diff --git a/.ipynb_checkpoints/multi-area-model-checkpoint.ipynb b/.ipynb_checkpoints/multi-area-model-checkpoint.ipynb
index 606d7bf867eb05a744e3d9c662a9f8c40578b23d..3ae191e745fc747284894f51529e25ea6c66c921 100644
--- a/.ipynb_checkpoints/multi-area-model-checkpoint.ipynb
+++ b/.ipynb_checkpoints/multi-area-model-checkpoint.ipynb
@@ -378,7 +378,7 @@
"output_type": "stream",
"text": [
"Initializing network from dictionary.\n",
- "RAND_DATA_LABEL 1644\n"
+ "RAND_DATA_LABEL 565\n"
]
},
{
@@ -554,72 +554,72 @@
"text": [
"Prepared simulation in 0.00 seconds.\n",
"Rank 0: created area V1 with 0 local nodes\n",
- "Memory after V1 : 1911.70 MB\n",
+ "Memory after V1 : 1912.21 MB\n",
"Rank 0: created area V2 with 0 local nodes\n",
- "Memory after V2 : 1938.30 MB\n",
+ "Memory after V2 : 1938.80 MB\n",
"Rank 0: created area VP with 0 local nodes\n",
- "Memory after VP : 1967.50 MB\n",
+ "Memory after VP : 1968.00 MB\n",
"Rank 0: created area V3 with 0 local nodes\n",
- "Memory after V3 : 1995.75 MB\n",
+ "Memory after V3 : 1996.25 MB\n",
"Rank 0: created area V3A with 0 local nodes\n",
- "Memory after V3A : 2015.70 MB\n",
+ "Memory after V3A : 2016.15 MB\n",
"Rank 0: created area MT with 0 local nodes\n",
- "Memory after MT : 2041.32 MB\n",
+ "Memory after MT : 2041.82 MB\n",
"Rank 0: created area V4t with 0 local nodes\n",
- "Memory after V4t : 2066.26 MB\n",
+ "Memory after V4t : 2066.72 MB\n",
"Rank 0: created area V4 with 0 local nodes\n",
- "Memory after V4 : 2093.21 MB\n",
+ "Memory after V4 : 2093.75 MB\n",
"Rank 0: created area VOT with 0 local nodes\n",
- "Memory after VOT : 2118.56 MB\n",
+ "Memory after VOT : 2118.94 MB\n",
"Rank 0: created area MSTd with 0 local nodes\n",
- "Memory after MSTd : 2140.03 MB\n",
+ "Memory after MSTd : 2140.57 MB\n",
"Rank 0: created area PIP with 0 local nodes\n",
- "Memory after PIP : 2161.34 MB\n",
+ "Memory after PIP : 2161.88 MB\n",
"Rank 0: created area PO with 0 local nodes\n",
- "Memory after PO : 2182.81 MB\n",
+ "Memory after PO : 2183.39 MB\n",
"Rank 0: created area DP with 0 local nodes\n",
- "Memory after DP : 2203.08 MB\n",
+ "Memory after DP : 2203.65 MB\n",
"Rank 0: created area MIP with 0 local nodes\n",
- "Memory after MIP : 2224.74 MB\n",
+ "Memory after MIP : 2225.15 MB\n",
"Rank 0: created area MDP with 0 local nodes\n",
- "Memory after MDP : 2246.09 MB\n",
+ "Memory after MDP : 2246.66 MB\n",
"Rank 0: created area VIP with 0 local nodes\n",
- "Memory after VIP : 2268.07 MB\n",
+ "Memory after VIP : 2268.48 MB\n",
"Rank 0: created area LIP with 0 local nodes\n",
- "Memory after LIP : 2292.13 MB\n",
+ "Memory after LIP : 2292.51 MB\n",
"Rank 0: created area PITv with 0 local nodes\n",
- "Memory after PITv : 2317.34 MB\n",
+ "Memory after PITv : 2317.84 MB\n",
"Rank 0: created area PITd with 0 local nodes\n",
- "Memory after PITd : 2342.52 MB\n",
+ "Memory after PITd : 2343.02 MB\n",
"Rank 0: created area MSTl with 0 local nodes\n",
- "Memory after MSTl : 2364.02 MB\n",
+ "Memory after MSTl : 2364.52 MB\n",
"Rank 0: created area CITv with 0 local nodes\n",
- "Memory after CITv : 2383.25 MB\n",
+ "Memory after CITv : 2383.66 MB\n",
"Rank 0: created area CITd with 0 local nodes\n",
- "Memory after CITd : 2402.54 MB\n",
+ "Memory after CITd : 2403.00 MB\n",
"Rank 0: created area FEF with 0 local nodes\n",
- "Memory after FEF : 2424.04 MB\n",
+ "Memory after FEF : 2424.47 MB\n",
"Rank 0: created area TF with 0 local nodes\n",
- "Memory after TF : 2439.69 MB\n",
+ "Memory after TF : 2440.11 MB\n",
"Rank 0: created area AITv with 0 local nodes\n",
- "Memory after AITv : 2462.29 MB\n",
+ "Memory after AITv : 2462.78 MB\n",
"Rank 0: created area FST with 0 local nodes\n",
- "Memory after FST : 2479.05 MB\n",
+ "Memory after FST : 2479.55 MB\n",
"Rank 0: created area 7a with 0 local nodes\n",
- "Memory after 7a : 2500.23 MB\n",
+ "Memory after 7a : 2500.77 MB\n",
"Rank 0: created area STPp with 0 local nodes\n",
- "Memory after STPp : 2518.98 MB\n",
+ "Memory after STPp : 2519.48 MB\n",
"Rank 0: created area STPa with 0 local nodes\n",
- "Memory after STPa : 2538.01 MB\n",
+ "Memory after STPa : 2538.62 MB\n",
"Rank 0: created area 46 with 0 local nodes\n",
- "Memory after 46 : 2553.46 MB\n",
+ "Memory after 46 : 2553.95 MB\n",
"Rank 0: created area AITd with 0 local nodes\n",
- "Memory after AITd : 2576.02 MB\n",
+ "Memory after AITd : 2576.51 MB\n",
"Rank 0: created area TH with 0 local nodes\n",
- "Memory after TH : 2588.73 MB\n",
- "Created areas and internal connections in 2.30 seconds.\n",
- "Created cortico-cortical connections in 23.09 seconds.\n",
- "Simulated network in 67.64 seconds.\n"
+ "Memory after TH : 2589.22 MB\n",
+ "Created areas and internal connections in 2.26 seconds.\n",
+ "Created cortico-cortical connections in 22.84 seconds.\n",
+ "Simulated network in 81.08 seconds.\n"
]
}
],
@@ -756,7 +756,6 @@
"cell_type": "markdown",
"id": "57ff902c-d6ce-4f96-9e4f-8e3e7166ab66",
"metadata": {
- "jp-MarkdownHeadingCollapsed": true,
"tags": []
},
"source": [
@@ -772,8 +771,7 @@
},
"outputs": [],
"source": [
- "label_spikes = M.simulation.label\n",
- "label = M.simulation.label"
+ "label_spikes, label = M.simulation.label"
]
},
{
@@ -1057,19 +1055,6 @@
"## S5. Simulation results visualziation <a class=\"anchor\" id=\"section_5\"></a>"
]
},
- {
- "cell_type": "code",
- "execution_count": 22,
- "id": "3659d4de-cb23-4980-bddb-0245cd4d1bb7",
- "metadata": {},
- "outputs": [],
- "source": [
- "# # visualization settings\n",
- "# icolor = 'r'\n",
- "# ecolor = 'b'\n",
- "# population_labels = ['2/3E', '2/3I', '4E', '4I', '5E', '5I', '6E', '6I']"
- ]
- },
{
"cell_type": "markdown",
"id": "38ddd973",
@@ -1102,8 +1087,8 @@
"# ax.set_ylim(0, 50)\n",
"# ax.legend()\n",
"\n",
- "# # from MAM2EBRAINS import plot_instan_mean_firing_rate\n",
- "# # plot_instan_mean_firing_rate(tsteps, rate, sim_params)"
+ "from MAM2EBRAINS import plot_instan_mean_firing_rate\n",
+ "plot_instan_mean_firing_rate(tsteps, rate, sim_params)"
]
},
{
@@ -1115,7 +1100,7 @@
{
"data": {
"text/plain": [
- "<matplotlib.legend.Legend at 0x7f162e6a25e0>"
+ "<matplotlib.legend.Legend at 0x7f93142a9ee0>"
]
},
"execution_count": 24,
@@ -1136,18 +1121,18 @@
}
],
"source": [
- "data = np.loadtxt(M.simulation.data_dir + '/recordings/' + M.simulation.label + \"-spikes-1-0.dat\", skiprows=3)\n",
- "tsteps, spikecount = np.unique(data[:,1], return_counts=True)\n",
- "rate = spikecount / M.simulation.params['dt'] * 1e3 / np.sum(M.N_vec)\n",
- "fig, ax = plt.subplots()\n",
- "ax.plot(tsteps, rate)\n",
- "ax.plot(tsteps, np.average(rate)*np.ones(len(tsteps)), label='mean')\n",
- "ax.set_title('instantaneous rate across all populations')\n",
- "ax.set_xlabel('time (ms)')\n",
- "ax.set_ylabel('rate (spikes / s)')\n",
- "ax.set_xlim(0, sim_params['t_sim'])\n",
- "ax.set_ylim(0, 50)\n",
- "ax.legend()"
+ "# data = np.loadtxt(M.simulation.data_dir + '/recordings/' + M.simulation.label + \"-spikes-1-0.dat\", skiprows=3)\n",
+ "# tsteps, spikecount = np.unique(data[:,1], return_counts=True)\n",
+ "# rate = spikecount / M.simulation.params['dt'] * 1e3 / np.sum(M.N_vec)\n",
+ "# fig, ax = plt.subplots()\n",
+ "# ax.plot(tsteps, rate)\n",
+ "# ax.plot(tsteps, np.average(rate)*np.ones(len(tsteps)), label='mean')\n",
+ "# ax.set_title('instantaneous rate across all populations')\n",
+ "# ax.set_xlabel('time (ms)')\n",
+ "# ax.set_ylabel('rate (spikes / s)')\n",
+ "# ax.set_xlim(0, sim_params['t_sim'])\n",
+ "# ax.set_ylim(0, 50)\n",
+ "# ax.legend()"
]
},
{
@@ -1173,494 +1158,434 @@
"metadata": {},
"outputs": [],
"source": [
- "import json\n",
- "import numpy as np\n",
- "import os\n",
+ "# import json\n",
+ "# import numpy as np\n",
+ "# import os\n",
"\n",
- "import sys\n",
- "sys.path.append('./figures/Schmidt2018_dyn')\n",
- "from helpers import original_data_path, population_labels\n",
- "from multiarea_model import MultiAreaModel\n",
- "from plotcolors import myred, myblue\n",
+ "# import sys\n",
+ "# sys.path.append('./figures/Schmidt2018_dyn')\n",
+ "# from helpers import original_data_path, population_labels\n",
+ "# from multiarea_model import MultiAreaModel\n",
+ "# from plotcolors import myred, myblue\n",
"\n",
- "%matplotlib inline\n",
- "import matplotlib\n",
- "import numpy as np\n",
- "import matplotlib.pyplot as pl\n",
- "from matplotlib import gridspec\n",
- "from matplotlib import rc_file\n",
- "rc_file('./figures/Schmidt2018_dyn/plotstyle.rc')\n",
+ "# %matplotlib inline\n",
+ "# import matplotlib\n",
+ "# import numpy as np\n",
+ "# import matplotlib.pyplot as pl\n",
+ "# from matplotlib import gridspec\n",
+ "# from matplotlib import rc_file\n",
+ "# rc_file('./figures/Schmidt2018_dyn/plotstyle.rc')\n",
"\n",
- "icolor = myred\n",
- "ecolor = myblue"
+ "# icolor = myred\n",
+ "# ecolor = myblue"
]
},
{
"cell_type": "code",
- "execution_count": 47,
+ "execution_count": 26,
"id": "d3bf5947-7387-4d95-a00e-2ed72d26b35c",
"metadata": {},
"outputs": [],
"source": [
- "def set_boxplot_props(d):\n",
- " for i in range(len(d['boxes'])):\n",
- " if i % 2 == 0:\n",
- " d['boxes'][i].set_facecolor(icolor)\n",
- " d['boxes'][i].set_color(icolor)\n",
- " else:\n",
- " d['boxes'][i].set_facecolor(ecolor)\n",
- " d['boxes'][i].set_color(ecolor)\n",
- " pl.setp(d['whiskers'], color='k')\n",
- " pl.setp(d['fliers'], color='k', markerfacecolor='k', marker='+')\n",
- " pl.setp(d['medians'], color='none')\n",
- " pl.setp(d['caps'], color='k')\n",
- " pl.setp(d['means'], marker='x', color='k',\n",
- " markerfacecolor='k', markeredgecolor='k', markersize=3.)\n",
+ "# def set_boxplot_props(d):\n",
+ "# for i in range(len(d['boxes'])):\n",
+ "# if i % 2 == 0:\n",
+ "# d['boxes'][i].set_facecolor(icolor)\n",
+ "# d['boxes'][i].set_color(icolor)\n",
+ "# else:\n",
+ "# d['boxes'][i].set_facecolor(ecolor)\n",
+ "# d['boxes'][i].set_color(ecolor)\n",
+ "# pl.setp(d['whiskers'], color='k')\n",
+ "# pl.setp(d['fliers'], color='k', markerfacecolor='k', marker='+')\n",
+ "# pl.setp(d['medians'], color='none')\n",
+ "# pl.setp(d['caps'], color='k')\n",
+ "# pl.setp(d['means'], marker='x', color='k',\n",
+ "# markerfacecolor='k', markeredgecolor='k', markersize=3.)\n",
" \n",
- "def plot_resting_state(A, label_spikes, label): \n",
- " \"\"\"\n",
- " Figure layout\n",
- " \"\"\"\n",
- " nrows = 4\n",
- " ncols = 4\n",
- " width = 7.0866\n",
- " panel_wh_ratio = 0.7 * (1. + np.sqrt(5)) / 2. # golden ratio\n",
- "\n",
- " height = width / panel_wh_ratio * float(nrows) / ncols\n",
- " pl.rcParams['figure.figsize'] = (width, height)\n",
- "\n",
- "\n",
- " fig = pl.figure()\n",
- " axes = {}\n",
- "\n",
- " gs1 = gridspec.GridSpec(1, 3)\n",
- " gs1.update(left=0.06, right=0.72, top=0.95, wspace=0.4, bottom=0.35)\n",
- " axes['A'] = pl.subplot(gs1[:1, :1])\n",
- " axes['B'] = pl.subplot(gs1[:1, 1:2])\n",
- " axes['C'] = pl.subplot(gs1[:1, 2:])\n",
- "\n",
- " gs2 = gridspec.GridSpec(3, 1)\n",
- " gs2.update(left=0.78, right=0.95, top=0.95, bottom=0.35)\n",
- " axes['D'] = pl.subplot(gs2[:1, :1])\n",
- " axes['E'] = pl.subplot(gs2[1:2, :1])\n",
- " axes['F'] = pl.subplot(gs2[2:3, :1])\n",
- "\n",
- "\n",
- " gs3 = gridspec.GridSpec(1, 1)\n",
- " gs3.update(left=0.1, right=0.95, top=0.3, bottom=0.075)\n",
- " axes['G'] = pl.subplot(gs3[:1, :1])\n",
- "\n",
- " areas = ['V1', 'V2', 'FEF']\n",
- "\n",
- " labels = ['A', 'B', 'C']\n",
- " for area, label in zip(areas, labels):\n",
- " label_pos = [-0.2, 1.01]\n",
- " # pl.text(label_pos[0], label_pos[1], r'\\bfseries{}' + label + ': ' + area,\n",
- " # fontdict={'fontsize': 10, 'weight': 'bold',\n",
- " # 'horizontalalignment': 'left', 'verticalalignment':\n",
- " # 'bottom'}, transform=axes[label].transAxes)\n",
- "\n",
- " label = 'G'\n",
- " label_pos = [-0.1, 0.92]\n",
- " # pl.text(label_pos[0], label_pos[1], r'\\bfseries{}' + label,\n",
- " # fontdict={'fontsize': 10, 'weight': 'bold',\n",
- " # 'horizontalalignment': 'left', 'verticalalignment':\n",
- " # 'bottom'}, transform=axes[label].transAxes)\n",
- "\n",
- "\n",
- " labels = ['E', 'D', 'F']\n",
- " for label in labels:\n",
- " label_pos = [-0.2, 1.05]\n",
- " # pl.text(label_pos[0], label_pos[1], r'\\bfseries{}' + label,\n",
- " # fontdict={'fontsize': 10, 'weight': 'bold',\n",
- " # 'horizontalalignment': 'left', 'verticalalignment':\n",
- " # 'bottom'}, transform=axes[label].transAxes)\n",
- "\n",
- " labels = ['A', 'B', 'C', 'D', 'E', 'F']\n",
- "\n",
- " for label in labels:\n",
- " axes[label].spines['right'].set_color('none')\n",
- " axes[label].spines['top'].set_color('none')\n",
- " axes[label].yaxis.set_ticks_position(\"left\")\n",
- " axes[label].xaxis.set_ticks_position(\"bottom\")\n",
- "\n",
- " for label in ['A', 'B', 'C']:\n",
- " axes[label].yaxis.set_ticks_position('none')\n",
- "\n",
- "\n",
- " \"\"\"\n",
- " Load data\n",
- " \"\"\"\n",
- " LOAD_ORIGINAL_DATA = False\n",
- "\n",
- "\n",
- " if LOAD_ORIGINAL_DATA:\n",
- " # use T=10500 simulation for spike raster plots\n",
- " label_spikes = '3afaec94d650c637ef8419611c3f80b3cb3ff539'\n",
- " # and T=100500 simulation for all other panels\n",
- " label = '99c0024eacc275d13f719afd59357f7d12f02b77'\n",
- " data_path = original_data_path\n",
- " else:\n",
- " from network_simulations import init_models\n",
- " from config import data_path\n",
- " # models = init_models('Fig5')\n",
- " # label_spikes = models[0].simulation.label\n",
- " label_spikes = label_spikes\n",
- " # label = models[1].simulation.label\n",
- " label = label\n",
- "\n",
- " \"\"\"\n",
- " Create MultiAreaModel instance to have access to data structures\n",
- " \"\"\"\n",
- " # M = MultiAreaModel({})\n",
- "\n",
- " # # spike data\n",
- " # spike_data = {}\n",
- " # for area in areas:\n",
- " # spike_data[area] = {}\n",
- " # for pop in M.structure[area]:\n",
- " # spike_data[area][pop] = np.load(os.path.join(data_path,\n",
- " # label_spikes,\n",
- " # 'recordings',\n",
- " # '{}-spikes-{}-{}.npy'.format(label_spikes,\n",
- " # area, pop)))\n",
- "\n",
- " # load spike data\n",
- " spike_data = A.spike_data\n",
- "\n",
- " # stationary firing rates\n",
- " print(data_path)\n",
- " fn = os.path.join(data_path, label, 'Analysis', 'pop_rates.json')\n",
- " print(fn)\n",
- " fn = '/opt/app-root/src/MAM2EBRAINS/simulations/27d81076e6d6e9e591684be053078477/Analysis/pop_rates.json'\n",
- " with open(fn, 'r') as f:\n",
- " pop_rates = json.load(f)\n",
- "\n",
- " # time series of firing rates\n",
- " rate_time_series = {}\n",
- " for area in areas:\n",
- " # fn = os.path.join(data_path, label,\n",
- " # 'Analysis',\n",
- " # 'rate_time_series_full',\n",
- " # 'rate_time_series_full_{}.npy'.format(area))\n",
- " fn = os.path.join(data_path, '27d81076e6d6e9e591684be053078477',\n",
- " 'Analysis',\n",
- " 'rate_time_series-{}.npy'.format(area))\n",
- " # fn = \"/opt/app-root/src/MAM2EBRAINS/simulations/27d81076e6d6e9e591684be053078477/Analysis/rate_time_series_full/rate_time_series_full_V1.npy\"\n",
- " rate_time_series[area] = np.load(fn)\n",
- "\n",
- " # # time series of firing rates convolved with a kernel\n",
- " # rate_time_series_auto_kernel = {}\n",
- " # for area in areas:\n",
- " # fn = os.path.join(data_path, str(label),\n",
- " # 'Analysis',\n",
- " # 'rate_time_series_auto_kernel',\n",
- " # 'rate_time_series_auto_kernel_{}.npy'.format(area))\n",
- " # rate_time_series_auto_kernel[area] = np.load(fn)\n",
- "\n",
- " # local variance revised (LvR)\n",
- " fn = os.path.join(data_path, '27d81076e6d6e9e591684be053078477', 'Analysis', 'pop_LvR.json')\n",
- " with open(fn, 'r') as f:\n",
- " pop_LvR = json.load(f)\n",
- "\n",
- " # correlation coefficients\n",
- " fn = os.path.join(data_path, '27d81076e6d6e9e591684be053078477', 'Analysis', 'synchrony.json')\n",
- " with open(fn, 'r') as f:\n",
- " corrcoeff = json.load(f)\n",
+ "# def plot_resting_state(A, label_spikes, label): \n",
+ "# \"\"\"\n",
+ "# Figure layout\n",
+ "# \"\"\"\n",
+ "# nrows = 4\n",
+ "# ncols = 4\n",
+ "# width = 7.0866\n",
+ "# panel_wh_ratio = 0.7 * (1. + np.sqrt(5)) / 2. # golden ratio\n",
+ "\n",
+ "# height = width / panel_wh_ratio * float(nrows) / ncols\n",
+ "# pl.rcParams['figure.figsize'] = (width, height)\n",
+ "\n",
+ "\n",
+ "# fig = pl.figure()\n",
+ "# axes = {}\n",
+ "\n",
+ "# gs1 = gridspec.GridSpec(1, 3)\n",
+ "# gs1.update(left=0.06, right=0.72, top=0.95, wspace=0.4, bottom=0.35)\n",
+ "# axes['A'] = pl.subplot(gs1[:1, :1])\n",
+ "# axes['B'] = pl.subplot(gs1[:1, 1:2])\n",
+ "# axes['C'] = pl.subplot(gs1[:1, 2:])\n",
+ "\n",
+ "# gs2 = gridspec.GridSpec(3, 1)\n",
+ "# gs2.update(left=0.78, right=0.95, top=0.95, bottom=0.35)\n",
+ "# axes['D'] = pl.subplot(gs2[:1, :1])\n",
+ "# axes['E'] = pl.subplot(gs2[1:2, :1])\n",
+ "# axes['F'] = pl.subplot(gs2[2:3, :1])\n",
+ "\n",
+ "\n",
+ "# gs3 = gridspec.GridSpec(1, 1)\n",
+ "# gs3.update(left=0.1, right=0.95, top=0.3, bottom=0.075)\n",
+ "# axes['G'] = pl.subplot(gs3[:1, :1])\n",
+ "\n",
+ "# areas = ['V1', 'V2', 'FEF']\n",
+ "\n",
+ "# labels = ['A', 'B', 'C']\n",
+ "# for area, label in zip(areas, labels):\n",
+ "# label_pos = [-0.2, 1.01]\n",
+ "# # pl.text(label_pos[0], label_pos[1], r'\\bfseries{}' + label + ': ' + area,\n",
+ "# # fontdict={'fontsize': 10, 'weight': 'bold',\n",
+ "# # 'horizontalalignment': 'left', 'verticalalignment':\n",
+ "# # 'bottom'}, transform=axes[label].transAxes)\n",
+ "\n",
+ "# label = 'G'\n",
+ "# label_pos = [-0.1, 0.92]\n",
+ "# # pl.text(label_pos[0], label_pos[1], r'\\bfseries{}' + label,\n",
+ "# # fontdict={'fontsize': 10, 'weight': 'bold',\n",
+ "# # 'horizontalalignment': 'left', 'verticalalignment':\n",
+ "# # 'bottom'}, transform=axes[label].transAxes)\n",
+ "\n",
+ "\n",
+ "# labels = ['E', 'D', 'F']\n",
+ "# for label in labels:\n",
+ "# label_pos = [-0.2, 1.05]\n",
+ "# # pl.text(label_pos[0], label_pos[1], r'\\bfseries{}' + label,\n",
+ "# # fontdict={'fontsize': 10, 'weight': 'bold',\n",
+ "# # 'horizontalalignment': 'left', 'verticalalignment':\n",
+ "# # 'bottom'}, transform=axes[label].transAxes)\n",
+ "\n",
+ "# labels = ['A', 'B', 'C', 'D', 'E', 'F']\n",
+ "\n",
+ "# for label in labels:\n",
+ "# axes[label].spines['right'].set_color('none')\n",
+ "# axes[label].spines['top'].set_color('none')\n",
+ "# axes[label].yaxis.set_ticks_position(\"left\")\n",
+ "# axes[label].xaxis.set_ticks_position(\"bottom\")\n",
+ "\n",
+ "# for label in ['A', 'B', 'C']:\n",
+ "# axes[label].yaxis.set_ticks_position('none')\n",
+ "\n",
+ "\n",
+ "# \"\"\"\n",
+ "# Load data\n",
+ "# \"\"\"\n",
+ "# LOAD_ORIGINAL_DATA = False\n",
+ "\n",
+ "\n",
+ "# if LOAD_ORIGINAL_DATA:\n",
+ "# # use T=10500 simulation for spike raster plots\n",
+ "# label_spikes = '3afaec94d650c637ef8419611c3f80b3cb3ff539'\n",
+ "# # and T=100500 simulation for all other panels\n",
+ "# label = '99c0024eacc275d13f719afd59357f7d12f02b77'\n",
+ "# data_path = original_data_path\n",
+ "# else:\n",
+ "# from network_simulations import init_models\n",
+ "# from config import data_path\n",
+ "# # models = init_models('Fig5')\n",
