Notebooks: add plot of PSF with emission position overlay

Author: tritemio

notebooks/PyBroMo - 2. Generate smFRET data, including mixtures.ipynb

@@ -556,7 +556,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "> **NOTE**: most positions are NaN when the timestamp is from background.\n",
+    "> **NOTE**: positions are NaN when the timestamp is from background.\n",
     "\n",
     "Check that we have NaNs if and only if the timestamp is from background:"
    ]
@@ -693,11 +693,25 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, ax = plt.subplots(figsize=(2, 5))\n",
-    "ax.plot(R, Z, 'o', alpha=0.1)\n",
-    "ax.set_xlim(0, 1)\n",
-    "ax.set_ylim(-2, 2)\n",
-    "ax.set(xlabel='R (μm)', ylabel='Z (μm)');"
+    "# Increase the resolution of the figures displayed in the notebook\n",
+    "%config InlineBackend.figure_format = 'retina' # 'png' for default res"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "psf = pbm.NumericPSF().hdata\n",
+    "cmap = plt.cm.YlGnBu\n",
+    "cmap.set_under(alpha=0)\n",
+    "kwargs = dict(interpolation='bicubic', origin='lower', cmap=cmap, vmin=1e-1, zorder=1)\n",
+    "\n",
+    "fig, ax = plt.subplots(figsize=(8, 2))\n",
+    "ax.imshow(psf.T, extent=(-6, 6, 0, 4), **kwargs)\n",
+    "ax.plot(Z, R, '.', ms=5, color='C1', alpha=0.3)\n",
+    "ax.set(ylabel='R (μm)', xlabel='Z (μm)', ylim=(0, 1), xlim=(-2, 2));"
    ]
   },
   {
@@ -733,7 +747,13 @@
    "sideBar": true,
    "skip_h1_title": false,
    "toc_cell": false,
-   "toc_position": {},
+   "toc_position": {
+    "height": "591.867px",
+    "left": "0px",
+    "right": "959px",
+    "top": "111.133px",
+    "width": "212px"
+   },
    "toc_section_display": "block",
    "toc_window_display": false
   }