def test_jacobian_missing_kwargs(kind):
dudcol = 0.25
dudrow = 0.1
dvdcol = -0.4
dvdrow = 0.34
col = 5.6
row = -10.4
if kind == 'row-col':
kwargs = dict(col=col,
row=row,
dudcol=dudcol,
dudrow=dudrow,
dvdcol=dvdcol,
dvdrow=dvdrow)
elif kind == 'x-y':
kwargs = dict(x=col,
y=row,
dudx=dudcol,
dudy=dudrow,
dvdx=dvdcol,
dvdy=dvdrow)
for key in kwargs:
tst_kwargs = {}
tst_kwargs.update(kwargs)
del tst_kwargs[key]
with pytest.raises(ValueError):
Jacobian(**tst_kwargs)
def test_pixels_smoke(x, y, wcs_g1, wcs_g2, ignore_zero_weight):
gs_wcs = galsim.ShearWCS(0.25, galsim.Shear(g1=wcs_g1,
g2=wcs_g2)).jacobian()
jac = Jacobian(y=y,
x=x,
dudx=gs_wcs.dudx,
dudy=gs_wcs.dudy,
dvdx=gs_wcs.dvdx,
dvdy=gs_wcs.dvdy)
dims = (13, 15)
rng = np.random.RandomState(seed=11)
image = rng.normal(size=dims)
weight = np.exp(rng.normal(size=dims))
weight[10, 9] = 0
weight[8, 7] = 0
pixels = make_pixels(image,
weight,
jac,
ignore_zero_weight=ignore_zero_weight)
assert np.allclose(pixels['area'], jac.area)
found_zero = 0
for i in range(len(pixels)):
y, x = jac.get_rowcol(pixels['v'][i], pixels['u'][i])
assert np.allclose(x, int(x + 0.5))
assert np.allclose(y, int(y + 0.5))
x = int(x + 0.5)
y = int(y + 0.5)
assert pixels['val'][i] == image[y, x]
assert np.allclose(pixels['ierr'][i], np.sqrt(weight[y, x]))
if x == 9 and y == 10:
found_zero += 1
if y == 8 and x == 7:
found_zero += 1
if ignore_zero_weight:
assert found_zero == 0
else:
assert found_zero == 2
def get_exp_list(self, psf2=None):
if psf2 is None:
psf2 = self.psfs
obs_list = ObsList()
psf_list = ObsList()
w = []
for i in range(len(self.gals)):
im = self.gals[i].array
im_psf = self.psfs[i].array
im_psf2 = psf2[i].array
weight = 1 / self.skys[i].array
jacob = self.gals[i].wcs.jacobian()
dx = self.offsets[i].x
dy = self.offsets[i].y
gal_jacob = Jacobian(row=self.gals[i].true_center.y + dy,
col=self.gals[i].true_center.x + dx,
dvdrow=jacob.dvdy,
dvdcol=jacob.dvdx,
dudrow=jacob.dudy,
dudcol=jacob.dudx)
psf_jacob2 = gal_jacob
mask = np.where(weight != 0)
w.append(np.mean(weight[mask]))
noise = old_div(np.ones_like(weight), w[-1])
psf_obs = Observation(im_psf,
jacobian=gal_jacob,
meta={
'offset_pixels': None,
'file_id': None
})
psf_obs2 = Observation(im_psf2,
jacobian=psf_jacob2,
meta={
'offset_pixels': None,
'file_id': None
})
obs = Observation(im,
weight=weight,
jacobian=gal_jacob,
psf=psf_obs,
meta={
'offset_pixels': None,
'file_id': None
})
obs.set_noise(noise)
obs_list.append(obs)
psf_list.append(psf_obs2)
return obs_list, psf_list, np.array(w)
def test_unit_jacobian_missing_kwargs(kind):
col = 5.6
row = -10.4
if kind == 'row-col':
kwargs = dict(col=col, row=row)
elif kind == 'x-y':
kwargs = dict(x=col, y=row)
for key in kwargs:
tst_kwargs = {}
tst_kwargs.update(kwargs)
del tst_kwargs[key]
with pytest.raises(Exception):
Jacobian(**tst_kwargs)
def get_jacobian(self, type='galaxy'):
"""
get the jacobian and return a Jacobian object
"""
jdict = self.meds.get_jacobian(self.mindex, 0)
row0 = jdict['row0']
col0 = jdict['col0']
if self['fix_centroid_bug'] and type == 'galaxy':
print("fixing centroid bug")
row0 = row0 - 1
col0 = col0 - 1
jacob = Jacobian(row0, col0, jdict['dudrow'], jdict['dudcol'],
jdict['dvdrow'], jdict['dvdcol'])
return jacob
def test_coords_smoke(x, y, wcs_g1, wcs_g2):
gs_wcs = galsim.ShearWCS(0.25, galsim.Shear(g1=wcs_g1,
g2=wcs_g2)).jacobian()
jac = Jacobian(y=y,
x=x,
dudx=gs_wcs.dudx,
dudy=gs_wcs.dudy,
dvdx=gs_wcs.dvdx,
dvdy=gs_wcs.dvdy)
dims = (13, 15)
coords = make_coords(dims, jac)
loc = 0
for y in range(dims[0]):
for x in range(dims[1]):
v, u = jac(y, x)
assert u == coords['u'][loc]
assert v == coords['v'][loc]
loc += 1
def get_exp_list(gals_array, psfs_array, offsets, skys_array, gal_true, gal_jacobs, psf2=None):
#def get_exp_list(gal, psf, sky_stamp, psf2=None):
if psf2 is None:
psf2 = psfs_array
obs_list=ObsList()
psf_list=ObsList()
w = []
for i in range(len(gals_array)):
im = gals_array[i]
im_psf = psfs_array[i]
im_psf2 = psf2[i]
weight = 1/skys_array[i]
jacob = gal_jacobs[i]
dx = offsets[i].x
dy = offsets[i].y
gal_jacob = Jacobian(
row=gal_true[i].y+dy,
col=gal_true[i].x+dx,
dvdrow=jacob.dvdy,
dvdcol=jacob.dvdx,
dudrow=jacob.dudy,
dudcol=jacob.dudx)
psf_jacob2 = gal_jacob
print(gal_jacob)
mask = np.where(weight!=0)
w.append(np.mean(weight[mask]))
noise = old_div(np.ones_like(weight),w[-1])
psf_obs = Observation(im_psf, jacobian=gal_jacob, meta={'offset_pixels':None,'file_id':None})
psf_obs2 = Observation(im_psf2, jacobian=psf_jacob2, meta={'offset_pixels':None,'file_id':None})
obs = Observation(im, weight=weight, jacobian=gal_jacob, psf=psf_obs, meta={'offset_pixels':None,'file_id':None})
obs.set_noise(noise)
obs_list.append(obs)
psf_list.append(psf_obs2)
return obs_list,psf_list,np.array(w)
def get_ngmix_jacobian(self, iobj, icutout):
"""Get an ngmix.Jacobian representation.
