def test_set_get_user_transform_do_set_something():
model = VTKSurfaceModel(None, (1.0, 0.0, 1.0))
vtk_matrix = vtk.vtkMatrix4x4()
vtk_matrix.Identity()
vtk_matrix.SetElement(0, 0, 2) # i.e. not identity
model.set_user_matrix(vtk_matrix)
result = model.get_user_matrix()
assert result is not None
assert result == vtk_matrix
def test_get_set_visibility():
input_file = 'tests/data/models/liver.ply'
model = VTKSurfaceModel(input_file, colors.red)
assert (isinstance(model.get_visibility(), bool))
assert (model.get_visibility())
model.set_visibility(False)
assert (not model.get_visibility())
model.set_visibility(True)
assert (model.get_visibility())
def test_set_model_transform_is_used():
model = VTKSurfaceModel(None, (1.0, 0.0, 1.0))
vtk_matrix = vtk.vtkMatrix4x4()
vtk_matrix.Identity()
vtk_matrix.SetElement(0, 0, 2) # i.e. not identity
model.set_model_transform(vtk_matrix)
result = model.get_model_transform()
assert result is not None
assert result.GetElement(0, 0) == vtk_matrix.GetElement(0, 0)
def test_valid_set_texture_with_jpg_format(vtk_overlay_with_gradient_image):
input_file = 'tests/data/models/liver.ply'
model = VTKSurfaceModel(input_file, colors.red)
model.set_texture('tests/data/images/image0232.jpg')
image, widget, _, app = vtk_overlay_with_gradient_image
widget.add_vtk_actor(model.actor)
widget.show()
#app.exec_()
return model
def test_set_texture_regression(vtk_overlay_with_gradient_image):
in_github_ci = os.environ.get('CI')
in_gitlab_ci = os.environ.get('GITLAB_CI')
print("Gitlab_CI: " + str(in_gitlab_ci))
print("Github CI: " + str(in_github_ci))
if sys.platform == "darwin":
pytest.skip("Test not working on Mac runner \
because the widget size is different")
if in_github_ci and sys.platform.startswith("linux"):
pytest.skip("Test not working on Linux runner \
because of unknown issue, see #60.")
if in_github_ci and sys.platform.startswith("win"):
pytest.skip("Skip on Windows on GitHub CI (use of MESA messes up \
result")
input_file = 'tests/data/models/liver.ply'
model = VTKSurfaceModel(input_file, colors.red)
model.set_texture('tests/data/images/image0232.png')
image, widget, _, _, app = vtk_overlay_with_gradient_image
widget.resize(400, 400)
widget.add_vtk_actor(model.actor)
widget.show()
# Read the saved scene and compare it with the current scene.
screenshot_filename = 'tests/data/images/set_texture_test.png'
screenshot = cv2.imread(screenshot_filename)
# OpenCV uses BGR while VTK uses RGB.
screenshot = cv2.cvtColor(screenshot, cv2.COLOR_BGR2RGB)
current_scene = widget.convert_scene_to_numpy_array()
tmp_dir = 'tests/output'
if not os.path.isdir(tmp_dir):
os.makedirs(tmp_dir)
cv2.imwrite(os.path.join(tmp_dir, 'screenshot.png'), screenshot)
cv2.imwrite(os.path.join(tmp_dir, 'current_scene.png'), current_scene)
# As the rendered images in Ubuntu, Mac and Windows are different,
# i.e., the pixel values are slightly different at the same location,
# we add some threshold for comparison.
# It checks if the number of values (in any channel)
# that are different by more than 3 is less than 5 per cent
# of the total number of pixels in the image.
diff = abs(screenshot - current_scene)
assert (np.sum(
(diff > 3).astype(int)) / (screenshot.shape[0] * screenshot.shape[1]) *
screenshot.shape[2]) < 0.05
def test_extract_points_and_normals_as_numpy_array():
input_file = 'tests/data/models/Prostate.vtk'
model = VTKSurfaceModel(input_file, colors.red)
number_of_points = model.get_number_of_points()
points = model.get_points_as_numpy()
assert isinstance(points, np.ndarray)
assert points.shape[0] == number_of_points
assert points.shape[1] == 3
normals = model.get_normals_as_numpy()
assert isinstance(normals, np.ndarray)
assert normals.shape[0] == number_of_points
assert normals.shape[1] == 3
def test_set_texture_regression(vtk_overlay_with_gradient_image):
in_github_ci = os.environ.get('CI')
in_gitlab_ci = os.environ.get('GITLAB_CI')
print("Gitlab_CI: " + str(in_gitlab_ci))
print("Github CI: " + str(in_github_ci))
if sys.platform == "darwin":
pass
#pytest.skip("Test not working on Mac runner \
# because the widget size is different")
if in_github_ci and sys.platform.startswith("linux"):
