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
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
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
rstiskalek
723ea0a38b
Update README
2023-12-13 20:43:28 +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
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
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
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
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
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
Richard Stiskalek
acb8d9571c
Update units to be consistent. ( #78 )
...
* Fix Quijote units
* Updates to units
* Fix how things are loaded
* Updating definitions & conventions
* Clear up how fiducial observers in quijote work
* Refactorize array manip
* Move function definition
* More code refactoring
* Remove unused argument
* Remove `convert_from_box`
* Make a note
* Converting particle units
* Add notes about units
* Remove box constants
* Add rho_crit0
* Fix spherical overdensity mass units
* Refactor more code
* Edit catalogue kwargs
* Edit the docstring
* Edit bounds
* Add new checks for empty array
* Remove unused import
* Remove old code
* Remove old function
* Update real 2 redshift
* Clear up the RSP conv
* Add comments
* Add some units
2023-07-28 21:07:28 +02:00
Richard Stiskalek
fb4b4edf19
Quijote snapshots support ( #77 )
...
* Renaming
* Edit docs
* Delete old function
* Add a blank space
* Rename particle reader
* Add comments
* Rename
* Rename
* edit get_snapshots
* More renaming
* Remove old correction
* Add import
* Add basics of the Quijote reader
* Add a blank space
* Fix paths
* Rename function
* Fix HID and path
* Add more FoF reading
* Move definition
* Adding arguments
* Renaming
* Add kwargs for backward comp
* FoF Quijote return only hids
* Add sorting of quijote
* Add path to CSiBORG ICs snapshot
* Add support for Quijote
* initmatch paths for quijote
* Add kwargs
* Fix blank lines
* Rename kwarg
* Remove unused import
* Remove hardcoded numbers
* Update for Quijote
* Do not store velocities in QUijote ICs
* Box units mass Quijote
* Fix typo
* Ensure particles are not right at the edge
* Add structfit paths for QUuijote
* Basic CSiBORG units
* Add more quijote halo reading
* Add Quijote fitting
* Docs changes
* Docs changes
2023-07-27 18:41:00 +02:00
Richard Stiskalek
eb8d070fff
CSiBORG FoF switch ( #75 )
...
* Add moving FoF membership files
* add FoF membership path
* Add notes where its PHEW
* Add FoF catalogue path
* Correct typo
* Add more functionalities
* Make work with halo IDs from FoF
* Edit print statement
* Fix copy bug
* copy
* Add FoF catalogue reading
* Clean up script
* Fix typo
* Little edits
* Fix naming convention
* Rename key
* Remove loading substructure particles
* Rename CSiBORG Cat
* Rename clumps cat
* Rename cat
* Remove misplaced import
* Switch to halos
* rm import
* structfit of only halos
* Add FoF halo reading
* Add a short comment
* Fix __getitem__ to work with int
* Fix problems
* Improve __getitem__
* Add more conversion
* Fix indexing
* Fix __getitem__ assertion
* Fix numbers
* Rename
* Fix verbosity flags
* Add full Quijote HMF option
* Add plot of Quijote only
* Add quijote full paths
* Fix the fit_init script
* Renam arg
* Update .gitignore
* add default argument name
* Change default verbosity flag
* Modernise script structure
* Fix dictionary
* Fix reading to include m200c
* Modernise script
* Add args
2023-07-24 14:10:21 +02:00
rstiskalek
fcd1a6b321
Remove comments
2023-07-03 15:37:22 +01:00
Richard Stiskalek
28e93e917f
More plotting ( #74 )
...
* Add a new plot
* Add a binned trend
* Fix bug
* Improve plot further
* Add new plotting
* add max overlap
* edit get_overlap
* Add max overlap plot
* Update plot
* Add max overlap key
* add max dist flag
* Improve plotting
2023-07-03 15:35:10 +01:00
Richard Stiskalek
fbf9c2a4b7
Better plots ( #73 )
...
* Edits paths of saved files
* Add upper threshold options
* Add upper threshold options
* add latex_float option
* Add weighted stats
* add new plot
2023-06-28 15:22:42 +01:00
Richard Stiskalek
de7def61d5
New RSP density distinction ( #72 )
...
* Edit docs
* Fix kernel units
* Add NGP interpolation
* Add Vobs but not implemented
* Add BORG density option
* Add BORG mcmc path
* Organise imports
* Add new density field distinction
2023-06-26 20:41:07 +01:00
Richard Stiskalek
cd6d448874
Update plotting ( #71 )
2023-06-23 15:31:48 +01:00
Richard Stiskalek
27e1c181a2
Moving environment to RS ( #70 )
...
* Drag several fields at once
* add env in RSP
* Add docstrings
* Make __main__
* Fix bug
* Fix plotting little bug
2023-06-18 11:42:21 +01:00
Richard Stiskalek
35ccfb5c67
New matches ( #69 )
...
* Remove old file
* Add velocity plotting
* add smooth scale
* Fix bug
* Improve paths
* Edit plotting
* Add smoothed density
* Update boundaries
* Add basics
* Further docs
* Remove blank
* Better catalog broadcasting
* Update high res size
* Update plotting routines
* Update routine
* Update plotting
* Fix field saving name
* Add better colormap for environemnt
2023-06-17 19:52:26 +01:00
Richard Stiskalek
73687fd8cc
Add comment
2023-06-16 20:57:07 +01:00
Richard Stiskalek
cbfd1cbc99
Fixing tidal field calculation ( #68 )
...