+ "# # label_spikes = models[0].simulation.label\n",
+ "# label_spikes = label_spikes\n",
+ "# # label = models[1].simulation.label\n",
+ "# label = label\n",
+ "\n",
+ "# \"\"\"\n",
+ "# Create MultiAreaModel instance to have access to data structures\n",
+ "# \"\"\"\n",
+ "# # M = MultiAreaModel({})\n",
+ "\n",
+ "# # # spike data\n",
+ "# # spike_data = {}\n",
+ "# # for area in areas:\n",
+ "# # spike_data[area] = {}\n",
+ "# # for pop in M.structure[area]:\n",
+ "# # spike_data[area][pop] = np.load(os.path.join(data_path,\n",
+ "# # label_spikes,\n",
+ "# # 'recordings',\n",
+ "# # '{}-spikes-{}-{}.npy'.format(label_spikes,\n",
+ "# # area, pop)))\n",
+ "\n",
+ "# # load spike data\n",
+ "# spike_data = A.spike_data\n",
+ "\n",
+ "# # stationary firing rates\n",
+ "# print(data_path)\n",
+ "# fn = os.path.join(data_path, label, 'Analysis', 'pop_rates.json')\n",
+ "# print(fn)\n",
+ "# fn = '/opt/app-root/src/MAM2EBRAINS/simulations/27d81076e6d6e9e591684be053078477/Analysis/pop_rates.json'\n",
+ "# with open(fn, 'r') as f:\n",
+ "# pop_rates = json.load(f)\n",
+ "\n",
+ "# # time series of firing rates\n",
+ "# rate_time_series = {}\n",
+ "# for area in areas:\n",
+ "# # fn = os.path.join(data_path, label,\n",
+ "# # 'Analysis',\n",
+ "# # 'rate_time_series_full',\n",
+ "# # 'rate_time_series_full_{}.npy'.format(area))\n",
+ "# fn = os.path.join(data_path, '27d81076e6d6e9e591684be053078477',\n",
+ "# 'Analysis',\n",
+ "# 'rate_time_series-{}.npy'.format(area))\n",
+ "# # fn = \"/opt/app-root/src/MAM2EBRAINS/simulations/27d81076e6d6e9e591684be053078477/Analysis/rate_time_series_full/rate_time_series_full_V1.npy\"\n",
+ "# rate_time_series[area] = np.load(fn)\n",
+ "\n",
+ "# # # time series of firing rates convolved with a kernel\n",
+ "# # rate_time_series_auto_kernel = {}\n",
+ "# # for area in areas:\n",
+ "# # fn = os.path.join(data_path, str(label),\n",
+ "# # 'Analysis',\n",
+ "# # 'rate_time_series_auto_kernel',\n",
+ "# # 'rate_time_series_auto_kernel_{}.npy'.format(area))\n",
+ "# # rate_time_series_auto_kernel[area] = np.load(fn)\n",
+ "\n",
+ "# # local variance revised (LvR)\n",
+ "# fn = os.path.join(data_path, '27d81076e6d6e9e591684be053078477', 'Analysis', 'pop_LvR.json')\n",
+ "# with open(fn, 'r') as f:\n",
+ "# pop_LvR = json.load(f)\n",
+ "\n",
+ "# # correlation coefficients\n",
+ "# fn = os.path.join(data_path, '27d81076e6d6e9e591684be053078477', 'Analysis', 'synchrony.json')\n",
+ "# with open(fn, 'r') as f:\n",
+ "# corrcoeff = json.load(f)\n",
" \n",
- " \"\"\"\n",
- " Plotting\n",
- " \"\"\"\n",
- " print(\"Raster plots\")\n",
- "\n",
- " t_min = 0.\n",
- " t_max = 2000.\n",
- "\n",
- " icolor = myred\n",
- " ecolor = myblue\n",
- "\n",
- " frac_neurons = 0.03\n",
- "\n",
- " for i, area in enumerate(areas):\n",
- " ax = axes[labels[i]]\n",
- "\n",
- " if area in spike_data:\n",
- " n_pops = len(spike_data[area])\n",
- " # Determine number of neurons that will be plotted for this area (for\n",
- " # vertical offset)\n",
- " offset = 0\n",
- " n_to_plot = {}\n",
- " for pop in M.structure[area]:\n",
- " n_to_plot[pop] = int(M.N[area][pop] * frac_neurons)\n",
- " offset = offset + n_to_plot[pop]\n",
- " y_max = offset + 1\n",
- " prev_pop = ''\n",
- " yticks = []\n",
- " yticklocs = []\n",
- " for jj, pop in enumerate(M.structure[area]):\n",
- " if pop[0:-1] != prev_pop:\n",
- " prev_pop = pop[0:-1]\n",
- " yticks.append('L' + population_labels[jj][0:-1])\n",
- " yticklocs.append(offset - 0.5 * n_to_plot[pop])\n",
- " ind = np.where(np.logical_and(\n",
- " spike_data[area][pop][:, 1] <= t_max, spike_data[area][pop][:, 1] >= t_min))\n",
- " pop_data = spike_data[area][pop][ind]\n",
- " pop_neurons = np.unique(pop_data[:, 0])\n",
- " neurons_to_ = np.arange(np.min(spike_data[area][pop][:, 0]), np.min(\n",
- " spike_data[area][pop][:, 0]) + n_to_plot[pop], 1)\n",
- "\n",
- " if pop.find('E') > (-1):\n",
- " pcolor = ecolor\n",
- " else:\n",
- " pcolor = icolor\n",
- "\n",
- " for kk in range(n_to_plot[pop]):\n",
- " spike_times = pop_data[pop_data[:, 0] == neurons_to_[kk], 1]\n",
- "\n",
- " _ = ax.plot(spike_times, np.zeros(len(spike_times)) +\n",
- " offset - kk, '.', color=pcolor, markersize=1)\n",
- " offset = offset - n_to_plot[pop]\n",
- " y_min = offset\n",
- " ax.set_xlim([t_min, t_max])\n",
- " ax.set_ylim([y_min, y_max])\n",
- " # ax.set_yticklabels(yticks)\n",
- " ax.set_yticks(yticklocs)\n",
- " # ax.set_xlabel('Time (s)', labelpad=-0.1)\n",
- " ax.set_xticks([t_min, t_min + 250., t_max])\n",
- " # ax.set_xticklabels([r'3.', r'3.25', r'3.5'])\n",
+ "# \"\"\"\n",
+ "# Plotting\n",
+ "# \"\"\"\n",
+ "# print(\"Raster plots\")\n",
+ "\n",
+ "# t_min = 0.\n",
+ "# t_max = 2000.\n",
+ "\n",
+ "# icolor = myred\n",
+ "# ecolor = myblue\n",
+ "\n",
+ "# frac_neurons = 0.03\n",
+ "\n",
+ "# for i, area in enumerate(areas):\n",
+ "# ax = axes[labels[i]]\n",
+ "\n",
+ "# if area in spike_data:\n",
+ "# n_pops = len(spike_data[area])\n",
+ "# # Determine number of neurons that will be plotted for this area (for\n",
+ "# # vertical offset)\n",
+ "# offset = 0\n",
+ "# n_to_plot = {}\n",
+ "# for pop in M.structure[area]:\n",
+ "# n_to_plot[pop] = int(M.N[area][pop] * frac_neurons)\n",
+ "# offset = offset + n_to_plot[pop]\n",
+ "# y_max = offset + 1\n",
+ "# prev_pop = ''\n",
+ "# yticks = []\n",
+ "# yticklocs = []\n",
+ "# for jj, pop in enumerate(M.structure[area]):\n",
+ "# if pop[0:-1] != prev_pop:\n",
+ "# prev_pop = pop[0:-1]\n",
+ "# yticks.append('L' + population_labels[jj][0:-1])\n",
+ "# yticklocs.append(offset - 0.5 * n_to_plot[pop])\n",
+ "# ind = np.where(np.logical_and(\n",
+ "# spike_data[area][pop][:, 1] <= t_max, spike_data[area][pop][:, 1] >= t_min))\n",
+ "# pop_data = spike_data[area][pop][ind]\n",
+ "# pop_neurons = np.unique(pop_data[:, 0])\n",
+ "# neurons_to_ = np.arange(np.min(spike_data[area][pop][:, 0]), np.min(\n",
+ "# spike_data[area][pop][:, 0]) + n_to_plot[pop], 1)\n",
+ "\n",
+ "# if pop.find('E') > (-1):\n",
+ "# pcolor = ecolor\n",
+ "# else:\n",
+ "# pcolor = icolor\n",
+ "\n",
+ "# for kk in range(n_to_plot[pop]):\n",
+ "# spike_times = pop_data[pop_data[:, 0] == neurons_to_[kk], 1]\n",
+ "\n",
+ "# _ = ax.plot(spike_times, np.zeros(len(spike_times)) +\n",
+ "# offset - kk, '.', color=pcolor, markersize=1)\n",
+ "# offset = offset - n_to_plot[pop]\n",
+ "# y_min = offset\n",
+ "# ax.set_xlim([t_min, t_max])\n",
+ "# ax.set_ylim([y_min, y_max])\n",
+ "# # ax.set_yticklabels(yticks)\n",
+ "# ax.set_yticks(yticklocs)\n",
+ "# # ax.set_xlabel('Time (s)', labelpad=-0.1)\n",
+ "# ax.set_xticks([t_min, t_min + 250., t_max])\n",
+ "# # ax.set_xticklabels([r'3.', r'3.25', r'3.5'])\n",
"\n",
" \n",
- " print(\"plotting Population rates\")\n",
- "\n",
- " rates = np.zeros((len(M.area_list), 8))\n",
- " for i, area in enumerate(M.area_list):\n",
- " for j, pop in enumerate(M.structure[area][::-1]):\n",
- " rate = pop_rates[area][pop][0]\n",
- " if rate == 0.0:\n",
- " rate = 1e-5\n",
- " if area == 'TH' and j > 3: # To account for missing layer 4 in TH\n",
- " rates[i][j + 2] = rate\n",
- " else:\n",
- " rates[i][j] = rate\n",
- "\n",
- "\n",
- " rates = np.transpose(rates)\n",
- " masked_rates = np.ma.masked_where(rates < 1e-4, rates)\n",
- "\n",
- " ax = axes['D']\n",
- " d = ax.boxplot(np.transpose(rates), vert=False,\n",
- " patch_artist=True, whis=1.5, showmeans=True)\n",
- " set_boxplot_props(d)\n",
- "\n",
- " ax.plot(np.mean(rates, axis=1), np.arange(\n",
- " 1., len(M.structure['V1']) + 1., 1.), 'x', color='k', markersize=3)\n",
- " ax.set_yticklabels(population_labels[::-1], size=8)\n",
- " ax.set_yticks(np.arange(1., len(M.structure['V1']) + 1., 1.))\n",
- " ax.set_ylim((0., len(M.structure['V1']) + .5))\n",
- "\n",
- " x_max = 220.\n",
- " ax.set_xlim((-1., x_max))\n",
- " # ax.set_xlabel(r'Rate (spikes/s)', labelpad=-0.1)\n",
- " ax.set_xticks([0., 50., 100.])\n",
- "\n",
- " print(\"plotting Synchrony\")\n",
- "\n",
- " syn = np.zeros((len(M.area_list), 8))\n",
- " for i, area in enumerate(M.area_list):\n",
- " for j, pop in enumerate(M.structure[area][::-1]):\n",
- " value = corrcoeff[area][pop]\n",
- " if value == 0.0:\n",
- " value = 1e-5\n",
- " if area == 'TH' and j > 3: # To account for missing layer 4 in TH\n",
- " syn[i][j + 2] = value\n",
- " else:\n",
- " syn[i][j] = value\n",
- "\n",
- "\n",
- " syn = np.transpose(syn)\n",
- " masked_syn = np.ma.masked_where(syn < 1e-4, syn)\n",
- "\n",
- " ax = axes['E']\n",
- " d = ax.boxplot(np.transpose(syn), vert=False,\n",
- " patch_artist=True, whis=1.5, showmeans=True)\n",
- " set_boxplot_props(d)\n",
- "\n",
- " ax.plot(np.mean(syn, axis=1), np.arange(\n",
- " 1., len(M.structure['V1']) + 1., 1.), 'x', color='k', markersize=3)\n",
- "\n",
- " ax.set_yticklabels(population_labels[::-1], size=8)\n",
- " ax.set_yticks(np.arange(1., len(M.structure['V1']) + 1., 1.))\n",
- " # ax.set_ylim((0., len(M.structure['V1']) + .5))\n",
- " ax.set_xticks(np.arange(0.0, 0.601, 0.2))\n",
- " # ax.set_xlabel('Correlation coefficient', labelpad=-0.1)\n",
- "\n",
- "\n",
- " print(\"plotting Irregularity\")\n",
- "\n",
- " LvR = np.zeros((len(M.area_list), 8))\n",
- " for i, area in enumerate(M.area_list):\n",
- " for j, pop in enumerate(M.structure[area][::-1]):\n",
- " value = pop_LvR[area][pop]\n",
- " if value == 0.0:\n",
- " value = 1e-5\n",
- " if area == 'TH' and j > 3: # To account for missing layer 4 in TH\n",
- " LvR[i][j + 2] = value\n",
- " else:\n",
- " LvR[i][j] = value\n",
- "\n",
- " LvR = np.transpose(LvR)\n",
- " masked_LvR = np.ma.masked_where(LvR < 1e-4, LvR)\n",
- "\n",
- " ax = axes['F']\n",
- " d = ax.boxplot(np.transpose(LvR), vert=False,\n",
- " patch_artist=True, whis=1.5, showmeans=True)\n",
- " set_boxplot_props(d)\n",
- "\n",
- " ax.plot(np.mean(LvR, axis=1), np.arange(\n",
- " 1., len(M.structure['V1']) + 1., 1.), 'x', color='k', markersize=3)\n",
- " # ax.set_yticklabels(population_labels[::-1], size=8)\n",
- " ax.set_yticks(np.arange(1., len(M.structure['V1']) + 1., 1.))\n",
- " ax.set_ylim((0., len(M.structure['V1']) + .5))\n",
- "\n",
- "\n",
- " x_max = 2.9\n",
- " # ax.set_xlim((0., x_max))\n",
- " # ax.set_xlabel('Irregularity', labelpad=-0.1)\n",
- " # ax.set_xticks([0., 1., 2.])\n",
- "\n",
- " axes['G'].spines['right'].set_color('none')\n",
- " axes['G'].spines['left'].set_color('none')\n",
- " axes['G'].spines['top'].set_color('none')\n",
- " axes['G'].spines['bottom'].set_color('none')\n",
- " axes['G'].yaxis.set_ticks_position(\"none\")\n",
- " axes['G'].xaxis.set_ticks_position(\"none\")\n",
- " axes['G'].set_xticks([])\n",
- " axes['G'].set_yticks([])\n",
- "\n",
- "\n",
- " print(\"Plotting rate time series\")\n",
- " pos = axes['G'].get_position()\n",
- " ax = []\n",
- " h = pos.y1 - pos.y0\n",
- " w = pos.x1 - pos.x0\n",
- " ax.append(pl.axes([pos.x0, pos.y0, w, 0.28 * h]))\n",
- " ax.append(pl.axes([pos.x0, pos.y0 + 0.33 * h, w, 0.28 * h]))\n",
- " ax.append(pl.axes([pos.x0, pos.y0 + 0.67 * h, w, 0.28 * h]))\n",
- "\n",
- " colors = ['0.5', '0.3', '0.0']\n",
- "\n",
- " t_min = 0.\n",
- " t_max = 2000.\n",
- " time = np.arange(500., t_max)\n",
- " for i, area in enumerate(areas[::-1]):\n",
- " ax[i].spines['right'].set_color('none')\n",
- " ax[i].spines['top'].set_color('none')\n",
- " ax[i].yaxis.set_ticks_position(\"left\")\n",
- " ax[i].xaxis.set_ticks_position(\"none\")\n",
- "\n",
- " binned_spikes = rate_time_series[area][np.where(\n",
- " np.logical_and(time >= t_min, time < t_max))]\n",
- " ax[i].plot(time, binned_spikes, color=colors[0], label=area)\n",
- " # rate = rate_time_series_auto_kernel[area]\n",
- " rate = rate_time_series[area]\n",
- " ax[i].plot(time, rate, color=colors[2], label=area)\n",
- " # ax[i].set_xlim((500., t_max))\n",
- "\n",
- " # ax[i].text(0.8, 0.7, area, transform=ax[i].transAxes)\n",
- "\n",
- " # if i > 0:\n",
- " # ax[i].spines['bottom'].set_color('none')\n",
- " # ax[i].set_xticks([])\n",
- " # ax[i].set_yticks([0., 30.])\n",
- " # else:\n",
- " # ax[i].set_xticks([1000., 5000., 10000.])\n",
- " # ax[i].set_xticklabels([r'1.', r'5.', r'10.'])\n",
- " # ax[i].set_yticks([0., 5.])\n",
- " # if i == 1:\n",
- " # ax[i].set_ylabel('Rate (spikes/s)')\n",
+ "# print(\"plotting Population rates\")\n",
+ "\n",
+ "# rates = np.zeros((len(M.area_list), 8))\n",
+ "# for i, area in enumerate(M.area_list):\n",
+ "# for j, pop in enumerate(M.structure[area][::-1]):\n",
+ "# rate = pop_rates[area][pop][0]\n",
+ "# if rate == 0.0:\n",
+ "# rate = 1e-5\n",
+ "# if area == 'TH' and j > 3: # To account for missing layer 4 in TH\n",
+ "# rates[i][j + 2] = rate\n",
+ "# else:\n",
+ "# rates[i][j] = rate\n",
+ "\n",
+ "\n",
+ "# rates = np.transpose(rates)\n",
+ "# masked_rates = np.ma.masked_where(rates < 1e-4, rates)\n",
+ "\n",
+ "# ax = axes['D']\n",
+ "# d = ax.boxplot(np.transpose(rates), vert=False,\n",
+ "# patch_artist=True, whis=1.5, showmeans=True)\n",
+ "# set_boxplot_props(d)\n",
+ "\n",
+ "# ax.plot(np.mean(rates, axis=1), np.arange(\n",
+ "# 1., len(M.structure['V1']) + 1., 1.), 'x', color='k', markersize=3)\n",
+ "# ax.set_yticklabels(population_labels[::-1], size=8)\n",
+ "# ax.set_yticks(np.arange(1., len(M.structure['V1']) + 1., 1.))\n",
+ "# ax.set_ylim((0., len(M.structure['V1']) + .5))\n",
+ "\n",
+ "# x_max = 220.\n",
+ "# ax.set_xlim((-1., x_max))\n",
+ "# # ax.set_xlabel(r'Rate (spikes/s)', labelpad=-0.1)\n",
+ "# ax.set_xticks([0., 50., 100.])\n",
+ "\n",
+ "# print(\"plotting Synchrony\")\n",
+ "\n",
+ "# syn = np.zeros((len(M.area_list), 8))\n",
+ "# for i, area in enumerate(M.area_list):\n",
+ "# for j, pop in enumerate(M.structure[area][::-1]):\n",
+ "# value = corrcoeff[area][pop]\n",
+ "# if value == 0.0:\n",
+ "# value = 1e-5\n",
+ "# if area == 'TH' and j > 3: # To account for missing layer 4 in TH\n",
+ "# syn[i][j + 2] = value\n",
+ "# else:\n",
+ "# syn[i][j] = value\n",
+ "\n",
+ "\n",
+ "# syn = np.transpose(syn)\n",
+ "# masked_syn = np.ma.masked_where(syn < 1e-4, syn)\n",
+ "\n",
+ "# ax = axes['E']\n",
+ "# d = ax.boxplot(np.transpose(syn), vert=False,\n",
+ "# patch_artist=True, whis=1.5, showmeans=True)\n",
+ "# set_boxplot_props(d)\n",
+ "\n",
+ "# ax.plot(np.mean(syn, axis=1), np.arange(\n",
+ "# 1., len(M.structure['V1']) + 1., 1.), 'x', color='k', markersize=3)\n",
+ "\n",
+ "# ax.set_yticklabels(population_labels[::-1], size=8)\n",
+ "# ax.set_yticks(np.arange(1., len(M.structure['V1']) + 1., 1.))\n",
+ "# # ax.set_ylim((0., len(M.structure['V1']) + .5))\n",
+ "# ax.set_xticks(np.arange(0.0, 0.601, 0.2))\n",
+ "# # ax.set_xlabel('Correlation coefficient', labelpad=-0.1)\n",
+ "\n",
+ "\n",
+ "# print(\"plotting Irregularity\")\n",
+ "\n",
+ "# LvR = np.zeros((len(M.area_list), 8))\n",
+ "# for i, area in enumerate(M.area_list):\n",
+ "# for j, pop in enumerate(M.structure[area][::-1]):\n",
+ "# value = pop_LvR[area][pop]\n",
+ "# if value == 0.0:\n",
+ "# value = 1e-5\n",
+ "# if area == 'TH' and j > 3: # To account for missing layer 4 in TH\n",
+ "# LvR[i][j + 2] = value\n",
+ "# else:\n",
+ "# LvR[i][j] = value\n",
+ "\n",
+ "# LvR = np.transpose(LvR)\n",
+ "# masked_LvR = np.ma.masked_where(LvR < 1e-4, LvR)\n",
+ "\n",
+ "# ax = axes['F']\n",
+ "# d = ax.boxplot(np.transpose(LvR), vert=False,\n",
+ "# patch_artist=True, whis=1.5, showmeans=True)\n",
+ "# set_boxplot_props(d)\n",
+ "\n",
+ "# ax.plot(np.mean(LvR, axis=1), np.arange(\n",
+ "# 1., len(M.structure['V1']) + 1., 1.), 'x', color='k', markersize=3)\n",
+ "# # ax.set_yticklabels(population_labels[::-1], size=8)\n",
+ "# ax.set_yticks(np.arange(1., len(M.structure['V1']) + 1., 1.))\n",
+ "# ax.set_ylim((0., len(M.structure['V1']) + .5))\n",
+ "\n",
+ "\n",
+ "# x_max = 2.9\n",
+ "# # ax.set_xlim((0., x_max))\n",
+ "# # ax.set_xlabel('Irregularity', labelpad=-0.1)\n",
+ "# # ax.set_xticks([0., 1., 2.])\n",
+ "\n",
+ "# axes['G'].spines['right'].set_color('none')\n",
+ "# axes['G'].spines['left'].set_color('none')\n",
+ "# axes['G'].spines['top'].set_color('none')\n",
+ "# axes['G'].spines['bottom'].set_color('none')\n",
+ "# axes['G'].yaxis.set_ticks_position(\"none\")\n",
+ "# axes['G'].xaxis.set_ticks_position(\"none\")\n",
+ "# axes['G'].set_xticks([])\n",
+ "# axes['G'].set_yticks([])\n",
+ "\n",
+ "\n",
+ "# print(\"Plotting rate time series\")\n",
+ "# pos = axes['G'].get_position()\n",
+ "# ax = []\n",
+ "# h = pos.y1 - pos.y0\n",
+ "# w = pos.x1 - pos.x0\n",
+ "# ax.append(pl.axes([pos.x0, pos.y0, w, 0.28 * h]))\n",
+ "# ax.append(pl.axes([pos.x0, pos.y0 + 0.33 * h, w, 0.28 * h]))\n",
+ "# ax.append(pl.axes([pos.x0, pos.y0 + 0.67 * h, w, 0.28 * h]))\n",
+ "\n",
+ "# colors = ['0.5', '0.3', '0.0']\n",
+ "\n",
+ "# t_min = 0.\n",
+ "# t_max = 2000.\n",
+ "# time = np.arange(500., t_max)\n",
+ "# for i, area in enumerate(areas[::-1]):\n",
+ "# ax[i].spines['right'].set_color('none')\n",
+ "# ax[i].spines['top'].set_color('none')\n",
+ "# ax[i].yaxis.set_ticks_position(\"left\")\n",
+ "# ax[i].xaxis.set_ticks_position(\"none\")\n",
+ "\n",
+ "# binned_spikes = rate_time_series[area][np.where(\n",
+ "# np.logical_and(time >= t_min, time < t_max))]\n",
+ "# ax[i].plot(time, binned_spikes, color=colors[0], label=area)\n",
+ "# # rate = rate_time_series_auto_kernel[area]\n",
+ "# rate = rate_time_series[area]\n",
+ "# ax[i].plot(time, rate, color=colors[2], label=area)\n",
+ "# # ax[i].set_xlim((500., t_max))\n",
+ "\n",
+ "# # ax[i].text(0.8, 0.7, area, transform=ax[i].transAxes)\n",
+ "\n",
+ "# # if i > 0:\n",
+ "# # ax[i].spines['bottom'].set_color('none')\n",
+ "# # ax[i].set_xticks([])\n",
+ "# # ax[i].set_yticks([0., 30.])\n",
+ "# # else:\n",
+ "# # ax[i].set_xticks([1000., 5000., 10000.])\n",
+ "# # ax[i].set_xticklabels([r'1.', r'5.', r'10.'])\n",
+ "# # ax[i].set_yticks([0., 5.])\n",
+ "# # if i == 1:\n",
+ "# # ax[i].set_ylabel('Rate (spikes/s)')\n",
" \n",
- " # ax[0].set_xlabel('Time (s)', labelpad=-0.05)\n",
+ "# # ax[0].set_xlabel('Time (s)', labelpad=-0.05)\n",
" \n",
- " fig.subplots_adjust(left=0.05, right=0.95, top=0.95,\n",
- " bottom=0.075, wspace=1., hspace=.5)\n",
+ "# fig.subplots_adjust(left=0.05, right=0.95, top=0.95,\n",
+ "# bottom=0.075, wspace=1., hspace=.5)\n",
"\n",
- " # pl.legend()"
+ "# # pl.legend()"
]
},
{
"cell_type": "code",
- "execution_count": 48,
+ "execution_count": 27,
"id": "ae19bcc3",
"metadata": {
"tags": []
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "27d81076e6d6e9e591684be053078477\n",
- "/opt/app-root/src/MAM2EBRAINS/simulations\n",
- "/opt/app-root/src/MAM2EBRAINS/simulations/C/Analysis/pop_rates.json\n",
- "Raster plots\n",
- "plotting Population rates\n",
- "plotting Synchrony\n",
- "plotting Irregularity\n",
- "Plotting rate time series\n"
- ]
- },
- {
- "ename": "RuntimeError",
