def save_mosaic(stack, nfiles, patch_size, name, diff_std, threshold):
stamps_per_row = int(np.sqrt(nfiles))
nrows = (nfiles - 1) / stamps_per_row + 1
mx = stamps_per_row * (patch_size + 1) + 1
my = nrows * (patch_size + 1) + 1
mosaic = np.ones((my, mx)) * 1000.0
for i in range(nfiles):
mosaic[(i / stamps_per_row) * (patch_size + 1) + 1:(
i / stamps_per_row + 1) * (
patch_size + 1), \
(i % stamps_per_row) * (patch_size + 1) + 1:(
i % stamps_per_row + 1) * (
patch_size + 1)] = stack[
i,
:,
:]
if diff_std[i] > threshold:
mosaic[(i / stamps_per_row) * (patch_size + 1) + 1:(
i / stamps_per_row + 1) * (
patch_size + 1), \
(i % stamps_per_row) * (patch_size + 1) + 1] = -1000.0
mosaic[(i / stamps_per_row) * (patch_size + 1) + 1:(
i / stamps_per_row + 1) * (
patch_size + 1), \
(i % stamps_per_row + 1) * (patch_size + 1) - 1] = -1000.0
mosaic[(i / stamps_per_row) * (patch_size + 1) + 1, \
(i % stamps_per_row) * (patch_size + 1) + 1:(
i % stamps_per_row + 1) * (
patch_size + 1)] = -1000.0
mosaic[(i / stamps_per_row + 1) * (patch_size + 1) - 1, \
(i % stamps_per_row) * (patch_size + 1) + 1:(
i % stamps_per_row + 1) * (
patch_size + 1)] = -1000.0
IO.write_image(mosaic, name)
def register_images(files, params):
"""Register the images in the given files list.
Registered images are placed in the loc_output dir with prefix r_
"""
# Have we specified a registration template?
if params.registration_image:
reg = DS.Observation(params.registration_image, params)
else:
reg = DS.EmptyBase()
reg.fw = 999.0
for f in files:
if (f.fw < reg.fw) and (f.fw > 1.2):
reg = f
print('Registration image:', reg.name)
# Register images
for f in files:
if f == reg:
f.image = f.data
rf = params.loc_output + os.path.sep + 'r_' + f.name
IO.write_image(f.image, rf)
else:
f.register(reg, params)
# delete image arrays to save memory
del f.image
del f.mask
del f.inv_variance
del reg.data
del reg.image
del reg.mask
del reg.inv_variance
return(files)
def process_image(f, args):
ref, params, stamp_positions, star_positions, star_group_boundaries, star_unsort_index, detector_mean_positions_x, detector_mean_positions_y = args
dtarget = params.loc_output + os.path.sep + 'd_' + f.name
if not (os.path.exists(dtarget)):
#
# Compute difference image
#
result = difference_image(
ref,
f,
params,
stamp_positions=stamp_positions,
psf_image=params.loc_output + os.path.sep + 'psf.fits',
star_positions=star_positions,
star_group_boundaries=star_group_boundaries,
detector_mean_positions_x=detector_mean_positions_x,
detector_mean_positions_y=detector_mean_positions_y)
del f.image
del f.mask
del f.inv_variance
#
# Save photometry to a file
#
if isinstance(result.flux, np.ndarray):
#if not(params.use_GPU):
print 'ungrouping fluxes'
result.flux = result.flux[star_unsort_index].copy()
result.dflux = result.dflux[star_unsort_index].copy()
np.savetxt(params.loc_output + os.path.sep + f.name + '.flux',
np.vstack((result.flux, result.dflux)).T)
f.flux = result.flux.copy()
f.dflux = result.dflux.copy()
#
# Save output images to files
#
if isinstance(result.diff, np.ndarray):
IO.write_image(result.diff,
params.loc_output + os.path.sep + 'd_' + f.name)
IO.write_image(result.model,
params.loc_output + os.path.sep + 'm_' + f.name)
IO.write_image(result.norm,
params.loc_output + os.path.sep + 'n_' + f.name)
IO.write_image(result.mask,
params.loc_output + os.path.sep + 'z_' + f.name)
return 0
def register(self, reg, params):
print(self.name)
self._image, self._mask, self._inv_variance = IM.register(
reg, self, params)
rf = os.path.join(self.output_dir, 'r_' + self.name)
IO.write_image(self._image, rf)
rf = os.path.join(self.output_dir, 'sm_' + self.name)
IO.write_image(self._mask, rf)
rf = os.path.join(self.output_dir, 'iv_' + self.name)
IO.write_image(self._inv_variance, rf)
del self.mask
del self.data
del self.inv_variance
def register(self, reg, params):
print self.name
self._image, self._mask, self._inv_variance = IM.register(
reg, self, params)
if self._image is None:
return False
print 'registered', self.name
rf = os.path.join(self.output_dir, 'r_' + self.name)
IO.write_image(self._image, rf)
rf = os.path.join(self.output_dir, 'sm_' + self.name)
IO.write_image(self._mask, rf)
rf = os.path.join(self.output_dir, 'iv_' + self.name)
IO.write_image(self._inv_variance, rf)
del self.mask
del self.data
del self.inv_variance
return True
def difference_image(ref,
target,
params,
stamp_positions=None,
psf_image=None,
star_positions=None,
star_group_boundaries=None,
detector_mean_positions_x=None,
detector_mean_positions_y=None,
star_sky=None,
kernelRadius=None,
kernel_inner_rad=7):
from scipy.linalg import lu_solve, lu_factor, LinAlgError
start = time.time()
print 'difference_image', ref.name, target.name
#
# Set the kernel size based on the difference in seeing from the reference
#
#kernelRadius = min(params.kernel_maximum_radius,
# max(params.kernel_minimum_radius,
# np.abs(target.fw-ref.fw)*params.fwhm_mult))
if kernelRadius is None:
kernelRadius = min(
params.kernel_maximum_radius,
max(params.kernel_minimum_radius,
np.sqrt(np.abs(target.fw**2 - ref.fw**2)) * params.fwhm_mult))
#
# Mask saturated pixels
#
#print 'Masking ',target.name,time.time()-start
#smask = compute_saturated_pixel_mask(target.image,kernelRadius,params)
#
# Define the kernel basis functions
#
print 'Defining kernel pixels', time.time() - start
if params.use_fft_kernel_pixels:
kernelIndex, extendedBasis = IM.define_kernel_pixels_fft(
ref,
target,
kernelRadius + 2,
INNER_RADIUS=20,
threshold=params.fft_kernel_threshold)
else:
kernelIndex, extendedBasis = IM.define_kernel_pixels(
kernelRadius, INNER_RADIUS=kernel_inner_rad)
nKernel = kernelIndex.shape[0]
#
# We dont want to use bad pixels in either the target or reference image
#
smask = target.mask * ref.mask
bmask = np.ones(smask.shape, dtype=bool)
g = DS.EmptyBase()
for iteration in range(params.iterations):
print 'Computing matrix', time.time() - start
tmask = bmask * smask
#
# Compute the matrix and vector
#
H, V, texref = CI.compute_matrix_and_vector_cuda(
ref.image,
ref.blur,
target.image,
target.inv_variance,
tmask,
kernelIndex,
extendedBasis,
kernelRadius,
params,
stamp_positions=stamp_positions)
#
# Solve the matrix equation to find the kernel coefficients
#
print 'Solving matrix equation', time.time() - start
try:
lu, piv = lu_factor(H)
c = lu_solve((lu, piv), V).astype(np.float32).copy()
except (LinAlgError, ValueError):
print 'LU decomposition failed'
g.model = None
g.flux = None
g.diff = None
print 'H'
print H
sys.stdout.flush()
return g
#
# Compute the model image
#
print 'Computing model', time.time() - start
g.model = CI.compute_model_cuda(ref.image.shape, texref, c,
kernelIndex, extendedBasis, params)
edges = np.where(ref.image < 1.0)
g.model[edges] = 0.0
#
# Compute the difference image
#
difference = (target.image - g.model)
g.norm = difference * np.sqrt(target.inv_variance)
#
# Recompute the variance image from the model
#
#target.inv_variance = 1.0/(g.model/params.gain +
# (params.readnoise/params.gain)**2) + (1-smask)
mp = np.where(tmask == 0)
if len(mp[0]) > 0:
target.inv_variance[mp] = 1.e-12
#
# Mask pixels that disagree with the model
#
if iteration > 2:
bmask = IM.kappa_clip(smask, g.norm,
params.pixel_rejection_threshold)
print 'Iteration', iteration, 'completed', time.time() - start
#
# Delete the target image array to save memory
#
del target.image
#
# Save the kernel coefficients to a file
#
if params.do_photometry and psf_image:
kf = params.loc_output + os.path.sep + 'k_' + os.path.basename(
target.name)
IO.write_kernel_table(kf, kernelIndex, extendedBasis, c, params)
print 'coeffs', c
g.norm = difference * np.sqrt(target.inv_variance)
g.variance = 1.0 / target.inv_variance
g.mask = tmask
#
# Do the photometry if requested
#
g.flux = None
if params.do_photometry and psf_image:
print 'star_positions', star_positions.shape
print 'star_group_boundaries', star_group_boundaries
if ref.name == target.name:
sky_image, _ = IO.read_fits_file(params.loc_output + os.path.sep +
'temp.sub2.fits')
phot_target = ref.image - sky_image
IO.write_image(
phot_target,
params.loc_output + os.path.sep + 'clean_' + ref.name)
g.flux, g.dflux = CIF.photom_all_stars_simultaneous(
phot_target, target.inv_variance, star_positions, psf_image, c,
kernelIndex, extendedBasis, kernelRadius, params,
star_group_boundaries, detector_mean_positions_x,
detector_mean_positions_y)
else:
phot_target = difference
g.flux, g.dflux = CI.photom_all_stars(
phot_target, target.inv_variance, star_positions, psf_image, c,
kernelIndex, extendedBasis, kernelRadius, params,
star_group_boundaries, detector_mean_positions_x,
detector_mean_positions_y)
