correlcalc 0.974rc1
Two-point correlation function (2pCF) calculation
Latest Version: 1.0
A Python package to calculate 2-point correlation function(2pCF) from galaxy redshift surveys for any generic model of Cosmology or geometry.
Summary
correlcalc calculates two-point correlation function (2pCF) of galaxies/quasars using redshift surveys. It can be used for any assumed geometry or Cosmology model. Using BallTree algorithms to reduce the computational effort for large datasets, it is faster than brute-force methods. It takes redshift (z), Right Ascension (RA) and Declination (DEC) data of galaxies and random catalogs given by redshift survey as inputs. If random catalog is not provided, it generates one of desired size based on the input redshift distribution and a mangle polygon file in .ply format describing the survey geometry. It also calculates anisotropic 2pCF. Optionally it makes healpix maps of the survey providing visualization.
Installation
To install this package type “pip install correlcalc” in your terminal. If this method doesn’t work
To install the package Download this git repositry and in terminal enter the folder that contains setup.py and type “pip install .” or “python setup.py install”
If you do not have root permission, you can install by adding “--user” at the end of above commands
A note on Dependencies:
All the required dependencies such as sklearn, cython, scipy, numpy etc. should get automatically installed if installed through pip. In case, if some of the dependencies do not automatically get installed. The list of dependencies can be seen in the setup.py file to manually install them. In case of any problems feel free to raise an issue. “healpix_util” package from http://github.com/esheldon/healpix_util is not available on pip. So it needs to be manually installed following the commands to install from git repositry in the above section
Theory
The algorithm and formulae used are presented in the paper entitled A `Generic’ Recipe for Quick Computation of Two-point Correlation function
It is available on arXiv:1710.01723 at https://arxiv.org/abs/1710.01723
Please cite the same if you use this package or the ‘recipe’ presented herein
Usage
Calculation of 2pCF
Usage of the package is given in jupyter notebook “Using correlcalc example.nb” and in main.py
All the methods in correlcalc can be imported using the following command
from correlcalc import *
We first need to define bins (in \(c/H_0\) units) to calculate 2pCF. For e.g. to calculate correlation between 0-180Mpc in steps of 6Mpc, we say
bins=np.arange(0.002,0.06,0.002)
To calculate 2pCF using input data file (both ascii and fits files are supported), use tpcf method as follows
correl, poserr=tpcf('/path/to/datfile.dat',bins, randfile='/path/to/randomfile.dat', weights=True)
If random file is not available or not provided, we can generate random catalog by providing the mangle mask file in .ply format along with specifying the size of the catalog in multiples of size of data catalog (default 2x size). To do this
correl, poserr=tpcf('/path/to/datfile.dat', bins, maskfile='/path/to/maskfile.ply', weights=True, randfact=3)
This returns correl and poserr numpy arrays corresponding to Two-point correlation and Poisson error
Keyword Arguments
The following keyword arguments can be included as needed
Data file (Mandatory)
Data file of galaxy/quasar redshift survey must be passed as the first argument to both tpcf and atpcf methods.
Supported filetypes: ascii text files with columns, csv files or fits files are all supported. Most files provided by SDSS Value added catalogs should be directly usable.
To contain: Any type of file provided must at least have columns named Z (redshift), RA (Right Ascension), DEC (Declination). These column names can be in any case.
If one intends to use weights=True option (must to obtain accurate results) the data file must also contain radial weights with column title radial_weight or WEIGHT_SYSTOT
bins (Mandatory)
A numpy array with ascending values in \(c/H_0\) units must be provided as the second argument to both tpcf and atpcf methods. In case of atpcf it automatically creates 2D bins as bins2d=(bins,bins) from provided 1D bins
randfile= Path to random file (semi-Optional)
If not provided, maskfile= argument must be given .ply file.
Supported filetypes: ascii text files with columns, csv files or fits files are all supported. Most files provided by SDSS Value added catalogs should be directly usable.
To contain: Any type of file provided must at least have columns named Z (redshift), RA (Right Ascension), DEC (Declination). These column names can be in any case.
