Update notebooks

Author: lxenard

notebooks/Custom properties.ipynb

@@ -24,7 +24,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,7 +42,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [
     {
@@ -118,14 +118,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [],
    "source": [
     "age_prop = pc.Property(\n",
     "    identifier=\"age\",\n",
     "    name=\"age\",\n",
-    "    description=\"Age of the cell since the beginning of the lineage\",\n",
+    "    description=\"Age of the cell since the start of the lineage\",\n",
     "    provenance=\"custom\",\n",
     "    prop_type=\"node\",\n",
     "    lin_type=\"CellLineage\",\n",
@@ -143,14 +143,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 22,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "age: Age of the cell since the beginning of the lineage in frame(s)\n"
+      "age: Age of the cell since the start of the lineage in frame(s)\n"
      ]
     }
    ],
@@ -192,7 +192,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 23,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -267,7 +267,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 24,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -304,7 +304,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 25,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -322,7 +322,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 26,
    "metadata": {},
    "outputs": [
     {
@@ -2507,7 +2507,7 @@
          "autorange": "reversed",
          "showgrid": true,
          "title": {
-          "text": "Time (frames)"
+          "text": "Time (timepoints)"
          },
          "zeroline": true
         }
@@ -2539,7 +2539,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2577,7 +2577,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 28,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2602,7 +2602,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 29,
    "metadata": {
     "tags": [
      "raises-exception"
@@ -2616,9 +2616,9 @@
      "traceback": [
       "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
       "\u001b[31mTypeError\u001b[39m                                 Traceback (most recent call last)",
-      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[11]\u001b[39m\u001b[32m, line 3\u001b[39m\n\u001b[32m      1\u001b[39m calc = ParityCalculator_incorrect(prop_incorrect)\n\u001b[32m      2\u001b[39m model.add_custom_property(calc)\n\u001b[32m----> \u001b[39m\u001b[32m3\u001b[39m \u001b[43mmodel\u001b[49m\u001b[43m.\u001b[49m\u001b[43mupdate\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
-      "\u001b[36mFile \u001b[39m\u001b[32m/media/lxenard/data/Code/pycellin/pycellin/pycellin/classes/model.py:575\u001b[39m, in \u001b[36mModel.update\u001b[39m\u001b[34m(self, props_to_update)\u001b[39m\n\u001b[32m    567\u001b[39m             \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[32m    569\u001b[39m \u001b[38;5;66;03m# self.data._freeze_lineage_data()\u001b[39;00m\n\u001b[32m    570\u001b[39m \n\u001b[32m    571\u001b[39m \u001b[38;5;66;03m# TODO: need to handle all the errors that can be raised\u001b[39;00m\n\u001b[32m    572\u001b[39m \u001b[38;5;66;03m# by the updater methods to avoid incoherent states.\u001b[39;00m\n\u001b[32m    573\u001b[39m \u001b[38;5;66;03m# => saving a copy of the model before the update so we can roll back?\u001b[39;00m\n\u001b[32m--> \u001b[39m\u001b[32m575\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_updater\u001b[49m\u001b[43m.\u001b[49m\u001b[43m_update\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mprops_to_update\u001b[49m\u001b[43m)\u001b[49m\n",
-      "\u001b[36mFile \u001b[39m\u001b[32m/media/lxenard/data/Code/pycellin/pycellin/pycellin/classes/updater.py:194\u001b[39m, in \u001b[36mModelUpdater._update\u001b[39m\u001b[34m(self, data, props_to_update)\u001b[39m\n\u001b[32m    190\u001b[39m \u001b[38;5;66;03m# Recompute the properties as needed.\u001b[39;00m\n\u001b[32m    191\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m calc \u001b[38;5;129;01min\u001b[39;00m cell_calculators:\n\u001b[32m    192\u001b[39m     \u001b[38;5;66;03m# Depending on the class of the calculator, a different version of\u001b[39;00m\n\u001b[32m    193\u001b[39m     \u001b[38;5;66;03m# the enrich() method is called.\u001b[39;00m\n\u001b[32m--> \u001b[39m\u001b[32m194\u001b[39m     \u001b[43mcalc\u001b[49m\u001b[43m.