rstiskalek
7d947f5421
Edit the particle paths
2023-04-30 12:12:37 +01:00
Richard Stiskalek
553eec8228
Update field calculations ( #51 )
...
* Update density field routines
* Add utils
* Add possibility to return 2d array
* Styling
* Fixed density field
* Fix bugs
* add mpc2box
* Fix evaluating sky
* Fix sky map making
* Rename file
* Add paths if only positions
* Add option to dump particles only
* Add comments
2023-04-29 22:57:05 +01:00
Richard Stiskalek
b5fefe4196
Update init matching procedure ( #50 )
...
* 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
* lala
* la
* Add overlap paths
* Update limit
* pep8
* Some pep8 stuff
* pep8
* Minor corrections
* Update paths
* Add number of particles check
* Fix bug
* pep8 comments
2023-04-29 14:38:21 +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
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
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
rstiskalek
035d7e0071
add crossfiles reader
2023-04-02 22:23:50 +01:00
Richard Stiskalek
9cbdef4350
kNN-CDF reader ( #37 )
...
* Add nb
* add the KNN reader
* Move reading functions
* Update boolean masking
* Update the nb
2023-04-02 20:26:15 +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
8fc4e614e3
unused variable
2023-04-01 07:55:17 +01:00
rstiskalek
7610def8a0
Add brute KNN
2023-04-01 07:52:34 +01:00
rstiskalek
070b9b6c1b
Add batch sizing for less memory
2023-04-01 07:11:39 +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
Richard Stiskalek
9b524db617
Add a shared reader ( #32 )
...
* add import
* Rename object
* Simplify how catalogs are handled
* Move functions around
* Add NPair reader
* Add counterpart Gaussian average
* Change what is returned in exp mass
* small bug
* Simplify stat calcu
* Add mptebppl
2023-03-16 18:02:21 +00:00
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
6e290ccfb4
Add support for inverting the reader ( #30 )
2023-03-09 21:54:13 +00:00
Richard Stiskalek
f2cef73977
Final overlap definition update.. ( #29 )
...
* Delete whitespace
* Update overlap definition
* Add documentation
* add overlap args
* Make the background array store only high density region
* Add nsims to args
* Remove conc as done inside the func
* Simplify the overlap calculation
* Rename variable
* Just some docs
* Docs
* Correct overlap definition
* Undo debug comment
* Remove old debug code
* Add prob of no match and exp couunterpart mass
* docs
* Update the overlap definition
2023-03-09 14:55:38 +00:00
Richard Stiskalek
1c859dbdac
Overlap reader ( #28 )
...
* Edit output path
* remove matching of many sims
* Add a class skeleton
* Add a setter for only nsim
* Deletei mport
* Simplify cross and delete combined halo catalogue
* Simplify reading in catalogues
* Add distance calculation
* Add mass ratio
* Clean up the submission script
* Add the summer overlap
* Docs
* Add array copying
* Add import
* Add resampling mean
2023-02-08 12:05:32 +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
beb811e84c
Switch initial radius definition ( #26 )
...
* Add search for neighbours at z = 0
* Add initial snapshot KNN
* Add initi search either z =0 or z = 70
* Add import
* Add clumps_pos2cell
* Add function argument
* Add import
* Add spherical overlap and speed up make_delta
* Add clump limits calculation
* Sped up make_delta
* Add patch size conversion
* Add patch sizes
* Add patch size calculation
* Force catalogues to be in float32
* Optimised script
* Option to remove points with no overlap
* Add spherical aproximate overlap
* Fix subboxing bug
* Remove print diagnostics
* Add Lagrangian patch size
* Add patch size documentation
* Move when clumpsx converted to int
* Edit docs
* Remove spherical overlap
* New Langrangian patch calculation
2023-01-31 15:09:35 +00:00
Richard Stiskalek
830b1b8daf
Fix weights definition ( #24 )
...
* Fix running script
* Increase outside boundary size
* Add new weight scheme
* Edit docs
2023-01-16 16:14:38 +00:00
Richard Stiskalek
279580e041
Fix overlap weights ( #23 )
...
* Remove overlapper change cells
* Remove Pylians MASL and replace with custom
* Add concatenate clumps
* Add weighted overlap
2023-01-14 14:34:37 +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
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
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
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
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
5435781e8d
add the grav field
2022-11-30 13:41:35 +00:00
Richard Stiskalek
6aa3721c83
Potential ( #13 )
...
* add basic density field
* Add TODO
* add field smoothing
* update how pos are calculated
* add transforms both ways
* add import
* add sky density
* add make skymap func
* update TODO
* update gitignore
* add potential field calculation
* delete boxsize setter
* add tidal tensor
2022-11-27 07:53:38 +00:00
rstiskalek
2a5d6a03b6
add distance cut
2022-11-25 16:45:27 +00:00
Richard Stiskalek
ca45fbd5d9
add ascii writing ( #12 )
2022-11-25 15:06:10 +00:00
rstiskalek
8d68f35cf9
swithc to own G
2022-11-25 12:28:46 +00:00
rstiskalek
69d1f28fcc
add lambda200c calc
2022-11-25 12:23:43 +00:00
rstiskalek
e5208ed070
add note
2022-11-25 11:52:31 +00:00
rstiskalek
91bddb1d3a
remove not good comments
2022-11-25 11:45:47 +00:00
rstiskalek
9fe745b0b4
add center of mass
2022-11-25 10:54:09 +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
