pc4nanobio.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9bbbe662fb724e74aae8485dd9a90b88",
       "version_major": 2,
       "version_minor": 0
      },
      "text/html": [
       "<p>Failed to display Jupyter Widget of type <code>VBox</code>.</p>\n",
       "<p>\n",
       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
       "  that the widgets JavaScript is still loading. If this message persists, it\n",
       "  likely means that the widgets JavaScript library is either not installed or\n",
       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
       "  Widgets Documentation</a> for setup instructions.\n",
       "</p>\n",
       "<p>\n",
       "  If you're reading this message in another frontend (for example, a static\n",
       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
       "  it may mean that your frontend doesn't currently support widgets.\n",
       "</p>\n"
      ],
      "text/plain": [
       "VBox(children=(Tab(children=(VBox(children=(HBox(children=(Button(button_style='info', description='Use defaults', style=ButtonStyle(), tooltip='Populate the GUI with default parameters'), Button(button_style='info', description='Read config (in ~)', style=ButtonStyle(), tooltip='Populate the GUI with info in your configuration file (in your home directory)'), Text(value='my_nanobio_settings.xml'))), Label(value='Domain ($\\\\mu M$):'), HBox(children=(FloatText(value=0.0, description='$X_{min}$', layout=Layout(width='180px')), FloatText(value=0.0, description='$X_{max}$', layout=Layout(width='180px')), BoundedFloatText(value=1.0, description='$X_{delta}$', layout=Layout(width='180px'), min=1.0))), HBox(children=(FloatText(value=0.0, description='$Y_{min}$', layout=Layout(width='180px')), FloatText(value=0.0, description='$Y_{max}$', layout=Layout(width='180px')), BoundedFloatText(value=1.0, description='$Y_{delta}$', layout=Layout(width='180px'), min=1.0))), HBox(children=(FloatText(value=0.0, description='$Z_{min}$', layout=Layout(width='180px')), FloatText(value=0.0, description='$Z_{max}$', layout=Layout(width='180px')), BoundedFloatText(value=1.0, description='$Z_{delta}$', layout=Layout(width='180px'), min=1.0))), Label(value=''), BoundedFloatText(value=0.0, description='$Time_{max}$', layout=Layout(width='180px'), max=100000000.0), BoundedIntText(value=1, description='# threads', layout=Layout(width='180px'), min=1), HBox(children=(BoundedFloatText(value=1.0, description='Tumor Radius', layout=Layout(width='180px'), max=99999.0, min=1.0, step=1.0, style=DescriptionStyle(description_width='initial')), HTMLMath(value='$\\\\mu M$'))), HBox(children=(Checkbox(value=False, description='SVG', layout=Layout(width='180px')), BoundedIntText(value=1, description='interval', layout=Layout(width='180px'), max=99999999, min=1), Checkbox(value=False, description='Full', layout=Layout(width='180px')), BoundedIntText(value=0, description='interval', disabled=True, layout=Layout(width='180px'), max=99999999)))), layout=Layout(height='500px', overflow_y='scroll', width='800px')), VBox(children=(HBox(children=(Text(value='untreated cancer', description='Cell line name', style=DescriptionStyle(description_width='initial')),)), Label(value='Cycle:'), HBox(children=(BoundedFloatText(value=0.0, description='Max birth rate', layout=Layout(width='200px'), style=DescriptionStyle(description_width='initial')), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='300px')), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$O_2$: Prolif sat', layout=Layout(width='180px')), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Prolif thresh', layout=Layout(width='180px')), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Ref', layout=Layout(width='180px')), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$Glc$: Prolif sat', layout=Layout(width='180px'), style=DescriptionStyle(description_width='initial')),), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Prolif thresh', layout=Layout(width='180px')),), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Ref', layout=Layout(width='180px')),), layout=Layout(width='230px')))), Label(value='Necrosis:'), HBox(children=(BoundedFloatText(value=0.0, description='Max rate', layout=Layout(width='180px')), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$O_2$: Thresh', layout=Layout(width='180px')), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Max', layout=Layout(width='180px')), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))), Label(value='Apoptosis:'), HBox(children=(BoundedFloatText(value=0.0, description='Rate', layout=Layout(width='180px')), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), Label(value='Metabolism (must sum to 1):'), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='Aerobic', layout=Layout(width='180px'), max=1.0, step=0.1),), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Glycolytic', layout=Layout(width='180px'), max=1.0, step=0.1),), layout=Layout(width='230px')))), Label(value='Motility:'), HBox(children=(Checkbox(value=False, description='Motile', layout=Layout(width='180px')), BoundedFloatText(value=0.0, description='Bias', layout=Layout(width='180px'), max=1.0, step=0.1))), Label(value='Mechanics:'), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='Max adhesion distance', layout=Layout(width='180px'), step=0.1),), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Adhesion strength', layout=Layout(width='180px'), step=0.1),), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Repulsion strength', layout=Layout(width='180px'), step=0.1),), layout=Layout(width='230px')))), Label(value='Hypoxia:'), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$O_2$: Thresh', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Response', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Saturation', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))), Label(value='Secretion:'), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$O_2$: Uptake rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Secretion rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Saturation', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$Glc$: Uptake rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Secretion rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Saturation', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$H$+: Uptake rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Secretion rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Saturation', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$ECM$: Uptake rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Secretion rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Saturation', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$NP1$: Uptake rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Secretion rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Saturation', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))), HBox(children=(HBox(children=(BoundedFloatText(value=0.0, description='$NP2$: Uptake rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Secretion rate', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='230px')), HBox(children=(BoundedFloatText(value=0.0, description='Saturation', layout=Layout(width='180px'), step=0.1), HTMLMath(value='$mmHg$')), layout=Layout(width='230px')))))), Tab(children=(VBox(children=(VBox(children=(Label(value='Pharmacokinetics:'), HBox(children=(BoundedFloatText(value=0.0, description='Diffusion coef', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')), HTMLMath(value='$\\\\frac{\\\\mu M^2}{min}$')), layout=Layout(width='320px')), HBox(children=(BoundedFloatText(value=0.0, description='Survival lifetime', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')), HTMLMath(value='$min$')), layout=Layout(width='320px')), HBox(children=(BoundedFloatText(value=0.0, description='ECM