Revision 4f75faeded2cb284dedbc856a8b2ae56075ea158 authored by Collin Capano on 20 June 2020, 18:27:09 UTC, committed by GitHub on 20 June 2020, 18:27:09 UTC
* use different acl for every chain in epsie

* create base burn in class, move common functions to there; rename MCMCBurnInTests EnsembleMCMC, first stab at creating MCMC tests for independent chains

* more changes to burn in module

* simplify the attributes in the burn in classes

* add write method to burn in classes

* add write_data method to base_hdf

* remove write_burn_in method from mcmc io; use the write method in burn in module instead

* make use of new burn in functions in sampler/base_mcmc

* have emcee and emcee pt use ensemble burn in tests

* add compute_acf function to epsie

* start separating ensemble and mcmc io methods

* stop saving thin settings to file; just return on the fly

* make read/write samples stand alone functions, and update emcee

* rename write functions; update emcee

* move multi temper read/write functions to stand alone and update emcee_pt

* pass kwargs from emcee(_pt) io functions

* simplify get_slice method

* add function to base_mcmc to calculate the number of samples in a chain

* use nsamples_in_chain function to calculate effective number of samples

* add read_raw_samples function that can handle differing number of samples from different chains

* add forgotten import

* use write/read functions from base_multitemper in epsie io

* use stand alone functions for computing ensemble acf/acls

* separate out ensemble-specific attributes in sampler module; update emcee and emcee_pt

* add acl and effective_nsample methods to epsie

* simplify writing acls and burn in

* fix various bugs and typos

* use a single function for writing both acl and raw_acls

* add some more logging info to burn in

* reduce identical blocks of code in burn in module

* fix self -> fp in read_raw_samples

* reduce code duplication in base io and simplify read raw samples function

* fix missed rename

* reduce code redundacy in sampler/base_multitemper

* whitespace

* fix bugs and typos in burn_in module

* fix code climate issues

* use map in compute_acl

* more code climate fixes

* remove unused variable; try to silence pylint

* fix issues reading epsie samples

* only load samples from burned in chains by default

* add act property to mcmc files

* fix act logging message

* fix effective number of samples calculation in epsie

* remap walkers option to chains for reading samples

* fix thinning update

* fix acceptance ratio and temperature data thinning in epsie

* allow for different fields to have differing number of temperatures when loading

* don't try to figure out how many samples will be loaded ahead of time

* store acts in file instead of acls

* write burn in status to file before computing acls

* drop write_acts function

* fix issue with getting specific chains

* fix typo

* code climate issues

* fix plot_acl
1 parent 926b628
History
File Mode Size
bank
hdfcoinc
hwinj
inference
live
minifollowups
plotting
population
pygrb
workflow_comparisons
workflows
pycbc_banksim -rw-r--r-- 19.1 KB
pycbc_banksim_combine_banks -rw-r--r-- 2.2 KB
pycbc_banksim_match_combine -rw-r--r-- 7.3 KB
pycbc_banksim_skymax -rw-r--r-- 21.9 KB
pycbc_coinc_time -rw-r--r-- 7.5 KB
pycbc_compress_bank -rwxr-xr-x 8.9 KB
pycbc_condition_strain -rw-r--r-- 5.2 KB
pycbc_copy_output_map -rw-r--r-- 3.0 KB
pycbc_create_injections -rw-r--r-- 8.9 KB
pycbc_dark_vs_bright_injections -rwxr-xr-x 8.7 KB
pycbc_data_store -rwxr-xr-x 1.9 KB
pycbc_faithsim -rw-r--r-- 11.0 KB
pycbc_fit_sngl_trigs -rw-r--r-- 17.0 KB
pycbc_get_ffinal -rw-r--r-- 8.8 KB
pycbc_hdf5_splitbank -rwxr-xr-x 5.8 KB
pycbc_inj_cut -rw-r--r-- 4.9 KB
pycbc_inspiral -rw-r--r-- 23.5 KB
pycbc_inspiral_skymax -rw-r--r-- 18.0 KB
pycbc_live -rwxr-xr-x 43.0 KB
pycbc_live_nagios_monitor -rw-r--r-- 2.2 KB
pycbc_losc_segment_query -rw-r--r-- 6.0 KB
pycbc_make_banksim -rw-r--r-- 17.1 KB
pycbc_make_faithsim -rw-r--r-- 12.4 KB
pycbc_make_html_page -rw-r--r-- 11.4 KB
pycbc_make_skymap -rwxr-xr-x 16.0 KB
pycbc_multi_inspiral -rwxr-xr-x 32.5 KB
pycbc_optimal_snr -rw-r--r-- 12.0 KB
pycbc_optimize_snr -rwxr-xr-x 14.0 KB
pycbc_process_sngls -rw-r--r-- 4.9 KB
pycbc_randomize_inj_dist_by_optsnr -rw-r--r-- 9.2 KB
pycbc_single_template -rwxr-xr-x 19.7 KB
pycbc_split_inspinj -rw-r--r-- 2.4 KB
pycbc_splitbank -rw-r--r-- 7.2 KB
pycbc_stageout_failed_workflow -rw-r--r-- 2.7 KB
pycbc_submit_dax -rw-r--r-- 21.9 KB
pycbc_upload_xml_to_gracedb -rwxr-xr-x 7.0 KB

back to top