8000 Use features instead of properties internally by andy-sweet · Pull Request #7084 · napari/napari · GitHub
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Use features instead of properties internally #7084

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Use features instead of properties internally #7084

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7514d50
Update qt layer tests
andy-sweet Jul 8, 2024
4e88ea6
Use in tracks and vectors controls
andy-sweet Jul 8, 2024
ee2adb9
Update vispy points
andy-sweet Jul 8, 2024
4d6e0f5
Use in vispy shapes tests
andy-sweet Jul 8, 2024
67f590b
Update builtin point read and write
andy-sweet Jul 8, 2024
c4df774
Simply test comparison
andy-sweet Jul 8, 2024
cec88a8
Use features in tracks layer
andy-sweet Jul 8, 2024
073dad5
Use features in points laye
andy-sweet Jul 8, 2024
279c979
Use features in shapes
andy-sweet Jul 8, 2024
d90d3e7
Use features in vectors layer
andy-sweet Jul 8, 2024
689269c
Remove last usage
andy-sweet Jul 8, 2024
21746e1
Fix property
andy-sweet Jul 8, 2024
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22 changes: 11 additions & 11 deletions napari/_qt/layer_controls/_tests/test_qt_layer_controls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ class LayerTypeWithData(NamedTuple):
type: type[Layer]
data: np.ndarray
colormap: Optional[DirectLabelColormap]
properties: Optional[dict]
features: Optional[dict]
expected_isinstance: type[QtLayerControlsContainer]


Expand All @@ -62,7 +62,7 @@ class LayerTypeWithData(NamedTuple):
type=Image,
data=np.random.rand(8, 8),
colormap=None,
properties=None,
features=None,
expected_isinstance=QtImageControls,
)
_LABELS_WITH_DIRECT_COLORMAP = LayerTypeWithData(
Expand All @@ -78,28 +78,28 @@ class LayerTypeWithData(NamedTuple):
None: 'black',
}
),
properties=None,
features=None,
expected_isinstance=QtLabelsControls,
)
_LABELS = LayerTypeWithData(
type=Labels,
data=np.random.randint(5, size=(10, 15)),
colormap=None,
properties=None,
features=None,
expected_isinstance=QtLabelsControls,
)
_POINTS = LayerTypeWithData(
type=Points,
data=np.random.random((5, 2)),
colormap=None,
properties=None,
features=None,
expected_isinstance=QtPointsControls,
)
_SHAPES = LayerTypeWithData(
type=Shapes,
data=np.random.random((10, 4, 2)),
colormap=None,
properties=None,
features=None,
expected_isinstance=QtShapesControls,
)
_SURFACE = LayerTypeWithData(
Expand All @@ -110,14 +110,14 @@ class LayerTypeWithData(NamedTuple):
np.random.random(10),
),
colormap=None,
properties=None,
features=None,
expected_isinstance=QtSurfaceControls,
)
_TRACKS = LayerTypeWithData(
type=Tracks,
data=np.zeros((2, 4)),
colormap=None,
properties={
features={
'track_id': [0, 0],
'time': [0, 0],
'speed': [50, 30],
Expand All @@ -128,7 +128,7 @@ class LayerTypeWithData(NamedTuple):
type=Vectors,
data=np.zeros((2, 2, 2)),
colormap=None,
properties=None,
features=None,
expected_isinstance=QtVectorsControls,
)
_LINES_DATA = np.random.random((6, 2, 2))
Expand All @@ -142,10 +142,10 @@ def _create_layer_controls(layer_type_with_data):
layer_type_with_data.data,
colormap=layer_type_with_data.colormap,
)
elif layer_type_with_data.properties:
elif layer_type_with_data.features:
layer = layer_type_with_data.type(
layer_type_with_data.data,
properties=layer_type_with_data.properties,
features=layer_type_with_data.features,
)
else:
layer = layer_type_with_data.type(layer_type_with_data.data)
Expand Down
42 changes: 19 additions & 23 deletions napari/_qt/layer_controls/_tests/test_qt_tracks_layer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,28 +12,26 @@ def null_data() -> np.ndarray:


@pytest.fixture()
def properties() -> dict[str, list]:
def features() -> dict[str, list]:
return {
'track_id': [0, 0],
'time': [0, 0],
'speed': [50, 30],
}


def test_tracks_controls_color_by(null_data, properties, qtbot):
def test_tracks_controls_color_by(null_data, features, qtbot):
"""Check updating of the color_by combobox."""
inital_color_by = 'time'
initial_color_by = 'time'
with pytest.warns(UserWarning) as wrn:
layer = Tracks(
null_data, properties=properties, color_by=inital_color_by
)
layer = Tracks(null_data, features=features, color_by=initial_color_by)
assert "Previous color_by key 'time' not present" in str(wrn[0].message)
qtctrl = QtTracksControls(layer)
qtbot.addWidget(qtctrl)