pass
#pytest.skip("Test not working on Linux runner \
# because of unknown issue, see #60.")
if in_github_ci and sys.platform.startswith("win"):
pass
#pytest.skip("Skip on Windows on GitHub CI (use of MESA messes up \
# result")
input_file = 'tests/data/models/liver.ply'
model = VTKSurfaceModel(input_file, colors.red)
model.set_texture('tests/data/images/image0232.png')
image, widget, _, app = vtk_overlay_with_gradient_image
widget.resize(400, 400)
widget.add_vtk_actor(model.actor)
widget.show()
# Read the saved scene and compare it with the current scene.
screenshot_filename = 'tests/data/images/set_texture_test.png'
screenshot = cv2.imread(screenshot_filename)
# OpenCV uses BGR while VTK uses RGB.
screenshot = cv2.cvtColor(screenshot, cv2.COLOR_BGR2RGB)
current_scene = widget.convert_scene_to_numpy_array()
tmp_dir = 'tests/output'
if not os.path.isdir(tmp_dir):
os.makedirs(tmp_dir)
cv2.imwrite(os.path.join(tmp_dir, 'screenshot.png'), screenshot)
cv2.imwrite(os.path.join(tmp_dir, 'current_scene.png'), current_scene)
# As the rendered images in Ubuntu, Mac and Windows are different, we'll
# use the are similar function from sksurgery image
assert are_similar(screenshot,
current_scene,
threshold=0.995,
metric=cv2.TM_CCOEFF_NORMED,
mean_threshold=0.005)
def test_regression_test1():
"""A regression test with manually init"""
parameters = [136.0, 151.0, -91.0, 8.0]
model = VTKSurfaceModel("data/CT_Level_1.vtp", [1., 0., 0.])
x_values = model.get_points_as_numpy()[:, 0]
y_values = model.get_points_as_numpy()[:, 1]
z_values = model.get_points_as_numpy()[:, 2]
result = sphere_fitting.fit_sphere_least_squares(x_values, y_values,
z_values, parameters)
numpy.testing.assert_approx_equal(result.x[0], 136.571, significant=3)
numpy.testing.assert_approx_equal(result.x[1], 151.973, significant=3)
numpy.testing.assert_approx_equal(result.x[2], -95.518, significant=3)
numpy.testing.assert_approx_equal(result.x[3], 8.119, significant=3)
def run_demo(model_file_name, output="", configfile=False):
""" Run the application """
model = VTKSurfaceModel(model_file_name, [1., 0., 0.])
x_values = model.get_points_as_numpy()[:, 0]
y_values = model.get_points_as_numpy()[:, 1]
z_values = model.get_points_as_numpy()[:, 2]
initial_parameters = [
mean(x_values),
mean(y_values),
mean(z_values),
std(x_values)
]
bounds = ((-inf, -inf, -inf, -inf), (inf, inf, inf, inf))
if configfile:
configurer = ConfigurationManager(configfile)
configuration = configurer.get_copy()
if "initial values" in configuration:
initial_parameters = configuration.get("initial values")
if "bounds" in configuration:
bounds = configuration.get("bounds")
if "fixed radius" in configuration:
radius = configuration.get("fixed radius")
bounds = ((-inf, -inf, -inf, radius - 1e-6), (inf, inf, inf,
radius + 1e-6))
result = sphere_fitting.fit_sphere_least_squares(x_values,
y_values,
z_values,
initial_parameters,
bounds=bounds)
print("Result is {}".format(result))
if output != "":
sphere = vtk.vtkSphereSource()
sphere.SetCenter(result.x[0], result.x[1], result.x[2])
sphere.SetRadius(result.x[3])
sphere.SetThetaResolution(60)
sphere.SetPhiResolution(60)
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName(output)
writer.SetInputData(sphere.GetOutput())
sphere.Update()
writer.Write()
def test_valid_set_texture_with_png_format(vtk_overlay_with_gradient_image):
input_file = 'tests/data/models/liver.ply'
model = VTKSurfaceModel(input_file, colors.red)
model.set_texture('tests/data/images/image0232.png')
image, widget, _, app = vtk_overlay_with_gradient_image
widget.add_vtk_actor(model.actor)
widget.show()
# Save the scene to a file for parity check.
# See test_set_texture_regression() below.
# This line should be run again if the code is (purposefully) changed.
#screenshot_filename = 'tests/data/images/set_texture_test.png'
#widget.save_scene_to_file(screenshot_filename)
#app.exec_()
return model
def make_source_and_target():
"""
Helper to make a source and target.
