def test_image_view_integration_filter(self, qtbot, tmp_path,
filter_value):
settings = BaseSettings(tmp_path)
ch_property = ChannelProperty(settings, "test")
image_view = ImageView(settings, ch_property, "test")
# image_view.show()
qtbot.addWidget(image_view)
qtbot.addWidget(ch_property)
image = TiffImageReader.read_image(
PartSegData.segmentation_analysis_default_image)
with qtbot.waitSignal(image_view.image_added, timeout=10**6):
settings.image = image
image_view.channel_control.set_active(1)
def check_parameters(name, index):
return name == "test" and index == 1
if filter_value is NoiseFilterType.No:
with qtbot.waitSignal(
image_view.channel_control.coloring_update
), qtbot.waitSignal(image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.use_filter.setCurrentEnum(NoiseFilterType.Gauss)
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.use_filter.setCurrentEnum(filter_value)
image4 = image_view.viewer_widget.screenshot()
assert (filter_value != NoiseFilterType.No and
np.any(image4 != 255)) or (filter_value == NoiseFilterType.No
and np.any(image4 == 255))
def __init__(self, settings: BaseSettings, parent=None):
super().__init__(parent)
self.settings = settings
self.file_list = QListWidget()
self.file_list.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.cancel_btn = QPushButton("Cancel", clicked=self.reject)
self.load_btn = QPushButton("Load", clicked=self.accept)
for name_list, method in settings.get_last_files_multiple():
entry = f"{name_list[0]} {method}"
item = QListWidgetItem(entry, self.file_list)
item.setData(Qt.UserRole, (name_list, method))
last_set = {(tuple(x), y)
for x, y in settings.get_last_files_multiple()}
for name_list, method in settings.get_last_files():
if (tuple(name_list), method) in last_set:
continue
entry = f"{name_list[0]} {method}"
item = QListWidgetItem(entry, self.file_list)
item.setData(Qt.UserRole, (name_list, method))
layout = QGridLayout()
layout.addWidget(QLabel("Select files"))
layout.addWidget(self.file_list, 1, 0, 1, 2)
layout.addWidget(self.cancel_btn, 2, 0)
layout.addWidget(self.load_btn, 2, 1)
self.setLayout(layout)
self.resize(
*self.settings.get_from_profile("multiple_files_dialog_size", (
self.size().width(), self.size().height())))
def test_channels(self, tmp_path, qtbot):
settings = BaseSettings(tmp_path)
assert not settings.has_channels
assert settings.channels == 0
settings.image = Image(np.zeros((10, 10, 2), dtype=np.uint8), (1, 1), axes_order="XYC")
assert settings.has_channels
assert settings.channels == 2
settings.image = Image(np.zeros((10, 10, 1), dtype=np.uint8), (1, 1), axes_order="XYC")
assert not settings.has_channels
assert settings.channels == 1
def test_empty_history(self, tmp_path):
settings = BaseSettings(tmp_path)
assert settings.history_size() == 0
assert settings.history_redo_size() == 0
with pytest.raises(IndexError):
settings.history_current_element()
with pytest.raises(IndexError):
settings.history_next_element()
settings.history_pop()
assert settings.history_index == -1
def test_image_view_integration(self, qtbot, tmp_path):
settings = BaseSettings(tmp_path)
channel_property = ChannelProperty(settings, "test")
image_view = ImageView(settings, channel_property, "test")
qtbot.addWidget(channel_property)
qtbot.addWidget(image_view)
color_list = PColormapList(settings, ["test"])
qtbot.addWidget(color_list)
image = TiffImageReader.read_image(
PartSegData.segmentation_analysis_default_image)
with qtbot.wait_signal(image_view.image_added, timeout=10**6):
settings.image = image
color_list.refresh()
assert image_view.channel_control.channels_count == image.channels
assert len(color_list.blocked()) == image.channels
block_count = 0
for el in settings.colormap_dict.keys():
widget = color_list.get_colormap_widget(el)
assert widget.is_checked or el not in starting_colors
if not widget.checked.isEnabled():
block_count += 1
assert block_count == image.channels
image_view.channel_control.change_selected_color(0, "Grayscale")
assert len(color_list.blocked()) == image.channels
assert "Grayscale" in color_list.blocked()
color_list.refresh()
assert color_list.get_colormap_widget(
"Grayscale").checked.isEnabled() is False
# this lines test if after refresh of widget checkbox stays checkable
block_count = 0
for el in settings.colormap_dict.keys():
widget = color_list.get_colormap_widget(el)
assert widget.is_checked or el not in starting_colors
if not widget.checked.isEnabled():
block_count += 1
assert block_count == image.channels
def test_verify_image(self):
assert BaseSettings.verify_image(Image(np.zeros((10, 10, 2), dtype=np.uint8), (1, 1), axes_order="XYC"))
with pytest.raises(SwapTimeStackException):
BaseSettings.verify_image(
Image(np.zeros((2, 10, 10), dtype=np.uint8), (1, 1, 1), axes_order="TXY"), silent=False
)
im = BaseSettings.verify_image(Image(np.zeros((2, 10, 10), dtype=np.uint8), (1, 1, 1), axes_order="TXY"))
assert not im.is_time
assert im.times == 1
assert im.is_stack
assert im.layers == 2
with pytest.raises(TimeAndStackException):
BaseSettings.verify_image(Image(np.zeros((2, 2, 10, 10), dtype=np.uint8), (1, 1, 1), axes_order="TZXY"))
def test_set_roi(self, tmp_path, qtbot):
settings = BaseSettings(tmp_path)
roi = np.zeros((10, 10), dtype=np.uint8)
