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
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
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
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
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
616b903aec
Remove nb
2023-05-15 23:32:42 +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
rstiskalek
7971fe2bc1
update nbs
2023-05-14 12:48:24 +01:00
Richard Stiskalek
1d847cbd06
Add Quijote ( #61 )
...
* Rename paths object
* Remove redshift calculation
* Explicit keywrod arg
* Rename box units
* Basic renaming
* Little docs
* Rename paths
* add imports
* Sort imports
* Add Quijote cat
* Split boxes
* add Quijote path
* Add origin argument
* Update nbs
2023-05-13 17:37:34 +01:00
Richard Stiskalek
b3fd14b81f
Gravitational potential calculation ( #60 )
...
* Rename file
* add velocity field
* Add velcoity field
* Move smoothening
* Add verbosity flags
* remove blank
* Simplify paths
* Add potential calculation
* Update paths
* Add potential field
* Add potential calculation
* Move away sky matching
* Move interpolation functions
* Update nbs
2023-05-12 13:07:58 +01:00
Richard Stiskalek
b710b8e89c
Add new ICs ( #59 )
...
* edit IC paths
* Remove import
* Edit path
* Change naming
* Add __main__
* Script to match everything
* Edit docs
* Remove test statement
* Move import
* Update nb
2023-05-09 16:18:01 +01:00
Richard Stiskalek
cb5d35b1be
Density field calculation ( #58 )
...
* Add iterative density field generation
* Edit particle halfwidth selection
* Update import
* Remove old file
* Add position wrapping
* Add RSD support
* Add density field calculation
* Edit paths to the density field
* Flip argument order
* Edit documentation
* Edit docs
* update nb
2023-05-08 14:02:20 +01:00
Richard Stiskalek
65564849f4
Add redshift space position ( #55 )
...
* Add docs
* Delete blank
* Add real to redshift space function
* RSD move back observer
* Convert velocoties to km/s
* Add units to RSP calculation
* Add RSP to catalogues
* Add RSD to angular neighbour search
2023-05-07 19:07:35 +01:00
Richard Stiskalek
56e39a8b1d
Overlapper improvements ( #53 )
...
* Store indices as f32
* Fix init sorting
* Organise imports
* Rename pathing
* Add particle loading
* Improve particle reading
* Add h5py reader
* edit particle path
* Update particles loading
* update particles loading
* Fix particle dumping
* Add init fitting
* Fix bug due to insufficient precision
* Add commnet
* Add comment
* Add clumps catalogue to halo cat
* Add comment
* Make sure PIDS never forced to float32
* fix pid reading
* fix pid reading
* Update matching to work with new arrays
* Stop using cubical sub boxes, turn off nshift if no smoothing
* Improve caching
* Move function definitions
* Simplify calculation
* Add import
* Small updates to the halo
* Simplify calculation
* Simplify looping calculation
* fix tonew
* Add initial data
* Add skip condition
* Add unit conversion
* Add loading background in batches
* Rename mmain index
* Switch overlaps to h5
* Add finite lagpatch check
* fix column name
* Add verbosity flags
* Save halo IDs instead.
* Switch back to npz
* Delte nbs
* Reduce size of the box
* Load correct bckg of halos being matched
* Remove verbosity
* verbosity edits
* Change lower thresholds
2023-05-06 16:52:48 +01:00
Richard Stiskalek
c14be720b5
Particle dumping ( #49 )
...
* Add paths
* Add dumping script
* Remove snap from density fields
* Add progress statement
* Update import ordering
* Update nb
2023-04-28 13:57:23 +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
04119a5314
Update initial matching & overlaps ( #47 )
...
* pep8
* fix convention
* Update script
* enforce optimisation boundaries to be finite
* Update TODO
* Remove sky matching
* FIx a small bug
* fix bug
* Remove import
* Add halo fitted quantities
* Update nbs
* update README
* Add load_initial comments
* Rename nbs
* Delete nb
* Update imports
* Rename function
* Update matcher
* Add overlap paths
* Update the matching script
* Update verbosity
* Add verbosity flags
* Simplify make_bckg_delta
* bug fix
* fix bug
2023-04-21 01:35:06 +02:00
Richard Stiskalek
39b3498621
Correct fitting script for both clumps and halos ( #46 )
...
