bilby issueshttps://git.ligo.org/lscsoft/bilby/-/issues2020-06-30T23:02:20Zhttps://git.ligo.org/lscsoft/bilby/-/issues/496Bug in the evidence from merged runs2020-06-30T23:02:20ZGregory Ashtongregory.ashton@ligo.orgBug in the evidence from merged runsThe evidence from merged runs is being over estimated due to [this line](https://git.ligo.org/lscsoft/bilby/-/blob/master/bilby/core/result.py#L1653).
To verify this, here is some example code:
```python
In [19]: from scipy.special imp...The evidence from merged runs is being over estimated due to [this line](https://git.ligo.org/lscsoft/bilby/-/blob/master/bilby/core/result.py#L1653).
To verify this, here is some example code:
```python
In [19]: from scipy.special import logsumexp
In [20]: a = np.array([11, 12, 13]) # Create fake Z's
In [21]: np.sqrt(np.mean(a**2)) # Actual RMS value calculated directly
Out[21]: 12.027745701779143
In [22]: lna = np.log(a) # Take the natural log
In [23]: np.exp(0.5 * logsumexp(2 * lna, b=1. / len(a))) # This is how the RMS should be calculated
Out[23]: 12.027745701779143
In [24]: np.exp(logsumexp(2 * lna, b=1. / len(a))) # This is how we do it currently
Out[24]: 144.66666666666666
```1.0.0Gregory Ashtongregory.ashton@ligo.orgGregory Ashtongregory.ashton@ligo.orghttps://git.ligo.org/lscsoft/bilby/-/issues/444Restructure prior module2020-01-15T04:09:08ZMoritz HuebnerRestructure prior moduleThe `prior.py` module is pushing towards 4000 lines of code since we had some recent additions (Joint priors, conditional priors). I suggest splitting this up into separate modules while maintaining backwards compatibility. I am happy t...The `prior.py` module is pushing towards 4000 lines of code since we had some recent additions (Joint priors, conditional priors). I suggest splitting this up into separate modules while maintaining backwards compatibility. I am happy to have a look into this soon.1.0.0https://git.ligo.org/lscsoft/bilby/-/issues/439Conditional Priors not working reliably with Nested conditions2019-12-10T00:14:47ZMoritz HuebnerConditional Priors not working reliably with Nested conditionsConditional prior dicts are currently not working if there are multiple conditional priors which partly depend on each other.
I thought I tested this, but I must have missed it.Conditional prior dicts are currently not working if there are multiple conditional priors which partly depend on each other.
I thought I tested this, but I must have missed it.1.0.0Moritz HuebnerMoritz Huebnerhttps://git.ligo.org/lscsoft/bilby/-/issues/390Calibration tests2019-10-28T23:28:21ZGregory Ashtongregory.ashton@ligo.orgCalibration testsDemonstrate that the calibration output of GW150914 for bilby and L.I. are consistentDemonstrate that the calibration output of GW150914 for bilby and L.I. are consistent1.0.0Sylvia BiscoveanuSylvia Biscoveanuhttps://git.ligo.org/lscsoft/bilby/-/issues/374How to stop bilby version info being written to console on import2019-10-01T05:16:35ZMatthew PitkinHow to stop bilby version info being written to console on importFor some reason I get irrationally annoyed that `bilby` outputs its version info when I import it. I'm writing a new package that uses bilby and in case it's useful to others, here's how I get bilby to suppress its version info (but stil...For some reason I get irrationally annoyed that `bilby` outputs its version info when I import it. I'm writing a new package that uses bilby and in case it's useful to others, here's how I get bilby to suppress its version info (but still keep the logging info for eveything else) when I import that new package:
```python
### import bilby removing the logger version info output ###
import logging
import io
bilby_logger = logging.getLogger('bilby')
handler = logging.StreamHandler(io.StringIO())
bilby_logger.addHandler(handler)
import bilby # the actual import
bilby_logger.removeHandler(handler)
# reset bilby logging handler to default
from bilby.core.utils import setup_logger
setup_logger()
###
```1.0.0Gregory Ashtongregory.ashton@ligo.orgGregory Ashtongregory.ashton@ligo.orghttps://git.ligo.org/lscsoft/bilby/-/issues/336Add a page of documentation on the marginalized likelihood2019-06-26T01:33:56ZGregory Ashtongregory.ashton@ligo.orgAdd a page of documentation on the marginalized likelihood1.0.0https://git.ligo.org/lscsoft/bilby/-/issues/331Save correct luminosity distance when distance marginalizing2019-03-05T10:47:42ZMoritz HuebnerSave correct luminosity distance when distance marginalizingCurrently, when we marginalize over distance only the reference distance of 10 Mpc is saved into the result file. Working with result files than might require you to manually dig through the log to figure out the true luminosity distance.Currently, when we marginalize over distance only the reference distance of 10 Mpc is saved into the result file. Working with result files than might require you to manually dig through the log to figure out the true luminosity distance.1.0.0https://git.ligo.org/lscsoft/bilby/-/issues/320Add checking to the ROQ usage2019-11-21T03:21:03ZGregory Ashtongregory.ashton@ligo.orgAdd checking to the ROQ usageThe ROQ-basis comes with a `params.dat` file specifying things like the minimum and maximum chirp mass and sampling frequency. We should add a check to the `ROQLikelihood` that makes sure the given prior/sampling frequency is suitable.
