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cailmdaleycailmdaley
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update cosmosis inference pipeline and cosmosis_fitting to allow more flexible naming conventions
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‎cosmo_inference/pipeline.sh‎

Lines changed: 25 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -28,48 +28,52 @@ do
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;;
2929
'c')
3030
read -p 'COVARIANCE FILE: ' covmat_file;
31+
read -p 'OUTPUT STUB (without extension): ' output_stub;
3132
echo "Processing covariance matrix";
32-
python scripts/cosmocov_process.py $covmat_file
33+
python scripts/cosmocov_process.py $covmat_file $output_stub
3334
;;
3435
'i')
35-
read -p 'ROOT: ' root;
36+
read -p 'XI ROOT: ' xi_root;
37+
read -p 'TAU ROOT: ' tau_root;
38+
read -p 'COSMOSIS ROOT: ' cosmosis_root;
3639
read -p 'COSMO_VAL OUTPUT FOLDER: ' output_folder;
3740
read -p 'NZ FILE:' nz_file;
3841
read -p 'USE RHO/TAU_STATS? (y/n): ' rhotau_stats;
3942
echo $rhotau_stats
4043
read -p 'COV_XI MAT TXT FILE:' covmat;
4144
read -p 'OUTPUT MCMC CHAIN FOLDER: ' data;
4245

43-
out_file="data/${root}/cosmosis_${root}.fits";
46+
# Use cosmosis_root for output file naming
47+
out_file="data/${cosmosis_root}/cosmosis_${cosmosis_root}.fits";
4448

4549
#LG: add check if xi_plus/xi_minus fits file exists
46-
python scripts/cosmosis_fitting.py $root $output_folder $covmat $nz_file $out_file $rhotau_stats;
50+
python scripts/cosmosis_fitting.py $xi_root $tau_root $utput_folder $covmat $nz_file $out_file $rhotau_stats;
4751

4852
if [ "${rhotau_stats}" == "y" ]; then
49-
cp cosmosis_config/cosmosis_pipeline_A_psf.ini cosmosis_config/cosmosis_pipeline_${root}.ini;
53+
cp cosmosis_config/cosmosis_pipeline_A_psf.ini cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
5054
else
51-
cp cosmosis_config/cosmosis_pipeline_A_ia.ini cosmosis_config/cosmosis_pipeline_${root}.ini;
55+
cp cosmosis_config/cosmosis_pipeline_A_ia.ini cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
5256
fi
5357

54-
sed -i "/^\[DEFAULT\]/a\SCRATCH = ${data}" cosmosis_config/cosmosis_pipeline_${root}.ini;
55-
sed -i "/^\[DEFAULT\]/a\FITS_FILE = ${out_file}" cosmosis_config/cosmosis_pipeline_${root}.ini;
56-
sed -i "/^\[output\]/a\filename = %(SCRATCH)s/${root}/samples_${root}.txt" cosmosis_config/cosmosis_pipeline_${root}.ini;
58+
sed -i "/^\[DEFAULT\]/a\SCRATCH = ${data}" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
59+
sed -i "/^\[DEFAULT\]/a\FITS_FILE = ${out_file}" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
60+
sed -i "/^\[output\]/a\filename = %(SCRATCH)s/${cosmosis_root}/samples_${cosmosis_root}.txt" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
5761
if [ "${rhotau_stats}" == "y" ]; then
58-
sed -i "/^\[pipeline\]/a\values = cosmosis_config/values_psf.ini" cosmosis_config/cosmosis_pipeline_${root}.ini;
59-
sed -i "/^\[pipeline\]/a\priors = cosmosis_config/priors_psf.ini" cosmosis_config/cosmosis_pipeline_${root}.ini;
60-
sed -i "/^\[2pt_like]/a\file = %(COSMOSIS_DIR)s/likelihood/2pt/2pt_like_xi_sys.py" cosmosis_config/cosmosis_pipeline_${root}.ini;
61-
sed -i "/^\[2pt_like]/a\data_sets=XI_PLUS XI_MINUS TAU_0_PLUS TAU_2_PLUS" cosmosis_config/cosmosis_pipeline_${root}.ini;
62-
sed -i "/^\[2pt_like]/a\add_xi_sys=T" cosmosis_config/cosmosis_pipeline_${root}.ini;
62+
sed -i "/^\[pipeline\]/a\values = cosmosis_config/values_psf.ini" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
63+
sed -i "/^\[pipeline\]/a\priors = cosmosis_config/priors_psf.ini" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
64+
sed -i "/^\[2pt_like]/a\file = %(COSMOSIS_DIR)s/likelihood/2pt/2pt_like_xi_sys.py" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
65+
sed -i "/^\[2pt_like]/a\data_sets=XI_PLUS XI_MINUS TAU_0_PLUS TAU_2_PLUS" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
66+
sed -i "/^\[2pt_like]/a\add_xi_sys=T" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
6367
else
64-
sed -i "/^\[pipeline\]/a\values = cosmosis_config/values_ia.ini" cosmosis_config/cosmosis_pipeline_${root}.ini;
65-
sed -i "/^\[pipeline\]/a\priors = cosmosis_config/priors.ini" cosmosis_config/cosmosis_pipeline_${root}.ini;
66-
sed -i "/^\[2pt_like]/a\file = %(COSMOSIS_DIR)s/likelihood/2pt/2pt_like.py" cosmosis_config/cosmosis_pipeline_${root}.ini;
67-
sed -i "/^\[2pt_like]/a\data_sets=XI_PLUS XI_MINUS" cosmosis_config/cosmosis_pipeline_${root}.ini;
68+
sed -i "/^\[pipeline\]/a\values = cosmosis_config/values_ia.ini" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
69+
sed -i "/^\[pipeline\]/a\priors = cosmosis_config/priors.ini" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
70+
sed -i "/^\[2pt_like]/a\file = %(COSMOSIS_DIR)s/likelihood/2pt/2pt_like.py" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
71+
sed -i "/^\[2pt_like]/a\data_sets=XI_PLUS XI_MINUS" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
6872
fi
69-
sed -i "/^\[polychord\]/a\polychord_outfile_root = ${root}" cosmosis_config/cosmosis_pipeline_${root}.ini;
73+
sed -i "/^\[polychord\]/a\polychord_outfile_root = ${cosmosis_root}" cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini;
7074

71-
echo "Prepared CosmoSIS configuration file in cosmosis_config/cosmosis_pipeline_${root}.ini";
72-
echo "You can now run the inference with the command: cosmosis cosmosis_config/cosmosis_pipeline_${root}.ini"
75+
echo "Prepared CosmoSIS configuration file in cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini";
76+
echo "You can now run the inference with the command: cosmosis cosmosis_config/cosmosis_pipeline_${cosmosis_root}.ini"
7377
;;
7478
'm')
7579
# LG: also convert this into a script to directly output contour plots

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