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ebrahimebrahimebrahimebrahim
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Fix TransducerArray reading of impulse_response #380 #381
When the impulse response is global to the transducer array, rather than per module, it is not converted to a numpy array when it should be.
1 parent d96b464 commit 5137075

5 files changed

Lines changed: 129 additions & 14 deletions

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‎src/openlifu/xdc/transducerarray.py‎

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -42,12 +42,11 @@ def from_dict(data: dict):
4242
if "type" in d:
4343
d.pop("type")
4444
d["modules"] = [TransformedTransducer.from_dict(t) for t in data["modules"]]
45-
if (
46-
"attrs" in d
47-
and "standoff_transform" in d["attrs"]
48-
and d["attrs"]["standoff_transform"] is not None
49-
):
50-
d["attrs"]["standoff_transform"] = np.array(d["attrs"]["standoff_transform"])
45+
if "attrs" in d:
46+
if "standoff_transform" in d["attrs"] and d["attrs"]["standoff_transform"] is not None:
47+
d["attrs"]["standoff_transform"] = np.array(d["attrs"]["standoff_transform"])
48+
if "impulse_response" in d["attrs"] and d["attrs"]["impulse_response"] is not None:
49+
d["attrs"]["impulse_response"] = np.array(d["attrs"]["impulse_response"])
5150
return TransducerArray(**d)
5251

5352

‎tests/resources/example_db/transducers/example_transducer_array2/example_transducer_array2.json‎

Lines changed: 101 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,101 @@
1+
{
2+
"type": "TransducerArray",
3+
"id": "example_transducer_array",
4+
"name": "test example of an *array* of *transformed* transducers -- this time with certain attributes moved to attrs rather than individual modules",
5+
"modules": [
6+
{
7+
"id": "module1",
8+
"name": "Module 1",
9+
"elements": [
10+
{
11+
"index": 1,
12+
"position": [-17.5, 17.5, 0.0],
13+
"orientation": [0.0, 0.0, 0.0],
14+
"size": [3.7, 3.7],
15+
"pin": 1,
16+
"units": "mm"
17+
},
18+
{
19+
"index": 2,
20+
"position": [-17.5, 13.5, 0.0],
21+
"orientation": [0.0, 0.0, 0.0],
22+
"size": [3.7, 3.7],
23+
"pin": 2,
24+
"units": "mm"
25+
}
26+
],
27+
"frequency": 175000.0,
28+
"units": "mm",
29+
"attrs": {},
30+
"registration_surface_filename": null,
31+
"transducer_body_filename": null,
32+
"standoff_transform": [
33+
[1.0, 0.0, 0.0, 0.0],
34+
[0.0, 1.0, 0.0, 0.0],
35+
[0.0, 0.0, 1.0, 0.0],
36+
[0.0, 0.0, 0.0, 1.0]
37+
],
38+
"sensitivity": 1200,
39+
"module_invert": [false],
40+
"transform": [
41+
[0.9, 0.0, -0.2, 22.8],
42+
[0.0, 1.0, 0.0, 0.0],
43+
[0.2, 0.0, 0.9, 3.3],
44+
[0.0, 0.0, 0.0, 1.0]
45+
]
46+
},
47+
{
48+
"id": "module2",
49+
"name": "Module 2",
50+
"elements": [
51+
{
52+
"index": 1,
53+
"position": [-17.5, 17.5, 0.0],
54+
"orientation": [0.0, 0.0, 0.0],
55+
"size": [3.7, 3.7],
56+
"pin": 1,
57+
"units": "mm"
58+
},
59+
{
60+
"index": 2,
61+
"position": [-17.5, 13.5, 0.0],
62+
"orientation": [0.0, 0.0, 0.0],
63+
"size": [3.7, 3.7],
64+
"pin": 2,
65+
"units": "mm"
66+
}
67+
],
68+
"frequency": 180000.0,
69+
"units": "mm",
70+
"attrs": {},
71+
"registration_surface_filename": null,
72+
"transducer_body_filename": null,
73+
"standoff_transform": [
74+
[1.0, 0.0, 0.0, 0.0],
75+
[0.0, 1.0, 0.0, 0.0],
76+
[0.0, 0.0, 1.0, 0.0],
77+
[0.0, 0.0, 0.0, 1.0]
78+
],
79+
"sensitivity": 1000,
80+
"module_invert": [false],
81+
"transform": [
82+
[0.9, 0.0, 0.2, -22.0],
83+
[0.0, 1.0, 0.0, 0.0],
84+
[-0.2, 0.0, 0.9, 4.2],
85+
[0.0, 0.0, 0.0, 1.0]
86+
]
87+
}
88+
],
89+
"attrs": {
90+
"standoff_transform": [
91+
[1.0, 0.0, 0.0, 0.0],
92+
[0.0, 0.9, -0.02, 0.0],
93+
[0.0, 0.02, 0.9, -4.0],
94+
[0.0, 0.0, 0.0, 1.0]
95+
],
96+
"impulse_response": [1000.0, 1000.0],
97+
"impulse_dt": 1,
98+
"registration_surface_filename": null,
99+
"transducer_body_filename": null
100+
}
101+
}

