Merge pull request #6 from LSSTDESC/develop

Migrating the Legacy Blinding Code from the other repo into this one

.github/workflows/CI.yml

@@ -0,0 +1,56 @@
+# Author - Stuart McAlpine - [email protected] - Jan 2023
+name: DESC Legacy Blinding for Cosmosis
+
+# How does the workflow get triggered?
+on:
+  # Triggers when push/pull-request made to the main branch.
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+      - develop
+
+# List of jobs for this workflow.
+
+jobs:
+  # Our pytest job.
+  legacy_blinding-pytest:
+    # Our strategy lists the OS and Python versions we want to test on.
+    strategy:
+      # Don't quit all jobs if only one job fails.
+      fail-fast: false
+      matrix:
+        python-version: ["3.9"]
+        os: [ubuntu-20.04, macos-latest]
+        include:
+          - os: ubuntu-20.04
+            INSTALL_DEPS: sudo apt-get update && sudo apt-get -y install gfortran-7 swig libopenmpi-dev openmpi-bin libopenblas-dev && sudo ln -s `which gfortran-7` /usr/local/bin/gfortran
+          - os: macos-latest
+            INSTALL_DEPS: brew update-reset && HOMEBREW_NO_AUTO_UPDATE=1  HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install gcc swig libomp open-mpi openblas && if [ ! -f /usr/local/bin/gfortran ]; then ln -s /usr/local/bin/gfortran-$(brew list --versions gcc | awk '{print $2}' | cut -d. -f1) /usr/local/bin/gfortran; fi
+
+    # What operating system is this job running on?
+    runs-on: ${{ matrix.os }}
+
+    # Our CI steps for this job.
+    steps:
+      # Check out this repository code.
+      - name: Check out repository code
+        uses: actions/checkout@v3
+
+      # Install Python.
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: ${{ matrix.INSTALL_DEPS }}
+
+      # Install our package.
+      - name: Install legacy_blinding
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .
+          pytest ./tests

.gitignore

@@ -2,6 +2,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
+*.DS_Store
 
 # C extensions
 *.so

README.md

@@ -1,2 +1,40 @@
-# legacy_blinding
-Repository with Legacy Cosmology Blinding for 3x2pt data-vector blinding using Cosmosis v2
+# Legacy Cosmosis Blinding for 2pt Data-Vectors using Cosmosis
+
+This repository contains an implementation of [Muir et al. 2020](https://arxiv.org/abs/1911.05929) data-vector blinding strategy using Cosmosis V2.
+The package in this repository is a direct adaptation of Jessie Muir's DES Y3 blinding scripts to the DESC context.
+
+For the DESC Blinding Library, see [here](https://github.com/LSSTDESC/Blinding).
+
+## Installation
+- Install cosmosis via `conda install -c conda-forge cosmosis`
+- Activate the cosmosis configuration via `source cosmosis-configure`
+- Install the cosmosis standard library via `conda install -c conda-forge cosmosis-build-standard-library`
+- Install the standard library in the correct cosmosis folder `cosmosis-build-standard-library -i`
+
+### Legacy Blinding installation 
+Simply install with 
+```bash
+python -m pip install -e .
+```
+
+### Test the installation
+To run the unit tests:
+```bash
+cd tests
+pytest .
+```
+
+## Usage
+> Don't forget to `source cosmosis-configure`
+
+To get the docstring on the command-line interface:
+```
+python -m blind_2pt_cosmosis --help
+```
+
+To run an example: 
+```bash
+python -m blind_2pt_cosmosis -u src/blind_2pt_cosmosis/cosmosis_files/sim_fiducial.fits [--log-level DEBUG]
+```
+
+[!] Note: You can also include all the command line arguments in a `.config` file and call `python -m blind_2pt_cosmosis @example.config` instead. This will be adapted to use `yaml` files in the near future.

pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "legacy_blinding"
+description = "Legacy Cosmosis Blinding for DESC. This is a Cosmosis V2 port of Jessie Muir's legacy_blinding scripts for DES-Y3."
+readme = "README.md"
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+maintainers = [
+    {name = "Arthur Loureiro", email = "[email protected]"},
+    {name = "Jessie Muir", email =  "[email protected]"},
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy>=1.24.0",
+    "scipy>=1.9.0",
+    "cosmosis>=2.5",
+    "astropy>=5.1",
+    "pytest>=7.2.5",
+    "argparse>=1.0",
+    "sacc>=0.12",
+]
+keywords = ["desc", "python", "blinding", "cosmosis"]
+dynamic = ["version"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"blind_2pt_cosmosis" = ["cosmosis_files/*.txt", "cosmosis_files/*.ini"]
+

src/blind_2pt_cosmosis/__init__.py

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+# Author: Arthur Loureiro <[email protected]> & Jessie Muir <[email protected]>
+from ._version import __version__

src/blind_2pt_cosmosis/__main__.py

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+import logging
+from .param_shifts import draw_flat_param_shift, get_factordict
+from .io import get_parser, get_stored_seed_and_tag
+from .run_cosmosis_2pt import run_cosmosis_togen_2ptdict
+from .twopt_utils import apply_2pt_blinding_and_save_fits
+
+
+def main():
+    """
+    main function to be called from command line
+    """
+    # gets the parser from the io module
+    parser = get_parser()
+    args = parser.parse_args()
+
+    # Configure the logger level based on the input argument
+    log_level = getattr(logging, args.log_level)
+    logging.basicConfig(level=log_level, format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+
+    # Create a logger for the __main__ module
+    logger = logging.getLogger("2pt_blinding")
+    logger.debug(args)
+
+    params_shifts = draw_flat_param_shift(args.seed, args.paramshifts)
+    logger.debug(f"Parameters shifts are: {params_shifts}")
+
+    #get blinding factors
+    reff_dict = run_cosmosis_togen_2ptdict(inifile=args.ini) #args.ini is a template
+    logger.debug(f"Calculated Reference Dict")
+    # FIXME: Add nz_file and angles_file to args
+    shift_dict = run_cosmosis_togen_2ptdict(inifile=args.ini, pdict=params_shifts,
+                                             nz_file=None, angles_file=None)
+    logger.debug(f"Calculated Shifted Dict")
+    #gets the blinding factors data vectors
+    factor_dict = get_factordict(reff_dict, shift_dict, bftype = args.bftype)
+    logger.debug(f"Calculated Blinded Data Vectors")
+
+    # Gets some I/O information
+    storeseed, tagstr = get_stored_seed_and_tag(args)
+
+    # applies the shift to the 2pt data-vector:
+    #FIXME: This function is also saving the file, we want to split it!
+    apply_2pt_blinding_and_save_fits(factor_dict, origfitsfile=args.origfits,
+                                    outfname=args.outfname, outftag=tagstr,
+                                    bftype=args.bftype, storeseed = storeseed)
+
+
+if __name__ == '__main__':
+    main()

src/blind_2pt_cosmosis/_version.py

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+__version__ = "2023.10.11"