binding rate', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='320px')), HBox(children=(BoundedFloatText(value=0.0, description='ECM unbinding rate', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='320px')), BoundedFloatText(value=0.0, description='ECM saturation conc', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')))), Label(value='Pharmacodynamics:')), layout=Layout(height='350px', overflow_y='scroll', width='800px')), VBox(children=(VBox(children=(Label(value='Pharmacokinetics:'), HBox(children=(BoundedFloatText(value=0.0, description='Diffusion coef', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')), HTMLMath(value='$\\\\frac{\\\\mu M^2}{min}$')), layout=Layout(width='320px')), HBox(children=(BoundedFloatText(value=0.0, description='Survival lifetime', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')), HTMLMath(value='$min$')), layout=Layout(width='320px')), HBox(children=(BoundedFloatText(value=0.0, description='ECM binding rate', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='320px')), HBox(children=(BoundedFloatText(value=0.0, description='ECM unbinding rate', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')), HTMLMath(value='$\\\\frac{1}{min}$')), layout=Layout(width='320px')), BoundedFloatText(value=0.0, description='ECM saturation conc', layout=Layout(width='270px'), style=DescriptionStyle(description_width='150px')))), Label(value='Pharmacodynamics:')), layout=Layout(height='350px', overflow_y='scroll', width='800px')), Text(value='.', description='dummy:', layout=Layout(height='500px', overflow_y='scroll', width='800px'))), _titles={'0': 'Preform (spherical)', '1': 'Reconfig (rod)', '2': 'Transformations'}), HBox(children=(interactive(children=(IntSlider(value=250, description='SVG', max=500), Output()), layout=Layout(height='500px', width='500px'), _dom_classes=('widget-interact',)),), layout=Layout(height='500px', overflow_y='scroll', width='800px')), HBox(children=(VBox(children=(Dropdown(layout=Layout(width='180px'), options=('oxygen', 'glucose', 'H+ ions', 'ECM', 'NP1', 'NP2'), value='oxygen'), HBox(children=(Text(value='viridis', description='Colormap', layout=Layout(width='180px')), Checkbox(value=False, description='Fix', layout=Layout(width='150px')))), HBox(children=(FloatText(value=0.0, description='Min', disabled=True, layout=Layout(width='150px'), step=0.0), FloatText(value=0.0, description='Max', disabled=True, layout=Layout(width='150px')))))), interactive(children=(IntSlider(value=100, description='FileId', max=200), Output()), layout=Layout(height='500px', width='500px'), _dom_classes=('widget-interact',))), layout=Layout(height='500px', overflow_y='scroll', width='800px'))), layout=Layout(height='500px', overflow_y='scroll', width='800px'), _titles={'0': 'Config Basics', '1': 'Cells', '2': 'Nanoparticles', '3': 'out:SVG', '4': 'out:Substrates'}), VBox(children=(HBox(children=(Button(button_style='success', description='Write config file', style=ButtonStyle(), tooltip='Generate XML'), Text(value='my_nanobio_settings.xml'))), VBox(children=(Button(button_style='success', description='Run', style=ButtonStyle(), tooltip='Run Simulation'),))))))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# %load bin/pc4nanobio.py\n",
    "\n",
    "\n",
    "# In[2]:\n",
    "\n",
    "\n",
    "# %load bin/pc4nanobio.py\n",
    "# %load pc4nanobio.py\n",
    "import ipywidgets as widgets\n",
    "from ipywidgets import Layout, Button, Box, HBox, VBox, BoundedFloatText\n",
    "#from ipywidgets import interact, interactive\n",
    "from subprocess import Popen, PIPE, STDOUT\n",
    "from hublib.cmd import runCommand\n",
    "from hublib.ui import RunCommand\n",
    "import xml.etree.ElementTree as ET\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "import matplotlib.colors as mplc\n",
    "import scipy.io\n",
    "import sys, os, glob, random, math, pathlib\n",
    "import numpy as np\n",
    "from collections import deque\n",
    "\n",
    "join_our_list = \"(Join/ask questions at https://groups.google.com/forum/#!forum/physicell-users)\\n\"\n",
    "\n",
    "get_ipython().run_line_magic('matplotlib', 'inline')\n",
    "\n",
    "#===== Units =====\n",
    "micron_units = widgets.HTMLMath(value=r\"$\\mu M$\")\n",
    "diffusion_coef_units = widgets.HTMLMath(value=r\"$\\frac{\\mu M^2}{min}$\")\n",
    "survival_lifetime_units = widgets.HTMLMath(value=r\"$min$\")\n",
    "min_units = widgets.HTMLMath(value=r\"$min$\")\n",
    "min_inv_units = widgets.HTMLMath(value=r\"$\\frac{1}{min}$\")\n",
    "mmHg_units = widgets.HTMLMath(value=r\"$mmHg$\")\n",
    "\n",
    "constWidth = '180px'\n",
    "constWidth2 = '150px'\n",
    "constWidth3 = '200px'\n",
    "tab_height = '400px'\n",
    "tab_height = '500px'\n",
    "tab_layout = widgets.Layout( width='800px',   # border='2px solid black',\n",
    "                            height=tab_height, overflow_y='scroll',)\n",
    "np_tab_layout = widgets.Layout( width='800px',  # border='2px solid black',\n",
    "                               height='350px', overflow_y='scroll',)\n",
    "#tab_layout.height = '500px'\n",
    "\n",
    "# my_domain = [0,0,-10, 2000,2000,10, 20,20,20]  # [x,y,zmin,  x,y,zmax, x,y,zdelta]\n",
    "label_domain = widgets.Label('Domain ($\\mu M$):')\n",
    "xmin = widgets.FloatText(\n",
    "    description='$X_{min}$',\n",
    "#     disabled=False,\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "ymin = widgets.FloatText(\n",
    "    description='$Y_{min}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "zmin = widgets.FloatText(\n",
    "    description='$Z_{min}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "xmax = widgets.FloatText(\n",
    "    description='$X_{max}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "ymax = widgets.FloatText(\n",
    "    description='$Y_{max}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "zmax = widgets.FloatText(\n",
    "    description='$Z_{max}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "tmax = widgets.BoundedFloatText(\n",
    "    min = 0.,\n",
    "    max = 100000000,\n",
    "    description='$Time_{max}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "xdelta = widgets.BoundedFloatText(\n",
    "    min = 1.,\n",
    "    description='$X_{delta}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "ydelta = widgets.BoundedFloatText(\n",
    "    min = 1.,\n",
    "    description='$Y_{delta}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "zdelta = widgets.BoundedFloatText(\n",
    "    min = 1.,\n",
    "    description='$Z_{delta}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "tdelta = widgets.BoundedFloatText(\n",
    "    min = 0.01,\n",
    "    description='$Time_{delta}$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "\n",
    "toggle2D = widgets.Checkbox(\n",
    "    description='2-D',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "def toggle2D_cb(b):\n",
    "    if (toggle2D.value):\n",
    "        #zmin.disabled = zmax.disabled = zdelta.disabled = True\n",
    "        zmin.disabled = True\n",
    "        zmax.disabled = True\n",
    "        zdelta.disabled = True\n",
    "    else:\n",
    "        zmin.disabled = False\n",
    "        zmax.disabled = False\n",
    "        zdelta.disabled = False\n",
    "    \n",
    "toggle2D.observe(toggle2D_cb)\n",
    "\n",
    "x_row = widgets.HBox([xmin,xmax,xdelta])\n",
    "y_row = widgets.HBox([ymin,ymax,ydelta])\n",
    "z_row = widgets.HBox([zmin,zmax,zdelta])\n",
    "# box_layout = Layout(display='flex',\n",
    "#                     flex_flow='column',\n",
    "#                     align_items='stretch',\n",
    "#                     border='1px solid black',\n",
    "#                     width='90%')\n",
