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jo-muellerjo-mueller
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Merge pull request #364 from BiAPoL/fix-cluster-memorization
Fix cluster memorization
2 parents 577e351 + aaf8f98 commit 17d3204

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-38
lines changed

4 files changed

+355
-38
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‎notebooks/demo_new_plotter.ipynb‎

Lines changed: 243 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -18,15 +18,7 @@
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
21-
"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
26-
"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"
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]
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}
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],
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"outputs": [],
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"source": [
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"viewer = napari.Viewer()"
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]
@@ -46,7 +38,7 @@
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{
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"data": {
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"text/plain": [
49-
"<Points layer 'points2' at 0x204f46b5c10>"
41+
"<Points layer 'points2' at 0x12998840130>"
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]
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},
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"execution_count": 3,
@@ -63,10 +55,10 @@
6355
"frame = np.arange(n_timeframes).repeat(n_samples//n_timeframes)\n",
6456
"# make some random points with random features\n",
6557
"points = np.random.random((n_samples, 4))\n",
66-
"points2 = np.random.random((n_samples, 4))\n",
58+
"points2 = np.random.random((n_samples-1, 4))\n",
6759
"\n",
6860
"points[:, 0] = frame\n",
69-
"points2[:, 0] = frame\n",
61+
"points2[:, 0] = frame[:-1]\n",
7062
"\n",
7163
"features = pd.DataFrame({\n",
7264
" 'frame': frame,\n",
@@ -76,13 +68,14 @@
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" 'feature4': np.random.normal(size=n_samples, loc=loc),})\n",
7769
"\n",
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"features2 = pd.DataFrame({\n",
79-
" 'frame': frame,\n",
80-
" 'feature2': np.random.normal(size=n_samples, loc=-loc),\n",
81-
" 'feature3': np.random.normal(size=n_samples, loc=-loc),\n",
82-
" 'feature4': np.random.normal(size=n_samples, loc=-loc),})\n",
71+
" 'frame': frame[:-1],\n",
72+
" 'feature2': np.random.normal(size=n_samples-1, loc=-loc),\n",
73+
" 'feature3': np.random.normal(size=n_samples-1, loc=-loc),\n",
74+
" 'feature4': np.random.normal(size=n_samples-1, loc=-loc),})\n",
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"\n",
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"layer = napari.layers.Points(points, features=features, size=0.1, blending='translucent_no_depth')\n",
8577
"layer2 = napari.layers.Points(points2, features=features2, size=0.1, translate=(0, 0, 2), blending='translucent_no_depth')\n",
78+
"viewer.layers.clear()\n",
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"viewer.add_layer(layer)\n",
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"viewer.add_layer(layer2)\n"
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]
@@ -105,7 +98,7 @@
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{
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"data": {
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"text/plain": [
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"<napari._qt.widgets.qt_viewer_dock_widget.QtViewerDockWidget at 0x2049456d3a0>"
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"<napari._qt.widgets.qt_viewer_dock_widget.QtViewerDockWidget at 0x1299a10a820>"
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]
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},
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"execution_count": 4,
@@ -118,6 +111,238 @@
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"viewer.window.add_dock_widget(plotter_widget, area='right')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/html": [
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"<div>\n",
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"<style scoped>\n",
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" .dataframe tbody tr th:only-of-type {\n",
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" vertical-align: middle;\n",
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" }\n",
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"\n",
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" .dataframe tbody tr th {\n",
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" vertical-align: top;\n",
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" }\n",
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"\n",
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" .dataframe thead th {\n",
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" text-align: right;\n",
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" }\n",
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"</style>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th></th>\n",
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" <th>frame</th>\n",
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" <th>feature2</th>\n",
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" <th>feature3</th>\n",
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" <th>feature4</th>\n",
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" <th>MANUAL_CLUSTER_ID</th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>0</th>\n",
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" <td>0</td>\n",
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" <td>-4.725088</td>\n",
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" <td>-4.325642</td>\n",
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" <td>-7.112442</td>\n",
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" <td>1</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>1</th>\n",
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" <td>0</td>\n",
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" <td>-4.386041</td>\n",
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" <td>-5.335577</td>\n",
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" <td>-6.063437</td>\n",
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" <td>1</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2</th>\n",
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" <td>0</td>\n",
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" <td>-5.730792</td>\n",
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" <td>-4.642161</td>\n",
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" <td>-4.429953</td>\n",
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" <td>1</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3</th>\n",
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" <td>0</td>\n",
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" <td>-6.089492</td>\n",
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" <td>-2.991715</td>\n",
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" <td>-5.544447</td>\n",
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" <td>0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>4</th>\n",
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" <td>0</td>\n",
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" <td>-4.740159</td>\n",
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" <td>-5.189429</td>\n",
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" <td>-4.769790</td>\n",
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" <td>1</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>...</th>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>94</th>\n",
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" <td>4</td>\n",
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" <td>-5.815555</td>\n",
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" <td>-4.737373</td>\n",
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" <td>-4.945831</td>\n",
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" <td>0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>95</th>\n",
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" <td>4</td>\n",
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" <td>-6.226173</td>\n",
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" <td>-3.972162</td>\n",
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" <td>-6.477352</td>\n",
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" <td>0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>96</th>\n",
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" <td>4</td>\n",
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" <td>-4.597238</td>\n",
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" <td>-3.308072</td>\n",
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" <td>-4.418548</td>\n",
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" <td>0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>97</th>\n",
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" <td>4</td>\n",
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" <td>-6.143753</td>\n",
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" <td>-5.130647</td>\n",
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" <td>-5.700410</td>\n",
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" <td>0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>98</th>\n",
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" <td>4</td>\n",
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" <td>-4.029651</td>\n",
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" <td>-5.172430</td>\n",
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" <td>-5.987246</td>\n",
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" <td>1</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"<p>99 rows × 5 columns</p>\n",
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"</div>"
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],
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"text/plain": [
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" frame feature2 feature3 feature4 MANUAL_CLUSTER_ID\n",
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"0 0 -4.725088 -4.325642 -7.112442 1\n",
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"1 0 -4.386041 -5.335577 -6.063437 1\n",
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"2 0 -5.730792 -4.642161 -4.429953 1\n",
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"3 0 -6.089492 -2.991715 -5.544447 0\n",
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"4 0 -4.740159 -5.189429 -4.769790 1\n",
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".. ... ... ... ... ...\n",
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"94 4 -5.815555 -4.737373 -4.945831 0\n",
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"95 4 -6.226173 -3.972162 -6.477352 0\n",
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"96 4 -4.597238 -3.308072 -4.418548 0\n",
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"97 4 -6.143753 -5.130647 -5.700410 0\n",
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"98 4 -4.029651 -5.172430 -5.987246 1\n",
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"\n",
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"[99 rows x 5 columns]"
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]
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},
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"execution_count": 7,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"viewer.layers[-1].features"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"(99, 4)"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"viewer.layers[1].data.shape"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"array([1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0,\n",
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" 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0,\n",
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" 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0,\n",
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" 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1,\n",
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" 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0])"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"viewer.layers.selection.active = viewer.layers[-1]\n",
309+
"plotter_widget._selectors['x'].setCurrentText('feature3')\n",
310+
"plotter_widget.plotting_widget.active_artist.color_indices = np.random.randint(0, 2, n_samples)\n",
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"plotter_widget.plotting_widget.active_artist.color_indices"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"array([1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0,\n",
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" 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0,\n",
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" 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0,\n",
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" 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1,\n",
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" 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0])"
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]
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},
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"execution_count": 7,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"viewer.layers.selection.active = viewer.layers[0]\n",
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"plotter_widget.plotting_widget.active_artist.color_indices"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.19"
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"version": "3.9.18"
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}
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},
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"nbformat": 4,