- "evalue": "latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../58e5732caba9df74dca26bf4003d5924.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 58e5732caba9df74dca26bf4003d5924.log.\n\n\n",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:233\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 232\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 233\u001b[0m report \u001b[38;5;241m=\u001b[39m \u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_output\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 234\u001b[0m \u001b[43m \u001b[49m\u001b[43mcommand\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mis\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mnot\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtexcache\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 235\u001b[0m \u001b[43m \u001b[49m\u001b[43mstderr\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mSTDOUT\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:415\u001b[0m, in \u001b[0;36mcheck_output\u001b[0;34m(timeout, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 413\u001b[0m kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124minput\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m empty\n\u001b[0;32m--> 415\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mpopenargs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstdout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mPIPE\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcheck\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 416\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mstdout\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:516\u001b[0m, in \u001b[0;36mrun\u001b[0;34m(input, capture_output, timeout, check, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m check \u001b[38;5;129;01mand\u001b[39;00m retcode:\n\u001b[0;32m--> 516\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CalledProcessError(retcode, process\u001b[38;5;241m.\u001b[39margs,\n\u001b[1;32m 517\u001b[0m output\u001b[38;5;241m=\u001b[39mstdout, stderr\u001b[38;5;241m=\u001b[39mstderr)\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m CompletedProcess(process\u001b[38;5;241m.\u001b[39margs, retcode, stdout, stderr)\n",
- "\u001b[0;31mCalledProcessError\u001b[0m: Command '['latex', '-interaction=nonstopmode', '--halt-on-error', '../58e5732caba9df74dca26bf4003d5924.tex']' returned non-zero exit status 1.",
- "\nThe above exception was the direct cause of the following exception:\n",
- "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/formatters.py:339\u001b[0m, in \u001b[0;36mBaseFormatter.__call__\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 338\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 339\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mprinter\u001b[49m\u001b[43m(\u001b[49m\u001b[43mobj\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 340\u001b[0m \u001b[38;5;66;03m# Finally look for special method names\u001b[39;00m\n\u001b[1;32m 341\u001b[0m method \u001b[38;5;241m=\u001b[39m get_real_method(obj, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprint_method)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/pylabtools.py:151\u001b[0m, in \u001b[0;36mprint_figure\u001b[0;34m(fig, fmt, bbox_inches, base64, **kwargs)\u001b[0m\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbackend_bases\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FigureCanvasBase\n\u001b[1;32m 149\u001b[0m FigureCanvasBase(fig)\n\u001b[0;32m--> 151\u001b[0m \u001b[43mfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcanvas\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprint_figure\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbytes_io\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkw\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 152\u001b[0m data \u001b[38;5;241m=\u001b[39m bytes_io\u001b[38;5;241m.\u001b[39mgetvalue()\n\u001b[1;32m 153\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m fmt \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msvg\u001b[39m\u001b[38;5;124m'\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backend_bases.py:2295\u001b[0m, in \u001b[0;36mFigureCanvasBase.print_figure\u001b[0;34m(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)\u001b[0m\n\u001b[1;32m 2289\u001b[0m renderer \u001b[38;5;241m=\u001b[39m _get_renderer(\n\u001b[1;32m 2290\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure,\n\u001b[1;32m 2291\u001b[0m functools\u001b[38;5;241m.\u001b[39mpartial(\n\u001b[1;32m 2292\u001b[0m print_method, orientation\u001b[38;5;241m=\u001b[39morientation)\n\u001b[1;32m 2293\u001b[0m )\n\u001b[1;32m 2294\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(renderer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_draw_disabled\u001b[39m\u001b[38;5;124m\"\u001b[39m, nullcontext)():\n\u001b[0;32m-> 2295\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2297\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches:\n\u001b[1;32m 2298\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtight\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:73\u001b[0m, in \u001b[0;36m_finalize_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;129m@wraps\u001b[39m(draw)\n\u001b[1;32m 72\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdraw_wrapper\u001b[39m(artist, renderer, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m---> 73\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m renderer\u001b[38;5;241m.\u001b[39m_rasterizing:\n\u001b[1;32m 75\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/figure.py:2837\u001b[0m, in \u001b[0;36mFigure.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 2834\u001b[0m \u001b[38;5;66;03m# ValueError can occur when resizing a window.\u001b[39;00m\n\u001b[1;32m 2836\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpatch\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[0;32m-> 2837\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 2838\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2840\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m sfig \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msubfigs:\n\u001b[1;32m 2841\u001b[0m sfig\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axes/_base.py:3091\u001b[0m, in \u001b[0;36m_AxesBase.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 3088\u001b[0m a\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[1;32m 3089\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n\u001b[0;32m-> 3091\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 3092\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3094\u001b[0m renderer\u001b[38;5;241m.\u001b[39mclose_group(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124maxes\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 3095\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstale \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1159\u001b[0m, in \u001b[0;36mAxis.draw\u001b[0;34m(self, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 1156\u001b[0m renderer\u001b[38;5;241m.\u001b[39mopen_group(\u001b[38;5;18m__name__\u001b[39m, gid\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_gid())\n\u001b[1;32m 1158\u001b[0m ticks_to_draw \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_update_ticks()\n\u001b[0;32m-> 1159\u001b[0m ticklabelBoxes, ticklabelBoxes2 \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_tick_bboxes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mticks_to_draw\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks_to_draw:\n\u001b[1;32m 1163\u001b[0m tick\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1085\u001b[0m, in \u001b[0;36mAxis._get_tick_bboxes\u001b[0;34m(self, ticks, renderer)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_tick_bboxes\u001b[39m(\u001b[38;5;28mself\u001b[39m, ticks, renderer):\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124;03m\"\"\"Return lists of bboxes for ticks' label1's and label2's.\"\"\"\u001b[39;00m\n\u001b[0;32m-> 1085\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ([tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1086\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_visible()],\n\u001b[1;32m 1087\u001b[0m [tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_visible()])\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1085\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_tick_bboxes\u001b[39m(\u001b[38;5;28mself\u001b[39m, ticks, renderer):\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124;03m\"\"\"Return lists of bboxes for ticks' label1's and label2's.\"\"\"\u001b[39;00m\n\u001b[0;32m-> 1085\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ([\u001b[43mtick\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlabel1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_window_extent\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1086\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_visible()],\n\u001b[1;32m 1087\u001b[0m [tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_visible()])\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:910\u001b[0m, in \u001b[0;36mText.get_window_extent\u001b[0;34m(self, renderer, dpi)\u001b[0m\n\u001b[1;32m 907\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCannot get window extent w/o renderer\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 909\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m cbook\u001b[38;5;241m.\u001b[39m_setattr_cm(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure, dpi\u001b[38;5;241m=\u001b[39mdpi):\n\u001b[0;32m--> 910\u001b[0m bbox, info, descent \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_layout\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_renderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 911\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_unitless_position()\n\u001b[1;32m 912\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_transform()\u001b[38;5;241m.\u001b[39mtransform((x, y))\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:309\u001b[0m, in \u001b[0;36mText._get_layout\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 306\u001b[0m ys \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 308\u001b[0m \u001b[38;5;66;03m# Full vertical extent of font, including ascenders and descenders:\u001b[39;00m\n\u001b[0;32m--> 309\u001b[0m _, lp_h, lp_d \u001b[38;5;241m=\u001b[39m \u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fontproperties\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 311\u001b[0m \u001b[43m \u001b[49m\u001b[43mismath\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mTeX\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_usetex\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 312\u001b[0m min_dy \u001b[38;5;241m=\u001b[39m (lp_h \u001b[38;5;241m-\u001b[39m lp_d) \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_linespacing\n\u001b[1;32m 314\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, line \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(lines):\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py:259\u001b[0m, in \u001b[0;36mRendererAgg.get_text_width_height_descent\u001b[0;34m(self, s, prop, ismath)\u001b[0m\n\u001b[1;32m 257\u001b[0m texmanager \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_texmanager()\n\u001b[1;32m 258\u001b[0m fontsize \u001b[38;5;241m=\u001b[39m prop\u001b[38;5;241m.\u001b[39mget_size_in_points()\n\u001b[0;32m--> 259\u001b[0m w, h, d \u001b[38;5;241m=\u001b[39m \u001b[43mtexmanager\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 260\u001b[0m \u001b[43m \u001b[49m\u001b[43ms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m w, h, d\n\u001b[1;32m 263\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ismath:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:335\u001b[0m, in \u001b[0;36mTexManager.get_text_width_height_descent\u001b[0;34m(self, tex, fontsize, renderer)\u001b[0m\n\u001b[1;32m 333\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m tex\u001b[38;5;241m.\u001b[39mstrip() \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 334\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m--> 335\u001b[0m dvifile \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmake_dvi\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 336\u001b[0m dpi_fraction \u001b[38;5;241m=\u001b[39m renderer\u001b[38;5;241m.\u001b[39mpoints_to_pixels(\u001b[38;5;241m1.\u001b[39m) \u001b[38;5;28;01mif\u001b[39;00m renderer \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m dviread\u001b[38;5;241m.\u001b[39mDvi(dvifile, \u001b[38;5;241m72\u001b[39m \u001b[38;5;241m*\u001b[39m dpi_fraction) \u001b[38;5;28;01mas\u001b[39;00m dvi:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:271\u001b[0m, in \u001b[0;36mTexManager.make_dvi\u001b[0;34m(self, tex, fontsize)\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[38;5;66;03m# Generate the dvi in a temporary directory to avoid race\u001b[39;00m\n\u001b[1;32m 263\u001b[0m \u001b[38;5;66;03m# conditions e.g. if multiple processes try to process the same tex\u001b[39;00m\n\u001b[1;32m 264\u001b[0m \u001b[38;5;66;03m# string at the same time. Having tmpdir be a subdirectory of the\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 268\u001b[0m \u001b[38;5;66;03m# the absolute path may contain characters (e.g. ~) that TeX does\u001b[39;00m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;66;03m# not support.)\u001b[39;00m\n\u001b[1;32m 270\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m TemporaryDirectory(\u001b[38;5;28mdir\u001b[39m\u001b[38;5;241m=\u001b[39mPath(dvifile)\u001b[38;5;241m.\u001b[39mparent) \u001b[38;5;28;01mas\u001b[39;00m tmpdir:\n\u001b[0;32m--> 271\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_run_checked_subprocess\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 272\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlatex\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m-interaction=nonstopmode\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m--halt-on-error\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 273\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m../\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mtexfile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtmpdir\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 274\u001b[0m (Path(tmpdir) \u001b[38;5;241m/\u001b[39m Path(dvifile)\u001b[38;5;241m.\u001b[39mname)\u001b[38;5;241m.\u001b[39mreplace(dvifile)\n\u001b[1;32m 275\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m dvifile\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:241\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 237\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 238\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFailed to process string with tex because \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m could not be \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 239\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfound\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(command[\u001b[38;5;241m0\u001b[39m])) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 240\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m subprocess\u001b[38;5;241m.\u001b[39mCalledProcessError \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[0;32m--> 241\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 242\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m was not able to process the following string:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{tex!r}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mHere is the full report generated by \u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 245\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{exc}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 246\u001b[0m prog\u001b[38;5;241m=\u001b[39mcommand[\u001b[38;5;241m0\u001b[39m],\n\u001b[1;32m 247\u001b[0m tex\u001b[38;5;241m=\u001b[39mtex\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124municode_escape\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m 248\u001b[0m exc\u001b[38;5;241m=\u001b[39mexc\u001b[38;5;241m.\u001b[39moutput\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m'\u001b[39m))) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 249\u001b[0m _log\u001b[38;5;241m.\u001b[39mdebug(report)\n\u001b[1;32m 250\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m report\n",
- "\u001b[0;31mRuntimeError\u001b[0m: latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../58e5732caba9df74dca26bf4003d5924.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 58e5732caba9df74dca26bf4003d5924.log.\n\n\n"
- ]
- },
- {
- "data": {
- "text/plain": [
- "<Figure size 1062.99x938.52 with 10 Axes>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
- "# from MAM2EBRAINS import plot_resting_state\n",
- "label_spikes = M.simulation.label\n",
- "label = M.simulation.label\n",
- "print(label)\n",
- "plot_resting_state(A, label_spikes, label)"
+ "# # from MAM2EBRAINS import plot_resting_state\n",
+ "# label_spikes = M.simulation.label\n",
+ "# label = M.simulation.label\n",
+ "# print(label)\n",
+ "# plot_resting_state(A, label_spikes, label)"
]
},
{
@@ -1701,51 +1626,26 @@
"metadata": {},
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/tmp/ipykernel_6580/362875631.py:71: UserWarning:FixedFormatter should only be used together with FixedLocator\n"
- ]
- },
- {
- "ename": "RuntimeError",
- "evalue": "latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../540885da22f8d5147f0088a11e43701a.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 540885da22f8d5147f0088a11e43701a.log.\n\n\n",
+ "ename": "NameError",
+ "evalue": "name 'population_labels' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:233\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 232\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 233\u001b[0m report \u001b[38;5;241m=\u001b[39m \u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_output\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 234\u001b[0m \u001b[43m \u001b[49m\u001b[43mcommand\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mis\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mnot\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtexcache\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 235\u001b[0m \u001b[43m \u001b[49m\u001b[43mstderr\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mSTDOUT\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:415\u001b[0m, in \u001b[0;36mcheck_output\u001b[0;34m(timeout, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 413\u001b[0m kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124minput\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m empty\n\u001b[0;32m--> 415\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mpopenargs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstdout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mPIPE\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcheck\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 416\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mstdout\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:516\u001b[0m, in \u001b[0;36mrun\u001b[0;34m(input, capture_output, timeout, check, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m check \u001b[38;5;129;01mand\u001b[39;00m retcode:\n\u001b[0;32m--> 516\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CalledProcessError(retcode, process\u001b[38;5;241m.\u001b[39margs,\n\u001b[1;32m 517\u001b[0m output\u001b[38;5;241m=\u001b[39mstdout, stderr\u001b[38;5;241m=\u001b[39mstderr)\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m CompletedProcess(process\u001b[38;5;241m.\u001b[39margs, retcode, stdout, stderr)\n",
