Merge pull request #284 from MC-kit/devel

save gbins table

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "xpypact"
-version = "0.5.1"
+version = "0.5.2"
 description = "\"Python workflow framework for FISPACT.\""
 authors = ["dvp <[email protected]>"]
 license = "MIT"
@@ -605,7 +605,7 @@ min_alias_length = 3
 # which will auto-detect the setting from the rest of the file. This
 # is less desirable in a new project and you may find this (slightly
 # more strict) setting more useful.
-# Typically we find users rely on syntax highlighting rather than
+# Typically, we find users rely on syntax highlighting rather than
 # capitalisation to distinguish between keywords and identifiers.
 # Clearly, if your organisation has already settled on uppercase
 # formatting for any of these syntax elements then set them to "upper".

src/xpypact/dao/duckdb/create_schema.sql

@@ -15,24 +15,24 @@ create table if not exists timestep (
     material_id uinteger not null,
     case_id uinteger not null,
     time_step_number uinteger not null,
-    elapsed_time float4 not null,
-    irradiation_time float4 not null,
-    cooling_time float4 not null,
-    duration float4 not null,
-    flux float4 not null,
-    total_atoms float4 not null,
-    total_activity float4 not null,
-    alpha_activity float4 not null,
-    beta_activity float4 not null,
-    gamma_activity float4 not null,
-    total_mass float4 not null,
-    total_heat float4 not null,
-    alpha_heat float4 null,
-    beta_heat float4 not null,
-    gamma_heat float4 not null,
-    ingest1ion_dose float4 not null,
-    inhalation_dose float4 not null,
-    dose_rate float4 not null,
+    elapsed_time real not null,
+    irradiation_time real not null,
+    cooling_time real not null,
+    duration real not null,
+    flux real not null,
+    total_atoms real not null,
+    total_activity real not null,
+    alpha_activity real not null,
+    beta_activity real not null,
+    gamma_activity real not null,
+    total_mass real not null,
+    total_heat real not null,
+    alpha_heat real null,
+    beta_heat real not null,
+    gamma_heat real not null,
+    ingest1ion real not null,
+    inhalation real not null,
+    dose real not null,
     primary key (material_id, case_id, time_step_number),
     foreign key (material_id, case_id) references rundata (material_id, case_id)
 );
@@ -43,7 +43,7 @@ create table if not exists nuclide (
     mass_number usmallint not null check (0 < mass_number),
     state varchar(1) not null,
     zai uinteger not null check (10010 <= zai) unique,
-    half_life float4 not null check (0 <= half_life),
+    half_life real not null check (0 <= half_life),
     primary key (element, mass_number, state)
 );
 
@@ -52,34 +52,40 @@ create table if not exists timestep_nuclide (
     case_id uinteger not null,
     time_step_number uinteger not null,
     zai uinteger not null,
-    atoms float4 not null,
-    grams float4 not null,
+    atoms real not null,
+    grams real not null,
 
-    activity float4 not null,
-    alpha_activity float4 not null,
-    beta_activity float4 not null,
-    gamma_activity float4 not null,
+    activity real not null,
+    alpha_activity real not null,
+    beta_activity real not null,
+    gamma_activity real not null,
 
-    heat float4 not null,
-    alpha_heat float4 not null,
-    beta_heat float4 not null,
-    gamma_heat float4 not null,
+    heat real not null,
+    alpha_heat real not null,
+    beta_heat real not null,
+    gamma_heat real not null,
 
-    dose float4 not null,
-    ingestion float4 not null,
-    inhalation float4 not null,
+    dose real not null,
+    ingestion real not null,
+    inhalation real not null,
 
     primary key (material_id, case_id, time_step_number, zai),
     foreign key (material_id, case_id, time_step_number) references timestep (material_id, case_id, time_step_number),
     foreign key (zai) references nuclide (zai)
 );
 
