deletions | additions
diff --git a/figures/weight_fret_hist_measurement/weight_fret_hist_measurement.png b/figures/weight_fret_hist_measurement/weight_fret_hist_measurement.png
index f3c909a..2d7bf4d 100644
Binary files a/figures/weight_fret_hist_measurement/weight_fret_hist_measurement.png and b/figures/weight_fret_hist_measurement/weight_fret_hist_measurement.png differ
diff --git a/figures/weight_fret_hist_sim_mixture/weight_fret_hist_sim_mixture.png b/figures/weight_fret_hist_sim_mixture/weight_fret_hist_sim_mixture.png
index 76f3c1d..9543894 100644
Binary files a/figures/weight_fret_hist_sim_mixture/weight_fret_hist_sim_mixture.png and b/figures/weight_fret_hist_sim_mixture/weight_fret_hist_sim_mixture.png differ
diff --git a/notebooks/Figures - Burst Weights.ipynb b/notebooks/Figures - Burst Weights.ipynb
index f06f0f2..97dabb0 100644
--- a/notebooks/Figures - Burst Weights.ipynb
+++ b/notebooks/Figures - Burst Weights.ipynb
...
},
"outputs": [],
"source": [
"url "#url =
'http://files.figshare.com/2182601/0023uLRpitc_NTP_20dT_0.5GndCl.hdf5'\n",
"download_file(url, 'http://files.figshare.com/4917046/smFRET_44f3da_P_20_s0_20_s20_D_6.0e11_6.0e11_E_75_30_EmTot_200k_200k_BgD1500_BgA800_t_max_600s.hdf5'\n",
"#download_file(url, save_dir='./data')"
]
},
{
...
},
"outputs": [],
"source": [
"filename "url =
'./data/' + url.split('/')[-1]\n",
"filename"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"url2 = 'http://files.figshare.com/4861018/004_dsDNA_17d_green100u_red40u.hdf5'\n",
"download_file(url2, 'http://files.figshare.com/4917049/smFRET_44f3da_P_20_s0_20_s20_D_6.0e11_6.0e11_E_75_30_EmTot_160k_160k_BgD1500_BgA800_t_max_600s.hdf5'\n",
"download_file(url, save_dir='./data')"
]
},
{
...
},
"outputs": [],
"source": [
"filename2 = './data/' + url2.split('/')[-1]\n",
"filename2"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"dir_ = '/Users/anto/Google Drive/notebooks/pybromo/mixture_sim/data/'\n",
"filename = dir_ + 'smFRET_44f3da_P_20_s0_20_s20_D_6.0e-11_6.0e-11_E_75_30_EmTot_200k_200k_BgD1500_BgA800_t_max_600s.hdf5'\n", "filename =
dir_ + 'smFRET_44f3da_P_20_s0_20_s20_D_6.0e-11_6.0e-11_E_75_30_EmTot_160k_160k_BgD1500_BgA800_t_max_600s.hdf5'"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"dir_ = '/Users/anto/Google Drive/notebooks/multispot/8spot_paper/data/2012-11-26/'\n",
"filename2 = dir_ + '004_dsDNA_17d_green100u_red40u.hdf5'"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"dir_ = '/Users/anto/Google Drive/notebooks/multispot/8spot_paper/data/2012-11-26/'\n",
"filename3 = dir_ './data/' +
'008_dsDNA_22d_500pM_green100u_red40u.hdf5'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Loading the Data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Unweighted Estimator" url.split('/')[-1]\n",
"filename"
]
},
{
...
},
"outputs": [],
"source": [
"Eh "url2 =
np.nanmean(EE, axis=1)\n",
"Eh.shape, np.nanmean(Eh), np.nanstd(Eh)*100\n",
"print('Unweighted E estimator')\n",
"print('Mean = %.5f Std.Dev. = %.4f %%' % (np.nanmean(Eh), np.nanstd(Eh)*100))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Weighted Estimator" 'http://files.figshare.com/4916914/008_dsDNA_22d_500pM_green100u_red40u.hdf5'\n",
"download_file(url2, save_dir='./data')"
]
},
{
...
},
"outputs": [],
"source": [
"Ehw "filename2 =
np.nansum(EE * nt, axis=1)/ np.nansum(nt, axis=1)\n",
"print('Weighted E estimator')\n",
"print('Mean = %.5f Std.Dev. = %.4f %%' % (np.nanmean(Ehw), np.nanstd(Ehw)*100))" './data/' + url2.split('/')[-1]\n",
"filename2"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Estimator distribution plots" "## Loading the Data"
]
},
{
...
"loader.alex_apply_period(d2)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"d3 = loader.photon_hdf5(filename3)\n",
"loader.alex_apply_period(d3)"
]
},
{
"cell_type": "markdown",
"metadata": {},
...
