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from astropy.table import Table
import astropy.constants as cons
import collections
from collections import OrderedDict
from scipy import interpolate
from astropy import units as u
# from numpy import *
import numpy as np
from pylab import *
import galsim
import sys
import os
def rotate90(array_orig=None, xc=0, yc=0, isClockwise=0):
if array_orig is None:
return
l1 = array_orig.shape[0]
l2 = array_orig.shape[1]
if xc < 0 or xc > l2 - 1 or yc < 0 or yc > l1 - 1:
return
n_xc = xc
n_yc = yc
array_final = np.zeros_like(array_orig.T)
if isClockwise == 1:
for i in np.arange(l2):
array_final[i] = array_orig[:, l2 - i - 1]
n_xc = yc
n_yc = l2 - 1 - xc
else:
for i in np.arange(l2):
array_final[i] = array_orig[::-1, i]
n_xc = l1 - 1 - yc
n_yc = xc
return array_final, n_xc, n_yc
class SpecDisperser(object):
def __init__(
self,
orig_img=None,
xcenter=0,
ycenter=0,
origin=[100, 100],
tar_spec=None,
band_start=6200,
band_end=10000,
isAlongY=0,
conf="../param/CONF/csst.conf",
gid=0,
flat_cube=None,
ignoreBeam=[],
):
"""
orig_img: normal image,galsim image
xcenter, ycenter: the center of galaxy in orig_img
origin : [int, int]
`origin` defines the lower left pixel index (y,x) of the `direct`
cutout from a larger detector-frame image
tar_spec: galsim.SED
"""
# self.img_x = orig_img.shape[1]
# self.img_y = orig_img.shape[0]
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# 5 orders, A, B ,
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self.orig_img_orders = OrderedDict()
if isinstance(orig_img, list):
orig_img_list = orig_img
list_len = len(orig_img_list)
if list_len < 5:
for i in np.arange(5 - list_len):
orig_img_list.append(orig_img_list[list_len - 1])
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for i, k in enumerate(orig_img_list):
self.orig_img_orders[orderName[i]] = k
if isinstance(orig_img, galsim.Image):
for i in np.arange(5):
self.orig_img_orders[orderName[i]] = orig_img
orig_img_one = self.orig_img_orders["A"]
self.thumb_img = np.abs(orig_img_one.array)
self.thumb_x = orig_img_one.center.x
self.thumb_y = orig_img_one.center.y
self.img_sh = orig_img_one.array.shape
self.id = gid
self.xcenter = xcenter
self.ycenter = ycenter
self.isAlongY = isAlongY
self.flat_cube = flat_cube
if self.isAlongY == 1:
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for order in orderName:
self.orig_img_orders[order], self.thumb_x, self.thumb_y = rotate90(
array_orig=self.orig_img_orders[order],
xc=orig_img_one.center.x,
yc=orig_img_one.center.y,
isClockwise=1,
)
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# self.thumb_img, self.thumb_x, self.thumb_y = rotate90(array_orig=self.thumb_img, xc=orig_img_one.center.x,
# yc=orig_img_one.center.y, isClockwise=1)
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self.img_sh = self.orig_img_orders[order].array.T.shape
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self.xcenter = ycenter
self.ycenter = xcenter
self.origin = origin
self.band_start = band_start
self.band_end = band_end
self.spec = tar_spec
self.beam_flux = OrderedDict()
self.grating_conf = aXeConf(conf)
self.grating_conf.get_beams()
self.grating_conf_file = conf
self.ignoreBeam = ignoreBeam
def compute_spec_orders(self):
all_orders = OrderedDict()
