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Merged
jo-mueller merged 19 commits into from
Feb 4, 2025
Merged

Fix cluster memorization #364

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1c58e12
added test for cluster memorization
jo-mueller Jan 29, 2025
10317f2
merged `get_data` function into `_replot function`
jo-mueller Jan 30, 2025
deb5089
merged `_get_data` function
jo-mueller Jan 30, 2025
1bd7d16
added `MANUAL_CLUSTER_ID` as feature to memorize a previous selection
jo-mueller Jan 30, 2025
402fff1
more explicit layer naming in test
jo-mueller Jan 30, 2025
f71382d
made point clouds of uneven size
jo-mueller Jan 30, 2025
d78de0c
used layers of uneven size in demo notebook
jo-mueller Jan 30, 2025
13e9ff2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 30, 2025
70723bf
return 'MANUAL_CLUSTER_ID' with all features and avoid adding to dro…
jo-mueller Jan 30, 2025
ea89793
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 30, 2025
756abe7
remove `MANUAL_CLUSTER_ID` only if it exists
jo-mueller Jan 30, 2025
cfd3b87
Merge branch 'fix-cluster-memorization' of https://github.com/BiAPoL/…
jo-mueller Jan 30, 2025
32f947a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 30, 2025
4c73c34
fixed adding features to dropdown
jo-mueller Jan 30, 2025
e16721e
Merge branch 'fix-cluster-memorization' of https://github.com/BiAPoL/…
jo-mueller Jan 30, 2025
7243c30
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 30, 2025
1a792f4
add a wait for update in test
jo-mueller Jan 30, 2025
b83d29b
Revert "add a wait for update in test"
jo-mueller Jan 30, 2025
aaf8f98
set biaplotter dependency to git repo for latest version
jo-mueller Feb 4, 2025
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261 changes: 243 additions & 18 deletions notebooks/demo_new_plotter.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,15 +18,7 @@
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"napari.manifest -> 'napari-vedo-bridge' could not be imported: The name field in the manifest ('napari-clusters-plotter') must match the package name ('napari-vedo-bridge')\n"
]
}
],
"outputs": [],
"source": [
"viewer = napari.Viewer()"
]
Expand All @@ -46,7 +38,7 @@
{
"data": {
"text/plain": [
"<Points layer 'points2' at 0x204f46b5c10>"
"<Points layer 'points2' at 0x12998840130>"
]
},
"execution_count": 3,
Expand All @@ -63,10 +55,10 @@
"frame = np.arange(n_timeframes).repeat(n_samples//n_timeframes)\n",
"# make some random points with random features\n",
"points = np.random.random((n_samples, 4))\n",
"points2 = np.random.random((n_samples, 4))\n",
"points2 = np.random.random((n_samples-1, 4))\n",
"\n",
"points[:, 0] = frame\n",
"points2[:, 0] = frame\n",
"points2[:, 0] = frame[:-1]\n",
"\n",
"features = pd.DataFrame({\n",
" 'frame': frame,\n",
Expand All @@ -76,13 +68,14 @@
" 'feature4': np.random.normal(size=n_samples, loc=loc),})\n",
"\n",
"features2 = pd.DataFrame({\n",
" 'frame': frame,\n",
" 'feature2': np.random.normal(size=n_samples, loc=-loc),\n",
" 'feature3': np.random.normal(size=n_samples, loc=-loc),\n",
" 'feature4': np.random.normal(size=n_samples, loc=-loc),})\n",
" 'frame': frame[:-1],\n",
" 'feature2': np.random.normal(size=n_samples-1, loc=-loc),\n",
" 'feature3': np.random.normal(size=n_samples-1, loc=-loc),\n",
" 'feature4': np.random.normal(size=n_samples-1, loc=-loc),})\n",
"\n",
"layer = napari.layers.Points(points, features=features, size=0.1, blending='translucent_no_depth')\n",
"layer2 = napari.layers.Points(points2, features=features2, size=0.1, translate=(0, 0, 2), blending='translucent_no_depth')\n",
"viewer.layers.clear()\n",
"viewer.add_layer(layer)\n",
"viewer.add_layer(layer2)\n"
]
Expand All @@ -105,7 +98,7 @@
{
"data": {
"text/plain": [
"<napari._qt.widgets.qt_viewer_dock_widget.QtViewerDockWidget at 0x2049456d3a0>"
"<napari._qt.widgets.qt_viewer_dock_widget.QtViewerDockWidget at 0x1299a10a820>"
]
},
"execution_count": 4,
Expand All @@ -118,6 +111,238 @@
"viewer.window.add_dock_widget(plotter_widget, area='right')"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>frame</th>\n",
" <th>feature2</th>\n",
" <th>feature3</th>\n",
" <th>feature4</th>\n",
" <th>MANUAL_CLUSTER_ID</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>0</td>\n",
" <td>-4.725088</td>\n",
" <td>-4.325642</td>\n",
" <td>-7.112442</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>0</td>\n",
" <td>-4.386041</td>\n",
" <td>-5.335577</td>\n",
" <td>-6.063437</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>0</td>\n",
" <td>-5.730792</td>\n",
" <td>-4.642161</td>\n",
" <td>-4.429953</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>0</td>\n",
" <td>-6.089492</td>\n",
" <td>-2.991715</td>\n",
" <td>-5.544447</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>0</td>\n",
" <td>-4.740159</td>\n",
" <td>-5.189429</td>\n",
" <td>-4.769790</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>94</th>\n",
" <td>4</td>\n",
" <td>-5.815555</td>\n",
" <td>-4.737373</td>\n",
" <td>-4.945831</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>95</th>\n",
" <td>4</td>\n",
" <td>-6.226173</td>\n",
" <td>-3.972162</td>\n",
" <td>-6.477352</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>96</th>\n",
" <td>4</td>\n",
" <td>-4.597238</td>\n",
" <td>-3.308072</td>\n",
" <td>-4.418548</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>97</th>\n",
" <td>4</td>\n",
" <td>-6.143753</td>\n",
" <td>-5.130647</td>\n",
" <td>-5.700410</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>98</th>\n",
" <td>4</td>\n",
" <td>-4.029651</td>\n",
" <td>-5.172430</td>\n",
" <td>-5.987246</td>\n",
" <td>1</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>99 rows × 5 columns</p>\n",
"</div>"
],
"text/plain": [
" frame feature2 feature3 feature4 MANUAL_CLUSTER_ID\n",
"0 0 -4.725088 -4.325642 -7.112442 1\n",
"1 0 -4.386041 -5.335577 -6.063437 1\n",
"2 0 -5.730792 -4.642161 -4.429953 1\n",
"3 0 -6.089492 -2.991715 -5.544447 0\n",
"4 0 -4.740159 -5.189429 -4.769790 1\n",
".. ... ... ... ... ...\n",
"94 4 -5.815555 -4.737373 -4.945831 0\n",
"95 4 -6.226173 -3.972162 -6.477352 0\n",
"96 4 -4.597238 -3.308072 -4.418548 0\n",
"97 4 -6.143753 -5.130647 -5.700410 0\n",
"98 4 -4.029651 -5.172430 -5.987246 1\n",
"\n",
"[99 rows x 5 columns]"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"viewer.layers[-1].features"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(99, 4)"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"viewer.layers[1].data.shape"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0,\n",
" 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0,\n",
" 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0,\n",
" 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1,\n",
" 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0])"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"viewer.layers.selection.active = viewer.layers[-1]\n",
"plotter_widget._selectors['x'].setCurrentText('feature3')\n",
"plotter_widget.plotting_widget.active_artist.color_indices = np.random.randint(0, 2, n_samples)\n",
"plotter_widget.plotting_widget.active_artist.color_indices"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0,\n",
" 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0,\n",
" 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0,\n",
" 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1,\n",
" 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0])"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"viewer.layers.selection.active = viewer.layers[0]\n",
"plotter_widget.plotting_widget.active_artist.color_indices"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 6,
Expand Down Expand Up @@ -377,7 +602,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.19"
"version": "3.9.18"
}
},
"nbformat": 4,
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ dependencies = [
"scikit-image",
"superqt",
"scipy",
"biaplotter"
"biaplotter@https://github.com/BiAPoL/biaplotter/archive/refs/heads/main.zip"
]


