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qMRLab · Oct 1, 2024 · b01f645 · b01f645
1 parent 28414b9
commit b01f645
Showing 1 changed file with 0 additions and 154 deletions.
diff --git 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 = 'T<sub>1</sub> = 0.9 s (White Matter)',\n",
-    "    text = 'T<sub>1</sub> = 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 = 'T<sub>1</sub> = 1.5 s (Grey Matter)',\n",
-    "    text = 'T<sub>1</sub> = 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 = 'T<sub>1</sub> = 4.0 s (Cerebrospinal Fluid)',\n",
-    "    text = 'T<sub>1</sub> = 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 (M<sub>z</sub>)',\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,