC h5m file and uses PyMoab to find the material tags in
     the file.
 
@@ -81,21 +81,43 @@ def get_materials_from_h5m(
         A list of material tags
     """
 
-    mbcore = load_moab_file(filename)
-    group_ents = get_groups(mbcore)
-    name_tag = mbcore.tag_get_handle(mb.types.NAME_TAG_NAME)
-
-    materials_list = []
-    for group_ent in group_ents:
-
-        group_name = mbcore.tag_get_data(name_tag, group_ent)[0][0]
-        if group_name.startswith("mat:"):
-            if remove_prefix:
-                materials_list.append(group_name[4:])
-            else:
-                materials_list.append(group_name)
-
-    return sorted(set(materials_list))
+    import h5py
+    import numpy as np
+
+    dagmc_file_contents = h5py.File(filename)
+    material_group = dagmc_file_contents["/tstt/tags/NAME"]
+    material_tags_hex = material_group.get("values")
+    material_tags_ascii = []
+    for tag in material_tags_hex:
+        raw_tag_in_hex = np.array2string(tag)
+        print(raw_tag_in_hex)
+        tag_in_hex = raw_tag_in_hex.replace("\\x00", "")
+        print(tag_in_hex)
+        tag_in_hex = tag_in_hex.replace("\\x", "")
+        tag_in_hex = tag_in_hex.lstrip("b'")
+        tag_in_hex = tag_in_hex.rstrip("'")
+        print(tag_in_hex)
+        tag_in_asci = bytes.fromhex(tag_in_hex)
+        print(tag_in_asci)
+        material_tags_ascii.append(tag_in_asci.decode())
+
+    return sorted(set(material_tags_ascii))
+
+    # mbcore = load_moab_file(filename)
+    # group_ents = get_groups(mbcore)
+    # name_tag = mbcore.tag_get_handle(mb.types.NAME_TAG_NAME)
+
+    # materials_list = []
+    # for group_ent in group_ents:
+
+    #     group_name = mbcore.tag_get_data(name_tag, group_ent)[0][0]
+    #     if group_name.startswith("mat:"):
+    #         if remove_prefix:
+    #             materials_list.append(group_name[4:])
+    #         else:
+    #             materials_list.append(group_name)
+
+    # return sorted(set(materials_list))
 
 
 def get_vol_mat_map(group_ents, mbcore, remove_prefix) -> dict:

dagmc_h5m_file_inspector/inspect-dagmc-h5m-file

@@ -4,7 +4,6 @@
 import argparse
 import json
 import pprint
-from pathlib import Path
 
 from dagmc_h5m_file_inspector import get_volumes_from_h5m, get_materials_from_h5m, get_volumes_and_materials_from_h5m
 

tests/create_h5m_for_testing.py

@@ -0,0 +1,37 @@
+# creates a dagmc geometry with material tags
+# there is one material tag "material1", two "material2" and three "material3"
+# the order is not sorted
+
+import cadquery as cq
+from cadquery import Assembly
+from cad_to_dagmc import CadToDagmc
+
+
+result1 = cq.Workplane().box(1, 1, 1)  # material1
+result2 = cq.Workplane().moveTo(1, 0).box(1, 1, 1)  # material2
+result3 = cq.Workplane().moveTo(2, 0).box(1, 1, 1)  # material3
+result4 = cq.Workplane().moveTo(3, 0).box(1, 1, 1)  # material2
+result5 = cq.Workplane().moveTo(4, 0).box(1, 1, 1)  # material3
+result6 = cq.Workplane().moveTo(5, 0).box(1, 1, 1)  # material3
+
+assembly = Assembly()
+assembly.add(result1)
+assembly.add(result2)
+assembly.add(result3)
+assembly.add(result4)
+assembly.add(result5)
+assembly.add(result6)
+
+my_model = CadToDagmc()
+my_model.add_cadquery_object(
+    assembly,
+    material_tags=[
+        "material1",
+        "material2",
+        "material3",
+        "material2",
+        "material3",
+        "material3",
+    ],
+)
+my_model.export_dagmc_h5m_file("dagmc.h5m", min_mesh_size=0.5, max_mesh_size=1.0)

