build.py

import yaml
import glob
import os

import numpy as np
from astropy.coordinates import SkyCoord
import astropy.table

from grizli import utils

## Read tables

files = glob.glob("tables/*csv")
files.sort()

tabs = []
ids = []

with open("tables/README.md", "w") as fpr:
    fpr.write("# References\n\n")
    fpr.write("| arXiv | Author | Title |\n")
    fpr.write("| ----- | ------ | ----- |\n")

    for file in files:
        meta = file.replace(".csv", ".meta")
        if not os.path.exists(meta):
            print(f"meta file {meta} not found for {file}")
            continue

        print(f"Read table: {file}")
        try:
            tab = utils.read_catalog(file)
        except:
            print(f"Failed to read table: {file}")
            continue

        with open(meta) as fp:
            try:
                _meta = yaml.load(fp, Loader=yaml.SafeLoader)
            except:
                print(
                    f'ERROR: Failed to parse {meta}, check that there are no ":" or incompatible linebreaks in `description`'
                )
                continue

        fpr.write(
            f"| [{_meta['arxiv']}](https://arxiv.org/abs/{_meta['arxiv']}) | {_meta['author']} | {_meta['description']} | \n"
        )

        meta_ok = True
        for k in ["arxiv", "author"]:
            if k not in _meta:
                print(f"ERROR: `{k}` keyword not found in {meta}")
                meta_ok = False

        if not meta_ok:
            continue

        for k in ["arxiv", "author"]:
            tab[k] = _meta[k]

        if "rah" in tab.colnames:
            try:
                coo = SkyCoord(tab["rah"], tab["decd"], unit=("hour", "deg"))
            except:
                print(f"Failed to parse rah/decd coordinates in  {file}")
                continue

            tab["ra"] = coo.ra.deg
            tab["dec"] = coo.dec.deg

        # tab['id'] =
        ids.extend([f"{_id}" for _id in tab["id"]])
        tab.remove_column("id")

        tab["jname"] = [
            utils.radec_to_targname(
                ra,
                dec,
                round_arcsec=(0.00001, 0.00001),
                precision=2,
                targstr="j{rah}{ram}{ras}.{rass}{sign}{ded}{dem}{des}.{dess}",
            )
            for ra, dec in zip(tab["ra"], tab["dec"])
        ]

        if len(tabs) > 0:
            # If matches exist in files already processed, get the
            # jname from there
            _full = utils.GTable(astropy.table.vstack(tabs))
            idx, dr = _full.match_to_catalog_sky(tab)
            hasm = dr.value < 0.5

            if hasm.sum() > 0:
                tab["jname"][hasm] = _full["jname"][idx][hasm]

        tabs.append(tab)

# Concatenated table

full = utils.GTable(astropy.table.vstack(tabs))
full["id"] = ids

jn = utils.Unique(full["jname"], verbose=False)
full["count"] = 1
for name, ct in zip(jn.values, jn.counts):
    full["count"][jn[name]] = ct

so = np.argsort(full["jname"])
full = full[so]
full["ra"].format = ".6f"
full["ra"].description = "Right Ascension, deg"

full["dec"].format = ".5f"
full["dec"].description = "Declination, deg"

full["zphot"].format = ".2f"
full["zphot"].description = "Photometric redshift"

if "zspec" not in full.colnames:
    full["zspec"] = -1.0

full["zspec"].format = ".3f"
full["zspec"].description = "Spectroscopic redshift"

full["count"].description = "Number of references"

thumb = '<img src="http://grizli-cutout.herokuapp.com/thumb?ra={ra}8&dec={dec}&filters={filt}&size=1&scl={scl}&invert=True" height=100px />'
full["F200W"] = [thumb.format(filt="f200w-clear", scl=16, **row) for row in full]
full["F444W"] = [thumb.format(filt="f444w-clear", scl=24, **row) for row in full]

full.write("jwst-sources.csv", overwrite=True)

sub = full[
    "jname",
    "count",
    "F200W",
    "F444W",
    "ra",
    "dec",
    "id",
    "zphot",
    "zspec",
    "arxiv",
    "author",
]

sub.write_sortable_html(
    "jwst-sources.html",
    localhost=False,
    max_lines=100000,
    filter_columns=["count", "ra", "dec", "zphot", "zspec"],
    use_json=True,
)