Index: wflow-py/notebooks/BMI-Test.ipynb
===================================================================
diff -u -r54d5ebe9f713a1e1647a642ca924e17c98523693 -r60deb0d27020da029709d73a4c08b424cfa9d1a6
--- wflow-py/notebooks/BMI-Test.ipynb	(.../BMI-Test.ipynb)	(revision 54d5ebe9f713a1e1647a642ca924e17c98523693)
+++ wflow-py/notebooks/BMI-Test.ipynb	(.../BMI-Test.ipynb)	(revision 60deb0d27020da029709d73a4c08b424cfa9d1a6)
@@ -1,294 +1,311 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<h1>Basic test of the wflow BMI interface"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Populating the interactive namespace from numpy and matplotlib\n"
-     ]
-    }
-   ],
-   "source": [
-    "import wflow.wflow_bmi as bmi\n",
-    "import logging\n",
-    "\n",
-    "reload(bmi)\n",
-    "%pylab inline \n",
-    "import datetime\n",
-    "from IPython.html.widgets import interact"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Startup two models:\n",
-    "\n",
-    "+ The wflow_sbm model calculates the runoff from each cell (the LA land-atmosphere model)\n",
-    "+ the wflow_routing model that uses a kinimatic wave for routing the flow (the RT routing model)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "# This is the LAnd Atmophere (LA) model\n",
-    "LA_model = bmi.wflowbmi_csdms()\n",
-    "LA_model.initialize('../../examples/wflow_rhine_sbm/wflow_sbm.ini',loglevel=logging.ERROR)\n",
-    "\n",
-    "# This is the routing (RT) model\n",
-    "RT_model = bmi.wflowbmi_csdms()\n",
-    "RT_model.initialize('../../examples/wflow_rhine_sbm/wflow_routing.ini',loglevel=logging.ERROR)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<h3>Now we can investigate some model parameters"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "86400\n",
-      "791506800.0\n"
-     ]
-    }
-   ],
-   "source": [
-    "print(LA_model.get_value(\"timestepsecs\"))\n",
-    "print LA_model.get_start_time()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "imshow(LA_model.get_value(\"Altitude\"))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "imshow(LA_model.get_value(\"Slope\"))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "imshow(LA_model.get_value(\"FirstZoneDepth\"))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "a =LA_model.get_value(\"TopoId\")\n",
-    "a[a==-2147483648] = 0\n",
-    "imshow(a)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "imshow(LA_model.get_value(\"River\"))"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<h3>Start and end times"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "t_end = RT_model.get_end_time()\n",
-    "t_start = RT_model.get_start_time()\n",
-    "t = RT_model.get_current_time()\n",
-    "\n",
-    "(t_end  - t_start)/(86400)\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<h3>Now start the models"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "t_end = RT_model.get_end_time()\n",
-    "t = RT_model.get_start_time()\n",
-    "\n",
-    "res = []\n",
-    "resq = []\n",
-    "\n",
-    "# Loop in time and put output of SBM in seperate routing module - 1way link\n",
-    "while t < t_end:\n",
-    "    LA_model.update()\n",
-    "    # Now set the output from the LA model (specific Q) as input to the RT model\n",
-    "    thevar = LA_model.get_value(\"InwaterMM\")\n",
-    "    RT_model.set_value(\"IW\",thevar) # The IW is set in the wflow_routing.ini var as a forcing\n",
-    "    RT_model.update()\n",
-    "    resq.append(RT_model.get_value(\"SurfaceRunoff\"))\n",
-    "    res.append(thevar)\n",
-    "    t = RT_model.get_current_time()\n",
-    "    \n",
-    "    print datetime.datetime.fromtimestamp(t)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "LA_model.finalize()\n",
-    "RT_model.finalize()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<h4>Define function to view the results"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "def browse_res(digits):\n",
-    "    n = len(digits)\n",
-    "    def view_image(i):\n",
-    "        plt.imshow(log(digits[i]+1))\n",
-    "        plt.title('Step: %d' % i)\n",
-    "        plt.colorbar()\n",
-    "        plt.show()\n",
-    "    interact(view_image, i=(0,n-1))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "browse_res(res)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    " browse_res(resq)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 2",
