SuperK Data Display.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# SuperKamiokande event 3D displayer + animation\n",
    "SuperKamiokande, ICRR has released their simulated data for plotting as below link.\n",
    "This tutorial shows how to use Plotly to draw interactive graphs.\n",
    "\n",
    "http://www-sk.icrr.u-tokyo.ac.jp/sk/detector/eventdisplay-data.html?fbclid=IwAR3XvOjN1BbrgbPzzWPxVKXy4DX0UXSx6BxNYJx-QYuPVHdDSCVHFYZvN7Q\n",
    "\n",
    "The interactive plots is made by using Plotly (website:https://plotly.com/python/) \n",
    "\n",
    "\n",
    "A muon sample draw by plotly is shown as below:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"figure/muon_ring.png\">"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Data lience belong to ICRR, Tokyo Univ.\n",
    "\n",
    "\n",
    "(website:http://www-sk.icrr.u-tokyo.ac.jp/sk/index.html)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# install pypi packages in requirements.txt (if needed)\n",
    "#!pip3 install -r requirements.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# import packages\n",
    "import os\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "from zipfile import ZipFile\n",
    "import glob\n",
    "\n",
    "# plotly importing with embedding in joupter notebook \n",
    "from plotly.offline import init_notebook_mode,iplot\n",
    "import plotly.graph_objs as go # old version of plotly.graph_objects (plotly version 3.10.0)\n",
    "\n",
    "import cufflinks as cf\n",
    "init_notebook_mode(connected=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "## download data zip file from icrr website\n",
    "!wget -O skdata/sample.zip http://www-sk.icrr.u-tokyo.ac.jp/sk/evdisplay-data/sample.zip\n",
    "#!wget -O skdata/1ring-mu.100_events.zip http://www-sk.icrr.u-tokyo.ac.jp/sk/evdisplay-data/1ring-mu.100_events.zip\n",
    "#!wget -O skdata/1ring-e.100_events.zip http://www-sk.icrr.u-tokyo.ac.jp/sk/evdisplay-data/1ring-e.100_events.zip\n",
    "#!wget -O skdata/multirings.100_events.zip http://www-sk.icrr.u-tokyo.ac.jp/sk/evdisplay-data/multirings.100_events.zip"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fpd={}\n",
    "names = ['cable', 'charge', 'time', 'x', 'y', 'z']\n",
    "with ZipFile('skdata/sample.zip') as zf:\n",
    "    allfiles = zf.namelist()\n",
    "    \n",
    "    sample_names = [file for file in allfiles if '.csv' in file if 'sample/' in file if '__MACOS' not in file]\n",
    "    #for sname in sample_names:\n",
    "    #    zf.extract(sname, path='skdata/')\n",
    "    #csvfiles = glob.glob('skdata/sample/*.csv')\n",
    "    #print(csvfiles)\n",
    "    #for filename in csvfiles:\n",
    "    for filename in sample_names:\n",
    "        print('readin file {}'.format(filename))\n",
    "        key = os.path.split(filename)[-1] [:-4]# remove path and '.csv' in the tail, then use it as key\n",
    "        fpd[key]=pd.read_csv(zf.open(filename),comment='#', names=names)\n",
    "\n",
    "print(sample_names)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cat_list = [key for key in fpd.keys()]\n",
    "print(cat_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# print out head of data\n",
    "fpd[cat_list[0]].head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#preparing dropdown list menu\n",
    "#defining list_updatemenus, data list\n",
    "list_updatemenus = []\n",
    "data = []\n",
    "for i,cat in enumerate(cat_list):\n",
    "    item_menu = dict(label=cat,method='update')\n",
    "    # args list\n",
    "    args_list = list()\n",
