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Update pulsar recipe #22

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Aug 30, 2024
Merged

Update pulsar recipe #22

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73f3417
update env file
MRegeard Jun 13, 2024
2aa7373
update and correct notebook
MRegeard Jun 13, 2024
3ee44c6
atreyee comments
MRegeard Jun 26, 2024
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kirsty comments
MRegeard Jun 28, 2024
d5c817b
Update recipes/pulsar_phase/pulsar_phase_computation.ipynb
AtreyeeS Jul 1, 2024
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MRegeard Jul 12, 2024
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MRegeard Jul 12, 2024
45f4f4b
make expolsed env simlink of env.yaml
MRegeard Jul 12, 2024
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6 changes: 3 additions & 3 deletions recipes/pulsar_phase/env.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@ channels:
- conda-forge

dependencies:
- gammapy=1.0.2
- python=3.9
- gammapy=1.2
- python=3.11
- scipy<1.12
- jupyter
- pip
- pip:
- pint-pulsar~=0.9.3
- pint-pulsar~=1.0
6 changes: 3 additions & 3 deletions recipes/pulsar_phase/gammapy-pint-environment.yml
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Expand Up @@ -5,8 +5,8 @@ channels:
- conda-forge

dependencies:
- gammapy=1.0.1
- python=3.9
- gammapy=1.2
- python=3.11
- pip
- pip:
- pint-pulsar~=0.9.5
- pint-pulsar~=1.0
128 changes: 92 additions & 36 deletions recipes/pulsar_phase/pulsar_phase_computation.ipynb
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Expand Up @@ -15,9 +15,9 @@
"source": [
"This notebook has been done for the following version of Gammapy and PINT:\n",
"\n",
"Gammapy version : 1.0.1\n",
"Gammapy version : 1.2\n",
"\n",
"PINT version : 0.9.5"
"PINT version : 1.0"
]
},
{
Expand Down Expand Up @@ -54,7 +54,7 @@
"In order to run this notebook, one needs to have installed Gammapy as well as PINT (see documentation above) in the same environment. We recommend to first install Gammapy and then install PINT using your prefered package manager.\n",
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"\n",
"\n",
"`$ conda env create -n gammapy-pint -f gammapy-1.0-environment.yml`\n",
"`$ conda env create -n gammapy-pint -f gammapy-pint-environment.yml`\n",
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What is this gammapy-pint-environment.yml ?

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I don't really know. I think that is was the original env file that was presented to the user. But then we also need this env.yml for the CI. In the end they are the same so I could make gammapy-pint-environment.yml a simlink to env.

