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fermi-lat / Fermitools-conda

Conda recipe files for the Fermi Sciencetools software analysis package: Fermitools
https://fermi.gsfc.nasa.gov/ssc/data/analysis/
BSD 3-Clause "New" or "Revised" License
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Picking pulsar ephemeris to use in gtpphase #149

Closed TheCriticalSpan closed 1 year ago

TheCriticalSpan commented 1 year ago

Hey everyone! So I'm trying to compute some pulsar phase light curves, Due to sparse photon counts I am trying to phase phold over a period of 5 years. To sort the photon events into phase bins you must use gtpphase, although this requires an ephemeris for the given pulsar. What I'm wondering is how should I go about picking an ephemeris if its validity period is shorter than the time period of my data? Should I pick an ephemeris with a reference epoch close to the center of my data time range? Does gtpphase extrapolate the ephemeris for data points that are too far from the reference epoch? Any clarification would be appreciated!

kerrm commented 1 year ago

Hi,

Because gtpphase can only use simple ephemerides, it is indeed generally not capable of folding long spans of data, and it is not the tool of choice for most pulsar analyses. Instead, we suggest the "fermi" plugin for tempo2 or the "fermiphase" script which is included with PINT: https://github.com/nanograv/PINT/blob/master/src/pint/scripts/fermiphase.py

PINT is particularly easy to install: pip install pulsar-pint

On Thu, 6 Jul 2023 at 23:54, TheCriticalSpan @.***> wrote:

Hey everyone! So I'm trying to compute some pulsar phase light curves, Due to sparse photon counts I am trying to phase phold over a period of 5 years. To sort the photon events into phase bins you must use gtpphase, although this requires an ephemeris for the given pulsar. What I'm wondering is how should I go about picking an ephemeris if its validity period is shorter than the time period of my data? Should I pick an ephemeris with a reference epoch close to the center of my data time range? Does gtpphase extrapolate the ephemeris for data points that are too far from the reference epoch? Any clarification would be appreciated!

— Reply to this email directly, view it on GitHub https://github.com/fermi-lat/Fermitools-conda/issues/149, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3LAG6AWRQQTKTMXQ3EWYDXO6B7TANCNFSM6AAAAAA2BIPYCU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

TheCriticalSpan commented 1 year ago

@kerrm Thanks for the help. I've been trying to use fermiphase -- addphase to add a phase column to my event .fits file. I see you need to give the command a .par file to work with. Is this the ephemeris information? Is there a standard format for the contents of this .par file? Also, fermiphase wants a weightcolumn file. What should I do if I don't have one? Thanks again for the help!

kerrm commented 1 year ago

Yes, the .par is the ephemeris. There isn't an official format, but there's a reasonably concrete working definition such that tempo, tempo2, and PINT will generally all be able to ingest a given .par file. Below is an example. For fermiphase, run with "-h" for more information, where you'll see you can specify "CALC" for it to add a weight column it's calculated. (Generally this won't be a very useful feature; it's better to use gtsrcprob for photon weights.)

PSR J0307+7443 EPHEM DE421 UNITS TDB START 54682.77779 FINISH 60067.81102 DILATEFREQ N DMDATA N NTOA 0 CHI2 0.0 RAJ 3:07:55.88475506 1 0.00075534937544957941 DECJ 74:43:13.44016166 1 0.00341834089928908002 PMRA -0.9509685374701923 1 0.7275533495716217 PMDEC 3.107213758757599 1 0.8067336635844139 PX 0.0 POSEPOCH 57500.0000000000000000 F0 316.8478765835501984 1 1.1935141741116026678e-11 F1 -1.7346738858211639935e-15 1 2.0036761470753919744e-19 PEPOCH 57373.6285511987298378 PLANET_SHAPIRO N BINARY ELL1 A1 16.108342562623445 1 6.880593532717682e-06 FB0 3.1190445639127643342e-07 1 5.1745077209856359077e-16 TASC 55599.3639411204605203 1 4.0799847117157039028e-06 EPS1 -0.0032990118726784147362 1 8.4883825264588695604e-07 EPS2 0.0003954025301586158781 1 8.4649299876273048543e-07 TZRMJD 55779.6860352153050232 TZRSITE 1 TZRFRQ 819.999

On Mon, 10 Jul 2023 at 01:01, TheCriticalSpan @.***> wrote:

@kerrm https://github.com/kerrm Thanks for the help. I've been trying to use fermiphase -- addphase to add a phase column to my event .fits file. I see you need to give the command a .par file to work with. Is this the ephemeris information? Is there a standard format for the contents of this .par file? Also, fermiphase wants a weightcolumn file. What should I do if I don't have one? Thanks again for the help!

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TheCriticalSpan commented 1 year ago

@kerrm Thanks for the info. I've tried to use fermiphase with a few .par files from the Stanford Fermi LAT pulsar catalog which I believe should be accepted by fermiphase, but I keep on getting the following error:

KeyError: "Observatory name 'fermi' is not defined"

Do you happen to have any idea what might be causing this?

kerrm commented 1 year ago

If the data aren't geocentered/barycentered, you need to provide the FT2 file with the --ft2 argument. Probably a more helpful error message could be given...!

On Tue, 11 Jul 2023 at 01:35, TheCriticalSpan @.***> wrote:

@kerrm https://github.com/kerrm Thanks for the info. I've tried to use fermiphase with a few .par files from the Stanford Fermi LAT pulsar catalog which I believe should be accepted by fermiphase, but I keep on getting the following error:

KeyError: "Observatory name 'fermi' is not defined"

Do you happen to have any idea what might be causing this?