print 'Photometry completed', time.time() - start
#
# Apply the photometric scale factor to the difference image.
# We don't do this prior to the photometry because the PSF is
# being convolved by the kernel, which already includes the
# photometric scale factor.
#
g.diff = IM.apply_photometric_scale(difference, c, params.pdeg)
sys.stdout.flush()
return g
def make_reference(files, reg, params, reference_image='ref.fits'):
seeing = {}
sky = {}
ref_seeing = 1000
#
# Have we specified the files to make the reference with?
#
if params.ref_include_file:
ref_list = []
for line in open(params.ref_include_file, 'r'):
for f in files:
if f.name == line.split()[0]:
ref_list.append(f)
print f.name, f.fw, f.signal
if f.fw < ref_seeing:
ref_sky = f.sky
ref_seeing = f.fw
best_seeing_ref = f
else:
#
# We try to choose the best images
#
reference_exclude = []
if params.ref_exclude_file:
for line in open(params.ref_exclude_file, 'r'):
reference_exclude.append(line.split()[0])
sig = []
for f in files:
sig.append(f.signal)
sig = np.asarray(sig)
sigcut = np.mean(sig) - 2.0 * np.std(sig)
print 'signal: mean, std, cut = ', np.mean(sig), np.std(sig), sigcut
print 'Searching for lowest-background image'
ref_sky = 1.e6
for f in files:
print f.name, f.fw, f.sky, f.signal
if (f.sky < ref_sky) and (f.fw > params.reference_min_seeing) and \
(f.roundness < params.reference_max_roundness) and (f.signal > sigcut) and not(f.name in reference_exclude):
ref_sky = f.sky
ref_sky = np.max([ref_sky, params.pixel_max / 1.e5])
print 'Searching for best-seeing image'
ref_seeing = 100.0
for f in files:
print f.name, f.fw, f.sky, f.signal
if (f.fw < ref_seeing) and (f.fw > params.reference_min_seeing) and \
(f.roundness < params.reference_max_roundness) and (f.signal > sigcut) and not(f.name in reference_exclude):
ref_seeing = f.fw
best_seeing_ref = f
ref_list = []
while len(ref_list) < params.min_ref_images:
ref_list = []
print 'Reference FWHM = ', ref_seeing
print 'Cutoff FWHM for reference = ', params.reference_seeing_factor * ref_seeing
print 'Cutoff background for reference = ', params.reference_sky_factor * ref_sky
print 'Combining for reference:'
for f in files:
if (f.fw < params.reference_seeing_factor*ref_seeing) and \
(f.roundness < params.reference_max_roundness) and (f.sky < params.reference_sky_factor*ref_sky) and \
(f.fw > params.reference_min_seeing) and (f.signal > sigcut) and not(f.name in reference_exclude):
ref_list.append(f)
print f.name, f.fw, f.sky, f.signal
params.reference_seeing_factor *= 1.02
params.reference_sky_factor *= 1.02
if len(ref_list) > params.max_ref_images:
ref_list = ref_list[:params.max_ref_images]
sig = []
for f in ref_list:
sig.append(f.signal)
sig = np.asarray(sig)
sigcut = np.mean(sig) - 2 * np.std(sig)
print 'signal: mean, std, cut = ', np.mean(sig), np.std(sig), sigcut
ref_seeing = 1000
ref_roundness = 2.0
for f in ref_list:
if (f.fw < ref_seeing) and (f.signal > sigcut):
ref_sky = f.sky
ref_seeing = f.fw
ref_roundness = f.roundness
best_seeing_ref = f
#
# Which ref image has the worst seeing?
#
worst_seeing = 0.0
for f in ref_list:
if f.fw > worst_seeing:
worst_seeing = f.fw
worst_seeing_ref = f
if params.ref_image_list:
with open(params.loc_output + os.path.sep + params.ref_image_list,
'w') as fid:
for f in ref_list:
fid.write(f.name + ' ' + str(f.fw) + ' ' + str(f.sky) +
' ' + str(f.signal) + '\n')
#
# Find the locations of the brightest stars to use as stamp positions
# if required
#
stamp_positions = None
if params.use_stamps:
stars = PH.choose_stamps(best_seeing_ref, params)
stamp_positions = stars[:, 0:2]
#
# Construct the reference image.
#
ref = np.zeros([1, 1])
sum1 = 0
sum2 = 0
good_ref_list = []
for f in ref_list:
f.blur = IM.boxcar_blur(f.image)
good_ref_list.append(f)
print 'difference_image:', f.name, best_seeing_ref.name
if not (params.use_GPU) and (params.n_parallel > 1):
#
# Use ParallelProcessing to process images in the reference list
#
pool = Pool(params.n_parallel)
results = pool.map(
process_reference_image_helper,
itertools.izip(
ref_list,
itertools.repeat((best_seeing_ref, params, stamp_positions))))
for i, f in enumerate(ref_list):
f.result = results[i]
else:
for f in ref_list:
f.result = process_reference_image(
f, (best_seeing_ref, params, stamp_positions))
#
# Remove bad reference models
#
rlist = [g for g in good_ref_list]
for g in rlist:
if not (isinstance(g.result.diff, np.ndarray)):
print 'removing', g.name
good_ref_list.remove(g)
print 'good reference list:'
for g in good_ref_list:
print g.name
print 'kappa-clipping reference list'
for iterations in range(5):
if len(good_ref_list) < 4:
break
sd = np.zeros(len(good_ref_list))
for i, g in enumerate(good_ref_list):
print g.name, g.result.diff
sd[i] = np.std(g.result.diff)
sds = sd.std()
sdm = sd.mean()
rlist = [g for g in good_ref_list]
for g in rlist:
if np.std(g.result.diff) > (sdm + 2.5 * sds):
print 'removing', g.name
good_ref_list.remove(g)
#
# Combine the good reference models
#
g = good_ref_list[0]
gstack = np.zeros(
[len(good_ref_list), g.result.model.shape[0], g.result.model.shape[1]])
var_ref = np.zeros_like(g.result.model)
mask = np.ones_like(g.result.model)
print 'final reference list'
for i, g in enumerate(good_ref_list):
if isinstance(g.result.model, np.ndarray):
print g.name, np.std(g.result.diff), np.median(g.result.model)
IO.write_image(g.result.model,
params.loc_output + os.path.sep + 'mr_' + g.name)
gstack[i, :, :] = g.result.model
var_ref += g.result.model / params.gain + (params.readnoise /
params.gain)**2
mask *= g.mask
rr = np.median(gstack, axis=0)
IO.write_image(rr, params.loc_output + os.path.sep + reference_image)
IO.write_image(mask,
params.loc_output + os.path.sep + 'mask_' + reference_image)
var_ref /= np.float(len(good_ref_list))
IO.write_image(var_ref,
params.loc_output + os.path.sep + 'var_' + reference_image)
if params.error_image_prefix is not None:
IO.write_image(
np.sqrt(var_ref), params.loc_output + os.path.sep +
params.error_image_prefix + reference_image)
for f in ref_list:
f.result = None
return stamp_positions
headers += [channel + str(n) for n in range(n) for channel in ['R', 'G', 'B', 'P']]
writer.writerow(headers)
for filename in images:
color = io_functions.read_image(os.path.join(input_folder, 'color_' + filename))
abdomen = io_functions.read_image(os.path.join(input_folder, 'abdomen_' + filename))[:, :, 0]
wings = io_functions.read_image(os.path.join(input_folder, 'wings_' + filename))[:, :, 0]
if color is not None and abdomen is not None and wings is not None:
HSV = rgb2hsv(color)
segments = [Segment('wings', wings, 10),
Segment('abdomen', abdomen, 5)]
current_row = [os.path.splitext(filename)[0]]
for segment in segments:
current_row += [segment.name,
np.mean(HSV[:, :, 0][np.where(segment.mask > 128)]),
np.mean(HSV[:, :, 1][np.where(segment.mask > 128)])]
dc = dominant_colors(color.astype('float32'), segment.num_colors, mask=segment.mask)
output = visualise_colors(dc, 100, 100 * segment.num_colors)
io_functions.write_image(os.path.join(output_folder,'{}_{}'.format(segment.name, filename)), output)
for c in dc:
current_row += [c.RGB[channel] for channel in range(0, 3)[::-1]] + [c.proportion]
writer.writerow(current_row)
def photom_variable_star(x0,
y0,
params,
patch_half_width=15,
converge=True,
save_stamps=False,
stamp_prefix='mosaic',
locate=True,
locate_iterations=2,
locate_half_width=14,
q_sigma_threshold=1.0,
locate_date_range=None):
from astropy.io import fits
def save_mosaic(stack, nfiles, patch_size, name, diff_std, threshold):
stamps_per_row = int(np.sqrt(nfiles))
nrows = (nfiles - 1) / stamps_per_row + 1
mx = stamps_per_row * (patch_size + 1) + 1
my = nrows * (patch_size + 1) + 1
mosaic = np.ones((my, mx)) * 1000.0
for i in range(nfiles):
mosaic[(i/stamps_per_row)*(patch_size+1)+1:(i/stamps_per_row+1)*(patch_size+1), \
(i%stamps_per_row)*(patch_size+1)+1:(i%stamps_per_row+1)*(patch_size+1)] \
= stack[i,:,:]
if diff_std[i] > threshold:
mosaic[(i/stamps_per_row)*(patch_size+1)+1:(i/stamps_per_row+1)*(patch_size+1), \
(i%stamps_per_row)*(patch_size+1)+1] = -1000.0
mosaic[(i/stamps_per_row)*(patch_size+1)+1:(i/stamps_per_row+1)*(patch_size+1), \
(i%stamps_per_row+1)*(patch_size+1)-1] = -1000.0
mosaic[(i/stamps_per_row)*(patch_size+1)+1, \
(i%stamps_per_row)*(patch_size+1)+1:(i%stamps_per_row+1)*(patch_size+1)] = -1000.0
mosaic[(i/stamps_per_row+1)*(patch_size+1)-1, \
