make sure cls are included in data fits file

Author: cailmdaley

.gitignore

@@ -180,4 +180,5 @@ cosmo_inference/cosmosis_config/*.ini
 !cosmo_inference/cosmosis_config/cosmosis_pipeline_A.ini
 !cosmo_inference/cosmosis_config/cosmosis_pipeline_glass_mock_00001_cell.ini
 !cosmo_inference/cosmosis_config/cosmosis_pipeline_glass_mock_00001.ini
-!cosmo_inference/cosmosis_config/cosmosis_pipeline_SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1.ini
+!cosmo_inference/cosmosis_config/cosmosis_pipeline_SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1.ini
+!cosmo_inference/cosmosis_config/cosmosis_pipeline_SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1_cell.ini

cosmo_inference/cosmosis_config/cosmosis_pipeline_SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1_cell.ini

@@ -0,0 +1,113 @@
+#parameters used elsewhere in this file
+[DEFAULT]
+SCRATCH = /n09data/guerrini/output_chains/SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1
+FITS_FILE = data/SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1/cosmosis_SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1.fits
+COSMOSIS_DIR = /home/guerrini/cosmosis-standard-library
+
+
+[pipeline]
+values = cosmosis_config/values_psf.ini
+priors = cosmosis_config/priors_psf.ini
+modules = consistency sample_S8 camb load_nz_fits photoz_bias linear_alignment projection add_intrinsic shear_m_bias 2pt_like 
+likelihoods = 2pt_like 
+extra_output = cosmological_parameters/omega_lambda cosmological_parameters/S_8 cosmological_parameters/sigma_8 cosmological_parameters/omega_m
+timing = T
+debug = T
+
+[runtime]
+sampler = polychord
+verbosity = debug
+
+[test]
+save_dir = %(SCRATCH)s/best_fit/SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1_cell
+
+
+[polychord]
+polychord_outfile_root = SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1_cell
+live_points = 192
+feedback = 3
+resume = T
+base_dir = %(SCRATCH)s/polychord
+
+[output]
+filename = %(SCRATCH)s/SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1/samples_SP_v1.4.6_A_minsep=1.0_maxsep=250.0_nbins=20_npatch=1_cell.txt
+format = text
+lock = F
+
+[consistency]
+file = %(COSMOSIS_DIR)s/utility/consistency/consistency_interface.py
+verbose = F
+
+[sample_S8]
+file = %(COSMOSIS_DIR)s/utility/sample_sigma8/sample_S8.py
+
+[camb]
+file = %(COSMOSIS_DIR)s/boltzmann/camb/camb_interface.py
+mode=power
+lmax=2508
+feedback=0
+do_reionization=F
+kmin=1e-5
+kmax=20.0
+nk=200
+zmax=5.0
+zmax_background=5.0
+nz_background=500
+halofit_version=mead2020_feedback
+nonlinear=pk
+neutrino_hierarchy=normal
+kmax_extrapolate = 500.0
+
+[load_nz_fits]
+file = %(COSMOSIS_DIR)s/number_density/load_nz_fits/load_nz_fits.py
+nz_file =%(FITS_FILE)s
+data_sets = SOURCE
+
+[photoz_bias]
+file = %(COSMOSIS_DIR)s/number_density/photoz_bias/photoz_bias.py
+mode = additive
+sample = nz_source
+bias_section = nofz_shifts
+interpolation = cubic
+output_deltaz_section_name = delta_z_out
+
+[linear_alignment]
+file = %(COSMOSIS_DIR)s/intrinsic_alignments/la_model/linear_alignments_interface_znla.py
+method = bk_corrected
+
+[projection]
+file = %(COSMOSIS_DIR)s/structure/projection/project_2d.py
+ell_min_logspaced = 1.0
+ell_max_logspaced = 25000.0
+n_ell_logspaced = 400
+shear-shear = source-source
+shear-intrinsic = source-source
+intrinsic-intrinsic = source-source
+get_kernel_peaks = F
+verbose = F
+
+[add_intrinsic]
+file = %(COSMOSIS_DIR)s/shear/add_intrinsic/add_intrinsic.py
+shear-shear=T
+position-shear=F
+perbin=F
+
+[shear_m_bias]
+file = %(COSMOSIS_DIR)s/shear/shear_bias/shear_m_bias.py
+m_per_bin = True
+; Despite the parameter name, this can operate on xi as well as C_ell.
+cl_section = shear_cl
+verbose = F
+
+[2pt_shear]
+file = %(COSMOSIS_DIR)s/shear/cl_to_xi_nicaea/nicaea_interface.so
+corr_type = 0  ; shear_cl -> shear_xi
+
+[2pt_like]
+file = %(COSMOSIS_DIR)s/likelihood/2pt/2pt_like.py
+data_sets=CELL_EE CELL_BB
+data_file=%(FITS_FILE)s
+gaussian_covariance=F
+covmat_name=COVMAT
+cut_zeros=F
+like_name=2pt_like

cosmo_inference/scripts/cosmosis_fitting.py

@@ -115,6 +115,18 @@ def load_glass_cl(cl_file):
     return ell, cl_ee, cl_bb
 
 
+def load_pseudo_cl_fits(cl_file):
+    """
+    Load pseudo-C_ell data stored in FITS format with columns (ELL, EE, EB, BB).
+    """
+    with fits.open(cl_file) as hdul:
+        data = hdul[1].data
+        ell = np.asarray(data["ELL"], dtype=np.float64)
+        cl_ee = np.asarray(data["EE"], dtype=np.float64)
+        cl_bb = np.asarray(data["BB"], dtype=np.float64)
+    return ell, cl_ee, cl_bb
+
+
 def glass_cl_to_fits(ell, cl_ee, cl_bb):
     """Convert GLASS C_ell arrays to CosmoSIS FITS HDUs for EE and BB."""
     nbins = len(ell)
@@ -545,6 +557,10 @@ def parse_args():
                 ell, cl_ee, cl_bb = load_glass_cl(args.cl_file)
                 cl_ee_hdu, cl_bb_hdu = glass_cl_to_fits(ell, cl_ee, cl_bb)
                 print(f"Loaded Cl: {len(ell)} multipoles")
+            elif args.cl_file.endswith(".fits"):
+                ell, cl_ee, cl_bb = load_pseudo_cl_fits(args.cl_file)
+                cl_ee_hdu, cl_bb_hdu = glass_cl_to_fits(ell, cl_ee, cl_bb)
+                print(f"Loaded Cl: {len(ell)} multipoles (FITS pseudo-Cl)")
             else:
                 raise NotImplementedError(f"Cl format not supported: {args.cl_file}")