Ecdc 3331 nxoff geometry

nexus_constructor/common_attrs.py

@@ -51,7 +51,7 @@ class TransformationType:
 NX_SAMPLE = "NXsample"
 NX_USER = "NXuser"
 NX_TRANSFORMATIONS = "NXtransformations"
-GEOMETRY_NX_CLASS = "NXgeometry"
+# GEOMETRY_NX_CLASS = "NXgeometry" # depreceated
 NX_BOX = "nxbox"
 SIZE = "size"
 TRANSFORMATIONS = "transformations"

nexus_constructor/component_type.py

@@ -64,7 +64,7 @@
     "NXfilter",
     "NXflipper",
     "NXfresnel_zone_plate",
-    "NXgeometry",
+    # "NXgeometry", # depreceated
     "NXgrating",
     "NXguide",
     "NXinsertion_device",

nexus_constructor/json/shape_reader.py

@@ -1,12 +1,10 @@
-from typing import Any, Dict, List, Union
+from typing import Any, Dict, List, Optional
 
 import numpy as np
 from PySide6.QtGui import QVector3D
 
 from nexus_constructor.common_attrs import (
     CYLINDRICAL_GEOMETRY_NX_CLASS,
-    GEOMETRY_NX_CLASS,
-    NX_BOX,
     OFF_GEOMETRY_NX_CLASS,
     PIXEL_SHAPE_GROUP_NAME,
     SHAPE_GROUP_NAME,
@@ -84,13 +82,6 @@ def add_shape_to_component(self):
             self._add_off_shape_to_component()
         elif shape_type == CYLINDRICAL_GEOMETRY_NX_CLASS:
             self._add_cylindrical_shape_to_component()
-        elif shape_type == GEOMETRY_NX_CLASS:
-            for child in self.shape_info[CommonKeys.CHILDREN][0][CommonKeys.CHILDREN]:
-                if (
-                    child[NodeType.CONFIG][CommonKeys.NAME] == SHAPE_GROUP_NAME
-                    and child[NodeType.CONFIG][CommonKeys.VALUES] == NX_BOX
-                ):
-                    self._add_box_shape_to_component()
         else:
             self.warnings.append(
                 InvalidShape(
@@ -203,9 +194,11 @@ def _add_box_shape_to_component(self):
         information can be found and passes validation then the geometry is created and written to the component,
         otherwise the function just returns without changing the component.
         """
-        children = self.children[0][CommonKeys.CHILDREN]
         name = self.name
-        if not children:
+        children = False
+        if self.children and self.children[0][CommonKeys.CHILDREN]:
+            children = self.children[0][CommonKeys.CHILDREN]
+        else:
             return
         tmp_dict = {}
         for child in children:
@@ -217,7 +210,7 @@ def _add_box_shape_to_component(self):
         size = tmp_dict[SIZE][CommonKeys.VALUES]
         box_geometry = BoxGeometry(size[0], size[1], size[2], name, units)
         self.component[name] = box_geometry
-        self.shape = box_geometry  # type:ignore
+        self.shape = box_geometry
 
     @staticmethod
     def __get_units(children):
@@ -226,7 +219,7 @@ def __get_units(children):
                 for attr in child[CommonKeys.ATTRIBUTES]:
                     if attr[CommonKeys.NAME] == CommonAttrs.UNITS:
                         return attr[CommonKeys.VALUES]
-        return None
+        return ""
 
     def _add_cylindrical_shape_to_component(self):
         """
@@ -297,7 +290,7 @@ def __create_cylindrical_geometry(
 
     def _get_shape_dataset_from_list(
         self, dataset_name: str, children: List[Dict], warning: bool = True
-    ) -> Union[Dict, None]:
+    ) -> Optional[Dict]:
         """
         Tries to find a given shape dataset from a list of datasets.
         :param dataset_name: The name of the dataset that the function will search for.
@@ -320,7 +313,7 @@ def _get_shape_dataset_from_list(
 
     def _find_and_validate_data_type(
         self, dataset: Dict, expected_types: List[str], parent_name: str
-    ) -> Union[str, None]:
+    ) -> Optional[str]:
         """
         Checks if the type in the dataset attribute has an expected value. Failing this check does not stop the geometry
         creation.
@@ -358,7 +351,7 @@ def _find_and_validate_data_type(
 
         return None
 
-    def _find_and_validate_units(self, vertices_dataset: Dict) -> Union[str, None]:
+    def _find_and_validate_units(self, vertices_dataset: Dict) -> Optional[str]:
         """
         Attempts to retrieve and validate the units data.
         :param vertices_dataset: The vertices dataset.
@@ -438,9 +431,7 @@ def _all_in_list_have_expected_type(
         )
         return False
 
