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16 commits

Author SHA1 Message Date
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
1a9e6177d7
Switch to h5py format (#52) 
* 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
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
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
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
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
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
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
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