diff --git a/datalab/datalab_session/data_operations/hr_diagram.py b/datalab/datalab_session/data_operations/hr_diagram.py new file mode 100644 index 0000000..2dc9a49 --- /dev/null +++ b/datalab/datalab_session/data_operations/hr_diagram.py @@ -0,0 +1,300 @@ +import logging + +import numpy as np +from django.contrib.auth.models import User + +from datalab.datalab_session.data_operations.data_operation import BaseDataOperation +from datalab.datalab_session.exceptions import ClientAlertException +from datalab.datalab_session.utils.catalog_utils import ( + cone_filter, + cross_match_one_to_one, + extract_calibrated_catalog, + wcs_contains_point, +) +from datalab.datalab_session.utils.filecache import FileCache +from datalab.datalab_session.utils.format import Format +from datalab.datalab_session.utils.gaia import estimate_membership, gaia_cone_search + +log = logging.getLogger(__name__) +log.setLevel(logging.INFO) + + +class HRDiagram(BaseDataOperation): + # Fixed blue<->red match tolerance. Deliberately not a wizard input: every input is hashed + # into the cache key, so exposing it would fragment the cache and force full recomputes + MATCH_RADIUS_ARCSEC = 2.0 + # Tighter tolerance for matching our stars to Gaia. Gaia DR3 positions are epoch 2016.0, + # so 1 arcsec also tolerates ~a decade of <100 mas/yr proper motion + GAIA_MATCH_RADIUS_ARCSEC = 1.0 + # Keep only the brightest N matched stars to bound the output payload + MAX_OUTPUT_SOURCES = 5000 + # Also emit up to this many of the brightest Gaia sources that did NOT match an image star + # (flagged gaia_only): the cluster's proper-motion clump and parallax peak stand out far + # better against the full Gaia field than against just the image-matched subset + MAX_GAIA_ONLY_SOURCES = 5000 + DEFAULT_SEARCH_RADIUS_ARCMIN = 15.0 + # Disjoint blue/red filter options so the wizard can only produce valid, wavelength-ordered + # (color = blue - red) pairs. BANZAI only reduces gp/rp/ip/zs, so gp is the only blue choice + BLUE_FILTER_OPTIONS = ['gp'] + RED_FILTER_OPTIONS = ['rp', 'ip', 'zs'] + # Gaia-only stars get CMD photometry from Gaia's synthetic SDSS-system magnitudes (see + # utils/gaia.py for the ~0.03 mag SDSS<->PS1 caveat baked into their errors) + GAIA_SYNTH_MAG = {'gp': 'g_sdss', 'rp': 'r_sdss', 'ip': 'i_sdss', 'zs': 'z_sdss'} + PROGRESS_STEPS = { + 'BLUE_CATALOG_DONE': 0.2, + 'RED_CATALOG_DONE': 0.4, + 'CROSS_MATCH_DONE': 0.5, + 'GAIA_QUERY_DONE': 0.80, + 'GAIA_MATCH_DONE': 0.95, + 'OUTPUT_DONE': 1.0, + } + + @staticmethod + def name(): + return 'HR Diagram' + + @staticmethod + def description(): + return """Builds a color-magnitude diagram (an observational HR diagram) of a star cluster from two images of it taken in different filters. + +The calibrated photometry catalogs of the two images are cross-matched by sky position, giving each star a color (blue - red magnitude) and a brightness. The output CMD can then be analyzed to estimate the cluster's distance, reddening, age, and metallicity by fitting isochrones.""" + + @staticmethod + def wizard_description(): + return { + 'name': HRDiagram.name(), + 'description': HRDiagram.description(), + 'category': 'image', + 'inputs': { + 'blue_filter_files': { + 'name': 'Blue Band Image', + 'description': 'The bluer filter image of the cluster', + 'type': Format.FITS, + 'single_filter': True, + 'filter_options': HRDiagram.BLUE_FILTER_OPTIONS, + 'minimum': 1, + 'maximum': 1, + }, + 'red_filter_files': { + 'name': 'Red Band Image', + 'description': 'The redder filter image of the cluster (color = blue - red)', + 'type': Format.FITS, + 'single_filter': True, + 'filter_options': HRDiagram.RED_FILTER_OPTIONS, + 'minimum': 1, + 'maximum': 1, + }, + 'cluster': { + 'name': 'Cluster Center', + 'description': 'The center of the star cluster to analyze', + 'type': Format.SOURCE, + }, + 'search_radius_arcmin': { + 'name': 'Search Radius (arcmin)', + 'description': 'Include stars within this radius of the cluster center', + 'type': Format.FLOAT, + 'default': HRDiagram.DEFAULT_SEARCH_RADIUS_ARCMIN, + }, + }, + } + + def _validate_cluster(self): + cluster = self.input_data.get('cluster') or {} + try: + cluster_ra = float(cluster.get('ra')) + cluster_dec = float(cluster.get('dec')) + except (TypeError, ValueError): + raise ClientAlertException(f'Operation {self.name()} requires a cluster center with ra and dec.') + return cluster.get('name', ''), cluster_ra, cluster_dec + + def _validate_search_radius(self): + try: + search_radius_arcmin = float(self.input_data.get('search_radius_arcmin') or HRDiagram.DEFAULT_SEARCH_RADIUS_ARCMIN) + except (TypeError, ValueError): + raise ClientAlertException('The search radius must be a number of arcminutes.') + if search_radius_arcmin <= 0: + raise ClientAlertException('The search radius must be greater than zero arcminutes.') + return search_radius_arcmin + + def _band_catalog(self, image: dict, user: User) -> dict: + """ Downloads one band's fits file and extracts its calibrated source catalog """ + basename = image.get('basename') + try: + fits_path = FileCache().get_fits(basename, image.get('source', 'archive'), user) + except TimeoutError: + raise ClientAlertException(f'Download of {basename} timed out') + + catalog = extract_calibrated_catalog(fits_path, basename=basename) + if len(catalog['ra']) == 0: + raise ClientAlertException(f'No calibrated sources found in the catalog of {basename}.') + catalog['fits_path'] = fits_path + return catalog + + def operate(self, submitter: User): + blue_image = self._validate_inputs(input_key='blue_filter_files')[0] + red_image = self._validate_inputs(input_key='red_filter_files')[0] + blue_filter = blue_image.get('filter', blue_image.get('primary_optical_element', '')) or '' + red_filter = red_image.get('filter', red_image.get('primary_optical_element', '')) or '' + cluster_name, cluster_ra, cluster_dec = self._validate_cluster() + search_radius_arcmin = self._validate_search_radius() + + log.info(f'HR Diagram for cluster ({cluster_ra}, {cluster_dec}) from images ' + f'{blue_image["basename"]} ({blue_filter}) and {red_image["basename"]} ({red_filter})') + + blue_catalog = self._band_catalog(blue_image, submitter) + self.set_operation_progress(HRDiagram.PROGRESS_STEPS['BLUE_CATALOG_DONE']) + red_catalog = self._band_catalog(red_image, submitter) + self.set_operation_progress(HRDiagram.PROGRESS_STEPS['RED_CATALOG_DONE']) + + # cheap pre-flight to catch mistyped coordinates before cross-matching + if not wcs_contains_point(blue_catalog['fits_path'], cluster_ra, cluster_dec) \ + and not wcs_contains_point(red_catalog['fits_path'], cluster_ra, cluster_dec): + raise ClientAlertException('The cluster center is outside both image footprints - ' + 'check that the cluster coordinates match your images.') + + blue_indices, red_indices = cross_match_one_to_one(blue_catalog, red_catalog, HRDiagram.MATCH_RADIUS_ARCSEC) + if len(blue_indices) == 0: + raise ClientAlertException('No stars matched between the two bands - ' + 'check that both images cover the same field.') + self.set_operation_progress(HRDiagram.PROGRESS_STEPS['CROSS_MATCH_DONE']) + + # the red (y-axis) band positions are the canonical star positions + ra = red_catalog['ra'][red_indices] + dec = red_catalog['dec'][red_indices] + blue_mag = blue_catalog['mag'][blue_indices] + blue_magerr = blue_catalog['magerr'][blue_indices] + red_mag = red_catalog['mag'][red_indices] + red_magerr = red_catalog['magerr'][red_indices] + + in_cone = cone_filter(ra, dec, cluster_ra, cluster_dec, search_radius_arcmin) + if not in_cone.any(): + raise ClientAlertException(f'No matched stars within {search_radius_arcmin} arcminutes of the ' + 'cluster center - try a larger search radius.') + n_stars_matched = int(in_cone.sum()) + + # keep the brightest stars first when capping the output size + brightest = np.argsort(red_mag[in_cone])[:HRDiagram.MAX_OUTPUT_SOURCES] + ra, dec = ra[in_cone][brightest], dec[in_cone][brightest] + blue_mag, blue_magerr = blue_mag[in_cone][brightest], blue_magerr[in_cone][brightest] + red_mag, red_magerr = red_mag[in_cone][brightest], red_magerr[in_cone][brightest] + + # Gaia enrichment: proper motions + parallaxes for cluster membership selection. + # A Gaia failure raises and fails the operation (re-runnable) rather than silently + # caching a membership-less result for 30 days + gaia_data = gaia_cone_search(cluster_ra, cluster_dec, search_radius_arcmin) + self.set_operation_progress(HRDiagram.PROGRESS_STEPS['GAIA_QUERY_DONE']) + star_indices, gaia_indices = cross_match_one_to_one({'ra': ra, 'dec': dec}, gaia_data, + HRDiagram.GAIA_MATCH_RADIUS_ARCSEC) + gaia_for_star = {int(star): int(gaia) for star, gaia in zip(star_indices, gaia_indices)} + + # the brightest Gaia sources without an image counterpart still map the cluster's + # kinematics, so they are emitted too (flagged gaia_only) for the membership plots + matched_gaia = np.asarray(gaia_indices, dtype=int) + unmatched_gaia = np.setdiff1d(np.arange(len(gaia_data['ra'])), matched_gaia) + unmatched_g_mag = gaia_data['phot_g_mean_mag'][unmatched_gaia] + by_brightness = np.argsort(np.where(np.isfinite(unmatched_g_mag), unmatched_g_mag, np.inf)) + gaia_only_indices = unmatched_gaia[by_brightness][:HRDiagram.MAX_GAIA_ONLY_SOURCES] + + # the membership guess uses the same star set the membership plots will show + membership_pool = np.concatenate([matched_gaia, gaia_only_indices]) + membership_guess = estimate_membership( + gaia_data['pmra'][membership_pool], + gaia_data['pmdec'][membership_pool], + gaia_data['parallax'][membership_pool], + gaia_data['r_med_geo'][membership_pool], + gaia_data['r_lo_geo'][membership_pool], + gaia_data['r_hi_geo'][membership_pool], + ) + self.set_operation_progress(HRDiagram.PROGRESS_STEPS['GAIA_MATCH_DONE']) + + def gaia_value(column, gaia_index): + # non-finite (masked) Gaia values become None to stay JSON-safe + value = float(gaia_data[column][gaia_index]) + return round(value, 4) if np.isfinite(value) else None + + def gaia_astrometry(gaia_index): + # proper motion, parallax, Bailer-Jones geometric distance, and the gaia_match flag for a + # star (r_med_geo estimate + r_lo_geo/r_hi_geo 16th/84th percentile bounds. + # The astrometry fields are None when the star has no match. + matched = gaia_index is not None + def value(column): + return gaia_value(column, gaia_index) if matched else None + return { + 'pmra': value('pmra'), + 'pmra_err': value('pmra_error'), + 'pmdec': value('pmdec'), + 'pmdec_err': value('pmdec_error'), + 'parallax': value('parallax'), + 'parallax_err': value('parallax_error'), + 'distance': value('r_med_geo'), + 'distance_lo': value('r_lo_geo'), + 'distance_hi': value('r_hi_geo'), + 'gaia_match': matched, + } + + cmd_points = [] + # Iterate over points found in our input images and fill in gaia extra details + for i in range(len(ra)): + point = { + 'ra': round(float(ra[i]), 6), + 'dec': round(float(dec[i]), 6), + 'color': round(float(blue_mag[i] - red_mag[i]), 4), + 'color_err': round(float(np.sqrt(blue_magerr[i] ** 2 + red_magerr[i] ** 2)), 4), + 'mag': round(float(red_mag[i]), 4), + 'magerr': round(float(red_magerr[i]), 4), + } + point.update(gaia_astrometry(gaia_for_star.get(i))) + point['gaia_only'] = False + cmd_points.append(point) + + n_image_stars = len(cmd_points) + # Gaia-only stars: no image detection, but their astrometry feeds the membership plots + # and Gaia's synthetic photometry (where the source has it) also places them on the CMD + blue_synth = HRDiagram.GAIA_SYNTH_MAG[blue_filter] + red_synth = HRDiagram.GAIA_SYNTH_MAG[red_filter] + for gaia_index in gaia_only_indices: + # synthetic blue/red mags only feed color and the y-axis mag; they are not emitted per-star + blue_synth_mag = gaia_value(f'{blue_synth}_mag', gaia_index) + red_synth_mag = gaia_value(f'{red_synth}_mag', gaia_index) + blue_err = gaia_value(f'{blue_synth}_mag_error', gaia_index) + red_err = gaia_value(f'{red_synth}_mag_error', gaia_index) + point = { + 'ra': round(float(gaia_data['ra'][gaia_index]), 6), + 'dec': round(float(gaia_data['dec'][gaia_index]), 6), + 'g_mag': gaia_value('phot_g_mean_mag', gaia_index), + 'mag': red_synth_mag, + 'magerr': red_err, + 'gaia_only': True, + } + point.update(gaia_astrometry(gaia_index)) + if blue_synth_mag is not None and red_synth_mag is not None: + point['color'] = round(blue_synth_mag - red_synth_mag, 4) + point['color_err'] = round(float(np.hypot(blue_err, red_err)), 4) \ + if blue_err is not None and red_err is not None else None + else: + point['color'] = None + point['color_err'] = None + cmd_points.append(point) + + output = { + 'output_data': [ + { + 'cluster': {'name': cluster_name, 'ra': cluster_ra, 'dec': cluster_dec, 'radius_arcmin': search_radius_arcmin}, + 'blue_filter': blue_filter, + 'red_filter': red_filter, + 'mag_band': red_filter, + 'cmd': cmd_points, + 'membership_guess': membership_guess, + 'n_gaia_matched': len(star_indices), + 'n_gaia_only': len(gaia_only_indices), + 'n_stars': n_image_stars, + 'n_stars_matched': n_stars_matched, + } + ] + } + log.info(f'HR Diagram output {n_image_stars} image stars from {len(blue_indices)} band matches, ' + f'{len(star_indices)} Gaia matched, plus {len(gaia_only_indices)} Gaia-only stars') + + self.set_output(output, is_raw=True) + self.set_operation_progress(HRDiagram.PROGRESS_STEPS['OUTPUT_DONE']) + self.set_status('COMPLETED') diff --git a/datalab/datalab_session/tests/test_operations.py b/datalab/datalab_session/tests/test_operations.py index bc1f338..b816033 100644 --- a/datalab/datalab_session/tests/test_operations.py +++ b/datalab/datalab_session/tests/test_operations.py @@ -7,12 +7,14 @@ import os from astropy.io import fits +from astropy.wcs import WCS import numpy as np from datalab.datalab_session.data_operations.data_operation import BaseDataOperation from datalab.datalab_session.data_operations.aperture_photometry import AperturePhotometry from datalab.datalab_session.data_operations.color_image import Color_Image from datalab.datalab_session.exceptions import ClientAlertException +from datalab.datalab_session.data_operations.hr_diagram import HRDiagram from datalab.datalab_session.data_operations.light_curve import LightCurve from datalab.datalab_session.data_operations.median import Median from datalab.datalab_session.data_operations.stacking import Stack @@ -450,6 +452,353 @@ def test_operate(self, mock_file_cache, mock_named_tempfile, mock_create_jpgs, m self.assertEqual(output, [self.temp_color_path]) +class TestHRDiagramOperation(FileExtendedTestCase): + temp_blue_path = f'{test_path}temp_hr_blue.fits' + temp_red_path = f'{test_path}temp_hr_red.fits' + + CENTER_RA = 150.0 + CENTER_DEC = 30.0 + + def tearDown(self): + self.clean_test_dir() + return super().tearDown() + + @staticmethod + def create_test_fits(path, center_ra, center_dec, ra, dec, mag, magerr, include_radec=True, include_mag=True): + """ Writes a fits file with a WCS'd SCI HDU and a CAT HDU like a reduced image's catalog """ + wcs = WCS(naxis=2) + wcs.wcs.ctype = ['RA---TAN', 'DEC--TAN'] + wcs.wcs.crval = [center_ra, center_dec] + wcs.wcs.crpix = [100.0, 100.0] + wcs.wcs.cdelt = [-1.0 / 3600.0, 1.0 / 3600.0] + sci_hdu = fits.ImageHDU(data=np.zeros((200, 200), dtype=np.float32), header=wcs.to_header(), name='SCI') + + x, y = wcs.all_world2pix(np.asarray(ra), np.asarray(dec), 1) + columns = [ + fits.Column(name='x', format='D', array=x), + fits.Column(name='y', format='D', array=y), + ] + if include_radec: + columns += [ + fits.Column(name='ra', format='D', array=np.asarray(ra)), + fits.Column(name='dec', format='D', array=np.asarray(dec)), + ] + if include_mag: + columns += [ + fits.Column(name='mag', format='D', array=np.asarray(mag)), + fits.Column(name='magerr', format='D', array=np.asarray(magerr)), + ] + cat_hdu = fits.BinTableHDU.from_columns(columns, name='CAT') + fits.HDUList([fits.PrimaryHDU(), sci_hdu, cat_hdu]).writeto(path, overwrite=True) + + def hr_input_data(self, search_radius_arcmin=None): + input_data = { + 'blue_filter_files': [{'basename': 'blue_fits', 'source': 'local', 'filter': 'gp'}], + 'red_filter_files': [{'basename': 'red_fits', 'source': 'local', 'filter': 'rp'}], + 'cluster': {'name': 'Test Cluster', 'ra': self.CENTER_RA, 'dec': self.CENTER_DEC}, + } + if search_radius_arcmin is not None: + input_data['search_radius_arcmin'] = search_radius_arcmin + return input_data + + def mock_band_fits(self, mock_file_cache): + """ FileCache is instantiated once per band, blue first """ + mock_fc_blue = mock.MagicMock() + mock_fc_blue.get_fits.return_value = self.temp_blue_path + mock_fc_red = mock.MagicMock() + mock_fc_red.get_fits.return_value = self.temp_red_path + mock_file_cache.side_effect = [mock_fc_blue, mock_fc_red] + + @classmethod + def empty_gaia_data(cls): + return cls.gaia_field(ra=[], dec=[], pmra=[], pmdec=[], parallax=[]) + + @staticmethod + def gaia_field(ra, dec, pmra, pmdec, parallax, g_mag=None, synth_g=None, synth_r=None, distance=None): + """ Builds a gaia_cone_search-shaped dict; synthetic i/z bands mirror r, and the + Bailer-Jones distance bounds bracket r_med_geo asymmetrically """ + n = len(ra) + data = { + 'ra': np.asarray(ra, dtype=float), + 'dec': np.asarray(dec, dtype=float), + 'pmra': np.asarray(pmra, dtype=float), + 'pmra_error': np.full(n, 0.05), + 'pmdec': np.asarray(pmdec, dtype=float), + 'pmdec_error': np.full(n, 0.06), + 'parallax': np.asarray(parallax, dtype=float), + 'parallax_error': np.full(n, 0.04), + 'phot_g_mean_mag': np.full(n, 14.0) if g_mag is None else np.asarray(g_mag, dtype=float), + } + distance = np.full(n, 800.0) if distance is None else np.asarray(distance, dtype=float) + data['r_med_geo'] = distance + data['r_lo_geo'] = distance - 50.0 + data['r_hi_geo'] = distance + 60.0 + synth_g = np.full(n, 15.0) if synth_g is None else np.asarray(synth_g, dtype=float) + synth_r = np.full(n, 14.4) if synth_r is None else np.asarray(synth_r, dtype=float) + for band, mags in [('g_sdss', synth_g), ('r_sdss', synth_r), ('i_sdss', synth_r), ('z_sdss', synth_r)]: + data[f'{band}_mag'] = mags + data[f'{band}_mag_error'] = np.where(np.isfinite(mags), 0.032, np.nan) + return data + + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.gaia_cone_search') + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.FileCache') + def test_operate(self, mock_file_cache, mock_gaia_cone_search): + # five cluster stars present in both bands, at 10-50 arcsec north of the center + common_dec = self.CENTER_DEC + np.array([10.0, 20.0, 30.0, 40.0, 50.0]) / 3600.0 + common_ra = np.full(5, self.CENTER_RA) + blue_common_mag = np.array([15.0, 15.5, 16.0, 16.5, 17.0]) + red_common_mag = np.array([14.5, 14.8, 15.2, 15.6, 16.0]) + + # a sixth red star 10 arcsec south with two blue sources nearby (0 and 1 arcsec away), + # to check one-to-one dedup keeps only the closest pair + crowded_dec = self.CENTER_DEC - 10.0 / 3600.0 + # plus per-band strays with no counterpart within the match radius + blue_ra = np.concatenate([common_ra, [self.CENTER_RA, self.CENTER_RA, self.CENTER_RA]]) + blue_dec = np.concatenate([common_dec, [crowded_dec, crowded_dec + 1.0 / 3600.0, self.CENTER_DEC + 80.0 / 3600.0]]) + blue_mag = np.concatenate([blue_common_mag, [18.0, 19.0, 15.5]]) + red_ra = np.concatenate([common_ra, [self.CENTER_RA, self.CENTER_RA]]) + red_dec = np.concatenate([common_dec, [crowded_dec, self.CENTER_DEC - 40.0 / 3600.0]]) + red_mag = np.concatenate([red_common_mag, [17.0, 15.0]]) + + self.create_test_fits(self.temp_blue_path, self.CENTER_RA, self.CENTER_DEC, + blue_ra, blue_dec, blue_mag, np.full(len(blue_mag), 0.02)) + self.create_test_fits(self.temp_red_path, self.CENTER_RA, self.CENTER_DEC, + red_ra, red_dec, red_mag, np.full(len(red_mag), 0.03)) + self.mock_band_fits(mock_file_cache) + + # Gaia knows the four brightest cluster stars, plus a stray with no photometric counterpart + gaia_dec = np.concatenate([common_dec[:4], [self.CENTER_DEC - 60.0 / 3600.0]]) + mock_gaia_cone_search.return_value = self.gaia_field( + ra=np.full(5, self.CENTER_RA), + dec=gaia_dec, + pmra=[-5.1, -4.9, -5.0, -5.05, 12.0], + pmdec=[3.0, 3.1, 2.9, 3.02, -8.0], + parallax=[1.2, 1.3, 1.25, 1.22, 0.1], + synth_g=[15.0, 15.5, 16.0, 16.5, 16.2], + synth_r=[14.5, 14.8, 15.2, 15.6, 15.4], + distance=[810.0, 820.0, 830.0, 840.0, np.nan], + ) + + hr_diagram = HRDiagram(self.hr_input_data()) + hr_diagram.operate(None) + output = hr_diagram.get_output()['output_data'][0] + + self.assertEqual(hr_diagram.get_status(), 'COMPLETED') + self.assertEqual(hr_diagram.get_operation_progress(), 1.0) + self.assertEqual(output['n_stars'], 6) + self.assertEqual(output['n_stars_matched'], 6) + self.assertEqual(output['blue_filter'], 'gp') + self.assertEqual(output['red_filter'], 'rp') + self.assertEqual(output['mag_band'], 'rp') + self.assertEqual(output['cluster']['name'], 'Test Cluster') + mock_gaia_cone_search.assert_called_once_with(self.CENTER_RA, self.CENTER_DEC, 15.0) + + # cmd points are sorted brightest first in the red (y-axis) band + expected_mags = [14.5, 14.8, 15.2, 15.6, 16.0, 17.0] + expected_colors = [0.5, 0.7, 0.8, 0.9, 1.0, 1.0] + for point, expected_mag, expected_color in zip(output['cmd'], expected_mags, expected_colors): + self.assertAlmostEqual(point['mag'], expected_mag, places=3) + self.assertAlmostEqual(point['color'], expected_color, places=3) + self.assertAlmostEqual(point['color_err'], np.sqrt(0.02 ** 2 + 0.03 ** 2), places=3) + + # the four brightest stars picked up Gaia proper motions and parallaxes, the rest did not + self.assertEqual(output['n_gaia_matched'], 4) + self.assertEqual([point['gaia_match'] for point in output['cmd'][:6]], [True] * 4 + [False] * 2) + self.assertAlmostEqual(output['cmd'][0]['pmra'], -5.1) + self.assertAlmostEqual(output['cmd'][0]['pmdec'], 3.0) + self.assertAlmostEqual(output['cmd'][0]['parallax'], 1.2) + self.assertIsNone(output['cmd'][4]['pmra']) + self.assertIsNone(output['cmd'][5]['parallax']) + # Bailer-Jones geometric distance rides along with each Gaia match, bracketed by its bounds + self.assertAlmostEqual(output['cmd'][0]['distance'], 810.0) + self.assertAlmostEqual(output['cmd'][0]['distance_lo'], 