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🧑‍💻 Optimise MultiTaskSegmentor Tests #1102

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🧑‍💻 Optimise MultiTaskSegmentor Tests #1102

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3f26405
:technologist: Optimise `MultiTaskSegmentor` Tests
shaneahmed Jul 24, 2026
0d3e919
:technologist: Optimise `NucleusInstanceSegmentor` Tests
shaneahmed Jul 24, 2026
8b8f2a0
Merge branch 'develop' into optimise-mtsegmentor-tests
shaneahmed Aug 6, 2026
6752f06
Merge branch 'develop' into optimise-mtsegmentor-tests
shaneahmed Aug 7, 2026
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45 changes: 45 additions & 0 deletions tests/engines/test_multi_task_segmentor.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@

OutputType = dict[str, Any] | Any
device = "cuda" if toolbox_env.has_gpu() else "cpu"
_RUNNING_ON_CI = toolbox_env.running_on_ci()


def test_mtsegmentor_init() -> None:
Expand All @@ -53,6 +54,10 @@ def test_mtsegmentor_init() -> None:
assert isinstance(segmentor.model, torch.nn.Module)


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_mtsegmentor_patches(remote_sample: Callable, track_tmp_path: Path) -> None:
"""Tests MultiTaskSegmentor on image patches."""
mtsegmentor = MultiTaskSegmentor(
Expand Down Expand Up @@ -211,6 +216,10 @@ def test_mtsegmentor_patches(remote_sample: Callable, track_tmp_path: Path) -> N
)


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_mtsegmentor_tiles_no_metadata(track_tmp_path: Path) -> None:
"""Tests MultiTaskSegmentor on a tile with no metadata."""
img_file_name = track_tmp_path / "tcga_hnscc.png"
Expand Down Expand Up @@ -249,6 +258,10 @@ def test_mtsegmentor_tiles_no_metadata(track_tmp_path: Path) -> None:
assert len(output_zarr["nuclei_segmentation"]["contours"][:]) == 1299


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_single_task_mtsegmentor(
remote_sample: Callable,
track_tmp_path: Path,
Expand Down Expand Up @@ -422,6 +435,10 @@ def test_single_task_mtsegmentor(
assert "Probability maps cannot be saved as AnnotationStore or JSON" in caplog.text


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_wsi_mtsegmentor_correct_nonsquare_shape(
remote_sample: Callable,
track_tmp_path: Path,
Expand Down Expand Up @@ -523,6 +540,10 @@ def test_wsi_mtsegmentor_correct_nonsquare_shape(
)


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_wsi_mtsegmentor_zarr(
remote_sample: Callable,
track_tmp_path: Path,
Expand Down Expand Up @@ -611,6 +632,10 @@ def test_wsi_mtsegmentor_zarr(
)


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_multi_input_wsi_mtsegmentor_zarr(
remote_sample: Callable,
track_tmp_path: Path,
Expand Down Expand Up @@ -660,6 +685,10 @@ def test_multi_input_wsi_mtsegmentor_zarr(
assert "count" not in output_


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_wsi_segmentor_annotationstore(
remote_sample: Callable, track_tmp_path: Path
) -> None:
Expand Down Expand Up @@ -698,6 +727,10 @@ def test_wsi_segmentor_annotationstore(
assert store_file_path == output[wsi4_512_512_svs][0]


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_wsi_segmentor_qupath(remote_sample: Callable, track_tmp_path: Path) -> None:
"""Test MultiTaskSegmentor for WSIs with AnnotationStore output."""
wsi4_512_512_svs = remote_sample("wsi4_512_512_svs")
Expand Down Expand Up @@ -739,6 +772,10 @@ def test_wsi_segmentor_qupath(remote_sample: Callable, track_tmp_path: Path) ->
weights_path.unlink()


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_wsi_segmentor_annotationstore_probabilities(
remote_sample: Callable, track_tmp_path: Path, caplog: pytest.CaptureFixture
) -> None:
Expand Down Expand Up @@ -773,6 +810,10 @@ def test_wsi_segmentor_annotationstore_probabilities(
assert task_name not in zarr_group


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_raise_value_error_return_labels_wsi(
remote_sample: Callable,
track_tmp_path: Path,
Expand Down Expand Up @@ -1564,6 +1605,10 @@ def convert_to_dask_single_task(
# -------------------------------------------------------------------------------------


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_cli_model_single_file(remote_sample: Callable, track_tmp_path: Path) -> None:
"""Test semantic segmentor CLI single file."""
wsi4_512_512_svs = remote_sample("wsi4_512_512_svs")
Expand Down
17 changes: 15 additions & 2 deletions tests/engines/test_nucleus_instance_segmentor.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
from typing import TYPE_CHECKING, Any, Final

import numpy as np
import pytest
import torch
import zarr
from click.testing import CliRunner
Expand All @@ -25,9 +26,8 @@
if TYPE_CHECKING:
from collections.abc import Callable

import pytest

device = "cuda" if toolbox_env.has_gpu() else "cpu"
_RUNNING_ON_CI = toolbox_env.running_on_ci()
OutputType = dict[str, Any] | Any


Expand All @@ -43,6 +43,10 @@ def test_mtsegmentor_init(caplog: pytest.LogCaptureFixture) -> None:
)


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_mtsegmentor_patches(remote_sample: Callable) -> None:
"""Tests NucleusInstanceSegmentor on image patches."""
mtsegmentor = NucleusInstanceSegmentor(
Expand Down Expand Up @@ -88,6 +92,10 @@ def test_mtsegmentor_patches(remote_sample: Callable) -> None:
# -------------------------------------------------------------------------------------


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_cli_model_single_file(remote_sample: Callable, track_tmp_path: Path) -> None:
"""Test semantic segmentor CLI single file."""
wsi4_512_512_svs = remote_sample("wsi4_512_512_svs")
Expand Down Expand Up @@ -117,6 +125,10 @@ def test_cli_model_single_file(remote_sample: Callable, track_tmp_path: Path) ->
assert "predictions" in zarr_group


@pytest.mark.skipif(
_RUNNING_ON_CI,
reason="Local test only.",
)
def test_cli_default_return_predictions(
remote_sample: Callable, track_tmp_path: Path
) -> None:
Expand All @@ -125,6 +137,7 @@ def test_cli_default_return_predictions(
Regression test: omitting ``--return-predictions`` leaves it as ``None``,
which previously reached the engine and raised
``TypeError: 'NoneType' is not iterable``.

"""
wsi4_512_512_svs = remote_sample("wsi4_512_512_svs")
runner = CliRunner()
Expand Down
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