def strehlframe(image, primary, secondary, dimension, f_number, pixel_scale,
lambda_mean, growth_step, find_source, xcenter, ycenter, fwhmpsf,
threshold, quiet):
start_time = time.time()
info("Started at:", start_time)
if not os.path.exists(image):
raise RuntimeError("No file named {0}".format(image))
# Were we given coordinates, or do we need to find the source?
if find_source:
bright = daofind_brightest(image, fwhmpsf, threshold)
center_col, center_row = bright['XCENTER'], bright['YCENTER']
else:
center_col, center_row = xcenter, ycenter
scale_to_physical, plate_scale_px, min_radius_real = compute_psf_scale(
dimension,
primary,
secondary,
f_number,
lambda_mean,
pixel_scale
)
scaled_psf, scaled_psf_ctr, max_aperture_radius = generate_scaled_psf(
dimension,
primary,
secondary,
scale_to_physical
)
# wrap psf in a frame
psf = Frame(scaled_psf, scaled_psf_ctr)
# precompute CoG and profile to be rescaled later
curve_of_growth(psf, max_aperture_radius, step=growth_step, quiet=quiet)
profile_from_growthcurve(psf)
# values and functions to rescale our PSF Frame computed values
# to physical counts
max_extent_px = 2.5 / plate_scale_px # After 2.5" we're almost certainly measuring noise
debug("after 2.5'' or", max_extent_px, "px we're almost certainly measuring noise")
def max_flux(frame):
"""Frame max integrated flux (for a radius less than 2.5'')"""
return np.max(frame.fluxes[frame.radii <= max_extent_px])
def scale_psf_fluxes(frame, psf):
"""
Returns a profile and curve of growth values for the ideal PSF
scaled such that the total integrated flux is equivalent to the
maximum flux in the frame passed as the first argument.
"""
scale_factor = (max_flux(frame) / max_flux(psf))
return psf.profile * scale_factor, psf.fluxes * scale_factor
image_base = os.path.splitext(os.path.basename(image))[0]
frame = Frame(pyfits.getdata(image), (float(center_col), float(center_row)))
debug("loaded frame from", image)
# subtract median row to handle light/charge leakage biasing measurements
exclude_from, exclude_to = frame.ybounds(r=int(max_extent_px)) # exclude region of max_extent_px around center of frame
avgrow_median_subtract(frame, exclude_from, exclude_to)
debug("median subtracted frame")
curve_of_growth(frame, max_aperture_radius, step=growth_step, quiet=quiet)
debug("curve of growth generated")
profile_from_growthcurve(frame)
debug("profile generated")
# scale psf.fluxes and psf.profile to a max value determined from frame
ideal_profile, ideal_fluxes = scale_psf_fluxes(frame, psf)
write_table("{0}_strehl.dat".format(image_base), (
("Pixel Radius", frame.radii),
("Enclosed Pixels", frame.npix),
("Image Enclosed Energy (counts)", frame.fluxes),
("Ideal Enclosed Energy (counts)", ideal_fluxes),
("Strehl Ratio (for peak in this radius)", frame.fluxes / ideal_fluxes),
("Image Radial Profile (counts at radius)", frame.profile),
("Ideal Radial Profile (counts at radius)", ideal_profile)
))
# Plot Curve of Growth with twinned axis in arcseconds
plot_with_arcseconds(
image_base + "_growth.pdf",
psf.radii,
frame.fluxes,
ideal_fluxes,
min_radius_real,
max_extent_px,
plate_scale_px,
ylabel="Enclosed Flux at Radius"
)
# fig, host = plt.subplots()
#
# plt.plot(frame.radii, frame.fluxes, 'r', label="Science Image")
# plt.plot(psf.radii, ideal_fluxes, 'g', label="Ideal PSF")
# plt.axvspan(0, min_radius_real, facecolor='g', alpha=0.25)
#
# plt.ylabel("Enclosed Flux at Radius")
# plt.xlabel("Radius (pixels from center)")
#
# plt.xlim(1, max_extent_px)
# plt.ylim(0, np.max(ideal_fluxes))
# xfrom, xto = fig.axes[0].get_xlim()
# par1 = host.twiny()
# par1.axes.set_xlabel("Radius (arcseconds from center)")
# par1.set_xlim((xfrom * plate_scale_px, xto * plate_scale_px))
# par1.grid()
# host.legend(loc=4)
#
# plt.savefig('{0}_growth.pdf'.format(image_base))
# debug("saved plot to", '{0}_growth.pdf'.format(image_base))
#
# Plot profile with twinned axis in arcseconds
plot_with_arcseconds(
image_base + "_profile.pdf",
psf.radii,
frame.profile,
ideal_profile,
min_radius_real,
10, # xlim max
plate_scale_px,
ylabel="Flux at Radius",
marker="."
