diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb
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+++ b/multi-area-model.ipynb
@@ -0,0 +1,1411 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "id": "7e07b0d0",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Defaulting to user installation because normal site-packages is not writeable\n",
+ "Requirement already satisfied: nested_dict in /opt/app-root/src/.local/lib/python3.8/site-packages (1.61)\n",
+ "Requirement already satisfied: dicthash in /opt/app-root/src/.local/lib/python3.8/site-packages (0.0.2)\n",
+ "Requirement already satisfied: future in /opt/app-root/src/.local/lib/python3.8/site-packages (from dicthash) (0.18.2)\n"
+ ]
+ }
+ ],
+ "source": [
+ "!pip install nested_dict dicthash"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "id": "61e83d47",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import numpy as np\n",
+ "import os\n",
+ "\n",
+ "from multiarea_model import MultiAreaModel"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "2cedd26b",
+ "metadata": {},
+ "source": [
+ "# Down-scaled model\n",
+ "\n",
+ "Neurons and indegrees are both scaled down to 1%.\n",
+ "Can usually be simulated on a local machine."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "e940bb6b",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "scale_down_to = 0.005"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "241db524",
+ "metadata": {},
+ "source": [
+ "**Warning: This will not yield reasonable dynamical results from the\n",
+ "network and is only meant to demonstrate the simulation workflow.**"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "7af3a191",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "d = {}\n",
+ "conn_params = {'replace_non_simulated_areas': 'het_poisson_stat',\n",
+ " 'g': -11.,\n",
+ " \n",
+ " 'K_stable': 'K_stable.npy',\n",
+ " 'fac_nu_ext_TH': 1.2,\n",
+ " 'fac_nu_ext_5E': 1.125,\n",
+ " 'fac_nu_ext_6E': 1.41666667,\n",
+ " 'av_indegree_V1': 3950.}\n",
+ "input_params = {'rate_ext': 10.}\n",
+ "neuron_params = {'V0_mean': -150.,\n",
+ " 'V0_sd': 50.}\n",
+ "network_params = {'N_scaling': scale_down_to,\n",
+ " 'K_scaling': scale_down_to,\n",
+ " 'fullscale_rates': 'tests/fullscale_rates.json',\n",
+ " 'input_params': input_params,\n",
+ " 'connection_params': conn_params,\n",
+ " 'neuron_params': neuron_params}\n",
+ "\n",
+ "sim_params = {'t_sim': 2000.,\n",
+ " 'num_processes': 1,\n",
+ " 'local_num_threads': 1,\n",
+ " 'recording_dict': {'record_vm': False}}\n",
+ "\n",
+ "theory_params = {'dt': 0.1}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "id": "d409be95",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Initializing network from dictionary.\n",
+ "RAND_DATA_LABEL 1349\n",
+ "Model data base path: /opt/app-root/src/multi-area-model/multiarea_model/data_multiarea\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/srv/test-build/spack/opt/spack/linux-centos7-broadwell/gcc-10.3.0/py-numpy-1.21.0-v2re3aybktzrk5wo5kutbfg4bea6oag3/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning:Mean of empty slice.\n",
+ "/srv/test-build/spack/opt/spack/linux-centos7-broadwell/gcc-10.3.0/py-numpy-1.21.0-v2re3aybktzrk5wo5kutbfg4bea6oag3/lib/python3.8/site-packages/numpy/core/_methods.py:189: RuntimeWarning:invalid value encountered in double_scalars\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "No R installation, taking hard-coded SLN fit parameters.\n",
+ "\n",
+ "\n",
+ "========================================\n",
+ "Customized parameters\n",
+ "--------------------\n",
+ "{'K_scaling': 0.005,\n",
+ " 'N_scaling': 0.005,\n",
+ " 'connection_params': {'K_stable': 'K_stable.npy',\n",
+ " 'av_indegree_V1': 3950.0,\n",
+ " 'fac_nu_ext_5E': 1.125,\n",
+ " 'fac_nu_ext_6E': 1.41666667,\n",
+ " 'fac_nu_ext_TH': 1.2,\n",
+ " 'g': -11.0,\n",
+ " 'replace_non_simulated_areas': 'het_poisson_stat'},\n",
+ " 'fullscale_rates': 'tests/fullscale_rates.json',\n",
+ " 'input_params': {'rate_ext': 10.0},\n",
+ " 'neuron_params': {'V0_mean': -150.0, 'V0_sd': 50.0}}\n",