‎pyproject.toml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ dependencies = [
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"scikit-image",
4949
"superqt",
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"scipy",
51-
"biaplotter"
51+
"biaplotter@https://github.com/BiAPoL/biaplotter/archive/refs/heads/main.zip"
5252
]
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‎src/napari_clusters_plotter/_new_plotter_widget.py‎

Lines changed: 28 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -152,8 +152,24 @@ def _replot(self):
152152
if self.x_axis == "" or self.y_axis == "":
153153
return
154154

155-
data_to_plot = self._get_data()
156-
self.plotting_widget.active_artist.data = data_to_plot
155+
# retrieve the data from the selected layers
156+
features = self._get_features()
157+
x_data = features[self.x_axis].values
158+
y_data = features[self.y_axis].values
159+
160+
# # if no hue is selected, set it to 0
161+
# if self.hue_axis == "None":
162+
# hue = np.zeros(len(features))
163+
# elif self.hue_axis != "":
164+
# hue = features[self.hue_axis].values
165+
166+
self.plotting_widget.active_artist.data = np.stack(
167+
[x_data, y_data], axis=1
168+
)
169+
if "MANUAL_CLUSTER_ID" in features.columns:
170+
self.plotting_widget.active_artist.color_indices = features[
171+
"MANUAL_CLUSTER_ID"
172+
].values
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158174
def _checkbox_status_changed(self):
159175
self._replot()
@@ -264,22 +280,6 @@ def n_selected_layers(self) -> int:
264280
"""
265281
return len(list(self.viewer.layers.selection))
266282

267-
def _get_data(self) -> np.ndarray:
268-
"""
269-
Get the data from the selected layers features.
270-
"""
271-
features = self._get_features()
272-
x_data = features[self.x_axis].values
273-
y_data = features[self.y_axis].values
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# # if no hue is selected, set it to 0
276-
# if self.hue_axis == "None":
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# hue = np.zeros(len(features))
278-
# elif self.hue_axis != "":
279-
# hue = features[self.hue_axis].values
280-
281-
return np.stack([x_data, y_data], axis=1)
282-
283283
def _on_update_layer_selection(
284284
self, event: napari.utils.events.Event
285285
) -> None:
@@ -327,7 +327,11 @@ def _update_feature_selection(
327327
self._selectors[dim].clear()
328328

329329
for dim in ["x", "y", "hue"]:
330-
self._selectors[dim].addItems(sorted(self.common_columns))
330+
features_to_add = sorted(self.common_columns)
331+
if "MANUAL_CLUSTER_ID" in features_to_add:
332+
features_to_add.remove("MANUAL_CLUSTER_ID")
333+
334+
self._selectors[dim].addItems(features_to_add)
331335

332336
# it should always be possible to select no color
333337
self._selectors["hue"].addItem("None")
@@ -361,6 +365,11 @@ def _color_layer_by_cluster_id(self):
361365
].index
362366
_apply_layer_color(selected_layer, colors[layer_indices])
363367

368+
# store cluster indeces in the features table
369+
selected_layer.features["MANUAL_CLUSTER_ID"] = color_indices[
370+
layer_indices
371+
]
372+
364373
def _reset(self):
365374
"""
366375
Reset the selection in the current plotting widget.

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