)` "
]
},
{
"cell_type": "markdown",
"id": "09cfe94f",
"metadata": {},
"source": [
"Next you can create the profiles acccording to the model option you selected. A diagnostic plot will be shown per default, but this behaviour can be turned off with the option `show_plot=False`. The plot will always show both the positve and negative axis."
]
},
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"cell_type": "markdown",
"id": "7f2286b2",
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"\n",
"\n",
"\n",
"\n",
"Note\n",
"\n",
"\n",
"The keyword ``opening_angle=40`` is only needed for the cone profile. The other modes do not accept this keyword! The angle itself is the opening angle of the full cone and NOT the angle between the central x-axis and the cone!\n",
"\n",
"\n",
"
"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0aa59e7e",
"metadata": {},
"outputs": [],
"source": [
"profile.create_profile(opening_angle=40)"
]
},
{
"cell_type": "markdown",
"id": "d619b5d0",
"metadata": {},
"source": [
"In many cases you only want a very specific region from the snapshot, e.g. cutting out the dense, optically thick regions. This can be acchieved using the keywords `inner_radius` and `outer_radius`."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "bd934289",
"metadata": {},
"outputs": [],
"source": [
"profile.create_profile(opening_angle=40, inner_radius=1e11, outer_radius=2e11)"
]
},
{
"cell_type": "markdown",
"id": "dd6310ec",
"metadata": {},
"source": [
"Once you have created a profile of the desired region, you can export the profile to a `csvy` using the commented-out code below, which in turn can be used in a TARDIS model. Here you have to specify how many shells you want to export. The profiles are rebinned using [Scipys binned_statistic function](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binned_statistic.html), using the mean value of the data in each bin."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e918835b",
"metadata": {},
"outputs": [],
"source": [
"profile.export(20, \"snapshot_converted_to_tardis.csvy\", overwrite=True)"
]
},
{
"cell_type": "markdown",
"id": "c478ccec",
"metadata": {
"raw_mimetype": "text/restructuredtext"
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"source": [
"\n",
"\n",
"Note\n",
"\n",
"By default, the `export` method will not overwrite existing files with the same file name. Setting `overwrite=True` allows overwriting -- for example, if `overwrite=True`, if you make changes and rerun the export your exported file will be updated without creaing an additional file.\n",
"\n",
"
"
]
},
{
"cell_type": "markdown",
"id": "7c4e8922",
"metadata": {},
"source": [
"During the export, the `yaml` header is automatically written and includes the time of the screenshot as the time for both the nuclear data as well as the density profile. Per default, the positive axis will be exported. the negative axis can be exported with `direction=\"neg\"`.\n",
"\n",
"All abundences will normalised such that roughly sum to 1, but slight deviations are expected to occur."
]
},
{
"cell_type": "markdown",
"id": "5a5ec37b",
"metadata": {},
"source": [
"### Manually rebinning the data\n",
"Using `profile.rebin(, statistic=)`, you can manually rebin the data and use all `` keywords accepted by the `scipy.stats.binned_statistic` function. In this case you should pass the `statistic=None` keyword to the `export` function, so the data does not get rebinned twice."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "15fd5925",
"metadata": {},
"outputs": [],
"source": [
"profile.create_profile(opening_angle=40, inner_radius=1e11, outer_radius=2e11, show_plot=False)\n",
"profile.rebin(20)\n",
"profile.plot_profile()\n",
"plt.show()\n",
"profile.export(20, \"rebinned_snapshot_converted_to_tardis.csvy\", overwrite=True)"
]
},
{
"cell_type": "markdown",
"id": "da49c11a",
"metadata": {},
"source": [
"## Using the parser as a command line tool"
]
},
{
"cell_type": "markdown",
"id": "e0302a53",
"metadata": {},
"source": [
"You can also use the `tardis.io.arepo` package as a command line utility, e.g. if you are running batch jobs and want to automatically convert your snapshots from within you job-script.\n",
"\n",
"To export the same profile as in the example above you can run:\n",
"```bash\n",
"python .//arepo.py snapshot.hdf5 snapshot_converted.csvy -o 40 -n 20 --inner_radius 1e11 --outer_radius 2e11 -e ni56 si28 --save_plot plot.png --resolution 32 --plot_rebinned plot_binned.png\n",
"```\n",
"\n",
"This will also save diagnostic plots of both the raw and rebinned profiles. For more information on how to use the command line tool run:\n",
"```bash\n",
"python .//arepo.py --help\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "8f988111",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"\n",
"\n",
"\n",
"\n",
"Note\n",
"\n",
"\n",
"The command line tool does only work with snapshot files, not with e.g. json files. It is in any case not advised to use json files as an intermediate step, as the become huge for higher resolutions.\n",
"\n",
"\n",
"
"
]
}
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