🎉 New feature: Integration point support (basic) (#400)

coverage for later, sorry to much work ;)

Author: fbordeu

src/plaid/constants.py

@@ -66,6 +66,7 @@
     "JFaceCenter",
     "KFaceCenter",
     "EdgeCenter",
+    "IntegrationPoint"
 ]
 
 CGNS_ELEMENT_NAMES = [

src/plaid/containers/features.py

@@ -1048,20 +1048,29 @@ def get_field_names_one_time_base_zone_location(
                 return []
 
             names = []
-            solution_paths = CGU.getPathsByTypeSet(search_node, [CGK.FlowSolution_t])
+            # try to find IntegrationPoint on UserDefinedData_t
+            solution_paths = CGU.getPathsByTypeSet(search_node, [CGK.FlowSolution_t, "UserDefinedData_t"])
             for f_path in solution_paths:
-                if (
-                    CGU.getValueByPath(search_node, f_path + "/GridLocation")
-                    .tobytes()
-                    .decode()
-                    != location
-                ):
-                    continue
+
+                grid_loc_node = CGU.getValueByPath(search_node, f_path + "/GridLocation")
+                if grid_loc_node is not None:
+                    if (grid_loc_node.tobytes().decode()!= location ):
+                        continue
+                else:
+                    ##possible an integration point data check Muscat Implementation for details
+                    grid_loc_node = CGU.getValueByPath(search_node, f_path + "/gridlocation")
+                    if grid_loc_node is not None:
+                        if (grid_loc_node.tobytes().decode()!= location ):
+                            continue
+                    else:
+                        continue
+
                 f_node = CGU.getNodeByPath(search_node, f_path)
                 for path in CGU.getPathByTypeFilter(f_node, CGK.DataArray_t):
                     field_name = path.split("/")[-1]
-                    if not (field_name == "GridLocation"):
+                    if field_name not in ["GridLocation","ItgRules","gridlocation","ItgPointStartOffset", "Ids","Path"]:
                         names.append(field_name)
+
             return names
 
         field_names = []
@@ -1117,12 +1126,22 @@ def get_field(
             return None
 
         full_field = []
-        solution_paths = CGU.getPathsByTypeSet(search_node, [CGK.FlowSolution_t])
+        solution_paths = CGU.getPathsByTypeSet(search_node, [CGK.FlowSolution_t, "UserDefinedData_t"])
 
         for f_path in solution_paths:
             grid_loc = CGU.getValueByPath(search_node, f_path + "/GridLocation")
-            if grid_loc.tobytes().decode() != location:
-                continue
+            if grid_loc is not None:
+                if grid_loc.tobytes().decode() != location:
+                    continue
+            else:
+                ##possible an integration point data
+                grid_loc = CGU.getValueByPath(search_node , f_path+"/gridlocation")
+                if grid_loc is not None:
+                    if (grid_loc.tobytes().decode()!= location ):
+                        continue
+                else:
+                    raise
+
 
             field = CGU.getValueByPath(search_node, f_path + "/" + name)
             if field is not None and field.size > 0:

src/plaid/storage/common/preprocessor.py

@@ -42,6 +42,8 @@ def infer_dtype(value: Any) -> dict[str, int | str]:
             dt = "int64"
         elif np.issubdtype(dtype, np.str_):
             dt = "string"
+        elif np.issubdtype(dtype, np.dtype('S1')):
+            dt = "S1"
         else:  # pragma: no cover
             raise ValueError(f"Unrecognized scalar dtype: {dtype}")
         return {"dtype": dt, "ndim": arr.ndim}
@@ -183,7 +185,8 @@ def _hash_value(value: Any) -> str:
         str: The MD5 hash of the value.
     """
     if isinstance(value, np.ndarray):
-        return hashlib.md5(value.view(np.uint8)).hexdigest()
+        contiguous_value = np.ascontiguousarray(value)
+        return hashlib.md5(contiguous_value.tobytes(order="C")).hexdigest()
     return hashlib.md5(str(value).encode("utf-8")).hexdigest()
 
 
@@ -535,10 +538,10 @@ def preprocess(
 
     # --- build features ---
     var_features = sorted(list(set().union(*split_var_path.values())))
-    if len(var_features) == 0:  # pragma: no cover
-        raise ValueError(
-            "no variable feature found, is your dataset variable through samples?"
-        )
+    #if len(var_features) == 0:  # pragma: no cover
+    #    raise ValueError(
+    #        "no variable feature found, is your dataset variable through samples?"
+    #    )
 
     for split_name in split_flat_cst.keys():
         for path in var_features:

src/plaid/utils/cgns_helper.py

@@ -433,6 +433,8 @@ def visit(tree, path=""):
             name, data, children, cgns_type = node
             new_path = f"{path}/{name}" if path else name
 