...The ROQ-basis comes with a `params.dat` file specifying things like the minimum and maximum chirp mass and sampling frequency. We should add a check to the `ROQLikelihood` that makes sure the given prior/sampling frequency is suitable.
Chatting with @eric.thrane and @cjhaster it seems to me to make sense that, if the user-specific-prior is narrower then we should print a statement saying "prior okay" and continue, if the prior is not given, we should set the bounds correctly, and if the user-specified-prior is larger than the allowed range, `bilby` should raise an Error.1.0.0Carl-Johan HasterMichael PuerrerCarl-Johan Hasterhttps://git.ligo.org/lscsoft/bilby/-/issues/319Make bilby (or bilby_pipe) default PSD creation equivalent to LALInference2019-03-05T11:37:13ZGregory Ashtongregory.ashton@ligo.orgMake bilby (or bilby_pipe) default PSD creation equivalent to LALInferenceWe want to (by default) recreate what happens in LALInference for the PSD creation. This might need a combination of changes between `bilby` and `bilby_pipe`.
### Notes
In !366 we allowed the PSD to overlap the analysis segment. This t...We want to (by default) recreate what happens in LALInference for the PSD creation. This might need a combination of changes between `bilby` and `bilby_pipe`.
### Notes
In !366 we allowed the PSD to overlap the analysis segment. This takes the PSD duration of data, cuts out the analysis segment, then creates a PSD from the remaining data. As such, if one requests 100s of data for the PSD, one actually gets to use 100 - segment_length s of data.
We could add a catch to actually calc psd_duration + segment_length amount of data which then gets reduced to the proper amount.
1.0.0Vivien RaymondRhys GreenCharlie HoyVivien Raymondhttps://git.ligo.org/lscsoft/bilby/-/issues/317ROQ Likelihood does not permit the calculation of SNRs (which breaks conversi...2019-03-11T01:20:04ZEthan PayneROQ Likelihood does not permit the calculation of SNRs (which breaks conversion functions)When trying to use `gw.conversion._generate_all_cbc_parameters`, using the ROQ likelihood will break the post-processing stage, when the SNR cannot be calculated. The traceback is:
```
21:29 bilby WARNING : linear not a polarization mod...When trying to use `gw.conversion._generate_all_cbc_parameters`, using the ROQ likelihood will break the post-processing stage, when the SNR cannot be calculated. The traceback is:
```
21:29 bilby WARNING : linear not a polarization mode!
Traceback (most recent call last):
...
File "bilby/gw/conversion.py", line 966, in compute_snrs
signal_polarizations, sample.iloc[ii])
File "bilby/gw/detector.py", line 1281, in get_detector_response
parameters['psi'], mode)
File "bilby/gw/detector.py", line 1259, in antenna_response
return np.einsum('ij,ij->', self.detector_tensor, polarization_tensor)
```
@colm.talbot @gregory.ashton1.0.0Nikhil SarinNikhil Sarinhttps://git.ligo.org/lscsoft/bilby/-/issues/314ROQ doesn't convert arguments to float2019-02-20T00:29:22ZColm Talbotcolm.talbot@ligo.orgROQ doesn't convert arguments to float`lalsimulation` functions require all arguments to be floats, otherwise you get errors like `Argument 8 of type REAL8`.