# verify the color_by argument is initialized correctly
assert layer.color_by == inital_color_by
assert qtctrl.color_by_combobox.currentText() == inital_color_by
assert layer.color_by == initial_color_by
assert qtctrl.color_by_combobox.currentText() == initial_color_by

# update color_by from the layer model
layer_update_color_by = 'speed'
Expand All @@ -52,44 +50,42 @@ def test_tracks_controls_color_by(null_data, properties, qtbot):


@pytest.mark.parametrize('color_by', ['track_id', 'speed'])
def test_color_by_same_after_properties_change(
null_data, properties, color_by, qtbot
def test_color_by_same_after_features_change(
null_data, features, color_by, qtbot
):
"""See https://github.com/napari/napari/issues/5330"""
layer = Tracks(null_data, properties=properties)
layer = Tracks(null_data, features=features)
layer.color_by = color_by
controls = QtTracksControls(layer)
qtbot.addWidget(controls)
assert controls.color_by_combobox.currentText() == color_by

# Change the properties value by removing the time column.
layer.properties = {
'track_id': properties['track_id'],
'speed': properties['speed'],
# Change the features value by removing the time column.
layer.features = {
'track_id': features['track_id'],
'speed': features['speed'],
}

assert layer.color_by == color_by
assert controls.color_by_combobox.currentText() == color_by


def test_color_by_missing_after_properties_change(
null_data, properties, qtbot
):
def test_color_by_missing_after_features_change(null_data, features, qtbot):
"""See https://github.com/napari/napari/issues/5330"""
layer = Tracks(null_data, properties=properties)
layer = Tracks(null_data, features=features)
layer.color_by = 'time'
controls = QtTracksControls(layer)
qtbot.addWidget(controls)
assert controls.color_by_combobox.currentText() == 'time'

# Change the properties value by removing the time column.
# Change the features value by removing the time column.
with pytest.warns(
UserWarning,
match="Previous color_by key 'time' not present in features. Falling back to track_id",
):
layer.properties = {
'track_id': properties['track_id'],
'speed': properties['speed'],
layer.features = {
'track_id': features['track_id'],
'speed': features['speed'],
}

assert layer.color_by == 'track_id'
Expand Down
12 changes: 6 additions & 6 deletions napari/_qt/layer_controls/qt_tracks_controls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,13 +51,13 @@ def __init__(self, layer) -> None:
self.layer.events.tail_width.connect(self._on_tail_width_change)
self.layer.events.tail_length.connect(self._on_tail_length_change)
self.layer.events.head_length.connect(self._on_head_length_change)
self.layer.events.properties.connect(self._on_properties_change)
self.layer.events.features.connect(self._on_features_change)
self.layer.events.colormap.connect(self._on_colormap_change)

# combo box for track coloring, we can get these from the properties
# combo box for track coloring, we can get these from the features
# keys
self.color_by_combobox = QComboBox()
self.color_by_combobox.addItems(self.layer.properties_to_color_by)
self.color_by_combobox.addItems(self.layer.features_to_color_by)

self.colormap_combobox = QComboBox()
for name, colormap in AVAILABLE_COLORMAPS.items():
Expand Down Expand Up @@ -136,11 +136,11 @@ def _on_head_length_change(self):
value = self.layer.head_length
self.head_length_slider.setValue(value)

def _on_properties_change(self):
"""Change the properties that can be used to color the tracks."""
def _on_features_change(self):
"""Change the features that can be used to color the tracks."""
with qt_signals_blocked(self.color_by_combobox):
self.color_by_combobox.clear()
self.color_by_combobox.addItems(self.layer.properties_to_color_by)
self.color_by_combobox.addItems(self.layer.features_to_color_by)
self._on_color_by_change()

def _on_colormap_change(self):
Expand Down
68 changes: 26 additions & 42 deletions napari/_qt/layer_controls/qt_vectors_controls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,10 +53,10 @@ class QtVectorsControls(QtLayerControls):
Dropdown widget to select vector_style for the vectors.
color_mode_comboBox : qtpy.QtWidgets.QComboBox
Dropdown widget to select edge_color_mode for the vectors.
color_prop_box : qtpy.QtWidgets.QComboBox
Dropdown widget to select _edge_color_property for the vectors.
edge_prop_label : qtpy.QtWidgets.QLabel
Label for color_prop_box
color_feature_box : qtpy.QtWidgets.QComboBox
Dropdown widget to select the edge_color feature for the vectors.
edge_feature_label : qtpy.QtWidgets.QLabel
Label for color_feature_box
layer : napari.layers.Vectors
An instance of a napari Vectors layer.
outOfSliceCheckBox : qtpy.QtWidgets.QCheckBox
Expand All @@ -78,15 +78,14 @@ class QtVectorsControls(QtLayerControls):
def __init__(self, layer) -> None:
super().__init__(layer)