(i%stamps_per_row)*(patch_size+1)+1:(i%stamps_per_row+1)*(patch_size+1)] = -1000.0
IO.write_image(mosaic, name)
# Obtain a list of files
all_files = os.listdir(params.loc_data)
all_files.sort()
filenames = []
nfiles = 0
print 'Searching in', params.loc_output, 'for', params.name_pattern
for f in all_files:
if fnmatch.fnmatch(f, params.name_pattern):
basename = os.path.basename(f)
dfile = params.loc_output + os.path.sep + 'd_' + basename
ktable = params.loc_output + os.path.sep + 'k_' + basename
if os.path.exists(dfile) and os.path.exists(ktable):
nfiles += 1
filenames.append(f)
# Load the kernel tables
# Load the difference images into a data cube
print len(filenames), 'files found'
dates = np.zeros(nfiles)
seeing = np.zeros(nfiles)
roundness = np.zeros(nfiles)
bgnd = np.zeros(nfiles)
signal = np.zeros(nfiles)
norm_std = np.zeros(nfiles, dtype=np.float64)
diff_std = np.zeros(nfiles, dtype=np.float64)
n_kernel = np.zeros(nfiles, dtype=np.int32)
n_coeffs = np.zeros(nfiles, dtype=np.int32)
kindex_x = np.arange(0, dtype=np.int32)
kindex_y = np.arange(0, dtype=np.int32)
kindex_ext = np.arange(0, dtype=np.int32)
coeffs = np.arange(0, dtype=np.float64)
filenames.sort()
if not converge:
locate_iterations = 1
threshold = -10
for iteration in range(np.max([1, locate_iterations])):
ix0 = np.int32(x0 + 0.5)
iy0 = np.int32(y0 + 0.5)
x_patch = x0 - ix0 + patch_half_width
y_patch = y0 - iy0 + patch_half_width
patch_size = 2 * patch_half_width + 1
patch_slice = (ix0 - patch_half_width, ix0 + patch_half_width + 1,
iy0 - patch_half_width, iy0 + patch_half_width + 1)
d_image_stack = np.zeros((nfiles, patch_size, patch_size),
dtype=np.float64)
inv_var_image_stack = np.zeros((nfiles, patch_size, patch_size),
dtype=np.float64)
for i, f in enumerate(filenames):
basename = os.path.basename(f)
ktable = params.loc_output + os.path.sep + 'k_' + basename
kernelIndex, extendedBasis, c, params = IO.read_kernel_table(
ktable, params)
coeffs = np.hstack((coeffs, c))
kindex_x = np.hstack((kindex_x, kernelIndex[:, 0].T))
kindex_y = np.hstack((kindex_y, kernelIndex[:, 1].T))
kindex_ext = np.hstack((kindex_ext, extendedBasis))
n_kernel[i] = kernelIndex.shape[0]
n_coeffs[i] = c.shape[0]
dates[i] = IO.get_date(params.loc_data + os.path.sep + basename,
key=params.datekey) - 2450000
seeing[i], roundness[i], bgnd[i], signal[i] = IM.compute_fwhm(
f, params, width=20, image_name=True)
dfile = params.loc_output + os.path.sep + 'd_' + basename
nfile = params.loc_output + os.path.sep + 'n_' + basename
zfile = params.loc_output + os.path.sep + 'z_' + basename
diff, _ = IO.read_fits_file(dfile)
mask, _ = IO.read_fits_file(zfile)
diff_sc = IM.undo_photometric_scale(diff, c, params.pdeg)
diff_sc *= mask
d_image_stack[i, :, :] = diff_sc[patch_slice[2]:patch_slice[3],
patch_slice[0]:patch_slice[1]]
norm, _ = IO.read_fits_file(nfile, slice=patch_slice)
inv_var_image_stack[i, :, :] = (norm / d_image_stack[i, :, :])**2
diff_std[i] = np.std(diff)
d_image_stack[i, :, :] -= np.median(d_image_stack[i, :, :])
if save_stamps:
save_mosaic(
d_image_stack, nfiles, patch_size,
params.loc_output + os.path.sep + stamp_prefix + '.fits',
diff_std, threshold)
print 'kappa-clipping'
qd1 = np.arange(len(filenames))
#qd = np.where(diff_std[qd1]<10)
#qd1 = qd1[qd]
for iter in range(10):
qd = np.where(diff_std[qd1] < np.mean(diff_std[qd1]) +
(4.0 - 1.5 * (iter / 9.0)) * np.std(diff_std[qd1]))
qd1 = qd1[qd]
print iter, np.mean(diff_std[qd1]), np.std(diff_std[qd1]), np.mean(
diff_std[qd1]) + (4.0 - 3 *
(iter / 9.0)) * np.std(diff_std[qd1])
print 'mean(diff) :', np.mean(diff_std[qd1])
print 'std(diff) :', np.std(diff_std[qd1])
print '1-sig threshold:', np.mean(
diff_std[qd1]) + 1 * np.std(diff_std[qd1])
print '2-sig threshold:', np.mean(
diff_std[qd1]) + 2 * np.std(diff_std[qd1])
print '3-sig threshold:', np.mean(
diff_std[qd1]) + 3 * np.std(diff_std[qd1])
print '1-sig diff reject:', np.where(
diff_std > np.mean(diff_std[qd1]) + 1 * np.std(diff_std[qd1]))
print '2-sig diff reject:', np.where(
diff_std > np.mean(diff_std[qd1]) + 2 * np.std(diff_std[qd1]))
print '3-sig diff reject:', np.where(
diff_std > np.mean(diff_std[qd1]) + 3 * np.std(diff_std[qd1]))
threshold = np.mean(
diff_std[qd1]) + q_sigma_threshold * np.std(diff_std[qd1])
threshold2 = np.mean(diff_std[qd1]) + 2 * np.std(diff_std[qd1])
threshold3 = np.mean(diff_std[qd1]) + 3 * np.std(diff_std[qd1])
if locate_date_range is not None:
diff_std_copy = diff_std.copy()
diff_std = diff_std * 0.0 + 2 * threshold
pp = np.where((dates > locate_date_range[0])
& (dates < locate_date_range[1]))[0]
if pp.any():
diff_std[pp] = diff_std_copy[pp]
else:
print 'Error: No images found in date range', locate_date_range
print 'Reverting to all dates.'
diff_std = diff_std_copy
dsum = np.zeros((patch_size, patch_size), dtype=np.float64)
for i in range(nfiles):
if diff_std[i] < threshold3:
dsum += d_image_stack[i, :, :]
IO.write_image(
dsum, params.loc_output + os.path.sep + 'dsum%d.fits' % iteration)
dr = patch_half_width - int(locate_half_width)
dsum[:dr, :] = 0.0
dsum[-dr:, :] = 0.0
dsum[:, :dr] = 0.0
dsum[:, -dr:] = 0.0
ind_dsum_max = np.unravel_index(dsum.argmax(), dsum.shape)
print 'Iteration', iteration, ': dsum maximum located at ', ind_dsum_max
if locate and converge:
y0 += ind_dsum_max[0] - patch_half_width
x0 += ind_dsum_max[1] - patch_half_width
# Read the PSF
psf_image = params.loc_output + os.path.sep + 'psf.fits'
psf, psf_hdr = fits.getdata(psf_image, 0, header='true')
psf_height = psf_hdr['PSFHEIGH']
psf_sigma_x = psf_hdr['PAR1'] * 0.8493218
psf_sigma_y = psf_hdr['PAR2'] * 0.8493218
psf_x = psf_hdr['PSFX']
psf_y = psf_hdr['PSFY']
psf_size = psf.shape[1]
psf_fit_rad = params.psf_fit_radius
psf_parameters = np.array([
psf_size, psf_height, psf_sigma_x, psf_sigma_y, psf_x, psf_y,
psf_fit_rad, params.gain
]).astype(np.float64)
if params.psf_profile_type == 'gaussian':
psf_sigma_x = psf_hdr['PAR1'] * 0.8493218
psf_sigma_y = psf_hdr['PAR2'] * 0.8493218
psf_parameters = np.array([
psf_size, psf_height, psf_sigma_x, psf_sigma_y, psf_x, psf_y,
psf_fit_rad, params.gain
]).astype(np.float64)
profile_type = 0
elif params.psf_profile_type == 'moffat25':
print 'params.psf_profile_type moffat25 not working yet. Exiting.'
sys.exit(0)
psf_sigma_x = psf_hdr['PAR1']
psf_sigma_y = psf_hdr['PAR2']
psf_sigma_xy = psf_hdr['PAR3']
psf_parameters = np.array([
psf_size, psf_height, psf_sigma_x, psf_sigma_y, psf_x, psf_y,
psf_fit_rad, params.gain, psf_sigma_xy
]).astype(np.float64)
profile_type = 1
else:
print 'params.psf_profile_type undefined'
sys.exit(0)
psf_0 = psf.astype(np.float64).copy()
psf_xd = psf.astype(np.float64).copy() * 0.0
psf_yd = psf.astype(np.float64).copy() * 0.0
flux = np.zeros(nfiles, dtype=np.float64)
dflux = np.zeros(nfiles, dtype=np.float64)
x0_arr = np.atleast_1d(np.array([x0], dtype=np.float64))
y0_arr = np.atleast_1d(np.array([y0], dtype=np.float64))
cu_photom_converge(
profile_type, patch_half_width, params.pdeg, params.sdeg, nfiles,
n_kernel, kindex_x, kindex_y, kindex_ext, n_coeffs,
coeffs.astype(np.float64), psf_parameters, psf_0, psf_xd, psf_yd,
np.float64(d_image_stack.ravel()), inv_var_image_stack, diff_std,
np.float64(threshold), x0_arr, y0_arr, x_patch, y_patch, diff.shape[1],
diff.shape[0], 16, 16, flux, dflux, np.float64(params.gain),
np.int32(converge), np.float64(2.5))
if save_stamps:
save_mosaic(
d_image_stack, nfiles, patch_size,
params.loc_output + os.path.sep + 'p' + stamp_prefix + '.fits',
diff_std, threshold)
if locate_date_range is not None:
diff_std = diff_std_copy
return dates, seeing, roundness, bgnd, signal, flux, dflux, diff_std / threshold, x0_arr[
0], y0_arr[0]
segments = [
Segment('wings', wings, 10),
Segment('abdomen', abdomen, 5)
]
current_row = [os.path.splitext(filename)[0]]
for segment in segments:
current_row += [
segment.name,
np.mean(HSV[:, :, 0][np.where(segment.mask > 128)]),
np.mean(HSV[:, :, 1][np.where(segment.mask > 128)])
]
dc = dominant_colors(color.astype('float32'),
segment.num_colors,
mask=segment.mask)
output = visualise_colors(dc, 100, 100 * segment.num_colors)
io_functions.write_image(
os.path.join(output_folder,
'{}_{}'.format(segment.name, filename)),
output)
for c in dc:
current_row += [
c.RGB[channel] for channel in range(0, 3)[::-1]
] + [c.proportion]
writer.writerow(current_row)
def make_diff_images(filenamelist, refim, params):
""" make a diff image for each file in filenamelist: file - refim.
