Skip to content

Correctly convert counts to cf when doing an autocorr #201

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Christopher-Bradshaw wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Correctly convert counts to cf when doing an autocorr #201

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
0dabb7a
Correctly convert counts to cf when doing an autocorr
Christopher-Bradshaw Oct 16, 2019
73ce920
add docs + autocorr option convert_rp_pi_counts_to_wp
Christopher-Bradshaw Oct 18, 2019
4db04f7
fix line lengths
Christopher-Bradshaw Oct 18, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 26 additions & 9 deletions Corrfunc/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@

def convert_3d_counts_to_cf(ND1, ND2, NR1, NR2,
D1D2, D1R2, D2R1, R1R2,
estimator='LS'):
estimator='LS', autocorr=False):
"""
Converts raw pair counts to a correlation function.

Expand Down Expand Up @@ -61,6 +61,9 @@
The kind of estimator to use for computing the correlation
function. Currently, only supports Landy-Szalay

autocorr: bool, default=False
Whether the counts are from an autocorrelation

Returns
---------

Expand Down Expand Up @@ -138,14 +141,24 @@

nonzero = pair_counts['R1R2'] > 0
if 'LS' in estimator or 'Landy' in estimator:
fN1 = np.float(NR1) / np.float(ND1)
fN2 = np.float(NR2) / np.float(ND2)
cf = np.zeros(nbins)
cf[:] = np.nan
cf[nonzero] = (fN1 * fN2 * pair_counts['D1D2'][nonzero] -
fN1 * pair_counts['D1R2'][nonzero] -
fN2 * pair_counts['D2R1'][nonzero] +
pair_counts['R1R2'][nonzero]) / pair_counts['R1R2'][nonzero]
if autocorr:
fN1 = np.float(NR1) / np.float(ND1)

Check warning on line 147 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHA&open=AZ3mkgdQB7jd3e8SfYHA&pullRequest=201

Check warning on line 147 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYG_&open=AZ3mkgdQB7jd3e8SfYG_&pullRequest=201

Check warning on line 147 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Rename this local variable "fN1" to match the regular expression ^[_a-z][a-z0-9_]*$. 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYG8&open=AZ3mkgdQB7jd3e8SfYG8&pullRequest=201
fN2 = (np.float(NR1) - 1) / (np.float(ND1) - 1)

Check warning on line 148 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Rename this local variable "fN2" to match the regular expression ^[_a-z][a-z0-9_]*$. 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYG9&open=AZ3mkgdQB7jd3e8SfYG9&pullRequest=201

Check warning on line 148 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHB&open=AZ3mkgdQB7jd3e8SfYHB&pullRequest=201

Check warning on line 148 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHC&open=AZ3mkgdQB7jd3e8SfYHC&pullRequest=201
fN3 = (np.float(NR1) - 1) / np.float(ND1)

Check warning on line 149 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Rename this local variable "fN3" to match the regular expression ^[_a-z][a-z0-9_]*$. 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYG-&open=AZ3mkgdQB7jd3e8SfYG-&pullRequest=201

Check warning on line 149 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHE&open=AZ3mkgdQB7jd3e8SfYHE&pullRequest=201

Check warning on line 149 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHD&open=AZ3mkgdQB7jd3e8SfYHD&pullRequest=201
cf[nonzero] = (fN1 * fN2 * pair_counts['D1D2'][nonzero] -
2 * fN3 * pair_counts['D1R2'][nonzero] +
pair_counts['R1R2'][nonzero]
) / pair_counts['R1R2'][nonzero]
else:
fN1 = np.float(NR1) / np.float(ND1)

Check warning on line 155 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHG&open=AZ3mkgdQB7jd3e8SfYHG&pullRequest=201

Check warning on line 155 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHF&open=AZ3mkgdQB7jd3e8SfYHF&pullRequest=201
fN2 = np.float(NR2) / np.float(ND2)

Check warning on line 156 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHI&open=AZ3mkgdQB7jd3e8SfYHI&pullRequest=201

Check warning on line 156 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHH&open=AZ3mkgdQB7jd3e8SfYHH&pullRequest=201
cf[nonzero] = (fN1 * fN2 * pair_counts['D1D2'][nonzero] -
fN1 * pair_counts['D1R2'][nonzero] -
fN2 * pair_counts['D2R1'][nonzero] +
pair_counts['R1R2'][nonzero]
) / pair_counts['R1R2'][nonzero]
if len(cf) != nbins:
msg = 'Bug in code. Calculated correlation function does not '\
'have the same number of bins as input arrays. Input bins '\
Expand All @@ -163,7 +176,7 @@
def convert_rp_pi_counts_to_wp(ND1, ND2, NR1, NR2,
D1D2, D1R2, D2R1, R1R2,
nrpbins, pimax, dpi=1.0,
estimator='LS'):
estimator='LS', autocorr=False):
"""
Converts raw pair counts to a correlation function.

Expand Down Expand Up @@ -210,6 +223,10 @@
The kind of estimator to use for computing the correlation
function. Currently, only supports Landy-Szalay

autocorr: bool, default=False
Whether the counts are from an autocorrelation


Returns
---------

Expand Down Expand Up @@ -289,7 +306,7 @@

xirppi = convert_3d_counts_to_cf(ND1, ND2, NR1, NR2,
D1D2, D1R2, D2R1, R1R2,
estimator=estimator)
estimator=estimator, autocorr=autocorr)
wp = np.empty(nrpbins)
npibins = len(xirppi) // nrpbins
if ((npibins * nrpbins) != len(xirppi)):
Expand Down Expand Up @@ -793,7 +810,7 @@

# Upper and lower limits of the declination bands
grid_dtype= np.dtype({'names':['dec_limit','ra_limit'],
'formats':[(np.float, (2, )), (np.float, (2, ))]

Check warning on line 813 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHK&open=AZ3mkgdQB7jd3e8SfYHK&pullRequest=201

Check warning on line 813 in Corrfunc/utils.py

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Replace this deprecated "numpy" type alias with the builtin type "float". 


See more on https://sonarcloud.io/project/issues?id=manodeep_Corrfunc&issues=AZ3mkgdQB7jd3e8SfYHJ&open=AZ3mkgdQB7jd3e8SfYHJ&pullRequest=201
})
if not link_in_ra:
sphere_grid = np.zeros(ngrid_dec, dtype=grid_dtype)
Expand Down