3D_scatter_Voila_matplotlibADJUSTABLE.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# 3D scatter plot with file reading & adjustable settings as Voila App\n",
    "\n",
    "**THIS ILLUSTRATES THIS FOR MATPLOTLIB-BASED 3D SCATTER PLOT.**\n",
    "\n",
    "In [this notebook](3D_scatter_adjustableVIAwidgets.ipynb) you saw widgets can be used to control settings for the plot. (This notebook builds on that, and so you'll probably want to review [that one](3D_scatter_adjustableVIAwidgets.ipynb) first, if you haven't already.)  \n",
    "This can be further combined with additional widgets and Voila to make a dashboard-like web app that allows file upload and plotting where you can then control the plot look in the app dashbaord.\n",
    "\n",
    "This is meant to demonstrate that. You'll need to edit things to match your data.\n",
    "\n",
    "Also note you can use Excel files directly. The code to convert that to Pandas is left in there as commented out code. You can remove the comment symbol and alter the code to handle you files..\n",
    "\n",
    "This opens as a notebook to introduce what is going on in the traditional notebook format. You can run the code as a notebook or switch to the Voila app style by clicking the `Voila` button on the toolbar just above the notebook.\n",
    "\n",
    "Alternatively, the Voila application without all this introductory cruft can be launched via the link below:\n",
    "\n",
    "[Click here for streamlined version of this notebook as an app](../voila/render/3D_scatter_Voila_matplotlibSTREAMLINED.ipynb)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "-------\n",
    "\n",
    "## Matplotlib example with colorbar legend and adjustable options\n",
    "\n",
    "A tab-delimited example data file is provided. This combines both the red and white wine data. You can go [here](https://archive.ics.uci.edu/ml/datasets/wine+quality), which leads to [here](http://www3.dsi.uminho.pt/pcortez/wine/), and get the white or red data only if you like and use the upload button to upload the data from your local computer. (The code here is set to deal with tab-delimited data and the wine data come as commas-separated values [CSV] and so you need to either edit the code or the data. I've included the code for CSV in comments.)  Alternatively, see the note about using Excel files at the top of this notebook.\n",
    "\n",
    "The palette, view angles, opacity of spheres, size of spheres, view, and color gradient atrribute is adjustable using widgets.\n",
    "\n",
    "This is based on the Matplotlib examples in the first notebook [here](https://github.com/fomightez/3Dscatter_plot-binder) combined with [ipywidgets adjusting plot options](https://github.com/binder-examples/jupyter-extension) and [the widgets example notebook](3D_scatter_adjustableVIAwidgets.ipynb)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from traitlets import dlink\n",
    "import ipywidgets as widgets\n",
    "from IPython.display import display\n",
    "from io import StringIO\n",
    "import glob\n",
    "import random \n",
    "\n",
    "# widgets\n",
    "file_uploader = widgets.FileUpload(multiple=True )\n",
    "#file_name = widgets.Text()\n",
    "#files = glob.glob(\"*.xlsx\")\n",
    "#files = glob.glob(\"*.csv\")\n",
    "files = glob.glob(\"*.tsv\")\n",
    "#print(files)  # FOR DEBUGGING ONLY\n",
    "current_file = None\n",
    "\n",
    "#upload_suggest = widgets.Label(value=\"Use above button to upload your data file if not listed among the choices below.)\")\n",
    "#select_markdown = widgets.HTML(value=markdown.markdown(\"\"\"Use above button to upload your data file if not among the choices you see listed below.<br/>**Choose the file with the data to plot from below**:\"\"\")) # based on https://github.com/jupyter-widgets/ipywidgets/issues/2428#issuecomment-500084610 and https://ipywidgets.readthedocs.io/en/stable/examples/Widget%20List.html#HTML ; need to pip install markdown first and import it\n",
