def callback(cutout):
grid.add_cutout(cutout, frame_index, time_index)
if grid.is_filled():
self._cutout_grids[grid.source] = grid
events.send(events.IMG_LOADED, grid.source)
logger.info("Triplet grid finished downloading.")
def __init__(self, working_directory, output_directory,
dry_run=False, debug=False):
self.dry_run = dry_run
logger.info("Input directory set to: %s" % working_directory)
logger.info("Output directory set to: %s" % output_directory)
working_context = context.get_context(working_directory)
output_context = context.get_context(output_directory)
if dry_run and working_context.is_remote():
sys.stdout.write("A dry run can only be done on local files.\n")
sys.exit(0)
if output_context.is_remote():
sys.stdout.write("The output directory must be local.\n")
sys.exit(0)
image_manager = self._create_image_manager()
progress_manager = working_context.get_progress_manager()
builder = self._create_workunit_builder(working_context,
output_context,
progress_manager)
workunit_provider = WorkUnitProvider(self.input_suffix,
working_context,
progress_manager, builder,
randomize=self.should_randomize_workunits)
prefetching_workunit_provider = PreFetchingWorkUnitProvider(workunit_provider,
config.read("PREFETCH.NUMBER"),
image_manager)
if working_context.is_remote():
synchronization_manager = SynchronizationManager(working_context)
else:
synchronization_manager = None
model = TransAckValidationModel(prefetching_workunit_provider,
image_manager,
synchronization_manager)
logger.debug("Created model.")
view = self._create_view(model, debug=debug)
logger.debug("Created view.")
model.start_work()
self.model = model
self.view = view
self.controller = view.controller
self.controller.display_current_image()
if not synchronization_manager:
self.view.disable_sync_menu()
self.view.show()
def mark_apertures(self, cutout):
logger.info("marking apertures on cutout.")
x, y = cutout.pixel_source_point
try:
radii = (cutout.apcor.aperture, cutout.apcor.sky, cutout.apcor.swidth+cutout.apcor.sky)
except:
radii = (4, 15,30)
self._displayables_by_cutout[cutout].place_annulus(x, y, radii, colour='r')
def show(self):
self.mainframe.Show()
if self.debug:
logger.info("Launching view in debug mode.")
wx.lib.inspection.InspectionTool().Show()
self.wx_app.MainLoop()
def show(self):
self.mainframe.Show()
if self.debug:
logger.info("Launching view in debug mode.")
wx.lib.inspection.InspectionTool().Show()
self.wx_app.MainLoop()
def refresh_certificate(self, username, password):
download_certificate(username, password)
logger.info("Downloaded new CADC certificate")
model = self.app.get_model()
model.refresh_vos_client()
self.app.get_view().show_image_loading_dialog()
model.start_loading_images()
def preload_iraf():
logger.info("Preloading IRAF")
# NOTE: Force expensive loading of libraries up front. These are
# libraries that the reals task needs but the candidates task
# doesn't. To make sure the candidates task doesn't load them, we
# import them directly in the functions/methods where they are used.
# TODO: find out what the best practice is for handling this sort of
# situation and refactor.
from pyraf import iraf
def refresh_certificate(self, username, password):
download_certificate(username, password)
logger.info("Downloaded new CADC certificate")
model = self.app.get_model()
model.refresh_vos_client()
self.app.get_view().show_image_loading_dialog()
model.start_loading_images()
def query_ssos(self, mpc_observations, lunation_count=None):
# we observe ~ a week either side of new moon
# but we don't know when in the dark run the discovery happened
# so be generous with the search boundaries, add extra 2 weeks
# current date just has to be the night of the triplet,
"""
:param mpc_observations: a list of mpc.Observations
:param lunation_count: how many dark runs (+ and -) to search into
:return: an SSOSData object
"""
if lunation_count is None:
search_start_date = Time('2013-02-08', scale='utc')
search_end_date = Time(datetime.datetime.now().strftime('%Y-%m-%d'), scale='utc')
else:
search_start_date = Time((mpc_observations[0].date.jd - (
self._nights_per_darkrun +
lunation_count*self._nights_separating_darkruns) ),
format='jd', scale='utc')
search_end_date = Time((mpc_observations[-1].date.jd + (
self._nights_per_darkrun +
lunation_count*self._nights_separating_darkruns) ),
format='jd', scale='utc')
query = Query(mpc_observations,
search_start_date=search_start_date,
search_end_date=search_end_date)
tracks_data = self.ssos_parser.parse(query.get())
tracks_data.mpc_observations = {}
for mpc_observation in mpc_observations:
