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Pull master into parameter_handling #148

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merged 307 commits into from
Apr 20, 2023
Merged

Pull master into parameter_handling #148

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19dcc02
Added axes property to PDFSet to be conistent with the PDF class
martwo Apr 29, 2022
0149360
Only use valid bins for the ang_err
martwo Apr 29, 2022
7173e58
fix typo and add better error message
martwo Apr 29, 2022
cb4e9b3
Implemented new signal pdf based on the smearing matrix. It's current…
martwo Apr 29, 2022
324d943
Handle PDFs that only return prob and no gradient
martwo Apr 29, 2022
4da68ad
Handle PDFs that only return prob and no gradient
martwo Apr 29, 2022
916a3ea
Extend grid to handle the edges
martwo Apr 29, 2022
77ceccf
Fix typo
martwo Apr 29, 2022
af97753
Fix typo and format
martwo May 2, 2022
6dfd0e0
Added methods to BinningDefinition
martwo May 2, 2022
cfb9c11
Added methods
martwo May 2, 2022
aac2ce6
Use log space for the PDF ratio
martwo May 2, 2022
a18b04c
Take the effective area into account for the signal pdf
martwo May 2, 2022
ab9ed28
Use the new unionized signal pdf
martwo May 2, 2022
73c9ce1
Added method to calculate detection probability density values
martwo May 3, 2022
b296a49
Don't use log and caching for now
martwo May 3, 2022
1c423dd
Calculate signal pdf conceptionally correct
martwo May 3, 2022
29e2227
Use the probability density instead of the probability per bin
martwo May 3, 2022
d717b98
Fixed typo.
chiarabellenghi May 4, 2022
8618911
Add function to get the module and class name of a class inst
martwo May 4, 2022
b7dfe23
Call the get_prob method of the signal pdf set instance
martwo May 4, 2022
173aa05
Add logging information and use 1d phase spaces
martwo May 4, 2022
e3ec646
Merge branch 'publicdata_ps' of https://github.com/IceCubeOpenSource/…
martwo May 4, 2022
5571762
Use linear interpolation
martwo May 5, 2022
f81233e
Use the integral of the Aeff within the E_nu bin
martwo May 6, 2022
b6adb80
Separate spatial and energy signal pdfs
martwo May 10, 2022
d3bfc7a
Use Rayleigh distribution for the PSF and split spatial and energy PDFs
martwo May 11, 2022
eba9879
Improve the get detection probability method
martwo May 12, 2022
b77cc84
Improve logging
martwo May 12, 2022
4f2babd
Smooth the energy PDF
martwo May 12, 2022
84611f1
Spline the energy PDF
martwo May 13, 2022
44f9c58
Merge reco energy bins of the unionized smearing matrix
martwo May 13, 2022
5b8e9f4
Merge remote-tracking branch 'origin/master' into publicdata_ps
martwo May 25, 2022
9ce19b7
new energy pdf without unionized matrix.
chiarabellenghi May 25, 2022
bfe94d4
Bug fix.
chiarabellenghi May 25, 2022
feefd5d
Fix pdf construction for southern sky.
chiarabellenghi May 25, 2022
1f251e2
Added some documentation.
chiarabellenghi May 26, 2022
2ceb355
Added effective area weight to true neutrino energy sampling.
chiarabellenghi May 27, 2022
d25b403
Added pdf property to smearing matrix class
martwo May 27, 2022
ff3be1b
Fix pdf property
martwo May 27, 2022
a1f9ffe
Use the pdf property of the smearing matrix to build the energy pdfs.
chiarabellenghi May 27, 2022
2c76161
Removed unused bin width calculation.
chiarabellenghi May 27, 2022
0740d0e
Bug fix in the true energy pdf calculation.
chiarabellenghi May 27, 2022
e6e5780
Add zero background prob detection
martwo May 27, 2022
a3fdba8
Use debug message
martwo May 27, 2022
c031841
Changed from pdf to probability per bin for the true neutrino energy.
chiarabellenghi May 27, 2022
2e24aef
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
chiarabellenghi May 27, 2022
4926a9d
Changed variables name.
chiarabellenghi May 27, 2022
288090d
Improve error message
martwo Jun 7, 2022
540b00e
Add method to generate the pdf key
martwo Jun 8, 2022
36e33ca
Adding logging information
martwo Jun 8, 2022
b17fe89
Simplify dataset definition
martwo Jun 8, 2022
20dcac4
Construct the p(E_reco|E_nu) PDF for the entire reco energy range.
martwo Jun 8, 2022
1f4ff58
Add feature to cap the enegry PDF ratio
martwo Jun 8, 2022
023a64c
Add feature to cap the enegry PDF ratio
martwo Jun 8, 2022
257b8a2
Merge remote-tracking branch 'origin/master' into publicdata_ps
martwo Jun 8, 2022
40a6248
Added script to generate MCeq fluxes
martwo Jun 13, 2022
37f4147
Removed psi floor related to the kde analysis.
chiarabellenghi Jun 14, 2022
de39de3
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
chiarabellenghi Jun 14, 2022
b727e7c
Renamed signal energy pdf classes.
chiarabellenghi Jun 14, 2022
0950e81
Add method to get the true energy bin index from the smearing matrix
martwo Jun 15, 2022
c2bb767
Limit energy range to 2 and 9
martwo Jun 15, 2022
e54779d
Define MCEq flux data files
martwo Jun 27, 2022
265ee3f
Use MCEq flux datafile definition from the dataset
martwo Jun 27, 2022
0eedadb
Add properties for the number of true_e and dec bins to smearing matrix
martwo Jun 27, 2022
42f99ff
Add file for background flux calculations
martwo Jun 27, 2022
699e7a8
Add module for effective area
martwo Jul 6, 2022
82fc3c0
commit current state of the art
martwo Jul 6, 2022
314a5e2
Be inclusive
martwo Jul 8, 2022
3758192
Fix doc strings
martwo Jul 8, 2022
8584a29
Some code restructuring
martwo Jul 8, 2022
4da24e2
Make all analysis modules consistent with the new effective area class.
chiarabellenghi Jul 13, 2022
2bcec68
Calculate the correct bin indices
martwo Jul 13, 2022
23a1c18
Make mceq_atm_bkg.py compatible with the new effective area class.
chiarabellenghi Jul 14, 2022
e56fd9e
Handle edges cases correctly
martwo Jul 14, 2022
c424a38
Merge branch 'publicdata_ps' of https://github.com/IceCubeOpenSource/…
martwo Jul 14, 2022
0536703
Rename directory
martwo Jul 14, 2022
7ef38ab
Rename analysis script
martwo Jul 14, 2022
9d8efcd
Correct imports
martwo Jul 14, 2022
6a8aee2
Correct imports
martwo Jul 14, 2022
39e3d56
Fix imports.
chiarabellenghi Jul 14, 2022
d45db46
Updated to new effective area properties.
chiarabellenghi Jul 28, 2022
4ff0ef0
Add bin number properties to Aeff and SM
martwo Aug 5, 2022
35cecf2
Merge branch 'publicdata_ps' of https://github.com/IceCubeOpenSource/…
martwo Aug 5, 2022
5aeb2b5
Add method to create sin_decnu_log10_enu 2D spline
martwo Aug 9, 2022
77c152b
Add property for ang_err binedges
martwo Aug 9, 2022
881ca56
Make the cumsum of the true energy inv PDF monotonically increasing
martwo Aug 11, 2022
58dbec7
Extend spline to entire enu range
martwo Aug 11, 2022
06937b7
Improve code formatting
martwo Aug 17, 2022
04071e0
Added background pdf with KDE smooting.
