diff --git a/examples/tutorials/visualising_the_results.ipynb b/examples/tutorials/visualising_the_results.ipynb
index 4a27fb2d1e5c496242424628f504847bed27895c..09c5660ad767fe38d210f2664e58d63fa0c45627 100644
--- a/examples/tutorials/visualising_the_results.ipynb
+++ b/examples/tutorials/visualising_the_results.ipynb
@@ -2,6 +2,7 @@
"cells": [
{
"cell_type": "code",
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -21,9 +22,138 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 2,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "10:31 bilby INFO : No power spectral density provided, using aLIGO,zero detuning, high power.\n",
+ "10:31 bilby INFO : Injected signal in H1:\n",
+ "10:31 bilby INFO : optimal SNR = 120.28\n",
+ "10:31 bilby INFO : matched filter SNR = 120.60-0.46j\n",
+ "10:31 bilby INFO : mass_1 = 36.0\n",
+ "10:31 bilby INFO : mass_2 = 29.0\n",
+ "10:31 bilby INFO : a_1 = 0.4\n",
+ "10:31 bilby INFO : a_2 = 0.3\n",
+ "10:31 bilby INFO : tilt_1 = 0.5\n",
+ "10:31 bilby INFO : tilt_2 = 1.0\n",
+ "10:31 bilby INFO : phi_12 = 1.7\n",
+ "10:31 bilby INFO : phi_jl = 0.3\n",
+ "10:31 bilby INFO : luminosity_distance = 200.0\n",
+ "10:31 bilby INFO : theta_jn = 0.4\n",
+ "10:31 bilby INFO : phase = 1.3\n",
+ "10:31 bilby INFO : ra = 1.375\n",
+ "10:31 bilby INFO : dec = -1.2108\n",
+ "10:31 bilby INFO : geocent_time = 1126259642.413\n",
+ "10:31 bilby INFO : psi = 2.659\n",
+ "10:31 bilby WARNING : The waveform_generator start_time is not equal to that of the provided interferometers. Overwriting the waveform_generator.\n",
+ "10:31 bilby INFO : Running for label 'example', output will be saved to 'visualising_the_results'\n",
+ "10:31 bilby INFO : Using LAL version Branch: None;Tag: lalsuite-v6.60;Id: 413788d4afeff8b759d8d75abe589ae4a846120c;;Builder: Unknown User <>;Repository status: CLEAN: All modifications committed\n",
+ "10:31 bilby INFO : Search parameters:\n",
+ "10:31 bilby INFO : mass_1 = Uniform(minimum=20, maximum=50, name='mass_1', latex_label='$m_1$', unit=None, boundary=None)\n",
+ "10:31 bilby INFO : mass_2 = Uniform(minimum=20, maximum=50, name='mass_2', latex_label='$m_2$', unit=None, boundary=None)\n",
+ "10:31 bilby INFO : luminosity_distance = Uniform(minimum=100, maximum=300, name='luminosity_distance', latex_label='$d_L$', unit=None, boundary=None)\n",
+ "10:31 bilby INFO : a_1 = 0.4\n",
+ "10:31 bilby INFO : a_2 = 0.3\n",
+ "10:31 bilby INFO : tilt_1 = 0.5\n",
+ "10:31 bilby INFO : tilt_2 = 1.0\n",
+ "10:31 bilby INFO : phi_12 = 1.7\n",
+ "10:31 bilby INFO : phi_jl = 0.3\n",
+ "10:31 bilby INFO : theta_jn = 0.4\n",
+ "10:31 bilby INFO : phase = 1.3\n",
+ "10:31 bilby INFO : ra = 1.375\n",
+ "10:31 bilby INFO : dec = -1.2108\n",
+ "10:31 bilby INFO : geocent_time = 1126259642.413\n",
+ "10:31 bilby INFO : psi = 2.659\n",
+ "10:31 bilby INFO : Single likelihood evaluation took 2.305e-03 s\n",
+ "10:31 bilby INFO : Using sampler Dynesty with kwargs {'bound': 'multi', 'sample': 'rwalk', 'verbose': True, 'periodic': None, 'reflective': None, 'check_point_delta_t': 600, 'nlive': 100, 'first_update': None, 'walks': 5, 'npdim': None, 'rstate': None, 'queue_size': None, 'pool': None, 'use_pool': None, 'live_points': None, 'logl_args': None, 'logl_kwargs': None, 'ptform_args': None, 'ptform_kwargs': None, 'enlarge': None, 'bootstrap': None, 'vol_dec': 0.5, 'vol_check': 2.0, 'facc': 0.5, 'slices': 5, 'update_interval': 60, 'print_func': <bound method Dynesty._print_func of <bilby.core.sampler.dynesty.Dynesty object at 0x1236747f0>>, 'dlogz': 0.1, 'maxiter': None, 'maxcall': None, 'logl_max': inf, 'add_live': True, 'print_progress': True, 'save_bounds': False, 'n_effective': None}\n",
