{
"cells": [
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
".. _to_hdf_notebook:\n",
"\n",
"********************\n",
"Example to_hdf calls\n",
"********************"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Initialize the simulation with the `tardis_example.yml` configuration file."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:72)\n",
"tardis.plasma.standard_plasmas - \u001b[1;37mINFO\u001b[0m - Reading Atomic Data from tardis_example/kurucz_cd23_chianti_H_He.h5\n",
"tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8\n",
"[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:197)\n",
"tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
"[\u001b[1mtardis.montecarlo.base\u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Electron scattering switched on (\u001b[1mbase.py\u001b[0m:393)\n",
"tardis.montecarlo.base - \u001b[1;34mDEBUG\u001b[0m - Electron scattering switched on\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/vaibhav/anaconda2/lib/python2.7/site-packages/astropy/units/equivalencies.py:74: RuntimeWarning: divide by zero encountered in double_scalars\n",
" (si.m, si.Hz, lambda x: _si.c.value / x),\n",
" (\u001b[1mequivalencies.py\u001b[0m:74)\n",
"py.warnings - \u001b[1;33mWARNING\u001b[0m - /home/vaibhav/anaconda2/lib/python2.7/site-packages/astropy/units/equivalencies.py:74: RuntimeWarning: divide by zero encountered in double_scalars\n",
" (si.m, si.Hz, lambda x: _si.c.value / x),\n",
"\n"
]
}
],
"source": [
"from tardis.io.config_reader import Configuration\n",
"from tardis.simulation import Simulation\n",
"\n",
"# Must have the tardis_example folder in the working directory.\n",
"config_fname = 'tardis_example/tardis_example.yml'\n",
"config = Configuration.from_yaml(config_fname)\n",
"\n",
"simulation = Simulation.from_config(config)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Run the simulation."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/5 (\u001b[1mbase.py\u001b[0m:196)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 1/5\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.10360e+42 erg / s Luminosity absorbed = 2.67587e+42 erg / s Luminosity requested = 1.07688e+43 erg / s (\u001b[1mbase.py\u001b[0m:273)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 8.10360e+42 erg / s Luminosity absorbed = 2.67587e+42 erg / s Luminosity requested = 1.07688e+43 erg / s\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n",
"\t t_rad next_t_rad w next_w\n",
"\tShell \n",
"\t0 9967.488442 10074.800724 0.400392 0.452516\n",
"\t5 9893.293062 10103.998786 0.211205 0.202916\n",
"\t10 9820.194102 10007.439423 0.142695 0.130205\n",
"\t15 9748.167438 9820.947309 0.104556 0.096257\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:264)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Plasma stratification:\n",
"\t t_rad next_t_rad w next_w\n",
"\tShell \n",
"\t0 9967.488442 10074.800724 0.400392 0.452516\n",
"\t5 9893.293062 10103.998786 0.211205 0.202916\n",
"\t10 9820.194102 10007.439423 0.142695 0.130205\n",
"\t15 9748.167438 9820.947309 0.104556 0.096257\n",
"\n",
"\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9974.969 K -- next t_inner 10736.934 K (\u001b[1mbase.py\u001b[0m:266)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - t_inner 9974.969 K -- next t_inner 10736.934 K\n",
"[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:197)\n",
"tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 2/5 (\u001b[1mbase.py\u001b[0m:196)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 2/5\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.08633e+43 erg / s Luminosity absorbed = 3.60272e+42 erg / s Luminosity requested = 1.07688e+43 erg / s (\u001b[1mbase.py\u001b[0m:273)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 1.08633e+43 erg / s Luminosity absorbed = 3.60272e+42 erg / s Luminosity requested = 1.07688e+43 erg / s\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n",
"\t t_rad next_t_rad w next_w\n",
"\tShell \n",
"\t0 10074.800724 10480.642737 0.452516 0.485511\n",
"\t5 10103.998786 10542.429569 0.202916 0.203942\n",
"\t10 10007.439423 10413.108276 0.130205 0.127795\n",
"\t15 9820.947309 10179.669303 0.096257 0.094281\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:264)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Plasma stratification:\n",