filenamelist : list of filenames for 'target' images
refim : reference image, either a filename or a DIA Observation object
params : DIA parameters object
"""
star_group_boundaries = None
detector_mean_positions_x = None
detector_mean_positions_y = None
star_unsort_index = None
star_positions = None
stamp_positions = None
sky = 0.0
if isinstance(refim, str) and os.path.exists(refim):
refim = DS.Observation(refim, params)
# TODO: investigate what is really being done here:
# Apply saturation mask and boxcar blurring to reference image
mask, _ = IO.read_fits_file(
params.loc_output + os.path.sep + 'mask_' + refim.name)
refim.mask = mask
pm = params.pixel_max
params.pixel_max *= 0.9
refim.mask *= IM.compute_saturated_pixel_mask(refim.image, 4, params)
params.pixel_max = pm
refim.blur = IM.boxcar_blur(refim.image)
if params.mask_cluster:
refim.mask *= IM.mask_cluster(refim.image, refim.mask, params)
# For each given filename, get a pyDIA observation object
image_list = get_observation_list(filenamelist, params)
# Register the images, using the ref image as the registration template,
# unless the user has specified otherwise
if not params.registration_image:
params.registration_image = refim.fullname
registered_image_list = register_images(image_list, params)
# make diff images: im - ref
for im in registered_image_list:
result = DIA.difference_image(
refim, im, params,
stamp_positions=stamp_positions,
psf_image=params.loc_output + os.path.sep + 'psf.fits',
star_positions=star_positions,
star_group_boundaries=star_group_boundaries,
detector_mean_positions_x=detector_mean_positions_x,
detector_mean_positions_y=detector_mean_positions_y)
del im.image
del im.mask
del im.inv_variance
hdr = fits.getheader(im.fullname)
# TODO : use astropy fits to propagate header with WCS from parent image
# Save output images to files
if isinstance(result.diff, np.ndarray):
IO.write_image(result.diff,
params.loc_output + os.path.sep + 'd_' + im.name,
header=hdr)
def do_photometry(params,
extname='newflux',
star_file='star_positions',
psf_file='psf.fits',
star_positions=None,
reference_image='ref.fits'):
#
# Determine our list of files
#
all_files = os.listdir(params.loc_data)
all_files.sort()
files = []
for f in all_files:
if fnmatch.fnmatch(f, params.name_pattern):
g = DS.Observation(params.loc_data + os.path.sep + f, params)
if g.fw > 0.0:
files.append(g)
ref = DS.Observation(params.loc_output + os.path.sep + reference_image,
params)
ref.register(ref, params)
#
# Detect stars and compute the PSF if necessary
#
psf_file = params.loc_output + os.path.sep + psf_file
star_file = params.loc_output + os.path.sep + star_file
print psf_file
print os.path.exists(psf_file)
print star_file
print os.path.exists(star_file)
if not (os.path.exists(psf_file)) or not (os.path.exists(star_file)):
stars = PH.compute_psf_image(params, ref, psf_image=psf_file)
if star_positions is None:
if os.path.exists(star_file):
star_positions = np.genfromtxt(star_file)[:, :2]
else:
star_positions = stars[:, 0:2]
#
# Group the stars by location
#
star_group_boundaries = None
detector_mean_positions_x = None
detector_mean_positions_y = None
star_sort_index,star_group_boundaries,detector_mean_positions_x,detector_mean_positions_y = \
PH.group_stars_ccd(params,star_positions,params.loc_output+os.path.sep+reference_image)
star_positions = star_positions[star_sort_index]
star_unsort_index = np.argsort(star_sort_index)
#
# Process the reference image
#
print 'Processing', reference_image
ref = DS.Observation(params.loc_output + os.path.sep + reference_image,
params)
#reg = Observation(params.loc_data+os.path.sep+
# params.registration_image,params)
mask, _ = IO.read_fits_file(params.loc_output + os.path.sep + 'mask_' +
reference_image)
variance, _ = IO.read_fits_file(params.loc_output + os.path.sep + 'var_' +
reference_image)
ref.mask = mask
ref.inv_variance = 1.0 / variance + (1 - mask)
ref.register(ref, params)
smask = IM.compute_saturated_pixel_mask(ref.image, params)
ref.inv_variance += (1 - (smask * mask)) * 1.e-12
ktable = params.loc_output + os.path.sep + 'k_' + os.path.basename(
reference_image)
kernelIndex, extendedBasis, c, params = IO.read_kernel_table(
ktable, params)
kernelRadius = np.max(kernelIndex[:, 0]) + 1
if np.sum(extendedBasis) > 0:
kernelRadius += 1
print 'kernelIndex', kernelIndex
print 'extendedBasis', extendedBasis
print 'coeffs', c
print 'kernelRadius', kernelRadius
print 'star_positions', star_positions.shape
phot_target, _ = IO.read_fits_file(params.loc_output + os.path.sep +
'clean_' + reference_image)
ref.flux, ref.dflux = CIF.photom_all_stars_simultaneous(
phot_target, ref.inv_variance, star_positions, psf_file, c,
kernelIndex, extendedBasis, kernelRadius, params,
star_group_boundaries, detector_mean_positions_x,
detector_mean_positions_y)
if isinstance(ref.flux, np.ndarray):
if not (params.use_GPU):
print 'ungrouping fluxes'
ref.flux = ref.flux[star_unsort_index].copy()
ref.dflux = ref.dflux[star_unsort_index].copy()
print ref.flux.shape, star_positions.shape
np.savetxt(
params.loc_output + os.path.sep + reference_image + '.' + extname,
np.vstack((ref.flux, ref.dflux)))
#
# Process difference images
#
for f in files:
if not (os.path.exists(params.loc_output + os.path.sep + f.name + '.' +
extname)):
print 'Processing', f.name
target = f.name
dtarget = params.loc_output + os.path.sep + 'd_' + os.path.basename(
target)
ntarget = params.loc_output + os.path.sep + 'n_' + os.path.basename(
target)
ztarget = params.loc_output + os.path.sep + 'z_' + os.path.basename(
target)
ktable = params.loc_output + os.path.sep + 'k_' + os.path.basename(
target)
if os.path.exists(dtarget) and os.path.exists(
ntarget) and os.path.exists(ktable):
norm, h = IO.read_fits_file(ntarget)
diff, h = IO.read_fits_file(dtarget)
mask, h = IO.read_fits_file(ztarget)
inv_var = (norm / diff)**2 + (1 - mask)
kernelIndex, extendedBasis, c, params = IO.read_kernel_table(
ktable, params)
kernelRadius = np.max(kernelIndex[:, 0]) + 1
if np.sum(extendedBasis) > 0:
kernelRadius += 1
print 'kernelIndex', kernelIndex
print 'extendedBasis', extendedBasis
print 'coeffs', c
print 'kernelRadius', kernelRadius
IO.write_image(diff,
params.loc_output + os.path.sep + 'diff1.fits')
diff = IM.undo_photometric_scale(diff, c, params.pdeg)
IO.write_image(diff,
params.loc_output + os.path.sep + 'diff2.fits')
IO.write_image(
inv_var, params.loc_output + os.path.sep + 'inv_var.fits')
IO.write_kernel_table(
params.loc_output + os.path.sep + 'ktable.fits',
kernelIndex, extendedBasis, c, params)
flux, dflux = CI.photom_all_stars(
diff, inv_var, star_positions, psf_file, c, kernelIndex,
extendedBasis, kernelRadius, params, star_group_boundaries,
detector_mean_positions_x, detector_mean_positions_y)
print 'flux[100:110]:'
print flux[100:110]
if isinstance(flux, np.ndarray):
if not (params.use_GPU):
print 'ungrouping fluxes'
flux = flux[star_unsort_index].copy()
dflux = dflux[star_unsort_index].copy()
print 'unsort flux[100:110]:'
print flux[100:110]
np.savetxt(
params.loc_output + os.path.sep + f.name + '.' +
extname,
np.vstack((flux, dflux)).T)
sys.exit(0)
def set_image(self, value):
self._image = value
image_name = os.path.join(self.output_dir, 'r_' + self.name)
IO.write_image(self._image, image_name)
