Beiler phot (#125)

* adding beiler2024 ydwarf photometry

* updated temp url for jwst ydwarfs fits

* patch for bytes spt

* add null flag to ydwarfs

* isinstance bytes and hosted fits

species/data/database.py

@@ -1920,7 +1920,7 @@ def add_photometry(self, phot_library: str) -> None:
         Parameters
         ----------
         phot_library : str
-            Photometric library ('vlm-plx' or 'leggett').
+            Photometric library ('vlm-plx', 'leggett', or 'beiler2024').
 
         Returns
         -------
@@ -1946,6 +1946,11 @@ def add_photometry(self, phot_library: str) -> None:
                 from species.data.phot_data.phot_leggett import add_leggett
 
                 add_leggett(self.data_folder, hdf5_file)
+
+            elif phot_library[0:10] == "beiler2024":
+                from species.data.phot_data.phot_jwst_ydwarfs import add_jwst_ydwarfs
+
+                add_jwst_ydwarfs(self.data_folder, hdf5_file)
 
     @typechecked
     def add_calibration(

species/data/phot_data/phot_jwst_ydwarfs.py

@@ -0,0 +1,102 @@
+"""
+Module for the photometric data and parallaxes from the JWST late T and early Y
+dwarf observations recorded in Beiler et al. 2024 (ApJ)
+"""
+
+from pathlib import Path
+
+import h5py
+import numpy as np
+import pooch
+
+from astropy.io import fits
+from typeguard import typechecked
+
+from species.util.data_util import update_sptype
+
+
+@typechecked
+def add_jwst_ydwarfs(input_path: str, database: h5py._hl.files.File) -> None:
+    """
+    Function for adding the synthesized pphotometry from 'Precise Bolometric Luminosities and Effective Temperatures of 23 Late-T and Y Dwarfs Obtained with JWST' by Beiler et al. (2024, ApJ).
+
+    Parameters
+    ----------
+    input_path : str
+        Data folder.
+    database : h5py._hl.files.File
+        The HDF5 database that has been opened.
+
+    Returns
+    -------
+    NoneType
+        None
+    """
+
+    input_file = "Beiler2024_synth_phot.fits"
+    data_file = Path(input_path) / "Beiler2024_synth_phot.fits"
+    url = "https://home.strw.leidenuniv.nl/~stolker/species/Beiler2024_synth_phot.fits"
+
+    if not data_file.exists():
+        print()
+
+        pooch.retrieve(
+            url=url,
+            known_hash=None,
+            fname=input_file,
+            path=input_path,
+            progressbar=True,
+        )
+
+    database.create_group("photometry/beiler2024")
+
+    with fits.open(data_file, mode='update') as hdu_list:
+        phot_data = hdu_list[1].data
+
+    parallax = np.array(phot_data['PLX'], dtype=float)  # (mas)
+    parallax_error = np.array(phot_data['EPLX'], dtype=float)  # (mas)
+
+    name = np.array(phot_data["Name"]).astype('str')
+
+    sptype_nir = np.array(phot_data["SpT"]).astype('str')
+    sptype_nir = np.core.defchararray.strip(sptype_nir)
+
+    sptype = update_sptype(sptype_nir)
+
+    dtype = h5py.special_dtype(vlen=str)
+
+    flag = np.repeat("null", np.size(name))
+
+    dset = database.create_dataset("photometry/beiler2024" + "/flag", (np.size(flag),), dtype=dtype)
+    dset[...] = flag
+
+    dset = database.create_dataset(
+        "photometry/beiler2024/name", (np.size(name),), dtype=dtype
+    )
+    dset[...] = name
+
+    dset = database.create_dataset(
+        "photometry/beiler2024/sptype", (np.size(sptype),), dtype=dtype
+    )
+    dset[...] = sptype
+
+    database.create_dataset("photometry/beiler2024/parallax", data=parallax)
+    database.create_dataset("photometry/beiler2024/parallax_error", data=parallax_error)
+
+
+    nirc_filts = ['F090W', 'F115W', 'F140M', 'F150W',
+       'F150W2', 'F162M', 'F164N', 'F182M', 'F187N', 'F200W', 'F210M',
+       'F212N', 'F250M', 'F277W', 'F300M', 'F322W2', 'F323N', 'F335M',
+       'F356W', 'F360M', 'F405N', 'F410M', 'F430M', 'F444W', 'F460M',
+       'F466N', 'F470N', 'F480M']
+
+    for filt in nirc_filts:
+        database.create_dataset(f"photometry/beiler2024/JWST/NIRCAM.{filt}", data=np.array(phot_data[f'{filt}'], dtype=float))
+
+    miri_filts = ['F560W', 'F770W', 'F1065C', 'F1130W',
+       'F1140C']
+
+    for filt in miri_filts:
+        database.create_dataset(f"photometry/beiler2024/JWST/MIRI.{filt}", data=np.array(phot_data[f'{filt}'], dtype=float))
+
+    database.close()

species/util/plot_util.py

@@ -64,6 +64,8 @@ def sptype_to_index(
         ]
 
         for i, item in enumerate(spec_types):
+            if isinstance(item, bytes):
+                item = item.decode("utf-8") # this catches spt names from fits files that are saved to the hdf5 as bytes
             if item[0:2] in ["O0", "O1", "O2", "O3", "O4"]:
                 spt_discrete[i] = 0.5
 
@@ -136,6 +138,8 @@ def sptype_to_index(
         spt_check = ["O", "B", "A", "F", "G", "K", "M", "L", "T", "Y"]
 
         for i, item in enumerate(spec_types):
+            if isinstance(item, bytes):
+                item = item.decode("utf-8") # this catches spt names from fits files that are saved to the hdf5 as bytes
             if item[0] == "O":
                 spt_discrete[i] = 0.5