Parameters
----------
iobj : int
Index of the object.
icutout : int
Index of the cutout for this object.
Returns
-------
jacob : ngmix.Jacobian
The `Jacobian` for the cutout.
"""
jd = self.get_jacobian(iobj, icutout)
return Jacobian(row=jd['row0'],
col=jd['col0'],
dudrow=jd['dudrow'],
dudcol=jd['dudcol'],
dvdrow=jd['dvdrow'],
dvdcol=jd['dvdcol'])
def test_jacobian_smoke(kind):
dudcol = 0.25
dudrow = 0.1
dvdcol = -0.4
dvdrow = 0.34
col = 5.6
row = -10.4
if kind == 'row-col':
jac = Jacobian(col=col,
row=row,
dudcol=dudcol,
dudrow=dudrow,
dvdcol=dvdcol,
dvdrow=dvdrow)
elif kind == 'x-y':
jac = Jacobian(x=col,
y=row,
dudx=dudcol,
dudy=dudrow,
dvdx=dvdcol,
dvdy=dvdrow)
else:
wcs = galsim.JacobianWCS(dudx=dudcol,
dudy=dudrow,
dvdx=dvdcol,
dvdy=dvdrow)
jac = Jacobian(x=col, y=row, wcs=wcs)
assert np.allclose(jac.row0, row)
assert np.allclose(jac.col0, col)
assert np.allclose(jac.dudcol, dudcol)
assert np.allclose(jac.dudrow, dudrow)
assert np.allclose(jac.dvdcol, dvdcol)
assert np.allclose(jac.dvdrow, dvdrow)
assert np.allclose(jac.det, dudcol * dvdrow - dudrow * dvdcol)
assert np.allclose(jac.sdet,
np.sqrt(np.abs(dudcol * dvdrow - dudrow * dvdcol)))
assert np.allclose(jac.scale,
np.sqrt(np.abs(dudcol * dvdrow - dudrow * dvdcol)))
r, c = 20.0, -44.5
v, u = jac.get_vu(r, c)
assert np.allclose(v, dvdrow * (r - row) + dvdcol * (c - col))
assert np.allclose(u, dudrow * (r - row) + dudcol * (c - col))
v, u = jac(r, c)
assert np.allclose(v, dvdrow * (r - row) + dvdcol * (c - col))
assert np.allclose(u, dudrow * (r - row) + dudcol * (c - col))
v, u = 20.0, -44.5
r, c = jac.get_rowcol(v, u)
assert np.allclose(r, (dudcol * v - dvdcol * u) / jac.det + row)
assert np.allclose(c, (-dudrow * v + dvdrow * u) / jac.det + col)
gs_wcs = jac.get_galsim_wcs()
assert np.allclose(gs_wcs.dudx, jac.dudcol)
assert np.allclose(gs_wcs.dudy, jac.dudrow)
assert np.allclose(gs_wcs.dvdx, jac.dvdcol)
assert np.allclose(gs_wcs.dvdy, jac.dvdrow)
cpy_jac = jac.copy()
cpy_jac.set_cen(row=-11, col=-12)
assert np.allclose(jac.row0, row)
assert np.allclose(jac.col0, col)
assert np.allclose(cpy_jac.row0, -11)
assert np.allclose(cpy_jac.col0, -12)
def multiband_coadd():
local_Hmeds = './fiducial_H158_2285117.fits'
local_Jmeds = './fiducial_J129_2285117.fits'
local_Fmeds = './fiducial_F184_2285117.fits'
truth = fio.FITS(
'/hpc/group/cosmology/phy-lsst/my137/roman_H158/g1002/truth/fiducial_lensing_galaxia_g1002_truth_gal.fits'
)[-1]
m_H158 = meds.MEDS(local_Hmeds)
m_J129 = meds.MEDS(local_Jmeds)
m_F184 = meds.MEDS(local_Fmeds)
indices_H = np.arange(len(m_H158['number'][:]))
indices_J = np.arange(len(m_J129['number'][:]))
indices_F = np.arange(len(m_F184['number'][:]))
roman_H158_psfs = get_psf_SCA('H158')
roman_J129_psfs = get_psf_SCA('J129')
roman_F184_psfs = get_psf_SCA('F184')
oversample = 1
metacal_keys = ['noshear', '1p', '1m', '2p', '2m']
res_noshear = np.zeros(len(m_H158['number'][:]),
dtype=[('ind', int), ('ra', float), ('dec', float),
('flags', int), ('coadd_px', float),
('coadd_py', float), ('coadd_flux', float),
('coadd_snr', float), ('coadd_e1', float),
('coadd_e2', float), ('coadd_hlr', float),
('coadd_psf_e1', float),
('coadd_psf_e2', float),
('coadd_psf_T', float)])
res_1p = np.zeros(len(m_H158['number'][:]),
dtype=[('ind', int), ('ra', float), ('dec', float),
('flags', int), ('coadd_px', float),
('coadd_py', float), ('coadd_flux', float),
('coadd_snr', float), ('coadd_e1', float),
('coadd_e2', float), ('coadd_hlr', float),
('coadd_psf_e1', float), ('coadd_psf_e2', float),
('coadd_psf_T', float)])
res_1m = np.zeros(len(m_H158['number'][:]),
dtype=[('ind', int), ('ra', float), ('dec', float),
('flags', int), ('coadd_px', float),
('coadd_py', float), ('coadd_flux', float),
('coadd_snr', float), ('coadd_e1', float),
('coadd_e2', float), ('coadd_hlr', float),
('coadd_psf_e1', float), ('coadd_psf_e2', float),
('coadd_psf_T', float)])
res_2p = np.zeros(len(m_H158['number'][:]),
dtype=[('ind', int), ('ra', float), ('dec', float),
('flags', int), ('coadd_px', float),
('coadd_py', float), ('coadd_flux', float),