def photom_variable_star(x0,y0,params,patch_half_width=15,converge=True,save_stamps=False,stamp_prefix='mosaic',locate=True,locate_iterations=2, locate_half_width=14,q_sigma_threshold=1.0,locate_date_range=None): from astropy.io import fits from scipy.ndimage.filters import median_filter outer_radius = 15 inner_radius = 12 diameter = 2*outer_radius + 1 x = np.arange(diameter)-outer_radius xx,yy = np.meshgrid(x,x) filter_kernel = np.zeros((diameter,diameter)) filter_kernel[xx**2+yy**2<=outer_radius**2] = 1 filter_kernel[xx**2+yy**2<=inner_radius**2] = 0 def save_mosaic(stack,nfiles,patch_size,name,diff_std,threshold): stamps_per_row = int(np.sqrt(nfiles)) nrows = (nfiles-1)/stamps_per_row+1; mx = stamps_per_row*(patch_size+1)+1 my = nrows*(patch_size+1)+1 mosaic = np.ones((my,mx))*1000.0 for i in range(nfiles): mosaic[(i/stamps_per_row)*(patch_size+1)+1:(i/stamps_per_row+1)*(patch_size+1), \ (i%stamps_per_row)*(patch_size+1)+1:(i%stamps_per_row+1)*(patch_size+1)] \ = stack[i,:,:] if diff_std[i] > threshold: mosaic[(i/stamps_per_row)*(patch_size+1)+1:(i/stamps_per_row+1)*(patch_size+1), \ (i%stamps_per_row)*(patch_size+1)+1] = -1000.0 mosaic[(i/stamps_per_row)*(patch_size+1)+1:(i/stamps_per_row+1)*(patch_size+1), \ (i%stamps_per_row+1)*(patch_size+1)-1] = -1000.0 mosaic[(i/stamps_per_row)*(patch_size+1)+1, \ (i%stamps_per_row)*(patch_size+1)+1:(i%stamps_per_row+1)*(patch_size+1)] = -1000.0 mosaic[(i/stamps_per_row+1)*(patch_size+1)-1, \ (i%stamps_per_row)*(patch_size+1)+1:(i%stamps_per_row+1)*(patch_size+1)] = -1000.0 IO.write_image(mosaic,name) # Obtain a list of files all_files = os.listdir(params.loc_data) all_files.sort() filenames = [] nfiles = 0 print 'Searching in', params.loc_output, 'for', params.name_pattern for f in all_files: if fnmatch.fnmatch(f,params.name_pattern): basename = os.path.basename(f) dfile = params.loc_output+os.path.sep+'d_'+basename ktable = params.loc_output+os.path.sep+'k_'+basename if os.path.exists(dfile) and os.path.exists(ktable): nfiles += 1 filenames.append(f) # Load the kernel tables # Load the difference images into a data cube print len(filenames), 'files found' dates = np.zeros(nfiles) seeing = np.zeros(nfiles) roundness = np.zeros(nfiles) bgnd = np.zeros(nfiles) signal = np.zeros(nfiles) norm_std = np.zeros(nfiles,dtype=np.float64) diff_std = np.zeros(nfiles,dtype=np.float64) n_kernel = np.zeros(nfiles,dtype=np.int32) n_coeffs = np.zeros(nfiles,dtype=np.int32) kindex_x = np.arange(0,dtype=np.int32) kindex_y = np.arange(0,dtype=np.int32) kindex_ext = np.arange(0,dtype=np.int32) coeffs = np.arange(0,dtype=np.float64) filenames.sort() if not converge: locate_iterations = 1 threshold = -10 for iteration in range(np.max([1,locate_iterations])): #ix0 = np.int32(x0+0.5) #iy0 = np.int32(y0+0.5) ix0 = np.int32(x0) iy0 = np.int32(y0) x_patch = x0 - ix0 + patch_half_width y_patch = y0 - iy0 + patch_half_width patch_size = 2*patch_half_width+1 patch_slice = np.array([ix0-patch_half_width, ix0+patch_half_width+1, iy0-patch_half_width, iy0+patch_half_width+1]) print 'patch_slice:', patch_slice # check that patch doesn't overlap the edge of the image f = filenames[0] diff, _ = IO.read_fits_file(params.loc_output+os.path.sep+'d_'+os.path.basename(f)) nx = diff.shape[1] ny = diff.shape[0] delta_patch_x = 0 delta_patch_y = 0 if patch_slice[0] < 0: delta_patch_x = -patch_slice[0] elif patch_slice[1] >= nx: delta_patch_x = nx - patch_slice[1] - 1 if patch_slice[2] < 0: delta_patch_y = -patch_slice[2] elif patch_slice[3] >= ny: delta_patch_y = ny - patch_slice[3] - 1 print 'delta_patch_x, delta_patch_y:', delta_patch_x, delta_patch_y patch_slice += np.array([delta_patch_x,delta_patch_x,delta_patch_y,delta_patch_y]) print 'patch_slice:', patch_slice x_patch -= delta_patch_x y_patch -= delta_patch_y d_image_stack = np.zeros((nfiles,patch_size,patch_size),dtype=np.float64) inv_var_image_stack = np.zeros((nfiles,patch_size,patch_size),dtype=np.float64) dmask = np.ones([patch_size,patch_size],dtype=np.bool) dmask_rad = 8.0 dmix = np.linspace(-patch_half_width,patch_half_width,patch_size) - delta_patch_x dmiy = np.linspace(-patch_half_width,patch_half_width,patch_size) - delta_patch_y dmx, dmy = np.meshgrid(dmix,dmiy,indexing='ij') dmask[dmx**2 + dmy**2 < dmask_rad**2] = False for i, f in enumerate(filenames): basename = os.path.basename(f) ktable = params.loc_output+os.path.sep+'k_'+basename kernelIndex, extendedBasis, c, params = IO.read_kernel_table(ktable,params) coeffs = np.hstack((coeffs,c)) kindex_x = np.hstack((kindex_x,kernelIndex[:,0].T)) kindex_y = np.hstack((kindex_y,kernelIndex[:,1].T)) kindex_ext = np.hstack((kindex_ext,extendedBasis)) n_kernel[i] = kernelIndex.shape[0] n_coeffs[i] = c.shape[0] dates[i] = IO.get_date(params.loc_data+os.path.sep+basename,key=params.datekey) if dates[i] > 2450000: dates[i] -= 2450000 seeing[i], roundness[i], bgnd[i], signal[i] = IM.compute_fwhm(f,params,width=20,image_name=True) dfile = params.loc_output+os.path.sep+'d_'+basename nfile = params.loc_output+os.path.sep+'n_'+basename zfile = params.loc_output+os.path.sep+'sm_'+basename ivfile = params.loc_output+os.path.sep+'iv_'+basename diff, _ = IO.read_fits_file(dfile) mask, _ = IO.read_fits_file(zfile) iv, _ = IO.read_fits_file(ivfile) diff_sc = IM.undo_photometric_scale(diff,c,params.pdeg) #diff_sc = diff #diff_sc -= median_filter(diff_sc,footprint=filter_kernel) diff_sc *= mask d_image_stack[i,:,:] = diff_sc[patch_slice[2]:patch_slice[3],patch_slice[0]:patch_slice[1]] inv_var_image_stack[i,:,:], _ = IO.read_fits_file(ivfile,slice=patch_slice) #inv_var_image_stack[i,:,:] = (norm / d_image_stack[i,:,:])**2 #diff_std[i] = np.std(diff) diff_std[i] = np.std(d_image_stack[i,:,:][dmask]) d_image_stack[i,:,:] -= np.median(d_image_stack[i,:,:]) print 'kappa-clipping' qd = np.arange(len(filenames)) qd1 = np.where(np.isfinite(diff_std))[0] for iter in range(10): qd = np.where(diff_std[qd1]<np.mean(diff_std[qd1])+(4.0-1.5*(iter/9.0))*np.std(diff_std[qd1]))[0] qd1 = qd1[qd] print iter, np.mean(diff_std[qd1]), np.std(diff_std[qd1]), np.mean(diff_std[qd1])+(4.0-3*(iter/9.0))*np.std(diff_std[qd1]) print 'mean(diff) :',np.mean(diff_std[qd1]) print 'std(diff) :',np.std(diff_std[qd1]) print '1-sig threshold:', np.mean(diff_std[qd1])+1*np.std(diff_std[qd1]) print '2-sig threshold:', np.mean(diff_std[qd1])+2*np.std(diff_std[qd1]) print '3-sig threshold:', np.mean(diff_std[qd1])+3*np.std(diff_std[qd1]) print '1-sig diff reject:',np.where(diff_std>np.mean(diff_std[qd1])+1*np.std(diff_std[qd1])) print '2-sig diff reject:',np.where(diff_std>np.mean(diff_std[qd1])+2*np.std(diff_std[qd1])) print '3-sig diff reject:',np.where(diff_std>np.mean(diff_std[qd1])+3*np.std(diff_std[qd1])) threshold = np.mean(diff_std[qd1])+q_sigma_threshold*np.std(diff_std[qd1]) threshold2 = np.mean(diff_std[qd1])+2*np.std(diff_std[qd1]) threshold3 = np.mean(diff_std[qd1])+3*np.std(diff_std[qd1]) if locate_date_range is not None: diff_std_copy = diff_std.copy() diff_std = diff_std*0.0 + 100.0*threshold pp = np.where((dates>locate_date_range[0]) & (dates<locate_date_range[1]))[0] if pp.any(): print 'Using images ',pp diff_std[pp] = diff_std_copy[pp] else: print 'Error: No images found in date range',locate_date_range print 'Reverting to all dates.' diff_std = diff_std_copy print 'zeros:' for i in range(nfiles): print i, np.sum(np.abs(d_image_stack[i,:,:]) < 1.e-6) if np.isnan(inv_var_image_stack[i,:,:]).any() or np.sum(np.abs(d_image_stack[i,:,:]) < 1.e-6) > 5: diff_std[i] = 100.0*threshold inv_var_image_stack[i,:,:] = inv_var_image_stack[i,:,:]*0.0 if save_stamps: save_mosaic(d_image_stack,nfiles,patch_size,params.loc_output+os.path.sep+stamp_prefix+'.fits',diff_std,threshold) dsum = np.zeros((patch_size,patch_size),dtype=np.float64) for i in range(nfiles): if