This was done previously, e.g., https://git.ligo.org/lscsoft/bilby/blob/master/bilby/gw/utils.py#L744. I didn't also...`lalsimulation` functions require all arguments to be floats, otherwise you get errors like `Argument 8 of type REAL8`.
This was done previously, e.g., https://git.ligo.org/lscsoft/bilby/blob/master/bilby/gw/utils.py#L744. I didn't also do this for the ROQ. We should...
@ethan.payne1.0.0https://git.ligo.org/lscsoft/bilby/-/issues/311Determine default for sampler, sampler settings, jump proposals2019-06-25T04:09:18ZEric ThraneDetermine default for sampler, sampler settings, jump proposalsThis work is already underway, but I'm creating a git issue to link to the review readiness [wiki](https://git.ligo.org/lscsoft/bilby/wikis/review_script).
@gregory.ashton, @christopher\-berry, @paul\-lasky, @vivienThis work is already underway, but I'm creating a git issue to link to the review readiness [wiki](https://git.ligo.org/lscsoft/bilby/wikis/review_script).
@gregory.ashton, @christopher\-berry, @paul\-lasky, @vivien1.0.0Christopher BerryChristopher Berryhttps://git.ligo.org/lscsoft/bilby/-/issues/308Support for time domain waveforms2020-07-14T15:28:29ZMichael PuerrerSupport for time domain waveformsBilby uses lalsimulation's [`XLALSimInspiralChooseFDWaveform()`](https://git.ligo.org/lscsoft/bilby/blob/master/bilby/gw/utils.py#L765) to obtain Fourier domain waveforms.
To add support for time domain waveforms I would recommend to ca...Bilby uses lalsimulation's [`XLALSimInspiralChooseFDWaveform()`](https://git.ligo.org/lscsoft/bilby/blob/master/bilby/gw/utils.py#L765) to obtain Fourier domain waveforms.
To add support for time domain waveforms I would recommend to call lalsimulation's [`XLALSimInspiralFD()`](https://git.ligo.org/lscsoft/lalsuite/blob/master/lalsimulation/src/LALSimInspiral.c#L2119) to obtain Fourier domain waveforms from time domain waveforms implemented in lalsimulation. This has the advantage that lalsimulation is handling the conditioning and FFT.
Carefully read the documentation about the input parameters of this function! The redshift can be passed in the LALDict.1.0.0Colm Talbotcolm.talbot@ligo.orgColm Talbotcolm.talbot@ligo.orghttps://git.ligo.org/lscsoft/bilby/-/issues/307Improve the PP plot2019-05-20T03:40:16ZGregory Ashtongregory.ashton@ligo.orgImprove the PP plot* [x] Add labels to each curve on the pp plot
* [x] Add sigma confidence levels* [x] Add labels to each curve on the pp plot
* [x] Add sigma confidence levels1.0.0Meg MillhouseMeg Millhousehttps://git.ligo.org/lscsoft/bilby/-/issues/305Waveforms don't match LALInference2019-02-20T05:08:11ZSylvia BiscoveanuWaveforms don't match LALInferenceI've compared waveforms generated directly in LALInference versus using Bilby's waveform generator. I'm using TaylorF2 and have made sure the srate, min frequency, seglen, etc. are the same between the two. In the frequency domain the sp...I've compared waveforms generated directly in LALInference versus using Bilby's waveform generator. I'm using TaylorF2 and have made sure the srate, min frequency, seglen, etc. are the same between the two. In the frequency domain the spectral shape is quite different, which is weird to me if it's the same approximant, but they seem to converge at the min and max frequencies. The four injections I've plotted are all 1.4 Msun equal mass, non-spinning binaries, so only the extrinsic parameters are different. In the time domain they line up and have the same overall amplitude, but the behavior at early times is a bit different. Any ideas what's going on? It's definitely not an issue of the antenna patterns since the amplitudes line up (and I've checked that the LAL and Bilby versions return the same values for the same extrinsic parameters).
