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Commit 741c0eb1 authored by JX's avatar JX 😵
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Merge remote-tracking branch 'origin/develop'

parents 6b76aa65 cdf5fb1f
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config/config_overall.yaml
View file @ 741c0eb1
......@@ -11,8 +11,8 @@
# can add some of the command-line arguments here as well;
# ok to pass either way or both, as long as they are consistent
work_dir: "/public/home/fangyuedong/project/workplace/"
run_name: "ext_on"
data_set: "csst-msc-c11-1000sqdeg-wide-v1"
run_name: "csst-msc-c11-test-wide-v1"
data_set: "csst-msc-c11-test-wide-v1"
# Project cycle and run counter are used to name the outputs
project_cycle: 11
......
config/obs_config_SCI.yaml
View file @ 741c0eb1
......@@ -9,14 +9,13 @@
###############################################
# Observation type
obs_type: "SCI"
obs_type: null
obs_type_code: "101"
obs_id: "00000001" # this setting will only be used if pointing list file is not given
# Define list of chips
# run_chips: [6,7,8,9,11,12,13,14,15,16,17,18,19,20,22,23,24,25] # Photometric chips
#run_chips: [1,2,3,4,5,10,21,26,27,28,29,30] # Spectroscopic chips
run_chips: [17, 22]
run_chips: [6,7,8,9,11,12,13,14,15,16,17,18,19,20,22,23,24,25] # Photometric chips
# run_chips: [1,2,3,4,5,10,21,26,27,28,29,30] # Spectroscopic chips
# Define observation sequence
call_sequence:
......@@ -55,11 +54,12 @@ call_sequence:
# Set it here is you want to override the default
# exptime: 150. # [s]
add_dark: YES
input_dark: YES
# Simulate brighter fatter effects
bright_fatter: {}
# Add detector defects: hot/warm pixels, bad columns
detector_defects:
hot_pixels: YES
# hot_pixels: NO
dead_pixels: YES
bad_columns: YES
# Apply CCD Saturation & Blooming
......
observation_sim/instruments/chip/Chip.py
View file @ 741c0eb1
......@@ -124,6 +124,7 @@ class Chip(FocalPlane):
self.rotate_angle = 0.
self.overscan = 1000
self.badfraction = 5e-5
self.chip_type = 'default'
# Override default values
# for key in ["gain", "bias_level, dark_exptime", "flat_exptime", "readout_time", "full_well", "read_noise", "dark_noise", "overscan"]:
# if key in config["ins_effects"]:
......
observation_sim/instruments/chip/chip_utils.py
View file @ 741c0eb1
......@@ -214,44 +214,72 @@ def get_poisson(seed=0, sky_level=0.):
return rng_poisson, poisson_noise
def get_base_img(img, chip, read_noise, readout_time, dark_noise, exptime=150., InputDark=None):
if InputDark is None:
def get_base_img(img, chip, read_noise, readout_time, dark_noise, exptime=150., InputDark=False):
if not InputDark:
# base_level = read_noise**2 + dark_noise*(exptime+0.5*readout_time)
# base_level = dark_noise*(exptime+0.5*readout_time)
base_level = dark_noise*(exptime)
base_img1 = base_level * np.ones_like(img.array)
else:
base_img1 = np.zeros_like(img.array)
ny = int(chip.npix_y/2)
nx = chip.npix_x
arr = np.arange(ny).reshape(ny, 1)
arr = np.broadcast_to(arr, (ny, nx))
base_img2 = np.zeros_like(img.array)
base_img2[:ny, :] = arr
base_img2[ny:, :] = arr[::-1, :]
base_img2[:, :] = base_img2[:, :]*(readout_time/ny)*dark_noise
return base_img1+base_img2
def add_poisson(img, chip, exptime=150., seed=0, sky_level=0., poisson_noise=None, dark_noise=None, InputDark=None):
ny = int(chip.npix_y/2)
nx = chip.npix_x
arr = np.arange(ny).reshape(ny, 1)
arr = np.broadcast_to(arr, (ny, nx))
base_img2 = np.zeros_like(img.array)
base_img2[:ny, :] = arr
base_img2[ny:, :] = arr[::-1, :]
base_img2[:, :] = base_img2[:, :]*(readout_time/ny)*dark_noise
else:
# base_img1 = np.zeros_like(img.array)
histfile = 'hist_dark_{:}.npz'.format(chip.chip_type)
try:
with pkg_resources.files('observation_sim.instruments.data.ccd').joinpath(histfile) as dark_histogram:
hist_dc = np.load(dark_histogram)
except AttributeError:
with pkg_resources.path('observation_sim.instruments.data.ccd', histfile) as dark_histogram:
hist_dc = np.load(dark_histogram)
hist = stats.rv_histogram((hist_dc['counts'], hist_dc['bins']), density=True)
xsize = chip.npix_x
ysize = chip.npix_y
seed = chip.chipID
samples = hist.rvs(size=xsize*ysize, random_state=seed)
map_dc = np.reshape(samples, [ysize, xsize])
base_img1 = map_dc*exptime
# base_img2
map_temp = np.zeros((ysize//2, 2*xsize))
map_temp[:, :xsize] = map_dc[:ysize//2, :]
map_temp[:, xsize:] = map_dc[:ysize//2-1:-1, :]
dt = readout_time/(ysize/2.)