    "select_markdown = widgets.HTML(value=\"Use the above 'Upload' button to \"\n",
    "                               \"upload your data file if it is not among the choices you see \"\n",
    "                               \"listed below.<br/><b>Click on the file name among list below \"\n",
    "                               \"to select the data to plot</b> and then click the \"\n",
    "                               \"'Plot Selected' button.\")\n",
    "\n",
    "select_file = widgets.Select(options = files, description='Data files:')\n",
    "button = widgets.Button(description=\"Plot Selected\")\n",
    "ax = None\n",
    "out = widgets.Output()\n",
    "\n",
    "@out.capture(clear_output=True,wait=True)\n",
    "def on_button_clicked(b):\n",
    "    global file_uploader,select_file, current_file, ax\n",
    "    # get data file to be used\n",
    "    current_file = select_file.value\n",
    "    print(f\"Using data from:\\t{current_file}\")\n",
    "    # bring data into Pandas\n",
    "    import pandas as pd\n",
    "    import matplotlib.pyplot as plt\n",
    "    import numpy as np\n",
    "    import seaborn as sns\n",
    "    from mpl_toolkits.mplot3d import Axes3D\n",
    "    from ipywidgets import interact\n",
    "    from ipywidgets.widgets import FloatSlider, IntSlider, Dropdown\n",
    "    #wines = pd.read_excel(current_file) # Uncomment for Excel files\n",
    "    #wines = pd.read_csv(current_file) # Uncomment for CSV files\n",
    "    wines = pd.read_csv(current_file, sep='\\t')\n",
    "    #print(wines.head(random.randint(2, 12) ))\n",
    "    #construct or update plot\n",
    "    \n",
    "    if ax is None:\n",
    "        '''\n",
    "        fig1, axes1 = plt.subplots()\n",
    "        df.hist(ax = axes1)\n",
    "        '''\n",
    "        # BOTH `plt.show(fig1)` and `plt.show(block=True)` seem to work\n",
    "        #plt.show(fig1) # based on https://stackoverflow.com/a/51060721/8508004\n",
    "        #plt.show(block=True) # based on https://stackoverflow.com/a/61993497/8508004\n",
    "        xs = wines['residual sugar']\n",
    "        ys = wines['fixed acidity']\n",
    "        zs = wines['alcohol']\n",
    "        cmaps = ['coolwarm', 'viridis', 'magma','plasma','RdYlBu','YlGnBu','hsv']\n",
    "        v_angles = [\"30, 185\",\"50, 185\",\"230,110\",\"1,140\"]\n",
    "\n",
    "        view_widget = Dropdown(options=v_angles)\n",
    "        elevation_widget= IntSlider(value=30, min=0, max=360,step=5, continuous_update=False)\n",
    "        azimuth_widget= IntSlider(value=185, min=0, max=360,step=5, continuous_update=False)\n",
    "        def update_elevation_and_azimuth(*args):\n",
    "            view_nums = view_widget.value.split(\",\")\n",
    "            view_nums = [int(x) for x in view_nums]\n",
    "            elevation_widget.value, azimuth_widget.value = view_nums\n",
    "        view_widget.observe(update_elevation_and_azimuth, 'value')\n",
    "\n",
    "        def plot_data(opacity, cmap, coloring,marker_size,view_choice,elevation,azimuth):\n",
    "            fig = plt.figure(figsize=(9.5, 6))\n",
    "            ax = fig.add_subplot(111, projection='3d')\n",
    "            #norm = mpl.colors.Normalize(vmin=min(wines[coloring],), vmax=max(wines[coloring],))\n",
    "            g = ax.scatter(xs, ys, zs, s=marker_size, alpha=opacity, edgecolors='w', marker='o', depthshade=False, c=wines[coloring], cmap=cmap)\n",
    "            ax.view_init(elevation,azimuth)\n",
    "            ax.set_xlabel('Residual Sugar')\n",
    "            ax.set_ylabel('Fixed Acidity')\n",
    "            ax.set_zlabel('Alcohol')\n",
    "            clb = fig.colorbar(g)\n",
