disable currentscape

BlueBrain · Oct 3, 2024 · b5909f4 · b5909f4
1 parent 10f34cd
commit b5909f4
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Showing 2 changed files with 10 additions and 39 deletions.
diff --git a/examples/simplecell/config/recipes.json b/examples/simplecell/config/recipes.json
@@ -18,7 +18,8 @@
                 "offspring_size": 20
             },
             "validation_protocols": ["IDrest_0.4"],
-            "morph_modifiers": []
+            "morph_modifiers": [],
+            "plot_currentscape": false
         }
     }
 }
diff --git a/examples/simplecell/simplecell.ipynb b/examples/simplecell/simplecell.ipynb
@@ -29,7 +29,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -67,7 +67,8 @@
     "  - `max_ngen`: Defines the maximum number of generations for the optimisation process, set to `5`.  \n",
     "  - `optimisation_params`: Additional optimisation parameters, such as `offspring_size` set to `20`, indicating the number of solutions generated per generation.  \n",
     "  - `validation_protocols`: Lists protocols used for validation, e.g., `[\"IDrest_0.4\"]`.  \n",
-    "  - `morph_modifiers`: Set to an empty list `[]`, meaning no specific modifications to morphologies are applied by default."
+    "  - `morph_modifiers`: Set to an empty list `[]`, meaning no specific modifications to morphologies are applied by default.\n",
+    "  - `plot_currentscape`: We set this to False because we are using NEURON's built-in HH mechanism, where the currents are not defined as RANGE variables. As a result, CurrenScape is unable to access and plot these currents."
    ]
   },
   {
@@ -101,7 +102,8 @@
       "            \"validation_protocols\": [\n",
       "                \"IDrest_0.4\"\n",
       "            ],\n",
-      "            \"morph_modifiers\": []\n",
+      "            \"morph_modifiers\": [],\n",
+      "            \"plot_currentscape\": false\n",
       "        }\n",
       "    }\n",
       "}\n"
@@ -822,46 +824,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The plots are stored in the `./figures/` directory, organised into subfolders: `efeatures_extraction` for e-feature figures by protocol, distributions for parameter distributions, `optimisation` for optimisation curves and progress, `parameter_evolution` for parameter changes over generations, `scores` for z-scores of optimised e-features, `traces` for optimised e-model traces, and `currentscape` for Currentscape plots."
+    "The plots are stored in the `./figures/` directory, organised into subfolders: `efeatures_extraction` for e-feature figures by protocol, distributions for parameter distributions, `optimisation` for optimisation curves and progress, `parameter_evolution` for parameter changes over generations, `scores` for z-scores of optimised e-features, `traces` for optimised e-model traces."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/gpfs/bbp.cscs.ch/home/ikilic/workspace/BluePyEModel/bluepyemodel/emodel_pipeline/plotting.py:802: UserWarning: Tight layout not applied. The bottom and top margins cannot be made large enough to accommodate all axes decorations.\n",
-      "  plt.tight_layout()\n",
-      "Could not find any step protocol in recording. Will take the first one.\n",
-      "Could not plot currentscape for emodel=simplecell__etype=cADpyr__species=rat__brain_region=SSCX__seed=1__currentscape.IDrest_0.2.soma: voltage or currents is empty.\n",
-      "Could not plot currentscape for emodel=simplecell__etype=cADpyr__species=rat__brain_region=SSCX__seed=1__currentscape.IDrest_0.4.soma: voltage or currents is empty.\n",
-      "Could not plot currentscape for emodel=simplecell__etype=cADpyr__species=rat__brain_region=SSCX__seed=1__currentscape.IV_-0.1.soma: voltage or currents is empty.\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "[<bluepyemodel.emodel_pipeline.emodel.EModel at 0x2aaafaf88190>]"
-      ]
-     },
-     "execution_count": 16,
-     "metadata": {},
-     "output_type": "execute_result"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "<Figure size 640x480 with 0 Axes>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "pipeline.plot()"
    ]