- "\u001b[0;31mCalledProcessError\u001b[0m: Command '['latex', '-interaction=nonstopmode', '--halt-on-error', '../540885da22f8d5147f0088a11e43701a.tex']' returned non-zero exit status 1.",
- "\nThe above exception was the direct cause of the following exception:\n",
- "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/formatters.py:339\u001b[0m, in \u001b[0;36mBaseFormatter.__call__\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 338\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 339\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mprinter\u001b[49m\u001b[43m(\u001b[49m\u001b[43mobj\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 340\u001b[0m \u001b[38;5;66;03m# Finally look for special method names\u001b[39;00m\n\u001b[1;32m 341\u001b[0m method \u001b[38;5;241m=\u001b[39m get_real_method(obj, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprint_method)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/pylabtools.py:151\u001b[0m, in \u001b[0;36mprint_figure\u001b[0;34m(fig, fmt, bbox_inches, base64, **kwargs)\u001b[0m\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbackend_bases\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FigureCanvasBase\n\u001b[1;32m 149\u001b[0m FigureCanvasBase(fig)\n\u001b[0;32m--> 151\u001b[0m \u001b[43mfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcanvas\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprint_figure\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbytes_io\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkw\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 152\u001b[0m data \u001b[38;5;241m=\u001b[39m bytes_io\u001b[38;5;241m.\u001b[39mgetvalue()\n\u001b[1;32m 153\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m fmt \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msvg\u001b[39m\u001b[38;5;124m'\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backend_bases.py:2295\u001b[0m, in \u001b[0;36mFigureCanvasBase.print_figure\u001b[0;34m(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)\u001b[0m\n\u001b[1;32m 2289\u001b[0m renderer \u001b[38;5;241m=\u001b[39m _get_renderer(\n\u001b[1;32m 2290\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure,\n\u001b[1;32m 2291\u001b[0m functools\u001b[38;5;241m.\u001b[39mpartial(\n\u001b[1;32m 2292\u001b[0m print_method, orientation\u001b[38;5;241m=\u001b[39morientation)\n\u001b[1;32m 2293\u001b[0m )\n\u001b[1;32m 2294\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(renderer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_draw_disabled\u001b[39m\u001b[38;5;124m\"\u001b[39m, nullcontext)():\n\u001b[0;32m-> 2295\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2297\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches:\n\u001b[1;32m 2298\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtight\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:73\u001b[0m, in \u001b[0;36m_finalize_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;129m@wraps\u001b[39m(draw)\n\u001b[1;32m 72\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdraw_wrapper\u001b[39m(artist, renderer, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m---> 73\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m renderer\u001b[38;5;241m.\u001b[39m_rasterizing:\n\u001b[1;32m 75\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/figure.py:2837\u001b[0m, in \u001b[0;36mFigure.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 2834\u001b[0m \u001b[38;5;66;03m# ValueError can occur when resizing a window.\u001b[39;00m\n\u001b[1;32m 2836\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpatch\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[0;32m-> 2837\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 2838\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2840\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m sfig \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msubfigs:\n\u001b[1;32m 2841\u001b[0m sfig\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axes/_base.py:3055\u001b[0m, in \u001b[0;36m_AxesBase.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 3052\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m spine \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mspines\u001b[38;5;241m.\u001b[39mvalues():\n\u001b[1;32m 3053\u001b[0m artists\u001b[38;5;241m.\u001b[39mremove(spine)\n\u001b[0;32m-> 3055\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_update_title_position\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3057\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39maxison:\n\u001b[1;32m 3058\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m _axis \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_axis_list():\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axes/_base.py:3005\u001b[0m, in \u001b[0;36m_AxesBase._update_title_position\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 3003\u001b[0m _log\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtop of Axes not in the figure, so title not moved\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 3004\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[0;32m-> 3005\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[43mtitle\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_window_extent\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mymin \u001b[38;5;241m<\u001b[39m top:\n\u001b[1;32m 3006\u001b[0m _, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtransAxes\u001b[38;5;241m.\u001b[39minverted()\u001b[38;5;241m.\u001b[39mtransform((\u001b[38;5;241m0\u001b[39m, top))\n\u001b[1;32m 3007\u001b[0m title\u001b[38;5;241m.\u001b[39mset_position((x, y))\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:910\u001b[0m, in \u001b[0;36mText.get_window_extent\u001b[0;34m(self, renderer, dpi)\u001b[0m\n\u001b[1;32m 907\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCannot get window extent w/o renderer\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 909\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m cbook\u001b[38;5;241m.\u001b[39m_setattr_cm(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure, dpi\u001b[38;5;241m=\u001b[39mdpi):\n\u001b[0;32m--> 910\u001b[0m bbox, info, descent \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_layout\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_renderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 911\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_unitless_position()\n\u001b[1;32m 912\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_transform()\u001b[38;5;241m.\u001b[39mtransform((x, y))\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:309\u001b[0m, in \u001b[0;36mText._get_layout\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 306\u001b[0m ys \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 308\u001b[0m \u001b[38;5;66;03m# Full vertical extent of font, including ascenders and descenders:\u001b[39;00m\n\u001b[0;32m--> 309\u001b[0m _, lp_h, lp_d \u001b[38;5;241m=\u001b[39m \u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fontproperties\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 311\u001b[0m \u001b[43m \u001b[49m\u001b[43mismath\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mTeX\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_usetex\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 312\u001b[0m min_dy \u001b[38;5;241m=\u001b[39m (lp_h \u001b[38;5;241m-\u001b[39m lp_d) \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_linespacing\n\u001b[1;32m 314\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, line \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(lines):\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py:259\u001b[0m, in \u001b[0;36mRendererAgg.get_text_width_height_descent\u001b[0;34m(self, s, prop, ismath)\u001b[0m\n\u001b[1;32m 257\u001b[0m texmanager \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_texmanager()\n\u001b[1;32m 258\u001b[0m fontsize \u001b[38;5;241m=\u001b[39m prop\u001b[38;5;241m.\u001b[39mget_size_in_points()\n\u001b[0;32m--> 259\u001b[0m w, h, d \u001b[38;5;241m=\u001b[39m \u001b[43mtexmanager\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 260\u001b[0m \u001b[43m \u001b[49m\u001b[43ms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m w, h, d\n\u001b[1;32m 263\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ismath:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:335\u001b[0m, in \u001b[0;36mTexManager.get_text_width_height_descent\u001b[0;34m(self, tex, fontsize, renderer)\u001b[0m\n\u001b[1;32m 333\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m tex\u001b[38;5;241m.\u001b[39mstrip() \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 334\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m--> 335\u001b[0m dvifile \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmake_dvi\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 336\u001b[0m dpi_fraction \u001b[38;5;241m=\u001b[39m renderer\u001b[38;5;241m.\u001b[39mpoints_to_pixels(\u001b[38;5;241m1.\u001b[39m) \u001b[38;5;28;01mif\u001b[39;00m renderer \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m dviread\u001b[38;5;241m.\u001b[39mDvi(dvifile, \u001b[38;5;241m72\u001b[39m \u001b[38;5;241m*\u001b[39m dpi_fraction) \u001b[38;5;28;01mas\u001b[39;00m dvi:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:271\u001b[0m, in \u001b[0;36mTexManager.make_dvi\u001b[0;34m(self, tex, fontsize)\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[38;5;66;03m# Generate the dvi in a temporary directory to avoid race\u001b[39;00m\n\u001b[1;32m 263\u001b[0m \u001b[38;5;66;03m# conditions e.g. if multiple processes try to process the same tex\u001b[39;00m\n\u001b[1;32m 264\u001b[0m \u001b[38;5;66;03m# string at the same time. Having tmpdir be a subdirectory of the\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 268\u001b[0m \u001b[38;5;66;03m# the absolute path may contain characters (e.g. ~) that TeX does\u001b[39;00m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;66;03m# not support.)\u001b[39;00m\n\u001b[1;32m 270\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m TemporaryDirectory(\u001b[38;5;28mdir\u001b[39m\u001b[38;5;241m=\u001b[39mPath(dvifile)\u001b[38;5;241m.\u001b[39mparent) \u001b[38;5;28;01mas\u001b[39;00m tmpdir:\n\u001b[0;32m--> 271\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_run_checked_subprocess\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 272\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlatex\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m-interaction=nonstopmode\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m--halt-on-error\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 273\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m../\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mtexfile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtmpdir\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 274\u001b[0m (Path(tmpdir) \u001b[38;5;241m/\u001b[39m Path(dvifile)\u001b[38;5;241m.\u001b[39mname)\u001b[38;5;241m.\u001b[39mreplace(dvifile)\n\u001b[1;32m 275\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m dvifile\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:241\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 237\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 238\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFailed to process string with tex because \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m could not be \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 239\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfound\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(command[\u001b[38;5;241m0\u001b[39m])) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 240\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m subprocess\u001b[38;5;241m.\u001b[39mCalledProcessError \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[0;32m--> 241\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 242\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m was not able to process the following string:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{tex!r}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mHere is the full report generated by \u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 245\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{exc}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 246\u001b[0m prog\u001b[38;5;241m=\u001b[39mcommand[\u001b[38;5;241m0\u001b[39m],\n\u001b[1;32m 247\u001b[0m tex\u001b[38;5;241m=\u001b[39mtex\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124municode_escape\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m 248\u001b[0m exc\u001b[38;5;241m=\u001b[39mexc\u001b[38;5;241m.\u001b[39moutput\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m'\u001b[39m))) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 249\u001b[0m _log\u001b[38;5;241m.\u001b[39mdebug(report)\n\u001b[1;32m 250\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m report\n",
- "\u001b[0;31mRuntimeError\u001b[0m: latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../540885da22f8d5147f0088a11e43701a.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 540885da22f8d5147f0088a11e43701a.log.\n\n\n"
+ "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
+ "Input \u001b[0;32mIn [30]\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 45\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m pop[\u001b[38;5;241m0\u001b[39m:\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m] \u001b[38;5;241m!=\u001b[39m prev_pop:\n\u001b[1;32m 46\u001b[0m prev_pop \u001b[38;5;241m=\u001b[39m pop[\u001b[38;5;241m0\u001b[39m:\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m]\n\u001b[0;32m---> 47\u001b[0m yticks\u001b[38;5;241m.\u001b[39mappend(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mL\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m+\u001b[39m \u001b[43mpopulation_labels\u001b[49m[jj][\u001b[38;5;241m0\u001b[39m:\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m])\n\u001b[1;32m 48\u001b[0m yticklocs\u001b[38;5;241m.\u001b[39mappend(offset \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m0.5\u001b[39m \u001b[38;5;241m*\u001b[39m n_to_plot[pop])\n\u001b[1;32m 49\u001b[0m ind \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mwhere(np\u001b[38;5;241m.\u001b[39mlogical_and(\n\u001b[1;32m 50\u001b[0m spike_data[area][pop][:, \u001b[38;5;241m1\u001b[39m] \u001b[38;5;241m<\u001b[39m\u001b[38;5;241m=\u001b[39m t_max, spike_data[area][pop][:, \u001b[38;5;241m1\u001b[39m] \u001b[38;5;241m>\u001b[39m\u001b[38;5;241m=\u001b[39m t_min))\n",
+ "\u001b[0;31mNameError\u001b[0m: name 'population_labels' is not defined"
]
},
{
"data": {
+ "image/png": "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\n",
"text/plain": [
- "<Figure size 1500x450 with 3 Axes>"
+ "<Figure size 720x216 with 1 Axes>"
]
},
- "metadata": {},
+ "metadata": {
+ "needs_background": "light"
+ },
"output_type": "display_data"
}
],
@@ -1839,7 +1739,7 @@
},
{
"cell_type": "code",
- "execution_count": 31,
+ "execution_count": null,
"id": "b069bc59-44ae-450a-b0a5-b073951e3604",
"metadata": {},
"outputs": [],
@@ -1854,63 +1754,10 @@
},
{
"cell_type": "code",
- "execution_count": 32,
+ "execution_count": null,
"id": "96baac8f-3a0e-4d69-92ac-1d7cb4aff0d8",
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "[<matplotlib.axis.XTick at 0x7f160b2e5250>,\n",
- " <matplotlib.axis.XTick at 0x7f160b2e5220>]"
- ]
- },
- "execution_count": 32,
- "metadata": {},
- "output_type": "execute_result"
- },
- {
- "ename": "RuntimeError",
- "evalue": "latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../540885da22f8d5147f0088a11e43701a.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 540885da22f8d5147f0088a11e43701a.log.\n\n\n",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:233\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 232\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 233\u001b[0m report \u001b[38;5;241m=\u001b[39m \u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_output\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 234\u001b[0m \u001b[43m \u001b[49m\u001b[43mcommand\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mis\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mnot\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtexcache\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 235\u001b[0m \u001b[43m \u001b[49m\u001b[43mstderr\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mSTDOUT\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:415\u001b[0m, in \u001b[0;36mcheck_output\u001b[0;34m(timeout, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 413\u001b[0m kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124minput\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m empty\n\u001b[0;32m--> 415\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mpopenargs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstdout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mPIPE\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcheck\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 416\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mstdout\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:516\u001b[0m, in \u001b[0;36mrun\u001b[0;34m(input, capture_output, timeout, check, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m check \u001b[38;5;129;01mand\u001b[39;00m retcode:\n\u001b[0;32m--> 516\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CalledProcessError(retcode, process\u001b[38;5;241m.\u001b[39margs,\n\u001b[1;32m 517\u001b[0m output\u001b[38;5;241m=\u001b[39mstdout, stderr\u001b[38;5;241m=\u001b[39mstderr)\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m CompletedProcess(process\u001b[38;5;241m.\u001b[39margs, retcode, stdout, stderr)\n",
- "\u001b[0;31mCalledProcessError\u001b[0m: Command '['latex', '-interaction=nonstopmode', '--halt-on-error', '../540885da22f8d5147f0088a11e43701a.tex']' returned non-zero exit status 1.",
- "\nThe above exception was the direct cause of the following exception:\n",