"\t t_rad next_t_rad w next_w\n",
"\tShell \n",
"\t0 10074.800724 10480.642737 0.452516 0.485511\n",
"\t5 10103.998786 10542.429569 0.202916 0.203942\n",
"\t10 10007.439423 10413.108276 0.130205 0.127795\n",
"\t15 9820.947309 10179.669303 0.096257 0.094281\n",
"\n",
"\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10736.934 K -- next t_inner 10713.534 K (\u001b[1mbase.py\u001b[0m:266)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - t_inner 10736.934 K -- next t_inner 10713.534 K\n",
"[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:197)\n",
"tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 3/5 (\u001b[1mbase.py\u001b[0m:196)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 3/5\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.08260e+43 erg / s Luminosity absorbed = 3.52022e+42 erg / s Luminosity requested = 1.07688e+43 erg / s (\u001b[1mbase.py\u001b[0m:273)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 1.08260e+43 erg / s Luminosity absorbed = 3.52022e+42 erg / s Luminosity requested = 1.07688e+43 erg / s\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n",
"\t t_rad next_t_rad w next_w\n",
"\tShell \n",
"\t0 10480.642737 10711.113330 0.485511 0.493541\n",
"\t5 10542.429569 10819.470987 0.203942 0.199112\n",
"\t10 10413.108276 10633.892704 0.127795 0.125270\n",
"\t15 10179.669303 10359.259776 0.094281 0.092971\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:264)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Plasma stratification:\n",
"\t t_rad next_t_rad w next_w\n",
"\tShell \n",
"\t0 10480.642737 10711.113330 0.485511 0.493541\n",
"\t5 10542.429569 10819.470987 0.203942 0.199112\n",
"\t10 10413.108276 10633.892704 0.127795 0.125270\n",
"\t15 10179.669303 10359.259776 0.094281 0.092971\n",
"\n",
"\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10713.534 K -- next t_inner 10699.352 K (\u001b[1mbase.py\u001b[0m:266)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - t_inner 10713.534 K -- next t_inner 10699.352 K\n",
"[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:197)\n",
"tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 4/5 (\u001b[1mbase.py\u001b[0m:196)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 4/5\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.07886e+43 erg / s Luminosity absorbed = 3.48159e+42 erg / s Luminosity requested = 1.07688e+43 erg / s (\u001b[1mbase.py\u001b[0m:273)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 1.07886e+43 erg / s Luminosity absorbed = 3.48159e+42 erg / s Luminosity requested = 1.07688e+43 erg / s\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n",
"\t t_rad next_t_rad w next_w\n",
"\tShell \n",
"\t0 10711.113330 10866.508115 0.493541 0.489288\n",
"\t5 10819.470987 11017.147737 0.199112 0.192830\n",
"\t10 10633.892704 10795.422555 0.125270 0.121775\n",
"\t15 10359.259776 10499.976778 0.092971 0.090524\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:264)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Plasma stratification:\n",
"\t t_rad next_t_rad w next_w\n",
"\tShell \n",
"\t0 10711.113330 10866.508115 0.493541 0.489288\n",
"\t5 10819.470987 11017.147737 0.199112 0.192830\n",
"\t10 10633.892704 10795.422555 0.125270 0.121775\n",
"\t15 10359.259776 10499.976778 0.092971 0.090524\n",
"\n",
"\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10699.352 K -- next t_inner 10694.430 K (\u001b[1mbase.py\u001b[0m:266)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - t_inner 10699.352 K -- next t_inner 10694.430 K\n",
"[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:197)\n",
"tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 5/5 (\u001b[1mbase.py\u001b[0m:196)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 5/5\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.07897e+43 erg / s Luminosity absorbed = 3.45406e+42 erg / s Luminosity requested = 1.07688e+43 erg / s (\u001b[1mbase.py\u001b[0m:273)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 1.07897e+43 erg / s Luminosity absorbed = 3.45406e+42 erg / s Luminosity requested = 1.07688e+43 erg / s\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 5 iterations and took 50.01 s (\u001b[1mbase.py\u001b[0m:223)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Simulation finished in 5 iterations and took 50.01 s\n"
]
}