* Add import
* Fix tidal calculation
* Add env to paths
* Improve plot routines
* Add env classification
2023-06-16 18:31:43 +01:00
Richard Stiskalek
ccbbbd24b4
Add better diagnostics & plotting ( #67 )
...
* Add caching functions
* Add limts
* Add new mass runs
* Update .gitignore
* Edit which CDFs are loaded
* Stop saving cross hindxs
* Change dist to half precision
* New nearest path
* Add neighbour counting
* Add neighbour kwargs
* Update work in progress
* Add new counting
* Add how dist is built
* Collect dist to 1 file
* Update reading routine
* Delete Quijote files
* Remove file
* Back to float32
* Fix bugs
* Rename utils
* Remove neighbuor kwargs
* Rename file
* Fix bug
* Rename plt utils
* Change where nghb kwargs from
* line length
* Remove old notebooks
* Move survey
* Add white space
* Update TODO
* Update CDF calculation
* Update temporarily plotting
* Merge branch 'add_diagnostics' of github.com:Richard-Sti/csiborgtools into add_diagnostics
* Start adding documentation to plotting
* Remove comments
* Better code documentation
* Some work on tidal tensor
* Better plotting
* Add comment
* Remove nb
* Remove comment
* Add documentation
* Update plotting
* Update submission
* Update KL vs KS plots
* Update the plotting routine
* Update plotting
* Update plotting routines
2023-06-16 14:33:27 +01:00
rstiskalek
004d9629a2
Add better colorbar
2023-06-06 08:41:39 +01:00
rstiskalek
70b173ccc5
Edit plotting routine
2023-06-05 22:29:51 +01:00
rstiskalek
524434c7de
Small updates
2023-06-05 22:28:37 +01:00
Richard Stiskalek
63b6cdbe72
Forward model fields to RSP ( #66 )
...
* Add radial velocity field
* Add overdensity plot
* Flip velocities too
* Add field calculations
* Add RSP mapping
* Add potential in RSP
* Add projected field plotting
2023-06-05 17:24:20 +02:00
rstiskalek
f7b8b782a0
Add note
2023-06-02 12:51:34 +01:00
rstiskalek
060ccf4feb
Fix labels
2023-06-02 12:48:38 +01:00
rstiskalek
ed47d77dc1
Fix label
2023-06-02 11:53:29 +01:00
rstiskalek
d5b14ebd97
Add sky map
2023-06-01 22:57:55 +01:00
Richard Stiskalek
dbf93b9416
Lagrangian patch + HMF calculation ( #65 )
...
* Rename lagpatch
* Fix old bug
* Fix small bug
* Add number of cells calculation
* Fix a small bug
* Rename column
* Move file
* Small changes
* Edit style
* Add plot script
* Add delta2ncells
* Add HMF calculation
* Move definition around
* Add HMF plot
* pep8
* Update HMF plotting routine
* Small edit
2023-06-01 14:45:52 +01:00
Richard Stiskalek
f1dbe6f03f
Add plotting ( #64 )
...
* Add verbosity statements
* More verbosity
* Save masses too
* Add CDF new plot
* Blank line
* Fix RVS sampling bug
* Add R200 conversion
* Simplify plotting routines
* Remove imoprt
2023-05-27 00:08:39 +01:00
rstiskalek
7c2d7a86f5
Merge plotting scritps
2023-05-25 15:54:24 +01:00
rstiskalek
48cd5da88c
Add KL vs KS plot
2023-05-25 15:47:15 +01:00
rstiskalek
371b4bd057
Update plotting routines
2023-05-24 11:25:22 +01:00
rstiskalek
14dc8f85af
Edit xlabel
2023-05-22 13:42:48 +01:00
rstiskalek
10b355954b
Add 1NN histogram
2023-05-22 13:42:10 +01:00
rstiskalek
9b4c02f3b0
pep8
2023-05-21 22:47:09 +01:00
Richard Stiskalek
2185846e90
CDF for nearest neighbour ( #63 )
...
* Updat ebounds
* fix mistake
* add plot script
* fix which sims
* Add Poisson
* Just docs
* Hide things to __main__
* Rename paths
* Move old script
* Remove radpos
* Paths renaming
* Paths renaming
* Remove trunk stuff
* Add import
* Add nearest neighbour search
* Add Quijote fiducial indices
* Add final snapshot matching
* Add fiducial observer selection
* add boxsizes
* Add reading functions
* Little stuff
* Bring back the fiducial observer
* Add arguments
* Add quijote paths
* Add notes
* Get this running
* Add yaml
* Remove Poisson stuff
* Get the 2PCF script running
* Add not finished htings
* Remove comment
* Verbosity only on 0th rank!
* Update plotting style
* Add nearest neighbour CDF
* Save radial distance too
* Add centres
* Add basic plotting
2023-05-21 22:46:28 +01:00
rstiskalek
369438f881
Correct limits
2023-05-16 00:13:44 +01:00
Richard Stiskalek
255bec9710
Quijote kNN adding ( #62 )
...
* Fix small bug
* Add fiducial observers
* Rename 1D knn
* Add new bounds system
* rm whitespace
* Add boudns
* Add simname to paths
* Add fiducial obserevrs
* apply bounds only if not none
* Add TODO
* add simnames
* update script
* Fix distance bug
* update yaml
* Update file reading
* Update gitignore
* Add plots
* add check if empty list
* add func to obtaining cross
* Update nb
* Remove blank lines
* update ignroes
* loop over a few ics
* update gitignore
* add comments
2023-05-15 23:30:10 +01:00
