update tutorial 4

AthenaEPI · Feb 1, 2018 · 79278d6 · 79278d6
1 parent 4af324a
commit 79278d6
Showing 1 changed file with 19 additions and 13 deletions.
diff --git a/examples/tutorial_combining_biophysical_models_into_microstructure_model.ipynb b/examples/tutorial_combining_biophysical_models_into_microstructure_model.ipynb
@@ -35,13 +35,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now to make our first multi-compartment model! Don't worry, we start with a simple Ball & Stick model, and the procedure will be very simple and similar as before. First, we instantiate the models we want:"
+    "To make our first multi-compartment model, we instantiate the models we want to include:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "stick = cylinder_models.C1Stick()\n",
@@ -52,7 +54,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, we combine them into one model using PartialVolumeCombinedMicrostructureModel.  \n",
+    "Next, we combine them into one model using MultiCompartmentModel.  \n",
     "Our new model will now be $E = vf_0 * E_{Ball} + vf_1 * E_{Stick}$ where $vf_0$ and $vf_1$ are volume fractions and add up to one."
    ]
   },
@@ -69,7 +71,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "That it! We can again figure out the required parameter names using parameter_cardinality. As we are combining models, the parameter names now have the corresponding model prepended to it."
+    "The MultiCompartmentModel automatically joins the parameters and other properties of the models that are given as input.\n",
+    "\n",
+    "We can again figure out the required parameter names using parameter_cardinality. As you can see, the parameter names now have the corresponding model prepended to it."
    ]
   },
   {
@@ -106,7 +110,9 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "mu = (np.pi / 2., np.pi / 2.)\n",
@@ -142,9 +148,9 @@
      "output_type": "stream",
      "text": [
       "Using parallel processing with 8 workers.\n",
-      "Setup brute2fine optimizer in 0.408539056778 seconds\n",
-      "Fitting of 1 voxels complete in 0.0619370937347 seconds.\n",
-      "Average of 0.0619370937347 seconds per voxel.\n"
+      "Setup brute2fine optimizer in 0.418382883072 seconds\n",
+      "Fitting of 1 voxels complete in 0.292662143707 seconds.\n",
+      "Average of 0.292662143707 seconds per voxel.\n"
      ]
     }
    ],
@@ -160,11 +166,11 @@
     {
      "data": {
       "text/plain": [
-       "{'C1Stick_1_lambda_par': array([  1.70004007e-09]),\n",
-       " 'C1Stick_1_mu': array([ 1.57079729, -1.57078812]),\n",
-       " 'G1Ball_1_lambda_iso': array([  3.00000000e-09]),\n",
-       " 'partial_volume_0': array([ 0.49999748]),\n",
-       " 'partial_volume_1': array([ 0.50000252])}"
+       "{'C1Stick_1_lambda_par': array([[  1.70004007e-09]]),\n",
+       " 'C1Stick_1_mu': array([[ 1.57079729, -1.57078812]]),\n",
+       " 'G1Ball_1_lambda_iso': array([[  3.00000000e-09]]),\n",
+       " 'partial_volume_0': array([[ 0.49999748]]),\n",
+       " 'partial_volume_1': array([[ 0.50000252]])}"
       ]
      },
      "execution_count": 7,