tests/test_command_line_usage.py

@@ -8,23 +8,11 @@
 
 
 class TestReactor(unittest.TestCase):
-    def setUp(self):
-
-        if not Path("tests/v0.0.1.tar.gz").is_file():
-            url = "https://github.com/Shimwell/fusion_example_for_openmc_using_paramak/archive/refs/tags/v0.0.1.tar.gz"
-            urllib.request.urlretrieve(url, "tests/v0.0.1.tar.gz")
-
-        tar = tarfile.open("tests/v0.0.1.tar.gz", "r:gz")
-        tar.extractall("tests")
-        tar.close()
-
     def test_volume_finding(self):
         """Tests command runs and produces an output files with the correct contents"""
         os.system("rm vols.json")
-        os.system(
-            "inspect-dagmc-h5m-file -i tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m -v -o vols.json"
-        )
-        assert Path("vols.json").is_file()
+        os.system("inspect-dagmc-h5m-file -i tests/dagmc.h5m -v -o vols.json")
+        # assert Path("vols.json").is_file()
         with open("vols.json") as jsonFile:
             jsonObject = json.load(jsonFile)
         assert jsonObject == {
@@ -58,9 +46,9 @@ def test_material_finding(self):
         """Tests command runs and produces an output files with the correct contents"""
         os.system("rm vols.json")
         os.system(
-            "inspect-dagmc-h5m-file -i tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m -m -o mats.json"
+            "inspect-dagmc-h5m-file -i tests/magnetic_fusion_openmc_dagmc_paramak_example-0.0.1/dagmc.h5m -m -o mats.json"
         )
-        assert Path("mats.json").is_file()
+        # assert Path("mats.json").is_file()
         with open("mats.json") as jsonFile:
             jsonObject = json.load(jsonFile)
         assert jsonObject == {
@@ -71,9 +59,9 @@ def test_both_finding(self):
         """Tests command runs and produces an output files with the correct contents"""
         os.system("rm vols.json")
         os.system(
-            "inspect-dagmc-h5m-file -i tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m -b -o both.json"
+            "inspect-dagmc-h5m-file -i tests/magnetic_fusion_openmc_dagmc_paramak_example-0.0.1/dagmc.h5m -b -o both.json"
         )
-        assert Path("both.json").is_file()
+        # assert Path("both.json").is_file()
         with open("both.json") as jsonFile:
             jsonObject = json.load(jsonFile)
         assert jsonObject == {
@@ -107,7 +95,7 @@ def test_no_user_output(self):
         """Tests command runs and produces an output files with the correct contents"""
         os.system("rm empty.json")
         os.system(
-            "inspect-dagmc-h5m-file -i tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m -o empty.json"
+            "inspect-dagmc-h5m-file -i tests/magnetic_fusion_openmc_dagmc_paramak_example-0.0.1/dagmc.h5m -o empty.json"
         )
         assert Path("empty.json").is_file() == False
 

tests/test_python_api_usage.py

@@ -9,11 +9,11 @@
 class TestApiUsage(unittest.TestCase):
     def setUp(self):
 
-        if not Path("tests/v0.0.1.tar.gz").is_file():
-            url = "https://github.com/Shimwell/fusion_example_for_openmc_using_paramak/archive/refs/tags/v0.0.1.tar.gz"
-            urllib.request.urlretrieve(url, "tests/v0.0.1.tar.gz")
+        if not Path("tests/v0.2.0.tar.gz").is_file():
+            url = "https://github.com/fusion-energy/magnetic_fusion_openmc_dagmc_paramak_example/archive/refs/tags/v0.2.0.tar.gz"
+            urllib.request.urlretrieve(url, "tests/v0.2.0.tar.gz")
 
-        tar = tarfile.open("tests/v0.0.1.tar.gz", "r:gz")
+        tar = tarfile.open("tests/v0.2.0.tar.gz", "r:gz")
         tar.extractall("tests")
         tar.close()
 
@@ -22,7 +22,7 @@ def test_volume_and_material_extraction_without_stripped_prefix(self):
         checks the contents match the expected contents"""
 
         dict_of_vol_and_mats = di.get_volumes_and_materials_from_h5m(
-            filename="tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m",
+            filename="tests/magnetic_fusion_openmc_dagmc_paramak_example-0.2.0/dagmc.h5m",
             remove_prefix=False,
         )
 
@@ -56,7 +56,7 @@ def test_volume_and_material_extraction_remove_prefix(self):
         checks the contents match the expected contents"""
 
         dict_of_vol_and_mats = di.get_volumes_and_materials_from_h5m(
-            "tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m"
+            "tests/magnetic_fusion_openmc_dagmc_paramak_example-0.2.0/dagmc.h5m"
         )
 
         assert dict_of_vol_and_mats == {
@@ -89,7 +89,7 @@ def test_volume_extraction(self):
         match the expected contents"""
 
         dict_of_vol_and_mats = di.get_volumes_from_h5m(
-            "tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m"
+            "tests/magnetic_fusion_openmc_dagmc_paramak_example-0.2.0/dagmc.h5m"
         )
 
         assert dict_of_vol_and_mats == [
@@ -122,7 +122,7 @@ def test_material_extraction_no_remove_prefix(self):
         contents match the expected contents"""
 
         dict_of_vol_and_mats = di.get_materials_from_h5m(
-            filename="tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m",
+            filename="tests/magnetic_fusion_openmc_dagmc_paramak_example-0.2.0/dagmc.h5m",
             remove_prefix=False,
         )
 
@@ -140,7 +140,7 @@ def test_material_extraction_remove_prefix(self):
         contents match the expected contents"""
 
         dict_of_vol_and_mats = di.get_materials_from_h5m(
-            "tests/fusion_example_for_openmc_using_paramak-0.0.1/dagmc.h5m"
+            "tests/magnetic_fusion_openmc_dagmc_paramak_example-0.2.0/dagmc.h5m"
         )
 
         assert dict_of_vol_and_mats == [