+ "========================================\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/opt/app-root/src/.local/lib/python3.8/site-packages/dicthash/dicthash.py:47: UserWarning:Float too small for safe conversion tointeger. Rounding down to zero.\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Simulation label: 3262d976c50ea3bf4743174127fdd9a8\n",
+ "Copied files.\n",
+ "Initialized simulation class.\n",
+ "Iteration: 0\n",
+ "Mean-field theory predicts an average rate of 29.588 spikes/s across all populations.\n"
+ ]
+ }
+ ],
+ "source": [
+ "M = MultiAreaModel(network_params, simulation=True,\n",
+ " sim_spec=sim_params,\n",
+ " theory=True,\n",
+ " theory_spec=theory_params)\n",
+ "p, r = M.theory.integrate_siegert()\n",
+ "print(\"Mean-field theory predicts an average \"\n",
+ " \"rate of {0:.3f} spikes/s across all populations.\".format(np.mean(r[:, -1])))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "id": "15778e9c",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Prepared simulation in 0.00 seconds.\n",
+ "Rank 0: created area V1 with 5587 local nodes\n",
+ "Memory after V1 : 1401.15 MB\n",
+ "Rank 0: created area V2 with 12359 local nodes\n",
+ "Memory after V2 : 1428.81 MB\n",
+ "Rank 0: created area VP with 19107 local nodes\n",
+ "Memory after VP : 1459.11 MB\n",
+ "Rank 0: created area V3 with 26024 local nodes\n",
+ "Memory after V3 : 1488.66 MB\n",
+ "Rank 0: created area V3A with 30934 local nodes\n",
+ "Memory after V3A : 1509.58 MB\n",
+ "Rank 0: created area MT with 36731 local nodes\n",
+ "Memory after MT : 1536.38 MB\n",
+ "Rank 0: created area V4t with 42326 local nodes\n",
+ "Memory after V4t : 1561.34 MB\n",
+ "Rank 0: created area V4 with 48809 local nodes\n",
+ "Memory after V4 : 1590.08 MB\n",
+ "Rank 0: created area VOT with 54420 local nodes\n",
+ "Memory after VOT : 1616.06 MB\n",
+ "Rank 0: created area MSTd with 59652 local nodes\n",
+ "Memory after MSTd : 1642.70 MB\n",
+ "Rank 0: created area PIP with 64596 local nodes\n",
+ "Memory after PIP : 1667.27 MB\n",
+ "Rank 0: created area PO with 69540 local nodes\n",
+ "Memory after PO : 1691.75 MB\n",
+ "Rank 0: created area DP with 74306 local nodes\n",
+ "Memory after DP : 1715.18 MB\n",
+ "Rank 0: created area MIP with 78788 local nodes\n",
+ "Memory after MIP : 1738.88 MB\n",
+ "Rank 0: created area MDP with 84084 local nodes\n",
+ "Memory after MDP : 1763.31 MB\n",
+ "Rank 0: created area VIP with 89562 local nodes\n",
+ "Memory after VIP : 1787.62 MB\n",
+ "Rank 0: created area LIP with 94428 local nodes\n",
+ "Memory after LIP : 1812.97 MB\n",
+ "Rank 0: created area PITv with 100292 local nodes\n",
+ "Memory after PITv : 1840.07 MB\n",
+ "Rank 0: created area PITd with 106164 local nodes\n",
+ "Memory after PITd : 1868.93 MB\n",
+ "Rank 0: created area MSTl with 111396 local nodes\n",
+ "Memory after MSTl : 1896.56 MB\n",
+ "Rank 0: created area CITv with 115931 local nodes\n",
+ "Memory after CITv : 1920.68 MB\n",
+ "Rank 0: created area CITd with 120331 local nodes\n",
+ "Memory after CITd : 1942.41 MB\n",
+ "Rank 0: created area FEF with 125182 local nodes\n",
+ "Memory after FEF : 1964.41 MB\n",
+ "Rank 0: created area TF with 129117 local nodes\n",
+ "Memory after TF : 1987.88 MB\n",
+ "Rank 0: created area AITv with 133873 local nodes\n",
+ "Memory after AITv : 2006.77 MB\n",
+ "Rank 0: created area FST with 138068 local nodes\n",
+ "Memory after FST : 2030.80 MB\n",
+ "Rank 0: created area 7a with 142669 local nodes\n",
+ "Memory after 7a : 2050.91 MB\n",
+ "Rank 0: created area STPp with 147072 local nodes\n",
+ "Memory after STPp : 2074.14 MB\n",
+ "Rank 0: created area STPa with 151352 local nodes\n",
+ "Memory after STPa : 2096.18 MB\n",
+ "Rank 0: created area 46 with 155019 local nodes\n",
+ "Memory after 46 : 2116.31 MB\n",
+ "Rank 0: created area AITd with 159809 local nodes\n",
+ "Memory after AITd : 2134.84 MB\n",
+ "Rank 0: created area TH with 122538 local nodes\n",
+ "Memory after TH : 2159.46 MB\n",
+ "Created areas and internal connections in 56.70 seconds.\n",
+ "Created cortico-cortical connections in 38.64 seconds.\n",
+ "Simulated network in 56.95 seconds.\n"
+ ]
+ }
+ ],
+ "source": [