# attach the input observations to the the SSOS query result.
assert isinstance(mpc_observation,mpc.Observation)
tracks_data.mpc_observations[mpc_observation.comment.frame] = mpc_observation
for source in tracks_data.get_sources():
astrom_observations = tracks_data.observations
source_readings = source.get_readings()
for idx in range(len(source_readings)):
source_reading = source_readings[idx]
astrom_observation = astrom_observations[idx]
logger.info("About to call orbfit predict")
self.orbit.predict(astrom_observation.header['MJD_OBS_CENTER'])
logger.info("Finished predict")
source_reading.pa = self.orbit.pa
# why are these being recorded just in pixels?
source_reading.dra = self.orbit.dra / astrom_observation.header['SCALE']
source_reading.ddec = self.orbit.ddec / astrom_observation.header['SCALE']
frame = astrom_observation.rawname
if frame in tracks_data.mpc_observations:
source_reading.discovery = tracks_data.mpc_observations[frame].discovery
return tracks_data # a SSOSData with .sources and .observations only
def get_workunit(self, ignore_list=None):
"""
Gets a new unit of work.
Args:
ignore_list: list(str)
A list of filenames which should be ignored. Defaults to None.
Returns:
new_workunit: WorkUnit
A new unit of work that has not yet been processed. A lock on
it has been acquired.
Raises:
NoAvailableWorkException
There is no more work available.
"""
if ignore_list is None:
ignore_list = []
potential_files = self.get_potential_files(ignore_list)
while len(potential_files) > 0:
potential_file = self.select_potential_file(potential_files)
potential_files.remove(potential_file)
if self._filter(potential_file):
continue
if self.directory_context.get_file_size(potential_file) == 0:
continue
if self.progress_manager.is_done(potential_file):
self._done.append(potential_file)
continue
else:
try:
self.progress_manager.lock(potential_file)
except FileLockedException:
continue
self._already_fetched.append(potential_file)
return self.builder.build_workunit(
self.directory_context.get_full_path(potential_file))
logger.info("No eligible workunits remain to be fetched.")
raise NoAvailableWorkException()
def _do_prefetch_workunit(self):
try:
workunit = self.workunit_provider.get_workunit(
ignore_list=self.fetched_files)
filename = workunit.get_filename()
# 2 or more threads created back to back could end up
# retrieving the same workunit. Only keep one of them.
if filename not in self.fetched_files:
self.fetched_files.append(filename)
self.workunits.append(workunit)
logger.info("%s was prefetched." % filename)
except NoAvailableWorkException:
self._all_fetched = True
def create_application(taskname, working_directory, output_directory,
dry_run=False, debug=False):
logger.info("Starting %s task." % taskname)
if taskname == tasks.CANDS_TASK:
ProcessCandidatesApplication(working_directory, output_directory,
dry_run=dry_run, debug=debug)
elif taskname == tasks.REALS_TASK:
ProcessRealsApplication(working_directory, output_directory,
dry_run=dry_run, debug=debug)
elif taskname == tasks.TRACK_TASK:
ProcessTracksApplication(working_directory, output_directory,
dry_run=dry_run, debug=debug)
else:
error_message = "Unknown task: %s" % taskname
logger.critical(error_message)
raise ValueError(error_message)
def get_workunit(self, ignore_list=None):
"""
Gets a new unit of work.
Args:
ignore_list: list(str)
A list of filenames which should be ignored. Defaults to None.
Returns:
new_workunit: WorkUnit
A new unit of work that has not yet been processed. A lock on
it has been acquired.
Raises:
NoAvailableWorkException
There is no more work available.
