diff --git a/figures/2 T1 mapping/figure_2-2.ipynb b/figures/2 T1 mapping/figure_2-2.ipynb
index f590aab..30573b0 100644
--- a/figures/2 T1 mapping/figure_2-2.ipynb
+++ b/figures/2 T1 mapping/figure_2-2.ipynb
@@ -1,159 +1,5 @@
{
"cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---\n",
- "jupytext:\n",
- " formats: md:myst\n",
- " text_representation:\n",
- " extension: .md\n",
- " format_name: myst\n",
- "kernelspec:\n",
- " display_name: Python 3\n",
- " language: python\n",
- " name: python3\n",
- "---"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 1,
- "metadata": {},
- "outputs": [
- {
- "ename": "ModuleNotFoundError",
- "evalue": "No module named 'repo2data'",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
- "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mrepo2data\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mrepo2data\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Repo2Data\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mos\u001b[39;00m \n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mpickle\u001b[39;00m\n",
- "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'repo2data'"
- ]
- }
- ],
- "source": [
- "from repo2data.repo2data import Repo2Data\n",
- "import os \n",
- "import pickle\n",
- "import matplotlib.pyplot as plt\n",
- "import chart_studio.plotly as py\n",
- "import plotly.graph_objs as go\n",
- "import numpy as np\n",
- "from plotly import __version__\n",
- "from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot\n",
- "from IPython.display import display, HTML\n",
- "from plotly import tools\n",
- "\n",
- "data_req_path = os.path.join(\"..\",\"..\", \"binder\", \"data_requirement.json\")\n",
- "repo2data = Repo2Data(data_req_path)\n",
- "DATA_ROOT = os.path.join(repo2data.install()[0],\"t1-book-neurolibre\")\n",
- "\n",
- "filename = os.path.join(DATA_ROOT,\"01\",'figure_2.pkl')\n",
- "\n",
- "with open(filename, 'rb') as f:\n",
- " params, signal_WM, signal_GM, signal_CSF = pickle.load(f)\n",
- "\n",
- "config={'showLink': False, 'displayModeBar': False}\n",
- "\n",
- "init_notebook_mode(connected=True)\n",
- "\n",
- "wm = go.Scatter(\n",
- " x = params[\"TI\"],\n",
- " y = signal_WM,\n",
- " name = 'T1 = 0.9 s (White Matter)',\n",
- " text = 'T1 = 0.9 s (White Matter)',\n",
- " hoverinfo = 'x+y+text'\n",
- ")\n",
- "\n",
- "gm = go.Scatter(\n",
- " x = params[\"TI\"],\n",
- " y = signal_GM,\n",
- " name = 'T1 = 1.5 s (Grey Matter)',\n",
- " text = 'T1 = 1.5 s (Grey Matter)',\n",
- " hoverinfo = 'x+y+text'\n",
- ")\n",
- "\n",
- "csf = go.Scatter(\n",
- " x = params[\"TI\"],\n",
- " y = signal_CSF,\n",
- " name = 'T1 = 4.0 s (Cerebrospinal Fluid)',\n",
- " text = 'T1 = 4.0 s (Cerebrospinal Fluid)',\n",
- " hoverinfo = 'x+y+text'\n",
- ")\n",
- "\n",
- "data = [wm, gm, csf]\n",
- "\n",
- "layout = go.Layout(\n",
- " width=600,\n",
- " height=350,\n",
- " margin=go.layout.Margin(\n",
- " l=100,\n",
- " r=50,\n",
- " b=60,\n",
- " t=0,\n",
- " ),\n",
- " annotations=[\n",
- " dict(\n",
- " x=0.5004254919715793,\n",
- " y=-0.175,\n",
- " showarrow=False,\n",
- " text='Inversion Time – TI (ms)',\n",
- " font=dict(\n",
- " family='Times New Roman',\n",
- " size=22\n",
- " ),\n",
- " xref='paper',\n",
- " yref='paper'\n",
- " ),\n",
- " dict(\n",
- " x=-0.15,\n",
- " y=0.50,\n",
- " showarrow=False,\n",
- " text='Long. Magnetization (Mz)',\n",
- " font=dict(\n",
- " family='Times New Roman',\n",
- " size=22\n",
- " ),\n",
- " textangle=-90,\n",
- " xref='paper',\n",
- " yref='paper'\n",
- " ),\n",
- " ],\n",
- " xaxis=dict(\n",
- " showgrid=False,\n",
- " linecolor='black',\n",
- " linewidth=2\n",
- " ),\n",
- " yaxis=dict(\n",
- " showgrid=False,\n",
- " linecolor='black',\n",
- " linewidth=2\n",
- " ),\n",
- " legend=dict(\n",
- " x=0.55,\n",
- " y=0.15,\n",
- " traceorder='normal',\n",
- " font=dict(\n",
- " family='Times New Roman',\n",
- " size=12,\n",
- " color='#000'\n",
- " ),\n",
- " bordercolor='#000000',\n",
- " borderwidth=2\n",
- " ),\n",
- " plot_bgcolor='white'\n",
- ")\n",
- "\n",
- "fig = dict(data=data, layout=layout)\n",
- "\n",
- "plot(fig, filename = 'ir_fig_2.html', config = config)\n",
- "\n",
- "display(HTML('ir_fig_2.html'))"
- ]
- },
{
"cell_type": "code",
"execution_count": 1,