Merge pull request #23 from CosmoStat/develop

Release v.0.0.4

Author: martinkilbinger

.github/pull_request_template.md

@@ -0,0 +1,18 @@
+## Summary
+
+> Developers should provide a summary of the proposed changes here and include "closes #<ISSUE NUMBER>" if this addresses an open issue.
+
+## Reviewer Checklist
+
+> Reviewers should tick the following boxes before approving and merging the PR.
+
+- [ ] The PR is assigned to the developer
+- [ ] The PR has appropriate labels
+- [ ] The PR is included in appropriate projects and/or milestones
+- [ ] The PR includes a clear description of the proposed changes
+- [ ] If the PR addresses an open issue the description includes "closes #<ISSUE NUMBER>"
+- [ ] The code and documentation style match the current standards
+- [ ] Documentation has been added/updated consistently with the code
+- [ ] All CI tests are passing
+- [ ] All changed files have been checked and comments provided to the developer
+- [ ] All of the reviewer's comments have been satisfactorily addressed by the developer

README.md

@@ -22,4 +22,10 @@ Utility library for CosmoStat
 
 ### Library
 
-### Scripts
+- Galaxy catalogue handling
+- Weak-lensing related cosmological quantities (e.g. surface mass density)
+- VOS (Virtual Observatory Software)
+- Command line logging
+- Plotting
+- Basic statistic calculations
+- UNIONS/CFIS weak-lensing survey handling

cs_util/__init__.py

@@ -1,6 +1,6 @@
 """cs_util PACKAGE.
 
-Provide a basic description of what your package contains.
+CosmoStat utilities for weak lensing and cosmology.
 
 References
 ----------
@@ -23,14 +23,4 @@
 
 from warnings import warn
 
-from importlib_metadata import version
-
-try:
-    _version = version('cs_util')
-except Exception:  # pragma: no cover
-    _version = 'Unkown'
-    warn(
-        'Could not extract package metadata. Make sure the package is '
-        + 'correctly installed.',
-    )
-__version__ = _version
+__version__ = "0.0.4"

cs_util/calc.py

@@ -1,10 +1,10 @@
-"""CALC.                                                                       
-                                                                                
-:Name: calc.py                                                                 
-                                                                                
+"""CALC.
+
+:Name: calc.py
+
 :Description: This file contains methods for general calculations
               and statistics.
-                                                                                
+
 :Author: Martin Kilbinger <martin.kilbinger@cea.fr>
 
 """
@@ -36,10 +36,10 @@ def weighted_avg_and_std(values, weights, corrected=False):
     average = np.average(values, weights=weights)
 
     # Fast and numerically precise:
-    variance = np.average((values-average)**2, weights=weights)
-    
+    variance = np.average((values - average) ** 2, weights=weights)
+
     if corrected:
         n = len(values)
-        variance  = variance * n / (n - 1)
+        variance = variance * n / (n - 1)
 
     return average, np.sqrt(variance)

cs_util/canfar.py

@@ -38,7 +38,6 @@ class vosHandler:
     """
 
     def __init__(self, command):
-
         self._avail_commands = tuple(vosc.__all__)
         self.command = command
 
@@ -58,10 +57,9 @@ def command(self):
 
     @command.setter
     def command(self, value):
-
         if value not in self._avail_commands:
             raise ValueError(
-                f'vos command must be one of {self._avail_commands}'
+                f"vos command must be one of {self._avail_commands}"
             )
 
         self._command = getattr(vosc, value)
@@ -81,9 +79,7 @@ def __call__(self, *args, **kwargs):
             self._command()
 
         except Exception:
-            raise vosError(
-                f'Error in VOs command: {self._command.__name__}'
-            )
+            raise vosError(f"Error in VOs command: {self._command.__name__}")
 
 
 def download(source, target, verbose=False):
@@ -106,20 +102,20 @@ def download(source, target, verbose=False):
         status, True/False or success/failure
 
     """
-    cmd = 'vcp'
+    cmd = "vcp"
 
     if not os.path.exists(target):
         sys.argv = [cmd, source, target]
         if verbose:
-            print(f'Downloading file {source} to {target}...')
+            print(f"Downloading file {source} to {target}...")
         vcp = vosHandler(cmd)
 
         vcp()
         if verbose:
-            print('Download finished.')
+            print("Download finished.")
     else:
         if verbose:
-            print(f'Target file {target} exists, skipping download.')
+            print(f"Target file {target} exists, skipping download.")
 
 
 def dir_list(path, verbose=False):
@@ -145,22 +141,22 @@ def dir_list(path, verbose=False):
         file or directory at path, type is str
 
     """
-    cmd = 'vls'
+    cmd = "vls"
     sys.argv = [cmd, path]
     vls = vosHandler(cmd)
 
     if verbose:
-        print('Getting vos directory content from vls...')
+        print("Getting vos directory content from vls...")
 
     f = StringIO()
 
     try:
         with redirect_stdout(f):
             vls()
     except Exception:
-        print('Error during vls command')
+        print("Error during vls command")
         raise
 
     vls_out = f.getvalue()
 
-    return vls_out.split('\n')
+    return vls_out.split("\n")

cs_util/cat.py

@@ -9,11 +9,12 @@
 """
 
 import os
-from datetime import datetime                                                   
+from datetime import datetime
 from astropy.io import fits
+from astropy.io import ascii
 
 
-def write_header_info_sp(primary_header, name='unknown', version='unknown'):
+def write_header_info_sp(primary_header, name="unknown", version="unknown"):
     """Write Header Info sp_validation.
 
     Write information about software and run to FITS header
@@ -33,16 +34,16 @@ def write_header_info_sp(primary_header, name='unknown', version='unknown'):
         updated FITS header information
 
     """
-    if 'USER' in os.environ:
-        author = os.environ['USER']
+    if "USER" in os.environ:
+        author = os.environ["USER"]
     else:
-        author = 'unknown'
-    primary_header['AUTHOR'] = (author, 'Who ran the software')
-    primary_header['SOFTNAME'] = (name, 'Name of the software')
-    primary_header['SOFTVERS'] = (version, 'Version of the software')
-    primary_header['DATE'] = (
-        datetime.now().strftime('%Y-%m-%d_%H-%M-%S'),
-        'When it was started',
+        author = "unknown"
+    primary_header["AUTHOR"] = (author, "Who ran the software")
+    primary_header["SOFTNAME"] = (name, "Name of the software")
+    primary_header["SOFTVERS"] = (version, "Version of the software")
+    primary_header["DATE"] = (
+        datetime.now().strftime("%Y-%m-%d_%H-%M-%S"),
+        "When it was started",
     )
 
     return primary_header
@@ -68,56 +69,41 @@ def add_shear_bias_to_header(primary_header, R, R_shear, R_select, c):
         additive bias
 
     """
-    primary_header['R'] = (
-        r'<R>',
-        r'Mean full response <R_shear> + <R_select>'
+    primary_header["R"] = (r"<R>", r"Mean full response <R_shear> + <R_select>")
+    primary_header["R_11"] = (R[0, 0], "Full response matrix comp 1 1")
+    primary_header["R_12"] = (R[0, 1], "Full response matrix comp 1 2")
+    primary_header["R_21"] = (R[1, 0], "Full response matrix comp 2 1")
+    primary_header["R_22"] = (R[1, 1], "Full response matrix comp 2 2")
+
+    primary_header["R_g"] = (r"<R_g>", r"Mean shear response matrix <R_shear>")
+    primary_header["R_g11"] = (R_shear[0, 0], "Mean shear resp matrix comp 1 1")
+    primary_header["R_g12"] = (R_shear[0, 1], "Mean shear resp matrix comp 1 2")
+    primary_header["R_g21"] = (R_shear[1, 0], "Mean shear resp matrix comp 2 1")
+    primary_header["R_g22"] = (R_shear[1, 1], "Mean shear resp matrix comp 2 2")
+
+    primary_header["R_S"] = (
+        r"<R_S>",
+        r"Global selection response matrix <R_select>",
     )
-    primary_header['R_11'] = (R[0, 0], 'Full response matrix comp 1 1')
-    primary_header['R_12'] = (R[0, 1], 'Full response matrix comp 1 2')
-    primary_header['R_21'] = (R[1, 0], 'Full response matrix comp 2 1')
-    primary_header['R_22'] = (R[1, 1], 'Full response matrix comp 2 2')
-
-    primary_header['R_g'] = (r'<R_g>', r'Mean shear response matrix <R_shear>')
-    primary_header['R_g11'] = (
-        R_shear[0, 0],
-        'Mean shear resp matrix comp 1 1'
-    )
-    primary_header['R_g12'] = (
-        R_shear[0, 1],
-        'Mean shear resp matrix comp 1 2'
-    )
-    primary_header['R_g21'] = (
-        R_shear[1, 0],
-        'Mean shear resp matrix comp 2 1'
-    )
-    primary_header['R_g22'] = (
-        R_shear[1, 1],
-        'Mean shear resp matrix comp 2 2'
-    )
-
-    primary_header['R_S'] = (
-        r'<R_S>',
-        r'Global selection response matrix <R_select>'
-    )
-    primary_header['R_S11'] = (
+    primary_header["R_S11"] = (
         R_select[0, 0],
-        'Global selection resp matrix comp 1 1'
+        "Global selection resp matrix comp 1 1",
     )
-    primary_header['R_S12'] = (
+    primary_header["R_S12"] = (
         R_select[0, 1],
-        'Global selection resp matrix comp 1 2'
+        "Global selection resp matrix comp 1 2",
     )
-    primary_header['R_S21'] = (
+    primary_header["R_S21"] = (
         R_select[1, 0],
-        'Global selection resp matrix comp 2 1'
+        "Global selection resp matrix comp 2 1",
     )
-    primary_header['R_S22'] = (
+    primary_header["R_S22"] = (
         R_select[1, 1],
-        'Global selection resp matrix comp 2 2'
+        "Global selection resp matrix comp 2 2",
     )
 
-    primary_header['c_1'] = (c[0], 'Additive bias 1st comp')
-    primary_header['c_2'] = (c[1], 'Additive bias 2nd comp')
+    primary_header["c_1"] = (c[0], "Additive bias 1st comp")
+    primary_header["c_2"] = (c[1], "Additive bias 2nd comp")
 
 
 def write_fits_BinTable_file(
@@ -159,3 +145,54 @@ def write_fits_BinTable_file(
 
     hdu_list = fits.HDUList([primary_hdu, table_hdu])
     hdu_list.writeto(output_path, overwrite=True)
+
+
+def bin_edges2centers(bin_edges):
+    """Bin Edges To Centers.
+
+    Transform bin edge values to central values.
+
+    Parameters
+    ----------
+    bin_edges : list
+        bin edge values
+
+    Returns
+    -------
+    list
+        bin central values
+
+    """
+    bin_means = 0.5 * (bin_edges[1:] + bin_edges[:-1])
+
+    return bin_means
+
+
+def read_dndz(file_path):
+    """Read Dndz.
+
+    Read redshift histogram from file.
+
+    Parameters
+    ----------
+    file_path : str
+        input file path
+
+    Returns
+    -------
+    list :
+        redshift bin centers
+    list :
+        number densities
+    list :
+        redshift bin edges
+
+    """
+    dat = ascii.read(file_path, format="commented_header")
+
+    # Remove last n(z) value which is zero, to match bin centers
+    nz = dat["dn_dz"][:-1]
+    z_edges = dat["z"]
+    z_centers = bin_edges2centers(z_edges)
+
+    return z_centers, nz, z_edges