},
"outputs": [],
"source": [
"d.calc_bg(bg.exp_fit,
time_s=20, time_s=40, tail_min_us='auto', F_bg=1.7)\n",
"d2.calc_bg(bg.exp_fit,
time_s=20, tail_min_us='auto', F_bg=1.7)\n",
"d3.calc_bg(bg.exp_fit, time_s=40, tail_min_us='auto', F_bg=1.7)"
]
},
{
...
},
"outputs": [],
"source": [
"dplot(d2,
timetrace_bg);\n",
"dplot(d3, timetrace_bg);"
]
},
{
...
"outputs": [],
"source": [
"fig, ax = default_figure()\n",
"kws = dict(hist_style='step',
hist_plot_style=dict(alpha=1))\n", hist_plot_style=dict(alpha=1, drawstyle='steps-mid', marker=None))\n",
"dplot(ds, hist_fret, **kws, ax=ax)\n",
"dplot(ds, hist_fret, weights='size', ax=ax, **kws)\n",
"ax.set_title('');\n",
"sns.despine()\n",
"ax.grid(False)\n",
"ax.legend(['Unweighted', 'Weighted'],\n",
" bbox_to_anchor=(0.6,
1), 1.05), loc=2,
borderaxespad=0.)" borderaxespad=0.)\n",
"\n",
"savefig('weight_fret_hist_sim_mixture.png')"
]
},
{
...
},
"outputs": [],
"source": [
"d2.burst_search(F=4)\n",
"d3.burst_search(F=4)" "d2.burst_search(F=4)"
]
},
{
...
},
"outputs": [],
"source": [
"dd2 = bext.burst_search_and_gate(d2,
F=4)\n",
"dd3 = bext.burst_search_and_gate(d3, F=4)"
]
},
{
...
},
"outputs": [],
"source": [
"d2t = dd2.select_bursts(select_bursts.time,
time_s2=5000)\n", time_s2=600)\n",
"ds2 = d2t.select_bursts(select_bursts.size, th1=10)\n",
"ds2a = d2t.select_bursts(select_bursts.naa, th1=10)\n",
"ds2h "#ds2h = d2t.select_bursts(select_bursts.size,
th1=10)\n",
"ds2ha th1=20)\n",
"#ds2ha = d2t.select_bursts(select_bursts.naa,
th1=10)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"kws = dict(hist_style='step', hist_plot_style=dict(alpha=1))\n",
"ax = dplot(ds2h, hist_fret, **kws)\n",
"dplot(ds2, hist_fret, weights='size', ax=ax, **kws)\n",
"dplot(ds2ha, hist_fret, **kws, ax=ax)\n",
"dplot(ds2a, hist_fret, weights='size', ax=ax, **kws)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"d3t = dd3.select_bursts(select_bursts.time, time_s2=600)\n",
"ds3 = d3t.select_bursts(select_bursts.size, th1=10)\n",
"ds3a = d3t.select_bursts(select_bursts.naa, th1=10)\n",
"ds3h = d3t.select_bursts(select_bursts.size, th1=10)\n",
"ds3ha = d3t.select_bursts(select_bursts.naa, th1=10)" th1=20)"
]
},
{
...
},
"outputs": [],
"source": [
"alex_jointplot(ds3)" "alex_jointplot(ds2)"
]
},
{
...
"source": [
"# 600s, DCBS, F=4, size th1 = 10\n",
"kws = dict(hist_style='step', hist_plot_style=dict(alpha=1))\n",
"ax =
dplot(ds3h, dplot(ds2, hist_fret, **kws)\n",
"dplot(ds3, "dplot(ds2, hist_fret, weights='size', ax=ax, **kws)"
]
},
{
...
"fig, ax = default_figure()\n",
"kws = dict(ax=ax, hist_style='step', \n",
" hist_plot_style=dict(alpha=1, linestyle='-', marker=None, drawstyle='steps-mid'))\n",
"dplot(ds3h, "dplot(ds2, hist_fret, **kws)\n",
"dplot(ds3, "dplot(ds2, hist_fret, weights='size', **kws)\n",
"sns.despine()\n",
"ax.set_title('')\n",
"ax.grid(False)\n",
"ax.legend(['Unweighted',
'Weighted']);" 'Weighted']);\n",
"\n",
"savefig('weight_fret_hist_measurement.png')"
]
},
{
...
"source": [
"bins = np.arange(-0.2, 1.2, 0.03)\n",
"kws = dict(bins=bins, normed=True)\n",
"counts, _ =
np.histogram(ds3.E_, np.histogram(ds2.E_, **kws)\n",
"countsw, _ =
np.histogram(ds3.E_, weights=ds3.burst_sizes()[0], np.histogram(ds2.E_, weights=ds2.burst_sizes()[0], **kws)\n",
"\n",
"bincenters = bins[:-1] + 0.5*(bins[1] - bins[0])\n",
"plt.plot(bincenters, counts)\n",
