rstiskalek
0f94457b7f
Update nb
2024-03-16 17:16:22 +00:00
rstiskalek
0d1c262df0
Merge branch 'master' of github.com:Richard-Sti/csiborgtools
2024-03-16 17:14:03 +00:00
Richard Stiskalek
fb4abebeb6
Add more flow modelling ( #115 )
...
* Add SN calibration model
* Update imports
* Scale Carrick field
* Minor updates to flow validation
* Update script
* Update flow model
* Add CSiBORG2
* Add CSiboRG2 params
* Update imports
* Add regular grid interpolator to LOS
* Add nb
* Remove old code
* Update scripts
* Minor updates
* Minor updates
* Add TF
* Minor update
* Update notebook
* Update imports
* Add scan and loss of numpyro
* Add Pantheon
* Update svript
* Updaten b
* Add model loader
* Add jackknife
* Add evidence
* Update dr
* Add BIC to the flow model
* Update srcipt
* Update nb
* Update nb
* Update scripts
2024-03-16 17:02:00 +00:00
rstiskalek
180c2559fe
Update script
2024-03-10 11:22:35 +00:00
rstiskalek
ba2baa0081
Minor updates to flow validation
2024-03-10 11:22:29 +00:00
rstiskalek
9a3e937afd
Scale Carrick field
2024-03-10 11:20:11 +00:00
rstiskalek
5cbcdf96dd
Update imports
2024-03-10 11:19:47 +00:00
rstiskalek
088b15429b
Add SN calibration model
2024-03-10 11:19:13 +00:00
rstiskalek
b503a6f003
Add new notebook
2024-03-08 14:46:38 +00:00
rstiskalek
95af8db8e7
Delete old notebooks
2024-03-08 14:46:34 +00:00
Richard Stiskalek
a65e3cb15b
Add simple distance flow model ( #114 )
...
* Add imports
* Add field LOS paths
* Add basic flow model
* Edit script
* Add nb
* Add nb
* Update nb
* Add some docs
* Add RA reading
* Add imoprts
* Updates to the flow model
* Update script
* Bring back A2
* Update imports
* Update imports
* Add Carrick to ICs
* Add Carrick boxsize
* Add Carrick and fix minor bugs
* Add Carrick box
* Update script
* Edit imports
* Add fixed flow!
* Update omega_m and add it
* Update nb
* Update nb
* Update nb
* Remove old print statements
* Update params
* Add thinning of chains
* Add import
* Add flow validation script
* Add submit script
* Add ksmooth
* Update nb
* Update params
* Update script
* Update string
* Move where distributions are defined
* Add density bias parameter
* Add lognorm mean
* Update scripts
* Update script
2024-03-08 10:44:19 +00:00
Richard Stiskalek
fb93f85543
Make sure dumpfolder created only on rank 0
2024-02-27 13:28:41 +00:00
Richard Stiskalek
66d9f46919
Evaluate LOS distances ( #113 )
...
* Add field_los
* fix typo
* add fix bug
* bug fixes
* Add docs
* Add more docs
2024-02-27 12:40:52 +00:00
Richard Stiskalek
fc51f75e16
Add field interpolation along LOS ( #112 )
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* Add attemtp
* Add import
* Update LOS code
* Add better docstrings
* Update nb
2024-02-26 15:02:48 +00:00
Richard Stiskalek
f61429be43
Add SPH paths ( #111 )
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* Add path to CSiBORG1
* Update nb
2024-02-26 12:56:58 +00:00
Richard Stiskalek
1c736aaede
Density field tests ( #110 )
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* Add imports
* Remove file
* Add boxsize argument
* Add script
* Update script
* Edit script
* Add nbs
2024-02-26 12:36:29 +00:00
Richard Stiskalek
b88c0703f6
SPH for CSiBORG1 support ( #109 )
...
* Add edited files
* Update scripts
* Updates
* Little fix
* Little ifx
2024-02-20 12:24:58 +00:00
Richard Stiskalek
f0ab6fc9b4
Add TNG field ( #108 )
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* Add TNG catalogue script
* Add imoprt
* Add TNG box
* Add import
* Fix little bug
* Add TNG300-1
* Add shell scripts
* Organize .gitignore
* Add scatter to file name
* Add argument scatter
* Add threshold on mass
* Update nb
* Add scatter argument
* Add scattering of radial positions
* Update nb
* Update script
2024-02-07 09:11:49 +00:00
Richard Stiskalek
9e4b34f579
Overlap fixing and more ( #107 )
...