+ "M.simulation.simulate()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "id": "cb8e3edd",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "data = np.loadtxt(M.simulation.label + \"-spikes-1-0.dat\", skiprows=3)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "id": "84dc3bde",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "array([[5.0000e+01, 1.0000e-01],\n",
+ " [8.2000e+01, 1.0000e-01],\n",
+ " [3.3700e+02, 1.0000e-01],\n",
+ " ...,\n",
+ " [1.8629e+04, 2.0000e+03],\n",
+ " [2.0259e+04, 2.0000e+03],\n",
+ " [2.0265e+04, 2.0000e+03]])"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "data"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "id": "9590223b",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "tsteps, spikecount = np.unique(data[:,1], return_counts=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 35,
+ "id": "0c3fc302",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import matplotlib.pyplot as plt"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 36,
+ "id": "9f21dd40",
+ "metadata": {},
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+ {
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+ " if (forward) {\n",
+ " canvas_div.style.width = width + 'px';\n",
+ " canvas_div.style.height = height + 'px';\n",
+ " }\n",
+ " };\n",
+ "\n",
+ " // Disable right mouse context menu.\n",
+ " this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n",
+ " event.preventDefault();\n",
+ " return false;\n",
+ " });\n",
+ "\n",
+ " function set_focus() {\n",
+ " canvas.focus();\n",
+ " canvas_div.focus();\n",
+ " }\n",
+ "\n",
+ " window.setTimeout(set_focus, 100);\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype._init_toolbar = function () {\n",
+ " var fig = this;\n",
+ "\n",
+ " var toolbar = document.createElement('div');\n",
+ " toolbar.classList = 'mpl-toolbar';\n",
+ " this.root.appendChild(toolbar);\n",
+ "\n",
+ " function on_click_closure(name) {\n",
+ " return function (_event) {\n",
+ " return fig.toolbar_button_onclick(name);\n",
+ " };\n",
+ " }\n",
+ "\n",
+ " function on_mouseover_closure(tooltip) {\n",
+ " return function (event) {\n",
+ " if (!event.currentTarget.disabled) {\n",
+ " return fig.toolbar_button_onmouseover(tooltip);\n",
+ " }\n",
+ " };\n",
+ " }\n",
+ "\n",
+ " fig.buttons = {};\n",
+ " var buttonGroup = document.createElement('div');\n",
+ " buttonGroup.classList = 'mpl-button-group';\n",
+ " for (var toolbar_ind in mpl.toolbar_items) {\n",
+ " var name = mpl.toolbar_items[toolbar_ind][0];\n",
+ " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n",
+ " var image = mpl.toolbar_items[toolbar_ind][2];\n",
+ " var method_name = mpl.toolbar_items[toolbar_ind][3];\n",
+ "\n",
+ " if (!name) {\n",
+ " /* Instead of a spacer, we start a new button group. */\n",
+ " if (buttonGroup.hasChildNodes()) {\n",
+ " toolbar.appendChild(buttonGroup);\n",
+ " }\n",
+ " buttonGroup = document.createElement('div');\n",
+ " buttonGroup.classList = 'mpl-button-group';\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " var button = (fig.buttons[name] = document.createElement('button'));\n",
+ " button.classList = 'mpl-widget';\n",
+ " button.setAttribute('role', 'button');\n",
+ " button.setAttribute('aria-disabled', 'false');\n",
+ " button.addEventListener('click', on_click_closure(method_name));\n",
+ " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n",
+ "\n",
+ " var icon_img = document.createElement('img');\n",
+ " icon_img.src = '_images/' + image + '.png';\n",
+ " icon_img.srcset = '_images/' + image + '_large.png 2x';\n",
+ " icon_img.alt = tooltip;\n",
+ " button.appendChild(icon_img);\n",
+ "\n",
+ " buttonGroup.appendChild(button);\n",
+ " }\n",
+ "\n",
+ " if (buttonGroup.hasChildNodes()) {\n",
+ " toolbar.appendChild(buttonGroup);\n",
+ " }\n",
+ "\n",
+ " var fmt_picker = document.createElement('select');\n",
+ " fmt_picker.classList = 'mpl-widget';\n",
+ " toolbar.appendChild(fmt_picker);\n",
+ " this.format_dropdown = fmt_picker;\n",
+ "\n",
+ " for (var ind in mpl.extensions) {\n",
+ " var fmt = mpl.extensions[ind];\n",
+ " var option = document.createElement('option');\n",
+ " option.selected = fmt === mpl.default_extension;\n",
+ " option.innerHTML = fmt;\n",
+ " fmt_picker.appendChild(option);\n",
+ " }\n",
+ "\n",
+ " var status_bar = document.createElement('span');\n",
+ " status_bar.classList = 'mpl-message';\n",