\u001b[49m\u001b[43menrich\u001b[49m\u001b[43m(\u001b[49m\n\u001b[32m    195\u001b[39m \u001b[43m        \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    196\u001b[39m \u001b[43m        \u001b[49m\u001b[43mnodes_to_enrich\u001b[49m\u001b[43m=\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_added_cells\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    197\u001b[39m \u001b[43m        \u001b[49m\u001b[43medges_to_enrich\u001b[49m\u001b[43m=\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_added_links\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    198\u001b[39m \u001b[43m        \u001b[49m\u001b[43mlineages_to_enrich\u001b[49m\u001b[43m=\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_added_lineages\u001b[49m\u001b[43m \u001b[49m\u001b[43m|\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_modified_lineages\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    199\u001b[39m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m    201\u001b[39m \u001b[38;5;66;03m# In case of modifications in the structure of some cell lineages,\u001b[39;00m\n\u001b[32m    202\u001b[39m \u001b[38;5;66;03m# we need to recompute the cycle lineages and their properties.\u001b[39;00m\n\u001b[32m    203\u001b[39m \u001b[38;5;66;03m# TODO: optimize so we don't have to recompute EVERYTHING for cycle lineages?\u001b[39;00m\n\u001b[32m    204\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m lin_ID \u001b[38;5;129;01min\u001b[39;00m (\u001b[38;5;28mself\u001b[39m._modified_lineages | \u001b[38;5;28mself\u001b[39m._added_lineages) - \u001b[38;5;28mself\u001b[39m._removed_lineages:\n",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[29]\u001b[39m\u001b[32m, line 3\u001b[39m\n\u001b[32m      1\u001b[39m calc = ParityCalculator_incorrect(prop_incorrect)\n\u001b[32m      2\u001b[39m model.add_custom_property(calc)\n\u001b[32m----> \u001b[39m\u001b[32m3\u001b[39m \u001b[43mmodel\u001b[49m\u001b[43m.\u001b[49m\u001b[43mupdate\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
+      "\u001b[36mFile \u001b[39m\u001b[32m/media/lxenard/data/Code/pycellin/pycellin/pycellin/classes/model.py:910\u001b[39m, in \u001b[36mModel.update\u001b[39m\u001b[34m(self, props_to_update)\u001b[39m\n\u001b[32m    903\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m time_step \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[32m    904\u001b[39m     \u001b[38;5;66;03m# TODO: add \"see documentation\" to the error message or explain\u001b[39;00m\n\u001b[32m    905\u001b[39m     \u001b[38;5;66;03m# directly how to set it?\u001b[39;00m\n\u001b[32m    906\u001b[39m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[32m    907\u001b[39m         \u001b[33m\"\u001b[39m\u001b[33mThe time step of the model is currently not defined \u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m    908\u001b[39m         \u001b[33m\"\u001b[39m\u001b[33mbut is required for cycle lineage computation.\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m    909\u001b[39m     )\n\u001b[32m--> \u001b[39m\u001b[32m910\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_updater\u001b[49m\u001b[43m.\u001b[49m\u001b[43m_update\u001b[49m\u001b[43m(\u001b[49m\n\u001b[32m    911\u001b[39m \u001b[43m    \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    912\u001b[39m \u001b[43m    \u001b[49m\u001b[43mtime_prop\u001b[49m\u001b[43m=\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mmodel_metadata\u001b[49m\u001b[43m.\u001b[49m\u001b[43mreference_time_property\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    913\u001b[39m \u001b[43m    \u001b[49m\u001b[43mtime_step\u001b[49m\u001b[43m=\u001b[49m\u001b[43mtime_step\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    914\u001b[39m \u001b[43m    \u001b[49m\u001b[43mprops_to_update\u001b[49m\u001b[43m=\u001b[49m\u001b[43mprops_to_update\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    915\u001b[39m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
+      "\u001b[36mFile \u001b[39m\u001b[32m/media/lxenard/data/Code/pycellin/pycellin/pycellin/classes/updater.py:280\u001b[39m, in \u001b[36mModelUpdater._update\u001b[39m\u001b[34m(self, data, time_prop, time_step, props_to_update)\u001b[39m\n\u001b[32m    276\u001b[39m \u001b[38;5;66;03m# Recompute the properties as needed.\u001b[39;00m\n\u001b[32m    277\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m calc \u001b[38;5;129;01min\u001b[39;00m cell_calculators:\n\u001b[32m    278\u001b[39m     \u001b[38;5;66;03m# Depending on the class of the calculator, a different version of\u001b[39;00m\n\u001b[32m    279\u001b[39m     \u001b[38;5;66;03m# the enrich() method is called.\u001b[39;00m\n\u001b[32m--> \u001b[39m\u001b[32m280\u001b[39m     \u001b[43mcalc\u001b[49m\u001b[43m.