‎tests/resources/example_db/transducers/transducers.json‎

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1 +1,7 @@
1-
{ "transducer_ids": ["example_transducer", "example_transducer_array"] }
1+
{
2+
"transducer_ids": [
3+
"example_transducer",
4+
"example_transducer_array",
5+
"example_transducer_array2"
6+
]
7+
}

‎tests/test_database.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -666,13 +666,13 @@ def test_session_date_modified_updates_on_write(example_database:Database, examp
666666
assert session.date_modified > initial_modified_time - tolerance
667667

668668
def test_get_transducer_ids(example_database:Database):
669-
assert(example_database.get_transducer_ids() == ["example_transducer", "example_transducer_array"])
669+
assert("example_transducer" in example_database.get_transducer_ids())
670670

671671
def test_write_transducer_nodata(example_database:Database, example_transducer: Transducer):
672672
example_transducer.id = "example_transducer_2"
673673

674674
example_database.write_transducer(example_transducer)
675-
assert(len(example_database.get_transducer_ids()) == 3)
675+
assert(len(example_database.get_transducer_ids()) == 4)
676676
assert("example_transducer" in example_database.get_transducer_ids())
677677
assert("example_transducer_2" in example_database.get_transducer_ids())
678678

‎tests/test_transducer.py‎

Lines changed: 14 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -13,9 +13,9 @@
1313
def example_transducer() -> Transducer:
1414
return Transducer.from_file(Path(__file__).parent/'resources/example_db/transducers/example_transducer/example_transducer.json')
1515

16-
@pytest.fixture()
17-
def example_transducer_array() -> TransducerArray:
18-
return TransducerArray.from_file(Path(__file__).parent/'resources/example_db/transducers/example_transducer_array/example_transducer_array.json')
16+
def load_transducer_array(transducer_array_id : str) -> TransducerArray:
17+
"""Load an example TransducerArray given the transducer ID."""
18+
return TransducerArray.from_file(Path(__file__).parent/f'resources/example_db/transducers/{transducer_array_id}/{transducer_array_id}.json')
1919

2020
@pytest.mark.parametrize("compact_representation", [True, False])
2121
def test_serialize_deserialize_transducer(example_transducer : Transducer, compact_representation: bool):
@@ -94,8 +94,17 @@ def test_read_data_types(example_transducer:Transducer):
9494
if len(example_transducer.elements) > 0:
9595
assert isinstance(example_transducer.elements[0], Element)
9696

97-
def test_transducer_array_to_transducer_data_types(example_transducer_array:TransducerArray):
98-
transducer = example_transducer_array.to_transducer()
97+
@pytest.mark.parametrize(
98+
"transducer_array_id",
99+
[
100+
"example_transducer_array",
101+
"example_transducer_array2",
102+
]
103+
)
104+
def test_transducer_array_to_transducer_data_types(transducer_array_id):
105+
transducer_array : TransducerArray = load_transducer_array(transducer_array_id)
106+
transducer = transducer_array.to_transducer()
99107
assert isinstance(transducer.standoff_transform, np.ndarray)
108+
assert isinstance(transducer.impulse_response, np.ndarray)
100109
if len(transducer.elements) > 0:
101110
assert isinstance(transducer.elements[0], Element)

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