)
# fig, host = plt.subplots()
#
# plt.plot(frame.radii, frame.profile, c='r', marker=".", label="Science Image")
# plt.plot(psf.radii, ideal_profile, c='g', marker='.', label="Ideal PSF")
# plt.axvspan(0, min_radius_real, facecolor='g', alpha=0.25)
#
# plt.ylabel("Flux at Radius")
# plt.xlabel("Radius (pixels from center)")
#
# plt.xlim(1, 10)
# plt.ylim(0, np.max(ideal_profile))
# xfrom, xto = fig.axes[0].get_xlim()
# par1 = host.twiny()
# par1.axes.set_xlabel("Radius (arcseconds from center)")
# par1.set_xlim((xfrom * plate_scale_px, xto * plate_scale_px))
# par1.grid()
# host.legend(loc=4)
#
# plt.savefig('{0}_profile.pdf'.format(image_base))
# debug("saved plot to", '{0}_profile.pdf'.format(image_base))
info("Completed at:", time.time())
info("Total time:", time.time() - start_time)
def photstrehl(cubefile, rangespec, primary, secondary, dimension, f_number,
pixel_scale, lambda_mean, growth_step, normalize_at, find_source, xcenter, ycenter,
fwhmpsf, threshold, quiet):
start_time = time.time()
info("Started at:", start_time)
if not os.path.exists(cubefile):
raise RuntimeError("No file named {0}".format(cubefile))
cubefile_base = os.path.splitext(os.path.basename(cubefile))[0]
# I: compute ideal psf
scale_to_physical, plate_scale_px, min_radius_real = compute_psf_scale(
dimension,
primary,
secondary,
f_number,
lambda_mean,
pixel_scale
)
info("The radius of the first minimum in physical pixels is", min_radius_real, "px")
scaled_psf, scaled_psf_ctr, max_aperture_radius = generate_scaled_psf(
dimension,
primary,
secondary,
scale_to_physical
)
# wrap psf in a frame
psf = Frame(scaled_psf, scaled_psf_ctr)
if normalize_at != 0:
max_extent_px = normalize_at
debug("Rescaling to max integrated flux @ r=", max_extent_px, "pixels")
else:
max_extent_px = 2.5 / plate_scale_px # After 2.5" we're almost certainly measuring noise
debug("after 2.5'' or", max_extent_px, "px we'll be almost certainly measuring noise")
growth_max = max_extent_px + growth_step * 3 # do 3 steps beyond the 2.5" mark
assert growth_max < max_aperture_radius, "Curve of Growth won't fit on PSF frame with this max extent"
# precompute CoG and profile to be rescaled later
# phot CoG needs a FITS file, so write one:
psftmpfilename = os.path.abspath('./{0}.fits'.format(uuid.uuid1()))
hdu = pyfits.PrimaryHDU(psf.data)
hdu.writeto(psftmpfilename)
debug("psf FITS file temporarily stored in", psftmpfilename)
phot_curve_of_growth(psf, psftmpfilename, growth_max, step=growth_step, quiet=quiet, fitsky=False)
profile_from_growthcurve(psf)
# II: analyze images
# functions to rescale our PSF Frame computed values
# to physical counts
def max_flux(frame):
"""Frame max integrated flux (for a radius less than 2.5'')"""
return np.max(frame.fluxes[frame.radii <= max_extent_px])
def scale_psf_fluxes(frame, psf):
"""
Returns a profile and curve of growth values for the ideal PSF
scaled such that the total integrated flux is equivalent to the
maximum flux in the frame passed as the first argument.