"\n",
"`$ conda activate gammapy-pint`\n",
"\n",
Expand Down Expand Up @@ -97,7 +97,10 @@
"from astropy.coordinates import SkyCoord\n",
"import numpy as np\n",
"from pathlib import Path\n",
"from gammapy.data import DataStore, EventList, Observation"
"from gammapy.data import DataStore, EventList, Observation\n",
"import logging\n",
"\n",
"log = logging.getLogger(__name__)"
]
},
{
Expand Down Expand Up @@ -143,7 +146,8 @@
"outputs": [],
"source": [
"# Define the directory containing the DL3 data\n",
"DL3_direc = \"$GAMMAPY_DATA/magic/rad_max/data\""
"DL3_dir = \"$GAMMAPY_DATA/magic/rad_max/data\"\n",
"DL3_dir = \"/Users/mregeard/Workspace/dev/code/gammapy/gammapy-data/magic/rad_max/data/\""
]
},
{
Expand All @@ -154,7 +158,7 @@
"outputs": [],
"source": [
"# Read DataStore from a directory\n",
"data_store = DataStore.from_dir(DL3_direc)"
"data_store = DataStore.from_dir(DL3_dir)"
]
},
{
Expand All @@ -173,7 +177,7 @@
"outputs": [],
"source": [
"target_pos = SkyCoord(\n",
" ra=083.6331144560900, dec=+22.0144871383400, unit=\"deg\", frame=\"icrs\"\n",
" ra=083.633, dec=+22.014, unit=\"deg\", frame=\"icrs\"\n",
")"
]
},
Expand Down Expand Up @@ -298,7 +302,7 @@
"\n",
"In the following, we will use an ephemeris file for the Crab provided by Fermi-LAT, see [Kerr, M.; Ray, P. S.; et al; 2015](https://arxiv.org/abs/1510.05099). This ephemeris file for the Crab pulsar can be found alongside other pulsar ephemeris files at this [confluence page]( https://confluence.slac.stanford.edu/display/GLAMCOG/LAT+Gamma-ray+Pulsar+Timing+Models). \n",
"\n",
"However, be aware that most of these ephemeris files are not up-to-date. Therefore they could give bad results on the phase computation. In particular, one should always checked that the MJD of the observations one wants to phased lies between the `START`and `FINISH`entry of the ephemeris file."
"However, be aware that most of these ephemeris files are not up-to-date. Therefore they could give bad results on the phase computation. In particular, one should always checked that the MJD of the observations one wants to phased lies between the `START`and `FINISH`entry of the ephemeris file (see next section)."
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]
},
{
Expand All @@ -309,15 +313,17 @@
"outputs": [],
"source": [
"# Path to the ephemeris file\n",
"ephemeris_file = \"./0534+2200_ApJ_708_1254_2010.par\""
"ephemeris_file = \"0534+2200_ApJ_708_1254_2010.par\""
]
},
{
"cell_type": "markdown",
"id": "52eb3086",
"metadata": {},
"source": [
"Note that sometimes one needs to change some of the parameters of the ephemeris file that are not used in gamma-ray astronomy by hand. For instance, here we have removed the 'JUMP' line since it does not have any effect in our computation and raise an error in PINT. The ephemeris file provided with this notebook does not have this line. "
"Note that *Fermi*-LAT ephemeris file are created primarily by and for [Tempo2](https://www.pulsarastronomy.net/pulsar/software/tempo2). Most of the time, using such ephemeris file with PINT will not raise any issues. However, in a few cases, PINT does not support feature from Tempo2. \n",
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"\n",
"In our case, an error occur when using the ephemeris file with PINT. This is due to the `JUMP` line. In order to proceed, one as to either comment (with #) or remove this line. Note that this line is not important for gamma-ray instrument, so it is totally fine to ignore it."
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]
},
{
Expand Down Expand Up @@ -348,9 +354,7 @@
"cell_type": "code",
"execution_count": null,
"id": "d24e1c92",
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"model = pmodels.get_model(ephemeris_file)\n",
Expand All @@ -366,7 +370,69 @@
"id": "0f8cd0d8",
"metadata": {},
"source": [
"There are multiple parameters such as the name of the source, the interval of validity of the model (START to FINISH), the frequencies of rotation and its derivatives (F0,F1,F2). There are other additional parameters that can be checked in the [PINT documentation](https://nanograv-pint.readthedocs.io)"
"There are multiple parameters such as the name of the source, the frequencies of rotation and its derivatives (F0,F1,F2), the dispersion measure, etc. There are other additional parameters that can be checked in the [PINT documentation](https://nanograv-pint.readthedocs.io). To get the complete set of parameter of the ephemeris file, one can simply print the model:\n",
