def test_load_projection_angles(self, getOpenFileName: mock.Mock,
StackSelectorDialog: mock.Mock,
ProjectionAngleFileParser: Mock,
QMessageBox: Mock):
StackSelectorDialog.return_value.exec.return_value = QDialog.Accepted
selected_stack = "selected_stack"
StackSelectorDialog.return_value.selected_stack = selected_stack
selected_file = "~/home/test/directory/selected_file.txt"
getOpenFileName.return_value = (selected_file, None)
proj_angles = ProjectionAngles(np.arange(0, 10))
ProjectionAngleFileParser.return_value.get_projection_angles.return_value = proj_angles
self.view.load_projection_angles()
StackSelectorDialog.assert_called_once_with(
main_window=self.view,
title='Stack Selector',
message=self.view.LOAD_PROJECTION_ANGLES_DIALOG_MESSAGE)
getOpenFileName.assert_called_once_with(
caption=self.view.LOAD_PROJECTION_ANGLES_FILE_DIALOG_CAPTION,
filter="All (*.*)")
self.presenter.add_projection_angles_to_sample.assert_called_once_with(
selected_stack, proj_angles)
QMessageBox.information.assert_called_once()
def test_set_projection_angles(self):
images = generate_images()
pangles = ProjectionAngles(list(range(0, 10)))
images.set_projection_angles(pangles)
actual = images.projection_angles()
self.assertEqual(10, len(actual.value))
self.assertAlmostEqual(images.projection_angles().value, pangles.value, places=4)
def projection_angles(self) -> ProjectionAngles:
angles = numpy.zeros(
len(self._data[IMATLogColumn.IMAGE_TYPE_IMAGE_COUNTER]))
for i, angle_str in enumerate(
self._data[IMATLogColumn.IMAGE_TYPE_IMAGE_COUNTER]):
assert "angle:" in angle_str
angles[i] = float(angle_str[angle_str.rfind(": ") + 1:])
return ProjectionAngles(numpy.deg2rad(angles))
def test_add_projection_angles_to_sample_no_stack(self):
proj_angles = ProjectionAngles(np.arange(0, 10))
stack_name = "stack name"
stack_mock = mock.MagicMock()
self.model.get_stack_by_name = stack_mock
stack_mock.return_value = None
self.assertRaises(RuntimeError, self.model.add_projection_angles_to_sample, stack_name, proj_angles)
stack_mock.assert_called_with(stack_name)
def generate(max_angle, number_radiograms) -> ProjectionAngles:
"""
Generate equidistance projection angles.
:param max_angle: The maximum angle of the tomography
:param number_radiograms: The number of radiograms in the tomography
:returns: list of projection angles
"""
return ProjectionAngles(
np.linspace(0, (math.tau / 360) * max_angle, number_radiograms))
def test_add_projection_angles_to_stack_success(self):
mock_stack = mock.Mock()
mock_stack.windowTitle.return_value = window_title = "window title"
stack_id = "stack-id"
self.presenter.stacks[stack_id] = mock_stack
projection_angles = ProjectionAngles(np.ndarray([1]))
self.presenter.add_projection_angles_to_sample(window_title,
projection_angles)
self.model.add_projection_angles_to_sample(stack_id, projection_angles)
def test_add_projection_angles_to_sample(self):
proj_angles = ProjectionAngles(np.arange(0, 10))
stack_name = "stack name"
stack_mock = mock.MagicMock()
self.model.get_stack_by_name = stack_mock
self.model.add_projection_angles_to_sample(stack_name, proj_angles)
stack_mock.assert_called_with(stack_name)
stack_mock.return_value.widget.return_value.presenter.images.set_projection_angles.assert_called_once_with(
proj_angles)
def test_add_projection_angles_to_sample(self):
proj_angles = ProjectionAngles(np.arange(0, 10))
images_id = "id"
get_images_mock = mock.MagicMock()
self.model.get_images_by_uuid = get_images_mock
self.model.add_projection_angles_to_sample(images_id, proj_angles)
get_images_mock.assert_called_with(images_id)
get_images_mock.return_value.set_projection_angles.assert_called_once_with(
proj_angles)
def test_add_projection_angles_to_sample_no_stack(self):
proj_angles = ProjectionAngles(np.arange(0, 10))
images_id = "id"
get_images_mock = mock.MagicMock()
self.model.get_images_by_uuid = get_images_mock
get_images_mock.return_value = None
self.assertRaises(RuntimeError,
self.model.add_projection_angles_to_sample,
images_id, proj_angles)
get_images_mock.assert_called_with(images_id)
def projection_angles(self) -> ProjectionAngles:
angles = numpy.zeros(
len(self._data[IMATLogColumn.IMAGE_TYPE_IMAGE_COUNTER]))
for i, angle_str in enumerate(
self._data[IMATLogColumn.IMAGE_TYPE_IMAGE_COUNTER]):
if "angle:" not in angle_str:
raise ValueError(
"Projection angles loaded from logfile do not have the correct formatting!"
