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
506d7a7c70
Fix paths ( #95 )
...
* Fix args
* Fix paths
* Get rid of quijote backup
2023-12-13 18:03:27 +00:00
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
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
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
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
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
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
ab8199be2c
Rename folder
2023-05-08 14:24:15 +01:00
Richard Stiskalek
f48eb6dcb0
Dump radial profile information ( #48 )
...
* add radial position path
* pep8
* Add basic fit profile dumping
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* Update TODO
* Fix parts is None bug
* Update nb
2023-04-27 00:18:30 +01:00
Richard Stiskalek
2e99b901ac
Environmental properties ( #20 )
...
* rm get_positions
* Add comment
* add halfwidth func
* Update docs
* Add imprt
* Evaluate multiple fields simulatenously
* add halfwidth selection
* Change order of grav field and tensor field
* Add gravitational field norm
* Add eigenvalue calculation
* Sorted eigenvalues
* add init script
* add progress
* Add surveys
* Add more survey flexibility
* Minor changes
* add survey names
* rm name
* Fix list bug
* Fig bugs when running the script
* add phi to dtype
* fix dump bug
* Add comment
* Add smoothing options
* Add further comment
* Update TODO
2022-12-31 17:46:05 +00:00
Richard Stiskalek
1bb4255874
SDSS galaxies and catalogs rework ( #15 )
...
* add SDSS skeleton
* rm nb
* update gitignore
* add docs
* add survey volume
* add masking
* add SDSS mask
* add SDSS comments
* add reference
* rm
* move planck to fits clusters
* Rm comment
* update masking routines
* rm masks
* Update docs
* rm data
* make MCXC fits surv
* change MCXC name
* Move to extrasapce
* Update paths
2022-12-05 11:36:41 +00:00
Richard Stiskalek
c748c87e45
New filesystem, basic neighbours calculation ( #10 )
...
* simplify Planck catalogue
* add MCXC and base survey
* Add 2MPP classes
* move match to MCXC to Planck
* add halo catalogue
* rm comment
* rm unused imports
* Move conversion to box
* add min mass
* Run on all simulations
* rm old function
* add combined catalogue
* add halo positions
* add knn neighbors
* set to 5 sims for testing
* add docstring
* Switch to neighbours in a catalogue
* rename io to read
* fix indentation
* rename to read
* io -> read
* add import
* add RealisationMatcher
* io -> read
* add docstrings
* add search_sim_indiices
* update todo
* keep make_cat at 10 for now
* update nb
2022-11-22 10:00:01 +00:00
rstiskalek
3352b06c1c
add units
2022-11-20 14:11:25 +00:00
Richard Stiskalek
17badf2652
X-ray data ( #9 )
...
* add xray reading
* add import
* add more comments
* add data
* add nb
* add MCXC shortcut
* add match indxs to Planck of MCXC
* add import
* update TODO
* update readme
* add famous clusters
* add 2mpp_groups
* shorten paths
* add 2M++ groups
* add import
* Update TODO
2022-11-10 07:40:44 +00:00
rstiskalek
d69012424e
simplify loading
2022-11-06 20:55:49 +00:00
Richard Stiskalek
d32eb5c134
Data loading shortcut ( #7 )
...
* add load_processed
* update TODO
2022-11-06 10:26:24 +00:00
Richard Stiskalek
8a56c22813
Within halo work and NFW fit ( #4 )
...
* add listing of snapshots
* change distance to comoving
* ignore cp files
* rename nb
* add str to list
* add NFW profile shapes
* add fits imports
* Rename to Nsnap
* in clumps_read only select props
* make clumpid int
* expand doc
* add import
* edit readme
* distribute halos
* add profile & posterior
* add import
* add import
* add documentation
* add rvs and init guess
* update todo
* update nb
* add file
* return end index too
* change clump_ids format to int32
* skeleton of dump particle
* update nb
* add func to drop 0 clump indxs parts
* add import
* add halo dump
* switch to float32
* Update TODO
* update TODO
* add func that loads a split
* add halo object
* Rename to clump
* make post work with a clump
* add optimiser
* add Nsplits
* ignore submission scripts
* ignore .out
* add dumppath
* add job splitting
* add split halos script
* rename file
* renaem files
* rm file
* rename imports
* edit desc
* add pick clump
* add number of particles
* update TODO
* update todo
* add script
* add dumping
* change dumpdir structure
* change dumpdir
* add import
* Remove tqdm
* Increase the number of splits
* rm shuffle option
* Change to remove split
* add emojis
* fix part counts in splits
* change num of splits
* rm with particle cut
* keep splits
* fit only if 10 part and more
* add min distance
* rm warning about not set vels
* update TODO
* calculate rho0 too
* add results collection
* add import
* add func to combine splits
* update TODO
* add extract cols
* update nb
* update TODO
2022-10-30 20:16:56 +00:00
rstiskalek
a47847cb7c
more renaming
2022-10-20 23:37:33 +01:00
Richard Stiskalek
942c36b142
Box units conversion ( #3 )
...
* linting
* fix long line
* rename nb
* rename import
* add group catalog
* move imports out of functions
* add array_to_structured
* add references
* fix subsampling
* fix coord bug
* add 2M++ dists
* save nb
* fix comment
* add snapshot path
* add snapshot path
* add read_info
* Move transforms
* add import radec
* expand docs
* Move flipcols
* update nb
* add flip_cols
* create file
* add blank line
* Move units transfs
* add blank line
* add units import
* rm imports
* add import
* add box_units
* add comments
2022-10-20 23:28:44 +01:00
Richard Stiskalek
53a0629d90
Basic matching ( #2 )
...
* add recarray manipulations
* add cart to radec
* add behav so x can be a list
* add import
* create empty files
* ignore plots file
* add planck data
* add read_mmain file
* add cols_to_structured import
* use cols_to_structured
* add cols_to_structued
* add read_mmain import
* add reading planck
* add mass conversion
* add brute force separation calculation
* update nb
* rename & int dtype
* add func to get csiborg ids
* add list to nd array conversion
* add utils
* rename file
* add 2M++
* add read 2mpp
* add 2mpp shortcut
* add randoms generator
* Change range of RA [0, 360]
* fix ang wrapping
* add code for sphere 2pcf
* rm wrapping
* optionally load only a few borgs
* update nb
2022-10-18 19:41:20 +01:00
