diff --git a/examples/simplecell/config/recipes.json b/examples/simplecell/config/recipes.json index ce088985..68a232f5 100644 --- 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 } } } \ No newline at end of file diff --git a/examples/simplecell/simplecell.ipynb b/examples/simplecell/simplecell.ipynb index 89c43167..4fb8ee06 100644 --- 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": [ - "[]" - ] - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - }, - { - "data": { - "text/plain": [ - "
" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "pipeline.plot()" ]