    "#z_row = Box(children=items, layout=box_layout)\n",
    "#z_row = Box([toggle2D,zmin,zmax,zdelta], layout=box_layout)\n",
    "#domain_range = Box([x_row,y_row,z_row], layout=box_layout)\n",
    "\n",
    "tumor_radius = widgets.BoundedFloatText(\n",
    "    min=1,\n",
    "    max=99999,  # TODO - wth\n",
    "    step=1,\n",
    "    description='Tumor Radius', style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "\n",
    "omp_threads = widgets.BoundedIntText(\n",
    "    min=1,\n",
    "    step=1,\n",
    "    description='# threads',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "\n",
    "toggle_prng = widgets.Checkbox(\n",
    "    description='Seed PRNG', style={'description_width': 'initial'},  # e.g. 'initial'  '120px'\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "prng_seed = widgets.BoundedIntText(\n",
    "    min = 1,\n",
    "    description='Seed', \n",
    "    disabled=True,\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "def toggle_prng_cb(b):\n",
    "    if (toggle_prng.value):\n",
    "        prng_seed.disabled = False\n",
    "    else:\n",
    "        prng_seed.disabled = True\n",
    "    \n",
    "toggle_prng.observe(toggle_prng_cb)\n",
    "\n",
    "#prng_row = widgets.HBox([toggle_prng, prng_seed])\n",
    "\n",
    "#----- Output ------\n",
    "# TODO: this changes when running on nanoHUB (= $RESULTSDIR)\n",
    "output_dir_str = os.getenv('RESULTSDIR') + \"/pc4nanobio/\"\n",
    "# output_dir_str = 'output'  # match the \"value\" of the widget below\n",
    "\n",
    "# NOTE: not used anymore\n",
    "output_dir = widgets.Text(\n",
    "#     value='output',\n",
    "    description='Output Dir',\n",
    ")\n",
    "def config_output_dir_cb(w):\n",
    "    global output_dir_str\n",
    "    output_dir_str = w.value\n",
    "    print(output_dir_str)\n",
    "    \n",
    "output_dir.on_submit(config_output_dir_cb)\n",
    "\n",
    "toggle_svg = widgets.Checkbox(\n",
    "    description='SVG',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "svg_t0 = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description='$T_0$',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "svg_interval = widgets.BoundedIntText(\n",
    "    min=1,\n",
    "    max=99999999,   # TODO: set max on all Bounded widgets to avoid unwanted default\n",
    "    description='interval',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "def toggle_svg_cb(b):\n",
    "    if (toggle_svg.value):\n",
    "        svg_t0.disabled = False #False\n",
    "        svg_interval.disabled = False\n",
    "    else:\n",
    "        svg_t0.disabled = True\n",
    "        svg_interval.disabled = True\n",
    "    \n",
    "toggle_svg.observe(toggle_svg_cb)\n",
    "\n",
    "\n",
    "toggle_mcds = widgets.Checkbox(\n",
    "#     value=False,\n",
    "    description='Full',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "mcds_t0 = widgets.FloatText(\n",
    "    description='$T_0$',\n",
    "    disabled=True,\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "mcds_interval = widgets.BoundedIntText(\n",
    "    min=0,\n",
    "    max=99999999,\n",
    "    description='interval',\n",
    "    disabled=True,\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "def toggle_mcds_cb(b):\n",
    "    if (toggle_mcds.value):\n",
    "        mcds_t0.disabled = False #False\n",
    "        mcds_interval.disabled = False\n",
    "    else:\n",
    "        mcds_t0.disabled = True\n",
    "        mcds_interval.disabled = True\n",
    "    \n",
    "toggle_mcds.observe(toggle_mcds_cb)\n",
    "\n",
    "#----------------------------\n",
    "# NOTE/TODO: any time the elm names change in the XML, need to change here!!!\n",
    "def read_config_file_cb(b):\n",
    "    config_file = os.getenv('HOME') + '/' + read_config_file.value\n",
    "    fill_gui_params(config_file)\n",
    "    \n",
    "def default_config_file_cb(b):\n",
    "    fill_gui_params('data/nanobio_settings.xml')  # NOTE: hard-coded for now\n",
    "\n",
    "def fill_gui_params(config_file):\n",
    "#    global pc4nanobio_config_xml\n",
    "    tree = ET.parse(config_file)\n",
    "    root = tree.getroot()\n",
    "    xmin.value = float(root.find(\".//x_min\").text)\n",
    "    \n",
    "    xmin.value = float(root.find(\".//x_min\").text)\n",
    "    xmax.value = float(root.find(\".//x_max\").text)\n",
    "    xdelta.value = float(root.find(\".//dx\").text)\n",
    "    \n",
    "    ymin.value = float(root.find(\".//y_min\").text)\n",
    "    ymax.value = float(root.find(\".//y_max\").text)\n",
    "    ydelta.value = float(root.find(\".//dy\").text)\n",
    "    \n",
    "    zmin.value = float(root.find(\".//z_min\").text)\n",
    "    zmax.value = float(root.find(\".//z_max\").text)\n",
    "    zdelta.value = float(root.find(\".//dz\").text)\n",
    "    \n",
    "    tmax.value = float(root.find(\".//max_time\").text)\n",
    "    \n",
    "    tumor_radius.value = float(root.find(\".//radius\").text)\n",
    "    omp_threads.value = int(root.find(\".//omp_num_threads\").text)\n",
    "    \n",
    "#     output_dir.value = (root.find(\".//folder\").text)\n",
    "    toggle_svg.value = bool(root.find(\".//SVG\").find(\".//enable\").text)\n",
    "    svg_interval.value = int(root.find(\".//SVG\").find(\".//interval\").text)\n",
    "    toggle_mcds.value = bool(root.find(\".//full_data\").find(\".//enable\").text)\n",
    "    mcds_interval.value = int(root.find(\".//full_data\").find(\".//interval\").text)\n",
    "    \n",
    "    cdp = root.find(\".//cell_definition\")\n",
    "#     e2 = e1.find('.//')\n",
    "    cell0_max_birth_rate.children[0].value = float(cdp.find(\".//max_birth_rate\").text)\n",
    "    cell0_o2_prolif_sat.children[0].value = float(cdp.find(\".//o2_proliferation_saturation\").text)\n",
    "    cell0_o2_prolif_thresh.children[0].value = float(cdp.find(\".//o2_proliferation_threshold\").text)\n",
    "    cell0_o2_ref.children[0].value = float(cdp.find(\".//o2_reference\").text)\n",
    "    \n",
    "    cell0_glucose_prolif_ref.children[0].value = float(root.find(\".//glucose_proliferation_reference\").text)\n",
    "    cell0_glucose_prolif_sat.children[0].value = float(root.find(\".//glucose_proliferation_saturation\").text)\n",
    "    cell0_glucose_prolif_thresh.children[0].value = float(root.find(\".//glucose_proliferation_threshold\").text)\n",
    "    \n",
    "    cell0_max_necrosis_rate.children[0].value = float(root.find(\".//max_necrosis_rate\").text)\n",
    "    cell0_o2_necrosis_thresh.children[0].value = float(root.find(\".//o2_necrosis_threshold\").text)\n",
    "    cell0_o2_necrosis_max.children[0].value = float(root.find(\".//o2_necrosis_max\").text)\n",
    "    \n",
    "    cell0_apoptosis_rate.children[0].value = float(cdp.find(\".//apoptosis_rate\").text)\n",
    "    \n",
    "    cell0_metab_aero.children[0].value = float(cdp.find(\".//relative_aerobic_effects\").text)\n",
    "    cell0_metab_glyco.children[0].value = float(cdp.find(\".//relative_glycolytic_effects\").text)\n",
    "    \n",
    "    cell0_toggle_motile.value = bool(cdp.find(\".//is_motile\").text)\n",
    "    cell0_motile_bias.value = float(cdp.find(\".//bias\").text)\n",
    "\n",
    "    return\n",
    "\n",
    "default_config_button = Button(\n",
    "    description='Use defaults', style={'description_width': 'initial'},\n",
    "    button_style='info', # 'success', 'info', 'warning', 'danger' or ''\n",
    "    tooltip='Populate the GUI with default parameters',\n",
    ")\n",
    "default_config_button.on_click(default_config_file_cb)\n",
    "\n",
    "read_config_button = Button(\n",
    "    description='Read config (in ~)', style={'description_width': 'initial'},\n",
    "    button_style='info', # 'success', 'info', 'warning', 'danger' or ''\n",