('coadd_snr', float), ('coadd_e1', float),
('coadd_e2', float), ('coadd_hlr', float),
('coadd_psf_e1', float), ('coadd_psf_e2', float),
('coadd_psf_T', float)])
res_2m = np.zeros(len(m_H158['number'][:]),
dtype=[('ind', int), ('ra', float), ('dec', float),
('flags', int), ('coadd_px', float),
('coadd_py', float), ('coadd_flux', float),
('coadd_snr', float), ('coadd_e1', float),
('coadd_e2', float), ('coadd_hlr', float),
('coadd_psf_e1', float), ('coadd_psf_e2', float),
('coadd_psf_T', float)])
res_tot = [res_noshear, res_1p, res_1m, res_2p, res_2m]
for i, ii in enumerate(
indices_H): # looping through all the objects in meds file.
if i % 100 == 0:
print('object number ', i)
ind = m_H158['number'][ii]
t = truth[ind]
sca_Hlist = m_H158[ii][
'sca'] # List of SCAs for the same object in multiple observations.
sca_Jlist = m_J129[ii]['sca']
sca_Flist = m_F184[ii]['sca']
m2_H158_coadd = [
roman_H158_psfs[j - 1] for j in sca_Hlist[:m_H158['ncutout'][i]]
]
m2_J129_coadd = [
roman_J129_psfs[j - 1] for j in sca_Jlist[:m_J129['ncutout'][i]]
]
m2_F184_coadd = [
roman_F184_psfs[j - 1] for j in sca_Flist[:m_F184['ncutout'][i]]
]
obs_Hlist, psf_Hlist, included_H, w_H = get_exp_list_coadd(
m_H158, ii, m2=m2_H158_coadd)
coadd_H = psc.Coadder(obs_Hlist, flat_wcs=True).coadd_obs
coadd_H.psf.image[
coadd_H.psf.image < 0] = 0 # set negative pixels to zero.
coadd_H.set_meta({'offset_pixels': None, 'file_id': None})
obs_Jlist, psf_Jlist, included_J, w_J = get_exp_list_coadd(
m_J129, ii, m2=m2_J129_coadd)
coadd_J = psc.Coadder(obs_Jlist, flat_wcs=True).coadd_obs
coadd_J.psf.image[
coadd_J.psf.image < 0] = 0 # set negative pixels to zero.
coadd_J.set_meta({'offset_pixels': None, 'file_id': None})
obs_Flist, psf_Flist, included_F, w_F = get_exp_list_coadd(
m_F184, ii, m2=m2_F184_coadd)
coadd_F = psc.Coadder(obs_Flist, flat_wcs=True).coadd_obs
coadd_F.psf.image[
coadd_F.psf.image < 0] = 0 # set negative pixels to zero.
coadd_F.set_meta({'offset_pixels': None, 'file_id': None})
coadd = [coadd_H, coadd_J, coadd_F]
mb_obs_list = MultiBandObsList()
#coadd = [coadd_H]
for band in range(3):
obs_list = ObsList()
new_coadd_psf_block = block_reduce(coadd[band].psf.image,
block_size=(4, 4),
func=np.sum)
new_coadd_psf_jacob = Jacobian(
row=15.5,
col=15.5,
dvdrow=(coadd[band].psf.jacobian.dvdrow * oversample),
dvdcol=(coadd[band].psf.jacobian.dvdcol * oversample),
dudrow=(coadd[band].psf.jacobian.dudrow * oversample),
dudcol=(coadd[band].psf.jacobian.dudcol * oversample))
coadd_psf_obs = Observation(new_coadd_psf_block,
jacobian=new_coadd_psf_jacob,
meta={
'offset_pixels': None,
'file_id': None
})
coadd[band].psf = coadd_psf_obs
obs_list.append(coadd[band])
mb_obs_list.append(obs_list)
iteration = 0
for key in metacal_keys:
res_tot[iteration]['ind'][i] = ind
res_tot[iteration]['ra'][i] = t['ra']
res_tot[iteration]['dec'][i] = t['dec']
iteration += 1
#print(i, t['size'], mb_obs_list[0][0].image.sum(), mb_obs_list[1][0].image.sum(), mb_obs_list[2][0].image.sum())
res_ = measure_shape_metacal_multiband(
mb_obs_list,
t['size'],
method='bootstrap',
fracdev=t['bflux'],
use_e=[t['int_e1'], t['int_e2']])
iteration = 0
for key in metacal_keys:
if res_ == 0:
res_tot[iteration]['ind'][i] = 0
elif res_[key]['flags'] == 0:
res_tot[iteration]['coadd_px'][i] = res_[key]['pars'][0]
res_tot[iteration]['coadd_py'][i] = res_[key]['pars'][1]
res_tot[iteration]['coadd_snr'][i] = res_[key]['s2n']
res_tot[iteration]['coadd_e1'][i] = res_[key]['pars'][2]
res_tot[iteration]['coadd_e2'][i] = res_[key]['pars'][3]
res_tot[iteration]['coadd_hlr'][i] = res_[key]['pars'][4]
iteration += 1
mask = res_tot[0]['ind'] != 0
print(len(res_tot[0]), len(res_tot[0][mask]))
#print(res_['noshear'].dtype.names)
print('done')
def get_exp_list_coadd(m, i, m2=None):
def make_jacobian(dudx, dudy, dvdx, dvdy, x, y):
j = galsim.JacobianWCS(dudx, dudy, dvdx, dvdy)
return j.withOrigin(galsim.PositionD(x, y))
oversample = 1
#def psf_offset(i,j,star_):
m3 = [0]
#relative_offset=[0]
for jj, psf_ in enumerate(m2): # m2 has psfs for each observation.