+            if  new_path in flat:
+                raise RuntimeError(f"Error: Non unique path for every entity. The path '{new_path}' points to multiple data. Try changing the name of your fields")
             flat[new_path] = data
             cgns_types[new_path] = cgns_type
 

tests/containers/test_sample.py

@@ -3,6 +3,7 @@
 import copy
 from pathlib import Path
 
+import CGNS.PAT.cgnslib as CGL
 import CGNS.PAT.cgnskeywords as CGK
 import CGNS.PAT.cgnsutils as CGU
 import numpy as np
@@ -573,9 +574,7 @@ def test_del_zone_no_cgns_tree(self, sample: Sample):
 
     def test_has_zone(self, sample, base_name, zone_name):
         sample.init_base(3, 3, base_name)
-        sample.init_zone(
-            np.array([[5, 3, 0]]), zone=zone_name, base=base_name
-        )
+        sample.init_zone(np.array([[5, 3, 0]]), zone=zone_name, base=base_name)
         sample.show_tree()
         assert sample.features.has_zone(zone_name, base_name)
         assert not sample.features.has_zone("not_present_zone_name", base_name)
@@ -617,18 +616,14 @@ def test_get_zone_type(self, sample: Sample, zone_name, base_name):
         sample.init_base(3, 3, base_name)
         with pytest.raises(KeyError):
             sample.features.get_zone_type(zone_name, base_name)
-        sample.init_zone(
-            np.array([[5, 3, 0]]), zone=zone_name, base=base_name
-        )
+        sample.init_zone(np.array([[5, 3, 0]]), zone=zone_name, base=base_name)
         assert sample.features.get_zone_type(zone_name, base_name) == CGK.Unstructured_s
 
     def test_get_zone(self, sample: Sample, zone_name, base_name):
         assert sample.features.get_zone(zone_name, base_name) is None
         sample.init_base(3, 3, base_name)
         assert sample.features.get_zone(zone_name, base_name) is None
-        sample.init_zone(
-            np.array([[5, 3, 0]]), zone=zone_name, base=base_name
-        )
+        sample.init_zone(np.array([[5, 3, 0]]), zone=zone_name, base=base_name)
         assert sample.features.get_zone() is not None
         assert sample.features.get_zone(zone_name, base_name) is not None
         sample.init_zone(
@@ -651,6 +646,21 @@ def test_get_global_names_at_specific_time(self, sample: Sample):
         assert sample.get_global_names(time=0.0) == ["g_t0"]
         assert sample.get_global_names(time=1.0) == ["g_t1"]
 
+    def test_add_global_string_and_update_existing(self, sample: Sample):
+        sample.add_global("g_str", "abc")
+        value = sample.get_global("g_str")
+        assert isinstance(value, np.ndarray)
+        assert value.tobytes().decode("ascii") == "abc"
+
+        sample.add_global("g_str", np.array([7.0]))
+        assert sample.get_global("g_str") == 7.0
+
+    def test_get_global_names_excludes_time_arrays(self, sample: Sample):
+        sample.init_base(2, 2, "Base_2_2", time=0.0)
+        sample.add_global("kept_name", np.array([1.0]), time=0.0)
+        names = sample.get_global_names(time=0.0)
+        assert names == ["kept_name"]
+
     def test_get_scalar_empty(self, sample):
         assert sample.get_global("missing_scalar_name") is None
 
@@ -709,7 +719,9 @@ def test_add_feature(self, sample_with_tree3d):
     def test_del_feature(self, sample_with_scalar: Sample, sample_with_tree3d: Sample):
         sample_with_scalar.del_feature_by_path(path="Global/test_scalar_1")
         assert sample_with_scalar.get_all_features_identifiers_by_type("scalar") == []
-        sample_with_tree3d.del_feature_by_path("Base_2_3/Zone/VertexFields/test_node_field_1")
+        sample_with_tree3d.del_feature_by_path(
+            "Base_2_3/Zone/VertexFields/test_node_field_1"
+        )
 
     # -------------------------------------------------------------------------#
     def test_get_nodal_tags_empty(self, sample):
@@ -737,15 +749,38 @@ def test_get_nodes_unknown_coordinate_name(self, sample_with_tree):
         with pytest.raises(ValueError):
             sample_with_tree.get_nodes(name="UnknownCoordinate")
 
+    # def test_get_nodes_returns_none_without_gridcoordinates(
+    #     self, sample: Sample, base_name: str, zone_name: str
+    # ):
+    #     sample.init_base(2, 2, base_name)
+    #     sample.init_zone(np.array([3, 0, 0]), zone=zone_name, base=base_name)
+    #     zone_node = sample.features.get_zone(zone=zone_name, base=base_name)
+    #     gc_node = CGU.getNodeByPath(zone_node, "GridCoordinates")
+    #     assert gc_node is not None
+    #     CGU.nodeDelete(zone_node, gc_node)
+    #    assert sample.get_nodes(zone=zone_name, base=base_name) is None
+
     def test_set_nodes(self, sample, nodes, zone_name, base_name):
         sample.init_base(3, 3, base_name)
         with pytest.raises(KeyError):
             sample.set_nodes(nodes, zone_name, base_name)
-        sample.init_zone(
-            np.array([len(nodes), 0, 0]), zone=zone_name, base=base_name
-        )
+        sample.init_zone(np.array([len(nodes), 0, 0]), zone=zone_name, base=base_name)
         sample.set_nodes(nodes, zone_name, base_name)
 