    "    tooltip='Populate the GUI with info in your configuration file (in your home directory)',\n",
    ")\n",
    "read_config_file = widgets.Text(\n",
    "    value='my_nanobio_settings.xml',\n",
    "    description='',\n",
    ")\n",
    "read_config_button.on_click(read_config_file_cb)\n",
    "\n",
    "#----------------------------\n",
    "def write_config_file_cb(b):\n",
    "#    print('writing config')\n",
    "\n",
    "    # TODO: verify template .xml file exists!\n",
    "    # read/parse existing template that we'll then overwrite\n",
    "    tree = ET.parse('data/nanobio_settings.xml')  \n",
    "    root = tree.getroot()\n",
    "    \n",
    "    # TODO: verify valid type (numeric) and range?\n",
    "    root.find(\".//x_min\").text = str(xmin.value)\n",
    "    root.find(\".//x_max\").text = str(xmax.value)\n",
    "    root.find(\".//dx\").text = str(xdelta.value)\n",
    "    root.find(\".//y_min\").text = str(ymin.value)\n",
    "    root.find(\".//y_max\").text = str(ymax.value)\n",
    "    root.find(\".//dy\").text = str(ydelta.value)\n",
    "    root.find(\".//z_min\").text = str(zmin.value)\n",
    "    root.find(\".//z_max\").text = str(zmax.value)\n",
    "    root.find(\".//dz\").text = str(zdelta.value)\n",
    "    \n",
    "    root.find(\".//max_time\").text = str(tmax.value)\n",
    "    \n",
    "    root.find(\".//radius\").text = str(tumor_radius.value)\n",
    "    root.find(\".//omp_num_threads\").text = str(omp_threads.value)\n",
    "    \n",
    "#     root.find(\".//folder\").text = str(output_dir.value)\n",
    "    \n",
    "#    user_details = ET.SubElement(root, \"user_details\")\n",
    "#    ET.SubElement(user_details, \"PhysiCell_settings\", name=\"version\").text = \"devel-version\"\n",
    "#    ET.SubElement(user_details, \"domain\")\n",
    "#    ET.SubElement(user_details, \"xmin\").text = \"-100\"\n",
    "\n",
    "#    tree = ET.ElementTree(root)\n",
    "#    tree.write(write_config_file.value)\n",
    "#    tree.write(\"test.xml\")\n",
    "\n",
    "    # TODO: verify can write to this filename and don't allow overwrite of default\n",
    "    # Q: where does this file get written/saved?\n",
    "    tree.write(write_config_file.value)\n",
    "    \n",
    "write_config_button = Button(\n",
    "    description='Write config file',\n",
    "    button_style='success', # 'success', 'info', 'warning', 'danger' or ''\n",
    "    tooltip='Generate XML',\n",
    ")\n",
    "write_config_button.on_click(write_config_file_cb)\n",
    "\n",
    "write_config_file = widgets.Text(\n",
    "    value='my_nanobio_settings.xml',\n",
    "    description='',\n",
    ")\n",
    "\n",
    "#----------------------------\n",
    "run_output = widgets.Output(layout=widgets.Layout(width='900px', height='100px', border='solid'))\n",
    "#run_output\n",
    "\n",
    "# This is NOT used for the RunCommand\n",
    "run_command_str = widgets.Text(\n",
    "    value='pc-nb nanobio_settings.xml',\n",
    "    description='',\n",
    ")\n",
    "\n",
    "# This is used now for the RunCommand\n",
    "def run_sim_func(s):\n",
    "    s.run(\"bin/pc-nb data/nanobio_settings.xml\")  # TODO: choose: nanoHUB vs local\n",
    "#     s.run(\"/Users/heiland/dev/run-nanobio/pc-nb nanobio_settings.xml\")\n",
    "   \n",
    "# This is NOT used now\n",
    "def run_cb(b):\n",
    "    global my_proc\n",
    "    print('running: ', run_command_str.value)\n",
    "    with run_output:\n",
    "#         print(type(run_button))\n",
    "#         print(dir(run_button))\n",
    "#         args = ['/Users/heiland/git/PhysiCell-nanobio-com-fork/trunk/src/PhysiCell-nanobio','nanobio_settings.xml']\n",
    "#         args = ['/Users/heiland/dev/run-nanobio/pc-nb','nanobio_settings.xml']\n",
    "        #my_proc = Popen(args, stdout=PIPE, stderr=STDOUT)\n",
    "        #runCommand('/Users/heiland/git/PhysiCell-nanobio-com-fork/trunk/src/PhysiCell-nanobio nanobio_settings.xml')\n",
    "        sys.path.insert(0, os.path.abspath('..'))\n",
    "#         runCommand('/Users/heiland/dev/run-nanobio/pc-nb nanobio_settings.xml')\n",
    "        runCommand('pc-nb nanobio_settings.xml')\n",
    "        \n",
    "    # NOTE: using the following approach will block us from other processes, e.g. visualizing results or executing a cmd in another cell\n",
    "    # This should be safe because we're not piping stdin to the process.\n",
    "    # It gets tricky if we are, because the process can be waiting for input while we're waiting for output.\n",
    "#     while True:\n",
    "#         # Wait for some output, read it and print it.\n",
    "#         with run_output:\n",
    "#             my_output = my_proc.stdout.read1(1024).decode('utf-8')\n",
    "#             print(my_output, end='')\n",
    "\n",
    "#         # Has the subprocess finished yet?\n",
    "#         if my_proc.poll() is not None:\n",
    "#             break\n",
    "\n",
    "    if my_proc.returncode != 0:\n",
    "        print(\"Exited with error code:\", my_proc.returncode)\n",
    "\n",
    "        \n",
    "run_button = RunCommand(start_func=run_sim_func)  # optionally: , done_func=read_data\n",
    "\n",
    "# run_button = Button(\n",
    "#     description='Run',\n",
    "#     disabled=False,\n",
    "#     button_style='success', # 'success', 'info', 'warning', 'danger' or ''\n",
    "#     tooltip='Run simulation',\n",
    "# )\n",
    "# run_button.on_click(run_cb)\n",
    "\n",
    "# def kill_cb(b):\n",
    "#     global my_proc\n",
    "#     print('kill sim...')\n",
    "#     my_proc.terminate()\n",
    "    \n",
    "# kill_button = Button(\n",
    "#     description='Kill',\n",
    "#     disabled=False,\n",
    "#     button_style='danger', # 'success', 'info', 'warning', 'danger' or ''\n",
    "#     tooltip='Kill simulation',\n",
    "# )\n",
    "# kill_button.on_click(kill_cb)\n",
    "\n",
    "read_config_row = widgets.HBox([default_config_button, read_config_button, read_config_file])\n",
    "#svg_output_row = widgets.HBox([toggle_svg, svg_t0, svg_interval])\n",
    "#mat_output_row = widgets.HBox([toggle_mcds, mcds_t0, mcds_interval])\n",
    "svg_mat_output_row = widgets.HBox([toggle_svg,svg_interval, toggle_mcds,mcds_interval])\n",
    "write_config_row = widgets.HBox([write_config_button, write_config_file])\n",
    "#run_sim_row = widgets.HBox([run_button, run_command_str, kill_button])\n",
    "# run_sim_row = widgets.HBox([run_button, run_command_str])\n",
    "# run_sim_row = widgets.HBox([run_button.w])  # need \".w\" for the custom RunCommand widget\n",
    "\n",
    "label_blankline = widgets.Label('')\n",
    "tumor_radius2 = HBox([tumor_radius,micron_units])\n",
    "# toggle_2D_seed_row = widgets.HBox([toggle_prng, prng_seed])  # toggle2D\n",
    "config_tab = widgets.VBox([read_config_row, label_domain,x_row,y_row,z_row,  \n",
    "                           label_blankline, tmax, omp_threads,  \n",
    "                           tumor_radius2,svg_mat_output_row], layout=tab_layout)  # output_dir, toggle_2D_seed_row\n",
    "\n",
    "\n",
    "#----------------------------------------------\n",
    "\n",
    "#current_idx = 0\n",
    "\n",
    "#for idx in range(len(sys.argv)):\n",
    "use_defaults = True\n",
    "show_nucleus = 0\n",
    "current_idx = 0\n",
    "axes_min = 0.0\n",
    "axes_max = 2000\n",
    "#axes_max = 1000\n",
    "scale_radius = 1.0\n",
    "\n",
    "# TODO: these change when running on nanoHUB \n",
    "#svg_dir_str = output_dir_str\n",
    "#mcds_dir_str = output_dir_str\n",
    "\n",
    "field_index = 4\n",
    "def plot_substrate(FileId):\n",
    "    global current_idx, axes_max, gFileId, field_index\n",
    "#    global svg_dir_str\n",
    "    #  dir = svg_dir.value\n",
    "#     print('debug> plot_substrate: idx=',FileId)\n",