- "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/formatters.py:339\u001b[0m, in \u001b[0;36mBaseFormatter.__call__\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 338\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 339\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mprinter\u001b[49m\u001b[43m(\u001b[49m\u001b[43mobj\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 340\u001b[0m \u001b[38;5;66;03m# Finally look for special method names\u001b[39;00m\n\u001b[1;32m 341\u001b[0m method \u001b[38;5;241m=\u001b[39m get_real_method(obj, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprint_method)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/pylabtools.py:151\u001b[0m, in \u001b[0;36mprint_figure\u001b[0;34m(fig, fmt, bbox_inches, base64, **kwargs)\u001b[0m\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbackend_bases\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FigureCanvasBase\n\u001b[1;32m 149\u001b[0m FigureCanvasBase(fig)\n\u001b[0;32m--> 151\u001b[0m \u001b[43mfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcanvas\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprint_figure\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbytes_io\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkw\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 152\u001b[0m data \u001b[38;5;241m=\u001b[39m bytes_io\u001b[38;5;241m.\u001b[39mgetvalue()\n\u001b[1;32m 153\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m fmt \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msvg\u001b[39m\u001b[38;5;124m'\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backend_bases.py:2295\u001b[0m, in \u001b[0;36mFigureCanvasBase.print_figure\u001b[0;34m(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)\u001b[0m\n\u001b[1;32m 2289\u001b[0m renderer \u001b[38;5;241m=\u001b[39m _get_renderer(\n\u001b[1;32m 2290\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure,\n\u001b[1;32m 2291\u001b[0m functools\u001b[38;5;241m.\u001b[39mpartial(\n\u001b[1;32m 2292\u001b[0m print_method, orientation\u001b[38;5;241m=\u001b[39morientation)\n\u001b[1;32m 2293\u001b[0m )\n\u001b[1;32m 2294\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(renderer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_draw_disabled\u001b[39m\u001b[38;5;124m\"\u001b[39m, nullcontext)():\n\u001b[0;32m-> 2295\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2297\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches:\n\u001b[1;32m 2298\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtight\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:73\u001b[0m, in \u001b[0;36m_finalize_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;129m@wraps\u001b[39m(draw)\n\u001b[1;32m 72\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdraw_wrapper\u001b[39m(artist, renderer, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m---> 73\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m renderer\u001b[38;5;241m.\u001b[39m_rasterizing:\n\u001b[1;32m 75\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/figure.py:2837\u001b[0m, in \u001b[0;36mFigure.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 2834\u001b[0m \u001b[38;5;66;03m# ValueError can occur when resizing a window.\u001b[39;00m\n\u001b[1;32m 2836\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpatch\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[0;32m-> 2837\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 2838\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2840\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m sfig \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msubfigs:\n\u001b[1;32m 2841\u001b[0m sfig\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axes/_base.py:3055\u001b[0m, in \u001b[0;36m_AxesBase.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 3052\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m spine \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mspines\u001b[38;5;241m.\u001b[39mvalues():\n\u001b[1;32m 3053\u001b[0m artists\u001b[38;5;241m.\u001b[39mremove(spine)\n\u001b[0;32m-> 3055\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_update_title_position\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3057\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39maxison:\n\u001b[1;32m 3058\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m _axis \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_axis_list():\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axes/_base.py:3005\u001b[0m, in \u001b[0;36m_AxesBase._update_title_position\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 3003\u001b[0m _log\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtop of Axes not in the figure, so title not moved\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 3004\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[0;32m-> 3005\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[43mtitle\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_window_extent\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mymin \u001b[38;5;241m<\u001b[39m top:\n\u001b[1;32m 3006\u001b[0m _, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtransAxes\u001b[38;5;241m.\u001b[39minverted()\u001b[38;5;241m.\u001b[39mtransform((\u001b[38;5;241m0\u001b[39m, top))\n\u001b[1;32m 3007\u001b[0m title\u001b[38;5;241m.\u001b[39mset_position((x, y))\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:910\u001b[0m, in \u001b[0;36mText.get_window_extent\u001b[0;34m(self, renderer, dpi)\u001b[0m\n\u001b[1;32m 907\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCannot get window extent w/o renderer\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 909\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m cbook\u001b[38;5;241m.\u001b[39m_setattr_cm(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure, dpi\u001b[38;5;241m=\u001b[39mdpi):\n\u001b[0;32m--> 910\u001b[0m bbox, info, descent \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_layout\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_renderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 911\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_unitless_position()\n\u001b[1;32m 912\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_transform()\u001b[38;5;241m.\u001b[39mtransform((x, y))\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:309\u001b[0m, in \u001b[0;36mText._get_layout\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 306\u001b[0m ys \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 308\u001b[0m \u001b[38;5;66;03m# Full vertical extent of font, including ascenders and descenders:\u001b[39;00m\n\u001b[0;32m--> 309\u001b[0m _, lp_h, lp_d \u001b[38;5;241m=\u001b[39m \u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fontproperties\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 311\u001b[0m \u001b[43m \u001b[49m\u001b[43mismath\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mTeX\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_usetex\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 312\u001b[0m min_dy \u001b[38;5;241m=\u001b[39m (lp_h \u001b[38;5;241m-\u001b[39m lp_d) \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_linespacing\n\u001b[1;32m 314\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, line \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(lines):\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py:259\u001b[0m, in \u001b[0;36mRendererAgg.get_text_width_height_descent\u001b[0;34m(self, s, prop, ismath)\u001b[0m\n\u001b[1;32m 257\u001b[0m texmanager \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_texmanager()\n\u001b[1;32m 258\u001b[0m fontsize \u001b[38;5;241m=\u001b[39m prop\u001b[38;5;241m.\u001b[39mget_size_in_points()\n\u001b[0;32m--> 259\u001b[0m w, h, d \u001b[38;5;241m=\u001b[39m \u001b[43mtexmanager\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 260\u001b[0m \u001b[43m \u001b[49m\u001b[43ms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m w, h, d\n\u001b[1;32m 263\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ismath:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:335\u001b[0m, in \u001b[0;36mTexManager.get_text_width_height_descent\u001b[0;34m(self, tex, fontsize, renderer)\u001b[0m\n\u001b[1;32m 333\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m tex\u001b[38;5;241m.\u001b[39mstrip() \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 334\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m--> 335\u001b[0m dvifile \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmake_dvi\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 336\u001b[0m dpi_fraction \u001b[38;5;241m=\u001b[39m renderer\u001b[38;5;241m.\u001b[39mpoints_to_pixels(\u001b[38;5;241m1.\u001b[39m) \u001b[38;5;28;01mif\u001b[39;00m renderer \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m dviread\u001b[38;5;241m.\u001b[39mDvi(dvifile, \u001b[38;5;241m72\u001b[39m \u001b[38;5;241m*\u001b[39m dpi_fraction) \u001b[38;5;28;01mas\u001b[39;00m dvi:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:271\u001b[0m, in \u001b[0;36mTexManager.make_dvi\u001b[0;34m(self, tex, fontsize)\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[38;5;66;03m# Generate the dvi in a temporary directory to avoid race\u001b[39;00m\n\u001b[1;32m 263\u001b[0m \u001b[38;5;66;03m# conditions e.g. if multiple processes try to process the same tex\u001b[39;00m\n\u001b[1;32m 264\u001b[0m \u001b[38;5;66;03m# string at the same time. Having tmpdir be a subdirectory of the\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 268\u001b[0m \u001b[38;5;66;03m# the absolute path may contain characters (e.g. ~) that TeX does\u001b[39;00m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;66;03m# not support.)\u001b[39;00m\n\u001b[1;32m 270\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m TemporaryDirectory(\u001b[38;5;28mdir\u001b[39m\u001b[38;5;241m=\u001b[39mPath(dvifile)\u001b[38;5;241m.\u001b[39mparent) \u001b[38;5;28;01mas\u001b[39;00m tmpdir:\n\u001b[0;32m--> 271\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_run_checked_subprocess\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 272\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlatex\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m-interaction=nonstopmode\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m--halt-on-error\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 273\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m../\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mtexfile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtmpdir\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 274\u001b[0m (Path(tmpdir) \u001b[38;5;241m/\u001b[39m Path(dvifile)\u001b[38;5;241m.\u001b[39mname)\u001b[38;5;241m.\u001b[39mreplace(dvifile)\n\u001b[1;32m 275\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m dvifile\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:241\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 237\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 238\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFailed to process string with tex because \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m could not be \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 239\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfound\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(command[\u001b[38;5;241m0\u001b[39m])) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 240\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m subprocess\u001b[38;5;241m.\u001b[39mCalledProcessError \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[0;32m--> 241\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 242\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m was not able to process the following string:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{tex!r}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mHere is the full report generated by \u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 245\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{exc}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 246\u001b[0m prog\u001b[38;5;241m=\u001b[39mcommand[\u001b[38;5;241m0\u001b[39m],\n\u001b[1;32m 247\u001b[0m tex\u001b[38;5;241m=\u001b[39mtex\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124municode_escape\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m 248\u001b[0m exc\u001b[38;5;241m=\u001b[39mexc\u001b[38;5;241m.\u001b[39moutput\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m'\u001b[39m))) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 249\u001b[0m _log\u001b[38;5;241m.\u001b[39mdebug(report)\n\u001b[1;32m 250\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m report\n",
- "\u001b[0;31mRuntimeError\u001b[0m: latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../540885da22f8d5147f0088a11e43701a.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 540885da22f8d5147f0088a11e43701a.log.\n\n\n"
- ]
- },
- {
- "data": {
- "text/plain": [
- "<Figure size 1062.99x938.52 with 1 Axes>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
"def set_boxplot_props(d):\n",
" for i in range(len(d['boxes'])):\n",
@@ -1977,95 +1824,10 @@
},
{
"cell_type": "code",
- "execution_count": 33,
+ "execution_count": null,
"id": "721d1f03-df25-468d-8075-a807025a9c58",
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "0 V1\n",
- "1 V2\n",
- "2 VP\n",
- "3 V3\n",
- "4 PIP\n",
- "5 V3A\n",
- "6 MT\n",
- "7 V4t\n",
- "8 V4\n",
- "9 PO\n",
- "10 VOT\n",
- "11 DP\n",
- "12 MIP\n",
- "13 MDP\n",
- "14 MSTd\n",
- "15 VIP\n",
- "16 LIP\n",
- "17 PITv\n",
- "18 PITd\n",
- "19 AITv\n",
- "20 MSTl\n",
- "21 FST\n",
- "22 CITv\n",
- "23 CITd\n",
- "24 7a\n",
- "25 STPp\n",
- "26 STPa\n",
- "27 FEF\n",
- "28 46\n",
- "29 TF\n",
- "30 TH\n",
- "31 AITd\n",
- "['23E', '23I', '4E', '4I', '5E', '5I', '6E', '6I']\n"
- ]
- },
- {
- "ename": "RuntimeError",
- "evalue": "latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../58e5732caba9df74dca26bf4003d5924.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 58e5732caba9df74dca26bf4003d5924.log.\n\n\n",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:233\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 232\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 233\u001b[0m report \u001b[38;5;241m=\u001b[39m \u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_output\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 234\u001b[0m \u001b[43m \u001b[49m\u001b[43mcommand\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mis\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mnot\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtexcache\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 235\u001b[0m \u001b[43m \u001b[49m\u001b[43mstderr\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mSTDOUT\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:415\u001b[0m, in \u001b[0;36mcheck_output\u001b[0;34m(timeout, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 413\u001b[0m kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124minput\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m empty\n\u001b[0;32m--> 415\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mpopenargs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstdout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mPIPE\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcheck\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 416\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mstdout\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:516\u001b[0m, in \u001b[0;36mrun\u001b[0;34m(input, capture_output, timeout, check, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m check \u001b[38;5;129;01mand\u001b[39;00m retcode:\n\u001b[0;32m--> 516\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CalledProcessError(retcode, process\u001b[38;5;241m.\u001b[39margs,\n\u001b[1;32m 517\u001b[0m output\u001b[38;5;241m=\u001b[39mstdout, stderr\u001b[38;5;241m=\u001b[39mstderr)\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m CompletedProcess(process\u001b[38;5;241m.\u001b[39margs, retcode, stdout, stderr)\n",
- "\u001b[0;31mCalledProcessError\u001b[0m: Command '['latex', '-interaction=nonstopmode', '--halt-on-error', '../58e5732caba9df74dca26bf4003d5924.tex']' returned non-zero exit status 1.",
- "\nThe above exception was the direct cause of the following exception:\n",