-    def _get_values_attribute(
-        self, dataset: Dict, parent_name: str
-    ) -> Union[List, None]:
+    def _get_values_attribute(self, dataset: Dict, parent_name: str) -> Optional[List]:
         """
         Attempts to get the values attribute in a dataset. Creates an error message if it cannot be found.
         :param dataset: The dataset we hope to find the values attribute in.
@@ -475,7 +466,7 @@ def _attribute_is_a_list(self, attribute: Any, parent_name: str) -> bool:
         return False
 
     @property
-    def children(self) -> Union[List, None]:
+    def children(self) -> Optional[List]:
         """
         Attempts to get the children list from the shape dictionary.
         :return: The children list if it could be found, otherwise None is returned.
@@ -508,7 +499,7 @@ def name(self) -> str:
 
     def _find_and_validate_values_list(
         self, dataset: Dict, expected_types: List[str], attribute_name: str
-    ) -> Union[List, None]:
+    ) -> Optional[List]:
         """
         Attempts to find and validate the contents of the values attribute from the dataset.
         :param dataset: The dataset containing the values list.
@@ -582,7 +573,12 @@ def _handle_mapping(self, children: List[Dict]):
             detector_faces_dataset = self._get_shape_dataset_from_list(
                 DETECTOR_FACES, shape_group[CommonKeys.CHILDREN], False
             )
-            self.shape.detector_faces = detector_faces_dataset[CommonKeys.VALUES]
+            if (
+                detector_faces_dataset
+                and not isinstance(self.shape, BoxGeometry)
+                and not isinstance(self.shape, CylindricalGeometry)
+            ):
+                self.shape.detector_faces = detector_faces_dataset[CommonKeys.VALUES]
 
     def _find_and_add_pixel_offsets_to_component(
         self, offset_name: str, children: List[Dict]

nexus_constructor/model/geometry.py

@@ -6,7 +6,7 @@
 from PySide6.QtGui import QMatrix4x4, QVector3D
 
 from nexus_constructor.common_attrs import (
-    GEOMETRY_NX_CLASS,
+    OFF_GEOMETRY_NX_CLASS,
     NX_BOX,
     SHAPE_GROUP_NAME,
     SHAPE_NX_CLASS,
@@ -191,11 +191,11 @@ def __init__(
         Group.__init__(self, name)
         self._size = [length, width, height]
         self._units = units
-        self.nx_class = GEOMETRY_NX_CLASS
+        self.nx_class = OFF_GEOMETRY_NX_CLASS
         self._create_datasets_and_add_to_shape_group()
 
     @property
-    def detector_number(self) -> List[int]:
+    def detector_number(self) -> Optional[List[int]]:
         if self._detector is None:
             return None
         return self._detector.tolist()

nexus_constructor/model/group.py

@@ -151,7 +151,9 @@ def nx_class(self):
     def nx_class(self, new_nx_class: str):
         self.attributes.set_attribute_value(CommonAttrs.NX_CLASS, new_nx_class)
 
-    def set_field_value(self, name: str, value: Any, dtype: str, unit: str = ""):
+    def set_field_value(
+        self, name: str, value: Any, dtype: Optional[str], unit: str = ""
+    ):
         self[name] = Dataset(parent_node=self, name=name, type=dtype, values=value)
         if unit:
             self[name].attributes.set_attribute_value(CommonAttrs.UNITS, unit)

nexus_constructor/model/module.py

@@ -210,7 +210,7 @@ def as_nexus(self, nexus_node, error_collector: List[str]):
 class Dataset(FileWriterModule):
     name: str = attr.ib()
     values: Union[List[ValueType], ValueType] = attr.ib()
-    type: str = attr.ib(default=None)
+    type: Optional[str] = attr.ib(default=None)
     writer_module: str = attr.ib(default=WriterModules.DATASET.value, init=False)
 
     def as_dict(self, error_collector: List[str]):

