Richard Stiskalek
ee222cd010
Fix overlap runs ( #125 )
...
* Update nb
* Update script
* Update script
* Rename
* Update script
* Update script
* Remove warning
* Ignore minors when extracting MAH
* Fix paths bug
* Move notebooks
* Move files
* Rename and delete things
* Rename file
* Move file
* Rename things
* Remove old print statement
* Add basic MAH plot
* Add random MAH path
* Output snapshot numbers
* Add MAH random extraction
* Fix redshift bug
* Edit script
* Add extracting random MAH
* Little updates
* Add CB2 redshift
* Add some caching
* Add diagnostic plots
* Add caching
* Minor updates
* Update nb
* Update notebook
* Update script
* Add Sorce randoms
* Add CB2 varysmall
* Update nb
* Update nb
* Update nb
* Use catalogue HMF
* Move definition of radec2galactic
* Update nb
* Update import
* Update import
* Add galatic coords to catalogues
* Update nb
2024-04-08 11:23:21 +02:00
Richard Stiskalek
380c2f8df0
Stacking p(zcosmo | ... ) ( #124 )
...
* Update nb
* Add import
* Add posterior stacking
2024-04-02 11:45:18 +02:00
Richard Stiskalek
da43031877
Tests on mock PV catalogues ( #123 )
...
* Rename nb
* Add nb
* Update scrtip
* Update script
* Add reading of CB2 mocks
* CB2 mocks support
* Add mock generator
* Add mock support
* Add CB2 mock support
* Update nb for mocks
* Update script
* Update nb
* Update nbs
2024-04-02 00:19:14 +02:00
Richard Stiskalek
8e9645e202
Add p(z_cosmo | z_obs) ( #122 )
...
* Add import
* Add draft of the p(zcosmo)
* Add option for additional uncertainty
* Variable renaming
* Add zcosmo predict for flow calibration
* Add flow map notebook
* Update notebook
* Add posterior mean & std
* Edit docstring
2024-04-01 15:44:20 +02:00
Richard Stiskalek
29b37172fa
Add SFI groups ( #121 )
...
* Update LOS sampling
* Bring SD back to speed
* Update nb
* Update script
* Update requirements
* Update flow chi2 calc
* Update script
* Add support for SFI groups
* Update plot
* Update script
* Update script
2024-03-26 15:11:04 +01:00
Richard Stiskalek
27c1f9249b
Observer velocity script ( #120 )
...
* Rename script
* Delete scripts
* Add script
* Edit script
* Add script
* Update nb
* Update plotting
* Update .gitignore
* Update nb
* Update nb
* Add option to keep beta fixed
2024-03-26 10:42:53 +01:00
Richard Stiskalek
4093186f9a
Add z_obs output ( #119 )
...
* Update SN model to output zobs too
* Add TF predicted zobs
* Add imoprt
* Update nb
* Calculate chi2
* Update nb
* Update script
2024-03-22 18:10:40 +01:00
Richard Stiskalek
f7285b2600
More flow ( #118 )
...
* Add GoF calculation
* Add import
* Add base flow
* Add reading of ndata
* Update nb
* Update plotting
* Update script
* Update plots
* Updaet plo
* Add script
* Update nb
* Update nb
* Update script
* Update script
* Update nb
* Remove imports
* Improve labelling
* Improve flow calibration
* Add bulk flow plots
* Update flow
* Update scrit
* Calculate more radial steps
* Update bulk
* Update script
* Update nb
2024-03-21 16:50:37 +01:00
Richard Stiskalek
0a859a9a06
Write particles to ASCII ( #117 )
...
* Add option to output high-resolution particles only
* Add ASCII writing of simulatios
2024-03-19 09:23:52 +01:00
Richard Stiskalek
d0266584fa
CSiBORG2 subhalo catalogue ( #116 )
...
* Add import
* Add CSiBORG2 subfind catalogue
* Add parent mass
* Update nb
2024-03-18 16:37:58 +01:00
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
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
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 )
...
* 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 )
...
* Add path to CSiBORG1
* Update nb
2024-02-26 12:56:58 +00:00
Richard Stiskalek
1c736aaede
Density field tests ( #110 )
...
* 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
f0ab6fc9b4
Add TNG field ( #108 )
...
* 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
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
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
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
41c22e2166
Improve observer peculiar velocity ( #96 )
...
* Fix peculiar velocity cacl
* Move files
* Remove import
2023-12-14 00:40:07 +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
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
Richard Stiskalek
9a2188348b
Quick environmental dependence ( #90 )
...
* Improve field interpolator
* Update imports
2023-09-05 14:05:34 +01:00
Richard Stiskalek
9ae93bed14
Add dumping to ASCII of halos ( #89 )
...
* Rename file
* Add argument
* Add ASCII positions paths
* Add halo positions dumping
* Update halo catalogues
2023-09-03 12:11:39 +01:00
Richard Stiskalek
eccd8e3507
Add galaxy sampling ( #88 )
...