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"`print(model)`"
]
},
{
"cell_type": "markdown",
"id": "f02f0ca5-09f2-44d4-ad76-518f8964b6a1",
"metadata": {},
"source": [
"As said above, we should make sure that the time of the observation lies within the ephemeris time definition. In our example, we only have one run, so we can check that manually:"
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]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2584b571-93a9-4fb6-b8e2-60b8810190f6",
"metadata": {},
"outputs": [],
"source": [
"print(f\"Ephemeris time definition:\\n{model.START.value} - {model.FINISH.value}\")\n",
"print(f\"Observation time definition:\\n{observation.tstart} - {observation.tstop}\")"
]
},
{
"cell_type": "markdown",
"id": "86041174-5ec4-43ba-9035-cf567b47a3bb",
"metadata": {},
"source": [
"In the case you have several observations, if you know that they are sorted by time, you can manually check for the start time of the first observation and the stop time of the last one. Otherwise, you can build a small function such as the following one:"
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]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8838ee6c-5b53-4d34-8fd7-94d32daa6bb3",
"metadata": {},
"outputs": [],
"source": [
"def check_time(observation, timing_model):\n",
" \"\"\"\n",
" Check that the observation time lies within the time definition of the pulsar\n",
" timing model.\n",
"\n",
" Parameters\n",
" ----------\n",
" observation: `gammapy.data.Observation`\n",
" Observation to check.\n",
" timing_model: `pint.models.TimingModel`\n",
" The timing model that will be used.\n",
" \"\"\"\n",
" model_time = Time([model.START.value, model.FINISH.value], scale=\"tt\", format='mjd')\n",
" if (model_time[0].value > observation.tstart.tt.mjd) or (model_time[1].value < observation.tstop.tt.mjd):\n",
" log.warning(f\"Warning: Observation time of observation {observation.obs_id} goes out of timing model validity time.\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0d37e6cc-2cae-4192-87d9-88d52216e83f",
"metadata": {},
"outputs": [],
"source": [
"check_time(observation, model)"
]
},
{
Expand All @@ -381,9 +447,7 @@
"cell_type": "code",
"execution_count": null,
"id": "a145cdde",
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"%%time\n",
Expand Down Expand Up @@ -462,13 +526,11 @@
"cell_type": "code",
"execution_count": null,
"id": "f3269a2c",
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"# Show original table\n",
"print(table)"
"table"
]
},
{
Expand All @@ -494,9 +556,7 @@
"cell_type": "code",
"execution_count": null,
"id": "7f29187e",
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"# Show table with phases\n",
Expand Down Expand Up @@ -525,9 +585,7 @@
"cell_type": "code",
"execution_count": null,
"id": "af220557",
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"table.meta"
Expand Down Expand Up @@ -697,15 +755,13 @@
"cell_type": "code",
"execution_count": null,
"id": "f339c797",
"metadata": {
"scrolled": true
},
"metadata": {},
"outputs": [],
"source": [
"# Save the observation object in the specified file_path\n",
"print(\"Writing outputfile in \" + str(file_path))\n",
"observation.events.write(\n",
" filename=file_path, gti=observation.gti, overwrite=True\n",
"print(\"Writing output file in \" + str(file_path))\n",
"new_obs.write(\n",
" path=file_path, include_irfs=False, overwrite=True\n",
")"
]
},
Expand Down Expand Up @@ -737,7 +793,7 @@
"outputs": [],
"source": [
"for entry in new_hdu:\n",
" if entry[\"HDU_NAME\"] == \"EVENTS\" and entry[\"OBS_ID\"] == observation.obs_id:\n",
" if (entry[\"HDU_NAME\"] == \"EVENTS\") and (entry[\"OBS_ID\"] == observation.obs_id):\n",
" entry[\"FILE_DIR\"] = \"./\" + str(output_directory)\n",
" entry[\"FILE_NAME\"] = filename"
]
Expand Down Expand Up @@ -812,7 +868,7 @@
"outputs": [],
"source": [
"pulsar_datastore = DataStore.from_dir(\n",
" DL3_direc, hdu_table_filename=\"hdu-index-pulsar.fits.gz\"\n",
" DL3_dir, hdu_table_filename=\"hdu-index-pulsar.fits.gz\"\n",
")"
]
},
Expand Down Expand Up @@ -889,7 +945,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.16"
"version": "3.11.9"
}
},
"nbformat": 4,
Expand Down
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