- "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/formatters.py:339\u001b[0m, in \u001b[0;36mBaseFormatter.__call__\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 338\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 339\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mprinter\u001b[49m\u001b[43m(\u001b[49m\u001b[43mobj\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 340\u001b[0m \u001b[38;5;66;03m# Finally look for special method names\u001b[39;00m\n\u001b[1;32m 341\u001b[0m method \u001b[38;5;241m=\u001b[39m get_real_method(obj, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprint_method)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/pylabtools.py:151\u001b[0m, in \u001b[0;36mprint_figure\u001b[0;34m(fig, fmt, bbox_inches, base64, **kwargs)\u001b[0m\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbackend_bases\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FigureCanvasBase\n\u001b[1;32m 149\u001b[0m FigureCanvasBase(fig)\n\u001b[0;32m--> 151\u001b[0m \u001b[43mfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcanvas\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprint_figure\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbytes_io\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkw\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 152\u001b[0m data \u001b[38;5;241m=\u001b[39m bytes_io\u001b[38;5;241m.\u001b[39mgetvalue()\n\u001b[1;32m 153\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m fmt \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msvg\u001b[39m\u001b[38;5;124m'\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backend_bases.py:2295\u001b[0m, in \u001b[0;36mFigureCanvasBase.print_figure\u001b[0;34m(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)\u001b[0m\n\u001b[1;32m 2289\u001b[0m renderer \u001b[38;5;241m=\u001b[39m _get_renderer(\n\u001b[1;32m 2290\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure,\n\u001b[1;32m 2291\u001b[0m functools\u001b[38;5;241m.\u001b[39mpartial(\n\u001b[1;32m 2292\u001b[0m print_method, orientation\u001b[38;5;241m=\u001b[39morientation)\n\u001b[1;32m 2293\u001b[0m )\n\u001b[1;32m 2294\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(renderer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_draw_disabled\u001b[39m\u001b[38;5;124m\"\u001b[39m, nullcontext)():\n\u001b[0;32m-> 2295\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2297\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches:\n\u001b[1;32m 2298\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtight\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:73\u001b[0m, in \u001b[0;36m_finalize_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;129m@wraps\u001b[39m(draw)\n\u001b[1;32m 72\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdraw_wrapper\u001b[39m(artist, renderer, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m---> 73\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m renderer\u001b[38;5;241m.\u001b[39m_rasterizing:\n\u001b[1;32m 75\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/figure.py:2837\u001b[0m, in \u001b[0;36mFigure.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 2834\u001b[0m \u001b[38;5;66;03m# ValueError can occur when resizing a window.\u001b[39;00m\n\u001b[1;32m 2836\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpatch\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[0;32m-> 2837\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 2838\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2840\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m sfig \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msubfigs:\n\u001b[1;32m 2841\u001b[0m sfig\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axes/_base.py:3091\u001b[0m, in \u001b[0;36m_AxesBase.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 3088\u001b[0m a\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[1;32m 3089\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n\u001b[0;32m-> 3091\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 3092\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3094\u001b[0m renderer\u001b[38;5;241m.\u001b[39mclose_group(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124maxes\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 3095\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstale \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1159\u001b[0m, in \u001b[0;36mAxis.draw\u001b[0;34m(self, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 1156\u001b[0m renderer\u001b[38;5;241m.\u001b[39mopen_group(\u001b[38;5;18m__name__\u001b[39m, gid\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_gid())\n\u001b[1;32m 1158\u001b[0m ticks_to_draw \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_update_ticks()\n\u001b[0;32m-> 1159\u001b[0m ticklabelBoxes, ticklabelBoxes2 \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_tick_bboxes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mticks_to_draw\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks_to_draw:\n\u001b[1;32m 1163\u001b[0m tick\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1085\u001b[0m, in \u001b[0;36mAxis._get_tick_bboxes\u001b[0;34m(self, ticks, renderer)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_tick_bboxes\u001b[39m(\u001b[38;5;28mself\u001b[39m, ticks, renderer):\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124;03m\"\"\"Return lists of bboxes for ticks' label1's and label2's.\"\"\"\u001b[39;00m\n\u001b[0;32m-> 1085\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ([tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1086\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_visible()],\n\u001b[1;32m 1087\u001b[0m [tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_visible()])\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1085\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_tick_bboxes\u001b[39m(\u001b[38;5;28mself\u001b[39m, ticks, renderer):\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124;03m\"\"\"Return lists of bboxes for ticks' label1's and label2's.\"\"\"\u001b[39;00m\n\u001b[0;32m-> 1085\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ([\u001b[43mtick\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlabel1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_window_extent\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1086\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_visible()],\n\u001b[1;32m 1087\u001b[0m [tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_visible()])\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:910\u001b[0m, in \u001b[0;36mText.get_window_extent\u001b[0;34m(self, renderer, dpi)\u001b[0m\n\u001b[1;32m 907\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCannot get window extent w/o renderer\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 909\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m cbook\u001b[38;5;241m.\u001b[39m_setattr_cm(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure, dpi\u001b[38;5;241m=\u001b[39mdpi):\n\u001b[0;32m--> 910\u001b[0m bbox, info, descent \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_layout\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_renderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 911\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_unitless_position()\n\u001b[1;32m 912\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_transform()\u001b[38;5;241m.\u001b[39mtransform((x, y))\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:309\u001b[0m, in \u001b[0;36mText._get_layout\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 306\u001b[0m ys \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 308\u001b[0m \u001b[38;5;66;03m# Full vertical extent of font, including ascenders and descenders:\u001b[39;00m\n\u001b[0;32m--> 309\u001b[0m _, lp_h, lp_d \u001b[38;5;241m=\u001b[39m \u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fontproperties\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 311\u001b[0m \u001b[43m \u001b[49m\u001b[43mismath\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mTeX\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_usetex\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 312\u001b[0m min_dy \u001b[38;5;241m=\u001b[39m (lp_h \u001b[38;5;241m-\u001b[39m lp_d) \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_linespacing\n\u001b[1;32m 314\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, line \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(lines):\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py:259\u001b[0m, in \u001b[0;36mRendererAgg.get_text_width_height_descent\u001b[0;34m(self, s, prop, ismath)\u001b[0m\n\u001b[1;32m 257\u001b[0m texmanager \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_texmanager()\n\u001b[1;32m 258\u001b[0m fontsize \u001b[38;5;241m=\u001b[39m prop\u001b[38;5;241m.\u001b[39mget_size_in_points()\n\u001b[0;32m--> 259\u001b[0m w, h, d \u001b[38;5;241m=\u001b[39m \u001b[43mtexmanager\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 260\u001b[0m \u001b[43m \u001b[49m\u001b[43ms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m w, h, d\n\u001b[1;32m 263\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ismath:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:335\u001b[0m, in \u001b[0;36mTexManager.get_text_width_height_descent\u001b[0;34m(self, tex, fontsize, renderer)\u001b[0m\n\u001b[1;32m 333\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m tex\u001b[38;5;241m.\u001b[39mstrip() \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 334\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m--> 335\u001b[0m dvifile \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmake_dvi\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 336\u001b[0m dpi_fraction \u001b[38;5;241m=\u001b[39m renderer\u001b[38;5;241m.\u001b[39mpoints_to_pixels(\u001b[38;5;241m1.\u001b[39m) \u001b[38;5;28;01mif\u001b[39;00m renderer \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m dviread\u001b[38;5;241m.\u001b[39mDvi(dvifile, \u001b[38;5;241m72\u001b[39m \u001b[38;5;241m*\u001b[39m dpi_fraction) \u001b[38;5;28;01mas\u001b[39;00m dvi:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:271\u001b[0m, in \u001b[0;36mTexManager.make_dvi\u001b[0;34m(self, tex, fontsize)\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[38;5;66;03m# Generate the dvi in a temporary directory to avoid race\u001b[39;00m\n\u001b[1;32m 263\u001b[0m \u001b[38;5;66;03m# conditions e.g. if multiple processes try to process the same tex\u001b[39;00m\n\u001b[1;32m 264\u001b[0m \u001b[38;5;66;03m# string at the same time. Having tmpdir be a subdirectory of the\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 268\u001b[0m \u001b[38;5;66;03m# the absolute path may contain characters (e.g. ~) that TeX does\u001b[39;00m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;66;03m# not support.)\u001b[39;00m\n\u001b[1;32m 270\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m TemporaryDirectory(\u001b[38;5;28mdir\u001b[39m\u001b[38;5;241m=\u001b[39mPath(dvifile)\u001b[38;5;241m.\u001b[39mparent) \u001b[38;5;28;01mas\u001b[39;00m tmpdir:\n\u001b[0;32m--> 271\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_run_checked_subprocess\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 272\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlatex\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m-interaction=nonstopmode\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m--halt-on-error\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 273\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m../\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mtexfile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtmpdir\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 274\u001b[0m (Path(tmpdir) \u001b[38;5;241m/\u001b[39m Path(dvifile)\u001b[38;5;241m.\u001b[39mname)\u001b[38;5;241m.\u001b[39mreplace(dvifile)\n\u001b[1;32m 275\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m dvifile\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:241\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 237\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 238\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFailed to process string with tex because \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m could not be \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 239\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfound\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(command[\u001b[38;5;241m0\u001b[39m])) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 240\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m subprocess\u001b[38;5;241m.\u001b[39mCalledProcessError \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[0;32m--> 241\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 242\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m was not able to process the following string:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{tex!r}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mHere is the full report generated by \u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 245\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{exc}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 246\u001b[0m prog\u001b[38;5;241m=\u001b[39mcommand[\u001b[38;5;241m0\u001b[39m],\n\u001b[1;32m 247\u001b[0m tex\u001b[38;5;241m=\u001b[39mtex\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124municode_escape\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m 248\u001b[0m exc\u001b[38;5;241m=\u001b[39mexc\u001b[38;5;241m.\u001b[39moutput\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m'\u001b[39m))) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 249\u001b[0m _log\u001b[38;5;241m.\u001b[39mdebug(report)\n\u001b[1;32m 250\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m report\n",
- "\u001b[0;31mRuntimeError\u001b[0m: latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../58e5732caba9df74dca26bf4003d5924.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 58e5732caba9df74dca26bf4003d5924.log.\n\n\n"
- ]
- },
- {
- "data": {
- "text/plain": [
- "<Figure size 900x600 with 2 Axes>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
"\"\"\"\n",
"Plot overview over time-averaged population rates encoded in colors\n",
@@ -2086,7 +1848,6 @@
"cell_type": "markdown",
"id": "06a595de",
"metadata": {
- "jp-MarkdownHeadingCollapsed": true,
"tags": []
},
"source": [
@@ -2095,7 +1856,7 @@
},
{
"cell_type": "code",
- "execution_count": 34,
+ "execution_count": null,
"id": "a8e77836-4c37-4b78-b7c4-5e11bc67b4fa",
"metadata": {},
"outputs": [],
@@ -2112,66 +1873,10 @@
},
{
"cell_type": "code",
- "execution_count": 35,
+ "execution_count": null,
"id": "218367da-82ef-47b6-bf15-083ef3d43013",
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "Text(0.5, 0, 'Correlation coefficient')"
- ]
- },
- "execution_count": 35,
- "metadata": {},
- "output_type": "execute_result"
- },
- {
- "ename": "RuntimeError",
- "evalue": "latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../58e5732caba9df74dca26bf4003d5924.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 58e5732caba9df74dca26bf4003d5924.log.\n\n\n",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:233\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 232\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 233\u001b[0m report \u001b[38;5;241m=\u001b[39m \u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_output\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 234\u001b[0m \u001b[43m \u001b[49m\u001b[43mcommand\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mis\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mnot\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtexcache\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 235\u001b[0m \u001b[43m \u001b[49m\u001b[43mstderr\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mSTDOUT\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:415\u001b[0m, in \u001b[0;36mcheck_output\u001b[0;34m(timeout, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 413\u001b[0m kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124minput\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m empty\n\u001b[0;32m--> 415\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mpopenargs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstdout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mPIPE\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcheck\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 416\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mstdout\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:516\u001b[0m, in \u001b[0;36mrun\u001b[0;34m(input, capture_output, timeout, check, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m check \u001b[38;5;129;01mand\u001b[39;00m retcode:\n\u001b[0;32m--> 516\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CalledProcessError(retcode, process\u001b[38;5;241m.\u001b[39margs,\n\u001b[1;32m 517\u001b[0m output\u001b[38;5;241m=\u001b[39mstdout, stderr\u001b[38;5;241m=\u001b[39mstderr)\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m CompletedProcess(process\u001b[38;5;241m.\u001b[39margs, retcode, stdout, stderr)\n",
- "\u001b[0;31mCalledProcessError\u001b[0m: Command '['latex', '-interaction=nonstopmode', '--halt-on-error', '../58e5732caba9df74dca26bf4003d5924.tex']' returned non-zero exit status 1.",
- "\nThe above exception was the direct cause of the following exception:\n",
- "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/formatters.py:339\u001b[0m, in \u001b[0;36mBaseFormatter.__call__\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 338\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 339\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mprinter\u001b[49m\u001b[43m(\u001b[49m\u001b[43mobj\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 340\u001b[0m \u001b[38;5;66;03m# Finally look for special method names\u001b[39;00m\n\u001b[1;32m 341\u001b[0m method \u001b[38;5;241m=\u001b[39m get_real_method(obj, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprint_method)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/pylabtools.py:151\u001b[0m, in \u001b[0;36mprint_figure\u001b[0;34m(fig, fmt, bbox_inches, base64, **kwargs)\u001b[0m\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbackend_bases\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FigureCanvasBase\n\u001b[1;32m 149\u001b[0m FigureCanvasBase(fig)\n\u001b[0;32m--> 151\u001b[0m \u001b[43mfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcanvas\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprint_figure\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbytes_io\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkw\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 152\u001b[0m data \u001b[38;5;241m=\u001b[39m bytes_io\u001b[38;5;241m.\u001b[39mgetvalue()\n\u001b[1;32m 153\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m fmt \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msvg\u001b[39m\u001b[38;5;124m'\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backend_bases.py:2295\u001b[0m, in \u001b[0;36mFigureCanvasBase.print_figure\u001b[0;34m(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)\u001b[0m\n\u001b[1;32m 2289\u001b[0m renderer \u001b[38;5;241m=\u001b[39m _get_renderer(\n\u001b[1;32m 2290\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure,\n\u001b[1;32m 2291\u001b[0m functools\u001b[38;5;241m.\u001b[39mpartial(\n\u001b[1;32m 2292\u001b[0m print_method, orientation\u001b[38;5;241m=\u001b[39morientation)\n\u001b[1;32m 2293\u001b[0m )\n\u001b[1;32m 2294\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(renderer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_draw_disabled\u001b[39m\u001b[38;5;124m\"\u001b[39m, nullcontext)():\n\u001b[0;32m-> 2295\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2297\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches:\n\u001b[1;32m 2298\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtight\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:73\u001b[0m, in \u001b[0;36m_finalize_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;129m@wraps\u001b[39m(draw)\n\u001b[1;32m 72\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdraw_wrapper\u001b[39m(artist, renderer, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m---> 73\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m renderer\u001b[38;5;241m.\u001b[39m_rasterizing:\n\u001b[1;32m 75\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/figure.py:2837\u001b[0m, in \u001b[0;36mFigure.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 2834\u001b[0m \u001b[38;5;66;03m# ValueError can occur when resizing a window.\u001b[39;00m\n\u001b[1;32m 2836\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpatch\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[0;32m-> 2837\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 2838\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2840\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m sfig \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msubfigs:\n\u001b[1;32m 2841\u001b[0m sfig\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axes/_base.py:3091\u001b[0m, in \u001b[0;36m_AxesBase.