Richard Stiskalek
ce55a2b47e
Add marginalization over boxes ( #131 )
...
* Parallelize over simulations
* Update docs
* Update dependency
* Update imports
* Add adtitional dependencies
* Update .gitignore
* Update ERADME
* Simplify numpyro GOF
* Speed up GOF
* Deepcopy samples
* Update scripts
* Add GPU acceleration
* Select boxes
* Update script
* Optionally sample beta
* Fix old code
* Simplify code
* Start saving log posterior
* Start popping log_likeliood
* Add imports
* Add converting samples
* Fix sctipt name
* Add evidence with harmonic
* Remove comment
* Update imports
* Update imports so that pylians not required
* Stop requiring Pylians to be installed
* Update submission scripts for loops
* Update nb
* Update nb
* Add Manticore boxes
* Add verbosity flag
* Add bulk flow
* Update script
* Update nb
* Update normalization
* Update submit
* Update nb
2024-06-26 10:43:26 +01:00
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
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
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
rstiskalek
723ea0a38b
Update README
2023-12-13 20:43:28 +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
harrydesmond
f6ad3b152d
Update README.md ( #81 )
2023-07-31 20:41:51 +02:00
rstiskalek
afb7c515bd
Add README
2023-05-14 12:48:18 +01:00
rstiskalek
1d871e7109
Clean up README
2023-05-07 23:30:03 +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
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
0b743756ef
File organisation ( #41 )
...
* Split summary files
* Rename script
* Cosmetics
* Minor changes
* Update TODO
2023-04-09 21:12:19 +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
rstiskalek
b1b08b8e53
Edit TODO
2023-04-01 11:43:39 +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
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
153f1c0002
Overlap reader thresholds ( #31 )
...
* Improve data
* Add comment
* Update how KNN is called
* Bring back indices
* New function output
* return catx["index"]
* Remove unnecessary arguments
* Remove useless arguments
* Rename output
* thin up catalogues
* Add thresholding
* Update README
2023-03-15 20:55:50 +00:00
Richard Stiskalek
8dea3da4de
Speed up overlap ( #27 )
...
* Edit improt
* Simplify patch size calculation
* Add patch size percentiles
* Add various percentiles
* Remove comment
* Update TODO
* Change to 95th percentile
* Add import
* Add KNN properties
* Add new matching initial condition
* Add import
* Remove import
* Add fast neighbours option
* Further edits to fast neighbours
* add imports
* add new overlap calculation and non-zero things
* Remove print
* Clean up code
* Fix small bug
* Remove comment
* Add run single cross match
* change values
* Edit hyperparams
* Add comment
* Add the argument parser
* Add new lagpatch calc
* New lagpatch calc
* Delete old patch definitions
* Make clump dumping once again optional
* Add lagpatch to the catalogue
* Edit print statement
* Fix small bug
* Remove init radius
* Change to lagpatch key
* Fix a small bug
* Fix little bug
2023-02-05 11:46:19 +00:00
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
rstiskalek
65059f3798
Update TODO
2022-12-27 17:33:07 +00:00
Richard Stiskalek
3dc559fec1
Overlap calculation ( #19 )
...
* Rm comment
* Add new fixed particle overlap
* Fix overlap calculation
* Update docs
* Add new overlapper support in matcher
* add filter optin
* Add the real space filter.
* Change filtering to real space only
* Update TODO
* add high-resolution switch
* add cross script
* Remove comment
* Add smoothing option
2022-12-27 18:32:12 +01:00
rstiskalek
1edb566792
Update TODO
2022-12-20 12:11:18 +00:00
Richard Stiskalek
18f09767f4
Overlap calculation ( #18 )
...
* Move cosine similarity out
* Basic overlap calculation
* add overlap import
* Add clump0 dict path
* Update README
* fix path bug
* Save as dict instead
* Change format to array of arrays
* Update paths
* Take fewer ICs for now
* Change to structured array
* Add overlap calculation
* Start saving IDs
* Add a blank space
* Update TODO
2022-12-19 11:58:22 +01:00
Richard Stiskalek
13a9d11afe
Particle init CM separation ( #17 )
...
* Rename
* rename module
* add new_ic_ids
* Add to_new support
* rm unnecessary comment
* Remove JUlia!
* add new package attempt
* add dump script
* simplify positions getter
* Remove unused code
* change dumpdirs
* update project
* Add sorting
* fix indexing bug
* add comment
* Add particle dumping
* Delete blank line
* Delete Julia things
* Update README
* add working script
* fix assignment bug
* fix bug
* save temp to temp folder
* fix indexing bug & path
* do not always crreate folder
* Rename file
* add initcm reader
* add x0, y0, z0 transforms
* add initcm to halo cat
* docs update
* add initial KNN
* add attempt at init match
* add initial fiducial radius
* rm blank space
* Add further KNN Init pos support
* Add init radius support
* Remove message about the bug
* Get rid of an error msg
* purge mention of knn_init
* Add init CM distance calc
2022-12-16 11:18:16 +01:00
Richard Stiskalek
c3c686fa60
Power spectrum stuff ( #16 )
...
