def planted(fk_candidate_observations, planted_objects, tolerance=10):
"""
Using the fk_candidate_observations as input get the Object.planted file from VOSpace and match
planted sources with found sources.
The Object.planted list is pulled from VOSpace based on the standard file-layout and name of the
first exposure as read from the .astrom file.
:param fk_candidate_observations: name of the fk*reals.astrom file to check against Object.planted
:param planted_objects: object containing the planted object information.
"""
found_pos = []
detections = fk_candidate_observations.get_sources()
for detection in detections:
reading = detection.get_reading(0)
# create a list of positions, to be used later by match_lists
found_pos.append([reading.x, reading.y])
# The match_list method expects a list that contains a position, not an x and a y vector, so we transpose.
planted_objects_table = planted_objects.table
planted_pos = numpy.transpose([planted_objects_table['x'].data, planted_objects_table['y'].data])
# match_idx is an order list. The list is in the order of the first list of positions and each entry
# is the index of the matching position from the second list.
(match_idx, match_fnd) = util.match_lists(numpy.array(planted_pos), numpy.array(found_pos), tolerance=tolerance)
return match_fnd, match_idx
def planted(fk_candidate_observations, planted_objects, tolerance=10):
"""
Using the fk_candidate_observations as input get the Object.planted file from VOSpace and match
planted sources with found sources.
The Object.planted list is pulled from VOSpace based on the standard file-layout and name of the
first exposure as read from the .astrom file.
:param fk_candidate_observations: name of the fk*reals.astrom file to check against Object.planted
:param planted_objects: object containing the planted object information.
"""
found_pos = []
detections = fk_candidate_observations.get_sources()
for detection in detections:
reading = detection.get_reading(0)
# create a list of positions, to be used later by match_lists
found_pos.append([reading.x, reading.y])
# The match_list method expects a list that contains a position, not an x and a y vector, so we transpose.
planted_objects_table = planted_objects.table
planted_pos = numpy.transpose(
[planted_objects_table['x'].data, planted_objects_table['y'].data])
# match_idx is an order list. The list is in the order of the first list of positions and each entry
# is the index of the matching position from the second list.
(match_idx, match_fnd) = util.match_lists(numpy.array(planted_pos),
numpy.array(found_pos),
tolerance=tolerance)
return match_fnd, match_idx
def match_planted(fk_candidate_observations, match_filename, bright_limit=BRIGHT_LIMIT, object_planted=OBJECT_PLANTED,
minimum_bright_detections=MINIMUM_BRIGHT_DETECTIONS, bright_fraction=MINIMUM_BRIGHT_FRACTION):
"""
Using the fk_candidate_observations as input get the Object.planted file from VOSpace and match
planted sources with found sources.
The Object.planted list is pulled from VOSpace based on the standard file-layout and name of the
first exposure as read from the .astrom file.
:param fk_candidate_observations: name of the fk*reals.astrom file to check against Object.planted
:param match_filename: a file that will contain a list of all planted sources and the matched found source
"""
found_pos = []
detections = fk_candidate_observations.get_sources()
for detection in detections:
reading = detection.get_reading(0)
# create a list of positions, to be used later by match_lists
found_pos.append([reading.x, reading.y])
# Now get the Object.planted file, either from the local FS or from VOSpace.
objects_planted_uri = object_planted
if not os.access(objects_planted_uri, os.F_OK):
objects_planted_uri = fk_candidate_observations.observations[0].get_object_planted_uri()
lines = storage.open_vos_or_local(objects_planted_uri).read()
# we are changing the format of the Object.planted header to be compatible with astropy.io.ascii but
# there are some old Object.planted files out there so we do these string/replace calls to reset those.
new_lines = lines.replace("pix rate", "pix_rate")
new_lines = new_lines.replace("""''/h rate""", "sky_rate")
rdr = ascii.get_reader(Reader=ascii.CommentedHeader)
planted_objects_table = rdr.read(new_lines)
# The match_list method expects a list that contains a position, not an x and a y vector, so we transpose.
planted_pos = numpy.transpose([planted_objects_table['x'].data, planted_objects_table['y'].data])