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 3088\u001b[0m a\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[1;32m 3089\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n\u001b[0;32m-> 3091\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 3092\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3094\u001b[0m renderer\u001b[38;5;241m.\u001b[39mclose_group(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124maxes\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 3095\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstale \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1159\u001b[0m, in \u001b[0;36mAxis.draw\u001b[0;34m(self, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 1156\u001b[0m renderer\u001b[38;5;241m.\u001b[39mopen_group(\u001b[38;5;18m__name__\u001b[39m, gid\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_gid())\n\u001b[1;32m 1158\u001b[0m ticks_to_draw \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_update_ticks()\n\u001b[0;32m-> 1159\u001b[0m ticklabelBoxes, ticklabelBoxes2 \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_tick_bboxes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mticks_to_draw\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks_to_draw:\n\u001b[1;32m 1163\u001b[0m tick\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1085\u001b[0m, in \u001b[0;36mAxis._get_tick_bboxes\u001b[0;34m(self, ticks, renderer)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_tick_bboxes\u001b[39m(\u001b[38;5;28mself\u001b[39m, ticks, renderer):\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124;03m\"\"\"Return lists of bboxes for ticks' label1's and label2's.\"\"\"\u001b[39;00m\n\u001b[0;32m-> 1085\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ([tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1086\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_visible()],\n\u001b[1;32m 1087\u001b[0m [tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_visible()])\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1085\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_tick_bboxes\u001b[39m(\u001b[38;5;28mself\u001b[39m, ticks, renderer):\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124;03m\"\"\"Return lists of bboxes for ticks' label1's and label2's.\"\"\"\u001b[39;00m\n\u001b[0;32m-> 1085\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ([\u001b[43mtick\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlabel1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_window_extent\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1086\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_visible()],\n\u001b[1;32m 1087\u001b[0m [tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_visible()])\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:910\u001b[0m, in \u001b[0;36mText.get_window_extent\u001b[0;34m(self, renderer, dpi)\u001b[0m\n\u001b[1;32m 907\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCannot get window extent w/o renderer\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 909\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m cbook\u001b[38;5;241m.\u001b[39m_setattr_cm(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure, dpi\u001b[38;5;241m=\u001b[39mdpi):\n\u001b[0;32m--> 910\u001b[0m bbox, info, descent \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_layout\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_renderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 911\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_unitless_position()\n\u001b[1;32m 912\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_transform()\u001b[38;5;241m.\u001b[39mtransform((x, y))\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:309\u001b[0m, in \u001b[0;36mText._get_layout\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 306\u001b[0m ys \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 308\u001b[0m \u001b[38;5;66;03m# Full vertical extent of font, including ascenders and descenders:\u001b[39;00m\n\u001b[0;32m--> 309\u001b[0m _, lp_h, lp_d \u001b[38;5;241m=\u001b[39m \u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fontproperties\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 311\u001b[0m \u001b[43m \u001b[49m\u001b[43mismath\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mTeX\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_usetex\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 312\u001b[0m min_dy \u001b[38;5;241m=\u001b[39m (lp_h \u001b[38;5;241m-\u001b[39m lp_d) \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_linespacing\n\u001b[1;32m 314\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, line \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(lines):\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py:259\u001b[0m, in \u001b[0;36mRendererAgg.get_text_width_height_descent\u001b[0;34m(self, s, prop, ismath)\u001b[0m\n\u001b[1;32m 257\u001b[0m texmanager \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_texmanager()\n\u001b[1;32m 258\u001b[0m fontsize \u001b[38;5;241m=\u001b[39m prop\u001b[38;5;241m.\u001b[39mget_size_in_points()\n\u001b[0;32m--> 259\u001b[0m w, h, d \u001b[38;5;241m=\u001b[39m \u001b[43mtexmanager\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 260\u001b[0m \u001b[43m \u001b[49m\u001b[43ms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m w, h, d\n\u001b[1;32m 263\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ismath:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:335\u001b[0m, in \u001b[0;36mTexManager.get_text_width_height_descent\u001b[0;34m(self, tex, fontsize, renderer)\u001b[0m\n\u001b[1;32m 333\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m tex\u001b[38;5;241m.\u001b[39mstrip() \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 334\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m--> 335\u001b[0m dvifile \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmake_dvi\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 336\u001b[0m dpi_fraction \u001b[38;5;241m=\u001b[39m renderer\u001b[38;5;241m.\u001b[39mpoints_to_pixels(\u001b[38;5;241m1.\u001b[39m) \u001b[38;5;28;01mif\u001b[39;00m renderer \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m dviread\u001b[38;5;241m.\u001b[39mDvi(dvifile, \u001b[38;5;241m72\u001b[39m \u001b[38;5;241m*\u001b[39m dpi_fraction) \u001b[38;5;28;01mas\u001b[39;00m dvi:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:271\u001b[0m, in \u001b[0;36mTexManager.make_dvi\u001b[0;34m(self, tex, fontsize)\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[38;5;66;03m# Generate the dvi in a temporary directory to avoid race\u001b[39;00m\n\u001b[1;32m 263\u001b[0m \u001b[38;5;66;03m# conditions e.g. if multiple processes try to process the same tex\u001b[39;00m\n\u001b[1;32m 264\u001b[0m \u001b[38;5;66;03m# string at the same time. Having tmpdir be a subdirectory of the\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 268\u001b[0m \u001b[38;5;66;03m# the absolute path may contain characters (e.g. ~) that TeX does\u001b[39;00m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;66;03m# not support.)\u001b[39;00m\n\u001b[1;32m 270\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m TemporaryDirectory(\u001b[38;5;28mdir\u001b[39m\u001b[38;5;241m=\u001b[39mPath(dvifile)\u001b[38;5;241m.\u001b[39mparent) \u001b[38;5;28;01mas\u001b[39;00m tmpdir:\n\u001b[0;32m--> 271\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_run_checked_subprocess\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 272\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlatex\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m-interaction=nonstopmode\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m--halt-on-error\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 273\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m../\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mtexfile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtmpdir\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 274\u001b[0m (Path(tmpdir) \u001b[38;5;241m/\u001b[39m Path(dvifile)\u001b[38;5;241m.\u001b[39mname)\u001b[38;5;241m.\u001b[39mreplace(dvifile)\n\u001b[1;32m 275\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m dvifile\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:241\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 237\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 238\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFailed to process string with tex because \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m could not be \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 239\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfound\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(command[\u001b[38;5;241m0\u001b[39m])) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 240\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m subprocess\u001b[38;5;241m.\u001b[39mCalledProcessError \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[0;32m--> 241\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 242\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m was not able to process the following string:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{tex!r}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mHere is the full report generated by \u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 245\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{exc}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 246\u001b[0m prog\u001b[38;5;241m=\u001b[39mcommand[\u001b[38;5;241m0\u001b[39m],\n\u001b[1;32m 247\u001b[0m tex\u001b[38;5;241m=\u001b[39mtex\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124municode_escape\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m 248\u001b[0m exc\u001b[38;5;241m=\u001b[39mexc\u001b[38;5;241m.\u001b[39moutput\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m'\u001b[39m))) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 249\u001b[0m _log\u001b[38;5;241m.\u001b[39mdebug(report)\n\u001b[1;32m 250\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m report\n",
- "\u001b[0;31mRuntimeError\u001b[0m: latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../58e5732caba9df74dca26bf4003d5924.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 58e5732caba9df74dca26bf4003d5924.log.\n\n\n"
- ]
- },
- {
- "data": {
- "text/plain": [
- "<Figure size 1062.99x938.52 with 1 Axes>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
"# print(\"plotting Synchrony\")\n",
"\n",
@@ -2220,7 +1925,7 @@
},
{
"cell_type": "code",
- "execution_count": 36,
+ "execution_count": null,
"id": "65377033-f3c0-4f90-be13-70594cfda292",
"metadata": {},
"outputs": [],
@@ -2235,68 +1940,10 @@
},
{
"cell_type": "code",
- "execution_count": 37,
+ "execution_count": null,
"id": "d7480a9b",
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "[<matplotlib.axis.XTick at 0x7f160ae58fd0>,\n",
- " <matplotlib.axis.XTick at 0x7f160ae58fa0>,\n",
- " <matplotlib.axis.XTick at 0x7f160ae58700>]"
- ]
- },
- "execution_count": 37,
- "metadata": {},
- "output_type": "execute_result"
- },
- {
- "ename": "RuntimeError",
- "evalue": "latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../58e5732caba9df74dca26bf4003d5924.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 58e5732caba9df74dca26bf4003d5924.log.\n\n\n",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:233\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 232\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 233\u001b[0m report \u001b[38;5;241m=\u001b[39m \u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_output\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 234\u001b[0m \u001b[43m \u001b[49m\u001b[43mcommand\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mis\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mnot\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtexcache\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 235\u001b[0m \u001b[43m \u001b[49m\u001b[43mstderr\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mSTDOUT\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m exc:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:415\u001b[0m, in \u001b[0;36mcheck_output\u001b[0;34m(timeout, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 413\u001b[0m kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124minput\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m empty\n\u001b[0;32m--> 415\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mpopenargs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstdout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mPIPE\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcheck\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 416\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mstdout\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/._view/6axslmv6jvf4v2nte3uwlayg4vhsjoha/lib/python3.8/subprocess.py:516\u001b[0m, in \u001b[0;36mrun\u001b[0;34m(input, capture_output, timeout, check, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m check \u001b[38;5;129;01mand\u001b[39;00m retcode:\n\u001b[0;32m--> 516\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CalledProcessError(retcode, process\u001b[38;5;241m.\u001b[39margs,\n\u001b[1;32m 517\u001b[0m output\u001b[38;5;241m=\u001b[39mstdout, stderr\u001b[38;5;241m=\u001b[39mstderr)\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m CompletedProcess(process\u001b[38;5;241m.\u001b[39margs, retcode, stdout, stderr)\n",
- "\u001b[0;31mCalledProcessError\u001b[0m: Command '['latex', '-interaction=nonstopmode', '--halt-on-error', '../58e5732caba9df74dca26bf4003d5924.tex']' returned non-zero exit status 1.",
- "\nThe above exception was the direct cause of the following exception:\n",
- "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/formatters.py:339\u001b[0m, in \u001b[0;36mBaseFormatter.__call__\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 338\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 339\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mprinter\u001b[49m\u001b[43m(\u001b[49m\u001b[43mobj\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 340\u001b[0m \u001b[38;5;66;03m# Finally look for special method names\u001b[39;00m\n\u001b[1;32m 341\u001b[0m method \u001b[38;5;241m=\u001b[39m get_real_method(obj, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprint_method)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/IPython/core/pylabtools.py:151\u001b[0m, in \u001b[0;36mprint_figure\u001b[0;34m(fig, fmt, bbox_inches, base64, **kwargs)\u001b[0m\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbackend_bases\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FigureCanvasBase\n\u001b[1;32m 149\u001b[0m FigureCanvasBase(fig)\n\u001b[0;32m--> 151\u001b[0m \u001b[43mfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcanvas\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprint_figure\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbytes_io\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkw\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 152\u001b[0m data \u001b[38;5;241m=\u001b[39m bytes_io\u001b[38;5;241m.\u001b[39mgetvalue()\n\u001b[1;32m 153\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m fmt \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msvg\u001b[39m\u001b[38;5;124m'\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backend_bases.py:2295\u001b[0m, in \u001b[0;36mFigureCanvasBase.print_figure\u001b[0;34m(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)\u001b[0m\n\u001b[1;32m 2289\u001b[0m renderer \u001b[38;5;241m=\u001b[39m _get_renderer(\n\u001b[1;32m 2290\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure,\n\u001b[1;32m 2291\u001b[0m functools\u001b[38;5;241m.\u001b[39mpartial(\n\u001b[1;32m 2292\u001b[0m print_method, orientation\u001b[38;5;241m=\u001b[39morientation)\n\u001b[1;32m 2293\u001b[0m )\n\u001b[1;32m 2294\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(renderer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_draw_disabled\u001b[39m\u001b[38;5;124m\"\u001b[39m, nullcontext)():\n\u001b[0;32m-> 2295\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2297\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches:\n\u001b[1;32m 2298\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m bbox_inches \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtight\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:73\u001b[0m, in \u001b[0;36m_finalize_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;129m@wraps\u001b[39m(draw)\n\u001b[1;32m 72\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdraw_wrapper\u001b[39m(artist, renderer, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[0;32m---> 73\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m renderer\u001b[38;5;241m.\u001b[39m_rasterizing:\n\u001b[1;32m 75\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/figure.py:2837\u001b[0m, in \u001b[0;36mFigure.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 2834\u001b[0m \u001b[38;5;66;03m# ValueError can occur when resizing a window.\u001b[39;00m\n\u001b[1;32m 2836\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpatch\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[0;32m-> 2837\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 2838\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2840\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m sfig \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msubfigs:\n\u001b[1;32m 2841\u001b[0m sfig\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axes/_base.py:3091\u001b[0m, in \u001b[0;36m_AxesBase.draw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 3088\u001b[0m a\u001b[38;5;241m.\u001b[39mdraw(renderer)\n\u001b[1;32m 3089\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstop_rasterizing()\n\u001b[0;32m-> 3091\u001b[0m \u001b[43mmimage\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_draw_list_compositing_images\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 3092\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martists\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfigure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msuppressComposite\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3094\u001b[0m renderer\u001b[38;5;241m.\u001b[39mclose_group(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124maxes\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 3095\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstale \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/image.py:132\u001b[0m, in \u001b[0;36m_draw_list_compositing_images\u001b[0;34m(renderer, parent, artists, suppress_composite)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m not_composite \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m has_images:\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m artists:\n\u001b[0;32m--> 132\u001b[0m \u001b[43ma\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 133\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 134\u001b[0m \u001b[38;5;66;03m# Composite any adjacent images together\u001b[39;00m\n\u001b[1;32m 135\u001b[0m image_group \u001b[38;5;241m=\u001b[39m []\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/artist.py:50\u001b[0m, in \u001b[0;36mallow_rasterization.