If one intends to use weights=True option (must to obtain accurate results) the data file must also contain radial weights with column title radial_weight or WEIGHT_SYSTOT
To add: In future support for other column titles for weights will be added. To also add calculation of weights from n(z) and for random catalog generation.
mask= Path to mangle polygon file (semi-Optional)
If not provided, randfile= argument must be provided.
Supported filetypes: .ply file containing Mangle polygons describing survey geometry in the standard format. Most files provided by SDSS Value added catalogs should be directly usable.
randfact= (Optional)
Size of the random catalog in integer multiples of size of data catalog if random catalog file is not provided. Default value is 2
weights= (Optional)
It is highly recommended to use weights argument by providing weights=True to obtain accurate two-point correlation calculations. This picks up radial weights in the prescribed format (with column title radial_weight or WEIGHT_SYSTOT ) from the data and random files provided.
If weights=False, by default +1 will be added for each galaxy/random pair found within the bin instead of adding total weight. For more details on weights and references, see http://www.sdss3.org/dr9/tutorials/lss_galaxy.php
geometry='flat' (Optional)
Available options:
'flat'(default) - for flat geometry of the Universe
'open' - for Open Universe models like Milne
'close' - for Closed Universe
Customization
Formulae for calculation of distances between two points (Z1, RA1, DEC1) and (Z2, RA2, DEC2) is taken from T. Matsubara, Correlation function in deep redshift space as a cosmological probe, The Astrophysical Journal 615 (2) (2004) 573. Using the formulae in this paper, distances squares (to reduce additional computational time distance squares are calculated to avoid using expensive sqrt function every time) are computed in the metrics.pyx file for all the above mentioned geometries. Cython is chosen for implementation to obtain faster results in building BallTrees calculating cdist and to reduce query time.
One can customize metric definitions as per one’s need by editing this file. Also K (curvature parameter) in the formulae given in this reference need to be manually changed in the metrics.pyx for closed and open cases as per the model. After changing this compile it using python metricsetup.py build_ext --inplace
cosmology='lcdm' (Optional)
Used to calculate co-moving distances from redshifts.
Available options:
'lcdm' (default)- for Lambda CDM model
'lc' - for \(R_h=ct\) and linear coasting models
To add: wcdm and other popular cosmology models soon
estimator= (Optional)
Available options:
'dp' - Davis - Peebles estimator (default - fastest)
'ls'- Landy - Szalay estimator
'ph' - Peebles- Hauser estimator
'hew' - Hewitt estimator
'h' - Hamilton estimator
For more details on estimator formulae see https://arxiv.org/pdf/1211.6211.pdf
Calculation of Anisotropic 2pCF
Calculation of 2pCF
Usage of the package is given in jupyter notebook “Using correlcalc example-anisotropic.nb” and in main.py
All the methods in correlcalc can be imported using the following command
from correlcalc import *
We first need to define bins (in \(c/H_0\) units) to calculate 2pCF. For e.g. to calculate correlation between 0-180Mpc in steps of 6Mpc, we say
bins=np.arange(0.002,0.06,0.002)
To calculate anisotropic 2pCF using input data file (both ascii and fits files are supported), use atpcf method as follows
correl2d, poserr=atpcf('/path/to/datfile.dat',bins, randfile='/path/to/randomfile.dat', permetric='apzdth', parmetric='apdz', weights=True)
If random file is not available or not provided, we can generate random catalog by providing the mangle mask file in .ply format along with specifying the size of the catalog in multiples of size of data catalog (default 2x size). To do this
correl2d, poserr=atpcf('/path/to/datfile.dat', bins, maskfile='/path/to/maskfile.ply', permetric='apzdth', parmetric='apdz', weights=True, randfact=3)
This returns correl2d and poserr numpy arrays corresponding to anisotropic Two-point correlation and Poisson error
Keyword Arguments
The following keyword arguments can be included as needed
Data file (Mandatory)
Data file of galaxy/quasar redshift survey must be passed as the first argument to both tpcf and atpcf methods.
Supported filetypes: ascii text files with columns, csv files or fits files are all supported. Most files provided by SDSS Value added catalogs should be directly usable.
