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Z bin refactoring #1125

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4755d3b
Refactor z-cuts to remove old code and update headers
andreicuceu Mar 23, 2026
baf1fc3
Update dmat as well
andreicuceu Mar 23, 2026
fcac517
Clean-up other files
andreicuceu Mar 23, 2026
9c42217
Update picca_export to propagate header flags
andreicuceu Mar 23, 2026
3197c01
Remove unnecessary tests and comment out tests that need to be updated
andreicuceu Mar 23, 2026
815aa71
Merge remote-tracking branch 'origin/copilot/refactor-numpy-in1d-repl…
andreicuceu Mar 23, 2026
7ad56cc
Initial plan
Copilot Mar 23, 2026
af3a7e9
Update zcuts tests: uncomment 7 test functions, regenerate reference …
Copilot Mar 23, 2026
7d08340
Merge remote-tracking branch 'origin/main' into z-bin-refactoring
andreicuceu Mar 23, 2026
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34 changes: 4 additions & 30 deletions py/picca/bin/picca_cf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,30 +134,6 @@ def main(cmdargs=None):
),
)

parser.add_argument(
"--z-cut-min",
type=float,
default=0.0,
required=False,
help=(
"Use only pairs of forest x object with the mean "
"of the last absorber redshift and the object "
"redshift larger than z-cut-min"
),
)

parser.add_argument(
"--z-cut-max",
type=float,
default=10.0,
required=False,
help=(
"Use only pairs of forest x object with the mean "
"of the last absorber redshift and the object "
"redshift smaller than z-cut-max"
),
)

parser.add_argument(
"--z-min-sources",
type=float,
Expand Down Expand Up @@ -350,8 +326,6 @@ def main(cmdargs=None):
cf.r_par_max = args.rp_max
cf.r_trans_max = args.rt_max
cf.r_par_min = args.rp_min
cf.z_cut_max = args.z_cut_max
cf.z_cut_min = args.z_cut_min
cf.z_min_pairs = args.z_min_pairs
cf.z_max_pairs = args.z_max_pairs
cf.num_bins_r_par = args.np
Expand Down Expand Up @@ -506,12 +480,12 @@ def main(cmdargs=None):
'value': cf.num_bins_r_trans,
'comment': 'Number of bins in r-transverse'
}, {
'name': 'ZCUTMIN',
'value': cf.z_cut_min,
'name': 'ZMIN',
'value': cf.z_min_pairs,
'comment': 'Minimum redshift of pairs'
}, {
'name': 'ZCUTMAX',
'value': cf.z_cut_max,
'name': 'ZMAX',
'value': cf.z_max_pairs,
'comment': 'Maximum redshift of pairs'
}, {
'name': 'NSIDE',
Expand Down
28 changes: 0 additions & 28 deletions py/picca/bin/picca_cf_angl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,24 +89,6 @@ def main(cmdargs):
required=False,
help='Number of angular bins')

parser.add_argument(
'--z-cut-min',
type=float,
default=0.,
required=False,
help=('Use only pairs of forest x object with the mean of the last '
'absorber redshift and the object redshift larger than '
'z-cut-min'))

parser.add_argument(
'--z-cut-max',
type=float,
default=10.,
required=False,
help=('Use only pairs of forest x object with the mean of the last '
'absorber redshift and the object redshift smaller than '
'z-cut-max'))

parser.add_argument(
'--z-min-sources',
type=float,
Expand Down Expand Up @@ -197,8 +179,6 @@ def main(cmdargs):
cf.r_par_min = args.wr_min
cf.r_par_max = args.wr_max
cf.r_trans_max = args.ang_max
cf.z_cut_max = args.z_cut_max
cf.z_cut_min = args.z_cut_min
cf.num_bins_r_par = args.np
cf.num_bins_r_trans = args.nt
cf.nside = args.nside
Expand Down Expand Up @@ -305,14 +285,6 @@ def main(cmdargs):
'name': 'NT',
'value': cf.num_bins_r_trans,
'comment': 'Number of bins in angle'
}, {
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@iprafols iprafols Mar 25, 2026

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In picca_cf.py, picca_dmat.py, picca_export.py, etc. this was replaced by ZMIN and ZMAX adding the minimum and maximum redshift of pairs. Shouldn't we do the same here for consistency?