# match_idx is an order list. The list is in the order of the first list of positions and each entry
# is the index of the matching position from the second list.
(match_idx, match_fnd) = util.match_lists(numpy.array(planted_pos), numpy.array(found_pos))
assert isinstance(match_idx, numpy.ma.MaskedArray)
assert isinstance(match_fnd, numpy.ma.MaskedArray)
false_positives_table = Table()
# Once we've matched the two lists we'll need some new columns to store the information in.
# these are masked columns so that object.planted entries that have no detected match are left 'blank'.
new_columns = [MaskedColumn(name="measure_x", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_y", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_rate", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_angle", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_mag1", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_merr1", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_mag2", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_merr2", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_mag3", length=len(planted_objects_table), mask=True),
MaskedColumn(name="measure_merr3", length=len(planted_objects_table), mask=True)]
planted_objects_table.add_columns(new_columns)
tlength = 0
new_columns = [MaskedColumn(name="measure_x", length=tlength, mask=True),
MaskedColumn(name="measure_y", length=tlength, mask=True),
MaskedColumn(name="measure_rate", length=0, mask=True),
MaskedColumn(name="measure_angle", length=0, mask=True),
MaskedColumn(name="measure_mag1", length=0, mask=True),
MaskedColumn(name="measure_merr1", length=0, mask=True),
MaskedColumn(name="measure_mag2", length=0, mask=True),
MaskedColumn(name="measure_merr2", length=0, mask=True),
MaskedColumn(name="measure_mag3", length=tlength, mask=True),
MaskedColumn(name="measure_merr3", length=tlength, mask=True)]
false_positives_table.add_columns(new_columns)
print len(false_positives_table)
# We do some 'checks' on the Object.planted match to diagnose pipeline issues. Those checks are made using just
# those planted sources we should have detected.
bright = planted_objects_table['mag'] < bright_limit
n_bright_planted = numpy.count_nonzero(planted_objects_table['mag'][bright])
for idx in range(len(match_idx)):
# The match_idx value is False if nothing was found.
if not match_idx.mask[idx]:
# Each 'source' has multiple 'readings'
measures = detections[match_idx[idx]].get_readings()
planted_objects_table[idx] = measure_mags(measures, planted_objects_table[idx])
for idx in range(len(match_fnd)):
if match_fnd.mask[idx]:
measures = detections[idx].get_readings()
false_positives_table.add_row()
false_positives_table[-1] = measure_mags(measures, false_positives_table[-1])
# Count an object as detected if it has a measured magnitude in the first frame of the triplet.
n_bright_found = numpy.count_nonzero(planted_objects_table['measure_mag1'][bright])