-   "language": "python",
-   "name": "python2"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.8"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<h1>Basic test of the wflow BMI interface"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "import wflow.wflow_bmi as bmi\n",
+    "import logging\n",
+    "\n",
+    "reload(bmi)\n",
+    "%pylab inline \n",
+    "import datetime\n",
+    "from IPython.html.widgets import interact"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Startup two models:\n",
+    "\n",
+    "+ The wflow_sbm model calculates the runoff from each cell (the LA land-atmosphere model)\n",
+    "+ the wflow_routing model that uses a kinimatic wave for routing the flow (the RT routing model)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "# This is the LAnd Atmophere (LA) model\n",
+    "LA_model = bmi.wflowbmi_csdms()\n",
+    "LA_model.initialize('../../examples/wflow_rhine_sbm/wflow_sbm.ini',loglevel=logging.ERROR)\n",
+    "\n",
+    "# This is the routing (RT) model\n",
+    "RT_model = bmi.wflowbmi_csdms()\n",
+    "RT_model.initialize('../../examples/wflow_rhine_sbm/wflow_routing.ini',loglevel=logging.ERROR)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<h3>Now we can investigate some model parameters"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "print(LA_model.get_value(\"timestepsecs\"))\n",
+    "print LA_model.get_start_time()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "LA_model.get_attribute_names()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "LA_model.get_attribute_value(\"run:reinit\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "LA_model.set_attribute_value(\"run:reinit\",'1')\n",
+    "LA_model.get_attribute_value(\"run:reinit\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "imshow(LA_model.get_value(\"Altitude\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "imshow(LA_model.get_value(\"Slope\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "imshow(LA_model.get_value(\"FirstZoneDepth\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "a =LA_model.get_value(\"TopoId\")\n",
+    "a[a==-2147483648] = 0\n",
+    "imshow(a)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "imshow(LA_model.get_value(\"River\"))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<h3>Start and end times"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "t_end = RT_model.get_end_time()\n",
+    "t_start = RT_model.get_start_time()\n",
+    "t = RT_model.get_current_time()\n",
+    "\n",
+    "(t_end  - t_start)/(86400)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<h3>Now start the models"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "t_end = RT_model.get_end_time()\n",
+    "t = RT_model.get_start_time()\n",
+    "\n",
+    "res = []\n",
+    "resq = []\n",
+    "\n",
+    "# Loop in time and put output of SBM in seperate routing module - 1way link\n",
+    "while t < t_end:\n",
+    "    LA_model.update()\n",
+    "    # Now set the output from the LA model (specific Q) as input to the RT model\n",
+    "    thevar = LA_model.get_value(\"InwaterMM\")\n",
+    "    RT_model.set_value(\"IW\",thevar) # The IW is set in the wflow_routing.ini var as a forcing\n",
+    "    RT_model.update()\n",
+    "    resq.append(RT_model.get_value(\"SurfaceRunoff\"))\n",
+    "    res.append(thevar)\n",
+    "    t = RT_model.get_current_time()\n",
+    "    \n",
+    "    print datetime.datetime.fromtimestamp(t)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "LA_model.finalize()\n",
+    "RT_model.finalize()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<h4>Define function to view the results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "def browse_res(digits):\n",
+    "    n = len(digits)\n",
+    "    def view_image(i):\n",
+    "        plt.imshow(log(digits[i]+1))\n",
+    "        plt.title('Step: %d' % i)\n",
+    "        plt.colorbar()\n",
+    "        plt.show()\n",
+    "    interact(view_image, i=(0,n-1))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "browse_res(res)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    " browse_res(resq)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}