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
rstiskalek
8f3220bff7
Update dumping
2023-09-05 10:36:15 +01:00
rstiskalek
f135a69b40
Little bug
2023-09-04 14:27:14 +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
ca3772ac6f
Make copy
2023-08-08 12:15:59 +01:00
rstiskalek
36f4177f6b
Add some blank spaces
2023-08-08 11:48:31 +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
rstiskalek
ff395af148
Little changes to plotting
2023-08-04 09:26:28 +01:00
Richard Stiskalek
99d0232d7d
Update plots ( #82 )
2023-07-31 21:44:58 +02:00
rstiskalek
46848a86eb
Edit docs
2023-07-31 20:23:56 +01:00
rstiskalek
f21abc28e7
Add lower and upper limits
2023-07-31 20:13:10 +01:00