    "    gFileId = FileId\n",
    "    fname = \"output%08d_microenvironment0.mat\" % FileId\n",
    "#    fullname = svg_dir_str + \"/\" + fname\n",
    "    fullname = output_dir_str + fname\n",
    "    if not pathlib.Path(fullname).is_file():\n",
    "        return\n",
    "\n",
    "    info_dict = {}\n",
    "    scipy.io.loadmat(fullname, info_dict)\n",
    "    M = info_dict['multiscale_microenvironment']\n",
    "#     global_field_index = int(mcds_field.value)\n",
    "#     print('plot_substrate: field_index =',field_index)\n",
    "#    print('plot_substrate: field_index=',field_index)\n",
    "    f = M[field_index,:]   # 4=tumor cells field, 5=blood vessel density, 6=growth substrate\n",
    "    #plt.clf()\n",
    "    #my_plot = plt.imshow(f.reshape(400,400), cmap='jet', extent=[0,20, 0,20])\n",
    "    \n",
    "    fig = plt.figure(figsize=(7.2,6))  # this strange figsize results in a ~square contour plot\n",
    "#     fig.set_tight_layout(True)\n",
    "#     ax = plt.axes([0, 0.05, 0.9, 0.9 ]) #left, bottom, width, height\n",
    "#     ax = plt.axes([0, 0.0, 1, 1 ])\n",
    "#     cmap = plt.cm.viridis # Blues, YlOrBr, ...\n",
    "#     im = ax.imshow(f.reshape(100,100), interpolation='nearest', cmap=cmap, extent=[0,20, 0,20])\n",
    "#     ax.grid(False)\n",
    "\n",
    "    grid2D = M[0,:].reshape(100,100)\n",
    "    xvec = grid2D[0,:]\n",
    "    #xvec.size\n",
    "    #xvec.shape\n",
    "    num_contours = 30\n",
    "    my_plot = plt.contourf(xvec,xvec,M[field_index,:].reshape(100,100), num_contours, cmap=field_cmap.value) #'viridis'\n",
    "    plt.colorbar(my_plot)\n",
    "    axes_min = 0\n",
    "    axes_max = 2000\n",
    "    plt.xlim(axes_min,axes_max)\n",
    "    plt.ylim(axes_min,axes_max)\n",
    "#     plt.title(fname)\n",
    "#     ax.set_title(fname)\n",
    "#     plt.axis('equal')\n",
    "    #plt.show()\n",
    "\n",
    "\n",
    "get_ipython().run_line_magic('matplotlib', 'inline')\n",
    "def plot_svg(SVG):\n",
    "  global current_idx, axes_max\n",
    "#  global svg_dir_str\n",
    "#  dir = svg_dir.value\n",
    "#   print('plot_svg: SVG=',SVG)\n",
    "  fname = \"snapshot%08d.svg\" % SVG\n",
    "  fullname = output_dir_str + fname\n",
    "  if not pathlib.Path(fullname).is_file():\n",
    "#    print(\"File does not exist: \",fname)\n",
    "    return\n",
    "\n",
    "  xlist = deque()\n",
    "  ylist = deque()\n",
    "  rlist = deque()\n",
    "  rgb_list = deque()\n",
    "\n",
    "#  print('\\n---- ' + fullname + ':')\n",
    "  tree = ET.parse(fullname)\n",
    "  root = tree.getroot()\n",
    "#  print('--- root.tag ---')\n",
    "#  print(root.tag)\n",
    "#  print('--- root.attrib ---')\n",
    "#  print(root.attrib)\n",
    "\n",
    "\n",
    "#  print('--- child.tag, child.attrib ---')\n",
    "  numChildren = 0\n",
    "  for child in root:\n",
    "#    print(child.tag, child.attrib)\n",
    "#    print(\"keys=\",child.attrib.keys())\n",
    "    if use_defaults and ('width' in child.attrib.keys()):\n",
    "      axes_max = float(child.attrib['width'])\n",
    "#       print(\"debug> found width --> axes_max =\", axes_max)\n",
    "    if child.text and \"Current time\" in child.text:\n",
    "      svals = child.text.split()\n",
    "      #title_str = \"(\" + str(current_idx) + \") Current time: \" + svals[2] + \"d, \" + svals[4] + \"h, \" + svals[7] + \"m\"\n",
    "      title_str = \"Current time: \" + svals[2] + \"d, \" + svals[4] + \"h, \" + svals[7] + \"m\"\n",
    "\n",
    "#    print(\"width \",child.attrib['width'])\n",
    "#    print('attrib=',child.attrib)\n",
    "#    if (child.attrib['id'] == 'tissue'):\n",
    "    if ('id' in child.attrib.keys()):\n",
    "#      print('-------- found tissue!!')\n",
    "      tissue_parent = child\n",
    "      break\n",
    "\n",
    "#  print('------ search tissue')\n",
    "  cells_parent = None\n",
    "\n",
    "  for child in tissue_parent:\n",
    "#    print('attrib=',child.attrib)\n",
    "    if (child.attrib['id'] == 'cells'):\n",
    "#      print('-------- found cells, setting cells_parent')\n",
    "      cells_parent = child\n",
    "      break\n",
    "    numChildren += 1\n",
    "\n",
    "\n",
    "  num_cells = 0\n",
    "#  print('------ search cells')\n",
    "  for child in cells_parent:\n",
    "#    print(child.tag, child.attrib)\n",
    "#    print('attrib=',child.attrib)\n",
    "    for circle in child:  # two circles in each child: outer + nucleus\n",
    "    #  circle.attrib={'cx': '1085.59','cy': '1225.24','fill': 'rgb(159,159,96)','r': '6.67717','stroke': 'rgb(159,159,96)','stroke-width': '0.5'}\n",
    "#      print('  --- cx,cy=',circle.attrib['cx'],circle.attrib['cy'])\n",
    "      xval = float(circle.attrib['cx'])\n",
    "\n",
    "      s = circle.attrib['fill']\n",
    "#      print(\"s=\",s)\n",
    "#      print(\"type(s)=\",type(s))\n",
    "      if (s[0:3] == \"rgb\"):  # if an rgb string, e.g. \"rgb(175,175,80)\" \n",
    "        rgb = list(map(int, s[4:-1].split(\",\")))  \n",
    "        rgb[:]=[x/255. for x in rgb]\n",
    "      else:     # otherwise, must be a color name\n",
    "        rgb_tuple = mplc.to_rgb(mplc.cnames[s])  # a tuple\n",
    "        rgb = [x for x in rgb_tuple]\n",
    "\n",
    "      # test for bogus x,y locations (rwh TODO: use max of domain?)\n",
    "      too_large_val = 10000.\n",
    "      if (math.fabs(xval) > too_large_val):\n",
    "        print(\"bogus xval=\",xval)\n",
    "        break\n",
    "      yval = float(circle.attrib['cy'])\n",
    "      if (math.fabs(yval) > too_large_val):\n",
    "        print(\"bogus xval=\",xval)\n",
    "        break\n",
    "\n",
    "      rval = float(circle.attrib['r'])\n",
    "#      if (rgb[0] > rgb[1]):\n",
    "#        print(num_cells,rgb, rval)\n",
    "      xlist.append(xval)\n",
    "      ylist.append(yval)\n",
    "      rlist.append(rval)\n",
    "      rgb_list.append(rgb)\n",
    "\n",
    "#     For .svg files with cells that *have* a nucleus, there will be a 2nd\n",
    "      if (show_nucleus == 0):\n",
    "        break\n",
    "\n",
    "    num_cells += 1\n",
    "\n",
    "#    if num_cells > 3:   # for debugging\n",
    "#      print(fname,':  num_cells= ',num_cells,\" --- debug exit.\")\n",
    "#      sys.exit(1)\n",
    "#      break\n",
    "\n",
    "  #print(fname,':  num_cells= ',num_cells)\n",
    "\n",
    "  xvals = np.array(xlist)\n",
    "  yvals = np.array(ylist)\n",
    "  rvals = np.array(rlist)\n",
    "  rgbs =  np.array(rgb_list)\n",
    "#print(\"xvals[0:5]=\",xvals[0:5])\n",
    "#print(\"rvals[0:5]=\",rvals[0:5])\n",
    "#  print(\"rvals.min, max=\",rvals.min(),rvals.max())\n",
    "\n",
    "#rwh - is this where I change size of render window?? (YES - yipeee!)\n",
    "#   plt.figure(figsize=(6, 6))\n",
    "#   plt.cla()\n",
    "  title_str += \" (\" + str(num_cells) + \" agents)\"\n",
    "#   plt.title(title_str)\n",
    "#   plt.xlim(axes_min,axes_max)\n",
    "#   plt.ylim(axes_min,axes_max)\n",
    "#   plt.scatter(xvals,yvals, s=rvals*scale_radius, c=rgbs)\n",
    "    \n",
    "  fig = plt.figure(figsize=(6,6))\n",
    "  ax = plt.axes([0, 0.05, 0.9, 0.9 ]) #left, bottom, width, height\n",
    "\n",
    "#   im = ax.imshow(f.reshape(100,100), interpolation='nearest', cmap=cmap, extent=[0,20, 0,20])\n",
    "#   ax.xlim(axes_min,axes_max)\n",
    "#   ax.ylim(axes_min,axes_max)\n",
    "  ax.scatter(xvals,yvals, s=rvals*scale_radius, c=rgbs)\n",
    "  plt.xlim(axes_min,axes_max)\n",
    "  plt.ylim(axes_min,axes_max)\n",
    "#   ax.grid(False)\n",
    "  ax.set_title(title_str)\n",
    "    \n",
    "#plt.xlim(0,2000)  # TODO - get these values from width,height in .svg at top\n",
    "#plt.ylim(0,2000)\n",