+ " toolbar.appendChild(status_bar);\n",
+ " this.message = status_bar;\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n",
+ " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n",
+ " // which will in turn request a refresh of the image.\n",
+ " this.send_message('resize', { width: x_pixels, height: y_pixels });\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.send_message = function (type, properties) {\n",
+ " properties['type'] = type;\n",
+ " properties['figure_id'] = this.id;\n",
+ " this.ws.send(JSON.stringify(properties));\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.send_draw_message = function () {\n",
+ " if (!this.waiting) {\n",
+ " this.waiting = true;\n",
+ " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n",
+ " }\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_save = function (fig, _msg) {\n",
+ " var format_dropdown = fig.format_dropdown;\n",
+ " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n",
+ " fig.ondownload(fig, format);\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_resize = function (fig, msg) {\n",
+ " var size = msg['size'];\n",
+ " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n",
+ " fig._resize_canvas(size[0], size[1], msg['forward']);\n",
+ " fig.send_message('refresh', {});\n",
+ " }\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n",
+ " var x0 = msg['x0'] / fig.ratio;\n",
+ " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n",
+ " var x1 = msg['x1'] / fig.ratio;\n",
+ " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n",
+ " x0 = Math.floor(x0) + 0.5;\n",
+ " y0 = Math.floor(y0) + 0.5;\n",
+ " x1 = Math.floor(x1) + 0.5;\n",
+ " y1 = Math.floor(y1) + 0.5;\n",
+ " var min_x = Math.min(x0, x1);\n",
+ " var min_y = Math.min(y0, y1);\n",
+ " var width = Math.abs(x1 - x0);\n",
+ " var height = Math.abs(y1 - y0);\n",
+ "\n",
+ " fig.rubberband_context.clearRect(\n",
+ " 0,\n",
+ " 0,\n",
+ " fig.canvas.width / fig.ratio,\n",
+ " fig.canvas.height / fig.ratio\n",
+ " );\n",
+ "\n",
+ " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n",
+ " // Updates the figure title.\n",
+ " fig.header.textContent = msg['label'];\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n",
+ " var cursor = msg['cursor'];\n",
+ " switch (cursor) {\n",
+ " case 0:\n",
+ " cursor = 'pointer';\n",
+ " break;\n",
+ " case 1:\n",
+ " cursor = 'default';\n",
+ " break;\n",
+ " case 2:\n",
+ " cursor = 'crosshair';\n",
+ " break;\n",
+ " case 3:\n",
+ " cursor = 'move';\n",
+ " break;\n",
+ " }\n",
+ " fig.rubberband_canvas.style.cursor = cursor;\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_message = function (fig, msg) {\n",
+ " fig.message.textContent = msg['message'];\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n",
+ " // Request the server to send over a new figure.\n",
+ " fig.send_draw_message();\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n",
+ " fig.image_mode = msg['mode'];\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n",
+ " for (var key in msg) {\n",
+ " if (!(key in fig.buttons)) {\n",
+ " continue;\n",
+ " }\n",
+ " fig.buttons[key].disabled = !msg[key];\n",
+ " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n",
+ " }\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n",
+ " if (msg['mode'] === 'PAN') {\n",
+ " fig.buttons['Pan'].classList.add('active');\n",
+ " fig.buttons['Zoom'].classList.remove('active');\n",
+ " } else if (msg['mode'] === 'ZOOM') {\n",
+ " fig.buttons['Pan'].classList.remove('active');\n",
+ " fig.buttons['Zoom'].classList.add('active');\n",
+ " } else {\n",
+ " fig.buttons['Pan'].classList.remove('active');\n",
+ " fig.buttons['Zoom'].classList.remove('active');\n",
+ " }\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.updated_canvas_event = function () {\n",
+ " // Called whenever the canvas gets updated.\n",
+ " this.send_message('ack', {});\n",
+ "};\n",
+ "\n",
+ "// A function to construct a web socket function for onmessage handling.\n",
+ "// Called in the figure constructor.\n",
+ "mpl.figure.prototype._make_on_message_function = function (fig) {\n",
+ " return function socket_on_message(evt) {\n",
+ " if (evt.data instanceof Blob) {\n",
+ " var img = evt.data;\n",
+ " if (img.type !== 'image/png') {\n",