diff_std[i] < threshold3: dsum += d_image_stack[i,:,:] IO.write_image(dsum,params.loc_output+os.path.sep+'dsum%d.fits'%iteration) dr = patch_half_width-int(locate_half_width) print 'dr:', dr dsum[:dr-delta_patch_y,:] = 0.0 dsum[-dr-delta_patch_y:,:] = 0.0 dsum[:,:dr-delta_patch_x] = 0.0 dsum[:,-dr-delta_patch_x:] = 0.0 IO.write_image(dsum,params.loc_output+os.path.sep+'dsum_m%d.fits'%iteration) ind_dsum_max = np.unravel_index(dsum.argmax(),dsum.shape) print 'Iteration',iteration,': dsum maximum located at ',ind_dsum_max if locate and converge: y0 += ind_dsum_max[0] - patch_half_width + delta_patch_y x0 += ind_dsum_max[1] - patch_half_width + delta_patch_x # Read the PSF psf_image = params.loc_output+os.path.sep+'psf.fits' psf,psf_hdr = fits.getdata(psf_image,0,header='true') psf_height = psf_hdr['PSFHEIGH'] psf_sigma_x = psf_hdr['PAR1']*0.8493218 psf_sigma_y = psf_hdr['PAR2']*0.8493218 psf_x = psf_hdr['PSFX'] psf_y = psf_hdr['PSFY'] psf_size = psf.shape[1] psf_fit_rad = params.psf_fit_radius psf_parameters = np.array([psf_size,psf_height,psf_sigma_x,psf_sigma_y,psf_x, psf_y,psf_fit_rad,params.gain]).astype(np.float64) if params.psf_profile_type == 'gaussian': psf_sigma_x = psf_hdr['PAR1']*0.8493218 psf_sigma_y = psf_hdr['PAR2']*0.8493218 psf_parameters = np.array([psf_size,psf_height,psf_sigma_x,psf_sigma_y,psf_x, psf_y,psf_fit_rad,params.gain]).astype(np.float64) profile_type = 0 elif params.psf_profile_type == 'moffat25': print 'params.psf_profile_type moffat25 not working yet. Exiting.' sys.exit(0) psf_sigma_x = psf_hdr['PAR1'] psf_sigma_y = psf_hdr['PAR2'] psf_sigma_xy = psf_hdr['PAR3'] psf_parameters = np.array([psf_size,psf_height,psf_sigma_x,psf_sigma_y,psf_x, psf_y, psf_fit_rad,params.gain,psf_sigma_xy]).astype(np.float64) profile_type = 1 else: print 'params.psf_profile_type undefined' sys.exit(0) psf_0 = psf.astype(np.float64).copy() psf_xd = psf.astype(np.float64).copy()*0.0 psf_yd = psf.astype(np.float64).copy()*0.0 flux = np.zeros(nfiles,dtype=np.float64) dflux = np.zeros(nfiles,dtype=np.float64) x0_arr = np.atleast_1d(np.array([x0],dtype=np.float64)) y0_arr = np.atleast_1d(np.array([y0],dtype=np.float64)) print 'Converging photometry' print 'x0, y0:', x0, y0 print 'x_patch, y_patch:', x_patch, y_patch good_images = np.where(diff_std < threshold)[0] print 'using images', good_images print 'threshold', threshold for i, f in enumerate(filenames): if i in good_images: print i, 'd_'+f, diff_std[i] cu_photom_converge(profile_type, patch_half_width, params.pdeg, params.sdeg, nfiles, n_kernel, kindex_x, kindex_y, kindex_ext, n_coeffs, coeffs.astype(np.float64), psf_parameters, psf_0, psf_xd, psf_yd, np.float64(d_image_stack.ravel()), np.float64(inv_var_image_stack.ravel()), diff_std, np.float64(threshold), x0_arr, y0_arr, x_patch, y_patch, diff.shape[1], diff.shape[0], 16, 16, flux, dflux, np.float64(params.gain),np.int32(converge),np.float64(2.5)) if save_stamps: save_mosaic(d_image_stack,nfiles,patch_size,params.loc_output+os.path.sep+'p'+stamp_prefix+'.fits',diff_std,threshold) if locate_date_range is not None: diff_std = diff_std_copy return dates, seeing, roundness, bgnd, signal, flux, dflux, diff_std/threshold, x0_arr[0], y0_arr[0]
def photom_all_stars_simultaneous(diff,inv_variance,positions,psf_image,c,kernelIndex, extendedBasis,kernelRadius,params, star_group_boundaries, detector_mean_positions_x,detector_mean_positions_y): from astropy.io import fits # Read the PSF psf,psf_hdr = fits.getdata(psf_image,0,header='true') psf_height = psf_hdr['PSFHEIGH'] psf_x = psf_hdr['PSFX'] psf_y = psf_hdr['PSFY'] psf_size = psf.shape[1] psf_fit_rad = params.psf_fit_radius #psf_fit_rad = 3.1 if params.psf_profile_type == 'gaussian': psf_sigma_x = psf_hdr['PAR1']*0.8493218 psf_sigma_y = psf_hdr['PAR2']*0.8493218 psf_parameters = np.array([psf_size,psf_height,psf_sigma_x,psf_sigma_y,psf_x, psf_y,psf_fit_rad,params.gain]).astype(np.float64) print 'psf_parameters',psf_parameters profile_type = 0 elif params.psf_profile_type == 'moffat25': print 'params.psf_profile_type moffat25 not working yet. Exiting.' sys.exit(0) psf_sigma_x = psf_hdr['PAR1'] psf_sigma_y = psf_hdr['PAR2'] psf_sigma_xy = psf_hdr['PAR3'] psf_parameters = np.array([psf_size,psf_height,psf_sigma_x,psf_sigma_y,psf_x, psf_y, psf_fit_rad,params.gain,psf_sigma_xy]).astype(np.float64) print 'psf_parameters',psf_parameters profile_type = 1 else: print 'params.psf_profile_type undefined' sys.exit(0) k0 = kernelIndex[:,0].astype(np.int32).copy() k1 = kernelIndex[:,1].astype(np.int32).copy() if params.star_file_is_one_based: posx = np.float64(positions[:,0]-1.0) posy = np.float64(positions[:,1]-1.0) else: posx = np.float64(positions[:,0]-0.0) posy = np.float64(positions[:,1]-0.0) psf_0 = psf.astype(np.float64) psf_xd = np.zeros_like(psf_0,dtype=np.float64) psf_yd = np.zeros_like(psf_0,dtype=np.float64) nstars = positions.shape[0] flux = np.zeros(nstars+1,dtype=np.float64) dflux = np.zeros(nstars+1,dtype=np.float64) c64 = c.astype(np.float64).copy() print 'nstars', nstars print 'flux', flux.shape print 'dflux', dflux.shape i_index = ctypes.POINTER(ctypes.c_int)() j_index = ctypes.POINTER(ctypes.c_int)() value = ctypes.POINTER(ctypes.c_double)() n_entries = ctypes.c_int() rvec = np.zeros(nstars).astype(np.float64).copy() for iteration in range(1): cu_multi_photom(np.int(profile_type), diff.shape[1], diff.shape[0], params.pdeg, params.sdeg, c.shape[0], kernelIndex.shape[0], np.int(kernelRadius), k0, k1, extendedBasis, psf_parameters, psf_0, psf_xd, psf_yd, posx, posy, c64, long(nstars), 16, 16, np.float64(diff), np.float64(inv_variance),np.int32(star_group_boundaries), np.float64(detector_mean_positions_x), np.float64(detector_mean_positions_y),star_group_boundaries.shape[0],ctypes.byref(n_entries), ctypes.byref(i_index), ctypes.byref(j_index), ctypes.byref(value), rvec, flux[:nstars], iteration) n_e = np.int32(n_entries) buf_from_mem = ctypes.pythonapi.PyBuffer_FromMemory buf_from_mem.restype = ctypes.py_object buffer = buf_from_mem(i_index, n_e*np.dtype(np.int32).itemsize) i_ind = np.frombuffer(buffer, np.int32) buffer = buf_from_mem(j_index, n_e*np.dtype(np.int32).itemsize) j_ind = np.frombuffer(buffer, np.int32) buffer = buf_from_mem(value, n_e*np.dtype(np.float64).itemsize) val = np.frombuffer(buffer, np.float64) #for row in range(20): # print 'Row', row # q = np.where(i_ind == row) # print q # for qq in q[0]: # print j_ind[qq], val[qq] # print rvec[row] A = csc_matrix((val,(i_ind,j_ind)),shape=(nstars, nstars)) flux = np.float64(sp_linalg.spsolve(A, rvec)) dflux = np.sqrt(sp_linalg.spsolve(A, np.ones_like(rvec))) print 'flux =', flux print 'dflux =', dflux cdiff = np.float64(diff).copy() cu_make_residual(np.int(profile_type), diff.shape[1], diff.shape[0], params.pdeg, params.sdeg, c.shape[0], kernelIndex.shape[0], np.int(kernelRadius), k0, k1, extendedBasis, psf_parameters, psf_0, psf_xd, psf_yd, posx, posy, c64, flux, dflux, long(nstars), 16, 16, cdiff, np.float64(inv_variance),np.int32(star_group_boundaries), np.float64(detector_mean_positions_x), np.float64(detector_mean_positions_y),star_group_boundaries.shape[0]) IO.write_image(cdiff,params.loc_output+os.path.sep+'p_clean_ref.fits') return flux, dflux
def imsub_all_fits(params, reference='ref.fits'):
#
# Create the output directory if it doesn't exist
#
if not (os.path.exists(params.loc_output)):
os.mkdir(params.loc_output)
#
# The degree of spatial shape changes has to be at least as
# high as the degree of spatial photometric scale
#
if (params.sdeg < params.pdeg):