settings.image = Image(roi, (1, 1), axes_order="XY")
roi[1:5, 1:5] = 1
roi[5:-1, 5:-1] = 3
with qtbot.waitSignal(settings.roi_changed):
settings.roi = roi
assert len(settings.roi_info.bound_info) == 2
assert set(settings.roi_info.bound_info) == {1, 3}
assert settings.roi_info.alternative == {}
assert settings.roi_info.annotations == {}
with qtbot.waitSignal(settings.roi_clean):
settings.roi = None
assert settings.roi is None
settings.image = None
assert settings.image is not None
def test_clean_redo(self, tmp_path):
settings = BaseSettings(tmp_path)
for i in range(10):
settings.add_history_element(i)
for _ in range(5):
settings.history_pop()
settings.history_current_element()
settings.history_redo_clean()
settings.history_current_element()
def test_modifying_history(self, tmp_path):
settings = BaseSettings(tmp_path)
for i in range(10):
settings.add_history_element(i)
assert settings.history_size() == 10
assert settings.history_redo_size() == 0
with pytest.raises(IndexError):
settings.history_next_element()
for i in range(9, 5, -1):
assert settings.history_current_element() == i
assert settings.history_pop() == i
assert settings.history_current_element() == 5
assert settings.history_size() == 6
assert settings.history_redo_size() == 4
settings.add_history_element(7)
assert settings.history_size() == 7
assert settings.history_redo_size() == 0
def base_settings(image, tmp_path, measurement_profiles):
settings = BaseSettings(tmp_path)
settings.image = image
return settings
def test_shape(self, tmp_path):
settings = BaseSettings(tmp_path)
assert settings.image_shape == ()
settings.image = Image(np.zeros((10, 10, 2), dtype=np.uint8), (1, 1), axes_order="XYC")
assert settings.image_shape == (1, 1, 10, 10, 2)
def test_add_point(self, tmp_path, qtbot):
settings = BaseSettings(tmp_path)
with qtbot.waitSignal(settings.points_changed):
settings.points = [1, 2, 3]
def test_image_view_integration(self, qtbot, tmp_path):
settings = BaseSettings(tmp_path)
ch_property = ChannelProperty(settings, "test")
image_view = ImageView(settings, ch_property, "test")
# image_view.show()
qtbot.addWidget(image_view)
qtbot.addWidget(ch_property)
image = TiffImageReader.read_image(
PartSegData.segmentation_analysis_default_image)
with qtbot.waitSignals(
[settings.image_changed, image_view.image_added], timeout=10**6):
settings.image = image
channels_num = image.channels
assert image_view.channel_control.channels_count == channels_num
image_view.viewer_widget.screenshot()
image1 = image_view.viewer_widget.canvas.render()
assert np.any(image1 != 255)
image_view.channel_control.set_active(1)
ch_property.minimum_value.setValue(100)
ch_property.maximum_value.setValue(10000)
ch_property.filter_radius.setValue(0.5)
image2 = image_view.viewer_widget.canvas.render()
assert np.any(image2 != 255)
assert np.all(image1 == image2)
def check_parameters(name, index):
return name == "test" and index == 1
# Test fixed range
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.fixed.setChecked(True)
image1 = image_view.viewer_widget.canvas.render()
assert np.any(image1 != 255)
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.minimum_value.setValue(20)
image2 = image_view.viewer_widget.canvas.render()
assert np.any(image2 != 255)
assert np.any(image1 != image2)
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.maximum_value.setValue(11000)
image3 = image_view.viewer_widget.screenshot()
assert np.any(image3 != 255)
assert np.any(image2 != image3)
assert np.any(image1 != image3)
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.fixed.setChecked(False)
image1 = image_view.viewer_widget.screenshot()
assert np.any(image1 != 255)
assert np.any(image1 != image2)
assert np.any(image1 != image3)
# Test gauss
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.use_filter.set_value(NoiseFilterType.Gauss)
image4 = image_view.viewer_widget.screenshot()
assert np.any(image4 != 255)
assert np.any(image1 != image4)
assert np.any(image2 != image4)
assert np.any(image3 != image4)
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.filter_radius.setValue(1)
image5 = image_view.viewer_widget.screenshot()
assert np.any(image5 != 255)
assert np.any(image1 != image5)
assert np.any(image2 != image5)
assert np.any(image3 != image5)
assert np.any(image4 != image5)
# Test gauss and fixed range
ch_property.minimum_value.setValue(100)
ch_property.maximum_value.setValue(10000)
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.fixed.setChecked(True)
image1 = image_view.viewer_widget.screenshot()
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.minimum_value.setValue(10)
image2 = image_view.viewer_widget.screenshot()
assert np.any(image2 != 255)
assert np.any(image1 != image2)
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.maximum_value.setValue(11000)
image3 = image_view.viewer_widget.screenshot()
assert np.any(image3 != 255)
assert np.any(image2 != image3)
assert np.any(image1 != image3)
with qtbot.waitSignal(
image_view.channel_control.coloring_update), qtbot.waitSignal(
image_view.channel_control.change_channel,
check_params_cb=check_parameters):
ch_property.fixed.setChecked(False)
image1 = image_view.viewer_widget.screenshot()
assert np.any(image1 != 255)
assert np.any(image1 != image2)
assert np.any(image1 != image3)