chiarabellenghi Aug 17, 2022
58e9c6d
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
chiarabellenghi Aug 17, 2022
50f3166
Use binning info
martwo Aug 17, 2022
0fe45d0
cleanup
martwo Aug 17, 2022
9da0493
Add bkg pdf data file definition
martwo Aug 17, 2022
405501f
Add MC background energy pdf class
martwo Aug 17, 2022
6a9d31d
Add analysis for using mc background energy pdf
martwo Aug 17, 2022
a41ad07
Generate the signal energy PDF only in the neutrino energy bins where…
chiarabellenghi Aug 31, 2022
5aa3d80
exchange PDF axes
martwo Sep 2, 2022
90aa221
Merge branch 'publicdata_ps' of https://github.com/IceCubeOpenSource/…
martwo Sep 2, 2022
b1981dc
Use the correct bin indices for the spline representation
martwo Sep 2, 2022
7b9c943
Cache smearing matrix and effective area for signal trials generation.
chiarabellenghi Sep 5, 2022
8379fff
Small changes.
chiarabellenghi Sep 5, 2022
1465445
Style changes.
chiarabellenghi Sep 5, 2022
548c8bf
Add doc string and rename arguments to more precise names
martwo Sep 5, 2022
c3610f2
Vectorize detection probability calculation function
martwo Sep 5, 2022
0df08ee
Added a minimizer implementation argument in create_analysis().
chiarabellenghi Sep 6, 2022
e1c6600
Fixed iminuit minimizer import.
chiarabellenghi Sep 6, 2022
da1143f
Add debug info
martwo Sep 6, 2022
4819c27
Calculate fill ratio value only when needed
martwo Sep 6, 2022
a74ef99
Use a finer tolerance for the minimizer to find the minimum
martwo Sep 6, 2022
eee18e5
Add sanity check for +inf pdf ratio values
martwo Sep 7, 2022
2c544e7
Support fixed-gamma flux models
martwo Sep 13, 2022
7c4d870
Create the signal energy pdf spline using the reco energy bin centers…
chiarabellenghi Sep 19, 2022
23b1c8a
Starting adding tutorial for public ps data
martwo Sep 30, 2022
fea586f
Merge branch 'publicdata_ps' of https://github.com/IceCubeOpenSource/…
martwo Sep 30, 2022
2acc2fa
Improve doc string and remove obsolete argument
martwo Oct 3, 2022
b423638
Add kwargs and pass it to underlaying function
martwo Oct 3, 2022
2f5701a
Added tutorial for public data
martwo Oct 3, 2022
cbad012
Added section about flux normalization
martwo Oct 11, 2022
d272745
Improve tutorial
martwo Oct 27, 2022
4d34155
bug fix
martwo Oct 27, 2022
2e662e6
Add disclaimer about the PS data release
martwo Oct 27, 2022
4af8149
Fix format
martwo Oct 27, 2022
b693e13
Change text
martwo Nov 3, 2022
8707f8e
Remove obsolete code for the signal energy pdf calculation.
chiarabellenghi Nov 14, 2022
6d4057d
Use correct argument name
martwo Nov 14, 2022
251b7bc
Improve logging and handle inf values
martwo Nov 14, 2022
273e08b
Merge pull request #111 from icecube/master
martwo Nov 14, 2022
f27ba68
Some error handling.
chiarabellenghi Nov 14, 2022
fad94b8
Renamed signal generator objects
chiarabellenghi Nov 14, 2022
66515aa
Merge branch 'master' into publicdata_ps
martwo Dec 8, 2022
3a14f45
First commit analysis with MC.
chiarabellenghi Dec 9, 2022
bb37675
Fix a bug where `keep_fields` argument gets overwritten when loading MC
tomaskontrimas Dec 9, 2022
0f2e905
Append `sin_dec` and `sin_true_dec` fields only when they do not alre…
tomaskontrimas Dec 9, 2022
3c215e2
Support loading mc dataset when it has different renaming dictionary …
tomaskontrimas Dec 9, 2022
768d0b2
Update comment
tomaskontrimas Dec 12, 2022
c0976f6
Add data preparation function.