+ " /* FIXME: We get \"Resource interpreted as Image but\n",
+ " * transferred with MIME type text/plain:\" errors on\n",
+ " * Chrome. But how to set the MIME type? It doesn't seem\n",
+ " * to be part of the websocket stream */\n",
+ " img.type = 'image/png';\n",
+ " }\n",
+ "\n",
+ " /* Free the memory for the previous frames */\n",
+ " if (fig.imageObj.src) {\n",
+ " (window.URL || window.webkitURL).revokeObjectURL(\n",
+ " fig.imageObj.src\n",
+ " );\n",
+ " }\n",
+ "\n",
+ " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n",
+ " img\n",
+ " );\n",
+ " fig.updated_canvas_event();\n",
+ " fig.waiting = false;\n",
+ " return;\n",
+ " } else if (\n",
+ " typeof evt.data === 'string' &&\n",
+ " evt.data.slice(0, 21) === 'data:image/png;base64'\n",
+ " ) {\n",
+ " fig.imageObj.src = evt.data;\n",
+ " fig.updated_canvas_event();\n",
+ " fig.waiting = false;\n",
+ " return;\n",
+ " }\n",
+ "\n",
+ " var msg = JSON.parse(evt.data);\n",
+ " var msg_type = msg['type'];\n",
+ "\n",
+ " // Call the \"handle_{type}\" callback, which takes\n",
+ " // the figure and JSON message as its only arguments.\n",
+ " try {\n",
+ " var callback = fig['handle_' + msg_type];\n",
+ " } catch (e) {\n",
+ " console.log(\n",
+ " \"No handler for the '\" + msg_type + \"' message type: \",\n",
+ " msg\n",
+ " );\n",
+ " return;\n",
+ " }\n",
+ "\n",
+ " if (callback) {\n",
+ " try {\n",
+ " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n",
+ " callback(fig, msg);\n",
+ " } catch (e) {\n",
+ " console.log(\n",
+ " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n",
+ " e,\n",
+ " e.stack,\n",
+ " msg\n",
+ " );\n",
+ " }\n",
+ " }\n",
+ " };\n",
+ "};\n",
+ "\n",
+ "// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n",
+ "mpl.findpos = function (e) {\n",
+ " //this section is from http://www.quirksmode.org/js/events_properties.html\n",
+ " var targ;\n",
+ " if (!e) {\n",
+ " e = window.event;\n",
+ " }\n",
+ " if (e.target) {\n",
+ " targ = e.target;\n",
+ " } else if (e.srcElement) {\n",
+ " targ = e.srcElement;\n",
+ " }\n",
+ " if (targ.nodeType === 3) {\n",
+ " // defeat Safari bug\n",
+ " targ = targ.parentNode;\n",
+ " }\n",
+ "\n",
+ " // pageX,Y are the mouse positions relative to the document\n",
+ " var boundingRect = targ.getBoundingClientRect();\n",
+ " var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n",
+ " var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n",
+ "\n",
+ " return { x: x, y: y };\n",
+ "};\n",
+ "\n",
+ "/*\n",
+ " * return a copy of an object with only non-object keys\n",
+ " * we need this to avoid circular references\n",
+ " * http://stackoverflow.com/a/24161582/3208463\n",
+ " */\n",
+ "function simpleKeys(original) {\n",
+ " return Object.keys(original).reduce(function (obj, key) {\n",
+ " if (typeof original[key] !== 'object') {\n",
+ " obj[key] = original[key];\n",
+ " }\n",
+ " return obj;\n",
+ " }, {});\n",
+ "}\n",
+ "\n",
+ "mpl.figure.prototype.mouse_event = function (event, name) {\n",
+ " var canvas_pos = mpl.findpos(event);\n",
+ "\n",
+ " if (name === 'button_press') {\n",
+ " this.canvas.focus();\n",
+ " this.canvas_div.focus();\n",
+ " }\n",
+ "\n",
+ " var x = canvas_pos.x * this.ratio;\n",
+ " var y = canvas_pos.y * this.ratio;\n",
+ "\n",
+ " this.send_message(name, {\n",
+ " x: x,\n",
+ " y: y,\n",
+ " button: event.button,\n",
+ " step: event.step,\n",
+ " guiEvent: simpleKeys(event),\n",
+ " });\n",
+ "\n",
+ " /* This prevents the web browser from automatically changing to\n",
+ " * the text insertion cursor when the button is pressed. We want\n",
+ " * to control all of the cursor setting manually through the\n",
+ " * 'cursor' event from matplotlib */\n",
+ " event.preventDefault();\n",
+ " return false;\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n",
+ " // Handle any extra behaviour associated with a key event\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.key_event = function (event, name) {\n",
+ " // Prevent repeat events\n",
+ " if (name === 'key_press') {\n",
+ " if (event.key === this._key) {\n",
+ " return;\n",
+ " } else {\n",
+ " this._key = event.key;\n",
+ " }\n",
+ " }\n",
+ " if (name === 'key_release') {\n",
+ " this._key = null;\n",
+ " }\n",
+ "\n",