'name': 'ZCUTMIN',
'value': cf.z_cut_min,
'comment': 'Minimum redshift of pairs'
}, {
'name': 'ZCUTMAX',
'value': cf.z_cut_max,
'comment': 'Maximum redshift of pairs'
}, {
'name': 'NSIDE',
'value': cf.nside,
Expand Down
8 changes: 6 additions & 2 deletions py/picca/bin/picca_coadd_zint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -382,8 +382,12 @@ def coadd_dmats(input_files,output_file):
return

def main(cmdargs):
"""Coadds correlation function from different redshift intervals"""
parser = argparse.ArgumentParser()
"""This script is deprecated and will be removed in future versions.
Coadds correlation function from different redshift intervals"""
parser = argparse.ArgumentParser(
description=("This script is deprecated and will be removed in future versions."
" Coadds correlation function from different redshift intervals")
)

parser.add_argument("--data",
type=str,
Expand Down
6 changes: 5 additions & 1 deletion py/picca/bin/picca_compute_pk_pksb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,11 @@
from picca.constants import SPEED_LIGHT

def main(cmdargs):
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=("This script is deprecated and will be removed in future versions."
" Use the make_template.py script in Vega instead.")
)

parser.add_argument('-i','--ini', type=str, required=True,
help='Input config file for CAMB')
Expand Down
34 changes: 4 additions & 30 deletions py/picca/bin/picca_dmat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -138,30 +138,6 @@ def main(cmdargs=None):
),
)

parser.add_argument(
"--z-cut-min",
type=float,
default=0.0,
required=False,
help=(
"Use only pairs of forest x object with the mean of the last "
"absorber redshift and the object redshift larger than "
"z-cut-min"
),
)

parser.add_argument(
"--z-cut-max",
type=float,
default=10.0,
required=False,
help=(
"Use only pairs of forest x object with the mean of the last "
"absorber redshift and the object redshift smaller than "
"z-cut-max"
),
)

parser.add_argument(
"--z-min-sources",
type=float,
Expand Down Expand Up @@ -357,8 +333,6 @@ def main(cmdargs=None):
cf.r_par_max = args.rp_max
cf.r_par_min = args.rp_min
cf.r_trans_max = args.rt_max
cf.z_cut_max = args.z_cut_max
cf.z_cut_min = args.z_cut_min
cf.z_min_pairs = args.z_min_pairs
cf.z_max_pairs = args.z_max_pairs
cf.num_bins_r_par = args.np
Expand Down Expand Up @@ -549,13 +523,13 @@ def main(cmdargs=None):
"comment": "Coefficient for model binning",
},
{
"name": "ZCUTMIN",
"value": cf.z_cut_min,
"name": "ZMIN",
"value": cf.z_min_pairs,
"comment": "Minimum redshift of pairs",
},
{
"name": "ZCUTMAX",
"value": cf.z_cut_max,
"name": "ZMAX",
"value": cf.z_max_pairs,
"comment": "Maximum redshift of pairs",
},
{"name": "REJ", "value": cf.reject, "comment": "Rejection factor"},
Expand Down
8 changes: 8 additions & 0 deletions py/picca/bin/picca_export.py
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@HiramHerrera HiramHerrera Mar 25, 2026

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These lines will cause the export code to fail for previously generated correlations. While this may not be common, it could still lead to issues.

For backward compatibility, I suggest guarding this block so it only executes when ZMIN and ZMAX are present in the headers.

Original file line number Diff line number Diff line change
Expand Up @@ -367,6 +367,14 @@ def main(cmdargs=None):
'name': 'NT',
'value': num_bins_r_trans,
'comment': 'Number of bins in r-transverse'
}, {
'name': 'ZMIN',
'value': head['ZMIN'],
'comment': 'Minimum redshift of pairs'
}, {
'name': 'ZMAX',
'value': head['ZMAX'],
'comment': 'Maximum redshift of pairs'
}, {
'name': 'OMEGAM',
'value': head['OMEGAM'],
Expand Down
32 changes: 3 additions & 29 deletions py/picca/bin/picca_fast_metal_dmat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,9 @@ def main(cmdargs=None):
absorption."""
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='Computes metal matrices')
description=('This script is deprecated and will be removed in future versions. '
'Use Vega functionality instead.')
)

parser.add_argument('--out',
type=str,
Expand Down Expand Up @@ -292,24 +294,6 @@ def main(cmdargs=None):
help=('Coefficient multiplying np and nt to get finner binning for the '
'model'))

parser.add_argument(
'--z-cut-min',
type=float,
default=0.,
required=False,
help=('Use only pairs of forest x object with the mean of the last '
'absorber redshift and the object redshift larger than '
'z-cut-min'))

parser.add_argument(
'--z-cut-max',
type=float,
default=10.,
required=False,
help=('Use only pairs of forest x object with the mean of the last '
'absorber redshift and the object redshift smaller than '
'z-cut-max'))