* Minor typos
* fix minor bugs
* pep8
* formatting
* pep8
* Fix minor bugs
* New path & pep8
* add splitt
* Updates
* Improve calculation within radius
* pep8
* pep8
* get the script working
* Add matter overdensity
* Add m200m to the script
* Fix looping bug
* add parents support
* add import
* Optionally concatenate velocities
* Make optional masking
* Ignore the error message
* Start reading in raw data
* Fix cat reading
* Additional units conversions
* Add clump reading
* Fix indexing
* Remove old comment
* Remove old comment
* set npart to 0 instead of overflow from NaN
* fix docs
* rm boring stuff
* Remove old stuff
* Remove old stuff
* Remove old comment
* Update nb
2023-04-19 16:39:35 +02:00
Richard Stiskalek
c2fde1566b
Cluster rough angular match ( #45 )
...
* Remove sim dump
* Remove unused things
* Remove warning
* Fix coordinate transforms
* Add imports
* Update coordinate transfers
* Add angular neighbours calculation
* Update nb
2023-04-18 18:49:21 +02:00
Richard Stiskalek
fdb0df8d4c
Add mmain and other major updates ( #44 )
...
* Move paths to a separate file
* Add mmain reader
* Add a verbosity flag
* Fix imports
* Fix bug
* Rename files
* Return ultimate parents
* Add script to generate mmain
* Remove mmain path
* edit path
* Add mmain path
* Change function name
* Rename function
* Turn off verbose
* Fix list requirement
* Edit init match paths
* Fix init pathing
* Edit paths docs
* Edit dumpdir name
* Rename path
* Fix split paths
* Remove unused import
* Add comment
* Update readme
* remove read mmain
* Rename haloatalogue
* Fix minor bugs
* Update nbs
* Add create directory option
* Move split jobs
* Move spliot jobs
* Remove splitting
* Add import
* Edit script
* Deeper split folder
* Fix paths bug
* Rename catalogue
* Rename Catalogue
* Add new clumpread
* Edit paths
* add knn paths
* Update commenting
* Update imports
* Add more conversions
* Update temp file
* Add a note
* Add catalogue
* Cooment
* Update TODO
* Update script
* add nb
* Update
* pep8
* edit paths & pep8
* Fix knn auto paths
* add paths docs
* Add auto and cross knn paths
* Add new paths
* Simplify tpcf reading
* pep8 patch
* update readme
* Update progress
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* pep8
* Pep 8 and restructure
* add lambda spin
* add clump and halo
* add checks
* Edit halo profile fit
* Update gitignore
* backup script
2023-04-18 11:02:36 +02:00
Richard Stiskalek
e0d3854277
Add cleaner paths ( #43 )
...
* ignore venv
* ignore pylians if unavaible
* Edit loading paths
* Edit paths
* Stop having default paths
* Add nb
* Add glamdring paths
---------
Co-authored-by: Richard Stiskalek <dc-stis1@login8b.pri.cosma7.alces.network>
Co-authored-by: Richard Stiskalek <dc-stis1@login8a.pri.cosma7.alces.network>
2023-04-14 23:24:52 +01:00
Richard Stiskalek
1344fa40b6
Add 2PCF calculation ( #42 )
...
* Add 2PCF calculation
* Add 2PCF reader
* Add tpcf scripts
* Add random state
* Fix marked typo
* Fix marks and more randoms
* Stop calculating projected
* Add mean 2PCF
* Remove pimax
* Edit submit script
* Update nb
* Add corrfunc check
2023-04-14 23:05:48 +01:00
Richard Stiskalek
5784011de0
kNN-CDF secondary halo bias ( #40 )
...
