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77 commits

Author SHA1 Message Date
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
4e87a96b97 fix bug(again) 2022-11-25 12:42:49 +00:00
rstiskalek
a3c7d03ceb fix bug 2022-11-25 12:28:41 +00:00
rstiskalek
377d6ebb7e add lambda200c support 2022-11-25 12:24:06 +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
rstiskalek
f5bf04c46e update nb 2022-11-20 14:11:35 +00:00
rstiskalek
3352b06c1c add units 2022-11-20 14:11:25 +00:00
rstiskalek
1d9789c08e add vx 2022-11-20 14:11:19 +00:00
rstiskalek
06d3fede95 add max snapshot 2022-11-14 16:24:53 +00:00
rstiskalek
76349bab3f add MPI and do for all boxes 2022-11-14 15:52:52 +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
d69012424e simplify loading 2022-11-06 20:55:49 +00:00
rstiskalek
9291414572 update nbs 2022-11-06 20:53:58 +00:00
Richard Stiskalek
d32eb5c134
Data loading shortcut (#7) 
* add load_processed

* update TODO
 2022-11-06 10:26:24 +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
rstiskalek
a47847cb7c more renaming 2022-10-20 23:37:33 +01:00
Richard Stiskalek
942c36b142
Box units conversion (#3) 
* linting

* fix long line

* rename nb

* rename import

* add group catalog

* move imports out of functions

* add array_to_structured

* add references

* fix subsampling

* fix coord bug

* add 2M++ dists

* save nb

* fix comment

* add snapshot path

* add snapshot path

* add read_info

* Move transforms

* add import radec

* expand docs

* Move flipcols

* update nb

* add flip_cols

* create file

* add blank line

* Move units transfs

* add blank line

* add units import

* rm imports

* add import

* add box_units

* add comments
 2022-10-20 23:28:44 +01:00
Richard Stiskalek
53a0629d90
Basic matching (#2) 
* add recarray manipulations

* add cart to radec

* add behav so x can be a list

* add import

* create empty files

* ignore plots file

* add planck data

* add read_mmain file

* add cols_to_structured import

* use cols_to_structured

* add cols_to_structued

* add read_mmain import

* add reading planck

* add mass conversion

* add brute force separation calculation

* update nb

* rename & int dtype

* add func to get csiborg ids

* add list to nd array conversion

* add utils

* rename file

* add 2M++

* add read 2mpp

* add 2mpp shortcut

* add randoms generator

* Change range of RA [0, 360]

* fix ang wrapping

* add code for sphere 2pcf

* rm wrapping

* optionally load only a few borgs

* update nb
 2022-10-18 19:41:20 +01:00
rstiskalek
4d24895d2f update nb 2022-10-11 16:35:21 +01:00
rstiskalek
54221a8ff5 first commit 2022-10-02 11:12:45 +01:00