chiarabellenghi Dec 20, 2022
99709c3
Effective area pre-calculation.
chiarabellenghi Jan 23, 2023
d25ba88
Update to main code restructuring.
chiarabellenghi Jan 23, 2023
aa50084
Merge branch 'master' into publicdata_ps
martwo Jan 23, 2023
1b36e9c
Merge pull request #119 from icecube/master
chiarabellenghi Feb 8, 2023
b5e706b
Fixed detection probability calculation.
chiarabellenghi Feb 8, 2023
f925113
Added some doc strings.
chiarabellenghi Feb 8, 2023
3f3244e
Construct the signal generator when the analysis is created.
chiarabellenghi Feb 8, 2023
b2a7b79
Remove prints.
chiarabellenghi Feb 8, 2023
eedd2bf
Fix for signal injection in the southern sky.
chiarabellenghi Feb 9, 2023
5dbfd76
Small fix for error handling.
chiarabellenghi Feb 9, 2023
1088ac6
Some restructuring.
chiarabellenghi Feb 9, 2023
a52dbc7
Bug fix and renaming.
chiarabellenghi Feb 9, 2023
5b4a435
Comment out outdated code for the signal energy pdf.
chiarabellenghi Feb 9, 2023
febf59a
Clean up.
chiarabellenghi Feb 9, 2023
aee77f5
Bug fix.
chiarabellenghi Feb 10, 2023
86d2020
Added dataset definition for analysis with unbinned MC.
chiarabellenghi Feb 16, 2023
6a62de9
added keywords for ns_max, gamma_min, and gamma_max in create_analysis
mskarl Feb 20, 2023
4789bf7
Merge pull request #122 from icecube/publicdata_martina_changed_5_lines
mskarl Feb 20, 2023
0910e2a
added ns_min, ns_max, gamma_min, gamma_max to the docstring in create…
mskarl Feb 21, 2023
7223e63
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
mskarl Feb 21, 2023
dc389cf
minor changes for compatibility with newer numpy versions (#123)
mskarl Mar 8, 2023
4065fe2
Fix #108 (#126)
martwo Mar 8, 2023
dc58832
Fix #108 (#127)
martwo Mar 8, 2023
d0daa9e
implementation of single dataset time dependence
mskarl Mar 14, 2023
b7b2736
fixed small bug in box pdf
mskarl Mar 15, 2023
404a345
time dependent signal injection
mskarl Mar 15, 2023
478ed4b
time dependent signal injection
mskarl Mar 15, 2023
476da47
Merge branch 'publicdata_ps_time_dependent' of github.com:icecube/sky…
mskarl Mar 15, 2023
8566a69
made signal generation more fool proof
mskarl Mar 15, 2023
4ba9c9e
split trad_ps.py in two files
mskarl Mar 30, 2023
0bce342
included expectation maximization in the time dependent analysis
mskarl Mar 30, 2023
24db698
Merge pull request #134 from icecube/publicdata_ps_time_dependent
chiarabellenghi Mar 30, 2023
409a3f2
Fixing issues #130, #131 and #132.
chiarabellenghi Mar 30, 2023
361ca69
Remove redundant analysis script.
chiarabellenghi Mar 30, 2023
c4d6d45
Moved the energy cut splines to
chiarabellenghi Mar 31, 2023
a5ac60c
Fix #125.
