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Fix Napari relared tests fails #376

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Fix Napari relared tests fails #376

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eae0d08
Fix: Refactor test_widget_open_file to use qtbot for consistent GUI t…
Dec 30, 2024
cf4359a
style(pre-commit.ci): auto fixes
pre-commit-ci[bot] Dec 30, 2024
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8 changes: 4 additions & 4 deletions tests/widgets/test_widget_open_file.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

import napari
import numpy as np
import pytest
from pytestqt import qtbot

from plantseg.io.h5 import create_h5
from plantseg.io.voxelsize import VoxelSize
Expand All @@ -11,8 +11,7 @@
IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true" # set to true in GitHub Actions by default to skip CUDA tests


@pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="GUI tests hangs in GitHub Actions.")
def test_widget_open_file(make_napari_viewer_proxy, path_h5):
def test_widget_open_file(qtbot, make_napari_viewer_proxy, path_h5):
viewer = make_napari_viewer_proxy()
shape = (10, 10, 10)
data = np.random.rand(*shape).astype(np.float32)
Expand All @@ -29,7 +28,8 @@ def test_widget_open_file(make_napari_viewer_proxy, path_h5):
stack_layout="ZYX",
update_other_widgets=False,
)
napari.run()

qtbot.wait(100)

assert viewer.layers[0].name == "test_raw"
assert viewer.layers[0].data.shape == shape
Expand Down
30 changes: 15 additions & 15 deletions tests/widgets/test_widget_preprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import pytest
from magicgui import magicgui
from napari.types import LayerDataTuple
from pytestqt import qtbot

from plantseg.core.image import ImageLayout, ImageProperties, PlantSegImage, SemanticType
from plantseg.io.voxelsize import VoxelSize
Expand Down Expand Up @@ -51,9 +52,8 @@ def widget_add_image(image: PlantSegImage) -> LayerDataTuple:
return image.to_napari_layer_tuple()


@pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="GUI tests hangs in GitHub Actions.")
class TestWidgetRescaling:
def test_rescaling_from_factor(self, make_napari_viewer_proxy, sample_image):
def test_rescaling_from_factor(self, qtbot, make_napari_viewer_proxy, sample_image):
viewer = make_napari_viewer_proxy()
widget_add_image(sample_image)

Expand All @@ -64,14 +64,14 @@ def test_rescaling_from_factor(self, make_napari_viewer_proxy, sample_image):
rescaling_factor=(factor, factor, factor),
update_other_widgets=False,
)
napari.run()
qtbot.wait(100)

old_layer = viewer.layers[sample_image.name]
new_layer = viewer.layers[sample_image.name + '_rescaled']
np.testing.assert_allclose(new_layer.data.shape, np.multiply(old_layer.data.shape, factor), rtol=1e-5)
np.testing.assert_allclose(np.multiply(new_layer.scale, factor), old_layer.scale, rtol=1e-5)

def test_rescaling_to_layer_voxel_size(self, make_napari_viewer_proxy, sample_image, sample_label):
def test_rescaling_to_layer_voxel_size(self, qtbot, make_napari_viewer_proxy, sample_image, sample_label):
viewer = make_napari_viewer_proxy()
widget_add_image(sample_image)
widget_add_image(sample_label)
Expand All @@ -82,15 +82,15 @@ def test_rescaling_to_layer_voxel_size(self, make_napari_viewer_proxy, sample_im
reference_layer=viewer.layers[sample_label.name],
update_other_widgets=False,
)
napari.run()
qtbot.wait(100)

reference_layer = viewer.layers[sample_label.name]
new_layer = viewer.layers[sample_image.name + '_rescaled']

np.testing.assert_allclose(new_layer.data.shape, reference_layer.data.shape, rtol=1e-5)
np.testing.assert_allclose(new_layer.scale, reference_layer.scale, rtol=1e-5)

def test_rescaling_to_model_voxel_size(self, make_napari_viewer_proxy, sample_image):
def test_rescaling_to_model_voxel_size(self, qtbot, make_napari_viewer_proxy, sample_image):
viewer = make_napari_viewer_proxy()
widget_add_image(sample_image)

