Add VELMASS analysis scripts
This commit is contained in:
Deaglan Bartlett
parent
6cde261fcf
commit
7ce772730a
8 changed files with 695 additions and 293 deletions
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@ -30,7 +30,13 @@
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" try:\n",
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" yield\n",
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" finally:\n",
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" sys.stdout = old_stdout"
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" sys.stdout = old_stdout\n",
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" \n",
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"from analysis import (\n",
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" get_mcmc_steps, load_param_samples, get_truths,\n",
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" crop_field, compute_ensemble_mean_field, \n",
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" get_mock_field, get_spectra, get_both_fields,\n",
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" get_likelihood_values)"
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]
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},
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{
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@ -41,290 +47,7 @@
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"tags": []
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},
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"outputs": [],
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"source": [
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"def get_mcmc_steps(dirname, nframe, iter_max, iter_min=0):\n",
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" \"\"\"\n",
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" Obtain evenly-spaced sample of MCMC steps to make movie from\n",
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" \"\"\"\n",
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" all_mcmc = glob.glob(dirname + '/mcmc_*.h5')\n",
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" x = [m[len(dirname + '/mcmc_'):-3] for m in all_mcmc]\n",
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" all_mcmc = np.sort([int(m[len(dirname + '/mcmc_'):-3]) for m in all_mcmc])\n",
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" if iter_max >= 0:\n",
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" all_mcmc = all_mcmc[all_mcmc <= iter_max]\n",
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" all_mcmc = all_mcmc[all_mcmc >= iter_min]\n",
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" if nframe > 0:\n",
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" max_out = max(all_mcmc)\n",
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" min_out = min(all_mcmc)\n",
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" step = max(int((max_out - min_out+1) / nframe), 1)\n",
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" all_mcmc = all_mcmc[::step]\n",
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" if max_out not in all_mcmc:\n",
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" all_mcmc = np.concatenate([all_mcmc, [max_out]])\n",
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" return all_mcmc\n",
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"\n",
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"def load_param_samples(ini_name, dirname, nframe, iter_max, iter_min):\n",
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" \n",
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" config = configparser.ConfigParser()\n",
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" config.read(ini_name)\n",
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" to_sample = []\n",
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" for k,v in config['block_loop'].items():\n",
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" if v.strip() == 'false':\n",
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" i = k.index('_sampler')\n",
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" if k[:i] not in ['hades', 'bias', 'nmean']:\n",
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" to_sample.append(k[:i])\n",
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" \n",
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" print(\"TO SAMPLE\", to_sample)\n",
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" nsamp = int(config['run']['nsamp'])\n",
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" new_to_sample = []\n",
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" for s in to_sample:\n",
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" if s in ['omega_m', 'sigma8', 'sig_v']:\n",
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" new_to_sample.append(s)\n",
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" elif s == 'bulk_flow':\n",
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" for d in ['_x', '_y', '_z']:\n",
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" new_to_sample.append(f'{s}{d}')\n",
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" else:\n",
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" for i in range(nsamp):\n",
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" new_to_sample.append(f'{s}{i}')\n",
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" \n",
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" # This is desired list to sample\n",
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" to_sample = new_to_sample\n",
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" \n",
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" # Which steps to use\n",
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" all_mcmc = get_mcmc_steps(dirname, nframe, iter_max, iter_min=iter_min)\n",
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" \n",
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" sampler = config['sampling']['algorithm'].lower()\n",
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" samples = np.empty((len(to_sample),len(all_mcmc)))\n",
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" \n",
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" print('MY SAMPLER IS', sampler)\n",
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" \n",
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" if sampler == 'slice': \n",
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"\n",
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" for i in tqdm(range(len(all_mcmc))):\n",
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" with h5.File(f'{dirname}/mcmc_{all_mcmc[i]}.h5', 'r') as f:\n",
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" for j, s in enumerate(to_sample):\n",