* add autok1d
* update TODO
* add basic cross pk
* del blank line
* fix small bugs
* fix loop bug
* rm nbs
* edit docstring
* Update TODO
* get rid of verbose flag
* take all ICs
* attempt better memory
* simplify ASCII dump
* rm verbose statement to get rid of bugs!
* close fortran files
* add MAS options
* add boxsize setter
* Move comment up
* paths chagne
* Update TODO
* Update TODO
* Forgotten units in Xpk
* Attempt at fixing the distance bug
* Update TODO
* Update TODO
* Remove comment
* add summary reader
* Update gitignore
2022-12-12 14:42:44 +00:00
Richard Stiskalek
91beb4df50
Angular momentum ( #14 )
...
* add ang mom
* Update TODO
* add ascii dump script
* add comment
* Updating TODO
* add angmom
* add garbage collector
2022-11-30 16:12:39 +00:00
rstiskalek
92699bfb0a
update TODO
2022-11-30 13:42:00 +00:00
rstiskalek
ea73dfcd56
Update TODO
2022-11-25 16:46:28 +00:00
rstiskalek
d8adf56614
edit TODO
2022-11-25 15:07:53 +00:00
rstiskalek
469f4988fa
update TODO
2022-11-25 12:45:47 +00:00
Richard Stiskalek
161c27d995
Particle match & file system & phase space ( #11 )
...
* Create file system
* add doc
* add n_sim n_snap directly to paths
* Move things to a single particle reader for consistency
* add docstring
* add srdcir, dumpdir and mmain_path
* make boxunits work with paths
* switch to using paths
* add tempdumpdir
* rm dependence on old functions
* rm comment
* rm unused import
* go back to all imports
* fix import bug
* rm dependence on old functions
* modernize code!
* fix typo
* fix typo
* update fits to new data structureing
* change docs
* add julia repo
* add setup
* add install commands
* ignore install files
* add array flattening
* update dependene
* add positions reader
* update manifest and projects
* add func
* update gitignore
* pos matching progress
* move file
* rm comment
* add velocities getter
* fix bug
* fix name bug
* fix path bug
* fix args func
* add redshift calculation to catalogues
* add shortcut to set n_sim and n_snap
* if cond bug
* add the cosine similarity
* add verbosit iterator
* add docs
* update README
* update README
* update README
2022-11-25 10:44:08 +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
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
a3ccc029cd
update TODO
2022-11-06 21:01:43 +00:00
rstiskalek
760ba06689
update TODO
2022-11-06 20:59:39 +00:00
rstiskalek
a0f187d660
update TODO
2022-11-06 10:28:32 +00:00
Richard Stiskalek
d32eb5c134
Data loading shortcut ( #7 )
...
* add load_processed
* update TODO
2022-11-06 10:26:24 +00:00
rstiskalek
5fa429ceb0
Update TODO
2022-11-06 09:11:21 +00:00
rstiskalek
91ad3166f8
Update TODO
2022-11-06 09:07:27 +00:00
Richard Stiskalek
7f58b1f78c
JAX and fix conc ( #6 )
...
* change to log10 initlogRs
* add uncertainty
* add check if hessian negative
* update TODO
* update TODO
* output the error too
* save e_logRs
* add concentration calculation
* calcul concentration
* missed comma in a list
* Update TODO
* fix bug
* add box units and pretty status
* make uncertainty optional
* add BIC function
* remove BIC again
* add new overdensity calculation
* change defualt values to max dist and mass
* change to r200
* new halo find
* speed up the calculation
* add commented fucn
* update TODO
* add check whether too close to outside boundary
* Update TODO
* extract velocity as well
* calculate m200 and m500
* update nb
* update TODO
2022-11-05 21:17:05 +00:00
Richard Stiskalek
ba98ecc299
Mass enclosed in a sphere calculation ( #5 )
...
* rename nb
* add merge func
* rm bug..
* add static methods
* save rmin, rmax
* add properties for box units
* move radial info to the clump
* add Npart explicit
* move where rmin, rmax obtained
* add box cosmo
* add __getattr__
* add comments in units
* add enclosed spherical mass
* rm unused variables
* add clump mass setter
* add the halo index
* add enclosed overdensity
* add enclosed_overdensity
* simplify loss func
* opt result to nan
* change Rs to log10
* change back to attribs
* add H0 and h props
* add setattrs
* Remove global constants
* move Msuncgs above
* add crit density
* add dots
* add r200c and r500c
* add M200 and M500
* make lowercase
* output r200, r500, m200, m500
* update TODO
* update README
* fit NFW only up to r200
* add r178, m178
* add m178, r178
* update TODO
2022-11-01 10:10:54 +00:00
rstiskalek
88e2132232
update README
2022-10-30 20:23:35 +00:00
rstiskalek
09ce7b4b5e
Update TODO
2022-10-30 20:21:48 +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
Richard Stiskalek
0a73256fe3
Update README.md
2022-10-20 23:31:19 +01:00