beam_names = self.grating_conf.beams
for beam in beam_names:
if beam in self.ignoreBeam:
continue
all_orders[beam] = self.compute_spec(beam)
return all_orders
def compute_spec(self, beam):
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# if beam == "B":
# return self.thumb_img, self.origin[1], self.origin[0], None, None, None
from .disperse_c import interp
from .disperse_c import disperse
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self.thumb_img = np.abs(self.orig_img_orders[beam].array)
self.thumb_x = self.orig_img_orders[beam].center.x
self.thumb_y = self.orig_img_orders[beam].center.y
self.img_sh = self.orig_img_orders[beam].array.shape
ytrace_beam, lam_beam = self.grating_conf.get_beam_trace(
x=self.xcenter, y=self.ycenter, dx=(dx + xoff), beam=beam
)
ysens = lam_beam * 0
lam_index = argsort(lam_beam)
conf_sens = self.grating_conf.sens[beam]
lam_intep = np.linspace(self.band_start, self.band_end, int(
(self.band_end - self.band_start) / 0.1))
thri = interpolate.interp1d(
conf_sens["WAVELENGTH"], conf_sens["SENSITIVITY"])
spci = interpolate.interp1d(self.spec["WAVELENGTH"], self.spec["FLUX"])
beam_thr = thri(lam_intep)
spec_sample = spci(lam_intep)
bean_thr_spec = beam_thr * spec_sample
# generate sensitivity file for aXe
# ysensitivity = lam_beam * 0
#
# ysensitivity[lam_index] = interp.interp_conserve_c(lam_beam[lam_index], lam_intep,
# beam_thr * math.pi * 100 * 100 * 1e-7 / (
# cons.h.value * cons.c.value / (
# lam_intep * 1e-10)), integrate=0, left=0,
# right=0)
#
# self.writerSensitivityFile(conffile = self.grating_conf_file, beam = beam, w = lam_beam[lam_index], sens = ysensitivity[lam_index])
ysens[lam_index] = interp.interp_conserve_c(
lam_beam[lam_index], lam_intep, bean_thr_spec, integrate=1, left=0, right=0
)
sensitivity_beam = ysens
len_spec_x = len(dx)
len_spec_y = int(
abs(ceil(ytrace_beam[-1]) - floor(ytrace_beam[0])) + 1)
beam_sh = (self.img_sh[0] + len_spec_y, self.img_sh[1] + len_spec_x)
modelf = zeros(product(beam_sh), dtype=float)
model = modelf.reshape(beam_sh)
idx = np.arange(modelf.size, dtype=int64).reshape(beam_sh)
x0 = array((self.thumb_y, self.thumb_x), dtype=int64)
dxpix = dx - dx[0] + x0[1]
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# dypix = cast[int](np.floor(ytrace_beam - dyc[0] + x0[0] + 0.5))
dypix = dyc - dyc[0] + x0[0]
frac_ids = yfrac_beam < 0
dypix[frac_ids] = dypix[frac_ids] - 1
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flat_index = idx[dypix, dxpix]
nonz = sensitivity_beam != 0
origin_in = zeros_like(self.origin)
dx0_in = dx[0]
dy0_in = dyc[0]
if self.isAlongY == 1:
origin_in[0] = self.origin[0]
origin_in[1] = self.origin[1] - len_spec_y
dx0_in = -dyc[0]
dy0_in = dx[0]
else:
origin_in[0] = self.origin[0]
origin_in[1] = self.origin[1]
dx0_in = dx[0]
dy0_in = dyc[0]
originOut_x = origin_in[1] + dx0_in
originOut_y = origin_in[0] + dy0_in
if self.flat_cube is None:
beam_flat = None
else:
beam_flat = zeros([len(modelf), len(self.flat_cube)])
sub_flat_cube = zeros(
[len(self.flat_cube), beam_sh[0], beam_sh[1]])
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overlap_flag = 1
sub_y_s = originOut_y
sub_y_e = originOut_y + beam_sh[0] - 1
sub_x_s = originOut_x
sub_x_e = originOut_x + beam_sh[1] - 1
beam_x_s = max(sub_x_s, 0)
if beam_x_s > self.flat_cube[0].shape[1] - 1:
overlap_flag = 0
if overlap_flag == 1:
beam_x_e = min(sub_x_e, self.flat_cube[0].shape[1] - 1)
if beam_x_e < 0:
overlap_flag = 0
if overlap_flag == 1:
beam_y_s = max(sub_y_s, 0)
if beam_y_s > self.flat_cube[0].shape[0] - 1:
overlap_flag = 0
if overlap_flag == 1:
beam_y_e = min(sub_y_e, self.flat_cube[0].shape[0] - 1)
if beam_y_e < 0:
overlap_flag = 0
if overlap_flag == 1:
beam_y_s - originOut_y: beam_y_e - originOut_y + 1,
beam_x_s - originOut_x: beam_x_e - originOut_x + 1,
] = self.flat_cube[:, beam_y_s: beam_y_e + 1, beam_x_s: beam_x_e + 1]
for i in arange(0, len(self.flat_cube), 1):
beam_flat[:, i] = sub_flat_cube[i].flatten()
# beam_flat = zeros([len(modelf), len(self.flat_cube)])
# flat_sh = self.flat_cube[0].shape
# for i in arange(0, beam_sh[0], 1):
# for j in arange(0, beam_sh[1], 1):
# k = i * beam_sh[1] + j
# if originOut_y + i >= flat_sh[0] or originOut_y + i < 0 or originOut_x + j>= flat_sh[1] or originOut_x+j < 0:
# temp_bf = np.zeros_like(self.flat_cube[:, 0, 0])
# temp_bf[0] = 1.0
# beam_flat[k] = temp_bf
# else:
# beam_flat[k] = self.flat_cube[:, originOut_y + i, originOut_x + j]
status = disperse.disperse_grism_object(
self.thumb_img.astype(np.float32),
flat_index[nonz],
yfrac_beam[nonz],
sensitivity_beam[nonz],
modelf,
x0,
array(self.img_sh, dtype=int64),
array(beam_sh, dtype=int64),
beam_flat,
lam_beam[lam_index][nonz],
)
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# n1 = np.sum(np.isinf(model))
# n2 = np.sum(np.isnan(model))
# n3 = np.sum(np.isinf(modelf))
# n4 = np.sum(np.isnan(modelf))
# if n1>0 or n2 > 0:
# print("DEBUG: SpecDisperser, inf:%d, nan:%d--------%d,%d"%(n1, n2, n3, n4))
# print(dypix)
# n1 = np.sum(np.isinf(self.thumb_img.astype(np.float32)))
# n2 = np.sum(np.isnan(self.thumb_img.astype(np.float32)))
# n3 = np.sum(np.isinf(yfrac_beam))
# n4 = np.sum(np.isnan(yfrac_beam))
# n5 = np.sum(np.isinf(sensitivity_beam))
# n6 = np.sum(np.isnan(sensitivity_beam))
# print("DEBUG: SpecDisperser, innput ---inf:%d, nan:%d, yfrac_beam:%d/%d, sensitivity_beam:%d/%d"%(n1, n2, n3, n4, n5, n6))
self.beam_flux[beam] = sum(modelf)
if self.isAlongY == 1:
model, _, _ = rotate90(array_orig=model, isClockwise=0)
return model, originOut_x, originOut_y, dxpix, dypix, lam_beam, ysens
def writerSensitivityFile(self, conffile="", beam="", w=None, sens=None):
orders = {"A": "1st", "B": "0st", "C": "2st", "D": "-1st", "E": "-2st"}
sens_file_name = conffile[0:-5] + \
"_sensitivity_" + orders[beam] + ".fits"
senstivity_out = Table(
array([w, sens]).T, names=("WAVELENGTH", "SENSITIVITY"))
"""
Demonstrate aXe trace polynomials.
"""
class aXeConf:
def __init__(self, conf_file="WFC3.IR.G141.V2.5.conf"):
"""Read an aXe-compatible configuration file
Parameters
----------
conf_file: str
Filename of the configuration file to read
"""
if conf_file is not None:
self.conf = self.read_conf_file(conf_file)
self.conf_file = conf_file
self.count_beam_orders()
# Global XOFF/YOFF offsets
if "XOFF" in self.conf.keys():
self.xoff = np.float(self.conf["XOFF"])
if "YOFF" in self.conf.keys():
self.yoff = np.float(self.conf["YOFF"])
def read_conf_file(self, conf_file="WFC3.IR.G141.V2.5.conf"):
"""Read an aXe config file, convert floats and arrays
Parameters
----------
conf_file: str
Filename of the configuration file to read.
