fesc LyA constraints added

Author: sambit-giri

requirements.txt

@@ -8,6 +8,7 @@ scikit-image
 tqdm
 joblib
 pandas
+openpyxl
 pytest
 # torch==2.1.0
 # numba

src/tools21cm/compare_constraints.py

@@ -1,9 +1,33 @@
 import numpy as np
 import matplotlib.pyplot as plt 
 import os, sys 
+from .read_files import get_package_resource_path
+
+class EscapeFractionLymanAlpha:
+    def __init__(self, verbose=True):
+        self.verbose = verbose
+        if self.verbose:
+            print('--- Lyman-alpha Escape Fraction ---')
+        self._load_constraints()
+    
+    def _load_constraints(self):
+        import pandas as pd
+
+        self.fesc_LymanAlpha_constraints = {}
+        filename = get_package_resource_path('tools21cm', 'input_data/fesc_LyA_constraints.xlsx')
+
+        name = 'Napolitano+2024'
+        df = pd.read_excel(filename, sheet_name=name, engine='openpyxl')
+        self.fesc_LymanAlpha_constraints[name] = df
+
+        if self.verbose:
+            print(f'Lyman-alpha escapse fraction references:\n{list(self.fesc_LymanAlpha_constraints.keys())}')
 
 class ReionizationHistory:
-    def __init__(self):
+    def __init__(self, verbose=True):
+        self.verbose = verbose
+        if self.verbose:
+            print('--- Reionization History ---')
         self._load_constraints() 
         self._load_models()
 
@@ -175,6 +199,9 @@ def _load_constraints(self):
                 {"redshift": 6.6, "redshift_error": [-0.0,0.0], "value": 0.21, "error": [-0.14,0.19], "type": "measurement", "method": method},
             ]
 
+        if self.verbose:
+            print(f'Observations:\n{list(self.neutral_fraction_constraints.keys())}')
+        
     def _load_models(self):
         self.neutral_fraction_models = {}
         method = 'pyC2Ray'
@@ -276,6 +303,9 @@ def _load_models(self):
                                     "method": method, "name": "Evolving IMF"},
         ]
 
+        if self.verbose:
+            print(f'Theory:\n{list(self.neutral_fraction_constraints.keys())}')
+
 if __name__ == "__main__":
     import matplotlib.pyplot as plt
     from matplotlib.cm import ScalarMappable

src/tools21cm/input_data/fesc_LyA_constraints.xlsx

@@ -5,7 +5,7 @@
 from . import cosmo as cm
 from . import conv
 from .const import KB_SI, c_light_cgs, c_light_SI, janskytowatt
-from importlib.resources import files
+from .read_files import get_package_resource_path
 import astropy.units as u
 from astropy.coordinates import EarthLocation
 
@@ -473,14 +473,14 @@ def get_SKA_Low_layout(subarray_type="AA4", unit='ecef', verbose=True):
         filename = 'input_data/skalow1_layout.txt'
 
     # Load lat, lon, height from file
-    lon, lat, height = np.loadtxt(str(files('tools21cm') / 'input_data/central_geographic_position.txt'))
+    lon, lat, height = np.loadtxt(get_package_resource_path('tools21cm', 'input_data/central_geographic_position.txt'))
 
     # EarthLocation of the array center
     core = EarthLocation(lat=lat * u.deg, lon=lon * u.deg, height=height * u.m)
     origin_ecef = np.array([core.x.value, core.y.value, core.z.value])  # in meters
 
     # Load ENU antenna positions
-    path_to_file = str(files('tools21cm') / filename)
+    path_to_file = get_package_resource_path('tools21cm', filename)
     ant_enu = np.loadtxt(path_to_file)  # shape (N_ant, 3)
 
     if verbose:

src/tools21cm/radio_telescope_layout.py

@@ -303,4 +303,68 @@ def recursive_save(h5obj, d):
 		df.to_excel(filename, index=False)
 
 	else:
-		raise ValueError(f"Unsupported format: {format}")
+		raise ValueError(f"Unsupported format: {format}")
+	
+def get_package_resource_path(package_name, resource_path):
+    """
+    Get the path to a resource file within a package, with automatic fallback
+    for older Python versions.
+    
+    Parameters
+    ----------
+    package_name : str
+        Name of the package (e.g., 'tools21cm')
+    resource_path : str
+        Path to the resource relative to the package root
+        (e.g., 'input_data/central_geographic_position.txt')
+    
+    Returns
+    -------
+    str or Path
+        Path to the resource file that can be used with file reading functions
+    
+    Examples
+    --------
+    >>> path = get_package_resource_path('tools21cm', 'input_data/central_geographic_position.txt')
+    >>> data = np.loadtxt(path)
+    """
+    
+    # Try importlib.resources first (Python 3.9+)
+    try:
+        from importlib.resources import files
+        resource_file = files(package_name) / resource_path
+        return str(resource_file)
+    
+    except ImportError:
+        # Fall back to importlib_resources (Python 3.6-3.8)
+        try:
+            from importlib_resources import files
+            resource_file = files(package_name) / resource_path
+            return str(resource_file)
+        
+        except ImportError:
+            # Fall back to pkg_resources (older versions)
+            try:
+                import pkg_resources
+                return pkg_resources.resource_filename(package_name, resource_path)
+            
+            except ImportError:
+                # Last resort: try relative path (development mode)
+                import os
+                from pathlib import Path
+                try:
+                    # Get the package's location
+                    package = __import__(package_name)
+                    package_dir = Path(package.__file__).parent
+                    resource_file = package_dir / resource_path
+                    
+                    if resource_file.exists():
+                        return str(resource_file)
+                    else:
+                        raise FileNotFoundError(f"Resource not found: {resource_path}")
+                        
+                except Exception as e:
+                    raise ImportError(
+                        f"Could not locate resource '{resource_path}' in package '{package_name}'. "
+                        f"Please install 'importlib_resources' for Python < 3.9 or ensure the package is properly installed."
+                    ) from e

src/tools21cm/read_files.py

@@ -108,7 +108,7 @@ def __init__(self, tta=1, verbose=False):
 
     def load_model(self):
         import tensorflow as tf
-        import importlib.resources as pkg_resources
+        from .read_files import get_package_resource_path
 
         METRICS = {
             'balanced_cross_entropy': balanced_cross_entropy,
@@ -118,7 +118,7 @@ def load_model(self):
             'recall': recall
         }
 
-        MODEL_NAME = pkg_resources.resource_filename('tools21cm', 'input_data/segunet_03-11T12-02-05_128slice_ep35.h5')
+        MODEL_NAME = get_package_resource_path('tools21cm', 'input_data/segunet_03-11T12-02-05_128slice_ep35.h5')
         self.MODEL_LOADED = tf.keras.models.load_model(MODEL_NAME, custom_objects=METRICS)
         print('Loaded model: %s' % MODEL_NAME)