To contain: Any type of file provided must at least have columns named Z (redshift), RA (Right Ascension), DEC (Declination). These column names can be in any case.
If one intends to use weights=True option (must to obtain accurate results) the data file must also contain radial weights with column title radial_weight or WEIGHT_SYSTOT
bins (Mandatory)
A numpy array with ascending values in \(c/H_0\) units must be provided as the second argument to both tpcf and atpcf methods. In case of atpcf it automatically creates 2D bins as bins2d=(bins,bins) from provided 1D bins
randfile= Path to random file (semi-Optional)
If not provided, maskfile= argument must be given .ply file.
Supported filetypes: ascii text files with columns, csv files or fits files are all supported. Most files provided by SDSS Value added catalogs should be directly usable.
To contain: Any type of file provided must at least have columns named Z (redshift), RA (Right Ascension), DEC (Declination). These column names can be in any case.
If one intends to use weights=True option (must to obtain accurate results) the data file must also contain radial weights with column title radial_weight or WEIGHT_SYSTOT
To add: In future support for other column titles for weights will be added. To also add calculation of weights from n(z) and for random catalog generation.
mask= Path to mangle polygon file (semi-Optional)
If not provided, randfile= argument must be provided.
Supported filetypes: .ply file containing Mangle polygons describing survey geometry in the standard format. Most files provided by SDSS Value added catalogs should be directly usable.
randfact= (Optional)
Size of the random catalog in integer multiples of size of data catalog if random catalog file is not provided. Default value is 2
weights= (Optional)
It is highly recommended to use weights argument by providing weights=True to obtain accurate two-point correlation calculations. This picks up radial weights in the prescribed format (with column title radial_weight or WEIGHT_SYSTOT ) from the data and random files provided.
If weights=False, by default +1 will be added for each galaxy/random pair found within the bin instead of adding total weight. For more details on weights and references, see http://www.sdss3.org/dr9/tutorials/lss_galaxy.php
Metrics in parallel and perpendicular directions
Currently calculates anisotropic 2pCF only in angular co-ordinates. Currently only small \(\Delta \theta\) and \(z \Delta\theta\) are supported. But results can be converted to any cosmology model of choice (ref: https://arxiv.org/pdf/1312.0003.pdf)
parmetric= (Mandatory)
Metric to calculate distance in the line-of-sight direction. Currently only 'apdz' is supported
permetric= (Mandatory)
Metric to calculate distance perpendicular to the line-of-sight direction. Currently only 'apzdth' is supported
Customization
Formulae for calculation of distances in parallel and perpendicular directions is taken from https://arxiv.org/pdf/1312.0003.pdf. Using the formulae in this paper, \(\Delta z\) and \(z \Delta \theta\) are computed in the metrics.pyx file for the above mentioned. Cython is chosen for implementation to obtain faster results in building BallTrees calculating cdist and to reduce query time.
One can customize metric definitions as per one’s need by editing the metrics.pyx file. After changing this compile it using python metricsetup.py build_ext --inplace
To add:
Direct calculation of distances in LOS and perpendicular to the LOS to be added to support standard model Cosmology and other popular models. For now, one needs to manually convert the angular bins to physical distances to get the approximate results
cosmology='lcdm' (Optional)
Used to calculate co-moving distances from redshifts.
Available options:
'lcdm' (default)- for Lambda CDM model
'lc' - for \(R_h=ct\) and linear coasting models
To add: wcdm and other popular cosmology models soon
estimator= (Optional)
Available options:
'dp' - Davis - Peebles estimator (default - fastest)
'ls'- Landy - Szalay estimator
'ph' - Peebles- Hauser estimator
'hew' - Hewitt estimator
'h' - Hamilton estimator
For more details on estimator formulae see https://arxiv.org/pdf/1211.6211.pdf
File | Type | Py Version | Uploaded on | Size | |
---|---|---|---|---|---|
correlcalc-0.974rc1.tar.gz (md5) | Source | 2017-10-13 | 252KB | ||
- Author: Rohin Kumar Y
- Home Page: http://github.com/rohinkumar/correlcalc
- License: MIT
- Package Index Owner: rohin
- DOAP record: correlcalc-0.974rc1.xml