Parameters are stored in an OrderedDict in `self.conf`.
"""
from collections import OrderedDict
conf = OrderedDict()
lines = open(conf_file).readlines()
for line in lines:
# empty / commented lines
if (line.startswith("#")) | (line.strip() == "") | ('"' in line):
continue
# split the line, taking out ; and # comments
param = spl[0]
if len(spl) > 2:
value = np.cast[float](spl[1:])
else:
try:
value = float(spl[1])
except:
value = spl[1]
conf[param] = value
return conf
def count_beam_orders(self):
"""Get the maximum polynomial order in DYDX or DLDP for each beam"""
for beam in ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J"]:
while "DYDX_{0:s}_{1:d}".format(beam, order) in self.conf.keys():
while "DLDP_{0:s}_{1:d}".format(beam, order) in self.conf.keys():
order += 1
self.orders[beam] = order - 1
def get_beams(self):
import os
from collections import OrderedDict
from astropy.table import Table, Column
self.dxlam = OrderedDict()
self.nx = OrderedDict()
self.sens = OrderedDict()
self.beams = []
for beam in self.orders:
if self.orders[beam] > 0:
self.beams.append(beam)
self.dxlam[beam] = np.arange(
self.conf["BEAM{0}".format(beam)].min(), self.conf["BEAM{0}".format(beam)].max(), dtype=int
)
self.nx[beam] = int(self.dxlam[beam].max() -
self.dxlam[beam].min()) + 1
"{0}/{1}".format(os.path.dirname(self.conf_file),
self.conf["SENSITIVITY_{0}".format(beam)])
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# self.sens[beam].wave = np.cast[np.double](self.sens[beam]['WAVELENGTH'])
# self.sens[beam].sens = np.cast[np.double](self.sens[beam]['SENSITIVITY'])
# Need doubles for interpolating functions
for col in self.sens[beam].colnames:
data = np.cast[np.double](self.sens[beam][col])
self.sens[beam].remove_column(col)
self.sens[beam].add_column(Column(data=data, name=col))
self.beams.sort()
def field_dependent(self, xi, yi, coeffs):
"""aXe field-dependent coefficients
See the `aXe manual <http://axe.stsci.edu/axe/manual/html/node7.html#SECTION00721200000000000000>`_ for a description of how the field-dependent coefficients are specified.
Parameters
----------
xi, yi : float or array-like
Coordinate to evaluate the field dependent coefficients, where
`xi = x-REFX` and `yi = y-REFY`.
coeffs : array-like
Field-dependency coefficients
Returns
-------
a : float or array-like
Evaluated field-dependent coefficients
"""
# number of coefficients for a given polynomial order
# 1:1, 2:3, 3:6, 4:10, order:order*(order+1)/2
if isinstance(coeffs, float):
order = 1
else:
order = int(-1 + np.sqrt(1 + 8 * len(coeffs))) // 2
# Build polynomial terms array
# $a = a_0+a_1x_i+a_2y_i+a_3x_i^2+a_4x_iy_i+a_5yi^2+$ ...
xy = []
for p in range(order):
for px in range(p + 1):
# print 'x**%d y**%d' %(p-px, px)
xy.append(xi ** (p - px) * yi ** (px))
# Evaluate the polynomial, allowing for N-dimensional inputs
a = np.sum((np.array(xy).T * coeffs).T, axis=0)
return a
def evaluate_dp(self, dx, dydx):
"""Evalate arc length along the trace given trace polynomial coefficients
Parameters
----------
dx : array-like
x pixel to evaluate
dydx : array-like
Coefficients of the trace polynomial
Returns
-------
dp : array-like
Arc length along the trace at position `dx`.