# Also compute the offset and standard deviation of the measured magnitude from that planted ones.
offset = numpy.mean(planted_objects_table['mag'][bright] - planted_objects_table['measure_mag1'][bright])
try:
offset = "{:5.2f}".format(offset)
except:
offset = "indef"
std = numpy.std(planted_objects_table['mag'][bright] - planted_objects_table['measure_mag1'][bright])
try:
std = "{:5.2f}".format(std)
except:
std = "indef"
if os.access(match_filename, os.R_OK):
fout = open(match_filename, 'a')
else:
fout = open(match_filename, 'w')
fout.write("#K {:10s} {:10s}\n".format("EXPNUM", "FWHM"))
for measure in detections[0].get_readings():
fout.write('#V {:10s} {:10s}\n'.format(measure.obs.header['EXPNUM'], measure.obs.header['FWHM']))
fout.write("#K ")
for keyword in ["RMIN", "RMAX", "ANGLE", "AWIDTH"]:
fout.write("{:10s} ".format(keyword))
fout.write("\n")
fout.write("#V ")
for keyword in ["RMIN", "RMAX", "ANGLE", "AWIDTH"]:
fout.write("{:10s} ".format(fk_candidate_observations.sys_header[keyword]))
fout.write("\n")
fout.write("#K ")
for keyword in ["NBRIGHT", "NFOUND", "OFFSET", "STDEV"]:
fout.write("{:10s} ".format(keyword))
fout.write("\n")
fout.write("#V {:<10} {:<10} {:<10} {:<10}\n".format(n_bright_planted,
n_bright_found,
offset,
std))
fpout = storage.open_vos_or_local(match_filename+".fp", 'a')
try:
writer = ascii.FixedWidth
# add a hash to the start of line that will have header columns: for JMP
fout.write("#")
ascii.write(planted_objects_table, output=fout, Writer=writer, delimiter=None)
fpout.write("#")
if len(false_positives_table) > 0:
ascii.write(false_positives_table, output=fpout, Writer=writer, delimiter=None)
else:
fpout.write(" no false positives\n")
except Exception as e:
print e
print str(e)
raise e
finally:
fout.close()
fpout.close()
# Some simple checks to report a failure how we're doing.
if n_bright_planted < minimum_bright_detections:
raise RuntimeError(1, "Too few bright objects planted.")
if n_bright_found / float(n_bright_planted) < bright_fraction:
raise RuntimeError(2, "Too few bright objects found.")
return "{} {} {} {}".format(n_bright_planted, n_bright_found, offset, std)
def align(expnums, ccd, version='s', dry_run=False):
"""Create a 'shifts' file that transforms the space/flux/time scale of all images to the first image.
This function relies on the .fwhm, .trans.jmp, .phot and .zeropoint.used files for inputs.
The scaling we are computing here is for use in planting sources into the image at the same sky/flux locations
while accounting for motions of sources with time.
:param expnums: list of MegaPrime exposure numbers to add artificial KBOs to,
the first frame in the list is the reference.
:param ccd: which ccd to work on.
:param version: Add sources to the 'o', 'p' or 's' images
:param dry_run: don't push results to VOSpace.
"""
# Get the images and supporting files that we need from the VOSpace area
# get_image and get_file check if the image/file is already on disk.
# re-computed fluxes from the PSF stars and then recompute x/y/flux scaling.
# some dictionaries to hold the various scale
pos = {}
apcor = {}
mags = {}
zmag = {}
mjdates = {}
for expnum in expnums:
filename = storage.get_image(expnum, ccd=ccd, version=version)
zmag[expnum] = storage.get_zeropoint(expnum,
ccd,
prefix=None,
version=version)
mjdates[expnum] = float(fits.open(filename)[0].header.get('MJD-OBS'))
apcor[expnum] = [
float(x) for x in open(
storage.get_file(
expnum, ccd=ccd, version=version,
ext=storage.APCOR_EXT)).read().split()
]
keys = ['crval1', 'cd1_1', 'cd1_2', 'crval2', 'cd2_1', 'cd2_2']
# load the .trans.jmp values into a 'wcs' like dictionary.
# .trans.jmp maps current frame to reference frame in pixel coordinates.
# the reference frame of all the frames supplied must be the same.
shifts = dict(
zip(keys, [
float(x) for x in open(
storage.get_file(
expnum, ccd=ccd, version=version,
ext='trans.jmp')).read().split()
]))
shifts['crpix1'] = 0.0
shifts['crpix2'] = 0.0
# now create a wcs object based on those transforms, this wcs links the current frame's
# pixel coordinates to the reference frame's pixel coordinates.
w = get_wcs(shifts)
# get the PHOT file that was produced by the mkpsf routine
phot = ascii.read(storage.get_file(expnum,
ccd=ccd,
version=version,
ext='phot'),
format='daophot')
# compute the small-aperture magnitudes of the stars used in the PSF
mags[expnum] = daophot.phot(filename,
phot['XCENTER'],
phot['YCENTER'],
aperture=apcor[expnum][0],
sky=apcor[expnum][1] + 1,
swidth=apcor[expnum][0],
zmag=zmag[expnum])
