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 )
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* 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
rstiskalek
26ef1661a4
Add verbosity flag
2023-05-09 17:43:18 +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
rstiskalek
ab8199be2c
Rename folder
2023-05-08 14:24:15 +01:00
Richard Stiskalek
cb5d35b1be
Density field calculation ( #58 )
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* 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
4265315b47
Revert "Run density field estimator ( #56 )" ( #57 )
...
This reverts commit 98d0578fa7
2023-05-08 13:59:55 +01:00
Richard Stiskalek
98d0578fa7
Run density field estimator ( #56 )
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* 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
2023-05-08 13:58:12 +01:00
rstiskalek
1d871e7109
Clean up README
2023-05-07 23:30:03 +01:00
Richard Stiskalek
65564849f4
Add redshift space position ( #55 )
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* 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
rstiskalek
3df771f1ee
Blank line
2023-05-07 16:36:42 +01:00
Richard Stiskalek
51b670d30b
Updates to the overlap reader. ( #54 )
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* Flag for loading clumps_cat
* Optionally load clumps catalogues
* Update single pair reading
* Edit reading many pairs
2023-05-07 16:34:55 +01:00
Richard Stiskalek
56e39a8b1d
Overlapper improvements ( #53 )
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* 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
rstiskalek
1c9dacfde5
Merge branch 'master' of github.com:Richard-Sti/csiborgtools
2023-05-02 14:09:42 +01:00
Richard Stiskalek
1a9e6177d7
Switch to h5py format ( #52 )
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* Edit the particle paths
* Remove script
* Add h5py to dumping
* Minor adjustments
* add h5py support
* remove split path
* h5py support
* Type
* Edit initmatch paths
* Shorten func
* dist_centmass to work with 2D arrays
* Forgot to return the centre of mass
* Fixed code
* Fix halo bug
* Start MPI broadcasting
* Mini bug
* Remove commenting
* Remove test statement
* Fix index
* Printing from rank 0 only
* Move where clump index stored
* Add dtype options
* Add dtype options
2023-05-02 13:57:13 +01:00
rstiskalek
7d947f5421
Edit the particle paths
2023-04-30 12:12:37 +01:00
Richard Stiskalek
553eec8228
Update field calculations ( #51 )
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* 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 )
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* 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 )
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* 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
rstiskalek
4f8335e0a3
Merge branch 'master' of github.com:Richard-Sti/csiborgtools
2023-04-27 10:40:35 +01:00
rstiskalek
8d5ea287d8
Remove old files
2023-04-27 10:40:18 +01:00
Richard Stiskalek
b7ea2ce28b
Create LICENSE
2023-04-27 10:38:59 +01:00
rstiskalek
b0752efdf4
fix indexing bug
2023-04-27 09:21:00 +01:00
Richard Stiskalek
f48eb6dcb0
Dump radial profile information ( #48 )
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* 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
rstiskalek
1a115f481d
Rename file
2023-04-21 00:40:11 +01:00
Richard Stiskalek
04119a5314
Update initial matching & overlaps ( #47 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* add p(V | k)
* Update nb
2023-04-05 14:47:30 +01:00
Richard Stiskalek
8d34b832af
Improve paths and documentation ( #38 )
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* 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 )
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* Add nb
* add the KNN reader
* Move reading functions
* Update boolean masking
* Update the nb
2023-04-02 20:26:15 +01:00
rstiskalek
b1b08b8e53
Edit TODO
2023-04-01 11:43:39 +01:00
Richard Stiskalek
522ee709c9
Joint kNN-CDF calculation ( #36 )
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* 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
cb67e326c4
Merge branch 'master' of github.com:Richard-Sti/csiborgtools
2023-04-01 07:57:45 +01:00
Richard Stiskalek
513872ceb6
kNN memory batching ( #35 )
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* Add batch sizing for less memory
* Add batch size to submission
* Update nb
* Add brute KNN
* unused variable
* Update nb
2023-04-01 07:57:21 +01:00
rstiskalek
f26cf087ab
Update nb
2023-04-01 07:56:52 +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
097b498da6
Update nb
2023-04-01 07:16:10 +01:00
rstiskalek
8d933e7ba9
Add batch size to submission
2023-04-01 07:15:44 +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 )
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* 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
rstiskalek
4d7827006a
test
2023-03-27 13:38:01 +01:00
Richard Stiskalek
5dd8c668fa
Gaussian smoothing of density fields ( #33 )
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* 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