+ " var value = '';\n",
+ " if (event.ctrlKey && event.key !== 'Control') {\n",
+ " value += 'ctrl+';\n",
+ " }\n",
+ " else if (event.altKey && event.key !== 'Alt') {\n",
+ " value += 'alt+';\n",
+ " }\n",
+ " else if (event.shiftKey && event.key !== 'Shift') {\n",
+ " value += 'shift+';\n",
+ " }\n",
+ "\n",
+ " value += 'k' + event.key;\n",
+ "\n",
+ " this._key_event_extra(event, name);\n",
+ "\n",
+ " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n",
+ " return false;\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n",
+ " if (name === 'download') {\n",
+ " this.handle_save(this, null);\n",
+ " } else {\n",
+ " this.send_message('toolbar_button', { name: name });\n",
+ " }\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n",
+ " this.message.textContent = tooltip;\n",
+ "};\n",
+ "\n",
+ "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n",
+ "// prettier-ignore\n",
+ "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n",
+ "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n",
+ "\n",
+ "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n",
+ "\n",
+ "mpl.default_extension = \"png\";/* global mpl */\n",
+ "\n",
+ "var comm_websocket_adapter = function (comm) {\n",
+ " // Create a \"websocket\"-like object which calls the given IPython comm\n",
+ " // object with the appropriate methods. Currently this is a non binary\n",
+ " // socket, so there is still some room for performance tuning.\n",
+ " var ws = {};\n",
+ "\n",
+ " ws.binaryType = comm.kernel.ws.binaryType;\n",
+ " ws.readyState = comm.kernel.ws.readyState;\n",
+ " function updateReadyState(_event) {\n",
+ " if (comm.kernel.ws) {\n",
+ " ws.readyState = comm.kernel.ws.readyState;\n",
+ " } else {\n",
+ " ws.readyState = 3; // Closed state.\n",
+ " }\n",
+ " }\n",
+ " comm.kernel.ws.addEventListener('open', updateReadyState);\n",
+ " comm.kernel.ws.addEventListener('close', updateReadyState);\n",
+ " comm.kernel.ws.addEventListener('error', updateReadyState);\n",
+ "\n",
+ " ws.close = function () {\n",
+ " comm.close();\n",
+ " };\n",
+ " ws.send = function (m) {\n",
+ " //console.log('sending', m);\n",
+ " comm.send(m);\n",
+ " };\n",
+ " // Register the callback with on_msg.\n",
+ " comm.on_msg(function (msg) {\n",
+ " //console.log('receiving', msg['content']['data'], msg);\n",
+ " var data = msg['content']['data'];\n",
+ " if (data['blob'] !== undefined) {\n",
+ " data = {\n",
+ " data: new Blob(msg['buffers'], { type: data['blob'] }),\n",
+ " };\n",
+ " }\n",
+ " // Pass the mpl event to the overridden (by mpl) onmessage function.\n",
+ " ws.onmessage(data);\n",
+ " });\n",
+ " return ws;\n",
+ "};\n",
+ "\n",
+ "mpl.mpl_figure_comm = function (comm, msg) {\n",
+ " // This is the function which gets called when the mpl process\n",
+ " // starts-up an IPython Comm through the \"matplotlib\" channel.\n",
+ "\n",
+ " var id = msg.content.data.id;\n",
+ " // Get hold of the div created by the display call when the Comm\n",
+ " // socket was opened in Python.\n",
+ " var element = document.getElementById(id);\n",
+ " var ws_proxy = comm_websocket_adapter(comm);\n",
+ "\n",
+ " function ondownload(figure, _format) {\n",
+ " window.open(figure.canvas.toDataURL());\n",
+ " }\n",
+ "\n",
+ " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n",
+ "\n",
+ " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n",
+ " // web socket which is closed, not our websocket->open comm proxy.\n",
+ " ws_proxy.onopen();\n",
+ "\n",
+ " fig.parent_element = element;\n",
+ " fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n",
+ " if (!fig.cell_info) {\n",
+ " console.error('Failed to find cell for figure', id, fig);\n",
+ " return;\n",
+ " }\n",
+ " fig.cell_info[0].output_area.element.on(\n",
+ " 'cleared',\n",
+ " { fig: fig },\n",
+ " fig._remove_fig_handler\n",
+ " );\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_close = function (fig, msg) {\n",
+ " var width = fig.canvas.width / fig.ratio;\n",
+ " fig.cell_info[0].output_area.element.off(\n",
+ " 'cleared',\n",
+ " fig._remove_fig_handler\n",
+ " );\n",
+ " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n",
+ "\n",
+ " // Update the output cell to use the data from the current canvas.\n",