"""
filename = "data/liverphantom-iso=-130_cleaned2_mc_smooth2.stl"
colour = [1.0, 1.0, 1.0]
source_poly = VTKSurfaceModel(filename, colour)
target_points = source_poly.source.GetPoints()
target_vtk_poly = vtkPolyData()
target_vtk_poly.SetPoints(target_points)
return source_poly.source, target_vtk_poly
def test_regression_test2():
"""A regression test with fixed radius"""
model = VTKSurfaceModel("data/US_Sphere_2.vtp", [1., 0., 0.])
x_values = model.get_points_as_numpy()[:, 0]
y_values = model.get_points_as_numpy()[:, 1]
z_values = model.get_points_as_numpy()[:, 2]
parameters = [
numpy.mean(x_values),
numpy.mean(y_values),
numpy.mean(z_values), 4.5
]
radius = 4.5
epsilon = 1e-6
bounds = ((-numpy.inf, -numpy.inf, -numpy.inf, radius - epsilon),
(numpy.inf, numpy.inf, numpy.inf, radius + epsilon))
result = sphere_fitting.fit_sphere_least_squares(x_values,
y_values,
z_values,
parameters,
bounds=bounds)
numpy.testing.assert_approx_equal(result.x[0], 86.474, significant=3)
numpy.testing.assert_approx_equal(result.x[1], -97.243, significant=3)
numpy.testing.assert_approx_equal(result.x[2], -208.528, significant=3)
numpy.testing.assert_approx_equal(result.x[3], 4.500, significant=3)
def test_flat_shaded_on_coloured_background(setup_vtk_overlay_window):
#input_file = 'tests/data/models/liver.ply' # Don't use this one. It renders Grey, regardless of what colour you create it at.
input_file = 'tests/data/liver/liver_sub.ply'
model = VTKSurfaceModel(input_file, colors.white)
widget, _, app = setup_vtk_overlay_window
widget.add_vtk_actor(model.actor)
model.set_no_shading(True)
widget.background_renderer.SetBackground(0, 0, 1)
widget.show()
model.set_no_shading(False)
widget.background_renderer.SetBackground(0, 1, 0)
widget.show()
def test_invalid_because_color_blue_not_float():
with pytest.raises(TypeError):
VTKSurfaceModel('tests/data/models/Prostate.vtk', (0.0, 0.0, 1))
def test_invalid_because_color_green_too_low():
with pytest.raises(ValueError):
VTKSurfaceModel('tests/data/models/Prostate.vtk', (0.0, -1.0, 0.0))
def test_its_valid_for_null_filename():
model = VTKSurfaceModel(None, colors.red)
assert model.source is not None
def test_invalid_because_filename_invalid():
with pytest.raises(TypeError):
VTKSurfaceModel(9, colors.red)
def test_invalid_because_visibility_not_bool():
with pytest.raises(TypeError):
VTKSurfaceModel('tests/data/models/Prostate.vtk', (1.0, 0.0, 1.0),
visibility=1.0)
def test_invalid_because_model_file_format():
input_file = 'tox.ini'
with pytest.raises(ValueError):
VTKSurfaceModel(input_file, colors.red)
def test_invalid_because_pickable_not_bool():
with pytest.raises(TypeError):
VTKSurfaceModel('tests/data/models/Prostate.vtk', (1.0, 0.0, 1.0),
pickable=1.0)
def test_ensure_setter_and_getter_set_something():
model = VTKSurfaceModel(None, (1.0, 0.0, 1.0))
assert model.get_name() == ""
model.set_name("banana")
assert model.get_name() == "banana"
def test_valid_stl_results_in_vtkstlreader():
input_file = 'tests/data/models/Fiducial.stl'
model = VTKSurfaceModel(input_file, colors.red)
assert isinstance(model.reader, vtk.vtkSTLReader)
def test_invalid_set_texture_because_texture_filename_empty():
input_file = 'tests/data/models/liver.ply'
model = VTKSurfaceModel(input_file, colors.red)
with pytest.raises(ValueError):
model.set_texture('')
def test_invalid_set_texture_because_texture_file_format():
input_file = 'tests/data/models/liver.ply'
model = VTKSurfaceModel(input_file, colors.red)
texture_file = 'tox.ini'
with pytest.raises(ValueError):
model.set_texture(texture_file)
def test_invalid_because_name_is_none():
with pytest.raises(TypeError):
model = VTKSurfaceModel(None, (1.0, 0.0, 1.0))
model.set_name(None)
def test_invalid_because_name_is_empty():
with pytest.raises(ValueError):
model = VTKSurfaceModel(None, (1.0, 0.0, 1.0))
model.set_name("")
def test_invalid_because_color_blue_too_high():
with pytest.raises(ValueError):
VTKSurfaceModel('tests/data/models/Prostate.vtk', (1.0, 0.0, 1.1))
def test_valid_ply_results_in_vtkplyreader():
input_file = 'tests/data/models/Tumor.ply'
model = VTKSurfaceModel(input_file, colors.red)
assert isinstance(model.reader, vtk.vtkPLYReader)
def test_invalid_because_opacity_not_float():
with pytest.raises(TypeError):
VTKSurfaceModel('tests/data/models/Prostate.vtk', (1.0, 0.0, 1.0),
opacity=1)
def valid_vtk_model():
input_file = 'tests/data/models/Prostate.vtk'
model = VTKSurfaceModel(input_file, colors.red)
return model