"""
scale_factor = (max_flux(frame) / max_flux(psf))
return psf.profile * scale_factor, psf.fluxes * scale_factor
tmp_target_dir = tempfile.mkdtemp()
ranges = parse_ranges(rangespec)
debug("splitting ranges", ranges)
fits_frames = split_frames(cubefile, ranges, tmp_target_dir)
debug("working in", tmp_target_dir, "with frames", fits_frames)
# set up array to hold each frame's analysis data
radii_count = psf.radii.shape[0]
frame_count = len(fits_frames)
shape = (frame_count, 5, radii_count)
analysis_frames = np.zeros(shape)
# [cog x count, prof x count, ideal x count, idealprof x count, strehl x count] x frames
strehl_rows = []
for fits_frame in fits_frames:
# this is slightly dumb... parse the frame # out of the filename
frame_num = int(re.findall(r'\d+', os.path.basename(fits_frame))[0])
if find_source:
bright = daofind_brightest(fits_frame, fwhmpsf, threshold)
center_col, center_row = bright['XCENTER'], bright['YCENTER']
debug("frame #", frame_num, "has brightest at", center_col, center_row)
center_coords = (float(center_col), float(center_row))
frame = Frame(pyfits.getdata(fits_frame), center_coords)
else:
center_coords = (float(xcenter), float(ycenter))
frame = Frame(pyfits.getdata(fits_frame), center_coords)
debug("loaded frame from", fits_frame)
# subtract median row to handle light/charge leakage biasing measurements
exclude_from, exclude_to = frame.ybounds(r=int(max_extent_px)) # exclude region of max_extent_px around center of frame
avgrow_median_subtract(frame, exclude_from, exclude_to)
debug("median subtracted frame")
phot_curve_of_growth(frame, fits_frame, growth_max, step=growth_step, quiet=quiet, fitsky=True)
debug("curve of growth generated")
profile_from_growthcurve(frame)
debug("profile generated")
# scale psf.fluxes and psf.profile to a max value determined from frame
ideal_profile, ideal_fluxes = scale_psf_fluxes(frame, psf)
strehls_for_all_radii = frame.fluxes / ideal_fluxes
strehl_rows.append((frame_num, center_coords, strehls_for_all_radii))
outfile = "{0}_{1}_strehlseries.txt".format(cubefile_base, rangespec)
debug("writing strehl series to", outfile)
with open(outfile, 'w') as f:
f.write("# columns 2 and up are the pixel radii at which we computed the Strehl ratio\n")
f.write("# frameidx\txcenter\tycenter\t")
f.write('\t'.join(map(str, psf.radii)))
f.write('\n')
for idx, center, ratios in strehl_rows:
f.write(str(idx))
f.write('\t')
f.write('\t'.join(map(str, center)))
f.write('\t')
f.write('\t'.join(map(str, ratios)))
f.write('\n')
debug("removing exploded cube from", tmp_target_dir)
shutil.rmtree(tmp_target_dir)
info("Completed at:", time.time())
info("Total time:", time.time() - start_time)
def photstrehlframe(image, primary, secondary, dimension, f_number, pixel_scale,
lambda_mean, growth_step, normalize_at, find_source, xcenter, ycenter, fwhmpsf,
threshold, quiet):
start_time = time.time()
info("Started at:", start_time)
if not os.path.exists(image):
raise RuntimeError("No file named {0}".format(image))