print 'Increasing params.sdeg to ', params.pdeg
params.sdeg = params.pdeg
#
# Print out the parameters for this run.
#
print 'Parameters:'
for par in dir(params):
print par, getattr(params, par)
print
#
# Determine our list of images
#
all_files = os.listdir(params.loc_data)
all_files.sort()
files = []
for f in all_files:
print 'file', f
if fnmatch.fnmatch(f, params.name_pattern):
g = DS.Observation(params.loc_data + os.path.sep + f, params)
del g.data
del g.mask
print 'fw', g.fw
if g.fw > 0.0:
files.append(g)
print g.name, 'accepted'
if len(files) < 3:
print 'Only', len(files), 'files found matching', params.name_pattern
print 'Exiting'
sys.exit(0)
#
# Have we specified a registration template?
#
if params.registration_image:
reg = DS.Observation(params.registration_image, params)
else:
reg = DS.EmptyBase()
reg.fw = 999.0
for f in files:
if (f.fw < reg.fw) and (f.fw > params.reference_min_seeing) and (
f.sky < params.registration_max_background):
reg = f
print 'Registration image:', reg.name
#
# Register images
#
print 'Registering images'
files_copy = [f for f in files]
for f in files:
print f.name
if f == reg:
f.image = f.data
rf = params.loc_output + os.path.sep + 'r_' + f.name
IO.write_image(f.image, rf)
else:
if not f.register(reg, params):
files_copy.remove(f)
# delete image arrays to save memory
del f.image
del f.mask
del f.inv_variance
del reg.data
del reg.image
del reg.mask
del reg.inv_variance
files = files_copy
#
# Write image names and dates to a file
#
if params.image_list_file:
try:
with open(params.loc_output + os.path.sep + params.image_list_file,
'w') as fid:
for f in files:
date = None
if params.datekey:
date = IO.get_date(
params.loc_data + os.path.sep + f.name,
key=params.datekey) - 2450000
if date:
fid.write(f.name + ' %10.5f\n' % date)
else:
fid.write(f.name)
except:
raise
#
# Make the photometric reference image if we don't have it.
# Find stamp positions if required.
#
if not (os.path.exists(params.loc_output + os.path.sep + reference)):
print 'Reg = ', reg.name
stamp_positions = make_reference(files,
reg,
params,
reference_image=reference)
ref = DS.Observation(params.loc_output + os.path.sep + reference,
params)
mask, _ = IO.read_fits_file(params.loc_output + os.path.sep + 'mask_' +
reference)
variance, _ = IO.read_fits_file(params.loc_output + os.path.sep +
'var_' + reference)
ref.mask = mask
ref.inv_variance = 1.0 / variance
ref.register(reg, params)
else:
ref = DS.Observation(params.loc_output + os.path.sep + reference,
params)
if os.path.exists(params.loc_output + os.path.sep + 'mask_' +
reference):
mask, _ = IO.read_fits_file(params.loc_output + os.path.sep +
'mask_' + reference)
else:
mask = np.ones_like(ref.data)
ref.mask = mask
ref.register(reg, params)
stamp_positions = None
if params.use_stamps:
stamp_file = params.loc_output + os.path.sep + 'stamp_positions'
if os.path.exists(stamp_file):
stamp_positions = np.genfromtxt(stamp_file)
else:
stars = PF.choose_stamps(ref, params)
stamp_positions = stars[:, 0:2]
np.savetxt(stamp_file, stamp_positions)
pm = params.pixel_max
params.pixel_max *= 0.9
ref.mask *= IM.compute_saturated_pixel_mask(ref.image, params)
params.pixel_max = pm
ref.blur = IM.boxcar_blur(ref.image)
if params.mask_cluster:
ref.mask *= IM.mask_cluster(ref.image, ref.mask, params)
#
# Detect stars and compute the PSF if we are doing photometry
#
star_positions = None
sky = 0.0
if params.do_photometry:
star_file = params.loc_output + os.path.sep + 'star_positions'
psf_file = params.loc_output + os.path.sep + 'psf.fits'
if not (os.path.exists(psf_file)) or not (os.path.exists(star_file)):
stars = PH.compute_psf_image(params, ref, psf_image=psf_file)
star_positions = stars[:, 0:2]
star_sky = stars[:, 4]
if os.path.exists(star_file):
star_positions = np.genfromtxt(star_file)
star_sky = star_positions[:, 0] * 0.0
else:
np.savetxt(star_file, star_positions)
print 'sky =', sky
#
# If we have pre-determined star positions
#
if params.star_file:
stars = np.genfromtxt(params.star_file)
star_positions = stars[:, 1:3]
if params.star_reference_image:
star_ref, h = IO.read_fits_file(params.star_reference_image)
offset, _, _ = register_translation(star_ref, ref.image, 1000)
dy, dx = offset
#dy, dx = IM.positional_shift(ref.image,star_ref)
print 'position shift =', dx, dy
star_positions[:, 0] -= dx
star_positions[:, 1] -= dy
np.savetxt(star_file, star_positions)
#
# If we are using a CPU, group the stars by location
#
print 'Group_check'
print 'params.do_photometry', params.do_photometry
print 'params.use_GPU', params.use_GPU
if params.do_photometry:
star_group_boundaries = None
detector_mean_positions_x = None
detector_mean_positions_y = None
star_unsort_index = None
star_sort_index,star_group_boundaries,detector_mean_positions_x,detector_mean_positions_y = \
PH.group_stars_ccd(params,star_positions,params.loc_output+os.path.sep+reference)
star_positions = star_positions[star_sort_index]
star_sky = star_sky[star_sort_index]
star_unsort_index = np.argsort(star_sort_index)
#
# Do photometry of the reference image
#
if params.do_photometry:
ref_flux_file = params.loc_output + os.path.sep + 'ref.flux'
if not (os.path.exists(ref_flux_file)):
result = difference_image(
ref,
ref,
params,
stamp_positions=stamp_positions,
psf_image=psf_file,
star_positions=star_positions,
star_group_boundaries=star_group_boundaries,
detector_mean_positions_x=detector_mean_positions_x,
detector_mean_positions_y=detector_mean_positions_y,
star_sky=star_sky)
if isinstance(result.flux, np.ndarray):
print 'ungrouping fluxes'
result.flux = result.flux[star_unsort_index].copy()
result.dflux = result.dflux[star_unsort_index].copy()
np.savetxt(ref_flux_file,
np.vstack((result.flux, result.dflux)).T)
#
# Process images
#
if params.make_difference_images:
if not (params.use_GPU) and (params.n_parallel > 1):
pool = Pool(params.n_parallel)
pool.map(
process_image_helper,
itertools.izip(
files,
itertools.repeat(
(ref, params, stamp_positions, star_positions,
star_group_boundaries, star_unsort_index,
detector_mean_positions_x,
detector_mean_positions_y))))
else:
for f in files:
process_image(
f, (ref, params, stamp_positions, star_positions,
star_group_boundaries, star_unsort_index,
detector_mean_positions_x, detector_mean_positions_y))
return files
def set_mask(self, value):
self._mask = value
mask_name = os.path.join(self.output_dir, 'sm_' + self.name)
IO.write_image(self._mask, mask_name)
def compute_psf_image(params,g,psf_deg=1,psf_rad=8,
star_file='phot.mags',psf_image='psf.fits',edge_dist=5):
iraf.digiphot()
iraf.daophot()
fp = params.loc_output+os.path.sep
f_im = g.image*g.mask
f = fp+'temp.ref.fits'
write_image(f_im,f)
g.fw = np.max([1.5,g.fw])
g.fw = np.min([0.5*params.psf_max_radius,g.fw])
logfile = fp+'psf.log'
fd = fits.getdata(f)
xmax = fd.shape[0] - edge_dist
ymax = fd.shape[1] - edge_dist
for d in ['temp.stars','temp.phot','temp.phot1','temp.phot2','temp.pst',
'temp.opst','temp.opst2',
'temp.psf.fits','temp.psf1.fits','temp.psf2.fits','temp.psg',
'temp.psg2','temp.psg3','temp.psg5','temp.rej','temp.rej2',
'temp.sub.fits','temp.sub1.fits',
'temp.sub2.fits','temp.opst1','temp.opst3','temp.rej3',
'temp.nst','temp.stars1','ref.mags',psf_image,'temp.als',
'temp.als2']:
if os.path.exists(fp+d):
os.remove(fp+d)
# locate stars
iraf.daofind(image=f,output=fp+'temp.stars',interactive='no',verify='no',
threshold=3,sigma=params.star_detect_sigma,fwhmpsf=g.fw,
datamin=1,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,
noise='poisson')
if params.star_file:
als_recenter = 'no'
all_template_stars = np.genfromtxt(params.star_file)
all_new_stars = np.genfromtxt(fp+'temp.stars')
if all_new_stars.shape[0] > params.star_file_number_match:
new_stars = all_new_stars[all_new_stars[:,2].argsort()][:params.star_file_number_match]
else:
new_stars = all_new_stars
if all_template_stars.shape[0] > params.star_file_number_match:
template_stars = all_template_stars[all_template_stars[:,3].argsort()][:params.star_file_number_match]
else:
template_stars = all_template_stars
tx, ty = compute_xy_shift(new_stars,template_stars[:,1:3],0.5,