    "    # preparing visible list\n",
    "    visible_list = [False]*len(cat_list)\n",
    "    visible_list[i] = True\n",
    "    args_list.append(dict(visible=visible_list))\n",
    "    # preparing title\n",
    "    title_dict = dict(title='SuperK {} Event'.format(cat))\n",
    "    args_list.append(title_dict)\n",
    "    \n",
    "    item_menu['args'] = args_list\n",
    "    list_updatemenus.append(item_menu)\n",
    "    # preparing 3d-scattering plot\n",
    "    # text for showing\n",
    "    text_tc = fpd[cat]['time'].map('Time:{:,.1f} ns\\t'.format) + fpd[cat]['charge'].map('Charge:{:,.1f} p.e.'.format)\n",
    "    data.append(go.Scatter3d(x=fpd[cat].x,y=fpd[cat].y,z=fpd[cat].z,mode='markers',text=text_tc,\n",
    "                marker=dict(size=3,color=fpd[cat].charge,colorscale='Portland',opacity=0.4,\n",
    "                            colorbar=dict(title=\"Charge(p.e.)\",thickness=10,x = 0.92, y = 0.5))))\n",
    "    \n",
    "# print(list_updatemenus[1])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Plotly color built-in pallet \n",
    "https://plotly.com/python/builtin-colorscales/\n",
    "\n",
    "colorscale options for colorbar: ['Greys', 'YlGnBu', 'Greens', 'YlOrRd', 'Bluered', 'RdBu','Reds', 'Blues', 'Picnic', 'Rainbow', 'Portland', 'Jet','Hot', 'Blackbody', 'Earth', 'Electric', 'Viridis', 'Cividis']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import plotly.graph_objs.layout.scene as scene\n",
    "#defining layout\n",
    "layout=go.Layout(title='SuperK Event 3D Scatter Plot',\n",
    "                 updatemenus=list([dict(buttons= list_updatemenus)]),barmode='overlay',\n",
    "                 scene=go.Scene(\n",
    "                     xaxis=scene.XAxis(title='x(cm)'),yaxis=scene.YAxis(title='y(cm)'),zaxis=scene.ZAxis(title='z(cm)'))\n",
    "                )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#defining figure and plotting\n",
    "fig = go.Figure(data,layout)\n",
    "iplot(fig)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Animation drawing \n",
    "Showing the charge by varing time \n",
    "However, the scatter3d type did not suupport animate, so only 2d plot is shown.\n",
    "\n",
    "\n",
    "Example of animate by plotly:\n",
    "\n",
    "https://plotly.com/python/animations/#adding-control-buttons-to-animations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "multiring_cat = 'multirings.0000.000014'\n",
    "datadf = fpd[multiring_cat]\n",
    "min_time = datadf['time'].min()\n",
    "max_time = datadf['time'].max()\n",
    "#print(min_time,max_time)\n",
    "stamp_first = 50*(min_time//50+1)\n",
    "stamp_last = 50*(max_time//50+1)\n",
    "times_list = np.linspace(stamp_first,stamp_last,int((stamp_last-stamp_first)/50+1))\n",
    "times_list=times_list.astype(int)\n",
    "#print(times_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# group data with time by 100 ns\n",
    "# create a new column (timehns): replace time with 100 ns for example 132 ns-->200ns\n",
    "datadf['timehns'] = ((datadf['time']//50+1)*50).astype(int)\n",
    "datadf.tail()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# make figure\n",
    "fig_dict = {\n",
    "    \"data\":[],\n",
    "    \"layout\":{},\n",
    "    \"frames\":[]\n",
    "}\n",
    "\n",
    "\n",
    "# prepare initial data\n",
    "data_by_time = datadf[datadf['timehns']==times_list[0]]\n",
    "text_tc = data_by_time['z'].map('Z(cm):{:,.1f}'.format) + data_by_time['charge'].map('\\tCharge:{:,.1f} p.e.'.format)\n",
    "\n",
    "data_dict = {\n",
