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small fixes to import path in example notebooks and to flow profiler #8

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Dec 3, 2024
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small fixes to import path in example notebooks and to flow profiler #8

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10 changes: 6 additions & 4 deletions docs/example_notebooks/example_chains_convergence_test.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@
"source": [
"# we start by importing several libraries:\n",
"import sys, os\n",
"os.environ['TF_USE_LEGACY_KERAS'] = '1' # needed for tensorflow KERAS compatibility\n",
"os.environ['DISPLAY'] = 'inline' # hack to get getdist working\n",
"sys.path.insert(0,os.path.realpath(os.path.join(os.getcwd(),'../..')))\n",
"from getdist import plots, MCSamples\n",
"from getdist.gaussian_mixtures import GaussianND\n",
Expand Down Expand Up @@ -55,9 +57,9 @@
"outputs": [],
"source": [
"# load the chains (remove no burn in since the example chains have already been cleaned):\n",
"chains_dir = './../../test_chains/'\n",
"chains_dir = os.path.realpath(os.path.join(os.getcwd(), '../..', 'test_chains'))\n",
"# the DES Y1 3x2 chain:\n",
"chain = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'DES', no_cache=True)"
"chain = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'DES'), no_cache=True)"
]
},
{
Expand Down Expand Up @@ -499,7 +501,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "tensiometer",
"language": "python",
"name": "python3"
},
Expand All @@ -513,7 +515,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
"version": "3.9.7"
}
},
"nbformat": 4,
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16 changes: 9 additions & 7 deletions docs/example_notebooks/example_gaussian_tension.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,8 @@
"%autoreload 1\n",
"# import libraries:\n",
"import sys, os\n",
"os.environ['TF_USE_LEGACY_KERAS'] = '1' # needed for tensorflow KERAS compatibility\n",
"os.environ['DISPLAY'] = 'inline' # hack to get getdist working\n",
"sys.path.insert(0,os.path.realpath(os.path.join(os.getcwd(),'../..')))\n",
"from getdist import plots, MCSamples\n",
"from getdist.gaussian_mixtures import GaussianND\n",
Expand Down Expand Up @@ -281,15 +283,15 @@
"outputs": [],
"source": [
"# load the samples (remove no burn in since the example chains have already been cleaned):\n",
"chains_dir = './../../test_chains/'\n",
"chains_dir = os.path.realpath(os.path.join(os.getcwd(), '../..', 'test_chains'))\n",
"# the Planck 2018 TTTEEE chain:\n",
"chain_1 = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'Planck18TTTEEE', no_cache=True)\n",
"chain_1 = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'Planck18TTTEEE'), no_cache=True)\n",
"# the DES Y1 3x2 chain:\n",
"chain_2 = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'DES', no_cache=True)\n",
"chain_2 = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'DES'), no_cache=True)\n",
"# the joint chain:\n",
"chain_12 = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'Planck18TTTEEE_DES', no_cache=True)\n",
"chain_12 = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'Planck18TTTEEE_DES'), no_cache=True)\n",
"# the prior chain:\n",
"prior_chain = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'prior', no_cache=True)"
"prior_chain = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'prior'), no_cache=True)"
]
},
{
Expand Down Expand Up @@ -557,7 +559,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "tensiometer",
"language": "python",
"name": "python3"
},
Expand All @@ -571,7 +573,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
"version": "3.9.7"
}
},
"nbformat": 4,
Expand Down
12 changes: 7 additions & 5 deletions docs/example_notebooks/example_measured_parameters.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,8 @@
"\n",
"# import libraries:\n",