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" if 'model_params_' + s in f['scalars'].keys():\n",
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" samples[j,i] = f['scalars/model_params_' + s][:][0]\n",
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" elif 'model_params_cosmology.' + s in f['scalars'].keys():\n",
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" samples[j,i] = f['scalars/model_params_cosmology.' + s][:][0]\n",
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" elif s == 'sig_v':\n",
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" samples[j,i] = float(config['model'][s])\n",
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" elif s.startswith('bulk_flow'):\n",
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" if s[-1] == 'x':\n",
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" samples[j,i] = np.array(ast.literal_eval(config['model']['bulk_flow']))[0]\n",
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" elif s[-1] == 'y':\n",
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" samples[j,i] = np.array(ast.literal_eval(config['model']['bulk_flow']))[1]\n",
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" elif s[-1] == 'z':\n",
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" samples[j,i] = np.array(ast.literal_eval(config['model']['bulk_flow']))[2]\n",
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" else:\n",
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" raise NotImplementedError\n",
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" else:\n",
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" if s in config[f'cosmology'].keys():\n",
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" samples[j,i] = float(config['cosmology'][s])\n",
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" else:\n",
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" print(\"NOT THERE\")\n",
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" samples[j,i] = float(config[f'sample_{s[-1]}'][s[:-1]]) \n",
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" \n",
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" elif sampler in ['hmc', 'mvslice', 'transformedblackjax', 'blackjax']:\n",
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" \n",
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" if sampler in ['hmc', 'transformedblackjax']:\n",
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" key_name = 'attributes'\n",
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" key_name = 'model_params'\n",
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" elif sampler in ['mvslice', 'blackjax']:\n",
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" key_name = 'model_paramsattributes'\n",
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" \n",
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" # Get order in which model parameters are stored\n",
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" if os.path.isfile(f'{dirname}/model_params.txt'):\n",
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" with open(f'{dirname}/model_params.txt', 'r') as file:\n",
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" model_params = [line.strip() for line in file]\n",
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" else:\n",
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" model_params = []\n",
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" \n",
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" print(model_params)\n",
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" \n",
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" for i in tqdm(range(len(all_mcmc))):\n",
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" with h5.File(f'{dirname}/mcmc_{all_mcmc[i]}.h5', 'r') as f:\n",
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" if key_name in f['scalars'].keys():\n",
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" data = f[f'scalars/{key_name}'][:]\n",
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" else:\n",
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" data = None\n",
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" for j, s in enumerate(to_sample):\n",
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" if s in model_params:\n",
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" samples[j,i] = data[model_params.index(s)]\n",
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" elif 'model_params_cosmology.' + s in f['scalars'].keys():\n",
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" samples[j,i] = f['scalars/model_params_cosmology.' + s][:][0]\n",
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" elif s == 'sig_v':\n",
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" samples[j,i] = float(config['model'][s])\n",
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" elif s in config[f'cosmology'].keys():\n",
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" samples[j,i] = float(config['cosmology'][s])\n",
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" elif s.startswith('bulk_flow'):\n",
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" idx = {'x':0, 'y':1, 'z':2}\n",
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" idx = idx[s[-1]]\n",
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" samples[j,i] = np.array(ast.literal_eval(config['model']['bulk_flow']))[idx]\n",
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" else:\n",
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" samples[j,i] = float(config[f'sample_{s[-1]}'][s[:-1]]) \n",
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" else:\n",
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" raise NotImplementedError\n",
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"\n",
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" return to_sample, all_mcmc, samples\n",
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"\n",
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"\n",
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"def get_truths(ini_name, to_sample):\n",
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" \n",
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" config = configparser.ConfigParser()\n",
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" config.read(ini_name)\n",
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" \n",
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" truths = [None] * len(to_sample)\n",
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" \n",
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" for i, s in enumerate(to_sample):\n",
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" if s in config[f'cosmology'].keys():\n",
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" truths[i] = float(config['cosmology'][s])\n",