![compare_lal_bilby_freq](/uploads/6cef78c33b7f2e4c8679d170ea7675db/compare_lal_bilby_freq.png)
![compare_lal_bilby_time](/uploads/84c65845456a8513c7bc0f7d35e02ac8/compare_lal_bilby_time.png)1.0.0https://git.ligo.org/lscsoft/bilby/-/issues/278ensure that Bilby can run on large-scale computing resources beyond the LIGO ...2019-06-25T04:03:04ZPeter Couvaresensure that Bilby can run on large-scale computing resources beyond the LIGO Data GridThere are an increasing number of dedicated LVC and external shared computing resources available via the Open Science Grid (e.g., dedicated LVC: Virgo computing centers, Georgia Tech Tier-3 cluster's, LSU's SMIC allocation, CIT/LLO/LHO ...There are an increasing number of dedicated LVC and external shared computing resources available via the Open Science Grid (e.g., dedicated LVC: Virgo computing centers, Georgia Tech Tier-3 cluster's, LSU's SMIC allocation, CIT/LLO/LHO clusters, etc.; and shared: OSG opportunistic cycles, XSEDE allocations, commercial cloud CPUs, etc.). Bilby should be designed to be able to use them.
Concretely this means: not relying on shared filesystems but rather using explicit Condor file i/o; understanding and being explicit about runtime CPU, memory, and disk requirements rather than assuming an unspecified system configuration; and managing runtime software/library/package dependencies via LDG Singularity containers (ideal), CVMFS (good), and/or self-contained packaging/deployment (also good but harder).
@james\-clark, @pfc, Josh Willis, and others are available to help consult and debug.1.0.0James Alexander Clark PhDJames Alexander Clark PhDhttps://git.ligo.org/lscsoft/bilby/-/issues/277Be ready for new injection infrastructure2019-06-25T03:43:54ZCarl-Johan HasterBe ready for new injection infrastructurePlaceholder issue for now.
As mentioned by Tom Dent in [this post on chat.ligo.org](https://chat.ligo.org/ligo/pl/6eumo4gbrjd63yrtmp6693dtjh) there are plans for a revamped CBC injection infrastructure (not relying on `inspinj` and the o...Placeholder issue for now.
As mentioned by Tom Dent in [this post on chat.ligo.org](https://chat.ligo.org/ligo/pl/6eumo4gbrjd63yrtmp6693dtjh) there are plans for a revamped CBC injection infrastructure (not relying on `inspinj` and the old xml table format).
Bilby should, and needs to, be part of that design process such that we can use it seamlessly in the future!1.0.0https://git.ligo.org/lscsoft/bilby/-/issues/272Unexpected behaviour when converting to all BBH parameters with phase margina...2019-05-09T00:46:36ZEthan PayneUnexpected behaviour when converting to all BBH parameters with phase marginalization turned onWhen undertaking a run, sampling in the LALInference spin parameters (a_1, a_2, tilt_1, etc) with phase marginalization, and then converting to a x,y,z spin vector, a phase of zero is used for the conversion function, as this is the defa...When undertaking a run, sampling in the LALInference spin parameters (a_1, a_2, tilt_1, etc) with phase marginalization, and then converting to a x,y,z spin vector, a phase of zero is used for the conversion function, as this is the default output from the sampler when running PE with phase marginalization.
This not correct, as the phase should be determined from the analytic marginalization. My key issue with this is that the code will gladly do this without warning, such that I can get spin*_x,y,z which are not computed correctly. Not sure what the best way to fix this is, but it shouldn't be silent...
Tagged: @eric.thrane @moritz.huebner1.0.0Colm Talbotcolm.talbot@ligo.orgColm Talbotcolm.talbot@ligo.orghttps://git.ligo.org/lscsoft/bilby/-/issues/248Reproducibility between LALInference and bilby2019-06-25T02:10:59ZVivien RaymondReproducibility between LALInference and bilbyFor review and comparison, we want to have documented how one runs identical analysis with LALInference and BilbyFor review and comparison, we want to have documented how one runs identical analysis with LALInference and Bilby1.0.0Simon Paul Stevensonsimon.stevenson@ligo.orgVirginia d'EmilioSimon Paul Stevensonsimon.stevenson@ligo.orghttps://git.ligo.org/lscsoft/bilby/-/issues/237Create summary file for detector information2019-06-26T01:33:56ZMoritz HuebnerCreate summary file for detector informationAs stated in #225 there is no place where the geographical information about the detectors is stored. This should find it's way into the documentation eventually.
This document was mentioned in #225
https://dcc.ligo.org/LIGO-T980044/p...As stated in #225 there is no place where the geographical information about the detectors is stored. This should find it's way into the documentation eventually.
This document was mentioned in #225
https://dcc.ligo.org/LIGO-T980044/public1.0.0