def run_scipt():
'''Run the script'''
print 'Running Check Residual Script...'
# Read data files.
data_rec = np.load(opts.rec_data)
data_noisy = np.load(opts.noise_data)
psf = np.load(opts.psf)
# Convolve PSF with reconstruction.
data_conv = convolve(data_rec, psf, psf_type=opts.psf_type,
data_format=opts.data_format)
# Convert cube data to map.
if opts.data_format == 'cube':
if isinstance(opts.layout, type(None)):
opts.layout = tuple(mfactor(data_noisy.shape[0]))
data_rec = cube2map(data_rec, opts.layout)
data_noisy = cube2map(data_noisy, opts.layout)
data_conv = cube2map(data_conv, opts.layout)
# Calculate the residual.
residual = (data_noisy - data_conv)
# Return all data.
return (data_noisy, data_rec, data_conv, residual)
def do_stuff():
print "1- Reading full clean image data cube from file."
# Read data cube binary and store first N objects.
data_cube = np.load(path + data_file)[: opts.n_obj]
# Save the sampled data cube sample to a binary file.
if opts.save_cube:
np.save(path + "deep_galaxy_cube_" + str(opts.n_obj) + ".npy", data_cube)
print "2- Constructing data map from cube sample."
# Find the most appropriate map layout for N objects.
layout = mfactor(data_cube.shape[0])
# Transform the data cube into a map.
data_map = transform.cube2map(data_cube, layout)
# Save the data map to a binary file.
if opts.save_map:
np.save(path + "deep_galaxy_map_" + str(opts.n_obj) + ".npy", data_map)
if opts.no_psf_gen:
print "3- Constructing pixel variant PSF from map."
# Generate the pixel variant PSF stack.
psf = psf_gen.pixel_var_psf(data_map.shape, opts.variance)
# Reshape the PSF stack to data cube format and save it to binary file.
# Notes: The default stack is the number of map pixels, followed by the
# PSF shape. The data cube format requires that the default stack be
# the number of galaxies, followed by the number of pixels per galaxy
# image and finally the PSF shape (hence the strange indexing below).
if not opts.full_map_psf:
index = np.arange(psf.shape[0]).reshape(data_map.shape)
index = transform.map2cube(index, layout=layout).reshape(index.size)
psf = psf[index].reshape([data_cube.shape[0]] + [np.prod(data_cube.shape[1:])] + list(psf.shape[-2:]))
np.save(path + "deep_galaxy_psf_cube_" + str(opts.n_obj) + ".npy", psf)
# Just save the PSF in map format to a binary file.
else:
np.save(path + "deep_galaxy_psf_map_" + str(opts.n_obj) + ".npy", psf)
def get_noise_est():
print '1- Estimating noise from PSF.'
if opts.full_map_psf:
form_tag = 'map_'
else:
form_tag = 'cube_'
if opts.psf_type == 'fixed':
psf_tag = 'fix'
psf = np.load(path + opts.psf + '.npy')
psf = psf_pcs.reshape([1] + list(psf_pcs))
elif opts.psf_type == 'variant':
psf_tag = 'var'
psf_pcs = np.load(path + 'psf_pcs_' + form_tag + str(opts.n_obj) +
'.npy')
psf_coef = np.load(path + 'psf_coef_' + form_tag + str(opts.n_obj) +
'.npy')
if not opts.full_map_psf:
psf_coef = np.transpose(psf_coef, axes=[1, 0, 2, 3])
psf_coef = psf_coef.reshape([psf_coef.shape[0]] +
list(mfactor(opts.n_obj) *
np.array(psf_coef.shape[2:])))
kernel_shape = np.array(psf_pcs[0].shape)
coef_shape = np.array(psf_coef.shape[-2:])
print coef_shape
vec_length = np.prod(kernel_shape)