    "#  plt.pause(time_delay)\n",
    "#   plt.axis('equal')   # doing this will cause the axes to scale dynamically, probably unwanted\n",
    "\n",
    "\n",
    "# keep last plot displayed\n",
    "#plt.ioff()\n",
    "#   plt.show()\n",
    "\n",
    "#def svg_dir_cb(w):\n",
    "#    global svg_dir_str\n",
    "#    svg_dir_str = w.value\n",
    "#    print(svg_dir_str)\n",
    "    \n",
    "#svg_dir = widgets.Text(\n",
    "#    value=svg_dir_str,\n",
    "#    description='Directory',\n",
    "#)\n",
    "#svg_dir.on_submit(svg_dir_cb)\n",
    "\n",
    "#rwh - is this where I change size of render window?? (apparently not)\n",
    "# TODO: dynamically change max value\n",
    "svg_plot = widgets.interactive(plot_svg, SVG=(0, 500), continuous_update=False)\n",
    "# output = svg_plot.children[-1]\n",
    "# output.layout.height = '300px'\n",
    "# output = svg_plot.children[1]\n",
    "svg_plot_size = '500px'\n",
    "svg_plot.layout.width = svg_plot_size\n",
    "svg_plot.layout.height = svg_plot_size\n",
    "\n",
    "# video-style widget - perhaps for future use\n",
    "# svg_play = widgets.Play(\n",
    "#     interval=1,\n",
    "#     value=50,\n",
    "#     min=0,\n",
    "#     max=100,\n",
    "#     step=1,\n",
    "#     description=\"Press play\",\n",
    "#     disabled=False,\n",
    "# )\n",
    "# def svg_slider_change(change):\n",
    "#     print('svg_slider_change: type(change)=',type(change),change.new)\n",
    "#     plot_svg(change.new)\n",
    "    \n",
    "#svg_play\n",
    "# svg_slider = widgets.IntSlider()\n",
    "# svg_slider.observe(svg_slider_change, names='value')\n",
    "\n",
    "# widgets.jslink((svg_play, 'value'), (svg_slider,'value')) #  (svg_slider, 'value'), (plot_svg, 'value'))\n",
    "\n",
    "# svg_slider = widgets.IntSlider()\n",
    "# widgets.jslink((play, 'value'), (slider, 'value'))\n",
    "# widgets.HBox([svg_play, svg_slider])\n",
    "\n",
    "# Using the following generates a new mpl plot; it doesn't use the existing plot!\n",
    "#svg_anim = widgets.HBox([svg_play, svg_slider])\n",
    "\n",
    "#svg_tab = widgets.VBox([svg_dir, svg_plot, svg_anim], layout=tab_layout)\n",
    "svg_tab = widgets.HBox([svg_plot], layout=tab_layout)  # svg_dir\n",
    "\n",
    "#svg_tab = widgets.VBox([svg_dir, svg_anim], layout=tab_layout)\n",
    "#---------------------\n",
    "\n",
    "#============ Cells tab ===================\n",
    "cell_name = widgets.Text(\n",
    "    value='untreated cancer',\n",
    "    description='Cell line name', style={'description_width': 'initial'},\n",
    ")\n",
    "#-------\n",
    "label_cycle = widgets.Label('Cycle:')   # no worky:  ,style={'font_weight': 'bold'})\n",
    "\n",
    "# NOTE: by adopting the \n",
    "cell0_max_birth_rate = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    #value = 0.0079,\n",
    "    description='Max birth rate', style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth3),\n",
    "    ), min_inv_units], layout=Layout(width='300px'))\n",
    "\n",
    "\n",
    "width_cell_params_units = '230px'\n",
    "cell0_o2_prolif_sat = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='$O_2$: Prolif sat',\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_o2_prolif_thresh = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='Prolif thresh',\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_o2_ref = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='Ref',\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "cell0_glucose_prolif_sat = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='$Glc$: Prolif sat',\n",
    "    layout = Layout(width = constWidth),style={'description_width': 'initial'},\n",
    "    ), ], layout=Layout(width=width_cell_params_units))\n",
    "cell0_glucose_prolif_thresh = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='Prolif thresh',\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), ], layout=Layout(width=width_cell_params_units))\n",
    "cell0_glucose_prolif_ref = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='Ref',\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), ], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "#-------\n",
    "label_necrosis = widgets.Label('Necrosis:')\n",
    "cell0_max_necrosis_rate = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='Max rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_o2_necrosis_thresh = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='$O_2$: Thresh',\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_o2_necrosis_max = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='Max',\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "#-------\n",
    "label_apoptosis = widgets.Label('Apoptosis:')\n",
    "cell0_apoptosis_rate = HBox([BoundedFloatText (\n",
    "    min=0,\n",
    "    description='Rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "#-------\n",
    "# TODO: enforce sum=1\n",
    "label_metabolism = widgets.Label('Metabolism (must sum to 1):')\n",
    "# TODO: assert these next 2 values sum to 1.0\n",
    "cell0_metab_aero = HBox([BoundedFloatText (\n",
    "    min=0,max=1,step=0.1,\n",
    "    description='Aerobic', #style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), ], layout=Layout(width=width_cell_params_units))\n",
    "cell0_metab_glyco = HBox([BoundedFloatText (\n",
    "    min=0,max=1,step=0.1,\n",
    "    description='Glycolytic', #style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), ], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "#-------\n",
    "label_motility = widgets.Label('Motility:')\n",
    "\n",
    "cell0_toggle_motile = widgets.Checkbox(\n",
    "    description='Motile',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "cell0_motile_bias = BoundedFloatText (\n",
    "    min=0,max=1,step=0.1,\n",
    "#     disabled = True,\n",
    "    description='Bias', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "def cell0_toggle_motile_cb(b):\n",
    "    if (cell0_toggle_motile.value):\n",
    "        cell0_motile_bias.disabled = False\n",
    "    else:\n",
    "        cell0_motile_bias.disabled = True\n",
    "    \n",
    "cell0_toggle_motile.observe(cell0_toggle_motile_cb)\n",
    "\n",
    "\n",
    "#-------\n",
    "label_mechanics = widgets.Label('Mechanics:')\n",
    "cell0_max_rel_adhesion_dist = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Max adhesion distance', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), ], layout=Layout(width=width_cell_params_units))\n",
    "cell0_adhesion_strength = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Adhesion strength', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), ], layout=Layout(width=width_cell_params_units))\n",
    "cell0_repulsion_strength = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Repulsion strength', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), ], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "#-------\n",
    "label_hypoxia = widgets.Label('Hypoxia:')\n",
    "cell0_o2_hypoxic_thresh = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='$O_2$: Thresh', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_o2_hypoxic_response = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Response', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_o2_hypoxic_sat = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Saturation', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "#-------\n",
    "label_secretion = widgets.Label('Secretion:')\n",