degree=params.star_file_transform_degree)
if params.star_file_has_magnitudes:
star_positions = all_template_stars[:,1:4]
xx = (star_positions[:,0]-np.mean(new_stars[:,0]))/np.mean(new_stars[:,0])
yy = (star_positions[:,1]-np.mean(new_stars[:,1]))/np.mean(new_stars[:,1])
for m in range(params.star_file_transform_degree+1):
for n in range(params.star_file_transform_degree+1-m):
star_positions[:,0] += tx[m,n]* xx**m * yy**n
star_positions[:,1] += ty[m,n]* xx**m * yy**n
np.savetxt(fp+'temp.stars.1',star_positions,fmt='%10.3f %10.3f %10.3f')
else:
star_positions = all_template_stars[:,1:3]
xx = (star_positions[:,0]-np.mean(new_stars[:,0]))/np.mean(new_stars[:,0])
yy = (star_positions[:,1]-np.mean(new_stars[:,1]))/np.mean(new_stars[:,1])
for m in range(params.star_file_transform_degree+1):
for n in range(params.star_file_transform_degree+1-m):
star_positions[:,0] += tx[m,n]* xx**m * yy**n
star_positions[:,1] += ty[m,n]* xx**m * yy**n
np.savetxt(fp+'temp.stars.1',star_positions,fmt='%10.3f %10.3f')
all_template_stars[:,1] = star_positions[:,0]
all_template_stars[:,2] = star_positions[:,1]
else:
als_recenter = 'yes'
star_positions = np.genfromtxt(fp+'temp.stars')
np.savetxt(fp+'temp.stars.1',star_positions[:,:2],fmt='%10.3f %10.3f')
iraf.phot(image=f,output=fp+'temp.phot',coords=fp+'temp.stars.1',interactive='no',
verify='no',
sigma=params.star_detect_sigma,fwhmpsf=g.fw,apertures=g.fw,
datamin=1,
datamax=2*params.pixel_max,epadu=params.gain,annulus=3*g.fw,
dannulus=3.0,
readnoise=params.readnoise,noise='poisson')
print 'fw = ',g.fw
#fw = np.max([4.0,fw])
#print 'fw = ',fw
# select PSF stars
iraf.pstselect(image=f,photfile=fp+'temp.phot',pstfile=fp+'temp.pst',maxnpsf=40,
interactive='no',verify='no',datamin=1,fitrad=2.0,
datamax=params.pixel_max,epadu=params.gain,psfrad=np.max([3.0,g.fw]),
readnoise=params.readnoise,noise='poisson')
if params.star_file and params.star_file_has_magnitudes:
# We don't need to do the photometry - only make the PSF
# Initial PSF estimate to generate PSF groups
#psfrad=3*np.max([g.fw,1.8])
iraf.psf(image=f,photfile=fp+'temp.phot',pstfile=fp+'temp.pst',psfimage=fp+'temp.psf',
function=params.psf_profile_type,opstfile=fp+'temp.opst',
groupfile=fp+'temp.psg',
interactive='no',
verify='no',varorder=0 ,psfrad=2*np.max([g.fw,1.8]),
datamin=-10000,datamax=0.95*params.pixel_max,
scale=1.0)
# construct a file of the psf neighbour stars
slist = []
psf_stars = np.loadtxt(fp+'temp.opst',usecols=(0,1,2))
for star in range(psf_stars.shape[0]):
xp = psf_stars[star,1]
yp = psf_stars[star,2]
xmin = np.max([np.int(xp-10*g.fw),0])
xmax = np.min([np.int(xp+10*g.fw),f_im.shape[0]])
ymin = np.max([np.int(yp-10*g.fw),0])
ymax = np.min([np.int(yp+10*g.fw),f_im.shape[1]])
p = star_positions[np.logical_and(np.logical_and(star_positions[:,0]>xmin,
star_positions[:,0]<xmax),
np.logical_and(star_positions[:,1]>ymin,
star_positions[:,1]<ymax))]
slist.append(p)
group_stars = np.concatenate(slist)
np.savetxt(fp+'temp.nst',group_stars,fmt='%10.3f %10.3f %10.3f')
# subtract PSF star neighbours
iraf.substar(image=f,photfile=fp+'temp.nst',psfimage=fp+'temp.psf',
exfile=fp+'temp.opst',fitrad=2.0,
subimage=fp+'temp.sub1',verify='no',datamin=1,
datamax=params.pixel_max,epadu=params.gain,
readnoise=params.readnoise,noise='poisson')
# final PSF
iraf.psf(image=fp+'temp.sub1',photfile=fp+'temp.phot',pstfile=fp+'temp.opst',
psfimage=psf_image,psfrad=2*g.fw,
function=params.psf_profile_type,opstfile=fp+'temp.opst2',
groupfile=fp+'temp.psg2',
interactive='no',
verify='no',varorder=0,
datamin=1,datamax=0.95*params.pixel_max,
scale=1.0)
np.savetxt(fp+'ref.mags',all_template_stars,fmt='%7d %10.3f %10.3f %10.3f')
stars = all_template_stars
else:
# initial PSF estimate
iraf.psf(image=f,photfile=fp+'temp.phot',pstfile=fp+'temp.pst',psfimage=fp+'temp.psf',
function=params.psf_profile_type,opstfile=fp+'temp.opst',
groupfile=fp+'temp.psg1',
interactive='no',
verify='no',varorder=0 ,psfrad=2*g.fw,
datamin=1,datamax=0.95*params.pixel_max,
scale=1.0)
# separation distance of near neighbours
separation = np.max([rewrite_psg(fp+'temp.psg1',fp+'temp.psg2'),3])
print 'separation = ',separation
# subtract all stars using truncated PSF
iraf.allstar(image=f,photfile=fp+'temp.phot',psfimage=fp+'temp.psf',
allstarfile=fp+'temp.als',rejfile='',
subimage=fp+'temp.sub',verify='no',psfrad=2*g.fw,fitrad=2.0,
recenter='yes',groupsky='yes',fitsky='yes',sannulus=7,wsannulus=10,
datamin=1,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,
noise='poisson')
if params.star_file:
os.system('cp '+fp+'temp.phot '+fp+'temp.phot2')
else:
# locate new stars
iraf.daofind(image=fp+'temp.sub',output=fp+'temp.stars1',interactive='no',verify='no',
threshold=3,sigma=params.star_detect_sigma,fwhmpsf=2*g.fw,
datamin=1,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,
noise='poisson')
# magnitudes for new stars
iraf.phot(image=fp+'temp.sub',output=fp+'temp.phot1',coords=fp+'temp.stars1',
interactive='no',
verify='no',sigma=params.star_detect_sigma,
fwhmpsf=g.fw,datamin=1,
datamax=params.pixel_max,epadu=params.gain,
readnoise=params.readnoise,noise='poisson')
# join star lists together
iraf.pconcat(infiles=fp+'temp.phot,'+fp+'temp.phot1',outfile=fp+'temp.phot2')
# new PSF estimate to generate PSF groups
iraf.psf(image=f,photfile=fp+'temp.phot2',pstfile=fp+'temp.pst',psfimage=fp+'temp.psf2',
function=params.psf_profile_type,opstfile=fp+'temp.opst2',
groupfile=fp+'temp.psg3',
interactive='no',
verify='no',varorder=0 ,psfrad=2*g.fw,
datamin=-10000,datamax=0.95*params.pixel_max,
scale=1.0)
# magnitudes for PSF group stars
iraf.nstar(image=f,groupfile=fp+'temp.psg3',psfimage=fp+'temp.psf2',
nstarfile=fp+'temp.nst',
rejfile='',verify='no',psfrad=2*g.fw,fitrad=2.0,
recenter='no',
groupsky='yes',fitsky='yes',sannulus=7,wsannulus=10,
datamin=1,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,noise='poisson')
# subtract PSF star neighbours
iraf.substar(image=f,photfile=fp+'temp.nst',psfimage=fp+'temp.psf2',
exfile=fp+'temp.opst2',fitrad=2.0,
subimage=fp+'temp.sub1',verify='no',datamin=1,
datamax=params.pixel_max,epadu=params.gain,
readnoise=params.readnoise,noise='poisson')
# final PSF
iraf.psf(image=fp+'temp.sub1',photfile=fp+'temp.phot2',
pstfile=fp+'temp.opst2',
psfimage=psf_image,psfrad=2*g.fw,
function=params.psf_profile_type,opstfile=fp+'temp.opst3',
groupfile=fp+'temp.psg5',
interactive='no',
verify='no',varorder=0,
datamin=1,datamax=0.95*params.pixel_max,
scale=1.0)
# final photometry
iraf.allstar(image=g.fullname,photfile=fp+'temp.phot2',psfimage=psf_image,
allstarfile=fp+'temp.als2',rejfile='',
subimage=fp+'temp.sub2',verify='no',psfrad=2*g.fw,
recenter=als_recenter,groupsky='yes',fitsky='yes',sannulus=7,
wsannulus=10,fitrad=2.0,
datamin=params.pixel_min,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,
noise='poisson')
psfmag = 10.0
for line in open(fp+'temp.als2','r'):
sline = line.split()
if sline[1] == 'PSFMAG':
psfmag = float(sline[3])
break
if params.star_file:
iraf.psort(infiles=fp+'temp.als2',field='ID')
os.system('cp '+fp+'temp.als2 '+fp+'temp.als3')
else:
selection = 'XCE >= '+str(edge_dist)+' && XCE <= '+str(xmax)+' && YCE >= '+str(edge_dist)+' && YCE <= '+str(ymax)+' && MAG != INDEF'
iraf.pselect(infiles=fp+'temp.als2',outfiles=fp+'temp.als3',expr=selection)
iraf.psort(infiles=fp+'temp.als3',field='MAG')
iraf.prenumber(infile=fp+'temp.als3')
s = iraf.pdump(infiles=fp+'temp.als3',Stdout=1,
fields='ID,XCENTER,YCENTER,MAG,MERR,MSKY,SHARPNESS,CHI',expr='yes')
sf = [k.replace('INDEF','22.00') for k in s]
stars = np.zeros([len(sf),5])
for i, line in enumerate(sf):
stars[i,:] = np.array(map(float,sf[i].split()[1:6]))
s = iraf.pdump(infiles=fp+'temp.als3',Stdout=1,
fields='ID,XCENTER,YCENTER,MAG,MERR,SHARPNESS,CHI,MSKY',expr='yes')
sf = [k.replace('INDEF','22.00') for k in s]
with open(fp+'ref.mags','w') as fid:
for s in sf:
fid.write(s+'\n')
return stars
def set_inv_variance(self, value):
self._inv_variance = value
inv_variance_name = os.path.join(self.output_dir, 'iv_' + self.name)
IO.write_image(self._inv_variance, inv_variance_name)