"""
if ignore_list is None:
ignore_list = []
potential_files = self.get_potential_files(ignore_list)
while len(potential_files) > 0:
potential_file = self.select_potential_file(potential_files)
potential_files.remove(potential_file)
if self.directory_context.get_file_size(potential_file) == 0:
continue
if self.progress_manager.is_done(potential_file):
self._done.append(potential_file)
continue
else:
try:
self.progress_manager.lock(potential_file)
except FileLockedException:
continue
self._already_fetched.append(potential_file)
return self.builder.build_workunit(
self.directory_context.get_full_path(potential_file))
logger.info("No eligible workunits remain to be fetched.")
raise NoAvailableWorkException()
def _do_prefetch_workunit(self):
try:
workunit = self.workunit_provider.get_workunit(
ignore_list=self.fetched_files)
filename = workunit.get_filename()
# 2 or more threads created back to back could end up
# retrieving the same workunit. Only keep one of them.
if filename not in self.fetched_files:
self.fetched_files.append(filename)
self.workunits.append(workunit)
self.image_manager.download_singlets_for_workunit(workunit)
logger.info("%s was prefetched." % filename)
except NoAvailableWorkException:
self._all_fetched = True
def retrieve_comparison_image(self, downloader):
"""
Search the DB for a comparison image for this cutout.
"""
# selecting comparator when on a comparator should load a new one.
ref_wcs = wcs.WCS(self.fits_header)
try:
ref_x = self.fits_header['NAXIS1'] / 2.0
ref_y = self.fits_header['NAXIS2'] / 2.0
(ref_ra, ref_dec) = ref_wcs.xy2sky(ref_x, ref_y)
except Exception as e:
logger.info(str(e))
logger.info(str(self.fits_header))
return None
dra = self.fits_header['CD1_1'] * self.fits_header['NAXIS1'] / 2.0
ddec = self.fits_header['CD2_2'] * self.fits_header['NAXIS2'] / 2.0
radius = max(dra, ddec)
logger.info("BOX({} {} {} {})".format(ref_ra, ref_dec, dra, ddec))
query_result = storage.cone_search(ref_ra, ref_dec, dra, ddec) # returns an astropy.table.table.Table
comparison = None
if len(query_result['collectionID']) > 0: # are there any comparison images even available on that sky?
for collectionID in query_result['collectionID']:
if collectionID not in self._bad_comparison_images:
comparison = collectionID
self._bad_comparison_images.append(comparison)
break
if comparison is None:
logger.critical(str(self.fits_header))
self._comparison_image = None
return
else:
query_result.pprint()
logger.info("No comparison images available for this piece of sky.")
print "No comparison images available for this piece of sky."
self._comparison_image = None
return
base_url = "https://www.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/vospace/nodes/OSSOS/dbimages/{}/{}p.fits".format(
comparison, comparison)
cutout = 'CIRCLE ICRS {} {} {}'.format(ref_ra, ref_dec, radius)
url = base_url + "?" + urllib.urlencode({'view': 'cutout', 'cutout': cutout})
hdu_list = downloader.download_hdulist(uri=None, URL=url)
comp_wcs = wcs.WCS(hdu_list[-1].header)
(x, y) = comp_wcs.sky2xy(ref_ra, ref_dec)
obs = Observation(str(comparison), 'p', ccdnum=str(hdu_list[-1].header.get('EXTVER', 0)))
reading = SourceReading(x, y, ref_x, ref_y, ref_ra, ref_dec, ref_x, ref_y, obs, is_inverted=False)
self._comparison_image = SourceCutout(reading, hdu_list, CoordinateConverter(0, 0))
def create_application(task_name,
working_directory,
output_directory,
dry_run=False,
debug=False,
name_filter=None,
user_id=None,
skip_previous=False):
logger.info("Starting %s task." % task_name)
if task_name == tasks.CANDS_TASK:
ProcessCandidatesApplication(working_directory,
output_directory,
dry_run=dry_run,
debug=debug,
name_filter=name_filter,
user_id=user_id)
elif task_name == tasks.REALS_TASK:
ProcessRealsApplication(working_directory,
output_directory,
dry_run=dry_run,
debug=debug,
name_filter=name_filter,
user_id=user_id)
elif task_name == tasks.TRACK_TASK:
ProcessTracksApplication(working_directory,
output_directory,
dry_run=dry_run,
debug=debug,
name_filter=name_filter,
skip_previous=skip_previous,
user_id=user_id)
else:
error_message = "Unknown task: %s" % task_name
logger.critical(error_message)
raise ValueError(error_message)
def enable_synchronization(self):
if self.synchronization_manager:
self.synchronization_manager.enable_sync()
logger.info("Synchronization enabled")
def do_synchronize(self, local_path):
remote_uri = self.get_remote_uri(local_path)
logger.info("Syncing %s to %s." % (local_path, remote_uri))
storage.copy(local_path, remote_uri)
def disable_synchronization(self):
if self.synchronization_manager:
self.synchronization_manager.disable_sync()
logger.info("Synchronization disabled")
def use_singlets(self):
logger.info("Model set to use image singlets.")