    "            \"type\":\"scatter\",\n",
    "            \"x\":list(data_by_time[\"x\"]),\n",
    "            \"y\":list(data_by_time[\"y\"]),\n",
    "            #\"z\":list(data_by_time[\"z\"]),\n",
    "            \"mode\":\"markers\",\n",
    "            \"text\":text_tc,\n",
    "            \"marker\":dict(size=3,color=list(data_by_time.charge),colorscale='Portland',opacity=0.4,\n",
    "                            colorbar=dict(title=\"Charge(p.e.)\",thickness=10,x = 1.02, y = 0.5)),\n",
    "            \"name\": str(times_list[0])\n",
    "    }\n",
    "fig_dict[\"data\"].append(data_dict)\n",
    "    \n",
    "\n",
    "# prepare layout \n",
    "fig_dict[\"layout\"][\"xaxis\"] = {\"title\": \"x (cm)\"}\n",
    "fig_dict[\"layout\"][\"yaxis\"] = {\"title\": \"y (cm)\"}\n",
    "#fig_dict[\"layout\"][\"zaxis\"] = {\"title\": \"z (cm)\"}\n",
    "fig_dict[\"layout\"][\"width\"] = 600\n",
    "fig_dict[\"layout\"][\"height\"] = 600\n",
    "\n",
    "fig_dict[\"layout\"][\"scene\"]=go.Scene(xaxis=scene.XAxis(title='x(cm)',range=[-1600, 1600], autorange=False),\n",
    "                                     yaxis=scene.YAxis(title='y(cm)',range=[-1600, 1600]))\n",
    "\n",
    "fig_dict[\"layout\"][\"xaxis\"] = go.layout.XAxis(title='x(cm)',range=[-1600, 1600], autorange=False)           \n",
    "fig_dict[\"layout\"][\"yaxis\"] = go.layout.YAxis(title='y(cm)',range=[-1700, 1700], autorange=False)           \n",
    "fig_dict[\"layout\"][\"hovermode\"] = \"closest\"\n",
    "fig_dict[\"layout\"][\"updatemenus\"] = [\n",
    "    {\n",
    "        \"buttons\": [\n",
    "            {\n",
    "                \"args\": [None, {\"frame\": {\"duration\": 1500, \"redraw\": False},\n",
    "                                \"fromcurrent\": True, \"transition\": {\"duration\": 300,\n",
    "                                                                    \"easing\": \"quadratic-in-out\"}}],\n",
    "                \"label\": \"Play\",\n",
    "                \"method\": \"animate\"\n",
    "            },\n",
    "            {\n",
    "                \"args\": [[None], {\"frame\": {\"duration\": 0, \"redraw\": False},\n",
    "                                  \"mode\": \"immediate\",\n",
    "                                  \"transition\": {\"duration\": 0}}],\n",
    "                \"label\": \"Pause\",\n",
    "                \"method\": \"animate\"\n",
    "            }\n",
    "        ],\n",
    "        \"direction\": \"left\",\n",
    "        \"pad\": {\"r\": 10, \"t\": 87},\n",
    "        \"showactive\": False,\n",
    "        \"type\": \"buttons\",\n",
    "        \"x\": 0.1,\n",
    "        \"xanchor\": \"right\",\n",
    "        \"y\": 0,\n",
    "        \"yanchor\": \"top\"\n",
    "    }\n",
    "]\n",
    "\n",
    "sliders_dict = {\n",
    "    \"active\": 0,\n",
    "    \"yanchor\": \"top\",\n",
    "    \"xanchor\": \"left\",\n",
    "    \"currentvalue\": {\n",
    "        \"font\": {\"size\": 20},\n",
    "        \"prefix\": \"Time(ns):\",\n",
    "        \"visible\": True,\n",
    "        \"xanchor\": \"right\"\n",
    "    },\n",
    "    \"transition\": {\"duration\": 300, \"easing\": \"cubic-in-out\"},\n",
    "    \"pad\": {\"b\": 10, \"t\": 50},\n",
    "    \"len\": 0.9,\n",
    "    \"x\": 0.1,\n",
    "    \"y\": 0,\n",
    "    \"steps\": []\n",
    "}\n",
    "\n",
    "# prepare frames\n",
    "\n",
    "for time_stamp in times_list:\n",
    "    frame = {\"data\": [], \"name\": str(time_stamp)}\n",
