Update BMI notebooks (#52)

* Use GitHub URLs for image paths * Copy current ESPIn logo image instead of linking * Update notebook for revisions to bmi-example-python
csdms · Aug 9, 2021 · 470dca7 · 470dca7
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diff --git a/lessons/bmi/bmi-run-model-from-bmi.ipynb b/lessons/bmi/bmi-run-model-from-bmi.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a href=\"https://bmi.readthedocs.io\"><img src=\"../../media/bmi-logo-header-text.png\"></a>"
+    "<a href=\"https://bmi.readthedocs.io\"><img src=\"https://raw.githubusercontent.com/csdms/espin/main/media/bmi-logo-header-text.png\"></a>"
    ]
   },
   {
@@ -185,7 +185,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, get attributes of the grid on which the temperature variable is defined:"
+    "Next, get the identifier for the grid on which the temperature variable is defined:"
    ]
   },
   {
@@ -197,37 +197,75 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Grid id: 0\n",
-      "Grid rank: 2\n",
-      "Grid shape: (6, 8)\n",
-      "Grid spacing: [1.0, 1.0]\n",
-      "Grid type: uniform_rectilinear_grid\n"
+      "Grid id: 0\n"
      ]
     }
    ],
    "source": [
     "grid_id = x.get_var_grid('plate_surface__temperature')\n",
-    "print('Grid id:', grid_id)\n",
-    "print('Grid rank:', x.get_grid_rank(grid_id))\n",
-    "print('Grid shape:', x.get_grid_shape(grid_id))\n",
-    "print('Grid spacing:', x.get_grid_spacing(grid_id))\n",
-    "print('Grid type:', x.get_grid_type(grid_id))"
+    "print('Grid id:', grid_id)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Through the model's BMI, zero out the initial temperature field, except for an impulse:"
+    "Then get the grid attributes:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 9,
    "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Grid type: uniform_rectilinear\n",
+      "Grid rank: 2\n",
+      "Grid shape: [6 8]\n",
+      "Grid spacing: [1. 1.]\n"
+     ]
+    }
+   ],
+   "source": [
+    "print('Grid type:', x.get_grid_type(grid_id))\n",
+    "\n",
+    "rank = x.get_grid_rank(grid_id)\n",
+    "print('Grid rank:', rank)\n",
+    "\n",
+    "shape = np.ndarray(rank, dtype=int)\n",
+    "x.get_grid_shape(grid_id, shape)\n",
+    "print('Grid shape:', shape)\n",
+    "\n",
+    "spacing = np.ndarray(rank, dtype=float)\n",
+    "x.get_grid_spacing(grid_id, spacing)\n",
+    "print('Grid spacing:', spacing)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "These commands are made somewhat un-Pythonic by the generic design of the BMI."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Through the model's BMI, zero out the initial temperature field, except for an impulse near the middle.\n",
+    "Note that *set_value* expects a one-dimensional array for input."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
    "outputs": [],
    "source": [
-    "temperature = np.zeros(x.get_grid_shape(grid_id))\n",
+    "temperature = np.zeros(shape)\n",
     "temperature[3, 4] = 100.0\n",
     "x.set_value('plate_surface__temperature', temperature)"
    ]
@@ -236,12 +274,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Check that the temperature field has been updated:"
+    "Check that the temperature field has been updated. Note that *get_value* expects a one-dimensional array to receive output."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -258,8 +296,9 @@
     }
    ],
    "source": [
-    "initial_temperature = x.get_value('plate_surface__temperature')\n",
-    "print(initial_temperature)"
+    "temperature_flat = np.empty_like(temperature).flatten()\n",
+    "x.get_value('plate_surface__temperature', temperature_flat)\n",
+    "print(temperature_flat.reshape(shape))"
    ]
   },
   {
@@ -271,7 +310,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -287,7 +326,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -304,8 +343,8 @@
     }
    ],
    "source": [
-    "updated_temperature = x.get_value('plate_surface__temperature')\n",
-    "print(updated_temperature)"
+    "x.get_value('plate_surface__temperature', temperature_flat)\n",
+    "print(temperature_flat.reshape(shape))"
    ]
   },
   {
@@ -324,7 +363,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -342,7 +381,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
@@ -359,9 +398,9 @@
     }
    ],
    "source": [
-    "final_temperature = x.get_value('plate_surface__temperature')\n",
     "np.set_printoptions(formatter={'float': '{: 5.1f}'.format})\n",
-    "print(final_temperature)"
+    "x.get_value('plate_surface__temperature', temperature_flat)\n",
+    "print(temperature_flat.reshape(shape))"
    ]
   },
   {
@@ -373,7 +412,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -385,7 +424,7 @@
     }
    ],
    "source": [
-    "print(final_temperature.sum())"
+    "print(temperature_flat.sum())"
    ]
   },
   {
@@ -397,7 +436,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -407,7 +446,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -421,7 +460,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.9.6"
   }
  },
  "nbformat": 4,

diff --git a/lessons/bmi/bmi-run-model.ipynb b/lessons/bmi/bmi-run-model.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a href=\"https://bmi.readthedocs.io\"><img src=\"../../media/bmi-logo-header-text.png\"></a>"
+    "<a href=\"https://bmi.readthedocs.io\"><img src=\"https://raw.githubusercontent.com/csdms/espin/main/media/bmi-logo-header-text.png\"></a>"
    ]
   },
   {
@@ -273,7 +273,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -287,7 +287,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.9.6"
   }
  },
  "nbformat": 4,

diff --git a/lessons/bmi/index.ipynb b/lessons/bmi/index.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a href=\"https://csdms.colorado.edu\"><img style=\"float: center; width: 75%\" src=\"../../media/ESPIn.png\"></a>"
+    "<a href=\"https://csdms.colorado.edu\"><img style=\"float: center; width: 75%\" src=\"https://raw.githubusercontent.com/csdms/espin/main/media/ESPIn.png\"></a>"
    ]
   },
   {
@@ -46,7 +46,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -60,7 +60,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.9.6"
   }
  },
  "nbformat": 4,

diff --git a/media/ESPIn.png b/media/ESPIn.png
diff --git a/media/ESPIn.png b/media/ESPIn.png