self.image_state = SingletState(self)
self.image_state.enter_state()
def use_triplets(self):
logger.info("Model set to use image triplets.")
self.image_state = TripletState(self)
self.image_state.enter_state()
def use_triplets(self):
logger.info("Model set to use image triplets.")
self.image_state = TripletState(self)
self.image_state.enter_state()
def enable_synchronization(self):
if self.synchronization_manager:
self.synchronization_manager.enable_sync()
logger.info("Synchronization enabled")
def __init__(self,
working_directory,
output_directory,
dry_run=False,
debug=False,
name_filter=None,
user_id=None):
self.dry_run = dry_run
self.user_id = user_id
logger.info("Input directory set to: %s" % working_directory)
logger.info("Output directory set to: %s" % output_directory)
working_context = context.get_context(working_directory,
userid=self.user_id)
output_context = context.get_context(output_directory,
userid=self.user_id)
if dry_run and working_context.is_remote():
sys.stdout.write("A dry run can only be done on local files.\n")
sys.exit(0)
if output_context.is_remote():
sys.stdout.write("The output directory must be local.\n")
sys.exit(0)
image_manager = self._create_image_manager()
progress_manager = working_context.get_progress_manager()
builder = self._create_workunit_builder(working_context,
output_context,
progress_manager)
workunit_provider = WorkUnitProvider(
self.input_suffix,
working_context,
progress_manager,
builder,
randomize=self.should_randomize_workunits,
name_filter=name_filter)
prefetching_workunit_provider = PreFetchingWorkUnitProvider(
workunit_provider, config.read("PREFETCH.NUMBER"), image_manager)
if working_context.is_remote():
synchronization_manager = SynchronizationManager(working_context,
sync_enabled=True)
else:
synchronization_manager = None
model = TransAckValidationModel(prefetching_workunit_provider,
image_manager, synchronization_manager)
logger.debug("Created model.")
view = self._create_view(model, debug=debug)
logger.debug("Created view.")
model.start_work()
self.model = model
self.view = view
self.controller = view.controller
self.controller.display_current_image()
if not synchronization_manager:
self.view.disable_sync_menu()
self.view.show()
def preload_iraf():
logger.info("Preloading IRAF")
def disable_synchronization(self):
if self.synchronization_manager:
self.synchronization_manager.disable_sync()
logger.info("Synchronization disabled")
def use_singlets(self):
logger.info("Model set to use image singlets.")
self.image_state = SingletState(self)
self.image_state.enter_state()
def download_cutout(self, reading, focus=None, needs_apcor=False):
"""
Downloads a cutout of the FITS image for a given source reading.
Args:
source_reading: ossos.astrom.SourceReading
The reading which will be the focus of the downloaded image.
focus: tuple(int, int)
The x, y coordinates that should be the focus of the downloaded
image. These coordinates should be in terms of the
source_reading parameter's coordinate system.
Default value is None, in which case the source reading's x, y
position is used as the focus.
needs_apcor: bool
If True, the apcor file with data needed for photometry
calculations is downloaded in addition to the image.
Defaults to False.