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" elif s == 'sig_v':\n",
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" truths[i] = float(config['model'][s])\n",
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" elif s.startswith('bulk_flow'):\n",
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" idx = {'x':0, 'y':1, 'z':2}\n",
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" idx = idx[s[-1]]\n",
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" truths[i] = np.array(ast.literal_eval(config['model']['bulk_flow']))[idx]\n",
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" else:\n",
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" truths[i] = float(config[f'sample_{s[-1]}'][s[:-1]]) \n",
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" \n",
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" return truths\n",
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"\n",
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"\n",
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"def crop_field(ini_name, field):\n",
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" \n",
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" config = configparser.ConfigParser()\n",
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" config.read(ini_name)\n",
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" Rmax = float(config['mock']['R_max'])\n",
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" xmin = float(config['system']['corner0'])\n",
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" L = float(config['system']['L0'])\n",
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" N = int(config['system']['N0'])\n",
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" x = np.linspace(xmin, xmin+L, N)\n",
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" m = np.abs(x) < Rmax\n",
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" L = x[m].max() - x[m].min()\n",
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" \n",
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" return field[m][:, m][:, :, m], L\n",
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"\n",
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"\n",
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"def compute_ensemble_mean_field(ini_name, dirname, nframe, iter_max, iter_min, cut_field=True):\n",
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" \"\"\"\n",
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" Compute the mean and std deviation of the inferred density field\n",
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" \"\"\"\n",
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"\n",
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" print('Computing ensemble mean field')\n",
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" \n",
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" # Which steps to use\n",
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" all_mcmc = get_mcmc_steps(dirname, nframe, iter_max, iter_min=iter_min)\n",
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"\n",
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" #COMPUTE THE MEAN-DENSITY FIELD\n",
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" for i in tqdm(range(len(all_mcmc))):\n",
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" idx = all_mcmc[i]\n",
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" with h5.File(dirname + \"/mcmc_%d.h5\" % idx,'r') as mcmc_file:\n",
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" temp_field = np.array(mcmc_file['scalars/BORG_final_density'][...],dtype=np.float64)\n",
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" if i == 0:\n",
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" mean_field = np.array(np.full(temp_field.shape,0),dtype=np.float64)\n",
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" std_field = np.array(np.full(temp_field.shape,0),dtype=np.float64)\n",
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" mean_field += temp_field\n",
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" std_field += temp_field*temp_field\n",
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" mean_field = mean_field/np.float64(len(all_mcmc))\n",
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" std_field = std_field/np.float64(len(all_mcmc)) # < delta^2 >\n",
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" std_field = np.sqrt(std_field - mean_field **2) # < delta^2 > - < delta >^2\n",
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" \n",
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" # Cut the density field if needed\n",
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" if cut_field:\n",
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" mean_field, _ = crop_field(ini_name, mean_field)\n",
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" std_field, _ = crop_field(ini_name, std_field)\n",
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" \n",
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" return mean_field, std_field\n",
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"\n",
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"\n",
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"def get_mock_field(ini_name, dirname, which_field='delta', cut_field=True):\n",
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" with h5.File(f'{dirname}/mock_data.h5', 'r') as f:\n",
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" if which_field == 'delta':\n",
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" dens = f['scalars/BORG_final_density'][:]\n",
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" elif which_field == 'ics':\n",
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" dens = f['scalars/s_field'][:]\n",
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" if cut_field:\n",
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" dens, L = crop_field(ini_name, dens)\n",
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" else:\n",
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" config = configparser.ConfigParser()\n",
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" config.read(ini_name)\n",
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" L = float(config['system']['L0'])\n",
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" return dens, L\n",
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"\n",
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"\n",
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"def get_spectra(ini_file, dirname, nframe, iter_max, iter_min, which_field='delta', cut_field=True):\n",
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" \n",
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" # Which steps to use\n",
