-
Notifications
You must be signed in to change notification settings - Fork 10
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* Refactor tests * Update tests/tests/test_integration/test_gui/test_tracks.py Co-authored-by: Alessandro Felder <[email protected]> * fix typo --------- Co-authored-by: Alessandro Felder <[email protected]>
- Loading branch information
1 parent
ca34331
commit 2269421
Showing
5 changed files
with
210 additions
and
120 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,90 @@ | ||
from filecmp import cmp | ||
from pathlib import Path | ||
|
||
import pandas as pd | ||
import pytest | ||
|
||
brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output" | ||
validate_regions_dir = ( | ||
brainreg_dir / "manual_segmentation" / "standard_space" / "regions" | ||
) | ||
|
||
|
||
@pytest.fixture | ||
def test_regions_dir(tmpdir): | ||
tmp_input_dir = tmpdir / "brainreg_output" | ||
test_regions_dir = ( | ||
tmp_input_dir / "manual_segmentation" / "standard_space" / "regions" | ||
) | ||
return test_regions_dir | ||
|
||
|
||
def test_region_widget_layer_numbers( | ||
segmentation_widget_with_data_atlas_space, test_regions_dir | ||
): | ||
assert len(segmentation_widget_with_data_atlas_space.viewer.layers) == 4 | ||
assert len(segmentation_widget_with_data_atlas_space.label_layers) == 1 | ||
|
||
|
||
def test_add_new_region( | ||
segmentation_widget_with_data_atlas_space, test_regions_dir | ||
): | ||
segmentation_widget_with_data_atlas_space.region_seg.add_new_region() | ||
assert len(segmentation_widget_with_data_atlas_space.viewer.layers) == 5 | ||
assert len(segmentation_widget_with_data_atlas_space.label_layers) == 2 | ||
assert ( | ||
segmentation_widget_with_data_atlas_space.label_layers[0].name | ||
== "test_region" | ||
) | ||
assert ( | ||
segmentation_widget_with_data_atlas_space.label_layers[1].name | ||
== "region_1" | ||
) | ||
|
||
|
||
def test_add_existing_region( | ||
segmentation_widget_with_data_atlas_space, test_regions_dir | ||
): | ||
test_layer = segmentation_widget_with_data_atlas_space.viewer.add_labels( | ||
segmentation_widget_with_data_atlas_space.label_layers[0].data, | ||
name="test_region_2", | ||
) | ||
segmentation_widget_with_data_atlas_space.viewer.layers.selection.select_only( | ||
test_layer | ||
) | ||
segmentation_widget_with_data_atlas_space.region_seg.add_region_from_existing_layer( | ||
override=True | ||
) | ||
assert len(segmentation_widget_with_data_atlas_space.viewer.layers) == 5 | ||
assert len(segmentation_widget_with_data_atlas_space.label_layers) == 2 | ||
|
||
|
||
def test_region_analysis( | ||
segmentation_widget_with_data_atlas_space, test_regions_dir | ||
): | ||
segmentation_widget_with_data_atlas_space.region_seg.run_region_analysis( | ||
override=True | ||
) | ||
region_csv_validate = pd.read_csv(validate_regions_dir / "test_region.csv") | ||
region_csv_test = pd.read_csv(test_regions_dir / "test_region.csv") | ||
pd.testing.assert_frame_equal(region_csv_test, region_csv_validate) | ||
|
||
summary_csv_validate = pd.read_csv(validate_regions_dir / "summary.csv") | ||
summary_csv_test = pd.read_csv(test_regions_dir / "summary.csv") | ||
pd.testing.assert_frame_equal(summary_csv_test, summary_csv_validate) | ||
|
||
|
||
def test_region_save(segmentation_widget_with_data_atlas_space): | ||
segmentation_widget_with_data_atlas_space.save(override=True) | ||
|
||
|
||
def test_region_export( | ||
segmentation_widget_with_data_atlas_space, test_regions_dir | ||
): | ||
segmentation_widget_with_data_atlas_space.export_to_brainrender( | ||
override=True | ||
) | ||
cmp( | ||
validate_regions_dir / "test_region.obj", | ||
test_regions_dir / "test_region.obj", | ||
) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,103 @@ | ||
from pathlib import Path | ||
|
||
import numpy as np | ||
import pandas as pd | ||
import pytest | ||
|
||
brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output" | ||
validate_tracks_dir = ( | ||
brainreg_dir / "manual_segmentation" / "standard_space" / "tracks" | ||
) | ||
|
||
|
||
@pytest.fixture | ||
def test_tracks_dir(tmpdir): | ||
tmp_input_dir = tmpdir / "brainreg_output" | ||
test_tracks_dir = ( | ||
tmp_input_dir / "manual_segmentation" / "standard_space" / "tracks" | ||
) | ||
return test_tracks_dir | ||
|
||
|
||
def test_track_widget_layer_numbers( | ||
segmentation_widget_with_data_atlas_space, test_tracks_dir | ||
): | ||
assert len(segmentation_widget_with_data_atlas_space.viewer.layers) == 4 | ||
assert len(segmentation_widget_with_data_atlas_space.track_layers) == 1 | ||
|
||
|
||
def test_add_new_track( | ||
segmentation_widget_with_data_atlas_space, test_tracks_dir | ||
): | ||
segmentation_widget_with_data_atlas_space.track_seg.add_track() | ||
assert len(segmentation_widget_with_data_atlas_space.viewer.layers) == 5 | ||
assert len(segmentation_widget_with_data_atlas_space.track_layers) == 2 | ||
assert ( | ||
segmentation_widget_with_data_atlas_space.track_layers[0].name | ||
== "test_track" | ||
) | ||
assert ( | ||
segmentation_widget_with_data_atlas_space.track_layers[1].name | ||
== "track_1" | ||
) | ||
assert ( | ||
len(segmentation_widget_with_data_atlas_space.track_layers[0].data) | ||
== 6 | ||
) | ||
|
||
|
||
def test_add_existing_track( | ||
segmentation_widget_with_data_atlas_space, test_tracks_dir | ||
): | ||
segmentation_widget = segmentation_widget_with_data_atlas_space | ||
|
||
# importing existing track | ||
points = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2], [3, 3, 3]]) | ||
test_layer = segmentation_widget.viewer.add_points( | ||
points, name="test_track2" | ||
) | ||
segmentation_widget.viewer.layers.selection.select_only(test_layer) | ||
segmentation_widget.track_seg.add_track_from_existing_layer(override=True) | ||
assert len(segmentation_widget.viewer.layers) == 5 | ||
assert len(segmentation_widget.track_layers) == 2 | ||
|
||
|
||
def test_add_surface_point( | ||
segmentation_widget_with_data_atlas_space, test_tracks_dir | ||
): | ||
segmentation_widget_with_data_atlas_space.track_seg.add_surface_points() | ||
assert ( | ||
len(segmentation_widget_with_data_atlas_space.track_layers[0].data) | ||
== 7 | ||
) | ||
|
||
|
||
def test_track_analysis( | ||
segmentation_widget_with_data_atlas_space, test_tracks_dir | ||
): | ||
segmentation_widget_with_data_atlas_space.track_seg.run_track_analysis( | ||
override=True | ||
) | ||
regions_validate = pd.read_csv(validate_tracks_dir / "test_track.csv") | ||
regions_test = pd.read_csv(test_tracks_dir / "test_track.csv") | ||
pd.testing.assert_frame_equal(regions_validate, regions_test) | ||
|
||
|
||
def test_track_save( | ||
segmentation_widget_with_data_atlas_space, test_tracks_dir, rtol=1e-10 | ||
): | ||
segmentation_widget_with_data_atlas_space.save(override=True) | ||
points_validate = pd.read_hdf(validate_tracks_dir / "test_track.points") | ||
points_test = pd.read_hdf(test_tracks_dir / "test_track.points") | ||
np.testing.assert_allclose(points_validate, points_test, rtol=rtol) | ||
|
||
|
||
def test_track_export( | ||
segmentation_widget_with_data_atlas_space, test_tracks_dir | ||
): | ||
segmentation_widget_with_data_atlas_space.export_to_brainrender( | ||
override=True | ||
) | ||
spline_validate = pd.read_hdf(validate_tracks_dir / "test_track.h5") | ||
spline_test = pd.read_hdf(test_tracks_dir / "test_track.h5") | ||
pd.testing.assert_frame_equal(spline_test, spline_validate) |