Returns:
cutout: ossos.downloads.data.SourceCutout
"""
if focus is None:
focus = reading.source_point
cutout_str, converter = self.cutout_calculator.build_cutout_str(
reading.get_extension(),
focus,
reading.get_original_image_size(),
dx = reading.dx,
dy = reading.dy,
inverted=reading.is_inverted())
image_uri = reading.get_image_uri()
cutout = re.findall(r'(\d+)', cutout_str)
y2 = int(cutout[-1])
y1 = int(cutout[-2])
logger.info("Calculated cutout: %s for %s"
% (cutout_str, image_uri))
hdulist = self.download_hdulist(image_uri, view="cutout",
cutout=cutout_str)
# modify the DATASEC to account for possible flip/flop and changes in dimensions of the image.
(NAXIS1, NAXIS2) = reading.get_original_image_size()
DATASEC = hdulist[0].header.get('DATASEC',None)
if DATASEC is not None:
datasec = re.findall(r'(\d+)', DATASEC)
if y2 < y1:
x2 = int(NAXIS1) - int(datasec[0]) + 1
x1 = int(NAXIS1) - int(datasec[1]) + 1
y2 = int(NAXIS2) - int(datasec[2]) + 1
y1 = int(NAXIS2) - int(datasec[3]) + 1
logger.info("Flip/Flopped DATASEC from {} to [{}:{}:{}:{}]".format(DATASEC, x1,x2,y1,y2))
datasec = (x1,x2,y1,y2)
(x1,y1) = converter.convert((int(datasec[0]),int(datasec[2])))
x1 = max(1,x1)
y1 = max(1,y1)
(x2,y2) = converter.convert((int(datasec[1]),int(datasec[3])))
x2 = min(x2, int(hdulist[0].header['NAXIS1']))
y2 = min(y2, int(hdulist[0].header['NAXIS2']))
datasec = "[{}:{},{}:{}]".format(x1,x2,y1,y2)
logger.info("Trimmed and offset DATASEC from {} to {}".format(DATASEC, datasec))
hdulist[0].header['DATASEC'] = datasec
apcor = None
if needs_apcor:
try:
apcor = self.download_apcor(reading.get_apcor_uri())
except:
apcor = None
zmag = None
try:
zmag = self.download_zmag(reading.get_zmag_uri())
except Exception as e:
logger.debug(str(e))
pass
return SourceCutout(reading, hdulist, converter, apcor, zmag=zmag)
def parse(self, ssos_result_filename_or_lines):
"""
given the result table create 'source' objects.
:type ssos_result_table: Table
:param ssos_result_table:
"""
table_reader = ascii.get_reader(Reader=ascii.Basic)
table_reader.inconsistent_handler = self._skip_missing_data
table_reader.header.splitter.delimiter = '\t'
table_reader.data.splitter.delimiter = '\t'
table = table_reader.read(ssos_result_filename_or_lines)
sources = []
observations = []
source_readings = []
ref_pvwcs = None
downloader = Downloader()
warnings.filterwarnings('ignore')
for row in table:
# check if a dbimages object exists
ccd = int(row['Ext']) - 1
expnum = row['Image'].rstrip('p')
# ADDING THIS TEMPORARILY TO GET THE NON-OSSOS DATA OUT OF THE WAY WHILE DEBUGGING
if (row['Telescope_Insturment'] != 'CFHT/MegaCam') or (row['Filter'] != 'r.MP9601'):
continue
# it's fine for OSSOS, go get the image
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=None,
version='p',
ext='.fits',
subdir=None)
logger.info('Trying to access %s\n%s' % (row.data, image_uri))
if not storage.exists(image_uri, force=False):
logger.warning('Image not in dbimages? Trying subdir.')