Expand All @@ -100,7 +100,7 @@ def test_rescaling_to_model_voxel_size(self, make_napari_viewer_proxy, sample_im
reference_model='PlantSeg_3Dnuc_platinum', # voxel size: (0.2837, 0.1268, 0.1268)
update_other_widgets=False,
)
napari.run()
qtbot.wait(200)

old_layer = viewer.layers[sample_image.name]
new_layer = viewer.layers[sample_image.name + '_rescaled']
Expand All @@ -116,7 +116,7 @@ def test_rescaling_to_model_voxel_size(self, make_napari_viewer_proxy, sample_im

np.testing.assert_allclose(new_shape * new_scale, old_shape * old_scale, atol=0.1)

def test_rescaling_to_voxel_size(self, make_napari_viewer_proxy, sample_image):
def test_rescaling_to_voxel_size(self, qtbot, make_napari_viewer_proxy, sample_image):
viewer = make_napari_viewer_proxy()
widget_add_image(sample_image)

Expand All @@ -127,7 +127,7 @@ def test_rescaling_to_voxel_size(self, make_napari_viewer_proxy, sample_image):
out_voxel_size=expected_scale,
update_other_widgets=False,
)
napari.run()
qtbot.wait(100)

old_layer = viewer.layers[sample_image.name]
new_layer = viewer.layers[sample_image.name + '_rescaled']
Expand All @@ -138,7 +138,7 @@ def test_rescaling_to_voxel_size(self, make_napari_viewer_proxy, sample_image):
np.testing.assert_allclose(new_layer.data.shape, expected_shape, rtol=1e-5)
np.testing.assert_allclose(new_layer.scale, expected_scale, rtol=1e-5)

def test_rescaling_to_layer_shape(self, make_napari_viewer_proxy, sample_image, sample_label):
def test_rescaling_to_layer_shape(self, qtbot, make_napari_viewer_proxy, sample_image, sample_label):
viewer = make_napari_viewer_proxy()
widget_add_image(sample_image)
widget_add_image(sample_label)
Expand All @@ -149,7 +149,7 @@ def test_rescaling_to_layer_shape(self, make_napari_viewer_proxy, sample_image,
reference_layer=viewer.layers[sample_label.name],
update_other_widgets=False,
)
napari.run()
qtbot.wait(100)

reference_layer = viewer.layers[sample_label.name]
new_layer = viewer.layers[sample_image.name + '_reshaped']
Expand All @@ -159,7 +159,7 @@ def test_rescaling_to_layer_shape(self, make_napari_viewer_proxy, sample_image,
# In our special case in this test, yes, the scale should be the same
np.testing.assert_allclose(new_layer.scale, reference_layer.scale, rtol=1e-5)

def test_rescaling_set_shape(self, make_napari_viewer_proxy, sample_image):
def test_rescaling_set_shape(self, qtbot, make_napari_viewer_proxy, sample_image):
viewer = make_napari_viewer_proxy()
widget_add_image(sample_image)

Expand All @@ -170,7 +170,7 @@ def test_rescaling_set_shape(self, make_napari_viewer_proxy, sample_image):
reference_shape=target_shape,
update_other_widgets=False,
)
napari.run()
qtbot.wait(100)

old_layer = viewer.layers[sample_image.name]
new_layer = viewer.layers[sample_image.name + '_reshaped']
Expand All @@ -182,7 +182,7 @@ def test_rescaling_set_shape(self, make_napari_viewer_proxy, sample_image):

np.testing.assert_allclose(new_layer.scale, expected_scale, rtol=1e-5)

def test_rescaling_set_voxel_size(self, make_napari_viewer_proxy, sample_image):
def test_rescaling_set_voxel_size(self, qtbot, make_napari_viewer_proxy, sample_image):
viewer = make_napari_viewer_proxy()
widget_add_image(sample_image)

Expand All @@ -193,7 +193,7 @@ def test_rescaling_set_voxel_size(self, make_napari_viewer_proxy, sample_image):
out_voxel_size=target_voxel_size,
update_other_widgets=False,
)
napari.run()
qtbot.wait(100)

new_layer = viewer.layers[sample_image.name + '_set_voxel_size']
np.testing.assert_allclose(new_layer.scale, target_voxel_size, rtol=1e-5)