Convert and Ingest Zhang18 Spectra

.gitignore

@@ -13,3 +13,4 @@ build/
 simple/version.py
 *.zip
 *.fits
+*sty2054_supplemental_files/

scripts/spectra_convert/zhang18/add_header.py

@@ -0,0 +1,118 @@
+import os
+import numpy as np
+import pandas as pd
+from astropy.io import fits
+from astropy.time import Time
+from datetime import date
+import astropy.units as u
+from specutils import Spectrum
+from astrodb_utils.fits import add_missing_keywords, add_wavelength_keywords, check_header
+from astrodb_utils.spectra import check_spectrum_plottable
+from astroquery.simbad import Simbad
+from pathlib import Path
+
+# Path config
+path = "/Users/guanying/SIMPLE db/SIMPLE-db/scripts/spectra_convert/zhang18/processed_spectra"
+
+
+def get_paper_metadata(filename):
+    if "-I_SIMPLE.fits" in filename or "-I_SMOOTHED_SIMPLE.fits" in filename:
+        title = "Primeval very low-mass stars and brown dwarfs - I. Six new L subdwarfs, classification and atmospheric properties"
+        voref = "10.1093/mnras/stw2438"
+    elif "-II.fits" in filename or "-II_SMOOTHED_SIMPLE.fits" in filename:
+        title = "Primeval very low-mass stars and brown dwarfs - II. The most metal-poor substellar object"
+        voref = "10.1093/mnras/stx350"
+    elif "-III.fits" in filename or "-III_SMOOTHED_SIMPLE.fits" in filename:
+        title = "Primeval very low-mass stars and brown dwarfs - III. The halo transitional brown dwarfs"
+        voref = "10.1093/mnras/sty1352"
+    elif "IV.fits" in filename or "IV_SMOOTHED_SIMPLE.fits" in filename:
+        title = "Primeval very low-mass stars and brown dwarfs - IV. New L subdwarfs, Gaia astrometry, population properties, and a blue brown dwarf binary"
+        voref = "10.1093/mnras/sty2054"
+    else:
+        title = "Unknown Paper"
+        voref = "Unknown DOI"
+
+    return title, voref
+
+
+def add_header(path):
+    missing_telescop_instrument = []
+    missing_dateobs = []
+    file_proceed = 0
+
+
+    fits_files = list(Path(path).glob("*.fits"))
+
+    for fits_file in fits_files:
+        filename = fits_file.name
+        print(f"\nProcessing {filename}...")
+        spectrum = Spectrum.read(fits_file)
+
+        title, voref = get_paper_metadata(filename)
+
+        with fits.open(fits_file, mode="update") as hdul:
+            header = hdul[0].header
+
+            # add SIMPLE FITS headers
+            header["SIMPLE"] = (True, "Conforms to FITS standard")
+            header["VOPUB"] = ("SIMPLE Archive", "Publication of the spectrum")
+
+            # object name
+            object_name = " ".join(filename.split("_")[:2])
+            header["OBJECT"] = (object_name, "Name of the object")
+
+            # Query simbad for ra/dec
+            try:
+                result = Simbad.query_object(object_name)
+                if result is not None and len(result) > 0:
+                    header["RA_TARG"] = (result[0]["ra"], "[ra] Pointing position")
+                    header["DEC_TARG"] = (result[0]["dec"], "[dec] Pointing position")
+            except Exception as e:
+                print(f"  SIMBAD lookup failed: {e}")
+
+            # Remove deprecated keyword
+            if "RADECSYS" in header:
+                header.remove("RADECSYS", ignore_missing=True)
+                print("  Removed RADECSYS")
+
+            # Check TELESCOP + INSTRUME
+            if "TELESCOP" not in header or "INSTRUME" not in header:
+                missing_telescop_instrument.append(filename)
+
+            # Paper metadata
+            header["TITLE"] = (title, "Title of the paper")
+            header["VOREF"] = (voref, "DOI of the paper")
+            header["AUTHOR"] = ("Zhang, Z.H. et al.", "Original authors")
+            header["DATE"] = (date.today().isoformat(), "Header update date")
+
+            # Fix flux units
+            if "BUNIT" not in header:
+                header["BUNIT"] = "erg / (cm2 s Angstrom)"
+            elif header["BUNIT"] == "erg/s/cm2/Angstrom":
+                header["BUNIT"] = "erg / (cm2 s Angstrom)"
+
+            # date-obs check
+            if "DATE-OBS" not in header or header["DATE-OBS"] in ["", "UNKNOWN", None]:
+                missing_dateobs.append(filename)
+
+            add_wavelength_keywords(header, spectrum.spectral_axis)
+            add_missing_keywords(header)
+            check_header(hdul[0].header)
+
+            hdul.flush()
+            print(f"  Finished {filename}")
+            file_proceed += 1
+
+    # Summary
+    print(f"\File processed: {file_proceed}/{len(fits_files)}")
+    if missing_telescop_instrument:
+        print("\nFiles missing TELESCOP or INSTRUME:")
+        for f in missing_telescop_instrument:
+            print(f"  - {f}")
+
+    if missing_dateobs:
+        print("\nFiles missing DATE-OBS:")
+        for f in missing_dateobs:
+            print(f"  - {f}")
+
+add_header(path)