)
angles[i] = float(angle_str[angle_str.rfind(": ") + 1:])
return ProjectionAngles(numpy.deg2rad(angles))
def projection_angles(self, max_angle: float = 360.0) -> ProjectionAngles:
"""
Return projection angles, in priority order:
- From a log
- From the manually loaded file with a list of angles
- Automatically generated with equidistant step
:param max_angle: The maximum angle up to which the angles will be generated.
Only used when the angles are generated, if they are provided
via a log or a file the argument will be ignored.
"""
if self._log_file is not None:
return self._log_file.projection_angles()
elif self._projection_angles is not None:
return self._projection_angles
else:
return ProjectionAngles(np.linspace(0, np.deg2rad(max_angle), self.num_projections))
def get_projection_angles(self) -> ProjectionAngles:
if "," in self.contents[0]:
if len(self.contents) > 2:
# allows a file that has a single line of CSV angles,
# and a new line after it
raise RuntimeError(self.ERROR_MESSAGE)
string_content = self.contents[0]
# Handles the angles provided as comma separated values
# angles are in CSV format 0,0.1,0.2...
values = np.deg2rad(
[float(angle.strip()) for angle in string_content.split(",")])
else:
# Handles the angles provided as a value per line
values = np.deg2rad(
[float(angle.strip()) for angle in self.contents])
return ProjectionAngles(values)
def test_create_new_stack_dataset_and_use_threshold_180(self):
dock_mock = self.view.create_stack_window.return_value
stack_visualiser_mock = mock.Mock()
self.dataset.sample.set_projection_angles(
ProjectionAngles(
np.linspace(0, np.pi, self.dataset.sample.num_images)))
dock_mock.widget.return_value = stack_visualiser_mock
dock_mock.windowTitle.return_value = "somename"
self.view.model_changed.emit = mock.Mock()
self.dataset.flat_before.filenames = ["filename"] * 10
self.dataset.dark_before.filenames = ["filename"] * 10
self.dataset.flat_after.filenames = ["filename"] * 10
self.dataset.dark_after.filenames = ["filename"] * 10
self.view.ask_to_use_closest_to_180.return_value = False
self.presenter.create_new_stack(self.dataset)
self.assertEqual(6, len(self.presenter.stacks))
self.view.model_changed.emit.assert_called_once()
def _create_sample_images(self):
"""
Creates the sample Images object.
:return: An Images object containing projections. If given, projection angles, pixel size, and 180deg are also
set.
"""
assert self.sample_array is not None
# Create sample array and Images object
self.sample_array = self.sample_array[self.view.start_widget.value(
):self.view.stop_widget.value():self.view.step_widget.value()]
sample_images = self._create_images(self.sample_array, "Projections")
# Set attributes
sample_images.pixel_size = int(self.view.pixelSizeSpinBox.value())
if self.projection_angles is not None:
sample_images.set_projection_angles(
ProjectionAngles(
self.projection_angles[self.view.start_widget.
value():self.view.stop_widget.value(
):self.view.step_widget.value()]))
return sample_images
def projection_angles(self) -> ProjectionAngles:
angles = numpy.zeros(len(self._data[IMATLogColumn.PROJECTION_ANGLE]))
angles[:] = self._data[IMATLogColumn.PROJECTION_ANGLE]
return ProjectionAngles(numpy.deg2rad(angles))
def test_add_projection_angles_to_stack_failure(self):
with self.assertRaises(RuntimeError):
self.presenter.add_projection_angles_to_sample(
"doesn't-exist", ProjectionAngles(np.ndarray([1])))
self.model.add_projection_angles_to_sample.assert_not_called()