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" all_mcmc = get_mcmc_steps(dirname, nframe, iter_max, iter_min=iter_min)\n",
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" \n",
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" if which_field == 'delta':\n",
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" MAS = \"CIC\"\n",
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" elif which_field == 'ics':\n",
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" MAS = None\n",
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" else:\n",
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" raise NotImplementedError\n",
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" \n",
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" # Compute original power spectrum\n",
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" delta1, boxsize = get_mock_field(ini_name, dirname, which_field=which_field, cut_field=cut_field)\n",
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" print(\"BOXSIZE\", boxsize)\n",
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" Pk = PKL.Pk(delta1.astype(np.float32), boxsize, axis=0, MAS=MAS, threads=1, verbose=True)\n",
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" k = Pk.k3D\n",
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" Pk_true = Pk.Pk[:,0]\n",
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" \n",
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" # Get other spectra\n",
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" all_pk = np.zeros((len(all_mcmc), len(k)))\n",
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" all_r = np.zeros((len(all_mcmc), len(k)))\n",
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" for i in tqdm(range(len(all_mcmc))):\n",
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" idx = all_mcmc[i]\n",
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" with h5.File(dirname + \"/mcmc_%d.h5\" % idx,'r') as mcmc_file:\n",
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" if which_field == 'delta':\n",
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" delta2= np.array(mcmc_file['scalars/BORG_final_density'][...],dtype=np.float64)\n",
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" elif which_field == 'ics':\n",
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" delta2 = np.array(mcmc_file['scalars/s_field'][...],dtype=np.float64)\n",
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" else:\n",
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" raise NotImplementedError\n",
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" if cut_field:\n",
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" delta2, _ = crop_field(ini_name, delta2)\n",
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" with suppress_stdout():\n",
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" Pk = PKL.XPk([delta1.astype(np.float32),delta2.astype(np.float32)], boxsize, axis=0, MAS=[MAS, MAS], threads=1)\n",
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" all_pk[i,:] = Pk.Pk[:,0,1] #monopole of field 2\n",
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" all_r[i,:] = Pk.XPk[:,0,0] / np.sqrt(Pk.Pk[:,0,1] * Pk.Pk[:,0,0])\n",
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" \n",
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" return k, Pk_true, all_pk, all_r\n",
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"\n",
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"\n",
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"def get_both_fields(ini_file, dirname, step, which_field='delta', cut_field=True):\n",
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" \n",
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" # Mock\n",
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" delta1, boxsize = get_mock_field(ini_name, dirname, which_field=which_field, cut_field=cut_field)\n",
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" \n",
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" # Step\n",
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" with h5.File(dirname + \"/mcmc_%d.h5\" % step,'r') as mcmc_file:\n",
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" if which_field == 'delta':\n",
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" delta2= np.array(mcmc_file['scalars/BORG_final_density'][...],dtype=np.float64)\n",
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" elif which_field == 'ics':\n",
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" delta2 = np.array(mcmc_file['scalars/s_field'][...],dtype=np.float64)\n",
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" else:\n",
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" raise NotImplementedError\n",
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" if cut_field:\n",
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" delta2, _ = crop_field(ini_name, delta2)\n",
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" \n",
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" return delta1, delta2\n",
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"\n",
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"\n",
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"def get_likelihood_values(dirname, nframe, iter_max, iter_min):\n",
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" \n",
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" all_mcmc = get_mcmc_steps(dirname, nframe, iter_max, iter_min=iter_min)\n",
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" \n",
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" all_logL = np.zeros(len(all_mcmc))\n",
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" all_logprior = np.zeros(len(all_mcmc))\n",
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" for i in tqdm(range(len(all_mcmc))):\n",
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" with h5.File(f'{dirname}/mcmc_{all_mcmc[i]}.h5', 'r') as f:\n",
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" s_hat = f['scalars/s_hat_field'][:]\n",
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" all_logL[i] = f['scalars/hmc_Elh'][:]\n",
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" all_logprior[i] = f['scalars/hmc_Eprior'][:]\n",
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" \n",
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" return all_logL, all_logprior"
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]
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"source": []
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},
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{
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"cell_type": "markdown",
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