parser.add_argument('--z-min-sources',
type=float,
default=0.,
Expand Down Expand Up @@ -439,8 +423,6 @@ def main(cmdargs=None):
cf.r_par_max = args.rp_max
cf.r_trans_max = args.rt_max
cf.r_par_min = args.rp_min
cf.z_cut_max = args.z_cut_max
cf.z_cut_min = args.z_cut_min
cf.num_bins_r_par = args.np * args.coef_binning_model
cf.num_bins_r_trans = args.nt * args.coef_binning_model
cf.num_model_bins_r_par = args.np * args.coef_binning_model
Expand Down Expand Up @@ -572,14 +554,6 @@ def main(cmdargs=None):
'name': 'COEFMOD',
'value': args.coef_binning_model,
'comment': 'Coefficient for model binning'
}, {
'name': 'ZCUTMIN',
'value': cf.z_cut_min,
'comment': 'Minimum redshift of pairs'
}, {
'name': 'ZCUTMAX',
'value': cf.z_cut_max,
'comment': 'Maximum redshift of pairs'
}, {
'name': 'REJ',
'value': cf.reject,
Expand Down
33 changes: 3 additions & 30 deletions py/picca/bin/picca_fast_metal_xdmat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -198,8 +198,9 @@ def main(cmdargs=None):
a list of IGM absorption."""
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=('Computes metal matrices for the cross-correlation '
'delta x object for a list of IGM absorption.'))
description=('This script is deprecated and will be removed in future versions. '
'Use Vega functionality instead.')
)

parser.add_argument('--out',
type=str,
Expand Down Expand Up @@ -287,24 +288,6 @@ def main(cmdargs=None):
required=False,
help='Max redshift for object field')

parser.add_argument(
'--z-cut-min',
type=float,
default=0.,
required=False,
help=('Use only pairs of forest x object with the mean of the last '
'absorber redshift and the object redshift larger than '
'z-cut-min'))

parser.add_argument(
'--z-cut-max',
type=float,
default=10.,
required=False,
help=('Use only pairs of forest x object with the mean of the last '
'absorber redshift and the object redshift smaller than '
'z-cut-max'))

parser.add_argument('--z-min-sources',
type=float,
default=0.,
Expand Down Expand Up @@ -414,8 +397,6 @@ def main(cmdargs=None):
xcf.r_par_max = args.rp_max
xcf.r_par_min = args.rp_min
xcf.r_trans_max = args.rt_max
xcf.z_cut_max = args.z_cut_max
xcf.z_cut_min = args.z_cut_min
xcf.num_bins_r_par = args.np * args.coef_binning_model
xcf.num_bins_r_trans = args.nt * args.coef_binning_model
xcf.num_model_bins_r_par = args.np * args.coef_binning_model
Expand Down Expand Up @@ -532,14 +513,6 @@ def main(cmdargs=None):
'name': 'COEFMOD',
'value': args.coef_binning_model,
'comment': 'Coefficient for model binning'
}, {
'name': 'ZCUTMIN',
'value': xcf.z_cut_min,
'comment': 'Minimum redshift of pairs'
}, {
'name': 'ZCUTMAX',
'value': xcf.z_cut_max,
'comment': 'Maximum redshift of pairs'
}, {
'name': 'OMEGAM',
'value': args.fid_Om,
Expand Down
30 changes: 0 additions & 30 deletions py/picca/bin/picca_metal_dmat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,24 +112,6 @@ def main(cmdargs=None):
help=('Coefficient multiplying np and nt to get finner binning for the '
'model'))

parser.add_argument(
'--z-cut-min',
type=float,
default=0.,
required=False,
help=('Use only pairs of forest x object with the mean of the last '
'absorber redshift and the object redshift larger than '
'z-cut-min'))

parser.add_argument(
'--z-cut-max',
type=float,
default=10.,
required=False,
help=('Use only pairs of forest x object with the mean of the last '
'absorber redshift and the object redshift smaller than '
'z-cut-max'))

parser.add_argument(
'--z-min-sources',
type=float,
Expand Down Expand Up @@ -297,8 +279,6 @@ def main(cmdargs=None):
cf.r_par_max = args.rp_max
cf.r_trans_max = args.rt_max
cf.r_par_min = args.rp_min
cf.z_cut_max = args.z_cut_max
cf.z_cut_min = args.z_cut_min
cf.num_bins_r_par = args.np * args.coef_binning_model
cf.num_bins_r_trans = args.nt * args.coef_binning_model
cf.num_model_bins_r_par = args.np * args.coef_binning_model
Expand Down Expand Up @@ -509,16 +489,6 @@ def main(cmdargs=None):
'value': args.coef_binning_model,
'comment': 'Coefficient for model binning'
},
{
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@iprafols iprafols Mar 25, 2026

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In picca_cf.py, picca_dmat.py, picca_export.py, etc. this was replaced by ZMIN and ZMAX adding the minimum and maximum redshift of pairs. Shouldn't we do the same here for consistency?

'name': 'ZCUTMIN',
'value': cf.z_cut_min,
'comment': 'Minimum redshift of pairs'
},
{
'name': 'ZCUTMAX',
'value': cf.z_cut_max,
'comment': 'Maximum redshift of pairs'
},
{
'name': 'REJ',
'value': cf.reject,
Expand Down
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