nx-class-documentation/html/index.html

@@ -109,7 +109,7 @@ <h1>User Manual and Reference Documentation<a class="headerlink" href="#user-man
 </div>
 <hr class="docutils" />
 <p class="rubric">Publishing Information</p>
-<p>This manual built Sep 21, 2023.</p>
+<p>This manual built Sep 26, 2023.</p>
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <p>This document is available in these formats online:</p>

tests/json/shape_json.py

@@ -278,54 +278,91 @@ def off_shape_json() -> Dict:
 def box_shape_json() -> dict:
     box_shape = """
     {
-      "name": "geometry",
-      "type": "group",
-      "attributes": [
+      "name":"geometry",
+      "attributes":[
         {
-          "name": "NX_class",
-          "dtype": "string",
-          "values": "NXgeometry"
+          "name":"NX_class",
+          "type":"string",
+          "values":"NXoff_geometry"
         }
       ],
-      "children": [
+      "type":"group",
+      "children":[
         {
-          "name": "shape",
-          "type": "group",
-          "attributes": [
+          "module":"dataset",
+          "config":{
+            "name":"faces",
+            "type":"int32",
+            "values":[
+              0, 4, 8, 12, 16, 20
+            ]
+          }
+        },
+        {
+          "module":"dataset",
+          "attributes":[
             {
-              "name": "NX_class",
-              "dtype": "string",
-              "values": "NXshape"
+              "name":"units",
+              "type":"string",
+              "values":"m"
             }
           ],
-          "children": [
-            {
-              "module": "dataset",
-              "config": {
-                "name": "size",
-                "values": [
-                  6.0,
-                  12.0,
-                  15.0
-                ],
-                "type": "double"
-              },
-              "attributes": [
-                {
-                  "name": "units",
-                  "dtype": "string",
-                  "values": "m"
-                }
+          "config":{
+            "name":"vertices",
+            "type":"float",
+            "values":[
+              [
+                0.0,
+                0.0,
+                0.0
+              ],
+              [
+                1.0,
+                0.0,
+                0.0
+              ],
+              [
+                1.0,
+                0.0,
+                1.0
+              ],
+              [
+                0.0,
+                0.0,
+                1.0
+              ],
+              [
+                0.0,
+                1.0,
+                0.0
+              ],
+              [
+                1.0,
+                1.0,
+                0.0
+              ],
+              [
+                1.0,
+                1.0,
+                1.0
+              ],
+              [
+                0.0,
+                1.0,
+                1.0
               ]
-            },
-            {
-              "module": "dataset",
-              "config": {
-                "name": "shape",
-                "values": "nxbox"
-              }
-            }
-          ]
+            ]
+          }
+        },
+        {
+          "module":"dataset",
+          "config":{
+            "name":"winding_order",
+            "type":"int32",
+            "values":[
+              0, 1, 2, 3, 4, 5, 6, 7, 0, 3, 7, 4, 1, 2, 6, 5, 0, 1, 5, 4, 3, 2, 6, 7
+            ]
+          }
         }
       ]
     }

tests/json/test_shape_reader.py

@@ -8,7 +8,6 @@
 from nexus_constructor.common_attrs import (
     CYLINDRICAL_GEOMETRY_NX_CLASS,
     GEOMETRY_GROUP_NAME,
-    GEOMETRY_NX_CLASS,
     OFF_GEOMETRY_NX_CLASS,
     PIXEL_SHAPE_GROUP_NAME,
     SHAPE_GROUP_NAME,
@@ -714,14 +713,14 @@ def test_GIVEN_valid_pixel_mapping_and_cylindrical_shape_WHEN_reading_pixel_data
 def test_GIVEN_box_shape_json_WHEN_reading_shape_THEN_geometry_object_has_expected_properties(
     box_shape_reader, box_shape_json, mock_component
 ):
+    # no detector faces
     name = box_shape_json[CommonKeys.NAME]
     box_shape_reader.add_shape_to_component()
     shape = mock_component[name]
-    assert isinstance(shape, BoxGeometry)
+    assert isinstance(shape, OFFGeometryNexus)
     assert shape.name == name
-    assert shape.nx_class == GEOMETRY_NX_CLASS
-    assert shape.size[0] == 6.0
-    assert shape.size[1] == 12.0
-    assert shape.size[2] == 15.0
+    assert shape.nx_class == OFF_GEOMETRY_NX_CLASS
+    assert len(shape.faces[0]) == 4
+    assert len(shape.faces) == 6
     assert shape.units == "m"
     assert shape.name == GEOMETRY_GROUP_NAME