* Update README
* Update density field reader
* Update name of SDSSxALFAFA
* Fix quick bug
* Add little fixes
* Update README
* Put back fit_init
* Add paths to initial snapshots
* Add export
* Remove some choices
* Edit README
* Add Jens' comments
* Organize imports
* Rename snapshot
* Add additional print statement
* Add paths to initial snapshots
* Add masses to the initial files
* Add normalization
* Edit README
* Update README
* Fix bug in CSiBORG1 so that does not read fof_00001
* Edit README
* Edit README
* Overwrite comments
* Add paths to init lag
* Fix Quijote path
* Add lagpatch
* Edit submits
* Update README
* Fix numpy int problem
* Update README
* Add a flag to keep the snapshots open when fitting
* Add a flag to keep snapshots open
* Comment out some path issue
* Keep snapshots open
* Access directly snasphot
* Add lagpatch for CSiBORG2
* Add treatment of x-z coordinates flipping
* Add radial velocity field loader
* Update README
* Add lagpatch to Quijote
* Fix typo
* Add setter
* Fix typo
* Update README
* Add output halo cat as ASCII
* Add import
* Add halo plot
* Update README
* Add evaluating field at radial distanfe
* Add field shell evaluation
* Add enclosed mass computation
* Add BORG2 import
* Add BORG boxsize
* Add BORG paths
* Edit run
* Add BORG2 overdensity field
* Add bulk flow clauclation
* Update README
* Add new plots
* Add nbs
* Edit paper
* Update plotting
* Fix overlap paths to contain simname
* Add normalization of positions
* Add default paths to CSiBORG1
* Add overlap path simname
* Fix little things
* Add CSiBORG2 catalogue
* Update README
* Add import
* Add TNG density field constructor
* Add TNG density
* Add draft of calculating BORG ACL
* Fix bug
* Add ACL of enclosed density
* Add nmean acl
* Add galaxy bias calculation
* Add BORG acl notebook
* Add enclosed mass calculation
* Add TNG300-1 dir
* Add TNG300 and BORG1 dir
* Update nb
2024-01-30 16:14:07 +00:00
rstiskalek
0984191dc8
Fix overload I/O system
2024-01-08 16:08:43 +00:00
rstiskalek
b49cc9ebee
Update README
2024-01-08 14:56:59 +00:00
Richard Stiskalek
1dfc11e462
Scripts for CSiBORG1 SPH calculation ( #106 )
...
* Rename files
* Delet efile
* Add new submission script
* Update README
* Add submit script
* Renaming file
* Correct typos
* Update README
* Add all nsims
2024-01-08 15:43:01 +01:00
rstiskalek
655f7a733c
Update README
2024-01-08 12:59:43 +00:00
Richard Stiskalek
1a5477805a
Update evaluate density scripts ( #105 )
...
* Edit docs
* Updated interpolated field paths
* Update field sampling script
* Add comments about flipping fields
* Fix little typo
* Edit docs
* Edit hard-coded values
* Fix paths issue
* Add docs
* Switch uncorrected dist to corrected
* Improve error message
* Convert numpy int to Python int
* Add flip of x and z
* Update README
* Edit README
* Fix bug in velocity field calculation
* Fix simple bug
* Add checked axes flipping
* Fix field units
* Update README
2024-01-08 13:56:22 +01:00
Richard Stiskalek
f61f69dfab
Read merger branch ( #104 )
...
* Add support to read merger tree main branch
* Add imports
* Add trees path
* Edit processing
2024-01-04 17:56:49 +01:00
Richard Stiskalek
78443e30b5
Fix reading varysmall ( #103 )
...
* Fix paths
* Add new chains options
* Remove old imports
2023-12-22 21:46:41 +01:00
Richard Stiskalek
b4a29aea85
Add correlation module to field ( #102 )
...
* Remove file
* Add boostrap corr as a module
2023-12-22 11:21:52 +01:00
rstiskalek
d04ae6b327
Remove olf file
2023-12-21 18:35:46 +00:00
rstiskalek
119d09e26e
Update file
2023-12-21 18:35:07 +00:00
Richard Stiskalek
a08109b997
Add snapshots optionally directly to catalogue ( #101 )
...
* Add isinstance check
* Add snapshot to cat
* Rename mass_kind to mass_key
* Remove import
* Fix compatiblility
* Remove old export
* Rename import
* Fix calling
* Remove paths dependence
* Update match script
* Add check if halo has no particles
2023-12-20 16:28:26 +01:00
Richard Stiskalek
7d5141cf7f
Add comments
2023-12-20 15:19:51 +01:00
Richard Stiskalek
279022d036
Preparing RAMSES for SPH. ( #100 )
...