if jj == 0:
continue
gal_stamp_center_row = m['orig_start_row'][i][jj] + m['box_size'][
i] / 2 - 0.5 # m['box_size'] is the galaxy stamp size.
gal_stamp_center_col = m['orig_start_col'][i][jj] + m['box_size'][
i] / 2 - 0.5 # m['orig_start_row/col'] is in SCA coordinates.
psf_stamp_size = 32
# Make the bounds for the psf stamp.
b = galsim.BoundsI(
xmin=(m['orig_start_col'][i][jj] +
(m['box_size'][i] - 32) / 2. - 1) * oversample + 1,
xmax=(m['orig_start_col'][i][jj] +
(m['box_size'][i] - 32) / 2. + psf_stamp_size - 1) *
oversample,
ymin=(m['orig_start_row'][i][jj] +
(m['box_size'][i] - 32) / 2. - 1) * oversample + 1,
ymax=(m['orig_start_row'][i][jj] +
(m['box_size'][i] - 32) / 2. + psf_stamp_size - 1) *
oversample)
# Make wcs for oversampled psf.
wcs_ = make_jacobian(
m.get_jacobian(i, jj)['dudcol'] / oversample,
m.get_jacobian(i, jj)['dudrow'] / oversample,
m.get_jacobian(i, jj)['dvdcol'] / oversample,
m.get_jacobian(i, jj)['dvdrow'] / oversample,
m['orig_col'][i][jj] * oversample,
m['orig_row'][i][jj] * oversample)
# Taken from galsim/roman_psfs.py line 266. Update each psf to an object-specific psf using the wcs.
scale = galsim.PixelScale(wfirst.pixel_scale / oversample)
psf_ = wcs_.toWorld(scale.toImage(psf_),
image_pos=galsim.PositionD(wfirst.n_pix / 2,
wfirst.n_pix / 2))
# Convolve with the star model and get the psf stamp.
#st_model = galsim.DeltaFunction(flux=1.)
#st_model = st_model.evaluateAtWavelength(wfirst.getBandpasses(AB_zeropoint=True)['H158'].effective_wavelength)
#st_model = st_model.withFlux(1.)
#st_model = galsim.Convolve(st_model, psf_)
psf_ = galsim.Convolve(psf_, galsim.Pixel(wfirst.pixel_scale))
psf_stamp = galsim.Image(b, wcs=wcs_)
# Galaxy is being drawn with some subpixel offsets, so we apply the offsets when drawing the psf too.
offset_x = m['orig_col'][i][jj] - gal_stamp_center_col
offset_y = m['orig_row'][i][jj] - gal_stamp_center_row
offset = galsim.PositionD(offset_x, offset_y)
if (offset_x <= -1.0 or offset_y <= -1.0):
print(offset)
elif (offset_x >= 1.0 or offset_y >= 1.0):
print(offset)
psf_.drawImage(image=psf_stamp, offset=offset, method='no_pixel')
m3.append(psf_stamp.array)
obs_list = ObsList()
psf_list = ObsList()
included = []
w = []
# For each of these objects create an observation
for j in range(m['ncutout'][i]):
if j == 0:
continue
# if j>1:
# continue
im = m.get_cutout(i, j, type='image')
weight = m.get_cutout(i, j, type='weight')
im_psf = m3[j]
im_psf2 = im_psf
if np.sum(im) == 0.:
#print(local_meds, i, j, np.sum(im))
print('no flux in image ', i, j)
continue
jacob = m.get_jacobian(i, j)
# Get a galaxy jacobian.
gal_jacob = Jacobian(
row=(m['orig_row'][i][j] - m['orig_start_row'][i][j]),
col=(m['orig_col'][i][j] - m['orig_start_col'][i][j]),
dvdrow=jacob['dvdrow'],
dvdcol=jacob['dvdcol'],
dudrow=jacob['dudrow'],
dudcol=jacob['dudcol'])