chiarabellenghi Mar 31, 2023
be46728
Merge branch 'master' of github.com:icecube/skyllh into publicdata_ps
tomaskontrimas Mar 31, 2023
d5c8a98
Update .gitignore
chiarabellenghi Apr 3, 2023
03901b2
Update doc/user_manual.tex
chiarabellenghi Apr 3, 2023
9342cbe
Update skyllh/analyses/i3/publicdata_ps/bkg_flux.py
martwo Apr 3, 2023
1ce1cda
Update backgroundpdf.py
chiarabellenghi Apr 3, 2023
d0531c6
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
chiarabellenghi Apr 3, 2023
e6f693d
Update detsigyield.py
chiarabellenghi Apr 3, 2023
11e5b12
Update skyllh/analyses/i3/publicdata_ps/bkg_flux.py
martwo Apr 3, 2023
0a15362
Clean PublicData_10y_ps_wMC.py
chiarabellenghi Apr 3, 2023
075750f
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
chiarabellenghi Apr 3, 2023
2c46722
Update skyllh/core/storage.py
chiarabellenghi Apr 3, 2023
f959389
Update skyllh/core/storage.py
chiarabellenghi Apr 3, 2023
5393704
Update utils.py
chiarabellenghi Apr 3, 2023
8af0d59
Update skyllh/core/signalpdf.py
mskarl Apr 3, 2023
b4d6dd1
Update skyllh/core/signalpdf.py
mskarl Apr 3, 2023
39a1580
Update skyllh/core/signalpdf.py
mskarl Apr 3, 2023
394f449
Update skyllh/core/signalpdf.py
mskarl Apr 3, 2023
12d1e09
Update skyllh/core/signalpdf.py
mskarl Apr 3, 2023
24417bb
Update skyllh/analyses/i3/publicdata_ps/expectation_maximization.py
mskarl Apr 3, 2023
058cc98
Update skyllh/analyses/i3/publicdata_ps/expectation_maximization.py
mskarl Apr 3, 2023
1ffd1ae
Update skyllh/analyses/i3/publicdata_ps/expectation_maximization.py
mskarl Apr 3, 2023
de1b5f1
Update skyllh/analyses/i3/publicdata_ps/expectation_maximization.py
mskarl Apr 3, 2023
1edb1f9
Update skyllh/analyses/i3/publicdata_ps/time_dependent_ps.py
mskarl Apr 3, 2023
a73d561
Update skyllh/analyses/i3/publicdata_ps/signal_generator.py
mskarl Apr 3, 2023
f2ca26a
Update skyllh/analyses/i3/publicdata_ps/signal_generator.py
mskarl Apr 3, 2023
6510f86
Update skyllh/core/signalpdf.py
mskarl Apr 3, 2023
fce9f63
Double quotes for doc-string.
chiarabellenghi Apr 3, 2023
ea92f38
Update skyllh/core/analysis.py
mskarl Apr 3, 2023
956a0ea
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
chiarabellenghi Apr 3, 2023
91a451f
Apply suggestions from code review
mskarl Apr 3, 2023
e698970
Update analysis path and fix typo
tomaskontrimas Apr 3, 2023
277b495
Remove unused, commented out functions.
chiarabellenghi Apr 3, 2023
5af0143
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
chiarabellenghi Apr 3, 2023
c7b50c7
Update skyllh/analyses/i3/publicdata_ps/signalpdf.py
chiarabellenghi Apr 3, 2023
bde66a8
Apply suggestions to signalpdf.py from code review
chiarabellenghi Apr 3, 2023
16a2d85
Apply suggestions to time_integrated_ps.py from code review
chiarabellenghi Apr 3, 2023
f94605d
Apply suggestions to signal_generator.py from code review
chiarabellenghi Apr 3, 2023
f862686
Update skyllh/core/binning.py
chiarabellenghi Apr 3, 2023
622e884
Update skyllh/core/signal_generator.py
chiarabellenghi Apr 3, 2023
3d6093d
Removed unused import.