# covert the x/y positions to positions in Frame 1 based on the trans.jmp values.
(x, y) = w.wcs_pix2world(mags[expnum]["XCENTER"],
mags[expnum]["YCENTER"], 1)
pos[expnum] = numpy.transpose([x, y])
# match this exposures PSF stars position against those in the first image of the set.
idx1, idx2 = util.match_lists(pos[expnums[0]], pos[expnum])
# compute the magnitdue offset between the current frame and the reference.
dmags = numpy.ma.array(mags[expnums[0]]["MAG"] - apcor[expnums[0]][2] -
(mags[expnum]["MAG"][idx1] - apcor[expnum][2]),
mask=idx1.mask)
dmags.sort()
# compute the median and determine if that shift is small compared to the scatter.
dmag = dmags[int(len(dmags) / 2.0)]
if math.fabs(dmag) > 3 * (dmags.std() + 0.01):
logging.warn(
"Magnitude shift {} between {} and {} is large: {}".format(
dmag, expnums[0], expnum, shifts[expnum]))
shifts['dmag'] = dmag
shifts['emag'] = dmags.std()
shifts['nmag'] = len(dmags.mask) - dmags.mask.sum()
shifts['dmjd'] = mjdates[expnums[0]] - mjdates[expnum]
shift_file = os.path.basename(
storage.get_uri(expnum, ccd, version, '.shifts'))
fh = open(shift_file, 'w')
fh.write(
json.dumps(shifts,
sort_keys=True,
indent=4,
separators=(',', ': ')))
fh.write('\n')
fh.close()
if not dry_run:
storage.copy(
shift_file,
os.path.basename(
storage.get_uri(expnum, ccd, version, '.shifts')))
def align(expnums, ccd, version='s', prefix='', dry_run=False, force=True):
"""Create a 'shifts' file that transforms the space/flux/time scale of all
images to the first image.
This function relies on the .fwhm, .trans.jmp, .phot and .zeropoint.used files for inputs.
The scaling we are computing here is for use in planting sources into the image at the same sky/flux locations
while accounting for motions of sources with time.
:param expnums: list of MegaPrime exposure numbers to add artificial KBOs to,
the first frame in the list is the reference.
:param ccd: which ccd to work on.
:param prefix: put this string in front of expnum when looking for exposure, normally '' or 'fk'
:param force: When true run task even if this task is recorded as having succeeded
:param version: Add sources to the 'o', 'p' or 's' images
:param dry_run: don't push results to VOSpace.
"""
message = storage.SUCCESS
if storage.get_status(task, prefix, expnums[0], version,
ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(
task, prefix, expnums[0], version, ccd))
return
# Get the images and supporting files that we need from the VOSpace area
# get_image and get_file check if the image/file is already on disk.
# re-computed fluxes from the PSF stars and then recompute x/y/flux scaling.
# some dictionaries to hold the various scale
pos = {}
apcor = {}
mags = {}
zmag = {}
mjdates = {}
with storage.LoggingManager(task, prefix, expnums[0], ccd, version,
dry_run):
try:
for expnum in expnums:
filename = storage.get_image(expnum, ccd=ccd, version=version)
zmag[expnum] = storage.get_zeropoint(expnum,
ccd,
prefix=None,
version=version)
mjdates[expnum] = float(
fits.open(filename)[0].header.get('MJD-OBS'))
apcor[expnum] = [
float(x) for x in open(
storage.get_file(
expnum,
ccd=ccd,
version=version,
ext=storage.APCOR_EXT)).read().split()
]
keys = ['crval1', 'cd1_1', 'cd1_2', 'crval2', 'cd2_1', 'cd2_2']