    "cell0_secretion_o2_uptake = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='$O_2$: Uptake rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_o2_secretion = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Secretion rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_o2_sat = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Saturation', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "cell0_secretion_glc_uptake = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='$Glc$: Uptake rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_glc_secretion = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Secretion rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_glc_sat = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Saturation', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "cell0_secretion_Hions_uptake = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='$H$+: Uptake rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_Hions_secretion = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Secretion rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_Hions_sat = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Saturation', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "cell0_secretion_ECM_uptake = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='$ECM$: Uptake rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_ECM_secretion = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Secretion rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_ECM_sat = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Saturation', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "cell0_secretion_NP1_uptake = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='$NP1$: Uptake rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_NP1_secretion = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Secretion rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_NP1_sat = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Saturation', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "cell0_secretion_NP2_uptake = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='$NP2$: Uptake rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_NP2_secretion = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Secretion rate', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), min_inv_units], layout=Layout(width=width_cell_params_units))\n",
    "cell0_secretion_NP2_sat = HBox([BoundedFloatText (\n",
    "    min=0, step=0.1, #max=1,  \n",
    "    description='Saturation', # style={'description_width': 'initial'},\n",
    "    layout = Layout(width = constWidth),\n",
    "    ), mmHg_units], layout=Layout(width=width_cell_params_units))\n",
    "\n",
    "\n",
    "#-----------------\n",
    "# cells_max_birth_rate2 = HBox([max_birth_rate,min_inv_units], layout=Layout(width='300px'))\n",
    "# cells_o2_prolif_sat2 = HBox([o2_prolif_sat,min_inv_units])\n",
    "# cells_o2_prolif_thresh2 = HBox([o2_prolif_thresh, mmHg_units])\n",
    "cells_row1 = HBox([cell_name])\n",
    "cells_row2 = HBox([cell0_o2_prolif_sat, cell0_o2_prolif_thresh, cell0_o2_ref])\n",
    "cells_row3 = HBox([cell0_glucose_prolif_sat, cell0_glucose_prolif_thresh, cell0_glucose_prolif_ref])\n",
    "cell0_necrosis_row = HBox([cell0_o2_necrosis_thresh, cell0_o2_necrosis_max]) #, layout=Layout(width=pk_widgets_width))\n",
    "cells_tab = VBox([cells_row1, \n",
    "    label_cycle, cell0_max_birth_rate, cells_row2, cells_row3,\n",
    "    label_necrosis, cell0_max_necrosis_rate, cell0_necrosis_row,\n",
    "    label_apoptosis, cell0_apoptosis_rate,\n",
    "    label_metabolism, HBox([cell0_metab_aero, cell0_metab_glyco]),\n",
    "    label_motility, HBox([cell0_toggle_motile, cell0_motile_bias]),\n",
    "    label_mechanics, HBox([cell0_max_rel_adhesion_dist,cell0_adhesion_strength,cell0_repulsion_strength]),\n",
    "    label_hypoxia, HBox([cell0_o2_hypoxic_thresh,cell0_o2_hypoxic_response,cell0_o2_hypoxic_sat]),\n",
    "    label_secretion, HBox([cell0_secretion_o2_uptake,cell0_secretion_o2_secretion,cell0_secretion_o2_sat]),\n",
    "                  HBox([cell0_secretion_glc_uptake,cell0_secretion_glc_secretion,cell0_secretion_glc_sat]),\n",
    "                  HBox([cell0_secretion_Hions_uptake,cell0_secretion_Hions_secretion,cell0_secretion_Hions_sat]),\n",
    "                  HBox([cell0_secretion_ECM_uptake,cell0_secretion_ECM_secretion,cell0_secretion_ECM_sat]),\n",
    "                  HBox([cell0_secretion_NP1_uptake,cell0_secretion_NP1_secretion,cell0_secretion_NP1_sat]),\n",
    "                  HBox([cell0_secretion_NP2_uptake,cell0_secretion_NP1_secretion,cell0_secretion_NP2_sat]),\n",
    "    ])  #, layout=tab_layout)\n",
    "\n",
    "#=========\n",
    "# PK\n",
    "half_conc_desc = '$T_{0.5}$'\n",
    "diffusion_coef_desc = 'Diffusion coef'\n",
    "survival_desc = 'Survival lifetime'\n",
    "binding_desc = 'ECM binding rate'\n",
    "unbinding_desc = 'ECM unbinding rate'\n",
    "sat_conc_desc = 'ECM saturation conc'\n",
    "desc_style = {'description_width': '150px'}  # vs. 'initial'\n",
    "\n",
    "# PD\n",
    "ec_50_desc = '$EC_{50}$'\n",
    "\n",
    "label_PK = widgets.Label('Pharmacokinetics:')\n",
    "pk_param_width = '270px'\n",
    "pd_param_width = '270px'\n",
    "#------------\n",
    "np1_diff_coef = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= diffusion_coef_desc, style=desc_style,\n",
    "    disabled=False,\n",
    "    layout = Layout(width = pk_param_width),  #flex_flow='row',align_items='stretch'),\n",
    ")\n",
    "np1_survival_lifetime = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= survival_desc, style=desc_style,\n",
    "    disabled=False,\n",
    "    layout = Layout(width = pk_param_width),  #flex_flow='row',align_items='stretch'),\n",
    ")\n",
    "np1_binding_rate = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= binding_desc, style=desc_style,\n",
    "    disabled=False,\n",
    "    layout = Layout(width = pk_param_width),\n",
    ")\n",
    "np1_unbinding_rate = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= unbinding_desc, style=desc_style,\n",
    "    layout = Layout(width = pk_param_width),\n",
    ")\n",
    "np1_saturation_conc = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= sat_conc_desc, style=desc_style,\n",
    "    layout = Layout(width = pk_param_width),\n",
    ")\n",
    "#box_layout = Layout(display='flex',flex_flow='column',align_items='stretch',border='1px solid black',width='30%')\n",
    "pk_widgets_width = '320px'\n",
    "np1_diff_coef2 = HBox([np1_diff_coef,diffusion_coef_units], layout=Layout(width=pk_widgets_width),)\n",
    "np1_survival_lifetime2 = HBox([np1_survival_lifetime,survival_lifetime_units], layout=Layout(width=pk_widgets_width),)\n",
    "np1_binding_rate2 = HBox([np1_binding_rate,min_inv_units], layout=Layout(width=pk_widgets_width),)\n",
    "np1_unbinding_rate2 = HBox([np1_unbinding_rate,min_inv_units], layout=Layout(width=pk_widgets_width),)\n",
    "#np1_sat_conc2 = widgets.HBox([np1_saturation_conc,min_inv_units], layout=Layout(width=pk_widgets_width),)\n",
    "\n",
    "np1_PK_params = VBox([label_PK,np1_diff_coef2,np1_survival_lifetime2,np1_binding_rate2,np1_unbinding_rate2,np1_saturation_conc]) #, layout=box_layout)\n",
    "\n",
    "#----------\n",
    "label_PD = widgets.Label('Pharmacodynamics:')\n",
    "\n",
    "np1_effect_model_choice = widgets.Dropdown(\n",
    "#     options=['1', '2', '3','4','5','6'],\n",
    "    options=['Simple (conc)', 'Intermed (AUC)', 'Details'],\n",
    "    value='Simple (conc)',\n",
    "#     description='Field',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "np1_EC_50 = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= ec_50_desc, style=desc_style,\n",
    "    layout = Layout(width = pd_param_width),\n",
    ")\n",
    "\n",
    "np1_tab = VBox([np1_PK_params, label_PD], layout=np_tab_layout)\n",
    "\n",
    "\n",
    "#------------\n",
    "#------------\n",
    "np2_diff_coef = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= diffusion_coef_desc, style=desc_style,\n",
