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Merge pull request #2 from OpenSMFS/gauss_psf
Implement GaussianPSF
2 parents 0491c46 + 10c602c commit 9f93859

8 files changed

Lines changed: 690 additions & 94 deletions

‎notebooks/PyBroMo - 1. Simulate 3D trajectories - single core.ipynb‎

Lines changed: 142 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -101,6 +101,7 @@
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"\n",
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"# PSF definition\n",
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"psf = pbm.NumericPSF()\n",
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"#psf = pbm.GaussianPSF(sx=0.2e-6, sy=0.2e-6, sz=0.8e-6)\n",
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"\n",
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"# Particle simulation definition\n",
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"S = pbm.ParticlesSimulation(t_step=t_step, t_max=t_max, \n",
@@ -143,6 +144,24 @@
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"S.compact_name()"
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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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"outputs": [],
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"source": [
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"S.psf.hash()"
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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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"outputs": [],
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"source": [
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"S.psf"
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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,
@@ -234,6 +253,15 @@
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"print('Simulation file size: %d MB' % (S.store.h5file.get_filesize()/1024./1024.))"
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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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"outputs": [],
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"source": [
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"S.compact_name()"
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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,
@@ -256,7 +284,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
259-
"S.hash()"
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"S.compact_name()"
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]
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},
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{
@@ -268,6 +296,15 @@
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"S = pbm.ParticlesSimulation.from_datafile(S.hash()[:4]) # Read-only by default"
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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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"outputs": [],
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"source": [
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"S.psf_pytables.attrs"
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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,
@@ -277,6 +314,22 @@
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"S"
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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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"outputs": [],
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"source": [
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"S.compact_name()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"> **BUG**: hash changed with GaussianPSF!"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
@@ -336,6 +389,50 @@
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"plot_emission(S, slice_=(0, 2e6, 10), em_th=0.05)"
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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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"outputs": [],
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"source": [
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"def plot_tracks_r(S, slice_=None, particles=None):\n",
399+
" if slice_ is None:\n",
400+
" slice_ = (0, 100e3, 100)\n",
401+
" duration = (slice_[1] - slice_[0])*S.t_step\n",
402+
" slice_ = slice(*slice_)\n",
403+
" em = S.emission[:, slice_]\n",
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" t = np.arange(em.shape[1])*(S.t_step*1e3)\n",
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" \n",
406+
" if particles is None:\n",
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" particles = range(S.num_particles)\n",
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" \n",
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" fig, ax = plt.subplots(1, 1, figsize=(11, 5), sharey=True)\n",
410+
" plt.subplots_adjust(left=0.05, right=0.93, top=0.95, bottom=0.09,\n",
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" wspace=0.05)\n",
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" plt.suptitle(\"Total: %.1f s, Visualized: %.2f ms\" % (\n",
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" S.t_step*S.n_samples, duration*1e3))\n",
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"\n",
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" for ip in particles:\n",
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" x, y, z = S.position[ip, :, slice_]\n",
417+
" r = np.sqrt(x**2 + y**2 + z**2) * 1e6\n",
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" plot_kwargs = dict(ls='', marker='o', mew=0, ms=4, alpha=0.8, \n",
419+
" label='P%d' % ip)\n",
420+
" ax.plot(t, r, **plot_kwargs)\n",
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"\n",
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" ax.set_ylabel(\"r (um)\")\n",
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" ax.legend(bbox_to_anchor=(1.01, 1), loc=2, borderaxespad=0.)\n",
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" ax.set_ylim(0)"
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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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"outputs": [],
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"source": [
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"plot_tracks_r(S, slice_=(0, 2e6, 1000))"
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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,
@@ -395,6 +492,15 @@
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"plot_tracks(S) #particles=[2, 5, 7, 22, 30])"
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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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"outputs": [],
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"source": [
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"#plot_tracks(S, slice_=(1.9e6, 2e6, 100), particles=[1])"
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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,
@@ -404,6 +510,16 @@
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"S.store.close()"
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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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"outputs": [],
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"source": [
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"if hasattr(S, 'ts_store'):\n",
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" S.ts_store.close() # needed if timestamp file is already present"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
@@ -415,6 +531,15 @@
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"- [PyBroMo - 2. Generate smFRET data, including mixtures](PyBroMo - 2. Generate smFRET data, including mixtures.ipynb)"
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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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"outputs": [],
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"source": [
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"S.compact_name()"
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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,
@@ -581,6 +706,16 @@
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"pos, ts"
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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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"outputs": [],
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"source": [
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"S.store.close()\n",
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"S.ts_store.close()"
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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,
@@ -592,9 +727,9 @@
592727
"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 3.6 (py36)",
730+
"display_name": "py37-sm",
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"language": "python",
597-
"name": "py36"
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"name": "py37-sm"
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},
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"language_info": {
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"codemirror_mode": {
@@ -606,13 +741,16 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
609-
"version": "3.6.7"
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"version": "3.7.2"
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},
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"toc": {
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"base_numbering": 1,
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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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"title_cell": "Table of Contents",
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"title_sidebar": "Contents",
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"toc_cell": false,
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"toc_position": {
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"height": "591.867px",

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

Lines changed: 31 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -81,7 +81,8 @@
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"metadata": {},
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"outputs": [],
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"source": [
84-
"code = 'e30f'\n",
84+
"code = 'e30f' # 1s simulation, NumericPSF\n",
85+
"#code = '10a1' # 1s simulation, GaussianPSF\n",
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"S = pbm.ParticlesSimulation.from_datafile(code, mode='w')"
8687
]
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},
@@ -694,9 +695,24 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"PSF = pbm.NumericPSF()\n",
698-
"psf = PSF.hdata\n",
699-
"z_peak = PSF.zi[PSF.zm] # z position of PSF peak in μm\n",
698+
"S.psf"
699+
]
700+
},
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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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"outputs": [],
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"source": [
707+
"if S.psf.kind == 'numeric':\n",
708+
" PSF = pbm.NumericPSF()\n",
709+
" psf = PSF.hdata\n",
710+
" z_peak = PSF.zi[PSF.zm] # z position of PSF peak in μm\n",
711+
"else:\n",
712+
" x = np.arange(0, 4, 0.01) * 1e-6\n",
713+
" z = np.arange(-6, 6, 0.01) * 1e-6\n",
714+
" X, Z = np.meshgrid(x, z)\n",
715+
" psf = S.psf.eval_xz(X, Z)\n",
700716
"cmap = plt.cm.YlGnBu\n",
701717
"cmap.set_under(alpha=0)\n",
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"kwargs = dict(interpolation='bicubic', origin='lower', cmap=cmap, vmin=1e-1, zorder=1)\n",
@@ -705,7 +721,7 @@
705721
"ax.imshow(psf.T, extent=(-6, 6, 0, 4), **kwargs)\n",
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"ax.plot(burstph.z_um, burstph.r_um, '.', ms=5, color='C1', alpha=0.3)\n",
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"ax.set(ylabel='R (μm)', xlabel='Z (μm)', ylim=(0, 1), xlim=(-2, 2),\n",
708-
" title='Position of photon emission');"
724+
" title=f'Position of photon emission (PSF {S.psf.kind})');"
709725
]
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},
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{
@@ -724,6 +740,16 @@
724740
" title='Position of photon emission by burst');"
725741
]
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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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"outputs": [],
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"source": [
749+
"S.store.close()\n",
750+
"S.ts_store.close()"
751+
]
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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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