pcst = [rot_and_roll(x.T) for x in psf_pcs]
pcs = [rot_and_roll(x) for x in psf_pcs]
mask = gen_mask(kernel_shape, coef_shape)
k_pat = kernel_pattern(kernel_shape, mask)
k_rolls = roll_sequence(kernel_shape)
m_rolls = roll_sequence(mask.shape)
res = []
i = 0
val = 0
widgets = ['Test: ', Percentage(), ' ', Bar(marker=RotatingMarker()),
' ', ETA(), ' ', FileTransferSpeed()]
pbar = ProgressBar(widgets=widgets, maxval=10000000).start()
for i in range(np.prod(coef_shape)):
for k1 in range(psf_pcs.shape[0]):
for k2 in range(psf_pcs.shape[0]):
pkt = roll_2d(pcst[k1],
roll_rad=k_rolls[k_pat[i]]).reshape(vec_length)
pk = roll_2d(pcs[k2],
roll_rad=k_rolls[k_pat[i]]).reshape(vec_length)
mi = roll_2d(mask, roll_rad=m_rolls[i])
dk1 = psf_coef[k1][mi]
dk2 = psf_coef[k2][mi]
val += sum(pkt * dk1 * dk2 * pk)
res.append(val)
pbar.update(10*i+1)
pbar.finish()
res = opts.sigma ** 2 * np.array(res).reshape(coef_shape)
if not opts.full_map_psf:
res = transform.map2cube(res, mfactor(opts.n_obj))
np.save(path + 'psf_noise_est_' + form_tag + str(opts.n_obj)+ '_' +
psf_tag + '.npy', res)
def deconvolve():
print '1- Performing deconvolution.'
print ' - with mode:', opts.mode
psf = None
psf_pcs = None
psf_coef = None
if opts.full_map_psf:
form_tag = 'map_'
else:
form_tag = 'cube_'
# Read in fixed PSF file.
if not isinstance(opts.psf, type(None)):
psf_tag = 'fix'
psf = np.load(path + opts.psf + '.npy')
noise_est = opts.sigma
# Read in PSF principal components and coefficients, and noise estiamte.
else:
psf_tag = 'var'
psf_pcs = np.load(path + 'psf_pcs_' + form_tag + str(opts.n_obj) +
'.npy')
psf_coef = np.load(path + 'psf_coef_' + form_tag + str(opts.n_obj) +
'.npy')
noise_est = np.load(path + 'psf_noise_est_' + form_tag +
str(opts.n_obj) + '_' + psf_tag + '.npy')
# Read in noisy data file.
data_noisy = np.load(path + 'deep_galaxy_noise_' + form_tag +
str(opts.n_obj) + '_' + psf_tag + '.npy')
# Set mr_transform wavelet type option.
wavelet_opt = '-t ' + opts.wavelet_type
# Perform reconstruction.
layout = mfactor(opts.n_obj)
# if opts.full_map_psf:
# data_rec = reconstruct4.reconstruct_map(data_noisy, noise_est, layout,
# psf, psf_pcs, psf_coef,
# opts.wavelet_levels,
# wavelet_opt,
# opts.wave_thresh_factor,
# opts.lowr_thresh_factor,
# opts.n_reweights, opts.mode)
if opts.full_map_psf:
data_format = 'map'
else:
data_format = 'cube'
primal_rec, dual_rec = reconstruct4.reconstruct(data_noisy, noise_est,
layout, psf, psf_pcs,
psf_coef,
opts.wavelet_levels,
wavelet_opt,
opts.wave_thresh_factor,
opts.lowr_thresh_factor,
opts.n_reweights,
opts.mode, opts.no_pos,
data_format)
# Save results to a binary file.
if isinstance(opts.output, type(None)):
np.save(path + 'deep_galaxy_rec_' + form_tag + str(opts.n_obj) + '_' +
psf_tag + '_' + opts.mode + '.npy', primal_rec)
np.save(path + 'deep_galaxy_dual_' + form_tag + str(opts.n_obj) + '_' +
psf_tag + '_' + opts.mode + '.npy', dual_rec)
else:
np.save(path + opts.output + '_primal', primal_rec)
np.save(path + opts.output + '_dual', dual_rec)
if opts.full_map_psf:
return (data_noisy, primal_rec)
else:
return (transform.cube2map(data_noisy, layout),
transform.cube2map(primal_rec, layout))