* Add seperate autoknn script & config file
* edit ics
* Edit submission script
* Add threshold values
* Edit batch sizign
* Remove print
* edit
* Rename files
* Rename
* Update nb
* edit runs
* Edit submit
* Add median threshold
* add new auto reader
* editt submit
* edit submit
* Edit submit
* Add mean prk
* Edit runs
* Remove correlation file
* Move split to clutering
* Add init
* Remove import
* Add the file
* Add correlation reading
* Edit scripts
* Add below and above median permutation for cross
* Update imports
* Move rvs_in_sphere
* Create utils
* Split
* Add import
* Add normalised marks
* Add import
* Edit readme
* Clean up submission file
* Stop tracking submit files
* Update gitignore
* Add poisson field analytical expression
* Add abstract generators
* Add generators
* Pass in the generator
* Add a check for if there are any files
* Start saving average density
* Update nb
* Update readme
* Update units
* Edit jobs
* Update submits
* Update reader
* Add random crossing
* Update crossing script
* Add crossing with random
* Update readme
* Update notebook
2023-04-09 20:57:05 +01:00
Richard Stiskalek
826ab61d2d
Add p(V | k) ( #39 )
...
* add p(V | k)
* Update nb
2023-04-05 14:47:30 +01:00
Richard Stiskalek
8d34b832af
Improve paths and documentation ( #38 )
...
* pep8
* style issue
* Documentation edits
* Remove old files
* Remove more old files
* Doc & stop setting snap and nsim in paths
* add nsnap, nsim support
* Remove blank space
* docs
* Docs edits
* Reduce redudant code
* docs
* Documentation
* Docs
* Simplify
* add nsnap nsim arguments
* Remove redundant docs
* Fix typos
* Shorten catalogue
* Remove import
* Remove blank line
* Docs only edits
* Rearrange imports
* Remove blank space
* Rearrange imports
* Rearrange imports
* Remove blank space
* Update submission scritp
* Edit docs
* Remove blank line
* new paths
* Update submission scripts
* Update file handling
* Remove blank line
* Move things around
* Ne paths
* Edit submission script
* edit paths
* Fix typo
* Fix bug
* Remove import
* Update nb
2023-04-04 15:22:00 +01:00
Richard Stiskalek
522ee709c9
Joint kNN-CDF calculation ( #36 )
...
* Add joint kNN CDF
* add jointKNN calculation
* change sub script
* Update readme
* update sub
* Small changes
* comments
* update nb
* Update submisison script
2023-04-01 11:16:11 +01:00
rstiskalek
f26cf087ab
Update nb
2023-04-01 07:56:52 +01:00
rstiskalek
097b498da6
Update nb
2023-04-01 07:16:10 +01:00
Richard Stiskalek
63ab3548b4
kNN-CDF implementation ( #34 )
...
* Rewrite doc
* add kNN
* edit loading of samples with no init
* Add verbosity flag
* add KNN submission script
* do not make peaked cdf by default
* Add submit script
* stop ignore sh
* Add mass thresholding
* Edit gitignore
* edits
* Space points in logspace
* Calculate for all ICs
* Update TODO
* Add dtype support
* Update readme
* Update nb
2023-03-31 18:13:41 +01:00
Richard Stiskalek
5dd8c668fa
Gaussian smoothing of density fields ( #33 )
...
* Simplify smoothing support and looping over nonzero
* Simplify comments
* add now()
* add cat length
* add smoothed calculation
* add smoothing
* Add sorting
* Edit what is ignored
* Move notebooks
* Add nonsymmetric smoothed overlap
* Update NB
* Add support for reading in the smoothed overlap
* Switch to the true overlap definition
* Reader of the true overlap
* rem occups
* Import moved to a class
* Move definition
* Edit submission script
* Update to account for the new definition
* backup nb
* Switch back to properly initialising arrays
* Fix addition bug
* Update NB
* Fix little bug
* Update nb
2023-03-27 09:22:03 +01:00