    "    layout = Layout(width = pk_param_width),  #flex_flow='row',align_items='stretch'),\n",
    ")\n",
    "np2_survival_lifetime = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= survival_desc, style=desc_style,\n",
    "    layout = Layout(width = pk_param_width),  #flex_flow='row',align_items='stretch'),\n",
    ")\n",
    "np2_binding_rate = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= binding_desc, style=desc_style,\n",
    "    layout = Layout(width = pk_param_width),\n",
    ")\n",
    "np2_unbinding_rate = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= unbinding_desc, style=desc_style,\n",
    "    layout = Layout(width = pk_param_width),\n",
    ")\n",
    "np2_saturation_conc = widgets.BoundedFloatText (\n",
    "    min=0,\n",
    "    description= sat_conc_desc, style=desc_style,\n",
    "    layout = Layout(width = pk_param_width),\n",
    ")\n",
    "#box_layout = Layout(display='flex',flex_flow='column',align_items='stretch',border='1px solid black',width='30%')\n",
    "np2_diff_coef2 = widgets.HBox([np2_diff_coef,diffusion_coef_units], layout=Layout(width=pk_widgets_width),)\n",
    "np2_survival_lifetime2 = widgets.HBox([np2_survival_lifetime,survival_lifetime_units], layout=Layout(width=pk_widgets_width),)\n",
    "np2_binding_rate2 = widgets.HBox([np2_binding_rate,min_inv_units], layout=Layout(width=pk_widgets_width),)\n",
    "np2_unbinding_rate2 = widgets.HBox([np2_unbinding_rate,min_inv_units], layout=Layout(width=pk_widgets_width),)\n",
    "\n",
    "np2_PK_params = widgets.VBox([label_PK,np2_diff_coef2,np2_survival_lifetime2,np2_binding_rate2,\n",
    "                              np2_unbinding_rate2,np2_saturation_conc]) #, layout=box_layout)\n",
    "\n",
    "#---------------\n",
    "label_PD = widgets.Label('Pharmacodynamics:')\n",
    "\n",
    "#---------------\n",
    "np2_tab = widgets.VBox([np2_PK_params, label_PD], layout=np_tab_layout)\n",
    "\n",
    "#-------------------\n",
    "xforms_tab = widgets.Text(\n",
    "    value='.',\n",
    "    description='dummy:',\n",
    "    layout=tab_layout,\n",
    ")\n",
    "np_tab = widgets.Tab(children=[np1_tab, np2_tab, xforms_tab])\n",
    "np_tab.set_title(0, 'Preform (spherical)')\n",
    "np_tab.set_title(1, 'Reconfig (rod)')\n",
    "np_tab.set_title(2, 'Transformations')\n",
    "\n",
    "\n",
    "\n",
    "#--------------------\n",
    "\n",
    "#def plot_mcds(MCDS):\n",
    "#    global current_idx, axes_max\n",
    "#    global mcds_dir_str\n",
    "#    fname = mcds_dir_str + \"/output%08d.mat\" % MCDS\n",
    "#    return\n",
    "\n",
    "#def mcds_dir_cb(w):\n",
    "#    global mcds_dir_str\n",
    "#    mcds_dir_str = w.value\n",
    "#    print(mcds_dir_str)\n",
    "    \n",
    "#mcds_dir = widgets.Text(\n",
    "#    value=mcds_dir_str,\n",
    "#    description='Directory',\n",
    "#)\n",
    "#mcds_dir.on_submit(mcds_dir_cb)\n",
    "\n",
    "# TODO: dynamically change max value\n",
    "mcds_plot = widgets.interactive(plot_substrate, FileId=(0, 200), continuous_update=False)  \n",
    "mcds_plot.layout.width = svg_plot_size\n",
    "mcds_plot.layout.height = svg_plot_size\n",
    "\n",
    "# mcds_play = widgets.Play(\n",
    "# #     interval=10,\n",
    "#     value=50,\n",
    "#     min=0,\n",
    "#     max=100,\n",
    "#     step=1,\n",
    "#     description=\"Press play\",\n",
    "#     disabled=False,\n",
    "# )\n",
    "# #mcds_slider = widgets.IntSlider()\n",
    "\n",
    "# widgets.jslink((mcds_play, 'value'), (mcds_slider, 'value'))\n",
    "# widgets.HBox([mcds_play, mcds_slider])\n",
    "\n",
    "mcds_field = widgets.Dropdown(\n",
    "#     options=['1', '2', '3','4','5','6'],\n",
    "    options=['oxygen', 'glucose', 'H+ ions','ECM','NP1','NP2'],\n",
    "    value='oxygen',\n",
    "#     description='Field',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "def mcds_field_cb(b):\n",
    "    global field_index\n",
    "#     field_index = int(mcds_field.value) + 3  # match actual (0-offset) field in data\n",
    "    field_index = mcds_field.options.index(mcds_field.value) + 4 # match actual (0-offset) field in data\n",
    "#    print('mcds_field_field_cb: field_index=',field_index)  # a 'print' causes flicker!\n",
    "#     print(gFileId)\n",
    "#     plot_substrate(gFileId)  # argh, this will create a *new* plot\n",
    "    \n",
    "mcds_field.observe(mcds_field_cb)\n",
    "\n",
    "field_cmap = widgets.Text(\n",
    "    value='viridis',\n",
    "    description='Colormap',\n",
    "    layout = Layout(width = constWidth),\n",
    ")\n",
    "    \n",
    "toggle_field_cmap_fixed = widgets.Checkbox(\n",
    "    description='Fix',\n",
    "    layout = Layout(width = constWidth2),\n",
    ")\n",
    "field_cmap_fixed_min = widgets.FloatText (\n",
    "    description='Min',\n",
    "    step=0,\n",
    "    disabled=True,\n",
    "    layout = Layout(width = constWidth2),\n",
    ")\n",
    "field_cmap_fixed_max = widgets.FloatText (\n",
    "    description='Max',\n",
    "    disabled=True,\n",
    "    layout = Layout(width = constWidth2),\n",
    ")\n",
    "def toggle_field_cmap_fixed_cb(b):\n",
    "    if (toggle_field_cmap_fixed.value):\n",
    "        field_cmap_fixed_min.disabled = False\n",
    "        field_cmap_fixed_max.disabled = False\n",
    "    else:\n",
    "        field_cmap_fixed_min.disabled = True\n",
    "        field_cmap_fixed_max.disabled = True\n",
    "\n",
    "toggle_field_cmap_fixed.observe(toggle_field_cmap_fixed_cb)\n",
    "\n",
    "field_cmap_row2 = widgets.HBox([field_cmap, toggle_field_cmap_fixed])\n",
    "field_cmap_row3 = widgets.HBox([field_cmap_fixed_min,field_cmap_fixed_max])\n",
    "# mcds_tab = widgets.VBox([mcds_dir, mcds_plot, mcds_play], layout=tab_layout)\n",
    "mcds_params = widgets.VBox([mcds_field, field_cmap_row2,field_cmap_row3]) # mcds_dir\n",
    "mcds_tab = widgets.HBox([mcds_params, mcds_plot], layout=tab_layout)\n",
    "\n",
    "#----------------------\n",
    "xml_editor = widgets.Textarea(\n",
    "    description=\"\",\n",
    "    layout = widgets.Layout(border='1px solid black', width='900px', height='500px'), #tab_layout,  #Layout(min_width = '900px', min_height='300px'),\n",
    ")\n",
    "#xml_editor.value = \"Mary had a lamb, yada yada...\\nfleece was white yada...\"\n",
    "#with open('nanobio_settings.xml') as xml_filep:\n",
    "#    xml_editor.value = xml_filep.read()\n",
    "#xml_filep.closed\n",
    "\n",
    "write_xml_button = Button(\n",
    "    description='Save XML config file',\n",
    "    button_style='success', # 'success', 'info', 'warning', 'danger' or ''\n",
    "    tooltip='Write XML',\n",
    ")\n",
    "\n",
    "#write_xml_button.on_click(read_config_file_cb)\n",
    "xml_tab = widgets.VBox([xml_editor,write_xml_button], layout=tab_layout)\n",
    "\n",
    "#----------------------\n",
    "tabs = widgets.Tab(children=[config_tab, cells_tab, np_tab, svg_tab, mcds_tab], layout=tab_layout)  # xml_tab\n",
    "tab_idx = 0\n",
    "tabs.set_title(tab_idx, 'Config Basics'); tab_idx += 1\n",
    "tabs.set_title(tab_idx, 'Cells'); tab_idx += 1\n",
    "tabs.set_title(tab_idx, 'Nanoparticles'); tab_idx += 1\n",
    "# tabs.set_title(tab_idx, 'XML'); tab_idx += 1\n",
    "tabs.set_title(tab_idx, 'out:SVG'); tab_idx += 1\n",
    "tabs.set_title(tab_idx, 'out:Substrates')\n",
    "\n",
    "# run_sim = widgets.VBox([write_config_row, run_sim_row, run_output])\n",
    "run_sim = widgets.VBox([write_config_row, run_button.w])\n",
    "\n",
    "gui = widgets.VBox(children=[tabs,run_sim]) #, layout=tab_layout)\n",
    "display(gui)\n",
    "\n"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "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": "3.6.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}