psf_center = (32 / 2.) + 0.5
# Get a oversampled psf jacobian.
if oversample == 1:
psf_jacob2 = Jacobian(
row=15.5 +
(m['orig_row'][i][j] - m['orig_start_row'][i][j] + 1 -
(m['box_size'][i] / 2. + 0.5)) * oversample,
col=15.5 +
(m['orig_col'][i][j] - m['orig_start_col'][i][j] + 1 -
(m['box_size'][i] / 2. + 0.5)) * oversample,
dvdrow=jacob['dvdrow'] / oversample,
dvdcol=jacob['dvdcol'] / oversample,
dudrow=jacob['dudrow'] / oversample,
dudcol=jacob['dudcol'] / oversample)
elif oversample == 4:
psf_jacob2 = Jacobian(
row=63.5 +
(m['orig_row'][i][j] - m['orig_start_row'][i][j] + 1 -
(m['box_size'][i] / 2. + 0.5)) * oversample,
col=63.5 +
(m['orig_col'][i][j] - m['orig_start_col'][i][j] + 1 -
(m['box_size'][i] / 2. + 0.5)) * oversample,
dvdrow=jacob['dvdrow'] / oversample,
dvdcol=jacob['dvdcol'] / oversample,
dudrow=jacob['dudrow'] / oversample,
dudcol=jacob['dudcol'] / oversample)
# Create an obs for each cutout
mask = np.where(weight != 0)
if 1. * len(weight[mask]) / np.product(np.shape(weight)) < 0.8:
continue
w.append(np.mean(weight[mask]))
noise = np.ones_like(weight) / w[-1]
psf_obs = Observation(im_psf,
jacobian=gal_jacob,
meta={
'offset_pixels': None,
'file_id': None
})
psf_obs2 = Observation(im_psf2,
jacobian=psf_jacob2,
meta={
'offset_pixels': None,
'file_id': None
})
#obs = Observation(im, weight=weight, jacobian=gal_jacob, psf=psf_obs, meta={'offset_pixels':None,'file_id':None})
# oversampled PSF
obs = Observation(im,
weight=weight,
jacobian=gal_jacob,
psf=psf_obs2,
meta={
'offset_pixels': None,
'file_id': None
})
obs.set_noise(noise)
obs_list.append(obs)
psf_list.append(psf_obs2)
included.append(j)
return obs_list, psf_list, np.array(included) - 1, np.array(w)
def single_vs_coadd_images():
local_Hmeds = './fiducial_F184_2285117.fits'
truth = fio.FITS('/hpc/group/cosmology/phy-lsst/my137/roman_F184/g1002/truth/fiducial_lensing_galaxia_g1002_truth_gal.fits')[-1]
m_H158 = meds.MEDS(local_Hmeds)
indices_H = np.arange(len(m_H158['number'][:]))
roman_H158_psfs = get_psf_SCA('F184')
oversample = 4
metacal_keys=['noshear', '1p', '1m', '2p', '2m']
res_noshear=np.zeros(len(m_H158['number'][:]),dtype=[('ind',int), ('ra',float), ('dec',float), ('flags',int),('int_e1',float), ('int_e2',float),('coadd_px',float), ('coadd_py',float), ('coadd_flux',float), ('coadd_snr',float), ('coadd_e1',float), ('coadd_e2',float), ('coadd_hlr',float),('coadd_psf_e1',float), ('coadd_psf_e2',float), ('coadd_psf_T',float)])
res_1p=np.zeros(len(m_H158['number'][:]),dtype=[('ind',int), ('ra',float), ('dec',float), ('flags',int),('int_e1',float), ('int_e2',float),('coadd_px',float), ('coadd_py',float), ('coadd_flux',float), ('coadd_snr',float), ('coadd_e1',float), ('coadd_e2',float), ('coadd_hlr',float),('coadd_psf_e1',float), ('coadd_psf_e2',float), ('coadd_psf_T',float)])
res_1m=np.zeros(len(m_H158['number'][:]),dtype=[('ind',int), ('ra',float), ('dec',float), ('flags',int),('int_e1',float), ('int_e2',float),('coadd_px',float), ('coadd_py',float), ('coadd_flux',float), ('coadd_snr',float), ('coadd_e1',float), ('coadd_e2',float), ('coadd_hlr',float),('coadd_psf_e1',float), ('coadd_psf_e2',float), ('coadd_psf_T',float)])
res_2p=np.zeros(len(m_H158['number'][:]),dtype=[('ind',int), ('ra',float), ('dec',float), ('flags',int),('int_e1',float), ('int_e2',float),('coadd_px',float), ('coadd_py',float), ('coadd_flux',float), ('coadd_snr',float), ('coadd_e1',float), ('coadd_e2',float), ('coadd_hlr',float),('coadd_psf_e1',float), ('coadd_psf_e2',float), ('coadd_psf_T',float)])
res_2m=np.zeros(len(m_H158['number'][:]),dtype=[('ind',int), ('ra',float), ('dec',float), ('flags',int),('int_e1',float), ('int_e2',float),('coadd_px',float), ('coadd_py',float), ('coadd_flux',float), ('coadd_snr',float), ('coadd_e1',float), ('coadd_e2',float), ('coadd_hlr',float),('coadd_psf_e1',float), ('coadd_psf_e2',float), ('coadd_psf_T',float)])
res_tot=[res_noshear, res_1p, res_1m, res_2p, res_2m]
for i,ii in enumerate(indices_H): # looping through all the objects in meds file.
if i%100==0:
print('object number ',i)
# if i not in [1,600]:
# continue
ind = m_H158['number'][ii]
t = truth[ind]
sca_Hlist = m_H158[ii]['sca'] # List of SCAs for the same object in multiple observations.
m2_H158_coadd = [roman_H158_psfs[j-1] for j in sca_Hlist[:m_H158['ncutout'][i]]]
obs_Hlist,psf_Hlist,included_H,w_H = get_exp_list_coadd(m_H158,ii,oversample,m2=m2_H158_coadd)
s2n_test = get_snr(obs_Hlist)
# if i in [1,600]: #in [ 309, 444, 622, 644, 854, 1070, 1282, 1529]:
# for l in range(len(obs_Hlist)):
# #print(i, obs_Hlist[l].jacobian, obs_Hlist[l].psf.jacobian)
# print(i, obs_Hlist[l].weight)
# np.savetxt('/hpc/group/cosmology/masaya/wfirst_simulation/paper/single_image_oversample4_08scaling_'+str(i)+'_'+str(l)+'.txt', obs_Hlist[l].image)
# np.savetxt('/hpc/group/cosmology/masaya/wfirst_simulation/paper/single_psf_oversample4_08scaling_'+str(i)+'.txt', obs_Hlist[0].psf.image)
coadd_H = psc.Coadder(obs_Hlist,flat_wcs=True).coadd_obs
coadd_H.psf.image[coadd_H.psf.image<0] = 0 # set negative pixels to zero.