760.0) + self.assertAlmostEqual(output['cmd'][0]['distance_hi'], 870.0) + # an unmatched image star has no Gaia distance + self.assertIsNone(output['cmd'][5]['distance']) + # five pool stars is below the clump threshold, so no automatic membership guess + self.assertIsNone(output['membership_guess']) + + # the unmatched Gaia stray is appended as a gaia_only star with synthetic photometry + self.assertEqual(output['n_gaia_only'], 1) + self.assertEqual(len(output['cmd']), 7) + self.assertEqual([point['gaia_only'] for point in output['cmd']], [False] * 6 + [True]) + gaia_only_point = output['cmd'][6] + self.assertAlmostEqual(gaia_only_point['pmra'], 12.0) + self.assertAlmostEqual(gaia_only_point['g_mag'], 14.0) + self.assertAlmostEqual(gaia_only_point['color'], 0.8, places=3) + self.assertAlmostEqual(gaia_only_point['mag'], 15.4, places=3) + # this stray has no Bailer-Jones entry (nan distance), so its distance is null while its pm rides along + self.assertIsNone(gaia_only_point['distance']) + + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.gaia_cone_search') + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.FileCache') + def test_gaia_only_stars_capped_and_brightest_first(self, mock_file_cache, mock_gaia_cone_search): + # two image stars near the center with no Gaia counterparts + star_dec = self.CENTER_DEC + np.array([10.0, 20.0]) / 3600.0 + star_ra = np.full(2, self.CENTER_RA) + red_mags = np.array([15.0, 16.0]) + self.create_test_fits(self.temp_blue_path, self.CENTER_RA, self.CENTER_DEC, + star_ra, star_dec, red_mags + 0.5, np.full(2, 0.02)) + self.create_test_fits(self.temp_red_path, self.CENTER_RA, self.CENTER_DEC, + star_ra, star_dec, red_mags, np.full(2, 0.03)) + self.mock_band_fits(mock_file_cache) + + # five unmatched Gaia field stars: G mags shuffled, one with no G mag at all, + # and the brightest one missing its synthetic photometry + gaia_dec = self.CENTER_DEC - np.array([60.0, 70.0, 80.0, 90.0, 100.0]) / 3600.0 + mock_gaia_cone_search.return_value = self.gaia_field( + ra=np.full(5, self.CENTER_RA), + dec=gaia_dec, + pmra=np.full(5, 4.0), pmdec=np.full(5, -2.0), parallax=np.full(5, 0.8), + g_mag=[15.0, 11.0, 13.0, np.nan, 12.0], + synth_g=[15.8, np.nan, 13.8, 14.1, 12.8], + synth_r=[15.1, np.nan, 13.1, 13.5, 12.1], + ) + + with mock.patch.object(HRDiagram, 'MAX_GAIA_ONLY_SOURCES', 3): + hr_diagram = HRDiagram(self.hr_input_data()) + hr_diagram.operate(None) + output = hr_diagram.get_output()['output_data'][0] + + self.assertEqual(output['n_stars'], 2) + self.assertEqual(output['n_gaia_matched'], 0) + self.assertEqual(output['n_gaia_only'], 3) + gaia_only_points = output['cmd'][2:] + # the cap keeps the brightest three by G mag, ascending; the source with no G mag lost out + self.assertEqual([point['g_mag'] for point in gaia_only_points], [11.0, 12.0, 13.0]) + self.assertTrue(all(point['gaia_only'] for point in gaia_only_points)) + # no synthetic photometry -> the star appears on the membership plots but not the CMD + self.assertIsNone(gaia_only_points[0]['color']) + self.assertIsNone(gaia_only_points[0]['mag']) + self.assertAlmostEqual(gaia_only_points[1]['color'], 0.7, places=3) + self.assertAlmostEqual(gaia_only_points[1]['mag'], 12.1, places=3) + # Bailer-Jones distance rides along even for gaia-only stars + self.assertAlmostEqual(gaia_only_points[1]['distance'], 800.0) + self.assertAlmostEqual(gaia_only_points[1]['distance_lo'], 750.0) + self.assertAlmostEqual(gaia_only_points[1]['distance_hi'], 860.0) + + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.gaia_cone_search') + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.FileCache') + def test_cone_filter_excludes_far_stars(self, mock_file_cache, mock_gaia_cone_search): + # two stars near the center and one 3 arcmin away, with a 1 arcmin search radius + ra = np.full(3, self.CENTER_RA) + dec = self.CENTER_DEC + np.array([10.0, 20.0, 180.0]) / 3600.0 + mag = np.array([15.0, 16.0, 17.0]) + magerr = np.full(3, 0.02) + + self.create_test_fits(self.temp_blue_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag + 0.5, magerr) + self.create_test_fits(self.temp_red_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag, magerr) + self.mock_band_fits(mock_file_cache) + mock_gaia_cone_search.return_value = self.empty_gaia_data() + + hr_diagram = HRDiagram(self.hr_input_data(search_radius_arcmin=1.0)) + hr_diagram.operate(None) + output = hr_diagram.get_output()['output_data'][0] + + self.assertEqual(output['n_stars'], 2) + self.assertEqual(output['cluster']['radius_arcmin'], 1.0) + # an empty Gaia field is not an error, the stars are just unmatched + self.assertEqual(output['n_gaia_matched'], 0) + self.assertIsNone(output['membership_guess']) + + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.gaia_cone_search') + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.FileCache') + def test_radec_from_wcs_fallback(self, mock_file_cache, mock_gaia_cone_search): + # the blue catalog has no ra/dec columns, so they are computed from its x/y and WCS + ra = np.full(3, self.CENTER_RA) + dec = self.CENTER_DEC + np.array([10.0, 20.0, 30.0]) / 3600.0 + mag = np.array([15.0, 16.0, 17.0]) + magerr = np.full(3, 0.02) + + self.create_test_fits(self.temp_blue_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag + 0.5, magerr, + include_radec=False) + self.create_test_fits(self.temp_red_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag, magerr) + self.mock_band_fits(mock_file_cache) + mock_gaia_cone_search.return_value = self.empty_gaia_data() + + hr_diagram = HRDiagram(self.hr_input_data()) + hr_diagram.operate(None) + output = hr_diagram.get_output()['output_data'][0] + + self.assertEqual(hr_diagram.get_status(), 'COMPLETED') + self.assertEqual(output['n_stars'], 3) + self.assertAlmostEqual(output['cmd'][0]['ra'], self.CENTER_RA, places=5) + self.assertAlmostEqual(output['cmd'][0]['color'], 0.5, places=3) + + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.gaia_cone_search') + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.FileCache') + def test_gaia_failure_fails_operation(self, mock_file_cache, mock_gaia_cone_search): + # a Gaia outage fails the operation (re-runnable) instead of caching a degraded result + ra = np.full(2, self.CENTER_RA) + dec = self.CENTER_DEC + np.array([10.0, 20.0]) / 3600.0 + mag = np.array([15.0, 16.0]) + magerr = np.full(2, 0.02) + + self.create_test_fits(self.temp_blue_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag + 0.5, magerr) + self.create_test_fits(self.temp_red_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag, magerr) + self.mock_band_fits(mock_file_cache) + mock_gaia_cone_search.side_effect = ClientAlertException('Could not fetch Gaia data for the cluster field') + + hr_diagram = HRDiagram(self.hr_input_data()) + with self.assertRaisesRegex(ClientAlertException, 'Gaia'): + hr_diagram.operate(None) + + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.FileCache') + def test_uncalibrated_band_fails(self, mock_file_cache): + ra = np.full(2, self.CENTER_RA) + dec = self.CENTER_DEC + np.array([10.0, 20.0]) / 3600.0 + mag = np.array([15.0, 16.0]) + magerr = np.full(2, 0.02) + + self.create_test_fits(self.temp_blue_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag, magerr, + include_mag=False) + self.create_test_fits(self.temp_red_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag, magerr) + self.mock_band_fits(mock_file_cache) + + hr_diagram = HRDiagram(self.hr_input_data()) + with self.assertRaisesRegex(ClientAlertException, 'zero-point calibrated'): + hr_diagram.operate(None) + + @mock.patch('datalab.datalab_session.data_operations.hr_diagram.FileCache') + def test_disjoint_fields_fail(self, mock_file_cache): + # the red image is a degree away, so no stars cross-match + ra = np.full(2, self.CENTER_RA) + dec = self.CENTER_DEC + np.array([10.0, 20.0]) / 3600.0 + mag = np.array([15.0, 16.0]) + magerr = np.full(2, 0.02) + + self.create_test_fits(self.temp_blue_path, self.CENTER_RA, self.CENTER_DEC, ra, dec, mag, magerr) + self.create_test_fits(self.temp_red_path, self.CENTER_RA + 1.0, self.CENTER_DEC, + ra + 1.0, dec, mag, magerr) + self.mock_band_fits(mock_file_cache) + + hr_diagram = HRDiagram(self.hr_input_data()) + with self.assertRaisesRegex(ClientAlertException, 'No stars matched'): + hr_diagram.operate(None) + + def test_missing_cluster_fails(self): + input_data = self.hr_input_data() + del input_data['cluster'] + hr_diagram = HRDiagram(input_data) + + with self.assertRaisesRegex(ClientAlertException, 'cluster center'): + hr_diagram.operate(None) + + def test_bad_search_radius_fails(self): + hr_diagram = HRDiagram(self.hr_input_data(search_radius_arcmin=-5.0)) + + with self.assertRaisesRegex(ClientAlertException, 'search radius'): + hr_diagram.operate(None) + + def test_missing_input_files_fails(self): + input_data = self.hr_input_data() + input_data['red_filter_files'] = [] + hr_diagram = HRDiagram(input_data) + + with self.assertRaises(ClientAlertException): + hr_diagram.operate(None) + + class TestStackOperation(FileExtendedTestCase): test_fits_1_path = f'{test_path}fits_1.fits.fz' test_fits_2_path = f'{test_path}fits_2.fits.fz' diff --git a/datalab/datalab_session/tests/test_utils.py b/datalab/datalab_session/tests/test_utils.py index a56a156..f2c4b9f 100644 --- a/datalab/datalab_session/tests/test_utils.py +++ b/datalab/datalab_session/tests/test_utils.py @@ -1,9 +1,16 @@ +from unittest import mock + +from astropy.table import Table, MaskedColumn + from datalab.datalab_session.utils.file_utils import * from datalab.datalab_session.utils.s3_utils import * from datalab.datalab_session.utils.flux_to_mag import flux_to_mag, flux_to_mag_array, flux_to_mag_scalar from datalab.datalab_session.utils.geometry import angular_distance_arcsec, distance_pixels from datalab.datalab_session.utils.centroiding import BackgroundModel, _fit_plane from datalab.datalab_session.utils.photometry import fractional_pixel_overlap, measure_aperture +from datalab.datalab_session.utils.catalog_utils import cross_match_one_to_one, cone_filter +from datalab.datalab_session.utils.gaia import GAIA_PARALLAX_ZERO_POINT_MAS, estimate_membership, gaia_cone_search +from datalab.datalab_session.exceptions import ClientAlertException from datalab.datalab_session.tests.test_files.file_extended_test_case import FileExtendedTestCase class FileUtilsTestClass(FileExtendedTestCase): @@ -167,3 +174,185 @@ def test_fit_plane_rejects_degenerate_points(self): ] self.assertIsNone(_fit_plane(points)) + +class CatalogUtilsTestClass(FileExtendedTestCase): + + @staticmethod + def catalog(dec_offsets_arcsec, ra=150.0, dec=30.0): + """ Builds a minimal catalog dict of points offset north of (ra, dec) by arcseconds """ + return { + 'ra': np.full(len(dec_offsets_arcsec), ra), + 'dec': dec + np.array(dec_offsets_arcsec) / 3600.0, + } + + def test_cross_match_matches_within_radius(self): + catalog_a = self.catalog([0.0, 10.0]) + catalog_b = self.catalog([0.5, 10.0]) + + a_indices, b_indices = cross_match_one_to_one(catalog_a, catalog_b, 2.0) + + self.assertEqual(a_indices.tolist(), [0, 1]) + self.assertEqual(b_indices.tolist(), [0, 1]) + + def test_cross_match_applies_separation_cut(self): + catalog_a = self.catalog([0.0]) + catalog_b = self.catalog([3.0]) # nearest neighbor is 3 arcsec away + + a_indices, b_indices = cross_match_one_to_one(catalog_a, catalog_b, 2.0) + + self.assertEqual(len(a_indices), 0) + self.assertEqual(len(b_indices), 0) + + def test_cross_match_dedups_to_closest_pair(self): + # two a sources share the same nearest b source, only the closer pair survives + catalog_a = self.catalog([0.0, 1.0]) + catalog_b = self.catalog([0.0]) + + a_indices, b_indices = cross_match_one_to_one(catalog_a, catalog_b, 2.0) + + self.assertEqual(a_indices.tolist(), [0]) + self.assertEqual(b_indices.tolist(), [0]) + + def test_cross_match_empty_catalogs(self): + empty = {'ra': np.array([]), 'dec': np.array([])} + catalog = self.catalog([0.0]) + + for catalog_a, catalog_b in [(empty, catalog), (catalog, empty), (empty, empty)]: + a_indices, b_indices = cross_match_one_to_one(catalog_a, catalog_b, 2.0) + self.assertEqual(len(a_indices), 0) + self.assertEqual(len(b_indices), 0) + + def test_cone_filter(self): + catalog = self.catalog([30.0, 120.0]) # 0.5 and 2 arcmin north of center + + in_cone = cone_filter(catalog['ra'], catalog['dec'], 150.0, 30.0, 1.0) + + self.assertEqual(in_cone.tolist(), [True, False]) + + +class GaiaUtilsTestClass(FileExtendedTestCase): + + @staticmethod + def gaia_table(): + """ A fake Gaia archive result: the second source is missing its astrometric solution, + its Bailer-Jones distance, and (like any source without published BP/RP spectra) its + synthetic photometry """ + columns = { + 'ra': [150.0, 150.001], + 'dec': [30.0, 30.001], + 'pmra': MaskedColumn([5.0, 0.0], mask=[False, True]), + 'pmra_error': MaskedColumn([0.05, 0.0], mask=[False, True]), + 'pmdec': MaskedColumn([-3.0, 0.0], mask=[False, True]), + 'pmdec_error': MaskedColumn([0.06, 0.0], mask=[False, True]), + 'parallax': MaskedColumn([1.25, 0.0], mask=[False, True]), + 'parallax_error': MaskedColumn([0.04, 0.0], mask=[False, True]), + 'phot_g_mean_mag': [14.2, 17.9], + 'r_med_geo': MaskedColumn([800.0, 0.0], mask=[False, True]), + 'r_lo_geo': MaskedColumn([760.0, 0.0], mask=[False, True]), + 'r_hi_geo': MaskedColumn([845.0, 0.0], mask=[False, True]), + } + for band in ['g_sdss', 'r_sdss', 'i_sdss', 'z_sdss']: + columns[f'{band}_mag'] = MaskedColumn([15.0, 0.0], mask=[False, True]) + columns[f'{band}_flux'] = MaskedColumn([1000.0, 0.0], mask=[False, True]) + columns[f'{band}_flux_error'] = MaskedColumn([10.0, 0.0], mask=[False, True]) + return Table(columns) + + @mock.patch('astroquery.gaia.Gaia') + def test_gaia_cone_search_parses_and_caches(self, mock_gaia): + mock_gaia.launch_job_async.return_value.get_results.return_value = self.gaia_table() + + # unique field so this test never hits another test's cache entry + gaia_data = gaia_cone_search(210.1234, -5.5678, 12.0) + + self.assertEqual(len(gaia_data['ra']), 2) + self.assertAlmostEqual(gaia_data['pmra'][0], 5.0) + self.assertAlmostEqual(gaia_data['parallax'][0], 1.25 + GAIA_PARALLAX_ZERO_POINT_MAS) + # masked values come back as nan + self.assertTrue(np.isnan(gaia_data['pmra'][1])) + self.assertTrue(np.isnan(gaia_data['parallax'][1])) + # Bailer-Jones geometric distance parses; the source without an entry comes back nan + self.assertAlmostEqual(gaia_data['r_med_geo'][0], 800.0) + self.assertAlmostEqual(gaia_data['r_lo_geo'][0], 760.0) + self.assertAlmostEqual(gaia_data['r_hi_geo'][0], 845.0) + self.assertTrue(np.isnan(gaia_data['r_med_geo'][1])) + # synthetic photometry parses, with flux errors propagated onto the systematic floor + self.assertAlmostEqual(gaia_data['g_sdss_mag'][0], 15.0) + expected_error = np.sqrt((2.5 / np.log(10) * 10.0 / 1000.0) ** 2 + 0.03 ** 2) + self.assertAlmostEqual(gaia_data['g_sdss_mag_error'][0], expected_error, places=5) + self.assertTrue(np.isnan(gaia_data['g_sdss_mag'][1])) + self.assertTrue(np.isnan(gaia_data['g_sdss_mag_error'][1])) + + # a second identical search is served from the cache without re-querying the archive + gaia_cone_search(210.1234, -5.5678, 12.0) + mock_gaia.launch_job_async.assert_called_once() + + @mock.patch('astroquery.gaia.Gaia') + def test_gaia_cone_search_failure_raises(self, mock_gaia): + mock_gaia.launch_job_async.side_effect = ConnectionError('archive down') + + with self.assertRaisesRegex(ClientAlertException, 'Gaia'): + gaia_cone_search(33.3333, 44.4444, 10.0) + + def test_estimate_membership_finds_clump(self): + rng = np.random.default_rng(42) + # a 40 star cluster clump at (-5, 3) mas/yr among 20 spread out field stars + pmra = np.concatenate([rng.normal(-5.0, 0.3, 40), rng.uniform(-20.0, 20.0, 20)]) + pmdec = np.concatenate([rng.normal(3.0, 0.3, 40), rng.uniform(-20.0, 20.0, 20)]) + parallax = np.concatenate([rng.normal(1.25, 0.05, 40), rng.uniform(0.1, 2.0, 20)]) + # cluster piled up near 800 pc, field stars scattered; +/-40 pc Bailer-Jones bounds per star + distance = np.concatenate([rng.normal(800.0, 20.0, 40), rng.uniform(100.0, 3000.0, 20)]) + distance_lo = distance - 40.0 + distance_hi = distance + 40.0 + + guess = estimate_membership(pmra, pmdec, parallax, distance, distance_lo, distance_hi) + + self.assertIsNotNone(guess) + self.assertAlmostEqual(guess['pmra'], -5.0, delta=0.5) + self.assertAlmostEqual(guess['pmdec'], 3.0, delta=0.5) + self.assertGreaterEqual(guess['pm_radius'], 0.5) + self.assertLessEqual(guess['pm_radius'], 5.0) + self.assertLess(guess['parallax_min'], 1.25) + self.assertGreater(guess['parallax_max'], 1.25) + self.assertLess(guess['distance_min'], 800.0) + self.assertGreater(guess['distance_max'], 800.0) + self.assertGreaterEqual(guess['distance_min'], 0.0) + + def test_estimate_membership_distance_window_optional(self): + rng = np.random.default_rng(42) + pmra = np.concatenate([rng.normal(-5.0, 0.3, 40), rng.uniform(-20.0, 20.0, 20)]) + pmdec = np.concatenate([rng.normal(3.0, 0.3, 40), rng.uniform(-20.0, 20.0, 20)]) + parallax = np.concatenate([rng.normal(1.25, 0.05, 40), rng.uniform(0.1, 2.0, 20)]) + + # no distances supplied - the distance window is left unset + guess = estimate_membership(pmra, pmdec, parallax) + + self.assertIsNotNone(guess) + self.assertIsNone(guess['distance_min']) + self.assertIsNone(guess['distance_max']) + + def test_estimate_membership_too_few_stars(self): + pmra = np.full(5, -5.0) + pmdec = np.full(5, 3.0) + parallax = np.full(5, 1.25) + + self.assertIsNone(estimate_membership(pmra, pmdec, parallax)) + + def test_estimate_membership_no_clump(self): + rng = np.random.default_rng(7) + # spread out field stars only, no concentration to call a cluster + pmra = rng.uniform(-20.0, 20.0, 40) + pmdec = rng.uniform(-20.0, 20.0, 40) + parallax = rng.uniform(0.1, 2.0, 40) + + self.assertIsNone(estimate_membership(pmra, pmdec, parallax)) + + def test_estimate_membership_tolerates_negative_parallax(self): + rng = np.random.default_rng(11) + pmra = rng.normal(0.0, 0.2, 15) + pmdec = rng.normal(0.0, 0.2, 15) + parallax = rng.normal(-0.05, 0.02, 15) # a distant clump can measure slightly negative + + guess = estimate_membership(pmra, pmdec, parallax) + + self.assertIsNotNone(guess) + self.assertLess(guess['parallax_min'], 0.0) diff --git a/datalab/datalab_session/utils/catalog_utils.py b/datalab/datalab_session/utils/catalog_utils.py new file mode 100644 index 0000000..bb9246f --- /dev/null +++ b/datalab/datalab_session/utils/catalog_utils.py @@ -0,0 +1,117 @@ +import logging + +import numpy as np +from astropy import units as u +from astropy.coordinates import SkyCoord +from astropy.wcs import WCS + +from datalab.datalab_session.exceptions import ClientAlertException +from datalab.datalab_session.utils.file_utils import get_hdu + +log = logging.getLogger() +log.setLevel(logging.INFO) + + +def extract_calibrated_catalog(fits_path: str, basename: str = '') -> dict: + """ + Reads the CAT HDU of a fits file and returns full-precision numpy arrays of the + source positions and zero-point calibrated photometry: {ra, dec, mag, magerr} + + - Requires calibrated mag/magerr columns, there is no instrumental flux fallback + since an un-zero-pointed magnitude makes a color meaningless + - Computes ra/dec from the x/y columns and the SCI WCS when the CAT lacks them + - Drops rows with non-finite values in any returned column + """ + cat_data = get_hdu(fits_path, 'CAT').data + + if 'mag' not in cat_data.names or 'magerr' not in cat_data.names: + raise ClientAlertException(f'{basename} has no zero-point calibrated magnitudes (CAT mag/magerr), ' + 'which the HR Diagram requires. Try an image in a calibrated filter.') + + mag = np.asarray(cat_data['mag'], dtype=float) + magerr = np.asarray(cat_data['magerr'], dtype=float) + + if 'ra' in cat_data.names and 'dec' in cat_data.names: + ra = np.asarray(cat_data['ra'], dtype=float) + dec = np.asarray(cat_data['dec'], dtype=float) + else: + ra, dec = _ra_dec_from_wcs(fits_path, cat_data, basename) + + valid = np.isfinite(ra) & np.isfinite(dec) & np.isfinite(mag) & np.isfinite(magerr) + return {'ra': ra[valid], 'dec': dec[valid], 'mag': mag[valid], 'magerr': magerr[valid]} + + +def _ra_dec_from_wcs(fits_path: str, cat_data, basename: str = ''): + """ + Fallback for CAT HDUs without ra/dec columns: compute them from the catalog x/y + pixel positions and the SCI extension's WCS solution + """ + if 'x' not in cat_data.names or 'y' not in cat_data.names: + raise ClientAlertException(f'{basename} catalog has no ra/dec or x/y columns to locate its sources') + + sci_header = get_hdu(fits_path, 'SCI').header + wcs = WCS(sci_header) + if not wcs.has_celestial: + raise ClientAlertException(f'{basename} catalog has no ra/dec columns and the image has no WCS solution to compute them') + + # origin=1: source extractor catalog x/y positions use the FITS 1-based convention + ra, dec = wcs.all_pix2world(cat_data['x'], cat_data['y'], 1) + return np.asarray(ra, dtype=float), np.asarray(dec, dtype=float) + + +def cross_match_one_to_one(catalog_a: dict, catalog_b: dict, match_radius_arcsec: float): + """ + Nearest-neighbor sky match of catalog_a sources to catalog_b sources within match_radius_arcsec, + deduplicated to one-to-one pairs (when multiple a sources share the same nearest b source, + only the closest pair is kept, avoiding double counted stars in crowded fields). + + Catalogs are dicts holding equal-length 'ra' and 'dec' arrays in degrees. + Returns (a_indices, b_indices) index arrays of the matched pairs. + """ + if len(catalog_a['ra']) == 0 or len(catalog_b['ra']) == 0: + return np.array([], dtype=int), np.array([], dtype=int) + + coords_a = SkyCoord(ra=catalog_a['ra'] * u.deg, dec=catalog_a['dec'] * u.deg) + coords_b = SkyCoord(ra=catalog_b['ra'] * u.deg, dec=catalog_b['dec'] * u.deg) + nearest_b, sep2d, _ = coords_a.match_to_catalog_sky(coords_b) + sep_arcsec = np.atleast_1d(sep2d.arcsec) + nearest_b = np.atleast_1d(nearest_b) + + # match_to_catalog_sky returns a nearest neighbor unconditionally, so apply the separation cut, + # then keep only the closest a for each