For `dydx` polynomial orders 0, 1 or 2, integrate analytically.
Higher orders must be integrated numerically.
**Constant:**
.. math:: dp = dx
**Linear:**
.. math:: dp = \sqrt{1+\mathrm{DYDX}[1]}\cdot dx
**Quadratic:**
.. math:: u = \mathrm{DYDX}[1] + 2\ \mathrm{DYDX}[2]\cdot dx
.. math:: dp = (u \sqrt{1+u^2} + \mathrm{arcsinh}\ u) / (4\cdot \mathrm{DYDX}[2])
"""
# dp is the arc length along the trace
# $\lambda = dldp_0 + dldp_1 dp + dldp_2 dp^2$ ...
poly_order = len(dydx) - 1
if np.abs(np.unique(dydx[2])).max() == 0:
poly_order = 1
if poly_order == 0: # dy=0
dp = dx
elif poly_order == 1: # constant dy/dx
dp = np.sqrt(1 + dydx[1] ** 2) * (dx)
elif poly_order == 2: # quadratic trace
u0 = dydx[1] + 2 * dydx[2] * (0)
dp0 = (u0 * np.sqrt(1 + u0**2) + np.arcsinh(u0)) / (4 * dydx[2])
dp = (u * np.sqrt(1 + u**2) + np.arcsinh(u)) / (4 * dydx[2]) - dp0
else:
# high order shape, numerical integration along trace
# (this can be slow)
xmin = np.minimum((dx).min(), 0)
xmax = np.maximum((dx).max(), 0)
xfull = np.arange(xmin, xmax)
dyfull = 0
for i in range(1, poly_order):
dyfull += i * dydx[i] * (xfull - 0.5) ** (i - 1)
# Integrate from 0 to dx / -dx
dpfull[lt0] = np.cumsum(
np.sqrt(1 + dyfull[lt0][::-1] ** 2))[::-1]
dpfull[lt0] *= -1
#
gt0 = xfull > 0
if gt0.sum() > 0:
dpfull[gt0] = np.cumsum(np.sqrt(1 + dyfull[gt0] ** 2))
dp = np.interp(dx, xfull, dpfull)
if dp[-1] == dp[-2]:
dp[-1] = dp[-2] + np.diff(dp)[-2]
return dp
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"""Get an aXe beam trace for an input reference pixel and list of output x pixels `dx`
Parameters
----------
x, y : float or array-like
Evaluate trace definition at detector coordinates `x` and `y`.
dx : float or array-like
Offset in x pixels from `(x,y)` where to compute trace offset and
effective wavelength
beam : str
Beam name (i.e., spectral order) to compute. By aXe convention,
`beam='A'` is the first order, 'B' is the zeroth order and
additional beams are the higher positive and negative orders.
Returns
-------
dy : float or array-like
Center of the trace in y pixels offset from `(x,y)` evaluated at
`dx`.
lam : float or array-like
Effective wavelength along the trace evaluated at `dx`.
"""
NORDER = self.orders[beam] + 1
xi, yi = x - self.xoff, y - self.yoff
xoff_beam = self.field_dependent(
xi, yi, self.conf["XOFF_{0}".format(beam)])
yoff_beam = self.field_dependent(
xi, yi, self.conf["YOFF_{0}".format(beam)])
# y offset of trace (DYDX)
dydx = np.zeros(NORDER) # 0 #+1.e-80
dydx = [0] * NORDER
for i in range(NORDER):
if "DYDX_{0:s}_{1:d}".format(beam, i) in self.conf.keys():
coeffs = self.conf["DYDX_{0:s}_{1:d}".format(beam, i)]
dydx[i] = self.field_dependent(xi, yi, coeffs)