coadd_H.set_meta({'offset_pixels':None,'file_id':None})
obs_list = ObsList()
if oversample == 4:
new_coadd_psf_block = block_reduce(coadd_H.psf.image, block_size=(4,4), func=np.sum)
new_coadd_psf_jacob = Jacobian( row=15.5,
col=15.5,
dvdrow=(coadd_H.psf.jacobian.dvdrow*oversample),
dvdcol=(coadd_H.psf.jacobian.dvdcol*oversample),
dudrow=(coadd_H.psf.jacobian.dudrow*oversample),
dudcol=(coadd_H.psf.jacobian.dudcol*oversample))
coadd_psf_obs = Observation(new_coadd_psf_block, jacobian=new_coadd_psf_jacob, meta={'offset_pixels':None,'file_id':None})
coadd_H.psf = coadd_psf_obs
obs_list.append(coadd_H)
s2n_coadd = get_snr(obs_list)
# if i in [1,600]:
# print(i, coadd_H.weight)
#np.savetxt('/hpc/group/cosmology/masaya/wfirst_simulation/paper/coadd_image_oversample4_08scaling_'+str(i)+'.txt', coadd_H.image)
# np.savetxt('/hpc/group/cosmology/masaya/wfirst_simulation/paper/coadd_weight_oversample4_08scaling_'+str(i)+'.txt', coadd_H.weight)
#np.savetxt('/hpc/group/cosmology/masaya/wfirst_simulation/paper/coadd_psf_over-downsample4_08scaling_'+str(i)+'.txt', coadd_H.psf.image)
iteration=0
for key in metacal_keys:
res_tot[iteration]['ind'][i] = ind
res_tot[iteration]['ra'][i] = t['ra']
res_tot[iteration]['dec'][i] = t['dec']
res_tot[iteration]['int_e1'][i] = t['int_e1']
res_tot[iteration]['int_e2'][i] = t['int_e2']
iteration+=1
res_ = measure_shape_metacal(obs_list, t['size'], method='bootstrap', fracdev=t['bflux'],use_e=[t['int_e1'],t['int_e2']])
print('signal to noise test', i, s2n_test, s2n_coadd, res_['noshear']['s2n_r'])
# if res_[key]['s2n'] > 1e7:
# print('coadd snr', res_[key]['s2n'])
# np.savetxt('large_coadd_snr_image.txt', coadd_H.image)
iteration=0
for key in metacal_keys:
if res_==0:
res_tot[iteration]['ind'][i] = 0
elif res_[key]['flags']==0:
res_tot[iteration]['coadd_px'][i] = res_[key]['pars'][0]
res_tot[iteration]['coadd_py'][i] = res_[key]['pars'][1]
res_tot[iteration]['coadd_snr'][i] = res_[key]['s2n']
res_tot[iteration]['coadd_e1'][i] = res_[key]['pars'][2]
res_tot[iteration]['coadd_e2'][i] = res_[key]['pars'][3]
res_tot[iteration]['coadd_hlr'][i] = res_[key]['pars'][4]
iteration+=1
mask=res_tot[0]['ind']!=0
print(len(res_tot[0]), len(res_tot[0][mask]))
#print(res_['noshear'].dtype.names)
print('done')
def _get_nbrs_data(self,cen_id,band,cutout_index):
"""
return cen and nbrs info for a given cen_id
Parameters
----------
cen_id: id of central object
band: integer for band (e.g., 0 for griz MOF)
cutout_index: index of epoch in MEDS file for nbrs
Returns
-------
cen_ind: index of central intp returned fit_data
cen_flags: flags for central from nbrs_data
cen_psf_gmix: an ngmix GMix for PSF of central
cen_jac: an ngmix Jacobian for the central
nbrs_inds: list of indexes into returned fit_data of nbrs
nbrs_flags: flags of nbrs (only use flags == 0)
nbrs_psf_gmixes: a list of ngmix GMixes of the PSF models for the nbrs
nbrs_jacs: a list of ngmix Jacobians for the nbrs
fit_data: entries of input fit_data corresponding to cen_ind and nbrs_inds
pixel_scale: the pixel_scale of the jacobian associated with the image
will return None if thete is an error or if not all quantities are found
"""
fit_inds = []
# get cen stuff
q, = numpy.where(self.fit_data['id'] == cen_id)
if len(q) != 1:
return None
cen_ind = 0
fit_inds.append(q[0])
q, = numpy.where(
(self.nbrs_data['id'] == cen_id)
& (self.nbrs_data['nbr_id'] == cen_id)
& (self.nbrs_data['band_num'] == band)
& (self.nbrs_data['cutout_index'] == cutout_index)
)
if len(q) != 1:
return None
ind = q[0]
cen_flags = self.nbrs_data['nbr_flags'][ind]
if cen_flags == 0:
cen_jac = Jacobian(
row=self.nbrs_data['nbr_jac_row0'][ind],
col=self.nbrs_data['nbr_jac_col0'][ind],
dudrow=self.nbrs_data['nbr_jac_dudrow'][ind],
dudcol=self.nbrs_data['nbr_jac_dudcol'][ind],
dvdrow=self.nbrs_data['nbr_jac_dvdrow'][ind],
dvdcol=self.nbrs_data['nbr_jac_dvdcol'][ind]
)
cen_psf_gmix = GMix(pars=self.nbrs_data['nbr_psf_fit_pars'][ind,:])
else:
cen_psf_gmix = None
cen_jac = None
pixel_scale = self.nbrs_data['pixel_scale'][ind]
# get nbr ids
q, = numpy.where(
(self.nbrs_data['id'] == cen_id)
& (self.nbrs_data['nbr_id'] != cen_id)
& (self.nbrs_data['band_num'] == band)
& (self.nbrs_data['cutout_index'] == cutout_index)
)
if len(q) == 0:
return None
n1 = len(numpy.unique(self.nbrs_data['nbr_id'][q]))
n2 = len(self.nbrs_data['nbr_id'][q])
mess=("nbrs list for given band %d and cutout_index "
"%d for object %d is not unique!" % (band,cutout_index,cen_id))
assert n1==n2, mess
nbrs_inds = [i+1 for i in xrange(len(q))]
# find location of nbrs in fit_data
for nbr_id in self.nbrs_data['nbr_id'][q]:
qq, = numpy.where(self.fit_data['id'] == nbr_id)
if len(qq) != 1:
return None
fit_inds.append(qq[0])
# doing fit data
fit_data = self.fit_data[fit_inds]
# build flag, psf and jacobian lists
nbrs_flags = []
nbrs_psf_gmixes = []
nbrs_jacs = []
for i,ind in enumerate(q):
check=fit_data['id'][i+1] == self.nbrs_data['nbr_id'][ind]
assert check,"Matching of nbr_ids to ids in fit_data did not work!"