Expand Down
47 changes: 28 additions & 19 deletions src/napari_clusters_plotter/_new_plotter_widget.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -152,8 +152,24 @@ def _replot(self):
if self.x_axis == "" or self.y_axis == "":
return

data_to_plot = self._get_data()
self.plotting_widget.active_artist.data = data_to_plot
# retrieve the data from the selected layers
features = self._get_features()
x_data = features[self.x_axis].values
y_data = features[self.y_axis].values

# # if no hue is selected, set it to 0
# if self.hue_axis == "None":
# hue = np.zeros(len(features))
# elif self.hue_axis != "":
# hue = features[self.hue_axis].values

self.plotting_widget.active_artist.data = np.stack(
[x_data, y_data], axis=1
)
if "MANUAL_CLUSTER_ID" in features.columns:
self.plotting_widget.active_artist.color_indices = features[
"MANUAL_CLUSTER_ID"
].values

def _checkbox_status_changed(self):
self._replot()
Expand Down Expand Up @@ -264,22 +280,6 @@ def n_selected_layers(self) -> int:
"""
return len(list(self.viewer.layers.selection))

def _get_data(self) -> np.ndarray:
"""
Get the data from the selected layers features.
"""
features = self._get_features()
x_data = features[self.x_axis].values
y_data = features[self.y_axis].values

# # if no hue is selected, set it to 0
# if self.hue_axis == "None":
# hue = np.zeros(len(features))
# elif self.hue_axis != "":
# hue = features[self.hue_axis].values

return np.stack([x_data, y_data], axis=1)

def _on_update_layer_selection(
self, event: napari.utils.events.Event
) -> None:
Expand Down Expand Up @@ -327,7 +327,11 @@ def _update_feature_selection(
self._selectors[dim].clear()

for dim in ["x", "y", "hue"]:
self._selectors[dim].addItems(sorted(self.common_columns))
features_to_add = sorted(self.common_columns)
if "MANUAL_CLUSTER_ID" in features_to_add:
features_to_add.remove("MANUAL_CLUSTER_ID")

self._selectors[dim].addItems(features_to_add)

# it should always be possible to select no color
self._selectors["hue"].addItem("None")
Expand Down Expand Up @@ -361,6 +365,11 @@ def _color_layer_by_cluster_id(self):
].index
_apply_layer_color(selected_layer, colors[layer_indices])

# store cluster indeces in the features table
selected_layer.features["MANUAL_CLUSTER_ID"] = color_indices[
layer_indices
]

def _reset(self):
"""
Reset the selection in the current plotting widget.
Expand Down
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