# load the .trans.jmp values into a 'wcs' like dictionary.
# .trans.jmp maps current frame to reference frame in pixel coordinates.
# the reference frame of all the frames supplied must be the same.
shifts = dict(
list(
zip(keys, [
float(x) for x in open(
storage.get_file(
expnum,
ccd=ccd,
version=version,
ext='trans.jmp')).read().split()
])))
shifts['crpix1'] = 0.0
shifts['crpix2'] = 0.0
# now create a wcs object based on those transforms, this wcs links the current frame's
# pixel coordinates to the reference frame's pixel coordinates.
w = get_wcs(shifts)
# get the PHOT file that was produced by the mkpsf routine
logging.debug("Reading .phot file {}".format(expnum))
phot = ascii.read(storage.get_file(expnum,
ccd=ccd,
version=version,
ext='phot'),
format='daophot')
# compute the small-aperture magnitudes of the stars used in the PSF
logging.debug("Running phot on {}".format(filename))
mags[expnum] = daophot.phot(filename,
phot['XCENTER'],
phot['YCENTER'],
aperture=apcor[expnum][0],
sky=apcor[expnum][1] + 1,
swidth=apcor[expnum][0],
zmag=zmag[expnum])
# covert the x/y positions to positions in Frame 1 based on the trans.jmp values.
logging.debug(
"Doing the XY translation to refrence frame: {}".format(w))
(x, y) = w.wcs_pix2world(mags[expnum]["XCENTER"],
mags[expnum]["YCENTER"], 1)
pos[expnum] = numpy.transpose([x, y])
# match this exposures PSF stars position against those in the first image of the set.
logging.debug("Matching lists")
idx1, idx2 = util.match_lists(pos[expnums[0]], pos[expnum])
# compute the magnitdue offset between the current frame and the reference.
dmags = numpy.ma.array(
mags[expnums[0]]["MAG"] - apcor[expnums[0]][2] -
(mags[expnum]["MAG"][idx1] - apcor[expnum][2]),
mask=idx1.mask)
dmags.sort()
# logging.debug("Computed dmags between input and reference: {}".format(dmags))
error_count = 0
error_count += 1
logging.debug("{}".format(error_count))
# compute the median and determine if that shift is small compared to the scatter.
try:
midx = int(
numpy.sum(numpy.any([~dmags.mask], axis=0)) / 2.0)
dmag = float(dmags[midx])
logging.debug("Computed a mag delta of: {}".format(dmag))
except Exception as e:
logging.error(str(e))
logging.error(
"Failed to compute mag offset between plant and found using: {}"
.format(dmags))
dmag = 99.99
error_count += 1
logging.debug("{}".format(error_count))
try:
if math.fabs(dmag) > 3 * (dmags.std() + 0.01):
logging.warning(
"Magnitude shift {} between {} and {} is large: {}"
.format(dmag, expnums[0], expnum, shifts))
except Exception as e:
logging.error(str(e))
error_count += 1
logging.debug("{}".format(error_count))
shifts['dmag'] = dmag
shifts['emag'] = dmags.std()
shifts['nmag'] = len(dmags.mask) - dmags.mask.sum()
shifts['dmjd'] = mjdates[expnums[0]] - mjdates[expnum]
shift_file = os.path.basename(
storage.get_uri(expnum, ccd, version, '.shifts'))
error_count += 1
logging.debug("{}".format(error_count))
try:
fh = open(shift_file, 'w')
fh.write(
json.dumps(shifts,
sort_keys=True,
indent=4,
separators=(',', ': '),
cls=NpEncoder))
fh.write('\n')
fh.close()
except Exception as e:
logging.error(
"Creation of SHIFTS file failed while trying to write: {}"
.format(shifts))
raise e
error_count += 1
logging.debug("{}".format(error_count))
if not dry_run:
storage.copy(
shift_file,
storage.get_uri(expnum, ccd, version, '.shifts'))
logging.info(message)
except Exception as ex:
message = str(ex)
logging.error(message)
if not dry_run:
storage.set_status(task,
prefix,
expnum,
version,
ccd,
status=message)