],
"source": [
"simulation.run()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You can now use `to_hdf` method, to save properties to a HDF file.\n",
"\n",
"#### Parameters \n",
"\n",
"`file_path`: Path where the HDF file should be stored. (Required) \n",
"`path`: Path inside the HDF store to store the elements. (Optional) \n",
"`name`: Name of the group inside HDF store, under which properties will be saved.(Optional)\n"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/vaibhav/anaconda2/lib/python2.7/site-packages/pandas/core/generic.py:1299: PerformanceWarning: \n",
"your performance may suffer as PyTables will pickle object types that it cannot\n",
"map directly to c-types [inferred_type->mixed,key->block0_values] [items->[0]]\n",
"\n",
" return pytables.to_hdf(path_or_buf, key, self, **kwargs)\n",
" (\u001b[1mpytables.py\u001b[0m:2675)\n",
"py.warnings - \u001b[1;33mWARNING\u001b[0m - /home/vaibhav/anaconda2/lib/python2.7/site-packages/pandas/core/generic.py:1299: PerformanceWarning: \n",
"your performance may suffer as PyTables will pickle object types that it cannot\n",
"map directly to c-types [inferred_type->mixed,key->block0_values] [items->[0]]\n",
"\n",
" return pytables.to_hdf(path_or_buf, key, self, **kwargs)\n",
"\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/vaibhav/anaconda2/lib/python2.7/site-packages/pandas/core/generic.py:1299: PerformanceWarning: \n",
"your performance may suffer as PyTables will pickle object types that it cannot\n",
"map directly to c-types [inferred_type->mixed,key->values] [items->None]\n",
"\n",
" return pytables.to_hdf(path_or_buf, key, self, **kwargs)\n",
" (\u001b[1mpytables.py\u001b[0m:2675)\n",
"py.warnings - \u001b[1;33mWARNING\u001b[0m - /home/vaibhav/anaconda2/lib/python2.7/site-packages/pandas/core/generic.py:1299: PerformanceWarning: \n",
"your performance may suffer as PyTables will pickle object types that it cannot\n",
"map directly to c-types [inferred_type->mixed,key->values] [items->None]\n",
"\n",
" return pytables.to_hdf(path_or_buf, key, self, **kwargs)\n",
"\n"
]
}
],
"source": [
"simulation.to_hdf('/tmp/full_example.hdf')\n",
"#simulation.to_hdf(file_path='/tmp/full_example.hdf', path='/', name='simulation')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Open the stored HDF file with pandas and print its structure."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'pandas.io.pytables.HDFStore'>\n",
"File path: /tmp/full_example.hdf\n",
"/simulation/model/homologous_density/density_0 series (shape->[21]) \n",
"/simulation/model/homologous_density/scalars series (shape->[1]) \n",
"/simulation/model/scalars series (shape->[1]) \n",
"/simulation/model/t_radiative series (shape->[20]) \n",
"/simulation/model/v_inner series (shape->[20]) \n",
"/simulation/model/v_outer series (shape->[20]) \n",
"/simulation/model/w series (shape->[20]) \n",
"/simulation/plasma/abundance frame (shape->[6,20]) \n",
"/simulation/plasma/atomic_mass series (shape->[6]) \n",
"/simulation/plasma/beta_rad series (shape->[20]) \n",
"/simulation/plasma/beta_sobolev frame (shape->[29224,20])\n",
"/simulation/plasma/density series (shape->[20]) \n",
"/simulation/plasma/electron_densities series (shape->[20]) \n",
"/simulation/plasma/excitation_energy series (shape->[4439]) \n",
"/simulation/plasma/f_lu series (shape->[29224]) \n",
"/simulation/plasma/g series (shape->[4439]) \n",
"/simulation/plasma/g_electron series (shape->[20]) \n",
"/simulation/plasma/general_level_boltzmann_factor frame (shape->[4439,20]) \n",
"/simulation/plasma/ion_number_density frame (shape->[94,20]) \n",
"/simulation/plasma/ionization_data frame (shape->[88,1]) \n",
"/simulation/plasma/j_blues frame (shape->[29224,20])\n",
"/simulation/plasma/level_boltzmann_factor frame (shape->[4439,20]) \n",
"/simulation/plasma/level_number_density frame (shape->[4439,20]) \n",
"/simulation/plasma/levels frame (shape->[1,1]) \n",
"/simulation/plasma/lines frame (shape->[29224,12])\n",
"/simulation/plasma/lines_lower_level_index series (shape->[29224]) \n",
"/simulation/plasma/lines_upper_level_index series (shape->[29224]) \n",
"/simulation/plasma/metastability series (shape->[4439]) \n",
"/simulation/plasma/nu series (shape->[29224]) \n",
"/simulation/plasma/number_density frame (shape->[6,20]) \n",
"/simulation/plasma/partition_function frame (shape->[94,20]) \n",