chiarabellenghi Apr 3, 2023
f5fc736
Improved documentation for the signal generator to comply with the co…
chiarabellenghi Apr 3, 2023
63e48a1
Update skyllh/datasets/i3/PublicData_10y_ps_wMC.py
martwo Apr 4, 2023
5bafaf4
Update skyllh/datasets/i3/PublicData_10y_ps.py
martwo Apr 4, 2023
4667f2c
Remove unused function
tomaskontrimas Apr 4, 2023
a75c728
Update skyllh/core/backgroundpdf.py
tomaskontrimas Apr 4, 2023
356a655
Update skyllh/analyses/i3/publicdata_ps/expectation_maximization.py
tomaskontrimas Apr 4, 2023
0b4f1f7
Rename `PublicDataSmearingMatrix` to `PDSmearingMatrix`
tomaskontrimas Apr 4, 2023
3fbe39d
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
tomaskontrimas Apr 4, 2023
7027937
Rename variables
tomaskontrimas Apr 4, 2023
12d7943
Update skyllh/analyses/i3/publicdata_ps/signal_generator.py
tomaskontrimas Apr 4, 2023
7678416
Apply suggestion based on code review by Martin
tomaskontrimas Apr 4, 2023
1b1548e
Minor changes following the code review of signalpdf.py
tomaskontrimas Apr 4, 2023
baa7987
Update skyllh/analyses/i3/publicdata_ps/signal_generator.py
tomaskontrimas Apr 4, 2023
1e047b1
Update skyllh/analyses/i3/publicdata_ps/signal_generator.py
tomaskontrimas Apr 4, 2023
f22ddcb
Remove `TimeSigOverBkgPDFRatio`
tomaskontrimas Apr 5, 2023
58f5f0d
Move expectation_maximization.py to skyllh.core
tomaskontrimas Apr 5, 2023
525238f
Refactor TimeDependentSingleDatasetSingleSourceAnalysis class as util…
tomaskontrimas Apr 5, 2023
a96eba1
Remove unused `sig_gen_list` property
tomaskontrimas Apr 5, 2023
9a79718
Remove redundant code
tomaskontrimas Apr 5, 2023
eecf3e5
Check if the pdfratio value is already cached.
chiarabellenghi Apr 6, 2023
40f4b55
Merge branch 'publicdata_ps' of github.com:icecube/skyllh into public…
chiarabellenghi Apr 6, 2023
6d50977
Fix import error and changed kwarg name
tomaskontrimas Apr 6, 2023
44904b1
Minor docstring fixes
tomaskontrimas Apr 11, 2023
b22bc9d
Add `time_pdf` and optimize time injection
tomaskontrimas Apr 11, 2023
3946064
Fix link in dataset references
tomaskontrimas Apr 11, 2023
9f865ae
Remove unused imports
tomaskontrimas Apr 12, 2023
7061347
Minor updates
tomaskontrimas Apr 12, 2023
61a3c38
Fix code width
tomaskontrimas Apr 12, 2023
d9959d9
Add explanation to docstring
tomaskontrimas Apr 12, 2023
049d838
Clean up PD data samples definitions
tomaskontrimas Apr 12, 2023
7ad80bc
Fixes #140, unifies the naming scheme for the public data scripts and…
chiarabellenghi Apr 14, 2023
a1662be
Comply with new naming scheme.
chiarabellenghi Apr 14, 2023
0630f78
Closes #124.
chiarabellenghi Apr 17, 2023
22a0eb1
Update dataset definition with MC.
chiarabellenghi Apr 17, 2023
242b6fc
Merge branch 'master' into publicdata_ps
martwo Apr 17, 2023
2e44059
Publicdata time dependent (#146)
mskarl Apr 19, 2023
a95cd6a
Merge pull request #138 from icecube/publicdata_ps
chiarabellenghi Apr 19, 2023
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1 change: 1 addition & 0 deletions doc/sphinx/tutorials/index.rst
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Expand Up @@ -8,5 +8,6 @@ Tutorials
:maxdepth: 3

getting_started
publicdata_ps
kdepdf_mcbg_ps
trad_ps_expbg
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