Fix standoff transform reading for TransducerArray #380 #381

It was not being converted to a numpy array on read

Author: ebrahimebrahim

src/openlifu/db/database.py

@@ -851,12 +851,13 @@ def load_system(self, sys_id=None):
         sys = UltrasoundSystem.from_file(sys_filename)
         return sys
 
-    def load_transducer(self, transducer_id, convert_array:bool = True) -> Transducer:
+    def load_transducer(self, transducer_id, convert_array:bool = True) -> Transducer|TransducerArray:
         """Given a transducer_id, reads the corresponding transducer file from database and returns a transducer object.
         Note: the transducer object includes the relative path to the affiliated transducer model data. `get_transducer_absolute_filepaths`, should
         be used to obtain the absolute data filepaths based on the Database directory path.
         Args:
             transducer_id: Transducer ID
+            convert_array: When enabled, if a TransducerArray is encountered then it is converted to a Transducer.
         Returns:
             Corresponding Transducer object
         """

src/openlifu/xdc/transducerarray.py

@@ -42,6 +42,12 @@ def from_dict(data: dict):
         if "type" in d:
             d.pop("type")
         d["modules"] = [TransformedTransducer.from_dict(t) for t in data["modules"]]
+        if (
+            "attrs" in d
+            and "standoff_transform" in d["attrs"]
+            and d["attrs"]["standoff_transform"] is not None
+        ):
+            d["attrs"]["standoff_transform"] = np.array(d["attrs"]["standoff_transform"])
         return TransducerArray(**d)
 
 

tests/resources/example_db/transducers/example_transducer_array/example_transducer_array.json

@@ -0,0 +1,99 @@
+{
+  "type": "TransducerArray",
+  "id": "example_transducer_array",
+  "name": "test example of an *array* of *transformed* transducers",
+  "modules": [
+    {
+      "id": "module1",
+      "name": "Module 1",
+      "elements": [
+        {
+          "index": 1,
+          "position": [-17.5, 17.5, 0.0],
+          "orientation": [0.0, 0.0, 0.0],
+          "size": [3.7, 3.7],
+          "pin": 1,
+          "units": "mm"
+        },
+        {
+          "index": 2,
+          "position": [-17.5, 13.5, 0.0],
+          "orientation": [0.0, 0.0, 0.0],
+          "size": [3.7, 3.7],
+          "pin": 2,
+          "units": "mm"
+        }
+      ],
+      "frequency": 175000.0,
+      "units": "mm",
+      "attrs": {},
+      "registration_surface_filename": null,
+      "transducer_body_filename": null,
+      "standoff_transform": [
+        [1.0, 0.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0, 0.0],
+        [0.0, 0.0, 1.0, 0.0],
+        [0.0, 0.0, 0.0, 1.0]
+      ],
+      "sensitivity": 1200,
+      "module_invert": [false],
+      "transform": [
+        [0.9, 0.0, -0.2, 22.8],
+        [0.0, 1.0, 0.0, 0.0],
+        [0.2, 0.0, 0.9, 3.3],
+        [0.0, 0.0, 0.0, 1.0]
+      ]
+    },
+    {
+      "id": "module2",
+      "name": "Module 2",
+      "elements": [
+        {
+          "index": 1,
+          "position": [-17.5, 17.5, 0.0],
+          "orientation": [0.0, 0.0, 0.0],
+          "size": [3.7, 3.7],
+          "pin": 1,
+          "units": "mm"
+        },
+        {
+          "index": 2,
+          "position": [-17.5, 13.5, 0.0],
+          "orientation": [0.0, 0.0, 0.0],
+          "size": [3.7, 3.7],
+          "pin": 2,
+          "units": "mm"
+        }
+      ],
+      "frequency": 180000.0,
+      "units": "mm",
+      "attrs": {},
+      "registration_surface_filename": null,
+      "transducer_body_filename": null,
+      "standoff_transform": [
+        [1.0, 0.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0, 0.0],
+        [0.0, 0.0, 1.0, 0.0],
+        [0.0, 0.0, 0.0, 1.0]
+      ],
+      "sensitivity": 1000,
+      "module_invert": [false],
+      "transform": [
+        [0.9, 0.0, 0.2, -22.0],
+        [0.0, 1.0, 0.0, 0.0],
+        [-0.2, 0.0, 0.9, 4.2],
+        [0.0, 0.0, 0.0, 1.0]
+      ]
+    }
+  ],
+  "attrs": {
+    "standoff_transform": [
+      [1.0, 0.0, 0.0, 0.0],
+      [0.0, 0.9, -0.02, 0.0],
+      [0.0, 0.02, 0.9, -4.0],
+      [0.0, 0.0, 0.0, 1.0]
+    ],
+    "registration_surface_filename": null,
+    "transducer_body_filename": null
+  }
+}

tests/resources/example_db/transducers/transducers.json

@@ -1 +1 @@
-{ "transducer_ids": ["example_transducer"] }
+{ "transducer_ids": ["example_transducer", "example_transducer_array"] }

tests/test_database.py

@@ -666,13 +666,13 @@ def test_session_date_modified_updates_on_write(example_database:Database, examp
         assert session.date_modified > initial_modified_time - tolerance
 
 def test_get_transducer_ids(example_database:Database):
-    assert(example_database.get_transducer_ids() == ["example_transducer"])
+    assert(example_database.get_transducer_ids() == ["example_transducer", "example_transducer_array"])
 
 def test_write_transducer_nodata(example_database:Database, example_transducer: Transducer):
     example_transducer.id = "example_transducer_2"
 
     example_database.write_transducer(example_transducer)
-    assert(len(example_database.get_transducer_ids()) == 2)
+    assert(len(example_database.get_transducer_ids()) == 3)
     assert("example_transducer" in example_database.get_transducer_ids())
     assert("example_transducer_2" in example_database.get_transducer_ids())
 

tests/test_transducer.py

@@ -6,13 +6,17 @@
 import pytest
 from helpers import dataclasses_are_equal
 
-from openlifu.xdc import Element, Transducer
+from openlifu.xdc import Element, Transducer, TransducerArray
 
 
 @pytest.fixture()
 def example_transducer() -> Transducer:
     return Transducer.from_file(Path(__file__).parent/'resources/example_db/transducers/example_transducer/example_transducer.json')
 
+@pytest.fixture()
+def example_transducer_array() -> TransducerArray:
+    return TransducerArray.from_file(Path(__file__).parent/'resources/example_db/transducers/example_transducer_array/example_transducer_array.json')
+
 @pytest.mark.parametrize("compact_representation", [True, False])
 def test_serialize_deserialize_transducer(example_transducer : Transducer, compact_representation: bool):
     reconstructed_transducer = example_transducer.from_json(example_transducer.to_json(compact_representation))
@@ -89,3 +93,9 @@ def test_read_data_types(example_transducer:Transducer):
     assert isinstance(example_transducer.standoff_transform, np.ndarray)
     if len(example_transducer.elements) > 0:
         assert isinstance(example_transducer.elements[0], Element)
+
+def test_transducer_array_to_transducer_data_types(example_transducer_array:TransducerArray):
+    transducer = example_transducer_array.to_transducer()
+    assert isinstance(transducer.standoff_transform, np.ndarray)
+    if len(transducer.elements) > 0:
+        assert isinstance(transducer.elements[0], Element)