\u001b[49m\u001b[43menrich\u001b[49m\u001b[43m(\u001b[49m\n\u001b[32m    281\u001b[39m \u001b[43m        \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m    282\u001b[39m \u001b[43m        \u001b[49m\u001b[43mnodes_to_enrich\u001b[49m\u001b[43m=\u001b[49m\u001b[43mnodes_to_process\u001b[49m\u001b[43m,\u001b[49m\u001b[43m  \u001b[49m\u001b[38;5;66;43;03m# self._added_cells,\u001b[39;49;00m\n\u001b[32m    283\u001b[39m \u001b[43m        \u001b[49m\u001b[43medges_to_enrich\u001b[49m\u001b[43m=\u001b[49m\u001b[43medges_to_process\u001b[49m\u001b[43m,\u001b[49m\u001b[43m  \u001b[49m\u001b[38;5;66;43;03m# self._added_links,\u001b[39;49;00m\n\u001b[32m    284\u001b[39m \u001b[43m        \u001b[49m\u001b[43mlineages_to_enrich\u001b[49m\u001b[43m=\u001b[49m\u001b[43mlins_to_process\u001b[49m\u001b[43m,\u001b[49m\u001b[43m  \u001b[49m\u001b[38;5;66;43;03m# self._added_lineages | self._modified_lineages\u001b[39;49;00m\n\u001b[32m    285\u001b[39m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m    287\u001b[39m \u001b[38;5;66;03m# In case of modifications in the structure of some cell lineages,\u001b[39;00m\n\u001b[32m    288\u001b[39m \u001b[38;5;66;03m# we need to recompute the cycle lineages and their properties.\u001b[39;00m\n\u001b[32m    289\u001b[39m \u001b[38;5;66;03m# TODO: optimize so we don't have to recompute EVERYTHING for cycle lineages?\u001b[39;00m\n\u001b[32m    290\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m lin_ID \u001b[38;5;129;01min\u001b[39;00m lins_to_process:\n",
       "\u001b[36mFile \u001b[39m\u001b[32m/media/lxenard/data/Code/pycellin/pycellin/pycellin/classes/property_calculator.py:181\u001b[39m, in \u001b[36mNodeLocalPropCalculator.enrich\u001b[39m\u001b[34m(self, data, nodes_to_enrich, **kwargs)\u001b[39m\n\u001b[32m    179\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m nid, lin_ID \u001b[38;5;129;01min\u001b[39;00m nodes_to_enrich:\n\u001b[32m    180\u001b[39m     lin = lineages[lin_ID]\n\u001b[32m--> \u001b[39m\u001b[32m181\u001b[39m     lin.nodes[nid][\u001b[38;5;28mself\u001b[39m.prop.identifier] = \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mcompute\u001b[49m\u001b[43m(\u001b[49m\u001b[43mlin\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mnid\u001b[49m\u001b[43m)\u001b[49m\n",
       "\u001b[31mTypeError\u001b[39m: ParityCalculator_incorrect.compute() takes 2 positional arguments but 3 were given"
      ]
@@ -2646,7 +2646,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2672,7 +2672,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 31,
    "metadata": {},
    "outputs": [
     {
@@ -2735,14 +2735,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 32,
    "metadata": {},
    "outputs": [],
    "source": [
     "age_prop2 = pc.Property(\n",
     "    identifier=\"relative_age\",\n",
     "    name=\"relative age\",\n",
-    "    description=\"Age of the cell since the beginning of the current cell cycle\",\n",
+    "    description=\"Age of the cell since the start of the current cell cycle\",\n",
     "    provenance=\"custom\",\n",
     "    prop_type=\"node\",\n",
     "    lin_type=\"CellLineage\",\n",
@@ -2751,7 +2751,7 @@
     ")\n",
     "\n",
     "\n",
-    "class RelativeAgeCalculator(pc.NodeGlobalPropCalculator):\n",
+    "class MyRelativeAgeCalculator(pc.NodeGlobalPropCalculator):\n",
     "    def __init__(self, property: pc.Property, time_step: float):\n",
     "        # Call the parent __init__ method.\n",
     "        super().__init__(property)\n",
@@ -2781,17 +2781,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 33,
    "metadata": {},
    "outputs": [],
    "source": [
-    "calc = RelativeAgeCalculator(age_prop2, model.get_time_step())\n",
+    "calc = MyRelativeAgeCalculator(age_prop2, model.get_time_step())\n",
     "model.add_custom_property(calc)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 34,
    "metadata": {},
    "outputs": [
     {
@@ -4976,7 +4976,7 @@
          "autorange": "reversed",
          "showgrid": true,
          "title": {
-          "text": "Time (frames)"
+          "text": "Time (timepoints)"
          },
          "zeroline": true
         }
@@ -5001,7 +5001,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 35,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -5036,7 +5036,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 36,
    "metadata": {},
    "outputs": [
     {
@@ -6199,8 +6199,9 @@
    ],
    "source": [
     "model.add_cycle_data()\n",
-    "# Division time is a Pycellin property, and it is needed to compute the growth rate.\n",
-    "model.add_division_time(in_time_unit=True)\n",
+    "# Division time is a Pycellin property, and it is needed to compute the growth rate,\n",
+    "# see line 23 in the code above.\n",
+    "model.add_division_time()\n",
     "model.add_custom_property(GrowthRateCalculator(gr_prop))\n",
     "model.update()\n",
     "model.data.cycle_data[0].plot(node_hover_props=[\"cycle_ID\", \"growth_rate\"])"