# Were we given coordinates, or do we need to find the source?
if find_source:
bright = daofind_brightest(image, fwhmpsf, threshold)
center_col, center_row = bright['XCENTER'], bright['YCENTER']
else:
center_col, center_row = xcenter, ycenter
scale_to_physical, plate_scale_px, min_radius_real = compute_psf_scale(
dimension,
primary,
secondary,
f_number,
lambda_mean,
pixel_scale
)
info("The radius of the first minimum in physical pixels is", min_radius_real, "px")
scaled_psf, scaled_psf_ctr, max_aperture_radius = generate_scaled_psf(
dimension,
primary,
secondary,
scale_to_physical
)
# wrap psf in a frame
psf = Frame(scaled_psf, scaled_psf_ctr)
if normalize_at != 0:
max_extent_px = normalize_at
debug("Rescaling to max integrated flux @ r=", max_extent_px, "pixels")
else:
max_extent_px = 2.5 / plate_scale_px # After 2.5" we're almost certainly measuring noise
debug("after 2.5'' or", max_extent_px, "px we'll be almost certainly measuring noise")
growth_max = max_extent_px + growth_step * 3 # do 3 steps beyond the 2.5" mark
assert growth_max < max_aperture_radius, "Curve of Growth won't fit on PSF frame with this max extent"
# phot CoG needs a FITS file, so write one:
psftmpfilename = os.path.abspath('./{0}.fits'.format(uuid.uuid1()))
hdu = pyfits.PrimaryHDU(psf.data)
hdu.writeto(psftmpfilename)
debug("psf FITS file temporarily stored in", psftmpfilename)
# precompute CoG and profile to be rescaled later
phot_curve_of_growth(psf, psftmpfilename, growth_max, step=growth_step, quiet=quiet, fitsky=False)
profile_from_growthcurve(psf)
# values and functions to rescale our PSF Frame computed values
# to physical counts
def max_flux(frame):
"""Frame max integrated flux (for a radius less than 2.5'')"""
return np.max(frame.fluxes[frame.radii <= max_extent_px])
def scale_psf_fluxes(frame, psf):
"""
Returns a profile and curve of growth values for the ideal PSF
scaled such that the total integrated flux is equivalent to the
maximum flux in the frame passed as the first argument.
"""
scale_factor = (max_flux(frame) / max_flux(psf))
return psf.profile * scale_factor, psf.fluxes * scale_factor
image_base = os.path.splitext(os.path.basename(image))[0]
frame = Frame(pyfits.getdata(image), (float(center_col), float(center_row)))
debug("loaded frame from", image)
# subtract median row to handle light/charge leakage biasing measurements
exclude_from, exclude_to = frame.ybounds(r=int(max_extent_px)) # exclude region of max_extent_px around center of frame
avgrow_median_subtract(frame, exclude_from, exclude_to)
debug("median subtracted frame")
phot_curve_of_growth(frame, image, growth_max, step=growth_step, quiet=quiet, fitsky=True)
debug("curve of growth generated")
profile_from_growthcurve(frame)
debug("profile generated")
# scale psf.fluxes and psf.profile to a max value determined from frame
ideal_profile, ideal_fluxes = scale_psf_fluxes(frame, psf)
write_table("{0}_strehl.dat".format(image_base), (
("Pixel Radius", frame.radii),
("Enclosed Pixels", frame.npix),
("Image Enclosed Energy (counts)", frame.fluxes),
("Ideal Enclosed Energy (counts)", ideal_fluxes),
("Strehl Ratio (for peak in this radius)", frame.fluxes / ideal_fluxes),
("Image Radial Profile (counts at radius)", frame.profile),
("Ideal Radial Profile (counts at radius)", ideal_profile)
))
# Plot Curve of Growth with twinned axis in arcseconds
plot_with_arcseconds(
image_base + "_growth.pdf",
psf.radii,
frame.fluxes,
ideal_fluxes,
min_radius_real,
max_extent_px,
plate_scale_px,
ylabel="Enclosed Flux at Radius"
)
# Plot profile with twinned axis in arcseconds
plot_with_arcseconds(
image_base + "_profile.pdf",
psf.radii,
frame.profile,
ideal_profile,
min_radius_real,
10, # xlim max
plate_scale_px,
ylabel="Flux at Radius",
marker="."
)
info("Completed at:", time.time())
info("Total time:", time.time() - start_time)