src/blind_2pt_cosmosis/cosmosis_files/blinding_values_template.ini

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+[cosmological_parameters]
+omega_m      =  0.1	0.3	0.9
+h0           =  0.55	0.69	0.91
+omega_b      =  0.03	0.048	0.12
+n_s          =  0.87	0.97	1.07
+sigma_8_input =  0.2  	0.843  	1.6
+A_s          =  0.5e-09	 2.19e-9  5.0e-09
+; omnuh2       =  0.0006	 0.00083 	   0.01 
+omnuh2       =  0.0
+massive_nu   =  0
+massless_nu  =  3.046
+omega_k      =  0.0
+tau          =  0.0697186
+w            =  -1.0
+;Helium mass fraction.  Needed for Planck 
+yhe          = 0.245341
+
+; %include ${METHODSDIR}/cosmosis/de_models/${DEMODEL}.ini
+
+[shear_calibration_parameters]
+m1 = -0.1  0.0  0.1
+m2 = -0.1  0.0  0.1 
+m3 = -0.1  0.0  0.1
+m4 = -0.1  0.0  0.1
+
+[wl_photoz_errors]
+bias_1 = -0.1   0.0   0.1
+bias_2 = -0.1   0.0   0.1
+bias_3 = -0.1   0.0   0.1
+bias_4 = -0.1   0.0   0.1
+
+[lens_photoz_errors]
+bias_1 = -0.05  0.0  0.05
+bias_2 = -0.05  0.0  0.05
+bias_3 = -0.05  0.0  0.05
+bias_4 = -0.05  0.0  0.05
+bias_5 = -0.05  0.0  0.05
+
+[bias_lens]
+b1 = 0.8  1.7   3.0
+b2 = 0.8  1.7   3.0
+b3 = 0.8  1.7   3.0
+b4 = 0.8  2.0    3.0
+b5 = 0.8  2.0    3.0
+
+[mag_alpha_lens]
+; alpha_1 = -4. 0.903125 4.
+; alpha_2 = -4. 0.68572965 4.
+; alpha_3 = -4. 0.65340057 4.
+; alpha_4 = -4. 1.58867862 4.
+; alpha_5 = -4. 1.93754879 4.
+alpha_1 = 0.903125 
+alpha_2 = 0.68572965 
+alpha_3 = 0.65340057 
+alpha_4 = 1.58867862 
+alpha_5 = 1.93754879 
+
+[intrinsic_alignment_parameters]
+z_piv = 0.62
+A1 = -5.0  0.7  5.0
+A2 = -5.0  -1.36  5.0 
+alpha1=-5.0  -1.7  5.0
+alpha2=-5.0  -2.5  5.0
+bias_ta = 0.0  1.0  2.0
+#bias_tt = 1.0
+
+
+
+

src/blind_2pt_cosmosis/cosmosis_files/default_blinding_template.ini

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+; ############################################################
+; This is a template file that is referenced by blind_2pt_usingcosmosis.py
+;   It is used as a template for running cosmosis to generate
+;   blinding factors to be applied to 2pt data vectors. To adapt
+;   for a specific pipeline:
+;   1. Edit the %include params.ini line to point towards your baseline pipeline file.
+;   2. The values file should be edited to match your fiducial run. Since we want
+;      to blind sigma8, sigma8_input needs to be in the cosmological parameters,
+;      so it may need to be a values file written specifically for blinding. You could
+;      always set it up to %include your standard values file though.
+;      >> the start values for each parameter is what will be used as reference vals
+;         when generating the blinding factors. 
+;   3. Make sure the file in 2PT_FILE points to a file with the format expected by
+;      your pipeline (with the same binning, etc.)
+;   4. The modules list in [pipeline] should match your standard pipeline with a one
+;      addition: you need sigma8_rescale to be able to include sigma8_input as a parameter
+; ############################################################
+
+
+; import baseline parameter file; change this to point towards the params.ini file for
+; whatever main pipeline you want to mimic
+%include ./src/blind_2pt_cosmosis/cosmosis_files/params.ini
+
+[DEFAULT]
+; this 2PT file is where we'll pull the n(z) info for computing blinding factors
+2PT_FILE = ./src/blind_2pt_cosmosis/cosmosis_files/sim_fiducial.fits
+;2PT_FILE = pipeline/2pt_sim_1110_baseline_Y3cov.fits 
+;should this be my 2pt measurement DV?
+
+[pipeline]
+; THIS MODULE LIST SHOULD MATCH YOUR SETTINGS FOR YOUR STANDARD ANALYSIS PIPELINE
+quiet=T
+timing=F
+debug=F
+priors = ./src/blind_2pt_cosmosis/cosmosis_files/priors.ini
+; sigma8_rescale included so we can set sigma8 as input
+modules = consistency camb extrapolate fits_nz lens_photoz_bias fast_pt source_photoz_bias unbiased_galaxies IA pk_to_cl_gg pk_to_cl add_magnification add_intrinsic 2pt_shear 2pt_gal 2pt_gal_shear shear_m_bias 2pt_like
+; if you want to blind sigma_8, set up values file to have sigma8_input as a parameter rather than A_s
+values = ./src/blind_2pt_cosmosis/cosmosis_files/blinding_values_template.ini
+
+
+[sigma8_rescale]
+file = cosmosis-standard-library/utility/sample_sigma8/sigma8_rescale.py
+
+[test]
+; if the sampler happens to be set to test, make sure it doesn't
+; save any output when we do blinding. We don't want to see the cosmology
+; and 2pt functions that go into making the blinding factor!
+save_dir=
+
+