b to enforce one-to-one matching + best_a_for_b = {} + for a_index in np.flatnonzero(sep_arcsec <= match_radius_arcsec): + b_index = int(nearest_b[a_index]) + if b_index not in best_a_for_b or sep_arcsec[a_index] < sep_arcsec[best_a_for_b[b_index]]: + best_a_for_b[b_index] = int(a_index) + + pairs = sorted((a_index, b_index) for b_index, a_index in best_a_for_b.items()) + a_indices = np.array([pair[0] for pair in pairs], dtype=int) + b_indices = np.array([pair[1] for pair in pairs], dtype=int) + return a_indices, b_indices + + +def cone_filter(ra, dec, center_ra: float, center_dec: float, radius_arcmin: float): + """ + Returns a boolean mask of the (ra, dec) points within radius_arcmin of the center point. + All coordinates in degrees. + """ + center = SkyCoord(ra=center_ra * u.deg, dec=center_dec * u.deg) + points = SkyCoord(ra=np.asarray(ra) * u.deg, dec=np.asarray(dec) * u.deg) + return center.separation(points).arcmin <= radius_arcmin + + +def wcs_contains_point(fits_path: str, ra: float, dec: float) -> bool: + """ + Best-effort check of whether (ra, dec) falls inside the image's WCS footprint. + Returns True when the WCS is missing or unusable so an inconclusive check never blocks an operation. + """ + try: + sci_header = get_hdu(fits_path, 'SCI').header + wcs = WCS(sci_header) + if not wcs.has_celestial: + return True + return bool(wcs.footprint_contains(SkyCoord(ra=ra * u.deg, dec=dec * u.deg))) + except Exception as e: + log.warning(f'Could not check WCS footprint for {fits_path}: {e}') + return True diff --git a/datalab/datalab_session/utils/gaia.py b/datalab/datalab_session/utils/gaia.py new file mode 100644 index 0000000..f3d42db --- /dev/null +++ b/datalab/datalab_session/utils/gaia.py @@ -0,0 +1,227 @@ +import logging + +import numpy as np +from django.core.cache import cache + +from datalab.datalab_session.exceptions import ClientAlertException + +log = logging.getLogger() +log.setLevel(logging.INFO) + +GAIA_TABLE = 'gaiadr3.gaia_source' +GAIA_SYNTH_TABLE = 'gaiadr3.synthetic_photometry_gspc' +# Bailer-Jones et al. (2021) geometric distances (external.gaiaedr3_distance): a Bayesian +# posterior with a direction-dependent distance prior, so the estimate is always positive and +# well behaved even where the parallax is negative or low-significance. +# r_med_geo is the point estimate (parsecs); r_lo_geo / r_hi_geo are the 16th / 84th +# percentiles (asymmetric, 1-sigma-like bounds). source_ids match gaiadr3.gaia_source. +# Photogeometric columns (r_med_photogeo,...) are sharper where BP/RP photometry is good but bake in a Galactic CMD population model; +# geometric is the robust default and assumes nothing photometric about the sources. +GAIA_DISTANCE_TABLE = 'external.gaiaedr3_distance' +GAIA_DISTANCE_COLUMNS = ['r_med_geo', 'r_lo_geo', 'r_hi_geo'] +GAIA_SOURCE_COLUMNS = ['ra', 'dec', 'pmra', 'pmra_error', 'pmdec', 'pmdec_error', 'parallax', 'parallax_error', + 'phot_g_mean_mag'] +# Synthetic SDSS-system AB magnitudes from the Gaia Synthetic Photometry Catalogue (computed +# from the BP/RP spectra, so only sources with published spectra have them, G <~ 17.65). +# GSPC standardizes griz to the SDSS system - within ~0.03 mag of the Pan-STARRS1 system the +# images are calibrated to, the same order as BANZAI's color-term-free zero-pointing +GAIA_SYNTH_BANDS = ['g_sdss', 'r_sdss', 'i_sdss', 'z_sdss'] +# columns queried per source; the result dict also carries a {band}_mag_error for each synth band +GAIA_COLUMNS = GAIA_SOURCE_COLUMNS + GAIA_DISTANCE_COLUMNS + [f'{band}_mag' for band in GAIA_SYNTH_BANDS] +# systematic floor on synthetic magnitude errors: SDSS<->PS1 system difference + GSPC calibration +GAIA_SYNTH_MAG_ERROR_FLOOR = 0.03 +# RUWE < 1.4 is the standard threshold for well behaved astrometric solutions from Lindegren's Gaia astrometry notes +GAIA_RUWE_LIMIT = 1.4 +# Mean Gaia DR3 parallax zero-point offset (Lindegren et al. 2021): observed parallaxes +# run ~17 microarcsec too small, so add it back +GAIA_PARALLAX_ZERO_POINT_MAS = 0.017 +# Gaia DR3 is a static catalog, so cached cone searches stay valid; cache them separately from +# the operation cache so unrelated input tweaks don't re-hit the TAP service +GAIA_CACHE_DURATION = 60 * 60 * 24 * 30 # 30 days + +# membership_guess tuning +MIN_GAIA_MATCHES_FOR_GUESS = 10 # too few matched stars to call a clump +PM_HISTOGRAM_HALF_WIDTH = 25.0 # mas/yr searched around the median proper motion +PM_HISTOGRAM_BIN = 1.0 # mas/yr cell size, ~cluster clump scale +MIN_CLUMP_COUNT = 5 # peak cells below this are noise, not a cluster +PM_RADIUS_BOUNDS = (0.5, 5.0) # mas/yr allowed range for the suggested clump radius + + +def gaia_cone_search(center_ra: float, center_dec: float, radius_arcmin: float) -> dict: + """ + Gaia DR3 cone search around (center_ra, center_dec) degrees, returning a dict of numpy + arrays for GAIA_COLUMNS with the RUWE cut and parallax zero-point correction applied. + Missing values (e.g. no proper motion solution) are np.nan. + + Results are cached by field + radius. Failures raise ClientAlertException so the + operation fails visibly and can be re-run, rather than caching a degraded result. + """ + # versioned key: whenever GAIA_COLUMNS changes (v2 added phot_g_mean_mag, v3 added the + # Bailer-Jones distance columns) a month-old cached response would be missing the new keys + cache_key = f'gaia_dr3_cone_v3_{center_ra:.4f}_{center_dec:.4f}_{radius_arcmin:.3f}' + gaia_data = cache.get(cache_key) + if gaia_data is not None: + return gaia_data + + gaia_data = _query_gaia(center_ra, center_dec, radius_arcmin) + cache.set(cache_key, gaia_data, GAIA_CACHE_DURATION) + return gaia_data + + +def _query_gaia(center_ra: float, center_dec: float, radius_arcmin: float) -> dict: + # astroquery is imported lazily so that Django startup (which imports every data operation + # to build available_operations) doesn't pay its import cost + from astroquery.gaia import Gaia + + source_columns = ', '.join(f'g.{column}' for column in GAIA_SOURCE_COLUMNS) + # raw Bailer-Jones column names + distance_columns = ', '.join(f'd.{column}' for column in GAIA_DISTANCE_COLUMNS) + synth_columns = ', '.join(f's.{band}_mag, s.{band}_flux, s.{band}_flux_error' + for band in GAIA_SYNTH_BANDS) + query = f""" + SELECT {source_columns}, {distance_columns}, {synth_columns} + FROM {GAIA_TABLE} AS g + LEFT JOIN {GAIA_DISTANCE_TABLE} AS d ON d.source_id = g.source_id + LEFT JOIN {GAIA_SYNTH_TABLE} AS s ON s.source_id = g.source_id + WHERE CONTAINS(POINT('ICRS', g.ra, g.dec), CIRCLE('ICRS', {center_ra}, {center_dec}, {radius_arcmin / 60.0})) = 1 + AND g.ruwe < {GAIA_RUWE_LIMIT} + """ + try: + # This launches off an async query to the GAIA service + job = Gaia.launch_job_async(query, verbose=False) + # This waits synchronously for the results of the GAIA query, which is fine since this operation happens in a worker. + # If this takes longer than the timeout limit of the worker task (1 hour), this task will die. + table = job.get_results() + except Exception as e: + log.error(f'Gaia cone search failed for ({center_ra}, {center_dec}) r={radius_arcmin}\': {e}') + raise ClientAlertException('Could not fetch Gaia data for the cluster field - the Gaia archive may ' + 'be temporarily unavailable, try re-running the operation later.') + + def column_values(name): + # Get rid of nans from the returned data + return