"/simulation/plasma/phi frame (shape->[88,20]) \n",
"/simulation/plasma/scalars series (shape->[1]) \n",
"/simulation/plasma/selected_atoms series (shape->[6]) \n",
"/simulation/plasma/stimulated_emission_factor frame (shape->[29224,20])\n",
"/simulation/plasma/t_electrons series (shape->[20]) \n",
"/simulation/plasma/t_rad series (shape->[20]) \n",
"/simulation/plasma/tau_sobolevs frame (shape->[29224,20])\n",
"/simulation/plasma/transition_probabilities frame (shape->[87672,20])\n",
"/simulation/plasma/w series (shape->[20]) \n",
"/simulation/plasma/wavelength_cm series (shape->[29224]) \n",
"/simulation/runner/j_estimator series (shape->[20]) \n",
"/simulation/runner/last_interaction_in_nu series (shape->[500000]) \n",
"/simulation/runner/last_interaction_type series (shape->[500000]) \n",
"/simulation/runner/last_line_interaction_in_id series (shape->[500000]) \n",
"/simulation/runner/last_line_interaction_out_id series (shape->[500000]) \n",
"/simulation/runner/last_line_interaction_shell_id series (shape->[500000]) \n",
"/simulation/runner/montecarlo_virtual_luminosity series (shape->[10000]) \n",
"/simulation/runner/nu_bar_estimator series (shape->[20]) \n",
"/simulation/runner/output_energy series (shape->[500000]) \n",
"/simulation/runner/output_nu series (shape->[500000]) \n",
"/simulation/runner/packet_luminosity series (shape->[500000]) \n",
"/simulation/runner/spectrum/_frequency series (shape->[10001]) \n",
"/simulation/runner/spectrum/luminosity series (shape->[10000]) \n",
"/simulation/runner/spectrum_reabsorbed/_frequency series (shape->[10001]) \n",
"/simulation/runner/spectrum_reabsorbed/luminosity series (shape->[10000]) \n",
"/simulation/runner/spectrum_virtual/_frequency series (shape->[10001]) \n",
"/simulation/runner/spectrum_virtual/luminosity series (shape->[10000]) \n"
]
}
],
"source": [
"import pandas as pd\n",
"data = pd.HDFStore('/tmp/full_example.hdf')\n",
"print data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Access `model.homologous_density.density_0` under simulation, which is a one-dimensional array"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 1970.527174\n",
"1 13.360318\n",
"2 10.146658\n",
"3 7.786621\n",
"4 6.033444\n",
"5 4.717122\n",
"6 3.718946\n",
"7 2.954982\n",
"8 2.365191\n",
"9 1.906156\n",
"10 1.546154\n",
"11 1.261789\n",
"12 1.035646\n",
"13 0.854653\n",
"14 0.708918\n",
"15 0.590901\n",
"16 0.494811\n",
"17 0.416168\n",
"18 0.351490\n",
"19 0.298047\n",
"20 0.253691\n",
"dtype: float64\n"
]
}
],
"source": [
"print data['/simulation/model/homologous_density/density_0']"
]
},
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
},
"source": [
"Scalars are stored in a `scalars` `pandas.Series` for every module. For example to access `model.t_inner` under simulation, one would need to do the following.\n",
"\n",
"Note: Quantities are always stored as their SI values."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"10694.430019\n"
]
}
],
"source": [
"print data['/simulation/model/scalars']['t_inner']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Breakdown of the various to_hdf methods\n",
"Every module in TARDIS has its own `to_hdf` method responsible to store its own data to an HDF file."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Plasma\n",
"The following call will store every plasma property to `/tmp/plasma_output.hdf` under `/parent/plasma`"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"simulation.plasma.to_hdf('/tmp/plasma_output.hdf', path='parent')"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'pandas.io.pytables.HDFStore'>\n",
"File path: /tmp/plasma_output.hdf\n",
"/parent/plasma/abundance frame (shape->[6,20]) \n",
"/parent/plasma/atomic_mass series (shape->[6]) \n",
"/parent/plasma/beta_rad series (shape->[20]) \n",
"/parent/plasma/beta_sobolev frame (shape->[29224,20])\n",
"/parent/plasma/density series (shape->[20]) \n",
"/parent/plasma/electron_densities series (shape->[20]) \n",
"/parent/plasma/excitation_energy series (shape->[4439]) \n",
"/parent/plasma/f_lu series (shape->[29224]) \n",
"/parent/plasma/g series (shape->[4439]) \n",
"/parent/plasma/g_electron series (shape->[20]) \n",
"/parent/plasma/general_level_boltzmann_factor frame (shape->[4439,20]) \n",
"/parent/plasma/ion_number_density frame (shape->[94,20]) \n",
