Update config interaction. Not yet working

Author: andreicuceu

lya_2pt/defaults.py

@@ -0,0 +1,48 @@
+
+cosmo = {
+    "use-picca-cosmo": False,
+    "omega_m": 0.315,
+    "omega_r": 7.963219132297603e-05,
+    "hubble-constant": 67.36,
+    "use-h-units": True,
+    "omega_k": 0.0,
+    "w0": -1,
+}
+
+
+settings = {
+    "nside": 16,
+    "num-cpu": 1,
+    "z_min": 0,
+    "z_max": 10,
+    "rp_min": 0,
+    "rp_max": 200,
+    "rt_max": 200,
+    "num_bins_rp": 50,
+    "num_bins_rt": 50,
+    "num_bins_rp_model": 50,
+    "num_bins_rt_model": 50,
+    "rejection_fraction": 0.99,
+    "get-old-distortion": True
+}
+
+tracer_reader = {
+    "tracer-type": "continuous",
+    "absorption-line": "LYA",
+    "project-deltas": True,
+    "projection-order": 1,
+    "use-old-projection": True,
+    "rebin": 1,
+    "redshift-evolution": 2.9,
+    "reference-redshift": 2.25,
+}
+
+output = {
+    "name": "lyaxlya",
+}
+
+export = {
+    "export-correlation": False,
+    "export-distortion": False,
+    "smooth-covariance": True,
+}

lya_2pt/export.py

@@ -3,16 +3,17 @@
 from multiprocessing import Pool
 
 from lya_2pt.utils import parse_config
+from lya_2pt import defaults
 
-accepted_options = [
-    "export-correlation", "export-distortion", "smooth-covariance"
-]
+# accepted_options = [
+#     "export-correlation", "export-distortion", "smooth-covariance"
+# ]
 
-defaults = {
-    "export-correlation": False,
-    "export-distortion": False,
-    "smooth-covariance": True,
-}
+# defaults = {
+#     "export-correlation": False,
+#     "export-distortion": False,
+#     "smooth-covariance": True,
+# }
 
 
 class Export:
@@ -22,7 +23,7 @@ class Export:
     Writes final correlation
     """
     def __init__(self, config, name, output_directory, num_cpu):
-        self.config = parse_config(config, defaults, accepted_options)
+        self.config = parse_config(config, defaults.export)
 
         self.num_cpu = num_cpu
         self.name = name

lya_2pt/forest_healpix_reader.py

@@ -6,23 +6,24 @@
 from lya_2pt.errors import ReaderException
 from lya_2pt.utils import parse_config
 from lya_2pt.read_io import read_from_image, read_from_hdu
-
-accepted_options = [
-    "input-dir", "tracer-type", "absorption-line", "project-deltas",
-    "projection-order", "use-old-projection", "rebin",
-    "redshift-evolution", "reference-redshift"
-]
-
-defaults = {
-    "tracer-type": "continuous",
-    "absorption-line": "LYA",
-    "project-deltas": True,
-    "projection-order": 1,
-    "use-old-projection": True,
-    "rebin": 1,
-    "redshift-evolution": 2.9,
-    "reference-redshift": 2.25,
-}
+from lya_2pt import defaults
+
+# accepted_options = [
+#     "input-dir", "tracer-type", "absorption-line", "project-deltas",
+#     "projection-order", "use-old-projection", "rebin",
+#     "redshift-evolution", "reference-redshift"
+# ]
+
+# defaults = {
+#     "tracer-type": "continuous",
+#     "absorption-line": "LYA",
+#     "project-deltas": True,
+#     "projection-order": 1,
+#     "use-old-projection": True,
+#     "rebin": 1,
+#     "redshift-evolution": 2.9,
+#     "reference-redshift": 2.25,
+# }
 
 
 class ForestHealpixReader:
@@ -73,7 +74,7 @@ def __init__(self, config, file, cosmo, auto_flag=False, need_distortion=False):
         ReaderException if the blinding strategy is not valid
         """
         # parse configuration
-        reader_config = parse_config(config, defaults, accepted_options)
+        reader_config = parse_config(config, defaults.tracer_reader)
         self.healpix_id = int(file.name.split("delta-")[-1].split(".fits")[0])
 
         # extract parameters from config

lya_2pt/interface.py

@@ -2,38 +2,41 @@
 
 import numpy as np
 import tqdm
+from lyacosmo import AstropyCosmo, PiccaCosmo
 
 import lya_2pt.global_data as globals
 from lya_2pt.correlation import compute_xi
 from lya_2pt.distortion import compute_dmat
-from lya_2pt.cosmo import Cosmology
+# from lya_2pt.cosmo import Cosmology
 from lya_2pt.forest_healpix_reader import ForestHealpixReader
 from lya_2pt.tracer2_reader import Tracer2Reader
 from lya_2pt.utils import find_path, parse_config, compute_ang_max
 from lya_2pt.output import Output
 from lya_2pt.export import Export
-
-accepted_options = [
-    "nside", "num-cpu", "z_min", "z_max", "rp_min", "rp_max", "rt_max",
-    "num_bins_rp", "num_bins_rt", "num_bins_rp_model", "num_bins_rt_model",
-    "rejection_fraction", "get-old-distortion"
-]
-
-defaults = {
-    "nside": 16,
-    "num-cpu": 1,
-    "z_min": 0,
-    "z_max": 10,
-    "rp_min": 0,
-    "rp_max": 200,
-    "rt_max": 200,
-    "num_bins_rp": 50,
-    "num_bins_rt": 50,
-    "num_bins_rp_model": 50,
-    "num_bins_rt_model": 50,
-    "rejection_fraction": 0.99,
-    "get-old-distortion": True
-}
+from lya_2pt import defaults
+
+
+# accepted_options = [
+#     "nside", "num-cpu", "z_min", "z_max", "rp_min", "rp_max", "rt_max",
+#     "num_bins_rp", "num_bins_rt", "num_bins_rp_model", "num_bins_rt_model",
+#     "rejection_fraction", "get-old-distortion"
+# ]
+
+# defaults = {
+#     "nside": 16,
+#     "num-cpu": 1,
+#     "z_min": 0,
+#     "z_max": 10,
+#     "rp_min": 0,
+#     "rp_max": 200,
+#     "rt_max": 200,
+#     "num_bins_rp": 50,
+#     "num_bins_rt": 50,
+#     "num_bins_rp_model": 50,
+#     "num_bins_rt_model": 50,
+#     "rejection_fraction": 0.99,
+#     "get-old-distortion": True
+# }
 
