Merge pull request #38 from chrishavlin/phaseplot_fixes

Phaseplot fixes

.github/workflows/build-test.yaml

@@ -32,4 +32,4 @@ jobs:
         python -m pip install -e .
     - name: Test with pytest
       run: |
-        pytest
+        pytest -v

analysis_schema/_model_instantiation.py

@@ -130,6 +130,25 @@ def process_pydantic(self, pydantic_instance, ds=None):
         return yt_func(*the_args, **kwarg_dict)
 
 
+class PhasePlot(YTGeneric):
+    def process_pydantic(self, pydantic_instance: data_classes.PhasePlot, ds=None):
+        if ds is None:
+            raise RuntimeError("ds required for a PhasePlot")
+
+        # before running the usual process_pydantic, need to set data_source
+        # if it does not exist, using values from the instantiated dataset
+        if pydantic_instance.data_source is None:
+            # this is equivalent to ds.all_data()
+            reg = data_classes.Region(
+                center=ds.domain_center.d.tolist(),
+                left_edge=ds.domain_left_edge.d.tolist(),
+                right_edge=ds.domain_right_edge.d.tolist(),
+            )
+            pydantic_instance.data_source = reg
+
+        return super().process_pydantic(pydantic_instance, ds=ds)
+
+
 class Visualizations(YTRunner):
     def _sanitize_viz(self, viz_model, yt_viz):
         if viz_model.output_type == "file":
@@ -156,12 +175,12 @@ def _sanitize_viz(self, viz_model, yt_viz):
             return yt_viz._repr_html_()
 
     def process_pydantic(self, pydantic_instance: data_classes.Visualizations, ds=None):
-        generic_runner = YTGeneric()
         viz_results = {}
         for attr in pydantic_instance.__fields__.keys():
             viz_model = getattr(pydantic_instance, attr)  # SlicePlot, etc.
+            viz_runner = yt_registry.get(viz_model)
             if viz_model is not None:
-                result = generic_runner.run(viz_model, ds=ds)
+                result = viz_runner.run(viz_model, ds=ds)
                 nme = f"{ds.basename}_{attr}"
                 viz_results[nme] = self._sanitize_viz(viz_model, result)
         return viz_results
@@ -192,3 +211,4 @@ def _is_yt_schema_instance(obj):
 yt_registry.register(data_classes.Visualizations, Visualizations())
 yt_registry.register(data_classes.Dataset, Dataset())
 yt_registry.register(data_classes.DataSource3D, DataSource3D())
+yt_registry.register(data_classes.PhasePlot, PhasePlot())

analysis_schema/_testing.py

@@ -24,8 +24,8 @@ def force_in_mem_dstore(wkflow, field_list: list = None, units_list: list = None
     # replace the data store datasets with in-memory datasets
     new_store = DataStore()
     if field_list is None:
-        field_list = [("gas", "density"), ("gas", "temperature")]
-        units_list = ["g/cm**3", "K"]
+        field_list = [("gas", "density"), ("gas", "temperature"), ("gas", "mass")]
+        units_list = ["g/cm**3", "K", "kg"]
     for dsname, dscon in wkflow.data_store.available_datasets.items():
         ds_ = fake_amr_ds(fields=field_list, units=units_list)
         new_store.store(dscon.filename, dataset_name=dsname, in_memory_ds=ds_)

analysis_schema/data_classes.py

@@ -140,10 +140,11 @@ def axis(self):
 class PhasePlot(ytVisualization):
     """A yt phase plot"""
 
-    data_source: Optional[Dataset] = Field(alias="Dataset")
+    ds: Optional[List[Dataset]] = Field(alias="Dataset")
+    data_source: Optional[DataSource3D] = Field(alias="DataSource")
     x_field: ytField = Field(alias="xField")
     y_field: ytField = Field(alias="yField")
-    z_fields: Union[ytField, List[ytField]] = Field(alias="zField(s)")
+    z_fields: Union[ytField, List[ytField]] = Field(alias="zFields")
     weight_field: Optional[ytField] = Field(alias="WegihtFieldName")
     x_bins: Optional[int] = Field(alias="xBins")
     y_bins: Optional[int] = Field(alias="yBins")

analysis_schema/yt_analysis_schema.json

@@ -388,16 +388,23 @@
           "type": "string"
         },
         "Dataset": {
-          "$ref": "#/definitions/Dataset"
+          "title": "Dataset",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Dataset"
+          }
+        },
+        "DataSource": {
+          "$ref": "#/definitions/DataSource3D"
         },
         "xField": {
           "$ref": "#/definitions/ytField"
         },
         "yField": {
           "$ref": "#/definitions/ytField"
         },
-        "zField(s)": {
-          "title": "Zfield(S)",
+        "zFields": {
+          "title": "Zfields",
           "anyOf": [
             {
               "$ref": "#/definitions/ytField"
@@ -460,7 +467,7 @@
         "output_type",
         "xField",
         "yField",
-        "zField(s)"
+        "zFields"
       ]
     },
     "Visualizations": {

tests/viz_phaseplot_1.json

@@ -0,0 +1,23 @@
+{
+    "$schema": "../analysis_schema/yt_analysis_schema.json",
+    "Plot": [
+      {
+        "PhasePlot": {
+            "Dataset": [
+              {
+                "FileName": "IsolatedGalaxy/galaxy0030/galaxy0030",
+                "DatasetName": "IG"
+              }
+            ],
+            "xField": {
+                "field": "density", "field_type": "gas"
+            },
+            "yField": {
+                "field_type": "gas", "field": "temperature"
+            },
+            "zFields": {"field": "mass", "field_type": "gas"},
+            "output_type": "file"
+          }
+      }
+    ]
+}

tests/viz_phaseplot_2.json

@@ -0,0 +1,29 @@
+{
+    "$schema": "../analysis_schema/yt_analysis_schema.json",
+    "Plot": [
+      {
+        "PhasePlot": {
+            "Dataset": [
+              {
+                "FileName": "IsolatedGalaxy/galaxy0030/galaxy0030",
+                "DatasetName": "IG"
+              }
+            ],
+            "DataSource": {
+                "sphere": {
+                    "Radius": 0.25,
+                    "Center": [0.25, 0.25, 0.25]
+                }
+            },
+            "xField": {
+                "field": "density", "field_type": "gas"
+            },
+            "yField": {
+                "field_type": "gas", "field": "temperature"
+            },
+            "zFields": {"field": "mass", "field_type": "gas"},
+            "output_type": "file"
+          }
+      }
+    ]
+}