A = map_temp
A_adjusted = np.vstack([np.zeros((1, A.shape[1])), A[:-1]])
cumsum_A = np.cumsum(A_adjusted, axis=0)
B = cumsum_A * dt
base_img2 = np.vstack([B[:, :xsize], B[::-1, xsize:]])
del hist_dc
del hist
del samples
del map_temp
del A
del A_adjusted
del cumsum_A
del B
return base_img1+base_img2, map_dc
def add_poisson(img, chip, exptime=150., seed=0, sky_level=0., poisson_noise=None, dark_noise=None, InputDark=False):
if poisson_noise is None:
_, poisson_noise = get_poisson(seed=seed, sky_level=sky_level)
read_noise = chip.read_noise
if dark_noise is None:
dark_noise = chip.dark_noise
base_img = get_base_img(img=img, chip=chip, read_noise=read_noise, readout_time=chip.readout_time,
dark_noise=dark_noise, exptime=exptime, InputDark=InputDark)
base_img, map_dc = get_base_img(img=img, chip=chip, read_noise=read_noise, readout_time=chip.readout_time, dark_noise=dark_noise, exptime=exptime, InputDark=InputDark)
img += base_img
img.addNoise(poisson_noise)
# img -= read_noise**2
if InputDark is not None:
# "Instrument/data/dark/dark_1000s_example_0.fits"
hdu = fits.open(InputDark)
img += hdu[0].data/hdu[0].header['exptime']*exptime
hdu.close()
return img, base_img
del base_img
return img, map_dc
def add_brighter_fatter(img):
......
observation_sim/instruments/data/ccd/chip_definition.json
View file @ 741c0eb1
{
"31": {
"chip_name": "FGS1A-D1",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -23,6 +24,7 @@
},
"32": {
"chip_name": "FGS1A-D2",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -45,6 +47,7 @@
},
"33": {
"chip_name": "FGS1B-D1",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -67,6 +70,7 @@
},
"34": {
"chip_name": "FGS1B-D2",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -89,6 +93,7 @@
},
"35": {
"chip_name": "FGS2A-D1",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -111,6 +116,7 @@
},
"36": {
"chip_name": "FGS2A-D2",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -133,6 +139,7 @@
},
"37": {
"chip_name": "FGS2B-D1",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -155,6 +162,7 @@
},
"38": {
"chip_name": "FGS2B-D2",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -177,6 +185,7 @@
},
"39": {
"chip_name": "FGS3-D1",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -199,6 +208,7 @@
},
"40": {
"chip_name": "FGS3-D2",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -221,6 +231,7 @@
},
"41": {
"chip_name": "FGS4-D1",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -243,6 +254,7 @@
},
"42": {
"chip_name": "FGS4-D2",
"chip_type": "default",
"pix_size": 0.0075,
"pix_scale": 0.0555,
"npix_x": 11264,
......@@ -265,6 +277,7 @@
},
"1": {
"chip_name": "GI-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -288,6 +301,7 @@
},
"2": {
"chip_name": "GV-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -311,6 +325,7 @@
},
"3": {
"chip_name": "GU-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -334,6 +349,7 @@
},
"4": {
"chip_name": "GU-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -357,6 +373,7 @@
},
"5": {
"chip_name": "GV-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -380,6 +397,7 @@
},
"6": {
"chip_name": "y-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -403,6 +421,7 @@
},
"7": {
"chip_name": "i-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -426,6 +445,7 @@
},
"8": {
"chip_name": "g-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -449,6 +469,7 @@
},
"9": {
"chip_name": "r-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -472,6 +493,7 @@
},
"10": {
"chip_name": "GI-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -495,6 +517,7 @@
},
"11": {
"chip_name": "z-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -518,6 +541,7 @@
},
"12": {
"chip_name": "NUV-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -541,6 +565,7 @@
},
"13": {
"chip_name": "NUV-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -564,6 +589,7 @@
},
"14": {
"chip_name": "u-1",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -587,6 +613,7 @@
},
"15": {
"chip_name": "y-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -610,6 +637,7 @@
},
"16": {
"chip_name": "y-3",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -633,6 +661,7 @@
},
"17": {
"chip_name": "u-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -656,6 +685,7 @@
},
"18": {
"chip_name": "NUV-3",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -679,6 +709,7 @@
},
"19": {
"chip_name": "NUV-4",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -702,6 +733,7 @@
},
"20": {
"chip_name": "z-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -725,6 +757,7 @@
},
"21": {
"chip_name": "GI-3",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -748,6 +781,7 @@
},
"22": {
"chip_name": "r-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -771,6 +805,7 @@
},
"23": {
"chip_name": "g-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -794,6 +829,7 @@
},
"24": {
"chip_name": "i-2",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -817,6 +853,7 @@
},
"25": {
"chip_name": "y-4",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -840,6 +877,7 @@
},
"26": {
"chip_name": "GV-3",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -863,6 +901,7 @@
},
"27": {
"chip_name": "GU-3",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -886,6 +925,7 @@
},
"28": {
"chip_name": "GU-4",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -909,6 +949,7 @@
},
"29": {
"chip_name": "GV-4",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......@@ -932,6 +973,7 @@
},
"30": {
"chip_name": "GI-4",
"chip_type": "default",
"pix_size": 0.01,
"pix_scale": 0.074,
"npix_x": 9216,
......
observation_sim/sim_steps/add_pattern_noise.py
View file @ 741c0eb1
......@@ -20,11 +20,13 @@ def add_poisson_and_dark(self, chip, filt, tel, pointing, catalog, obs_param):
exptime = pointing.exp_time
if obs_param["add_dark"] is True:
if obs_param["input_dark"]:
self.chip_output.Log_info(" Applying input_dark")
chip.img, _ = chip_utils.add_poisson(img=chip.img,
chip=chip,
exptime=exptime,
poisson_noise=chip.poisson_noise,
InputDark=None)
InputDark=obs_param["input_dark"])
else:
chip.img, _ = chip_utils.add_poisson(img=chip.img,
chip=chip,
......
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