nbrs_flags.append(self.nbrs_data['nbr_flags'][ind])
if nbrs_flags[-1] == 0:
nbrs_jacs.append(
Jacobian(
row=self.nbrs_data['nbr_jac_row0'][ind],
col=self.nbrs_data['nbr_jac_col0'][ind],
dudrow=self.nbrs_data['nbr_jac_dudrow'][ind],
dudcol=self.nbrs_data['nbr_jac_dudcol'][ind],
dvdrow=self.nbrs_data['nbr_jac_dvdrow'][ind],
dvdcol=self.nbrs_data['nbr_jac_dvdcol'][ind]
)
)
tgm = GMix(pars=self.nbrs_data['nbr_psf_fit_pars'][ind,:])
nbrs_psf_gmixes.append(tgm)
else:
nbrs_jacs.append(None)
nbrs_psf_gmixes.append(None)
return cen_ind, cen_flags, cen_psf_gmix, cen_jac, \
nbrs_inds, nbrs_flags, nbrs_psf_gmixes, nbrs_jacs, \
fit_data, pixel_scale
def render_central(self,
cen_id,
meds_data,
mindex,
cutout_index,
model,
band,
image_shape):
"""
just render the central. This is needed since Matt does not
store data for the central i the nbrs data structure if there
are no neighbors
you must send epoch_data= to the constructor
"""
import esutil as eu
#
# set and check some parameters
#
if self.epoch_data is None:
raise RuntimeError(
"send epoch_data= to the constructor to render centrals"
)
pars_tag = '%s_max_pars' % model
if model == 'cm':
fracdev_tag = 'cm_fracdev'
TdByTe_tag = 'cm_TdByTe'
else:
fracdev_tag=None
TdByTe_tag=None
#
# get data needed to render the central
#
we,=numpy.where(
(self.epoch_data['id'] == cen_id)
& (self.epoch_data['cutout_index'] == cutout_index)
)
if we.size == 0:
print(" central not in epochs data")
return None
psf_pars=self.epoch_data['psf_fit_pars'][we[0],:]
psf_gmix = GMix(pars=psf_pars)
e1,e2,T=psf_gmix.get_e1e2T()
if T <= 0.0:
print(" bad psf fit for central")
return None
pixel_scale=self.epoch_data['pixel_scale'][we[0]]
jdict=meds_data.get_jacobian(mindex, cutout_index)
jac=Jacobian(
row=jdict['row0'],
col=jdict['col0'],
dudrow=jdict['dudrow'],
dudcol=jdict['dudcol'],
dvdrow=jdict['dvdrow'],
dvdcol=jdict['dvdcol'],
)
# fit information for central
wfit, = numpy.where(self.fit_data['id'] == cen_id)
if wfit.size != 1:
# not sure why this would happen
print(" Central not found in fit_data")
return None
fit_data = self.fit_data[wfit]
cen_flags=fit_data['flags'][0]
if cen_flags != 0:
print(" bad central fit:",cen_flags)
return None
cen_img = RenderNGmixNbrs._render_single(
model,
band,
image_shape,
pars_tag,
fit_data,
psf_gmix,
jac,
fracdev_tag=fracdev_tag,TdByTe_tag=TdByTe_tag,
)
if cen_img is None:
return None
return cen_img, pixel_scale
def _get_nbrs_data(self, cen_id, band, cutout_index):
"""
return cen and nbrs info for a given cen_id
Parameters
----------
cen_id: id of central object
band: integer for band (e.g., 0 for griz MOF)
cutout_index: index of epoch in MEDS file for nbrs
Returns
-------
cen_ind: index of central intp returned fit_data
cen_flags: flags for central from nbrs_data
cen_psf_gmix: an ngmix GMix for PSF of central
cen_jac: an ngmix Jacobian for the central
nbrs_inds: list of indexes into returned fit_data of nbrs
nbrs_flags: flags of nbrs (only use flags == 0)
nbrs_psf_gmixes: a list of ngmix GMixes of the PSF models for the nbrs
nbrs_jacs: a list of ngmix Jacobians for the nbrs
fit_data: entries of input fit_data corresponding to cen_ind and nbrs_inds
pixel_scale: the pixel_scale of the jacobian associated with the image
will return None if thete is an error or if not all quantities are found
"""
fit_inds = []
# get cen stuff
qids, = numpy.where(self.fit_ids == cen_id)
if len(qids) != 1:
print(" no cen match in fits")
return None
cen_ind = 0
fit_inds.append(qids[0])
qnbrs_ids, = numpy.where(self.nbrs_ids == cen_id)
if len(qnbrs_ids) == 0:
return None
# extract just the data we need
nbrs_data = self._fits['nbrs_data'][qnbrs_ids]
qcen, = numpy.where((nbrs_data['nbr_id'] == cen_id)
& (nbrs_data['band_num'] == band)
& (nbrs_data['cutout_index'] == cutout_index))
if len(qcen) != 1:
return None
ind = qcen[0]
cen_flags = nbrs_data['nbr_flags'][ind]
if cen_flags == 0:
cen_jac = Jacobian(row=nbrs_data['nbr_jac_row0'][ind],
col=nbrs_data['nbr_jac_col0'][ind],
dudrow=nbrs_data['nbr_jac_dudrow'][ind],
dudcol=nbrs_data['nbr_jac_dudcol'][ind],
dvdrow=nbrs_data['nbr_jac_dvdrow'][ind],
dvdcol=nbrs_data['nbr_jac_dvdcol'][ind])
cen_psf_gmix = GMix(pars=nbrs_data['nbr_psf_fit_pars'][ind, :])
else:
cen_psf_gmix = None
cen_jac = None
pixel_scale = nbrs_data['pixel_scale'][ind]
# get nbr ids
qnbr, = numpy.where((nbrs_data['nbr_id'] != cen_id)
& (nbrs_data['band_num'] == band)
& (nbrs_data['cutout_index'] == cutout_index))
if len(qnbr) == 0:
return None
n1 = len(numpy.unique(nbrs_data['nbr_id'][qnbr]))
n2 = len(nbrs_data['nbr_id'][qnbr])
if n1 != n2:
# not sure why this happens, but it seems to be very rare.
# For now ignore
mess = ("nbrs list for given band %d and cutout_index "
"%d for object %d is not unique! %d:%d" %
(band, cutout_index, cen_id, n1, n2))
print(nbrs_data['nbr_id'][qnbr])
print(mess)
return None
#raise RuntimeError(mess)
nbrs_inds = [i + 1 for i in xrange(len(qnbr))]
# find location of nbrs in fit_data
for nbr_id in nbrs_data['nbr_id'][qnbr]:
qq, = numpy.where(self.fit_ids == nbr_id)
if len(qq) != 1:
print(" nbr", nbr_id, "not found in fit data")
return None
fit_inds.append(qq[0])
# doing fit data
# the data come out in row order, we need to reorder
fit_data_list = []
for tmp_ind in fit_inds:
fit_data_list.append(self._fits['model_fits'][tmp_ind])
fit_data = eu.numpy_util.combine_arrlist(fit_data_list)
# build flag, psf and jacobian lists
nbrs_flags = []
nbrs_psf_gmixes = []
nbrs_jacs = []
for i, ind in enumerate(qnbr):
check = fit_data['id'][i + 1] == nbrs_data['nbr_id'][ind]
assert check, "Matching of nbr_ids to ids in fit_data did not work!"
nbrs_flags.append(nbrs_data['nbr_flags'][ind])
if nbrs_flags[-1] == 0:
nbrs_jacs.append(
Jacobian(row=nbrs_data['nbr_jac_row0'][ind],
col=nbrs_data['nbr_jac_col0'][ind],
dudrow=nbrs_data['nbr_jac_dudrow'][ind],
dudcol=nbrs_data['nbr_jac_dudcol'][ind],
dvdrow=nbrs_data['nbr_jac_dvdrow'][ind],
dvdcol=nbrs_data['nbr_jac_dvdcol'][ind]))
tgm = GMix(pars=nbrs_data['nbr_psf_fit_pars'][ind, :])
nbrs_psf_gmixes.append(tgm)
else:
nbrs_jacs.append(None)
nbrs_psf_gmixes.append(None)
return cen_ind, cen_flags, cen_psf_gmix, cen_jac, \
nbrs_inds, nbrs_flags, nbrs_psf_gmixes, nbrs_jacs, \
fit_data, pixel_scale
def get_exp_list(gal, psf, offsets, sky_stamp, psf2=None):
#def get_exp_list(gal, psf, sky_stamp, psf2=None):
if psf2 is None:
psf2 = psf
obs_list = ObsList()
psf_list = ObsList()
w = []
for i in range(len(gal)):
im = gal[i].array
im_psf = psf[i].array
im_psf2 = psf2[i].array
weight = 1 / sky_stamp[i].array
jacob = gal[i].wcs.jacobian()
dx = offsets[i].x
dy = offsets[i].y
gal_jacob = Jacobian(row=gal[i].true_center.y + dy,
col=gal[i].true_center.x + dx,
dvdrow=jacob.dvdy,
dvdcol=jacob.dvdx,
dudrow=jacob.dudy,
dudcol=jacob.dudx)
#gal_jacob = Jacobian(
# row=gal[i].true_center.x+dx,
# col=gal[i].true_center.y+dy,
# dvdrow=jacob.dudx,
# dvdcol=jacob.dudy,
# dudrow=jacob.dvdx,
# dudcol=jacob.dvdy)
psf_jacob2 = gal_jacob
mask = np.where(weight != 0)
w.append(np.mean(weight[mask]))
noise = old_div(np.ones_like(weight), w[-1])
psf_obs = Observation(im_psf,
jacobian=gal_jacob,
meta={
'offset_pixels': None,
'file_id': None
})
psf_obs2 = Observation(im_psf2,
jacobian=psf_jacob2,
meta={
'offset_pixels': None,
'file_id': None
})
obs = Observation(im,
weight=weight,
jacobian=gal_jacob,
psf=psf_obs,
meta={
'offset_pixels': None,
'file_id': None
})
obs.set_noise(noise)
obs_list.append(obs)
psf_list.append(psf_obs2)
#print(obs_list)
return obs_list, psf_list, np.array(w)