+ "10:31 bilby INFO : Checkpoint every n_check_point = 300000\n",
+ "10:31 bilby INFO : Using dynesty version 0.9.7\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " 1864| logz ratio=7255.416 +/- 0.541 | dlogz: 0.118 > 0.100000"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "10:32 bilby WARNING : Run terminated with signal 2\n",
+ "10:32 bilby INFO : Writing checkpoint file visualising_the_results/example_resume.pickle\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Exception while calling loglikelihood function:\n",
+ " params: [ 35.99600559 28.99205241 200.17592464]\n",
+ " args: []\n",
+ " kwargs: {}\n",
+ " exception:\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "Traceback (most recent call last):\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/core/sampler/dynesty.py\", line 279, in _run_nested_wrapper\n",
+ " self.sampler.run_nested(**kwargs)\n",
+ "TypeError: run_nested() got an unexpected keyword argument 'n_effective'\n",
+ "\n",
+ "During handling of the above exception, another exception occurred:\n",
+ "\n",
+ "Traceback (most recent call last):\n",
+ " File \"/Users/virginiademilio/anaconda3/envs/bilby_source/lib/python3.7/site-packages/dynesty/dynesty.py\", line 805, in __call__\n",
+ " return self.func(x, *self.args, **self.kwargs)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/core/sampler/base_sampler.py\", line 583, in log_likelihood\n",
+ " return Sampler.log_likelihood(self, theta)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/core/sampler/base_sampler.py\", line 381, in log_likelihood\n",
+ " return self.likelihood.log_likelihood_ratio()\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/gw/likelihood.py\", line 244, in log_likelihood_ratio\n",
+ " self.waveform_generator.frequency_domain_strain(self.parameters)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/gw/waveform_generator.py\", line 119, in frequency_domain_strain\n",
+ " transformed_model_data_points=self.time_array)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/gw/waveform_generator.py\", line 158, in _calculate_strain\n",
+ " model_strain = self._strain_from_model(model_data_points, model)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/gw/waveform_generator.py\", line 170, in _strain_from_model\n",
+ " return model(model_data_points, **self.parameters)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/gw/source.py\", line 71, in lal_binary_black_hole\n",
+ " phi_jl=phi_jl, **waveform_kwargs)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/gw/source.py\", line 272, in _base_lal_cbc_fd_waveform\n",
+ " waveform_dictionary, approximant)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/gw/utils.py\", line 798, in lalsim_SimInspiralChooseFDWaveform\n",
+ " waveform_dictionary, approximant)\n",
+ " File \"/Users/virginiademilio/Documents/Bilby/bilby/bilby/core/sampler/dynesty.py\", line 385, in write_current_state_and_exit\n",
+ " sys.exit(130)\n",
+ "SystemExit: 130\n"
+ ]
+ },
+ {
+ "ename": "SystemExit",
+ "evalue": "130",
+ "output_type": "error",
+ "traceback": [
+ "An exception has occurred, use %tb to see the full traceback.\n",