"import sys, os\n",
"os.environ['TF_USE_LEGACY_KERAS'] = '1' # needed for tensorflow KERAS compatibility\n",
"os.environ['DISPLAY'] = 'inline' # hack to get getdist working\n",
"sys.path.insert(0,os.path.realpath(os.path.join(os.getcwd(),'../..')))\n",
"from getdist import plots, MCSamples\n",
"from getdist.gaussian_mixtures import GaussianND\n",
Expand Down Expand Up @@ -70,12 +72,12 @@
"outputs": [],
"source": [
"# load the chains (remove no burn in since the example chains have already been cleaned):\n",
"chains_dir = './../../test_chains/'\n",
"chains_dir = os.path.realpath(os.path.join(os.getcwd(), '../..', 'test_chains'))\n",
"# the DES Y1 3x2 chain:\n",
"settings = {'ignore_rows':0, 'smooth_scale_1D':0.3, 'smooth_scale_2D':0.3}\n",
"chain = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'DES', no_cache=True, settings=settings)\n",
"chain = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'DES'), no_cache=True, settings=settings)\n",
"# the prior chain:\n",
"prior_chain = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'prior', no_cache=True, settings=settings)\n",
"prior_chain = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'prior'), no_cache=True, settings=settings)\n",
"\n",
"# we add a couple of derived parameters that have been removed from the chains (to save a little space on github):\n",
"for ch in [chain, prior_chain]:\n",
Expand Down Expand Up @@ -617,7 +619,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "tensiometer",
"language": "python",
"name": "python3"
},
Expand All @@ -631,7 +633,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
"version": "3.9.7"
}
},
"nbformat": 4,
Expand Down
12 changes: 7 additions & 5 deletions docs/example_notebooks/example_non_gaussian_tension.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,8 @@
"%autoreload 1\n",
"# import libraries:\n",
"import sys, os\n",
"os.environ['TF_USE_LEGACY_KERAS'] = '1' # needed for tensorflow KERAS compatibility\n",
"os.environ['DISPLAY'] = 'inline' # hack to get getdist working\n",
"sys.path.insert(0,os.path.realpath(os.path.join(os.getcwd(),'../..')))\n",
"from getdist import plots\n",
"import getdist\n",
Expand Down Expand Up @@ -54,11 +56,11 @@
"outputs": [],
"source": [
"# load the samples (remove no burn in since the example chains have already been cleaned):\n",
"chains_dir = './../../test_chains/'\n",
"chains_dir = os.path.realpath(os.path.join(os.getcwd(), '../..', 'test_chains'))\n",
"# the Planck 2018 TTTEEE chain:\n",
"chain_1 = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'Planck18TTTEEE', no_cache=True)\n",
"chain_1 = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'Planck18TTTEEE'), no_cache=True)\n",
"# the DES Y1 3x2 chain:\n",
"chain_2 = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'DES', no_cache=True)"
"chain_2 = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'DES'), no_cache=True)"
]
},
{
Expand Down Expand Up @@ -463,7 +465,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "tensiometer",
"language": "python",
"name": "python3"
},
Expand All @@ -477,7 +479,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
"version": "3.9.7"
}
},
"nbformat": 4,
Expand Down
10 changes: 6 additions & 4 deletions docs/example_notebooks/example_posterior_profiles.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,8 @@
"\n",
"# import libraries:\n",
"import sys, os\n",
"os.environ['TF_USE_LEGACY_KERAS'] = '1' # needed for tensorflow KERAS compatibility\n",
"os.environ['DISPLAY'] = 'inline' # hack to get getdist working\n",
"sys.path.insert(0,os.path.realpath(os.path.join(os.getcwd(),'../..')))\n",
"from getdist import plots, MCSamples\n",
"from getdist.gaussian_mixtures import GaussianND\n",
Expand Down Expand Up @@ -469,9 +471,9 @@
"# we start by loading up the posterior:\n",
"\n",
"# load the samples (remove no burn in since the example chains have already been cleaned):\n",
"chains_dir = './../../test_chains/'\n",