+    def test_set_nodes_replaces_existing_coordinates(
+        self, sample: Sample, base_name: str, zone_name: str
+    ):
+        sample.init_base(3, 3, base_name)
+        sample.init_zone(np.array([3, 0, 0]), zone=zone_name, base=base_name)
+
+        nodes_a = np.array([[0.0, 0.0], [1.0, 0.0], [1.0, 1.0]])
+        nodes_b = np.array([[2.0, 2.0], [3.0, 2.0], [3.0, 3.0]])
+        sample.set_nodes(nodes_a, zone=zone_name, base=base_name)
+        sample.set_nodes(nodes_b, zone=zone_name, base=base_name)
+
+        got = sample.get_nodes(zone=zone_name, base=base_name)
+        assert np.allclose(got, nodes_b)
+
     # -------------------------------------------------------------------------#
     def test_get_elements_empty(self, sample: Sample):
         assert sample.features.get_elements() == {}
@@ -768,18 +803,10 @@ def test_get_field_names_several_bases(self):
         sample = Sample()
         sample.init_tree(time=-0.1)
         sample.init_tree(time=1.0)
-        sample.init_base(
-            topological_dim=1, physical_dim=2, base="Base_1_2", time=-0.1
-        )
-        sample.init_base(
-            topological_dim=2, physical_dim=2, base="Base_2_2", time=-0.1
-        )
-        sample.init_base(
-            topological_dim=1, physical_dim=3, base="Base_1_3", time=1.0
-        )
-        sample.init_base(
-            topological_dim=3, physical_dim=3, base="Base_3_3", time=1.0
-        )
+        sample.init_base(topological_dim=1, physical_dim=2, base="Base_1_2", time=-0.1)
+        sample.init_base(topological_dim=2, physical_dim=2, base="Base_2_2", time=-0.1)
+        sample.init_base(topological_dim=1, physical_dim=3, base="Base_1_3", time=1.0)
+        sample.init_base(topological_dim=3, physical_dim=3, base="Base_3_3", time=1.0)
         sample.init_zone(
             zone_shape=np.array([[5, 3, 0]]),
             zone="Zone_1",
@@ -998,6 +1025,28 @@ def test_get_field(self, sample_with_tree):
             "test_elem_field_1", location="CellCenter"
         ).shape == (3,)
 
+    def test_get_field_from_user_defined_data_lowercase_gridlocation(
+        self, sample: Sample, base_name: str, zone_name: str
+    ):
+        sample.init_base(2, 2, base_name)
+        sample.init_zone(np.array([3, 0, 0]), zone=zone_name, base=base_name)
+
+        zone_node = sample.features.get_zone(zone=zone_name, base=base_name)
+        udd = CGL.newUserDefinedData(zone_node, "ItgPointData")
+        CGL.newDataArray(
+            udd,
+            "gridlocation",
+            value=np.frombuffer("Vertex".encode("ascii"), dtype="S1"),
+        )
+        CGL.newDataArray(udd, "my_udd_field", value=np.array([1.0, 2.0, 3.0]))
+
+        assert (
+            sample.get_field("my_udd_field", zone=zone_name, base=base_name) is not None
+        )
+        assert "my_udd_field" in sample.get_field_names(
+            zone=zone_name, base=base_name, location="Vertex"
+        )
+
     def test_add_field_vertex(self, sample: Sample, vertex_field, zone_name, base_name):
         sample.init_base(3, 3, base_name)
         with pytest.raises(KeyError):
@@ -1014,9 +1063,7 @@ def test_add_field_vertex(self, sample: Sample, vertex_field, zone_name, base_na
                 zone=zone_name,
                 base=base_name,
             )
-        sample.init_zone(
-            np.array([[5, 3, 0]]), zone=zone_name, base=base_name
-        )
+        sample.init_zone(np.array([[5, 3, 0]]), zone=zone_name, base=base_name)
         sample.add_field(
             name="test_node_field_2",
             field=vertex_field,
@@ -1043,9 +1090,7 @@ def test_add_field_cell_center(
                 zone=zone_name,
                 base=base_name,
             )
-        sample.init_zone(
-            np.array([[5, 3, 0]]), zone=zone_name, base=base_name
-        )
+        sample.init_zone(np.array([[5, 3, 0]]), zone=zone_name, base=base_name)
         sample.add_field(
             name="test_elem_field_2",
             location="CellCenter",
@@ -1117,9 +1162,7 @@ def test_del_field_nonexistent(self, base_name):
     def test_del_field_in_zone(self, zone_name, base_name, cell_center_field):
         sample = Sample()
         sample.init_base(3, 3, base_name)
-        sample.init_zone(
-            np.array([[5, 3, 0]]), zone=zone_name, base=base_name
-        )
+        sample.init_zone(np.array([[5, 3, 0]]), zone=zone_name, base=base_name)
         sample.add_field(
             name="test_elem_field_1",
             field=cell_center_field,