    "    data_by_time = datadf[datadf['timehns']==time_stamp]\n",
    "    #print(data_by_time.shape)\n",
    "    text_tc = data_by_time['z'].map('Z(cm):{:,.1f}'.format) + data_by_time['charge'].map('\\tCharge:{:,.1f} p.e.'.format)\n",
    "    data_dict = {\n",
    "                \"type\":\"scatter\",\n",
    "                \"x\":list(data_by_time[\"x\"]),\n",
    "                \"y\":list(data_by_time[\"y\"]),\n",
    "                #\"z\":list(data_by_time[\"z\"]),\n",
    "                \"mode\":\"markers\",\n",
    "                \"text\":text_tc,\n",
    "                \"marker\":dict(size=3,color=list(data_by_time[\"charge\"]),colorscale='Portland',opacity=0.4,\n",
    "                                colorbar=dict(title=\"Charge(p.e.)\",thickness=10,x = 1.02, y = 0.5)),\n",
    "                \"name\": str(data_by_time)\n",
    "        }\n",
    "    frame[\"data\"].append(data_dict)\n",
    "    fig_dict[\"frames\"].append(frame)\n",
    "    slider_step = {\"args\": [\n",
    "        [str(time_stamp)], # first argument should be string \n",
    "        {\"frame\": {\"duration\": 300, \"redraw\": False},\n",
    "         \"mode\": \"immediate\",\n",
    "         \"transition\": {\"duration\": 300}}\n",
    "    ],\n",
    "        \"label\": str(time_stamp),\n",
    "        \"method\": \"animate\"}\n",
    "    sliders_dict[\"steps\"].append(slider_step)\n",
    "\n",
    "    #print(\"append data tme:{}\".format(time_stamp))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig_dict[\"layout\"][\"sliders\"] = [sliders_dict]\n",
    "\n",
    "fig = go.Figure(fig_dict)\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Then, draw y-z plots\n",
    "# make figure\n",
    "fig_dict = {\n",
    "    \"data\":[],\n",
    "    \"layout\":{},\n",
    "    \"frames\":[]\n",
    "}\n",
    "\n",
    "\n",
    "# prepare initial data\n",
    "data_by_time = datadf[datadf['timehns']==times_list[0]]\n",
    "text_tc = data_by_time['x'].map('X(cm):{:,.1f}'.format) + data_by_time['charge'].map('\\tCharge:{:,.1f} p.e.'.format)\n",
    "\n",
    "data_dict = {\n",
    "            \"type\":\"scatter\",\n",
    "            \"x\":list(data_by_time[\"y\"]),\n",
    "            \"y\":list(data_by_time[\"x\"]),\n",
    "            #\"z\":list(data_by_time[\"z\"]),\n",
    "            \"mode\":\"markers\",\n",
    "            \"text\":text_tc,\n",
    "            \"marker\":dict(size=3,color=list(data_by_time.charge),colorscale='Portland',opacity=0.4,\n",
    "                            colorbar=dict(title=\"Charge(p.e.)\",thickness=10,x = 1.02, y = 0.5)),\n",
    "            \"name\": str(times_list[0])\n",
    "    }\n",
    "fig_dict[\"data\"].append(data_dict)\n",
    "    \n",
    "\n",
    "# prepare layout \n",
    "fig_dict[\"layout\"][\"xaxis\"] = {\"title\": \"y (cm)\"}\n",
    "fig_dict[\"layout\"][\"yaxis\"] = {\"title\": \"z (cm)\"}\n",
    "#fig_dict[\"layout\"][\"zaxis\"] = {\"title\": \"z (cm)\"}\n",
    "fig_dict[\"layout\"][\"width\"] = 600\n",
    "fig_dict[\"layout\"][\"height\"] = 600\n",
    "\n",
    "\n",
    "fig_dict[\"layout\"][\"xaxis\"] = go.layout.XAxis(title='y(cm)',range=[-1600, 1600], autorange=False)           \n",
    "fig_dict[\"layout\"][\"yaxis\"] = go.layout.YAxis(title='z(cm)',range=[-1700, 1700], autorange=False)           \n",
    "fig_dict[\"layout\"][\"hovermode\"] = \"closest\"\n",
    "fig_dict[\"layout\"][\"updatemenus\"] = [\n",
    "    {\n",
    "        \"buttons\": [\n",
    "            {\n",
    "                \"args\": [None, {\"frame\": {\"duration\": 1500, \"redraw\": False},\n",