np.ma.filled(np.ma.masked_invalid(table[name].data), np.nan).astype(float) + + gaia_data = {column: column_values(column) for column in GAIA_COLUMNS} + # Adjust the parallax by the adjustment factor + gaia_data['parallax'] = gaia_data['parallax'] + GAIA_PARALLAX_ZERO_POINT_MAS + # propagate synthetic flux errors to magnitude errors, on a systematic floor + for band in GAIA_SYNTH_BANDS: + flux = column_values(f'{band}_flux') + flux_error = column_values(f'{band}_flux_error') + with np.errstate(divide='ignore', invalid='ignore'): + mag_error = 2.5 / np.log(10.0) * flux_error / flux + gaia_data[f'{band}_mag_error'] = np.sqrt(mag_error ** 2 + GAIA_SYNTH_MAG_ERROR_FLOOR ** 2) + + log.info(f'Gaia cone search returned {len(gaia_data["ra"])} sources ' + f'for ({center_ra}, {center_dec}) r={radius_arcmin}\'') + return gaia_data + + +def _member_distance_window(distance, distance_lo, distance_hi, finite_pm, members): + """ + Builds a (distance_min, distance_max) parsec window from the clump members' Bailer-Jones + distances, or (None, None) when distances weren't supplied or too few members have one. + + Members scatter around the true cluster distance from both real depth and measurement error, + so the half-window is 3x the larger of the robust scatter of the r_med_geo point estimates and + the members' typical per-star uncertainty (median (r_hi_geo - r_lo_geo) / 2). distance_min is + clamped non-negative since Bailer-Jones distances are always positive. + """ + if distance is None: + return None, None + distance = np.asarray(distance, dtype=float) + distance_lo = np.asarray(distance_lo, dtype=float) + distance_hi = np.asarray(distance_hi, dtype=float) + + member_distance = distance[finite_pm][members] + member_lo = distance_lo[finite_pm][members] + member_hi = distance_hi[finite_pm][members] + has_distance = np.isfinite(member_distance) & (member_distance > 0) + if has_distance.sum() < 3: + return None, None + + distances = member_distance[has_distance] + distance_median = np.median(distances) + robust_scatter = 1.4826 * np.median(np.abs(distances - distance_median)) + # per-star measurement uncertainty floor, using the asymmetric lo/hi bounds where present + half_widths = (member_hi[has_distance] - member_lo[has_distance]) / 2.0 + half_widths = half_widths[np.isfinite(half_widths) & (half_widths > 0)] + per_star_sigma = np.median(half_widths) if len(half_widths) else 0.0 + distance_sigma = max(robust_scatter, per_star_sigma) + + distance_min = round(float(max(distance_median - 3.0 * distance_sigma, 0.0)), 1) + distance_max = round(float(distance_median + 3.0 * distance_sigma), 1) + return distance_min, distance_max + + +def estimate_membership(pmra, pmdec, parallax, distance=None, distance_lo=None, distance_hi=None): + """ + Suggests a default cluster membership selection from the proper motions, parallaxes, and + Bailer-Jones distances of the Gaia-matched stars: the dominant proper-motion clump (2D + histogram peak, robust to the cluster being a minority of the field) plus parallax and + distance windows around the clump members. + + distance / distance_lo / distance_hi are the Bailer-Jones r_med_geo point estimate and its + r_lo_geo / r_hi_geo 16th / 84th percentile bounds (parsecs); pass them to also get a distance + window. When omitted (or too few members have a distance) the distance window is left None. + + Returns {'pmra', 'pmdec', 'pm_radius', 'parallax_min', 'parallax_max', 'distance_min', + 'distance_max'} in mas(/yr) and parsecs, or None when there are too few stars or no clear + clump - the user then selects manually. Negative parallaxes are tolerated throughout. + """ + pmra = np.asarray(pmra, dtype=float) + pmdec = np.asarray(pmdec, dtype=float) + parallax = np.asarray(parallax, dtype=float) + + finite_pm = np.isfinite(pmra) & np.isfinite(pmdec) + if finite_pm.sum() < MIN_GAIA_MATCHES_FOR_GUESS: + return None + pmra_finite = pmra[finite_pm] + pmdec_finite = pmdec[finite_pm] + + # histogram the proper motions around their median and take the densest cell as the clump + bins = np.arange(-PM_HISTOGRAM_HALF_WIDTH, PM_HISTOGRAM_HALF_WIDTH + PM_HISTOGRAM_BIN, PM_HISTOGRAM_BIN) + median_pmra, median_pmdec = np.median(pmra_finite), np.median(pmdec_finite) + histogram, pmra_edges, pmdec_edges = np.histogram2d(pmra_finite - median_pmra, pmdec_finite - median_pmdec, bins=(bins, bins)) + peak_index = np.unravel_index(np.argmax(histogram), histogram.shape) + peak_pmra = median_pmra + (pmra_edges[peak_index[0]] + pmra_edges[peak_index[0] + 1]) / 2.0 + peak_pmdec = median_pmdec + (pmdec_edges[peak_index[1]] + pmdec_edges[peak_index[1] + 1]) / 2.0 + + # judge the clump by the stars within a small neighborhood of the peak cell rather than the + # single cell count, so a clump straddling bin edges isn't split below the threshold + near_peak = np.hypot(pmra_finite - peak_pmra, pmdec_finite - peak_pmdec) <= 2.0 * PM_HISTOGRAM_BIN + if near_peak.sum() < MIN_CLUMP_COUNT: + return None + + # refine the clump center with the stars near the peak, then size the radius from their scatter + clump_pmra = float(np.median(pmra_finite[near_peak])) + clump_pmdec = float(np.median(pmdec_finite[near_peak])) + clump_distances = np.hypot(pmra_finite[near_peak] - clump_pmra, pmdec_finite[near_peak] - clump_pmdec) + robust_sigma = 1.4826 * np.median(np.abs(clump_distances - np.median(clump_distances))) + pm_radius = float(np.clip(3.0 * max(robust_sigma, np.median(clump_distances)), *PM_RADIUS_BOUNDS)) + + # parallax window from the clump members with measured parallaxes + members = np.hypot(pmra_finite - clump_pmra, pmdec_finite - clump_pmdec) <= pm_radius + member_parallaxes = parallax[finite_pm][members] + member_parallaxes = member_parallaxes[np.isfinite(member_parallaxes)] + if len(member_parallaxes) >= 3: + parallax_median = np.median(member_parallaxes) + parallax_sigma = max(1.4826 * np.median(np.abs(member_parallaxes - parallax_median)), 0.05) + parallax_min = round(float(parallax_median - 3.0 * parallax_sigma), 4) + parallax_max = round(float(parallax_median + 3.0 * parallax_sigma), 4) + else: + parallax_min = None + parallax_max = None + + # distance window from the clump members' Bailer-Jones distances, when provided + distance_min, distance_max = _member_distance_window(distance, distance_lo, distance_hi, finite_pm, members) + + return { + 'pmra': round(clump_pmra, 3), + 'pmdec': round(clump_pmdec, 3), + 'pm_radius': round(pm_radius, 3), + 'parallax_min': parallax_min, + 'parallax_max': parallax_max, + 'distance_min': distance_min, + 'distance_max': distance_max, + } diff --git a/datalab/settings.py b/datalab/settings.py index 9528671..b82242e 100644 --- a/datalab/settings.py +++ b/datalab/settings.py @@ -234,4 +234,4 @@ def get_list_from_env(variable, default=None): CORS_ORIGIN_ALLOW_ALL = True CORS_ALLOW_CREDENTIALS = True -CSRF_TRUSTED_ORIGINS = get_list_from_env('CSRF_TRUSTED_ORIGINS', 'http://localhost:8080,http://127.0.0.1:8000,http://127.0.0.1:8001,http://localhost:8000,') +CSRF_TRUSTED_ORIGINS = get_list_from_env('CSRF_TRUSTED_ORIGINS', 'http://localhost:8080,http://127.0.0.1:8080,http://127.0.0.1:8081,http://localhost:8081,') diff --git a/poetry.lock b/poetry.lock index 1fb9f3c..ba1df13 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,143 +1,144 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand. 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