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run_photometry.py
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#!/usr/bin/env python
import argparse
import logging
import os
import simplejson as json
import sys
import urllib
import django
from django.conf import settings
from django.utils import timezone
os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'settings')
sys.path.insert(0, os.getcwd())
django.setup()
import catalog
import imageflow.s3_util as s3_util
import point_source_extraction
from astropy_util import get_fits_from_raw
from imageflow.models import ImageAnalysis
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
class PhotometryRunner(object):
def __init__(self, analysis, args):
self.analysis = analysis
self.image_fits_data = None
def get_upload_key_prefix(self):
# TODO(ian): Yuck. This is a really weird way to access submission id,
# from its child...
return 'processed/%d' % (self.analysis.astrometry_job.submission.subid)
def run(self):
self.load()
# Point source extraction processing.
self.process_point_sources()
# Apparent magnitude processing.
# TODO(ian): These inputs could be made more efficient by just passing
# in the data from this function, rather than loading them again from
# urls.
self.process_magnitudes()
# ID numbering may have changed.
self.analysis.target_id = None
# Done!
self.analysis.status = ImageAnalysis.REVIEW_PENDING
self.analysis.save()
def load(self):
# TODO(ian): Dedupe with astrometry step.
job = self.analysis.astrometry_job
new_image_fits_url = 'http://35.202.61.141:8081/new_fits_file/%d' \
% (job.jobid)
self.image_fits_data = urllib.urlopen(new_image_fits_url).read()
def process_point_sources(self):
job = self.analysis.astrometry_job
submission = job.submission
logger.info('-> Processing fits image for analysis %d' % (self.analysis.id))
fitsobj = get_fits_from_raw(self.image_fits_data)
data = point_source_extraction.extract_image_data_from_fits(fitsobj)
'''
sources, residual_image, std = \
point_source_extraction.compute_sextractor(self.analysis.get_or_create_photometry_settings(),
self.image_fits_data,
data)
'''
sources, residual_image, std = \
point_source_extraction.compute_sextractor(self.analysis.get_or_create_photometry_settings(),
self.image_fits_data,
data)
self.analysis.sigma_clipped_std = std
# Unaltered image.
image_path = '%d_%d_display_image.png' % (submission.subid, job.jobid)
point_source_extraction.save_image(data, image_path);
logger.info(' -> Uploading %s...' % image_path)
if not args.dry_run:
'''
self.analysis.original_display_url = \
s3_util.upload_to_s3_via_file(image_path, \
self.get_upload_key_prefix())
'''
# Astrometry image looks much better.
self.analysis.original_display_url = self.analysis.astrometry_original_display_url
# Coords.
'''
coords_plot_path = '%d_%d_plot.png' % (submission.subid, job.jobid)
point_source_extraction.plot(sources, data, coords_plot_path)
logger.info(' -> Uploading %s...' % coords_plot_path)
if not args.dry_run:
self.analysis.coords_plot_url = \
s3_util.upload_to_s3_via_file(coords_plot_path, \
self.get_upload_key_prefix())
'''
coords_fits_path = '%d_%d_coords.fits' % (submission.subid, job.jobid)
point_source_extraction.save_fits(sources, coords_fits_path)
logger.info(' -> Uploading %s...' % coords_fits_path)
if not args.dry_run:
self.analysis.coords_fits_url = \
s3_util.upload_to_s3_via_file(coords_fits_path, \
self.get_upload_key_prefix())
coords_json_path = '%d_%d_coords.json' % (submission.subid, job.jobid)
point_source_extraction.save_json(sources, coords_json_path)
logger.info(' -> Uploading %s...' % coords_json_path)
if not args.dry_run:
self.analysis.coords = point_source_extraction.format_for_json_export(sources)
self.analysis.coords_json_url = \
s3_util.upload_to_s3_via_file(coords_json_path, \
self.get_upload_key_prefix())
# PSF.
psf_residual_path = '%d_%d_psf_residual.png' % (submission.subid, job.jobid)
point_source_extraction.save_image(residual_image, psf_residual_path);
logger.info(' -> Uploading %s' % psf_residual_path)
if not args.dry_run:
self.analysis.psf_residual_image_url = \
s3_util.upload_to_s3_via_file(psf_residual_path, \
self.get_upload_key_prefix())
# TODO(ian): Should delete the files afterwards, or create them as
# temporary files.
logger.info('-> Processed fits image for submission %d' % (submission.subid))
def process_magnitudes(self):
job = self.analysis.astrometry_job
submission = job.submission
logger.info('-> Processing reference stars/magnitudes for submission %d' % \
(submission.subid))
coords = urllib.urlopen(self.analysis.coords_json_url).read()
correlations = urllib.urlopen(self.analysis.astrometry_corr_fits_url).read()
# Compute reference stars and their apparent magnitudes.
ref_stars, unknown_stars = \
catalog.choose_reference_stars(self.image_fits_data, correlations, coords)
name = '%d_%d_image_reference_stars.json' % (submission.subid, job.jobid)
logger.info(' -> Uploading %s...' % name)
if not args.dry_run:
self.analysis.image_reference_stars = ref_stars
self.analysis.image_reference_stars_json_url = \
s3_util.upload_to_s3(json.dumps(ref_stars, indent=2, use_decimal=True), \
self.get_upload_key_prefix(), name)
logger.info('-> Uploaded reference stars for submission %d' % \
(submission.subid))
name = '%d_%d_image_unknown_stars.json' % (submission.subid, job.jobid)
logger.info(' -> Uploading %s...' % name)
if not args.dry_run:
self.analysis.image_unknown_stars = unknown_stars
self.analysis.image_unknown_stars_json_url = \
s3_util.upload_to_s3(json.dumps(unknown_stars, indent=2, use_decimal=True), \
self.get_upload_key_prefix(), name)
logger.info('-> Uploaded unknown stars for submission %d' % \
(submission.subid))
# Get reference star standard magnitudes.
standard_mags = catalog.get_standard_magnitudes_urat1(ref_stars)
name = '%d_%d_catalog_reference_stars.json' % (submission.subid, job.jobid)
logger.info(' -> Uploading %s...' % name)
if not args.dry_run:
self.analysis.catalog_reference_stars = standard_mags
self.analysis.catalog_reference_stars_json_url = \
s3_util.upload_to_s3(json.dumps(standard_mags, indent=2, use_decimal=True), \
self.get_upload_key_prefix(), name)
# Combine into single annotated point sources object.
all_points = catalog.merge_known_with_unknown(standard_mags, unknown_stars)
name = '%d_%d_annotated_point_sources.json' % (submission.subid, job.jobid)
logger.info(' -> Uploading %s...' % name)
if not args.dry_run:
self.analysis.annotated_point_sources = all_points
self.analysis.annotated_point_sources_json_url = \
s3_util.upload_to_s3(json.dumps(all_points, indent=2, use_decimal=True), \
self.get_upload_key_prefix(), name)
logger.info('-> Uploaded annotated point sources for submission %d' % \
(submission.subid))
def process_pending(args):
analyses = ImageAnalysis.objects.filter(status=ImageAnalysis.PHOTOMETRY_PENDING)
for analysis in analyses:
handler = PhotometryRunner(analysis, args)
handler.run()
def get_args():
parser = argparse.ArgumentParser('Process outstanding photometry jobs')
parser.add_argument('--dry_run', help='don\'t actually do anything', action='store_true')
return parser.parse_args()
if __name__ == '__main__':
args = get_args()
process_pending(args)
logger.info('Done.')