Merge pull request #37 from Image-Analysis-Hub/feature/geff_io

Feature/geff io

Author: lxenard

.gitignore

@@ -18,3 +18,4 @@ cov.xml
 
 # Data
 sample_data/FakeTracks.tif
+

notebooks/Custom properties.ipynb

@@ -24,7 +24,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,7 +42,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -95,7 +95,7 @@
     "Where does the property come from? For Pycellin computed properties, Pycellin uses `Pycellin`. For imported properties, Pycellin uses the name of the tool the data was imported from, like `TrackMate` or `CTC`. For custom properties, you can use `custom`, your initials or whatever works for you. This field is useful for traceability (e.g. reopening a model after a long time, sharing a model with other people...).\n",
     "\n",
     "**prop_type**  \n",
-    "The type of graph element the property applies to, either `node`, `edge`, `lineage`.\n",
+    "The type of graph element the property applies to, either `node`, `edge`, `lineage` or a combination of those.\n",
     "\n",
     "**lin_type**    \n",
     "Either `CellLineage`, `CycleLineage` or just `Lineage` depending on which type of lineage your property is related to. See [Pycellin data structure](./Pycellin%20data%20structure.ipynb) if in doubt.\n",
@@ -118,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -143,7 +143,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -192,14 +192,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
     "class AgeCalculator(pc.NodeGlobalPropCalculator):\n",
     "    def compute(self, data: pc.Data, lineage: pc.CellLineage, nid: int) -> int:\n",
     "        root = lineage.get_root()\n",
-    "        return lineage.nodes[nid][\"frame\"] - lineage.nodes[root][\"frame\"]"
+    "        # FRAME is the name of the one of the time properties in TrackMate.\n",
+    "        return lineage.nodes[nid][\"FRAME\"] - lineage.nodes[root][\"FRAME\"]"
    ]
   },
   {
@@ -267,7 +268,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -304,7 +305,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -322,7 +323,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -2539,7 +2540,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2577,7 +2578,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2602,7 +2603,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 11,
    "metadata": {
     "tags": [
      "raises-exception"
@@ -2616,8 +2617,8 @@
      "traceback": [
       "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
       "\u001b[31mTypeError\u001b[39m                                 Traceback (most recent call last)",
-      "\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[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:963\u001b[39m, in \u001b[36mModel.update\u001b[39m\u001b[34m(self, props_to_update)\u001b[39m\n\u001b[32m    956\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    957\u001b[39m     \u001b[38;5;66;03m# TODO: add \"see documentation\" to the error message or explain\u001b[39;00m\n\u001b[32m    958\u001b[39m     \u001b[38;5;66;03m# directly how to set it?\u001b[39;00m\n\u001b[32m    959\u001b[39m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[32m    960\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    961\u001b[39m         \u001b[33m\"\u001b[39m\u001b[33mbut is required for cycle lineage computation.\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m    962\u001b[39m     )\n\u001b[32m--> \u001b[39m\u001b[32m963\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    964\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    965\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    966\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    967\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    968\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 +2647,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2672,7 +2673,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -2688,7 +2689,7 @@
     "calc = ParityCalculator_correct(prop_correct)\n",
     "model.add_custom_property(calc)\n",
     "\n",
-    "# We clean the model by removing the improper property,\n",
+    "# We clean the model by removing the incorrect property,\n",
     "# otherwise we won't be able to update the model.\n",
     "model.remove_property(\"node_ID_parity_incorrect\")\n",
     "model.update()\n",
@@ -2735,7 +2736,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2747,29 +2748,28 @@
     "    prop_type=\"node\",\n",
     "    lin_type=\"CellLineage\",\n",
     "    dtype=\"float\",\n",
-    "    unit=model.get_time_step(),\n",
+    "    unit=model.get_time_unit(),\n",
     ")\n",
     "\n",
     "\n",
     "class MyRelativeAgeCalculator(pc.NodeGlobalPropCalculator):\n",
-    "    def __init__(self, property: pc.Property, time_step: float):\n",
+    "    def __init__(self, property: pc.Property, time_prop_name: float):\n",
     "        # Call the parent __init__ method.\n",
     "        super().__init__(property)\n",
     "        # Do whatever you want with the additional argument(s).\n",
     "        # Usually you store them in the object to be able to use them\n",
     "        # in the `compute` method.\n",
-    "        self.time_step = time_step\n",
+    "        self.time_prop_name = time_prop_name\n",
     "\n",
     "    def compute(self, data: pc.Data, lineage: pc.CellLineage, nid: int):\n",
     "        # As said before, the signature of the `compute` method must be respected,\n",
     "        # even if we don't use the `data` argument here.\n",
     "        first_cell = lineage.get_cell_cycle(nid)[0]\n",
-    "        first_cell_frame = lineage.nodes[first_cell][\"frame\"]\n",
-    "        current_cell_frame = lineage.nodes[nid][\"frame\"]\n",
-    "        age_in_frame = current_cell_frame - first_cell_frame\n",
-    "        # Here we use the additional time step argument.\n",
-    "        age_in_time = age_in_frame * self.time_step\n",
-    "        return age_in_time"
+    "        # We use the additional time_prop_name argument so that this method can work\n",
+    "        # with any time property, including the reference time property of the model.\n",
+    "        first_cell_time = lineage.nodes[first_cell][self.time_prop_name]\n",
+    "        current_cell_time = lineage.nodes[nid][self.time_prop_name]\n",
+    "        return current_cell_time - first_cell_time"
    ]
   },
   {
@@ -2781,17 +2781,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
-    "calc = MyRelativeAgeCalculator(age_prop2, model.get_time_step())\n",
+    "calc = MyRelativeAgeCalculator(age_prop2, model.reference_time_property)\n",
     "model.add_custom_property(calc)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -5001,7 +5001,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -5036,7 +5036,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {