Update the notebooks

OpenSMFS · Jan 22, 2015 · 3d5657d · 3d5657d
1 parent 3dfaa6c
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Showing 2 changed files with 31 additions and 5 deletions.
diff --git a/notebooks/Example - usALEX histogram.ipynb b/notebooks/Example - usALEX histogram.ipynb
@@ -1,7 +1,7 @@
 {
  "metadata": {
   "name": "",
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+  "signature": "sha256:5967497198e54e8f7d76b35446f4c89e8466d31b2f7583f98aa2c86e7ae36e8e"
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  "nbformat": 3,
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@@ -353,12 +353,11 @@
       "                                      values=['YlGnBu_crop', 'YlOrRd', 'Blues', 'PuBuGn', \n",
       "                                              'PuBu', 'GnBu', 'YlGnBu', 'afmhot', 'alex_lv',\n",
       "                                              'copper', 'summer', 'winter', 'cubehelix']),\n",
-      "          zero_transparent = True,\n",
       "          reverse_cmap = False,\n",
       "          vmax_fret = True,\n",
       "          )\n",
       "def plot_(min_size=50, cmap_compensate=False, overlay='KDE', binwidth=0.03, bandwidth=0.03, gridsize=50, cmap='YlGnBu_crop', \n",
-      "          reverse_cmap=False, vmax_fret=True, zero_transparent=True):\n",
+      "          reverse_cmap=False, vmax_fret=True):\n",
       "    dx = Sel(d, select_bursts.size, add_naa=True, th1=min_size)\n",
       "    bext.bursts_fitter(dx, 'E', binwidth=binwidth, bandwidth=bandwidth, \n",
       "                       model=mfit.factory_three_gaussians())\n",
@@ -373,7 +372,7 @@
       "        marginal_kws = dict(binwidth=binwidth, show_model=True)\n",
       "    else:\n",
       "        marginal_kws = dict(binwidth=binwidth, show_kde=True, bandwidth=bandwidth)\n",
-      "    alex_jointplot(dx, cmap=cmap, gridsize=gridsize, zero_transparent=zero_transparent, vmax_fret=vmax_fret, \n",
+      "    alex_jointplot(dx, cmap=cmap, gridsize=gridsize, vmax_fret=vmax_fret, \n",
       "                   cmap_compensate=cmap_compensate, marginal_kws=marginal_kws, joint_kws=dict(edgecolor='grey', lw=0.2))\n",
       "    \n",
       "    fig = gcf()\n",

diff --git a/notebooks/FRETBursts - us-ALEX smFRET burst analysis.ipynb b/notebooks/FRETBursts - us-ALEX smFRET burst analysis.ipynb
@@ -1,7 +1,7 @@
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@@ -541,6 +541,33 @@
      "metadata": {},
      "outputs": []
     },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "## Background timetrace"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "d.calc_bg(bg.exp_fit, time_s=30, tail_min_us='auto', F_bg=1.7)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "dplot(d, timetrace_bg)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
     {
      "cell_type": "markdown",
      "metadata": {},