Merge remote-tracking branch 'origin/update-weights-varlss-mod' into …

…update-weights-varlss-mod

bin/picca_cf.py

@@ -238,6 +238,8 @@ def main(cmdargs):
     parser.add_argument('--attributes', type=str, default=None,
                         help='Attributes file with VAR_FUNC extension with '
                              'lambda, eta, var_lss columns.')
+    parser.add_argument('--attributes2', type=str, default=None, required=False,
+                        help='Attributes file for 2nd tracer')
     parser.add_argument('--renormalize-deltas', action="store_true",
                         help="Stacks deltas and renormalizes deltas.")
 
@@ -294,6 +296,8 @@ def main(cmdargs):
         cf.alpha2 = args.z_evol2
         if args.in_dir2 is None:
             args.in_dir2 = args.in_dir
+        if args.attributes2 is None:
+            args.attributes2 = args.attributes
         if args.lambda_abs2:
             cf.lambda_abs2 = constants.ABSORBER_IGM[args.lambda_abs2]
         else:
@@ -313,7 +317,7 @@ def main(cmdargs):
             z_min_qso=args.z_min_sources,
             z_max_qso=args.z_max_sources,
             varlss_mod_factor=args.varlss_mod_factor,
-            attributes=args.attributes,
+            attributes=args.attributes2,
             renormalize_deltas=args.renormalize_deltas)
         del z_max2
         cf.data2 = data2

bin/picca_dmat.py

@@ -249,6 +249,18 @@ def main(cmdargs):
                         action='store_true',
                         help='Ignore redshift evolution when computing distortion matrix')
 
+    parser.add_argument('--varlss-mod-factor', type=float, default=None,
+                        help='Modifies weights with this factor. Requires '
+                             'IVAR column to be present in deltas and an input'
+                             ' attributes file.')
+    parser.add_argument('--attributes', type=str, default=None,
+                        help='Attributes file with VAR_FUNC extension with '
+                             'lambda, eta, var_lss columns.')
+    parser.add_argument('--attributes2', type=str, default=None, required=False,
+                        help='Attributes file for 2nd tracer')
+    parser.add_argument('--renormalize-deltas', action="store_true",
+                        help="Stacks deltas and renormalizes deltas.")
+
     args = parser.parse_args(cmdargs)
 
     if args.nproc is None:
@@ -310,7 +322,10 @@ def main(cmdargs):
                                                   nproc=args.nproc,
                                                   rebin_factor=args.rebin_factor,
                                                   z_min_qso=args.z_min_sources,
-                                                  z_max_qso=args.z_max_sources)
+                                                  z_max_qso=args.z_max_sources,
+                                                  varlss_mod_factor=args.varlss_mod_factor,
+                                                  attributes=args.attributes,
+                                                  renormalize_deltas=args.renormalize_deltas)
     del z_max
     cf.data = data
     cf.num_data = num_data
@@ -325,6 +340,8 @@ def main(cmdargs):
         cf.alpha2 = args.z_evol2
         if args.in_dir2 is None:
             args.in_dir2 = args.in_dir
+        if args.attributes2 is None:
+            args.attributes2 = args.attributes
         if args.lambda_abs2:
             cf.lambda_abs2 = constants.ABSORBER_IGM[args.lambda_abs2]
         else:
@@ -341,7 +358,10 @@ def main(cmdargs):
             nproc=args.nproc,
             rebin_factor=args.rebin_factor,
             z_min_qso=args.z_min_sources,
-            z_max_qso=args.z_max_sources)
+            z_max_qso=args.z_max_sources,
+            varlss_mod_factor=args.varlss_mod_factor,
+            attributes=args.attributes2,
+            renormalize_deltas=args.renormalize_deltas)
         del z_max2
         cf.data2 = data2
         cf.num_data2 = num_data2

bin/picca_xdmat.py

@@ -248,6 +248,17 @@ def main(cmdargs):
                         action='store_true',
                         help='Ignore redshift evolution when computing distortion matrix')
 
+
+    parser.add_argument('--varlss-mod-factor', type=float, default=None,
+                        help='Modifies weights with this factor. Requires '
+                             'IVAR column to be present in deltas and an input'
+                             ' attributes file.')
+    parser.add_argument('--attributes', type=str, default=None,
+                        help='Attributes file with VAR_FUNC extension with '
+                             'lambda, eta, var_lss columns.')
+    parser.add_argument('--renormalize-deltas', action="store_true",
+                        help="Stacks deltas and renormalizes deltas.")
+
     args = parser.parse_args(cmdargs)
     if args.nproc is None:
         args.nproc = cpu_count() // 2
@@ -303,7 +314,10 @@ def main(cmdargs):
                                                   nproc=args.nproc,
                                                   rebin_factor=args.rebin_factor,
                                                   z_min_qso=args.z_min_sources,
-                                                  z_max_qso=args.z_max_sources)
+                                                  z_max_qso=args.z_max_sources,
+                                                  varlss_mod_factor=args.varlss_mod_factor,
+                                                  attributes=args.attributes,
+                                                  renormalize_deltas=args.renormalize_deltas)
     xcf.data = data
     xcf.num_data = num_data
     userprint("\n")

py/picca/utils.py

@@ -13,6 +13,7 @@
 import sys
 import numpy as np
 import fitsio
+from astropy.io import fits
 import iminuit
 
 from scipy import interpolate
@@ -507,15 +508,19 @@ def modify_weights_with_varlss_factor(data, attributes, varlss_mod_factor):
         varlss_mod_factor: float
             Multiplicative factor for var_lss
     """
+    att = fits.open(attributes) # need astropy's case-insensitivity to work with qsonic and picca attributes files
     try:
-        varfunc = fitsio.read(attributes, ext="VAR_FUNC")
+        varfunc = att['VAR_FUNC']
     except OSError:
-        varfunc = fitsio.read(attributes, ext="VAR_FUNC-fit")
-    varfunc['lambda'] = np.log10(varfunc['lambda'])
+        varfunc = att['VAR_FUNC-fit']
+    try:
+        loglam = np.log10(varfunc.data['lambda'])
+    except KeyError:
+        loglam = varfunc.data['loglam']
     interp_eta = interpolate.interp1d(
-        varfunc['lambda'], varfunc['eta'], fill_value='extrapolate', kind='cubic')
+        loglam, varfunc.data['eta'], fill_value='extrapolate', kind='cubic')
     interp_varlss = interpolate.interp1d(
-        varfunc['lambda'], varfunc['var_lss'], fill_value='extrapolate', kind='cubic')
+        loglam, varfunc.data['var_lss'], fill_value='extrapolate', kind='cubic')
 
     for delta in data:
         if delta.ivar is None: