--n-qso support modified

qsoabsfind/absfinder.py

@@ -16,7 +16,6 @@
 from .config import load_constants
 from .spec import QSOSpecRead
 from numba import jit
-from astropy.table import Table
 
 constants = load_constants()
 lines, oscillator_parameters, speed_of_light = constants.lines, constants.oscillator_parameters, constants.speed_of_light

qsoabsfind/io.py

@@ -88,6 +88,5 @@ def save_results_to_fits(results, input_file, output_file, headers, absorber):
 
     _, _, _, metadata = read_fits_file(input_file, index=np.array(results['index_spec']))
     qso_hdu = fits.BinTableHDU(metadata, name='METADATA')
-    import pdb;pdb.set_trace()
     hdul = fits.HDUList([fits.PrimaryHDU(header=hdr), hdu, qso_hdu])
     hdul.writeto(output_file, overwrite=True)

qsoabsfind/parallel_convolution.py

@@ -12,6 +12,7 @@
 import os
 import pkg_resources
 from .config import load_constants
+from .utils import read_nqso_from_header
 
 def get_package_versions():
     """
@@ -144,7 +145,7 @@ def parallel_convolution_method_absorber_finder_QSO_spectra(fits_file, spec_indi
 def main():
     parser = argparse.ArgumentParser(description='Run convolution-based adaptive S/N method to search for metal doublets in SDSS/DESI-like QSO spectra in parallel.')
     parser.add_argument('--input-fits-file', type=str, required=True, help='Path to the input FITS file.')
-    parser.add_argument('--n-qso', type=str, required=True, help="Number of QSO spectra to process, or a bash-like sequence (e.g., '1-1000', '1-1000:10').")
+    parser.add_argument('--n-qso', type=str, required=False, help="Number of QSO spectra to process, or a bash-like sequence (e.g., '1-1000', '1-1000:10'). If not provided, code will run all the spectra")
     parser.add_argument('--absorber', type=str, required=True, help='Absorber name for searching doublets (MgII, CIV).')
     parser.add_argument('--constant-file', type=str, help='Path to the constants .py file, please follow the exact same structure as qsoabsfind.constants, i.e the default parameter that the code uses')
     parser.add_argument('--output', type=str, required=True, help='Path to the output FITS file.')
@@ -194,6 +195,9 @@ def main():
     # Start timing
     start_time = time.time()
 
+    if not args.n_qso:
+        nqso = read_nqso_from_header(args.input_fits_file)
+        args.n_qso = nqso
     # Parse the QSO sequence
     spec_indices = parse_qso_sequence(args.n_qso)
 

qsoabsfind/utils.py

@@ -8,6 +8,7 @@
 from .config import load_constants
 import matplotlib.pyplot as plt
 import os
+from astropy.io import fits
 
 # Configure logging
 #logging.basicConfig(level=logging.DEBUG, format='%(asctime)s - %(levelname)s - %(message)s')
@@ -348,3 +349,35 @@ def plot_absorber(lam, residual, absorber, zabs, xlabel='obs wave (ang)', ylabel
         print(f"Plot saved as {plot_path}")
     else:
         plt.show()
+
+def read_nqso_from_header(file_path, hdu_name='METADATA'):
+    """
+    Read the NAXIS1 value from the header of a specified HDU in a FITS file.
+
+    Parameters:
+    - file_path: str, path to the FITS file.
+    - hdu_name: str, name of the HDU from which to read NAXIS1 (default: 'METADATA').
+
+    Returns:
+    - naxis1_value: int, value of NAXIS1 from the specified HDU header.
+    """
+    # Check if the file exists
+    if not os.path.isfile(file_path):
+        raise FileNotFoundError(f"The FITS file {file_path} does not exist.")
+
+    # Open the FITS file in read-only mode and load headers only
+    with fits.open(file_path, mode='readonly') as hdul:
+        # Attempt to access the specified HDU by name
+        try:
+            # Load only the header of the specified HDU
+            header = hdul[hdu_name].header
+
+            # Read the NAXIS1 value from the header
+            naxis1_value = header.get('NAXIS1', None)
+
+            if naxis1_value is None:
+                raise KeyError(f"NAXIS1 not found in the '{hdu_name}' HDU header.")
+            return naxis1_value
+
+        except KeyError:
+            raise ValueError(f"No '{hdu_name}' HDU found in {file_path}.")