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TheCriticalSpan commented 1 year ago

@kerrm By FT2 file are you referring to the Fermi spacecraft file?

kerrm commented 1 year ago

Yes.

On Tue, 11 Jul 2023 at 11:07, TheCriticalSpan @.***> wrote:

@kerrm https://github.com/kerrm By FT2 file are you referring to the Fermi spacecraft file?

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TheCriticalSpan commented 1 year ago

@kerrm I see, thanks for the guidance! Sorry about asking so many questions, I'm fairly new to working with Fermi LAT data. So just to be clear, fermiphase should work even if the data I'm analyzing is fairly far in time from the reference epoch of the ephemeris I'm using, right? Does fermiphase extrapolate the ephemeris for different time in the data?

kerrm commented 1 year ago

fermiphase will happily extrapolate the ephemeris, yes, but it will depend on the pulsar as to whether or not the extrapolation will be any good. If there's lots of timing noise, then the ephemeris will really only be reliable between START and FINISH. (These typically reflect the span of the data used to make the ephemeris, so are usually a good indicator of the range of validity. Of course, someone might have made a really bad ephemeris and it won't be good anywhere! But hopefully not...)

On Wed, 12 Jul 2023 at 05:03, TheCriticalSpan @.***> wrote:

@kerrm https://github.com/kerrm I see, thanks for the guidance! Sorry about asking so many questions, I'm fairly new to working with Fermi LAT data. So just to be clear, fermiphase should work even if the data I'm analyzing is fairly far in time from the reference epoch of the ephemeris I'm using, right? Does fermiphase extrapolate the ephemeris for different time in the data?

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TheCriticalSpan commented 1 year ago

@kerrm Great, thanks a lot! I still occasionally get an error saying the following: "KeyError: "Observatory name '8.0' is not defined," even after having provided the ft2 file. Is this a common issue?

kerrm commented 1 year ago

I haven't seen that before. Perhaps you could post the ephemeris that gives the problem?

On Thu, 13 Jul 2023 at 00:38, TheCriticalSpan @.***> wrote:

@kerrm https://github.com/kerrm Great, thanks a lot! I still occasionally get an error saying the following: "KeyError: "Observatory name '8.0' is not defined," even after having provided the ft2 file. Is this a common issue?

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TheCriticalSpan commented 1 year ago

@kerrm Sure thing. It's an ephemeris for the Crab pulsar, here's what it looks like:

PSRJ J0534+2200
RAJ 05:34:31.94 DECJ +22:00:52.1 PMRA -11.8 1.0
PMDEC 4.4 1.0
POSEPOCH 50739
F0 29.716913767510206412 0 7.4407601857728877803e-08 F1 -3.7105744257791078768e-10 0 7.1826463672770942706e-16 PEPOCH 55555
DMEPOCH 55107.807158553281624
DM 56.785579397589822356
DM1 0.031279168349770640344
GLEP_1 55875.675439999999998
GLPH_1 0
GLF0_1 3.7919867922922049662e-07 GLF1_1 -6.7584711344759838211e-14 GLF2_1 -5.9401094997596437912e-22 GLF0D_1 1.199959850289066081e-06
GLTD_1 13.613075016131585777
START 54686.1526259
FINISH 56583.1591704
TZRMJD 55638.155277599951660
TZRFRQ 0
TZRSITE coe
EPHVER 5
CLK TT(TAI)
MODE 1
EPHEM DE405
NITS 1
NTOA 272
CHI2R -nan 0
JUMP TEL 8 -0.00065347246224967 0
TRACK -2
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kerrm commented 1 year ago

I think if you delete this you'll be alright: JUMP TEL 8 -0.00065347246224967 0 (It tells it what to do with TOAs from a specific telescope, but that's a tempo2-style encoding.)

On Fri, 14 Jul 2023 at 00:30, TheCriticalSpan @.***> wrote:

@kerrm https://github.com/kerrm Sure thing. It's an ephemeris for the Crab pulsar, here's what it looks like:

PSRJ J0534+2200 RAJ 05:34:31.94 DECJ +22:00:52.1 PMRA -11.8 1.0 PMDEC 4.4 1.0 POSEPOCH 50739 F0 29.716913767510206412 0 7.4407601857728877803e-08 F1 -3.7105744257791078768e-10 0 7.1826463672770942706e-16 PEPOCH 55555 DMEPOCH 55107.807158553281624 DM 56.785579397589822356 DM1 0.031279168349770640344 GLEP_1 55875.675439999999998 GLPH_1 0 GLF0_1 3.7919867922922049662e-07 GLF1_1 -6.7584711344759838211e-14 GLF2_1 -5.9401094997596437912e-22 GLF0D_1 1.199959850289066081e-06 GLTD_1 13.613075016131585777 START 54686.1526259 FINISH 56583.1591704 TZRMJD 55638.155277599951660 TZRFRQ 0 TZRSITE coe EPHVER 5 CLK TT(TAI) MODE 1 EPHEM DE405 NITS 1 NTOA 272 CHI2R -nan 0 JUMP TEL 8 -0.00065347246224967 0 TRACK -2 F2 1.1633675551229037574e-20 0 2.4873069815300371171e-23 F3 -8.6724769747827286635e-31 0 0 SIFUNC 2 0 IFUNC1 54658.15528904736856929958 0.0233293128 0.0 IFUNC2 54661.65528904736856929958 0.0234380536 0.0 IFUNC3 54665.15528904736856929958 0.0235667779 0.0 IFUNC4 54668.65528904736856929958 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TheCriticalSpan commented 1 year ago

@kerrm Great, thanks a bunch! Should be able to work through the analysis now.