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p')
if not storage.exists(image_uri, force=False):
logger.warning("Image doesn't exist in ccd subdir. %s" % image_uri)
continue
if row['X'] == -9999 or row['Y'] == -9999 :
logger.warning("Skipping %s as x/y not resolved." % ( row['Image']))
continue
mopheader_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p',
ext='.mopheader')
if not mopheader_uri in mopheaders:
if not storage.exists(mopheader_uri, force=False):
logger.warning('mopheader missing, but images exists')
continue
# raise flag if no MOPHEADER
mopheader_fpt = cStringIO.StringIO(storage.open_vos_or_local(mopheader_uri).read())
mopheader = fits.open(mopheader_fpt)
mopheaders[mopheader_uri] = mopheader
mopheader = mopheaders[mopheader_uri]
# Build astrom.Observation
observation = astrom.Observation(expnum=str(expnum),
ftype='p',
ccdnum=str(ccd),
fk="")
observation.rawname = os.path.splitext(os.path.basename(image_uri))[0]+str(ccd).zfill(2)
observation.header = mopheader[0].header
MJD_OBS_CENTER = mpc.Time(observation.header['MJD-OBSC'],
format='mjd',
scale='utc', precision=5 ).replicate(format='mpc')
observation.header['MJD_OBS_CENTER'] = str(MJD_OBS_CENTER)
observation.header['MAXCOUNT'] = MAXCOUNT
observation.header['SCALE'] = observation.header['PIXSCALE']
#observation.header['CHIP'] = str(observation.header['CHIPNUM']).zfill(2)
observation.header['NAX1'] = observation.header['NAXIS1']
observation.header['NAX2'] = observation.header['NAXIS2']
observation.header['MOPversion'] = observation.header['MOP_VER']
observation.header['FWHM'] = 4
# a download pixel 1,1 of this data to due offsets with.
x_cen = int(min(max(1,row['X']),observation.header['NAX1']))
y_cen = int(min(max(1,row['Y']),observation.header['NAX2']))
if image_uri not in astheaders:
hdulist = downloader.download_hdulist(
uri=image_uri,
view='cutout',
cutout='[{}][{}:{},{}:{}]'.format(ccd+1, x_cen, x_cen, y_cen, y_cen))
astheaders[image_uri] = hdulist
hdulist = astheaders[image_uri]
pvwcs = wcs.WCS(hdulist[0].header)
(ra,dec) = pvwcs.xy2sky(x_cen, y_cen)
if ref_pvwcs is None:
ref_pvwcs = pvwcs
xref = row['X']
yref = row['Y']
(x0, y0) = ref_pvwcs.sky2xy(ra,dec)
x0 += row['X'] - x_cen
y0 += row['Y'] - y_cen
# Build astrom.SourceReading
observations.append(observation)
from_input_file = observation.rawname in self.input_rawnames
null_observation = observation.rawname in self.null_observations
print observation.rawname, observation.header['MJD_OBS_CENTER'], null_observation, from_input_file
source_reading = astrom.SourceReading(x=row['X'], y=row['Y'],
xref=xref, yref=yref,
x0=x0, y0=y0,
ra=row['Object_RA'], dec=row['Object_Dec'],
obs=observation,
ssos=True,
from_input_file=from_input_file,
null_observation=null_observation)
#if observation.rawname in self.input_rawnames:
# source_readings.insert(0, source_reading)
#else:
source_readings.append(source_reading)
# build our array of SourceReading objects
sources.append(source_readings)
warnings.filterwarnings('once')
return SSOSData(observations, sources, self.provisional_name)
args = parser.parse_args()
astrom.DATASET_ROOT = args.dbimages
storage.DBIMAGES = args.dbimages
storage.MEASURE3 = args.measure3
## only measure if we have completed 'reals' on this file.
reals_filepath = ( args.reals is not None and args.reals ) or args.measure3
cands_filepath = args.measure3
cands_filelist = storage.my_glob(cands_filepath+"/fk*.cands.astrom")
eff_file_list = []
for cands in cands_filelist:
cands_filename = os.path.basename(cands)
if os.path.exists(cands_filename+".eff"):
logger.info("{}.eff exists, skipping".format(cands_filename))
continue
reals_filename = reals_filepath + cands_filename.replace('cands','reals')
if not (( reals_filename[0:4] == 'vos:' and storage.exists(reals_filename+".DONE") ) or os.access(reals_filename+".DONE",os.R_OK)) :
# skipping incomplete field/ccd combo
continue
sys.stderr.write("Getting list of .mpc files for input "+reals_filename+" ...")
# find and load any .mpc files associated with this candidate file.
mpc_list = storage.my_glob(reals_filename+".*.mpc")
sys.stderr.write(" got {} detections \n".format(len(mpc_list)))
if not len(mpc_list) > 0 :
continue
measures = {}
for mpc_fname in mpc_list:
provisional = mpc_fname.split(".")[-2]
measures[provisional] = []