"/parent/plasma/ionization_data frame (shape->[88,1]) \n",
"/parent/plasma/j_blues frame (shape->[29224,20])\n",
"/parent/plasma/level_boltzmann_factor frame (shape->[4439,20]) \n",
"/parent/plasma/level_number_density frame (shape->[4439,20]) \n",
"/parent/plasma/levels frame (shape->[1,1]) \n",
"/parent/plasma/lines frame (shape->[29224,12])\n",
"/parent/plasma/lines_lower_level_index series (shape->[29224]) \n",
"/parent/plasma/lines_upper_level_index series (shape->[29224]) \n",
"/parent/plasma/metastability series (shape->[4439]) \n",
"/parent/plasma/nu series (shape->[29224]) \n",
"/parent/plasma/number_density frame (shape->[6,20]) \n",
"/parent/plasma/partition_function frame (shape->[94,20]) \n",
"/parent/plasma/phi frame (shape->[88,20]) \n",
"/parent/plasma/scalars series (shape->[1]) \n",
"/parent/plasma/selected_atoms series (shape->[6]) \n",
"/parent/plasma/stimulated_emission_factor frame (shape->[29224,20])\n",
"/parent/plasma/t_electrons series (shape->[20]) \n",
"/parent/plasma/t_rad series (shape->[20]) \n",
"/parent/plasma/tau_sobolevs frame (shape->[29224,20])\n",
"/parent/plasma/transition_probabilities frame (shape->[87672,20])\n",
"/parent/plasma/w series (shape->[20]) \n",
"/parent/plasma/wavelength_cm series (shape->[29224]) \n"
]
}
],
"source": [
"import pandas\n",
"with pandas.HDFStore('/tmp/plasma_output.hdf') as data:\n",
" print data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Plasma's `to_hdf` method can also accept a `collection` parameter which can specify which types of plasma properties will be stored. For example if we wanted to only store Input plasma properties, we would do the following:"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"from tardis.plasma.properties.base import Input\n",
"simulation.plasma.to_hdf('/tmp/plasma_input_output.hdf', collection=[Input])"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'pandas.io.pytables.HDFStore'>\n",
"File path: /tmp/plasma_input_output.hdf\n",
"/plasma/abundance frame (shape->[6,20])\n",
"/plasma/density series (shape->[20]) \n",
"/plasma/scalars series (shape->[1]) \n",
"/plasma/t_rad series (shape->[20]) \n",
"/plasma/w series (shape->[20]) \n"
]
}
],
"source": [
"import pandas\n",
"with pandas.HDFStore('/tmp/plasma_input_output.hdf') as data:\n",
" print data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Model\n",
"The following call will store properties of the `Radial1DModel` to `/tmp/model_output.hdf` under `/model`."
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"simulation.model.to_hdf('/tmp/model_output.hdf')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### MontecarloRunner\n",
"The following call will store properties of the `MontecarloRunner` to `/tmp/runner_output.hdf` under `/runner`"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"simulation.runner.to_hdf('/tmp/runner_output.hdf')"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'pandas.io.pytables.HDFStore'>\n",
"File path: /tmp/runner_output.hdf\n",
"/runner/j_estimator series (shape->[20]) \n",
"/runner/last_interaction_in_nu series (shape->[500000])\n",
"/runner/last_interaction_type series (shape->[500000])\n",
"/runner/last_line_interaction_in_id series (shape->[500000])\n",
"/runner/last_line_interaction_out_id series (shape->[500000])\n",
"/runner/last_line_interaction_shell_id series (shape->[500000])\n",
"/runner/montecarlo_virtual_luminosity series (shape->[10000]) \n",
"/runner/nu_bar_estimator series (shape->[20]) \n",
"/runner/output_energy series (shape->[500000])\n",
"/runner/output_nu series (shape->[500000])\n",
"/runner/packet_luminosity series (shape->[500000])\n",
"/runner/spectrum/_frequency series (shape->[10001]) \n",
"/runner/spectrum/luminosity series (shape->[10000]) \n",
"/runner/spectrum_reabsorbed/_frequency series (shape->[10001]) \n",
"/runner/spectrum_reabsorbed/luminosity series (shape->[10000]) \n",
"/runner/spectrum_virtual/_frequency series (shape->[10001]) \n",
"/runner/spectrum_virtual/luminosity series (shape->[10000]) \n"
]
}
],
"source": [
"import pandas\n",
"with pandas.HDFStore('/tmp/runner_output.hdf') as data:\n",
" print data"
]
}
],
"metadata": {
"celltoolbar": "Raw Cell Format",
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.8"
}
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