    "            clb.solids.set_edgecolor(\"face\") #based on https://stackoverflow.com/a/5495912/8508004; \n",
    "            # addition of `.solids.set_edgecolor(\"face\")` based on https://matplotlib.org/3.1.0/api/_as_gen/matplotlib.pyplot.colorbar.html to \n",
    "            # avoid banding seen with just `fig.colorbar(g)` along with ipywidgets use; note it needed further adjusting to \n",
    "            # clb.solids.set_edgecolor(\"face\") when added title to colorbar based on https://stackoverflow.com/a/33740567/8508004\n",
    "            clb.ax.set_title(coloring) #adding title based on https://stackoverflow.com/a/33740567/8508004\n",
    "            plt.show()\n",
    "\n",
    "        p = interact(plot_data,\n",
    "                     opacity=FloatSlider(value=0.75, min=0, max=1.0, step=0.05, readout_format='.3f', continuous_update=False),\n",
    "                     cmap=Dropdown(value='magma',options=cmaps),\n",
    "                     coloring=Dropdown(value='alcohol',options=['residual sugar','fixed acidity','alcohol']),\n",
    "                     marker_size= IntSlider(value=50, min=10, max=180,step=10, continuous_update=False),\n",
    "                     view_choice=view_widget,\n",
    "                     elevation= elevation_widget,\n",
    "                     azimuth= azimuth_widget\n",
    "                    )\n",
    "    else:\n",
    "        print(\"updating...\")\n",
    "        #ax = fig.add_subplot(111, projection='3d')\n",
    "    #display(fig1)\n",
    "    vbox.children = [file_uploader, select_markdown, select_file,button, out]\n",
    "    \n",
    "\n",
    "button.on_click(on_button_clicked)\n",
    "vbox = widgets.VBox([file_uploader, select_markdown, select_file,button])\n",
    "\n",
    "def on_file_upload(change):\n",
    "    global file_uploader,select_file, current_file\n",
    "    #for filename in change['new'].keys(): #worked last time I tried, now `change['new']` is a tuple for each file with a dictionary as each item\n",
    "    for details_dict in change['new']:\n",
    "\n",
    "        #files.append(filename) #worked with `for filename in change['new'].keys():`\n",
    "        files.append(details_dict['name'])\n",
    "\n",
    "        #with open(details_dict['name'], \"wb\") as f: #worked with `for filename in change['new'].keys():`\n",
    "        with open(details_dict['name'], \"wb\") as f:\n",
    "            #f.write(change['new'][filename]['content']) #worked with `for filename in change['new'].keys():`\n",
    "            f.write(details_dict['content'])\n",
    "    #select_file.options=tuple(files)\n",
    "\n",
    "    current_file = select_file.value\n",
    "    select_file.options=tuple(files)\n",
    "    select_file.value\n",
    "    #print(current_file)\n",
    "\n",
    "# links between widgets\n",
    "#color_picker.observe(change_input, 'value')\n",
    "#dlink((file_uploader, 'value'), (select_file, 'value'), get_name)\n",
    "#file_picker.observe(change_input, 'value')\n",
    "file_uploader.observe(on_file_upload, 'value')\n",
    "\n",
    "vbox"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "----\n",
    "\n",
    "As discussed above, you can switch away from the notebook interface to the Voila web-app style by clicking the `Voila` button on the toolbar just above the notebook.\n",
    "\n",
    "Alternatively, the Voila application without all this introductory cruft can be launched via the link below:\n",
    "\n",
    "[Click here for streamlined version of this notebook as an app](../voila/render/3D_scatter_Voila_matplotlibSTREAMLINED.ipynb)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.12"
  },
  "rise": {
   "autolaunch": true,
   "enable_chalkboard": true,
   "scroll": true,
   "theme": "white",
   "transition": "zoom"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}