+ "\u001b[0;31mSystemExit\u001b[0m\u001b[0;31m:\u001b[0m 130\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/Users/virginiademilio/anaconda3/envs/bilby_source/lib/python3.7/site-packages/IPython/core/interactiveshell.py:3334: UserWarning: To exit: use 'exit', 'quit', or Ctrl-D.\n",
+ " warn(\"To exit: use 'exit', 'quit', or Ctrl-D.\", stacklevel=1)\n"
+ ]
+ }
+ ],
"source": [
"import bilby\n",
"import matplotlib.pyplot as plt\n",
@@ -34,6 +164,7 @@
"outdir = 'visualising_the_results' # directory in which to store output\n",
"label = 'example' # identifier to apply to output files\n",
"\n",
+ "# specify injection parameters\n",
"injection_parameters = dict(\n",
"mass_1=36., # source frame (non-redshifted) primary mass (solar masses)\n",
"mass_2=29., # source frame (non-redshifted) secondary mass (solar masses)\n",
@@ -44,22 +175,25 @@
"phi_12=1.7, # azimuthal angle between primary and secondary spin (radians)\n",
"phi_jl=0.3, # azimuthal angle between total angular momentum and orbital angular momentum (radians)\n",
"luminosity_distance=200., # luminosity distance to source (Mpc)\n",
- "iota=0.4, # inclination angle between line of sight and orbital angular momentum (radians)\n",
+ "theta_jn=0.4, # inclination angle between line of sight and orbital angular momentum (radians)\n",
"phase=1.3, # phase (radians)\n",
- "waveform_approximant='IMRPhenomPv2', # waveform approximant name\n",
- "reference_frequency=50., # gravitational waveform reference frequency (Hz)\n",
"ra=1.375, # source right ascension (radians)\n",
"dec=-1.2108, # source declination (radians)\n",
"geocent_time=1126259642.413, # reference time at geocentre (time of coalescence or peak amplitude) (GPS seconds)\n",
"psi=2.659 # gravitational wave polarisation angle\n",
")\n",
"\n",
+ "# specify waveform arguments\n",
+ "waveform_arguments = dict(\n",
+ "waveform_approximant='IMRPhenomPv2', # waveform approximant name\n",
+ "reference_frequency=50., # gravitational waveform reference frequency (Hz)\n",
+ ")\n",
"\n",
"# set up the waveform generator\n",
"waveform_generator = bilby.gw.waveform_generator.WaveformGenerator(\n",
" sampling_frequency=sampling_frequency, duration=time_duration,\n",
" frequency_domain_source_model=bilby.gw.source.lal_binary_black_hole,\n",
- " parameters=injection_parameters)\n",
+ " parameters=injection_parameters, waveform_arguments=waveform_arguments)\n",
"# create the frequency domain signal\n",
"hf_signal = waveform_generator.frequency_domain_strain()\n",
"\n",
@@ -69,7 +203,7 @@
" sampling_frequency=sampling_frequency, outdir=outdir)]\n",
"\n",
"# first, set up all priors to be equal to a delta function at their designated value\n",
- "priors = injection_parameters.copy()\n",
+ "priors = bilby.gw.prior.BBHPriorDict(injection_parameters.copy())\n",
"# then, reset the priors on the masses and luminosity distance to conduct a search over these parameters\n",
"priors['mass_1'] = bilby.core.prior.Uniform(20, 50, 'mass_1')\n",
"priors['mass_2'] = bilby.core.prior.Uniform(20, 50, 'mass_2')\n",
@@ -233,21 +367,30 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 2",
+ "display_name": "Bilby (source-install)",
"language": "python",
- "name": "python2"
+ "name": "bilby_source"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
- "version": 2
+ "version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
- "pygments_lexer": "ipython2",
- "version": "2.7.14"
+ "pygments_lexer": "ipython3",
+ "version": "3.7.3"
+ },
+ "pycharm": {
+ "stem_cell": {
+ "cell_type": "raw",
+ "metadata": {
+ "collapsed": false
+ },
+ "source": []
+ }
}
},
"nbformat": 4,