 
 class Interface:
@@ -79,11 +82,23 @@ def __init__(self, config):
         """
         self.config = config
 
-        # intialize cosmology
-        self.cosmo = Cosmology(config["cosmology"])
+        # Intialize cosmology
+        cosmo_config = parse_config(config["cosmology"], defaults.cosmo)
+        if cosmo_config.getboolean("use-picca-cosmo"):
+            self.cosmo = PiccaCosmo(
+                cosmo_config.getfloat('omega_m'), cosmo_config.getfloat('omega_k'),
+                cosmo_config.getfloat('omega_r'), cosmo_config.getfloat('w0')
+            )
+        else:
+            self.cosmo = AstropyCosmo(
+                cosmo_config.getfloat('omega_m'), cosmo_config.getfloat('omega_k'),
+                cosmo_config.getfloat('omega_r'), cosmo_config.getfloat('w0'),
+                cosmo_config.getfloat('hubble-constant'), cosmo_config.getboolean('use-h-units'),
+            )
+        # self.cosmo = Cosmology(config["cosmology"])
 
         # parse config
-        self.settings = parse_config(config["settings"], defaults, accepted_options)
+        self.settings = parse_config(config["settings"], defaults.settings)
         globals.z_min = self.settings.getfloat("z_min")
         globals.z_max = self.settings.getfloat("z_max")
         globals.rp_min = self.settings.getfloat('rp_min')

lya_2pt/output.py

@@ -1,19 +1,20 @@
 import fitsio
 
 from lya_2pt.utils import check_dir, parse_config, find_path
+from lya_2pt import defaults
 
-accepted_options = [
-    "name", "output-dir"
-]
+# accepted_options = [
+#     "name", "output-dir"
+# ]
 
-defaults = {
-    "name": "lyaxlya",
-}
+# defaults = {
+#     "name": "lyaxlya",
+# }
 
 
 class Output:
     def __init__(self, config):
-        self.config = parse_config(config, defaults, accepted_options)
+        self.config = parse_config(config, defaults.output)
         self.name = self.config.get('name')
         self.output_directory = find_path(self.config.get('output-dir'), enforce=False)
         check_dir(self.output_directory)

lya_2pt/tracer2_reader.py

@@ -7,13 +7,14 @@
 from lya_2pt.forest_healpix_reader import ForestHealpixReader
 from lya_2pt.utils import find_path, parse_config
 from lya_2pt.errors import ReaderException
+from lya_2pt import defaults
 
 # Read defaults from the healpix reader and add tracer2 specific options
-accepted_options = forest_healpix_reader.accepted_options
-accepted_options += []
+# accepted_options = forest_healpix_reader.accepted_options
+# accepted_options += []
 
-defaults = forest_healpix_reader.defaults
-defaults |= {}
+# defaults = forest_healpix_reader.defaults
+# defaults |= {}
 
 
 class Tracer2Reader:
@@ -44,7 +45,7 @@ def __init__(self, config, healpix_neighbours, cosmo, num_cpu, need_distortion=F
         Fiducial cosmology used to go from angles and redshift to distances
         """
         # parse configuration
-        reader_config = parse_config(config, defaults, accepted_options)
+        reader_config = parse_config(config, defaults.tracer_reader)
 
         self.tracers = {}
 

lya_2pt/utils.py

@@ -8,7 +8,7 @@
 from lya_2pt.errors import ParserError
 
 
-def parse_config(config, defaults, accepted_options):
+def parse_config(config, defaults):
     """Parse the given configuration
 
     Check that all required variables are present
@@ -22,9 +22,6 @@ def parse_config(config, defaults, accepted_options):
     defaults: dict
     The default options for the given config section
 
-    accepted_options: list of str
-    The accepted keys for the given config section
-
     Return
     ------
     config: configparser.SectionProxy
@@ -35,17 +32,11 @@ def parse_config(config, defaults, accepted_options):
         if key not in config:
             config[key] = str(value)
 
-    # make sure all the required variables are present
-    for key in accepted_options:
-        if key not in config:
-            raise ParserError(f"Missing option {key}")
-
     # check that all arguments are valid
     for key in config:
-        if key not in accepted_options:
+        if key not in defaults:
             raise ParserError(
-                f"Unrecognised option. Found: '{key}'. Accepted options are "
-                f"{accepted_options}")
+                f"Unrecognised option. Found: '{key}'. Accepted options are {defaults.keys()}")
 
     return config
 

requirements.txt

@@ -3,6 +3,7 @@ scipy
 astropy
 healpy
 fitsio
+lyacosmo
 numba
 setuptools
 gitpython