* Remove unused import
* Draft of preparing for SPH
* Edit script
2023-12-20 11:40:47 +01:00
Richard Stiskalek
b8863a903e
Sorting of CSiBORG2 initial snapshot ( #99 )
...
* Attempt at the sorting script
* Fix bug in CSiBORG2 sorting
* and check sstatement
* Simplify paths
* Improve paths too
* Update .gitignroe
* Just rewrite commands..
2023-12-20 11:00:26 +01:00
Richard Stiskalek
7dfc7514d2
Fix catalogues and add CSiBORG 2 catalogue support ( #98 )
...
* Add box selection to snapshot
* Edit imports
* Rename catalogue
* Add beautified catalogues
* Fix paths issue
* Create params to avoid circular import
* Add CSiBORG2 catalogue support
* Remove print statement
* Edit docs
2023-12-19 13:08:09 +01:00
Richard Stiskalek
eb1797e8a9
Clean density calculation ( #97 )
...
* Get rid of utils
* Clean up imports
* Move some utils here
* Rename file
* Add simname to boxsize
* Add imports
* Delete old files
* Update README
* Update imports
* Add a new draft of the density calculator
* Update fields
* Draft of new density field calculatiosn
* Add snapshot
* Add boxsizes
* Little updates
* Bring back utils
* Edit docstrings
* Edits imports
* Add progress on snapshots
* edit improts
* add basic snapshot catalogue
* Add support for CSiBORG2 snapshot reader
* add paths to fofcat for csiborg2
* Add more imports
* Add more boxsize
* Add more imports
* Add field readers
* Simplify field paths
* Fix typo
* Add observer vp
* Clean up density field calculation
* Add a short note
* Edit args
* Remove old comments
* Edit docs
* Remove blank line
* Stop flipping RAMSES
* Remove comment
* Edit desc
* Remove normalization
* Remove old dist array
* Remove non-volume weighting
* Remove non-volume weight
* Add ignore of flake8 notebooks
* Fix path typo
* Fix units
* Edit paths docs
* Update nb
2023-12-18 18:09:08 +01:00
Richard Stiskalek
eeff8f0ab9
Remove files that are not meant to be tracked..
2023-12-14 00:41:28 +00:00
Richard Stiskalek
41c22e2166
Improve observer peculiar velocity ( #96 )
...
* Fix peculiar velocity cacl
* Move files
* Remove import
2023-12-14 00:40:07 +00:00
rstiskalek
832d943fe7
Update not
2023-12-13 20:48:55 +00:00
rstiskalek
723ea0a38b
Update README
2023-12-13 20:43:28 +00:00
rstiskalek
2be20f763b
Add matching to no selection
2023-12-13 20:42:58 +00:00
Richard Stiskalek
506d7a7c70
Fix paths ( #95 )
...
* Fix args
* Fix paths
* Get rid of quijote backup
2023-12-13 18:03:27 +00:00
rstiskalek
963a382362
Remove old import
2023-12-13 16:20:10 +00:00
Richard Stiskalek
aaa14fc880
Add density field plot and start preparing CSiBORG2 ( #94 )
...
* Add RAMSES2HDF5 conversion
* Upload changes
* Clean up
* More clean up
* updates
* Little change
* pep9
* Add basic SPH calculation for a snapshot
* Add submit script
* Remove echo
* Little changes
* Send off changes
* Little formatting
* Little updates
* Add nthreads argument
* Upload chagnes
* Add nthreads arguemnts
* Some local changes..
* Update scripts
* Add submission script
* Update script
* Update params
* Rename CSiBORGBox to CSiBORG1box
* Rename CSiBORG1 reader
* Move files
* Rename folder again
* Add basic plotting here
* Add new skeletons
* Move def
* Update nbs
* Edit directories
* Rename files
* Add units to converted snapshots
* Fix empty dataset bug
* Delete file
* Edits to submission scripts
* Edit paths
* Update .gitignore
* Fix attrs
* Update weighting
* Fix RA/dec bug
* Add FORNAX cluster
* Little edit
* Remove boxes since will no longer need
* Move func back
* Edit to include sort by membership
* Edit paths
* Purge basic things
* Start removing
* Bring file back
* Scratch
* Update the rest
* Improve the entire file
* Remove old things
* Remove old
* Delete old things
* Fully updates
* Rename file
* Edit submit script
* Little things
* Add print statement
* Add here cols_to_structured
* Edit halo cat
* Remove old import
* Add comment
* Update paths manager
* Move file
* Remove file
* Add chains
2023-12-13 16:08:25 +00:00
Richard Stiskalek
6042a87111
Update README
2023-12-08 12:41:02 +00:00
Richard Stiskalek
944fea5510
Remove old merger tree ( #93 )
...
