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,