+create table if not exists gbins (
+    g utinyint primary key,
+    boundary real not null check (0.0 <= boundary) unique
+);
+
 create table if not exists timestep_gamma (
     material_id uinteger not null,
     case_id uinteger not null,
     time_step_number uinteger not null,
-    boundary real not null check (0 <= boundary),
+    g utinyint not null, -- only upper bin boundaries in this table
     rate real not null,
-    primary key (material_id, case_id, time_step_number, boundary),
-    foreign key (material_id, case_id, time_step_number) references timestep (material_id, case_id, time_step_number)
+    primary key (material_id, case_id, time_step_number, g),
+    foreign key (material_id, case_id, time_step_number) references timestep (material_id, case_id, time_step_number),
+    foreign key (g) references gbins (g)
 );

src/xpypact/dao/duckdb/implementation.py

@@ -89,6 +89,7 @@ def save(self, inventory: Inventory, material_id=1, case_id=1) -> None:
         _save_nuclides(cursor, inventory)
         _save_time_steps(cursor, inventory, material_id, case_id)
         _save_time_step_nuclides(cursor, inventory, material_id, case_id)
+        _save_gbins(cursor, inventory)
         _save_gamma(cursor, inventory, material_id, case_id)
 
     def load_rundata(self) -> db.DuckDBPyRelation:
@@ -123,6 +124,14 @@ def load_time_step_nuclides(self) -> db.DuckDBPyRelation:
         """
         return self.con.table("timestep_nuclide")
 
+    def load_gbins(self) -> db.DuckDBPyRelation:
+        """Load gbins table.
+
+        Returns:
+            gbins table
+        """
+        return self.con.table("gbins")
+
     def load_gamma(self, time_step_number: int | None = None) -> db.DuckDBPyRelation:
         """Load time step x gamma table.
 
@@ -259,23 +268,27 @@ def _save_time_step_nuclides(
 
 
 # noinspection SqlNoDataSourceInspection
-def _save_gamma(cursor: db.DuckDBPyConnection, inventory: Inventory, material_id=1, case_id=1):
-    """Material_id uinteger not null,.
-
-    case_id uinteger not null,
-    time_step_number uinteger not null,
-    boundary real not null check (0 <= boundary),
-    rate real not null,
+def _save_gbins(cursor: db.DuckDBPyConnection, inventory: Inventory) -> None:
+    gs = inventory[0].gamma_spectrum
+    if gs is None:
+        return
+    sql = """
+        insert into gbins values(?, ?);
     """
+    cursor.executemany(sql, enumerate(gs.boundaries))
+
+
+# noinspection SqlNoDataSourceInspection
+def _save_gamma(cursor: db.DuckDBPyConnection, inventory: Inventory, material_id=1, case_id=1):
     sql = """
         insert into timestep_gamma values(?, ?, ?, ?, ?);
     """
     cursor.executemany(
         sql,
         (
-            (material_id, case_id, t.number, x[0], x[1])
+            (material_id, case_id, t.number, x[0] + 1, x[1][1])  # timestep number  # g  # rate
             for t in inventory.inventory_data
             if t.gamma_spectrum
-            for x in zip(t.gamma_spectrum.boundaries[1:], t.gamma_spectrum.values)
+            for x in enumerate(zip(t.gamma_spectrum.boundaries[1:], t.gamma_spectrum.values))
         ),
     )

tests/test_duckdb_dao.py

@@ -61,7 +61,7 @@ def test_save(inventory_with_gamma) -> None:
         assert not time_step_nuclides.loc[2, 290630].empty
         gamma = dao.load_gamma().df()
         assert not gamma.empty
-        gamma = gamma.set_index(["time_step_number", "boundary"])
-        assert not gamma.loc[2, 1.0].empty
+        gamma = gamma.set_index(["time_step_number", "g"])
+        assert not gamma.loc[2, 1].empty
         gamma2 = dao.load_gamma(2).df()
         assert not gamma2.empty