* Improve calculations
* Improve flags
* Add smoothed options
* Remove some old comments
* Edit little things
* Save smoothed
* Move files
* Edit imports
* Edit imports
* Renaming imports
* Renaming imports
* Sort imports
* Sort files
* Sorting
* Optionally make copies of the field
* Add quijote backup check
* Add direct field smoothing
* Shorten stupid documentation
* Shorten stupid docs
* Update conversion
* Add particles to ASCII conversion
* Add a short comment
* Add SDSS uncorrected distance
* Adjust comment
* Add FITS index to galaxies
* Remove spare space
* Remove a stupid line
* Remove blank line
* Make space separated
* Add interpolated field path
* Add field sampling
* Sort imports
* Return density in cells
* Clear out observer velocity
* Add 170817 sampling
* Fix normalization
* Update plot
2023-09-01 16:29:50 +01:00
Richard Stiskalek
0af925e26a
Minor code improvements ( #87 )
...
* Shorten docs
* Renames
2023-08-31 09:57:53 +01:00
Richard Stiskalek
ae92fd9b72
Velocity observer ( #86 )
...
* Continue if r200c not defined
* Remove smooth scale
* Remove smooth scale
* Edit Max Matching plot
* Add peculiar velocity
* Add Vobs calculation
* Edit docs
* Add Vobs plot
* Improve plotting
* Edit naming convention
* Make a note
* Add new cat options
* Update density field RSP calculation
* Update field 2 rsp
* Move functions and shorten documentation
* Improve transforms and comments
* Update docs
* Update imports
* Edit calculation
* Add docs
* Remove imports
* Add Quijote flags
* Edit documentation
* Shorten documentation
* Edit func calls
* Shorten
* Docs edits
* Edit docs
* Shorten docs
* Short docs edits
* Simplify docs a little bit
* Save plotting
* Update env
2023-08-30 23:27:20 +01:00
Richard Stiskalek
8e3127f4d9
New plots ( #85 )
...
* Update verbosity messages
* Update verbosity messags
* Update more verbosity flags
* Update the iterator settings
* Add basic plots
* Update verbosity flags
* Update arg parsre
* Update plots
* Remove some older code
* Fix some definitions
* Update plots
* Update plotting
* Update plots
* Add support functions
* Update nb
* Improve plots, move back to scripts
* Update plots
* pep8
* Add max overlap plot
* Add blank line
* Upload changes
* Update changes
* Add weighted stats
* Remove
* Add import
* Add Max's matching
* Edit submission
* Add paths to Max's matching
* Fix matching
* Edit submission
* Edit plot
* Add max overlap separation plot
* Add periodic distance
* Update overlap summaries
* Add nsim0 for Max matvhing
* Add Max's agreement plot
* Add Quijote for Max method
* Update ploitting
* Update name
2023-08-18 19:20:47 +01:00
rstiskalek
7ef36c7ac0
Add mass to name
2023-08-08 11:46:56 +01:00
rstiskalek
6ba0c04ab8
Add mass to name
2023-08-08 11:46:46 +01:00
Richard Stiskalek
c7b600d0ad
Periodic neighbours ( #84 )
...
* Edit the HMF plot
* Add periodic dist 2 points
* Add boxsize to RVSSphere
* Add periodic distance
* Adding periodic distance
* Add imports
* Change arguments
* Update bounds
* Lower min number of particles
* Change kwargs
* Add paths overlap quijote
* Add some comments
2023-08-08 12:19:40 +02:00
rstiskalek
c7e447df01
Add blank line
2023-08-07 10:38:37 +01:00
Richard Stiskalek
f4a7cb0d16
Remove halo fitting. ( #83 )
...
* Rename file
* Remove old content
* Remove halo fit
* Completely remove fits
* Add utils here
* Account for renaming
2023-08-07 11:33:27 +02:00
Richard Stiskalek
344ff8e091
Fixing overlaps and halo definitions. ( #80 )
...
* Add imports
* Refactor code
* Rename fof velocities
* Clean up and add Quijote
* Edit docstrings
* Update submission script
* Fix bug
* Start loading fitted properties
* Edit docstrings
* Update fitting for new `halo`
* Update CM definition and R200c
* Tune the minimum number of particles
* Enforce crossing threshold & tune hypers
* Fix periodiity when calculating angmom
* Doc strings
* Relax checkip
* Minor edit
* Fix old kwarg bug
* Fix CSiBORG bounds
* Catch warnings!
* Add `mass_kind` and new boundaries
2023-07-31 16:13:21 +02:00
rstiskalek
169a5e5bd7
Fix a small bug in paths
2023-07-29 09:27:45 +01:00
rstiskalek
a1141408ea
Add subselection of Quijote snapshots
2023-07-29 09:25:03 +01:00
rstiskalek
ab9002a45a
Delete unused import
2023-07-29 09:18:57 +01:00
Richard Stiskalek
5acc4684bb
Edits paths ( #79 )
2023-07-29 10:16:43 +02:00