<locals>.draw_wrapper\u001b[0;34m(artist, renderer)\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 48\u001b[0m renderer\u001b[38;5;241m.\u001b[39mstart_filter()\n\u001b[0;32m---> 50\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mdraw\u001b[49m\u001b[43m(\u001b[49m\u001b[43martist\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m artist\u001b[38;5;241m.\u001b[39mget_agg_filter() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1159\u001b[0m, in \u001b[0;36mAxis.draw\u001b[0;34m(self, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m 1156\u001b[0m renderer\u001b[38;5;241m.\u001b[39mopen_group(\u001b[38;5;18m__name__\u001b[39m, gid\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_gid())\n\u001b[1;32m 1158\u001b[0m ticks_to_draw \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_update_ticks()\n\u001b[0;32m-> 1159\u001b[0m ticklabelBoxes, ticklabelBoxes2 \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_tick_bboxes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mticks_to_draw\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks_to_draw:\n\u001b[1;32m 1163\u001b[0m tick\u001b[38;5;241m.\u001b[39mdraw(renderer)\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1085\u001b[0m, in \u001b[0;36mAxis._get_tick_bboxes\u001b[0;34m(self, ticks, renderer)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_tick_bboxes\u001b[39m(\u001b[38;5;28mself\u001b[39m, ticks, renderer):\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124;03m\"\"\"Return lists of bboxes for ticks' label1's and label2's.\"\"\"\u001b[39;00m\n\u001b[0;32m-> 1085\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ([tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1086\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_visible()],\n\u001b[1;32m 1087\u001b[0m [tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_visible()])\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/axis.py:1085\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 1083\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_tick_bboxes\u001b[39m(\u001b[38;5;28mself\u001b[39m, ticks, renderer):\n\u001b[1;32m 1084\u001b[0m \u001b[38;5;124;03m\"\"\"Return lists of bboxes for ticks' label1's and label2's.\"\"\"\u001b[39;00m\n\u001b[0;32m-> 1085\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ([\u001b[43mtick\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlabel1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_window_extent\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrenderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1086\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel1\u001b[38;5;241m.\u001b[39mget_visible()],\n\u001b[1;32m 1087\u001b[0m [tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_window_extent(renderer)\n\u001b[1;32m 1088\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m tick \u001b[38;5;129;01min\u001b[39;00m ticks \u001b[38;5;28;01mif\u001b[39;00m tick\u001b[38;5;241m.\u001b[39mlabel2\u001b[38;5;241m.\u001b[39mget_visible()])\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:910\u001b[0m, in \u001b[0;36mText.get_window_extent\u001b[0;34m(self, renderer, dpi)\u001b[0m\n\u001b[1;32m 907\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCannot get window extent w/o renderer\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 909\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m cbook\u001b[38;5;241m.\u001b[39m_setattr_cm(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfigure, dpi\u001b[38;5;241m=\u001b[39mdpi):\n\u001b[0;32m--> 910\u001b[0m bbox, info, descent \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_layout\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_renderer\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 911\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_unitless_position()\n\u001b[1;32m 912\u001b[0m x, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_transform()\u001b[38;5;241m.\u001b[39mtransform((x, y))\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/text.py:309\u001b[0m, in \u001b[0;36mText._get_layout\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m 306\u001b[0m ys \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 308\u001b[0m \u001b[38;5;66;03m# Full vertical extent of font, including ascenders and descenders:\u001b[39;00m\n\u001b[0;32m--> 309\u001b[0m _, lp_h, lp_d \u001b[38;5;241m=\u001b[39m \u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fontproperties\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 311\u001b[0m \u001b[43m \u001b[49m\u001b[43mismath\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mTeX\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_usetex\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 312\u001b[0m min_dy \u001b[38;5;241m=\u001b[39m (lp_h \u001b[38;5;241m-\u001b[39m lp_d) \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_linespacing\n\u001b[1;32m 314\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, line \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(lines):\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/backends/backend_agg.py:259\u001b[0m, in \u001b[0;36mRendererAgg.get_text_width_height_descent\u001b[0;34m(self, s, prop, ismath)\u001b[0m\n\u001b[1;32m 257\u001b[0m texmanager \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_texmanager()\n\u001b[1;32m 258\u001b[0m fontsize \u001b[38;5;241m=\u001b[39m prop\u001b[38;5;241m.\u001b[39mget_size_in_points()\n\u001b[0;32m--> 259\u001b[0m w, h, d \u001b[38;5;241m=\u001b[39m \u001b[43mtexmanager\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_text_width_height_descent\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 260\u001b[0m \u001b[43m \u001b[49m\u001b[43ms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrenderer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m w, h, d\n\u001b[1;32m 263\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ismath:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:335\u001b[0m, in \u001b[0;36mTexManager.get_text_width_height_descent\u001b[0;34m(self, tex, fontsize, renderer)\u001b[0m\n\u001b[1;32m 333\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m tex\u001b[38;5;241m.\u001b[39mstrip() \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 334\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m--> 335\u001b[0m dvifile \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmake_dvi\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfontsize\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 336\u001b[0m dpi_fraction \u001b[38;5;241m=\u001b[39m renderer\u001b[38;5;241m.\u001b[39mpoints_to_pixels(\u001b[38;5;241m1.\u001b[39m) \u001b[38;5;28;01mif\u001b[39;00m renderer \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m dviread\u001b[38;5;241m.\u001b[39mDvi(dvifile, \u001b[38;5;241m72\u001b[39m \u001b[38;5;241m*\u001b[39m dpi_fraction) \u001b[38;5;28;01mas\u001b[39;00m dvi:\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:271\u001b[0m, in \u001b[0;36mTexManager.make_dvi\u001b[0;34m(self, tex, fontsize)\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[38;5;66;03m# Generate the dvi in a temporary directory to avoid race\u001b[39;00m\n\u001b[1;32m 263\u001b[0m \u001b[38;5;66;03m# conditions e.g. if multiple processes try to process the same tex\u001b[39;00m\n\u001b[1;32m 264\u001b[0m \u001b[38;5;66;03m# string at the same time. Having tmpdir be a subdirectory of the\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 268\u001b[0m \u001b[38;5;66;03m# the absolute path may contain characters (e.g. ~) that TeX does\u001b[39;00m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;66;03m# not support.)\u001b[39;00m\n\u001b[1;32m 270\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m TemporaryDirectory(\u001b[38;5;28mdir\u001b[39m\u001b[38;5;241m=\u001b[39mPath(dvifile)\u001b[38;5;241m.\u001b[39mparent) \u001b[38;5;28;01mas\u001b[39;00m tmpdir:\n\u001b[0;32m--> 271\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_run_checked_subprocess\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 272\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mlatex\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m-interaction=nonstopmode\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m--halt-on-error\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 273\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m../\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mtexfile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtmpdir\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 274\u001b[0m (Path(tmpdir) \u001b[38;5;241m/\u001b[39m Path(dvifile)\u001b[38;5;241m.\u001b[39mname)\u001b[38;5;241m.\u001b[39mreplace(dvifile)\n\u001b[1;32m 275\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m dvifile\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/var/spack/environments/ebrains-23-02/.spack-env/view/lib/python3.8/site-packages/matplotlib/texmanager.py:241\u001b[0m, in \u001b[0;36mTexManager._run_checked_subprocess\u001b[0;34m(self, command, tex, cwd)\u001b[0m\n\u001b[1;32m 237\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 238\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mFailed to process string with tex because \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m could not be \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 239\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfound\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(command[\u001b[38;5;241m0\u001b[39m])) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 240\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m subprocess\u001b[38;5;241m.\u001b[39mCalledProcessError \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[0;32m--> 241\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m 242\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m was not able to process the following string:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{tex!r}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mHere is the full report generated by \u001b[39m\u001b[38;5;132;01m{prog}\u001b[39;00m\u001b[38;5;124m:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 245\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{exc}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 246\u001b[0m prog\u001b[38;5;241m=\u001b[39mcommand[\u001b[38;5;241m0\u001b[39m],\n\u001b[1;32m 247\u001b[0m tex\u001b[38;5;241m=\u001b[39mtex\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124municode_escape\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m 248\u001b[0m exc\u001b[38;5;241m=\u001b[39mexc\u001b[38;5;241m.\u001b[39moutput\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m'\u001b[39m))) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mexc\u001b[39;00m\n\u001b[1;32m 249\u001b[0m _log\u001b[38;5;241m.\u001b[39mdebug(report)\n\u001b[1;32m 250\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m report\n",
- "\u001b[0;31mRuntimeError\u001b[0m: latex was not able to process the following string:\nb'lp'\n\nHere is the full report generated by latex:\nThis is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex)\n restricted \\write18 enabled.\nentering extended mode\n(../58e5732caba9df74dca26bf4003d5924.tex\nLaTeX2e <2020-02-02> patch level 2\nL3 programming layer <2020-02-14>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2019/12/20 v1.4l Standard LaTeX document class\n(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))\n(/usr/share/texlive/texmf-dist/tex/latex/type1cm/type1cm.sty)\n\n! LaTeX Error: File `type1ec.sty' not found.\n\nType X to quit or <RETURN> to proceed,\nor enter new name. (Default extension: sty)\n\nEnter file name: \n! Emergency stop.\n<read *> \n \nl.6 \\usepackage\n [utf8]{inputenc}^^M\nNo pages of output.\nTranscript written on 58e5732caba9df74dca26bf4003d5924.log.\n\n\n"
- ]
- },
- {
- "data": {
- "text/plain": [
- "<Figure size 1062.99x938.52 with 1 Axes>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
"# print(\"plotting Irregularity\")\n",
"\n",
@@ -2355,23 +2002,10 @@
},
{
"cell_type": "code",
- "execution_count": 38,
+ "execution_count": null,
"id": "0308d50a-1906-4860-9194-7f8664bd1f9d",
"metadata": {},
- "outputs": [
- {
- "ename": "FileNotFoundError",
- "evalue": "[Errno 2] No such file or directory: '/opt/app-root/src/MAM2EBRAINS/simulations/27d81076e6d6e9e591684be053078477/Analysis/rate_time_series_full/rate_time_series_full_V1.npy'",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
- "Input \u001b[0;32mIn [38]\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m area \u001b[38;5;129;01min\u001b[39;00m areas:\n\u001b[1;32m 6\u001b[0m fn \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(data_path, label,\n\u001b[1;32m 7\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mAnalysis\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m 8\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrate_time_series_full\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m 9\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrate_time_series_full_\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m.npy\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(area))\n\u001b[0;32m---> 10\u001b[0m rate_time_series[area] \u001b[38;5;241m=\u001b[39m \u001b[43mnp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mload\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfn\u001b[49m\u001b[43m)\u001b[49m\n",
- "File \u001b[0;32m/srv/main-spack-instance-2302/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.21.6-6fewtq7oarp3vtwlxrrcofz5sxwt55s7/lib/python3.8/site-packages/numpy/lib/npyio.py:417\u001b[0m, in \u001b[0;36mload\u001b[0;34m(file, mmap_mode, allow_pickle, fix_imports, encoding)\u001b[0m\n\u001b[1;32m 415\u001b[0m own_fid \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m 416\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 417\u001b[0m fid \u001b[38;5;241m=\u001b[39m stack\u001b[38;5;241m.\u001b[39menter_context(\u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mos_fspath\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mrb\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m)\n\u001b[1;32m 418\u001b[0m own_fid \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m 420\u001b[0m \u001b[38;5;66;03m# Code to distinguish from NumPy binary files and pickles.\u001b[39;00m\n",
- "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '/opt/app-root/src/MAM2EBRAINS/simulations/27d81076e6d6e9e591684be053078477/Analysis/rate_time_series_full/rate_time_series_full_V1.npy'"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# load data\n",
"\n",
diff --git a/figures/.ipynb_checkpoints/MAM2EBRAINS-checkpoint.py b/figures/.ipynb_checkpoints/MAM2EBRAINS-checkpoint.py
index 5de3bf190e5710ecceabb94c04c636fde1ba2ac5..e9fc09654daa0791e60c12aeb2be4c6c1711df6a 100644
--- a/figures/.ipynb_checkpoints/MAM2EBRAINS-checkpoint.py
+++ b/figures/.ipynb_checkpoints/MAM2EBRAINS-checkpoint.py
@@ -10,8 +10,8 @@ from plotcolors import myred, myblue
import matplotlib.pyplot as pl
from matplotlib import gridspec
-from matplotlib import rc_file
-rc_file('./figures/Schmidt2018_dyn/plotstyle.rc')
+# from matplotlib import rc_file
+# rc_file('./figures/Schmidt2018_dyn/plotstyle.rc')
icolor = myred
ecolor = myblue
diff --git a/figures/MAM2EBRAINS.py b/figures/MAM2EBRAINS.py
index 5de3bf190e5710ecceabb94c04c636fde1ba2ac5..e9fc09654daa0791e60c12aeb2be4c6c1711df6a 100644
--- a/figures/MAM2EBRAINS.py
+++ b/figures/MAM2EBRAINS.py
@@ -10,8 +10,8 @@ from plotcolors import myred, myblue
import matplotlib.pyplot as pl
from matplotlib import gridspec
-from matplotlib import rc_file
-rc_file('./figures/Schmidt2018_dyn/plotstyle.rc')
+# from matplotlib import rc_file
+# rc_file('./figures/Schmidt2018_dyn/plotstyle.rc')
icolor = myred
ecolor = myblue
diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb
index 65fa04ab8226d2ec623373c144b7d086ad2d8ba5..3ae191e745fc747284894f51529e25ea6c66c921 100644
--- a/multi-area-model.ipynb
+++ b/multi-area-model.ipynb
@@ -51,6 +51,7 @@
"cell_type": "markdown",
"id": "d782e527",
"metadata": {
+ "jp-MarkdownHeadingCollapsed": true,
"tags": []
},
"source": [
@@ -755,7 +756,6 @@
"cell_type": "markdown",
"id": "57ff902c-d6ce-4f96-9e4f-8e3e7166ab66",
"metadata": {
- "jp-MarkdownHeadingCollapsed": true,
"tags": []
},
"source": [
@@ -771,8 +771,7 @@
},
"outputs": [],
"source": [
- "label_spikes = M.simulation.label\n",
- "label = M.simulation.label"
+ "label_spikes, label = M.simulation.label"
]
},
{
@@ -1056,19 +1055,6 @@
"## S5. Simulation results visualziation <a class=\"anchor\" id=\"section_5\"></a>"
]
},
- {
- "cell_type": "code",
- "execution_count": 22,
- "id": "3659d4de-cb23-4980-bddb-0245cd4d1bb7",
- "metadata": {},
- "outputs": [],
- "source": [
- "# # visualization settings\n",
- "# icolor = 'r'\n",
- "# ecolor = 'b'\n",
- "# population_labels = ['2/3E', '2/3I', '4E', '4I', '5E', '5I', '6E', '6I']"
- ]
- },
{
"cell_type": "markdown",
"id": "38ddd973",
@@ -1101,8 +1087,8 @@
"# ax.set_ylim(0, 50)\n",
"# ax.legend()\n",
"\n",
- "# # from MAM2EBRAINS import plot_instan_mean_firing_rate\n",
- "# # plot_instan_mean_firing_rate(tsteps, rate, sim_params)"
+ "from MAM2EBRAINS import plot_instan_mean_firing_rate\n",
+ "plot_instan_mean_firing_rate(tsteps, rate, sim_params)"
]
},
{
@@ -1135,18 +1121,18 @@
}
],
"source": [
- "data = np.loadtxt(M.simulation.data_dir + '/recordings/' + M.simulation.label + \"-spikes-1-0.dat\", skiprows=3)\n",
- "tsteps, spikecount = np.unique(data[:,1], return_counts=True)\n",
- "rate = spikecount / M.simulation.params['dt'] * 1e3 / np.sum(M.N_vec)\n",
- "fig, ax = plt.subplots()\n",
- "ax.plot(tsteps, rate)\n",
- "ax.plot(tsteps, np.average(rate)*np.ones(len(tsteps)), label='mean')\n",
- "ax.set_title('instantaneous rate across all populations')\n",
- "ax.set_xlabel('time (ms)')\n",
- "ax.set_ylabel('rate (spikes / s)')\n",
- "ax.set_xlim(0, sim_params['t_sim'])\n",
- "ax.set_ylim(0, 50)\n",
- "ax.legend()"
+ "# data = np.loadtxt(M.simulation.data_dir + '/recordings/' + M.simulation.label + \"-spikes-1-0.dat\", skiprows=3)\n",
+ "# tsteps, spikecount = np.unique(data[:,1], return_counts=True)\n",
+ "# rate = spikecount / M.simulation.params['dt'] * 1e3 / np.sum(M.N_vec)\n",
+ "# fig, ax = plt.subplots()\n",
+ "# ax.plot(tsteps, rate)\n",
+ "# ax.plot(tsteps, np.average(rate)*np.ones(len(tsteps)), label='mean')\n",
+ "# ax.set_title('instantaneous rate across all populations')\n",
+ "# ax.set_xlabel('time (ms)')\n",
+ "# ax.set_ylabel('rate (spikes / s)')\n",
+ "# ax.set_xlim(0, sim_params['t_sim'])\n",
+ "# ax.set_ylim(0, 50)\n",
+ "# ax.legend()"
]
},
{