"chains_dir = os.path.realpath(os.path.join(os.getcwd(), '../..', 'test_chains'))\n",
"# the DES Y1 3x2 chain:\n",
"data_chain = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'DES', no_cache=True, settings=getdist_settings)\n",
"data_chain = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'DES'), no_cache=True, settings=getdist_settings)\n",
"\n",
"# let's add omegab as a derived parameter:\n",
"for _ch in [data_chain]:\n",
Expand Down Expand Up @@ -889,7 +891,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "base",
"display_name": "mlg",
"language": "python",
"name": "python3"
},
Expand All @@ -903,7 +905,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
"version": "3.9.7"
}
},
"nbformat": 4,
Expand Down
16 changes: 9 additions & 7 deletions docs/example_notebooks/example_synthetic_probability.ipynb
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Expand Up @@ -32,6 +32,8 @@
"\n",
"# import libraries:\n",
"import sys, os\n",
"os.environ['TF_USE_LEGACY_KERAS'] = '1' # needed for tensorflow KERAS compatibility\n",
"os.environ['DISPLAY'] = 'inline' # hack to get getdist working\n",
"sys.path.insert(0,os.path.realpath(os.path.join(os.getcwd(),'../..')))\n",
"from getdist import plots, MCSamples\n",
"from getdist.gaussian_mixtures import GaussianND\n",
Expand Down Expand Up @@ -380,13 +382,13 @@
"# we start by loading up the posteriors:\n",
"\n",
"# load the samples (remove no burn in since the example chains have already been cleaned):\n",
"chains_dir = './../../test_chains/'\n",
"chains_dir = os.path.realpath(os.path.join(os.getcwd(), '../..', 'test_chains'))\n",
"# the Planck 2018 TTTEEE chain:\n",
"chain_1 = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'Planck18TTTEEE', no_cache=True, settings=getdist_settings)\n",
"chain_1 = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'Planck18TTTEEE'), no_cache=True, settings=getdist_settings)\n",
"# the DES Y1 3x2 chain:\n",
"chain_2 = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'DES', no_cache=True, settings=getdist_settings)\n",
"chain_2 = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'DES'), no_cache=True, settings=getdist_settings)\n",
"# the joint chain:\n",
"chain_12 = getdist.mcsamples.loadMCSamples(file_root=chains_dir+'Planck18TTTEEE_DES', no_cache=True, settings=getdist_settings)\n",
"chain_12 = getdist.mcsamples.loadMCSamples(file_root=os.path.join(chains_dir, 'Planck18TTTEEE_DES'), no_cache=True, settings=getdist_settings)\n",
"\n",
"# let's add omegab as a derived parameter:\n",
"for _ch in [chain_1, chain_2, chain_12]:\n",
Expand Down Expand Up @@ -463,7 +465,7 @@
"# now we can define the joint posterior:\n",
"def joint_log_posterior(H0, omegam, sigma8, ns, omegab):\n",
" params = [H0, omegam, sigma8, ns, omegab]\n",
" return [flow_1.log_probability(flow_1.cast(params)).numpy() + flow_2.log_probability(flow_2.cast(params)).numpy()]\n",
" return [flow_1.log_probability(flow_1.cast([params])).numpy()[0] + flow_2.log_probability(flow_2.cast([params])).numpy()[0]]\n",
"\n",
"# and sample it:\n",
"from cobaya.run import run\n",
Expand Down Expand Up @@ -937,7 +939,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "base",
"display_name": "mlg",
"language": "python",
"name": "python3"
},
Expand All @@ -951,7 +953,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
"version": "3.9.7"
}
},
"nbformat": 4,
Expand Down
1 change: 1 addition & 0 deletions tensiometer/synthetic_probability/flow_profiler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -816,6 +816,7 @@ def _initialize_likestats(self, profile_lims=True):
m.complexity = 2 * (maxlike - m.meanLogLike)
m.logMeanInvLike = np.log(np.mean(np.exp(-_temp_loglikes + maxlike))) - maxlike
m.logMeanLike = -np.log(np.mean(np.exp(_temp_loglikes - maxlike))) + maxlike
m.varLogLike = np.var(_temp_loglikes)
m.names = self.paramNames.names

if profile_lims:
Expand Down
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