    "                                \"fromcurrent\": True, \"transition\": {\"duration\": 300,\n",
    "                                                                    \"easing\": \"quadratic-in-out\"}}],\n",
    "                \"label\": \"Play\",\n",
    "                \"method\": \"animate\"\n",
    "            },\n",
    "            {\n",
    "                \"args\": [[None], {\"frame\": {\"duration\": 0, \"redraw\": False},\n",
    "                                  \"mode\": \"immediate\",\n",
    "                                  \"transition\": {\"duration\": 0}}],\n",
    "                \"label\": \"Pause\",\n",
    "                \"method\": \"animate\"\n",
    "            }\n",
    "        ],\n",
    "        \"direction\": \"left\",\n",
    "        \"pad\": {\"r\": 10, \"t\": 87},\n",
    "        \"showactive\": False,\n",
    "        \"type\": \"buttons\",\n",
    "        \"x\": 0.1,\n",
    "        \"xanchor\": \"right\",\n",
    "        \"y\": 0,\n",
    "        \"yanchor\": \"top\"\n",
    "    }\n",
    "]\n",
    "\n",
    "sliders_dict = {\n",
    "    \"active\": 0,\n",
    "    \"yanchor\": \"top\",\n",
    "    \"xanchor\": \"left\",\n",
    "    \"currentvalue\": {\n",
    "        \"font\": {\"size\": 20},\n",
    "        \"prefix\": \"Time(ns):\",\n",
    "        \"visible\": True,\n",
    "        \"xanchor\": \"right\"\n",
    "    },\n",
    "    \"transition\": {\"duration\": 300, \"easing\": \"cubic-in-out\"},\n",
    "    \"pad\": {\"b\": 10, \"t\": 50},\n",
    "    \"len\": 0.9,\n",
    "    \"x\": 0.1,\n",
    "    \"y\": 0,\n",
    "    \"steps\": []\n",
    "}\n",
    "\n",
    "# prepare frames\n",
    "\n",
    "for time_stamp in times_list:\n",
    "    frame = {\"data\": [], \"name\": str(time_stamp)}\n",
    "    data_by_time = datadf[datadf['timehns']==time_stamp]\n",
    "    #print(data_by_time.shape)\n",
    "    text_tc = data_by_time['x'].map('X(cm):{:,.1f}'.format) + data_by_time['charge'].map('\\tCharge:{:,.1f} p.e.'.format)\n",
    "    data_dict = {\n",
    "                \"type\":\"scatter\",\n",
    "                \"x\":list(data_by_time[\"y\"]),\n",
    "                \"y\":list(data_by_time[\"z\"]),\n",
    "                #\"z\":list(data_by_time[\"z\"]),\n",
    "                \"mode\":\"markers\",\n",
    "                \"text\":text_tc,\n",
    "                \"marker\":dict(size=3,color=list(data_by_time[\"charge\"]),colorscale='Portland',opacity=0.4,\n",
    "                                colorbar=dict(title=\"Charge(p.e.)\",thickness=10,x = 1.02, y = 0.5)),\n",
    "                \"name\": str(data_by_time)\n",
    "        }\n",
    "    frame[\"data\"].append(data_dict)\n",
    "    fig_dict[\"frames\"].append(frame)\n",
    "    slider_step = {\"args\": [\n",
    "        [str(time_stamp)], # first argument should be string \n",
    "        {\"frame\": {\"duration\": 300, \"redraw\": False},\n",
    "         \"mode\": \"immediate\",\n",
    "         \"transition\": {\"duration\": 300}}\n",
    "    ],\n",
    "        \"label\": str(time_stamp),\n",
    "        \"method\": \"animate\"}\n",
    "    sliders_dict[\"steps\"].append(slider_step)\n",
    "\n",
    "    #print(\"append data tme:{}\".format(time_stamp))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig_dict[\"layout\"][\"sliders\"] = [sliders_dict]\n",
    "\n",
    "fig = go.Figure(fig_dict)\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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