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tritemiotritemio
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Fix typo TimestapSimulation -> TimestampSimulation
1 parent c61ee16 commit 7fd6bf8

5 files changed

Lines changed: 46 additions & 86 deletions

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

Lines changed: 40 additions & 80 deletions
Original file line numberDiff line numberDiff line change
@@ -40,9 +40,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"%matplotlib inline\n",
@@ -80,9 +78,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"S = pbm.ParticlesSimulation.from_datafile('0168', mode='w')"
@@ -91,9 +87,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"S.particles.diffusion_coeff_counts"
@@ -102,9 +96,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"#S = pbm.ParticlesSimulation.from_datafile('0168')"
@@ -148,12 +140,10 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"mix_sim = pbm.TimestapSimulation(S, **params)\n",
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"mix_sim = pbm.TimestampSimulation(S, **params)\n",
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"mix_sim.summarize()"
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]
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},
@@ -167,9 +157,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"rs = np.random.RandomState(1234)\n",
@@ -186,9 +174,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"mix_sim.save_photon_hdf5(identity=dict(author='John Doe', \n",
@@ -226,21 +212,17 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"mix_sim = pbm.TimestapSimulation(S, **params)\n",
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"mix_sim = pbm.TimestampSimulation(S, **params)\n",
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"mix_sim.summarize()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"rs = np.random.RandomState(1234)\n",
@@ -250,9 +232,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"mix_sim.save_photon_hdf5()"
@@ -272,9 +252,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"import fretbursts as fb"
@@ -283,9 +261,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"filepath = list(Path('./').glob('smFRET_*'))\n",
@@ -295,9 +271,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"d = fb.loader.photon_hdf5(str(filepath[1]))"
@@ -306,9 +280,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"d"
@@ -317,9 +289,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"d.A_em"
@@ -328,9 +298,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"fb.dplot(d, fb.timetrace);"
@@ -339,9 +307,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"d.calc_bg(fun=fb.bg.exp_fit, tail_min_us='auto', F_bg=1.7)"
@@ -350,9 +316,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"d.bg_dd, d.bg_ad"
@@ -361,9 +325,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"d.burst_search(F=7)"
@@ -372,9 +334,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"d.num_bursts"
@@ -383,9 +343,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"ds = d.select_bursts(fb.select_bursts.size, th1=20)"
@@ -394,9 +352,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"ds.num_bursts"
@@ -405,9 +361,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"fb.dplot(d, fb.timetrace, bursts=True);"
@@ -416,9 +370,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"fb.dplot(ds, fb.hist_fret, pdf=False)\n",
@@ -435,9 +387,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"fb.bext.burst_data(ds)"
@@ -456,7 +406,7 @@
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python [default]",
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
@@ -470,9 +420,19 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.5.2"
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"version": "3.6.7"
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},
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"toc": {
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"nav_menu": {},
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"number_sections": true,
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"sideBar": true,
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"skip_h1_title": false,
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"toc_cell": false,
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"toc_position": {},
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"toc_section_display": "block",
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"toc_window_display": false
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}
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},
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"nbformat": 4,
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"nbformat_minor": 0
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"nbformat_minor": 1
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}

‎notebooks/PyBroMo - 4. Two-state dynamics - Static smFRET simulation.ipynb‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -291,7 +291,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"mix_sim = pbm.TimestapSimulation(S, **params1)\n",
294+
"mix_sim = pbm.TimestampSimulation(S, **params1)\n",
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"mix_sim.summarize()"
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]
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},
@@ -349,7 +349,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"mix_sim = pbm.TimestapSimulation(S, **params2)\n",
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"mix_sim = pbm.TimestampSimulation(S, **params2)\n",
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"mix_sim.summarize()"
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]
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},
@@ -393,7 +393,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"mix_sim = pbm.TimestapSimulation(S, **params_mix)\n",
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"mix_sim = pbm.TimestampSimulation(S, **params_mix)\n",
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"mix_sim.summarize()"
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]
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},

‎pybromo/__init__.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,4 +18,4 @@
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from .diffusion import Box, Particles, ParticlesSimulation, hash_
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from .psflib import GaussianPSF, NumericPSF
21-
from .timestamps import TimestapSimulation
21+
from .timestamps import TimestampSimulation

‎pybromo/tests/test_diffusion.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -218,7 +218,7 @@ def test_TimestampSimulation():
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bg_rate_a = 800, # Poisson background rate (cps) Acceptor channel
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)
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221-
mix_sim = pbm.TimestapSimulation(S, **params)
221+
mix_sim = pbm.TimestampSimulation(S, **params)
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mix_sim.summarize()
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rs = np.random.RandomState(_SEED)

‎pybromo/timestamps.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -99,7 +99,7 @@ def populations_slices(particles, num_pop_list):
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return slices
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102-
class TimestapSimulation:
102+
class TimestampSimulation:
103103
"""Simulate timestamps for a mixture of two populations.
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Attributes set by input arguments:

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