# $dy = dydx_0+dydx_1 dx+dydx_2 dx^2+$ ...
dy = yoff_beam
for i in range(NORDER):
dy += dydx[i] * (dx - xoff_beam) ** i
# wavelength solution
dldp = np.zeros(NORDER)
dldp = [0] * NORDER
for i in range(NORDER):
if "DLDP_{0:s}_{1:d}".format(beam, i) in self.conf.keys():
coeffs = self.conf["DLDP_{0:s}_{1:d}".format(beam, i)]
self.eval_input = {"x": x, "y": y, "beam": beam, "dx": dx}
self.eval_output = {
"xi": xi,
"yi": yi,
"dldp": dldp,
"dydx": dydx,
"xoff_beam": xoff_beam,
"yoff_beam": yoff_beam,
"dy": dy,
}
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dp = self.evaluate_dp(dx - xoff_beam, dydx)
# ## dp is the arc length along the trace
# ## $\lambda = dldp_0 + dldp_1 dp + dldp_2 dp^2$ ...
# if self.conf['DYDX_ORDER_%s' %(beam)] == 0: ## dy=0
# dp = dx-xoff_beam
# elif self.conf['DYDX_ORDER_%s' %(beam)] == 1: ## constant dy/dx
# dp = np.sqrt(1+dydx[1]**2)*(dx-xoff_beam)
# elif self.conf['DYDX_ORDER_%s' %(beam)] == 2: ## quadratic trace
# u0 = dydx[1]+2*dydx[2]*(0)
# dp0 = (u0*np.sqrt(1+u0**2)+np.arcsinh(u0))/(4*dydx[2])
# u = dydx[1]+2*dydx[2]*(dx-xoff_beam)
# dp = (u*np.sqrt(1+u**2)+np.arcsinh(u))/(4*dydx[2])-dp0
# else:
# ## high order shape, numerical integration along trace
# ## (this can be slow)
# xmin = np.minimum((dx-xoff_beam).min(), 0)
# xmax = np.maximum((dx-xoff_beam).max(), 0)
# xfull = np.arange(xmin, xmax)
# dyfull = 0
# for i in range(1, NORDER):
# dyfull += i*dydx[i]*(xfull-0.5)**(i-1)
#
# ## Integrate from 0 to dx / -dx
# dpfull = xfull*0.
# lt0 = xfull <= 0
# if lt0.sum() > 1:
# dpfull[lt0] = np.cumsum(np.sqrt(1+dyfull[lt0][::-1]**2))[::-1]
# dpfull[lt0] *= -1
# #
# gt0 = xfull >= 0
# if gt0.sum() > 0:
# dpfull[gt0] = np.cumsum(np.sqrt(1+dyfull[gt0]**2))
#
# dp = np.interp(dx-xoff_beam, xfull, dpfull)
# Evaluate dldp
"""
Make a demo plot of the beams of a given configuration file
"""
import matplotlib.pyplot as plt
x0, x1 = 507, 507
dx = np.arange(-800, 1200)
x0, x1 = 2124, 1024
dx = np.arange(-1200, 1200)
s = 200 # marker size
fig = plt.figure(figsize=[10, 3])
plt.scatter(0, 0, marker="s", s=s, color="black",
edgecolor="0.8", label="Direct")
xoff = self.field_dependent(
x0, x1, self.conf["XOFF_{0}".format(beam)])
dy, lam = self.get_beam_trace(x0, x1, dx=dx, beam=beam)
plt.scatter(dx[ok] + xoff, dy[ok], c=lam[ok] / 1.0e4,
marker="s", s=s, alpha=0.5, edgecolor="None")
plt.text(np.median(dx[ok]), np.median(
dy[ok]) + 1, beam, ha="center", va="center", fontsize=14)
print("Beam {0}, lambda=({1:.1f} - {2:.1f})".format(beam,
lam[ok].min(), lam[ok].max()))
# """Load parameters from an aXe configuration file
# Parameters
# ----------
# conf_file : str
# Filename of the configuration file
# Returns
# -------
# conf : `~grizli.grismconf.aXeConf`
# Configuration file object. Runs `conf.get_beams()` to read the
# sensitivity curves.
# """
# conf = aXeConf(conf_file)
# conf.get_beams()
# return conf