+ " fig.push_to_output();\n",
+ " var dataURL = fig.canvas.toDataURL();\n",
+ " // Re-enable the keyboard manager in IPython - without this line, in FF,\n",
+ " // the notebook keyboard shortcuts fail.\n",
+ " IPython.keyboard_manager.enable();\n",
+ " fig.parent_element.innerHTML =\n",
+ " '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n",
+ " fig.close_ws(fig, msg);\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.close_ws = function (fig, msg) {\n",
+ " fig.send_message('closing', msg);\n",
+ " // fig.ws.close()\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n",
+ " // Turn the data on the canvas into data in the output cell.\n",
+ " var width = this.canvas.width / this.ratio;\n",
+ " var dataURL = this.canvas.toDataURL();\n",
+ " this.cell_info[1]['text/html'] =\n",
+ " '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.updated_canvas_event = function () {\n",
+ " // Tell IPython that the notebook contents must change.\n",
+ " IPython.notebook.set_dirty(true);\n",
+ " this.send_message('ack', {});\n",
+ " var fig = this;\n",
+ " // Wait a second, then push the new image to the DOM so\n",
+ " // that it is saved nicely (might be nice to debounce this).\n",
+ " setTimeout(function () {\n",
+ " fig.push_to_output();\n",
+ " }, 1000);\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype._init_toolbar = function () {\n",
+ " var fig = this;\n",
+ "\n",
+ " var toolbar = document.createElement('div');\n",
+ " toolbar.classList = 'btn-toolbar';\n",
+ " this.root.appendChild(toolbar);\n",
+ "\n",
+ " function on_click_closure(name) {\n",
+ " return function (_event) {\n",
+ " return fig.toolbar_button_onclick(name);\n",
+ " };\n",
+ " }\n",
+ "\n",
+ " function on_mouseover_closure(tooltip) {\n",
+ " return function (event) {\n",
+ " if (!event.currentTarget.disabled) {\n",
+ " return fig.toolbar_button_onmouseover(tooltip);\n",
+ " }\n",
+ " };\n",
+ " }\n",
+ "\n",
+ " fig.buttons = {};\n",
+ " var buttonGroup = document.createElement('div');\n",
+ " buttonGroup.classList = 'btn-group';\n",
+ " var button;\n",
+ " for (var toolbar_ind in mpl.toolbar_items) {\n",
+ " var name = mpl.toolbar_items[toolbar_ind][0];\n",
+ " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n",
+ " var image = mpl.toolbar_items[toolbar_ind][2];\n",
+ " var method_name = mpl.toolbar_items[toolbar_ind][3];\n",
+ "\n",
+ " if (!name) {\n",
+ " /* Instead of a spacer, we start a new button group. */\n",
+ " if (buttonGroup.hasChildNodes()) {\n",
+ " toolbar.appendChild(buttonGroup);\n",
+ " }\n",
+ " buttonGroup = document.createElement('div');\n",
+ " buttonGroup.classList = 'btn-group';\n",
+ " continue;\n",
+ " }\n",
+ "\n",
+ " button = fig.buttons[name] = document.createElement('button');\n",
+ " button.classList = 'btn btn-default';\n",
+ " button.href = '#';\n",
+ " button.title = name;\n",
+ " button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n",
+ " button.addEventListener('click', on_click_closure(method_name));\n",
+ " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n",
+ " buttonGroup.appendChild(button);\n",
+ " }\n",
+ "\n",
+ " if (buttonGroup.hasChildNodes()) {\n",
+ " toolbar.appendChild(buttonGroup);\n",
+ " }\n",
+ "\n",
+ " // Add the status bar.\n",
+ " var status_bar = document.createElement('span');\n",
+ " status_bar.classList = 'mpl-message pull-right';\n",
+ " toolbar.appendChild(status_bar);\n",
+ " this.message = status_bar;\n",
+ "\n",
+ " // Add the close button to the window.\n",
+ " var buttongrp = document.createElement('div');\n",
+ " buttongrp.classList = 'btn-group inline pull-right';\n",
+ " button = document.createElement('button');\n",
+ " button.classList = 'btn btn-mini btn-primary';\n",
+ " button.href = '#';\n",
+ " button.title = 'Stop Interaction';\n",
+ " button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n",
+ " button.addEventListener('click', function (_evt) {\n",
+ " fig.handle_close(fig, {});\n",
+ " });\n",
+ " button.addEventListener(\n",
+ " 'mouseover',\n",
+ " on_mouseover_closure('Stop Interaction')\n",
+ " );\n",
+ " buttongrp.appendChild(button);\n",
+ " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n",
+ " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype._remove_fig_handler = function (event) {\n",