* Edit docs
* Delete merger tree files
* Edit README
* Edit docs
2023-12-07 14:45:06 +00:00
Richard Stiskalek
e972f8e3f2
Add pynbody and other support ( #92 )
...
* Simplify box units
* Move old scripts
* Add printing
* Update readers
* Disable boundscheck
* Add new ordering
* Clean up imports
* Enforce dtype and add mass to quijote
* Simplify print statements
* Fix little typos
* Fix key bug
* Bug fixing
* Delete boring comments
* Improve ultimate clumps for PHEW
* Delete boring comments
* Add basic reading
* Remove 0th index HID
* Add flipping of X and Z
* Updates to halo catalogues
* Add ordered caching
* Fix flipping
* Add new flags
* Fix PHEW empty clumps
* Stop over-wrriting
* Little improvements to angular neighbours
* Add catalogue masking
* Change if-else statements
* Cache only filtered data
* Add PHEW cats
* Add comments
* Sort imports
* Get Quijote workign
* Docs
* Add HMF calculation
* Move to old
* Fix angular
* Add great circle distance
* Update imports
* Update impotrts
* Update docs
* Remove unused import
* Fix a quick bug
* Update compatibility
* Rename files
* Renaming
* Improve compatiblity
* Rename snapsht
* Fix snapshot bug
* Update interface
* Finish updating interface
* Update all paths
* Add old scripts
* Add basic halo
* Update imports
* Improve snapshot processing
* Update ordering
* Fix how CM positions accessed
* Add merger paths
* Add imports
* Add merger reading
* Add making a merger tree
* Add a basic merger tree reader
* Add imports
* Add main branch walking + comments + debuggin
* Get tree running
* Add working merger tree walking along main branch
* Add units conversion for merger data
* Add hid_to_array_index
* Update merger tree
* Add mergertree mass to PHEWcat
* Edit comments
* Add this to track changes...
* Fix a little bug
* Add mergertree mass
* Add cache clearing
* Improve summing substructure code
* Littbe bug
* Little updates to the merger tree reader
* Update .giignore
* Add box selection
* Add optional deletingf of a group
* add to keep track of changes
* Update changes
* Remove
* Add manual tracker
* Fix bug
* Add m200c_to_r200c
* Add manual halo tracking
* Remove skipped snapshots
* update cosmo params to match csiborg
* remove old comments
* Add SDSSxALFALFA
* Fix bugs
* Rename
* Edit paths
* Updates
* Add comments
* Add comment
* Add hour conversion
* Add imports
* Add new observation class
* Add selection
* Add imports
* Fix small bug
* Add field copying for safety
* Add matching to survey without masking
* Add P(k) calculation
* Add nb
* Edit comment
* Move files
* Remove merger import
* Edit setup.yp
* Fix typo
* Edit import warnigns
* update nb
* Update README
* Update README
* Update README
* Add skeleton
* Add skeleton
2023-12-07 14:23:32 +00:00
Richard Stiskalek
5500fbd2b9
Matching paper plots ( #91 )
...
* Fix calculations of expected mass
* Add paper plots
* Edits to pltos
* Add overlap summary
* Add imports
* Add import
* Add binned stat
* Add fit
* Add more plots
* Add basic env
* Add histogram mode
* Edit expected mass
* Improve expected plots
* Clean up plot
* Improve separation plot
* Update plots
* Edit expected calculation
* Update plotting
* Update plots
* Update plots
* Update plots
* Add conc fraction
* Add halo maker sorting
* Renaming
* Add import
* Add NaN treatment
* add import
* Move cosine smi
* Update plots
* Move similarity
* Fix little bugs
* Shorten documentation
* Update plots
2023-10-17 12:11:15 +01:00
rstiskalek
136c552369
Update dumping
2023-09-05 14:55:31 +01:00
rstiskalek
a63b51bef1
Edit pos
2023-09-05 14:14:28 +01:00
Richard Stiskalek
9a2188348b
Quick environmental dependence ( #90 )
...
* Improve field interpolator
* Update imports
2023-09-05 14:05:34 +01:00