# dropdown to select the property for mapping edge_color
color_properties = self._get_property_values()
self.color_prop_box = QComboBox(self)
self.color_prop_box.currentTextChanged.connect(
self.change_edge_color_property
# dropdown to select the feature for mapping edge_color
self.color_feature_box = QComboBox(self)
self.color_feature_box.currentTextChanged.connect(
self.change_edge_color_feature
)
self.color_prop_box.addItems(color_properties)
self.color_feature_box.addItems(self.layer.features.columns)

self.edge_prop_label = QLabel(trans._('edge property:'))
self.edge_feature_label = QLabel(trans._('edge feature:'))

# vector direct color mode adjustment and widget
self.edgeColorEdit = QColorSwatchEdit(
Expand Down Expand Up @@ -157,7 +156,7 @@ def __init__(self, layer) -> None:
trans._('edge color mode:'), self.color_mode_comboBox
)
self.layout().addRow(self.edge_color_label, self.edgeColorEdit)
self.layout().addRow(self.edge_prop_label, self.color_prop_box)
self.layout().addRow(self.edge_feature_label, self.color_feature_box)
self.layout().addRow(trans._('out of slice:'), self.outOfSliceCheckBox)

self.layer.events.edge_width.connect(self._on_edge_width_change)
Expand All @@ -171,21 +170,20 @@ def __init__(self, layer) -> None:
)
self.layer.events.edge_color.connect(self._on_edge_color_change)

def change_edge_color_property(self, property_name: str):
"""Change edge_color_property of vectors on the layer model.
This property is the property the edge color is mapped to.
def change_edge_color_feature(self, feature: str):
"""Change edge_color feature of vectors on the layer model.

Parameters
----------
property_name : str
property to map the edge color to
feature : str
feature to map the edge color to
"""
mode = self.layer.edge_color_mode
try:
self.layer.edge_color = property_name
self.layer.edge_color = feature
self.layer.edge_color_mode = mode
except TypeError:
# if the selected property is the wrong type for the current color mode
# if the selected feature is the wrong type for the current color mode
# the color mode will be changed to the appropriate type, so we must update
self._on_edge_color_mode_change()
raise
Expand Down Expand Up @@ -282,30 +280,14 @@ def _update_edge_color_gui(self, mode: str):
if mode in {'cycle', 'colormap'}:
self.edgeColorEdit.setHidden(True)
self.edge_color_label.setHidden(True)
self.color_prop_box.setHidden(False)
self.edge_prop_label.setHidden(False)
self.color_feature_box.setHidden(False)
self.edge_feature_label.setHidden(False)

elif mode == 'direct':
self.edgeColorEdit.setHidden(False)
self.edge_color_label.setHidden(False)
self.color_prop_box.setHidden(True)
self.edge_prop_label.setHidden(True)

def _get_property_values(self):
"""Get the current property values from the Vectors layer

Returns
-------
property_values : np.ndarray
array of all of the union of the property names (keys)
in Vectors.properties and Vectors.property_choices

"""
property_choices = [*self.layer.property_choices]
properties = [*self.layer.properties]
property_values = np.union1d(property_choices, properties)

return property_values
self.color_feature_box.setHidden(True)
self.edge_feature_label.setHidden(True)

def _on_length_change(self):
"""Change length of vectors."""
Expand Down Expand Up @@ -354,7 +336,9 @@ def _on_edge_color_change(self):
ColorMode.CYCLE,
ColorMode.COLORMAP,
):
with qt_signals_blocked(self.color_prop_box):
with qt_signals_blocked(self.color_feature_box):
prop = self.layer._edge.color_properties.name
index = self.color_prop_box.findText(prop, Qt.MatchFixedString)
self.color_prop_box.setCurrentIndex(index)
index = self.color_feature_box.findText(
prop, Qt.MatchFixedString
)
self.color_feature_box.setCurrentIndex(index)
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