+ " var fig = event.data.fig;\n",
+ " if (event.target !== this) {\n",
+ " // Ignore bubbled events from children.\n",
+ " return;\n",
+ " }\n",
+ " fig.close_ws(fig, {});\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype._root_extra_style = function (el) {\n",
+ " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype._canvas_extra_style = function (el) {\n",
+ " // this is important to make the div 'focusable\n",
+ " el.setAttribute('tabindex', 0);\n",
+ " // reach out to IPython and tell the keyboard manager to turn it's self\n",
+ " // off when our div gets focus\n",
+ "\n",
+ " // location in version 3\n",
+ " if (IPython.notebook.keyboard_manager) {\n",
+ " IPython.notebook.keyboard_manager.register_events(el);\n",
+ " } else {\n",
+ " // location in version 2\n",
+ " IPython.keyboard_manager.register_events(el);\n",
+ " }\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype._key_event_extra = function (event, _name) {\n",
+ " var manager = IPython.notebook.keyboard_manager;\n",
+ " if (!manager) {\n",
+ " manager = IPython.keyboard_manager;\n",
+ " }\n",
+ "\n",
+ " // Check for shift+enter\n",
+ " if (event.shiftKey && event.which === 13) {\n",
+ " this.canvas_div.blur();\n",
+ " // select the cell after this one\n",
+ " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n",
+ " IPython.notebook.select(index + 1);\n",
+ " }\n",
+ "};\n",
+ "\n",
+ "mpl.figure.prototype.handle_save = function (fig, _msg) {\n",
+ " fig.ondownload(fig, null);\n",
+ "};\n",
+ "\n",
+ "mpl.find_output_cell = function (html_output) {\n",
+ " // Return the cell and output element which can be found *uniquely* in the notebook.\n",
+ " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n",
+ " // IPython event is triggered only after the cells have been serialised, which for\n",
+ " // our purposes (turning an active figure into a static one), is too late.\n",
+ " var cells = IPython.notebook.get_cells();\n",
+ " var ncells = cells.length;\n",
+ " for (var i = 0; i < ncells; i++) {\n",
+ " var cell = cells[i];\n",
+ " if (cell.cell_type === 'code') {\n",
+ " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n",
+ " var data = cell.output_area.outputs[j];\n",
+ " if (data.data) {\n",
+ " // IPython >= 3 moved mimebundle to data attribute of output\n",
+ " data = data.data;\n",
+ " }\n",
+ " if (data['text/html'] === html_output) {\n",
+ " return [cell, data, j];\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ "};\n",
+ "\n",
+ "// Register the function which deals with the matplotlib target/channel.\n",
+ "// The kernel may be null if the page has been refreshed.\n",
+ "if (IPython.notebook.kernel !== null) {\n",
+ " IPython.notebook.kernel.comm_manager.register_target(\n",
+ " 'matplotlib',\n",
+ " mpl.mpl_figure_comm\n",
+ " );\n",
+ "}\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Javascript object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "<div id='ee555bc3-e4a9-4dda-ac23-66d7f15c2987'></div>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/plain": [
+ "[<matplotlib.lines.Line2D at 0x7f24f81183d0>]"
+ ]
+ },
+ "execution_count": 36,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "fig, ax = plt.subplots()\n",
+ "ax.plot(tsteps, spikecount)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 37,
+ "id": "41028d2c",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "plt.show()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 54,
+ "id": "c6091457",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "(19979, 36.330497021872965)"
+ ]
+ },
+ "execution_count": 54,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "len(spikecount), np.average(spikecount)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 52,
+ "id": "ad2bd7b2",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "36.55876300127927"
+ ]
+ },
+ "execution_count": 52,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "np.average(spikecount[2000:])"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "EBRAINS_release_20210930",
+ "language": "python",
+ "name": "spack_python_kernel_release_20210930"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.8.11"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}