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Commit a6664237 authored by Fang Yuedong's avatar Fang Yuedong
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new sim: modified ways to add detector effects: e.g. brighter-fatter etc.

parent f540664f
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ObservationSim/Instrument/Chip/Chip.py
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...@@ -12,6 +12,7 @@ from ObservationSim.Instrument.Chip import Effects as effects ...@@ -12,6 +12,7 @@ from ObservationSim.Instrument.Chip import Effects as effects
from ObservationSim.Instrument.FocalPlane import FocalPlane from ObservationSim.Instrument.FocalPlane import FocalPlane
from ObservationSim.Config.Header import generatePrimaryHeader, generateExtensionHeader from ObservationSim.Config.Header import generatePrimaryHeader, generateExtensionHeader
from ObservationSim.Instrument._util import rotate_conterclockwise from ObservationSim.Instrument._util import rotate_conterclockwise
from ObservationSim.Instrument.Chip import ChipUtils as chip_utils
try: try:
import importlib.resources as pkg_resources import importlib.resources as pkg_resources
...@@ -22,11 +23,7 @@ except ImportError: ...@@ -22,11 +23,7 @@ except ImportError:
class Chip(FocalPlane): class Chip(FocalPlane):
def __init__(self, chipID, ccdEffCurve_dir=None, CRdata_dir=None, sls_dir=None, config=None, treering_func=None, logger=None): def __init__(self, chipID, ccdEffCurve_dir=None, CRdata_dir=None, sls_dir=None, config=None, treering_func=None, logger=None):
# Get focal plane (instance of paraent class) info # Get focal plane (instance of paraent class) info
# TODO: use chipID to config individual chip?
super().__init__() super().__init__()
# self.npix_x = 9216
# self.npix_y = 9232
# self.pix_scale = 0.074 # pixel scale
self.nsecy = 2 self.nsecy = 2
self.nsecx = 8 self.nsecx = 8
self.gain_channel = np.ones(self.nsecy* self.nsecx) self.gain_channel = np.ones(self.nsecy* self.nsecx)
...@@ -42,12 +39,10 @@ class Chip(FocalPlane): ...@@ -42,12 +39,10 @@ class Chip(FocalPlane):
self.filter_id, self.filter_type = self.getChipFilter() self.filter_id, self.filter_type = self.getChipFilter()
self.survey_type = self._getSurveyType() self.survey_type = self._getSurveyType()
# [TODO]
if self.filter_type != "FGS": if self.filter_type != "FGS":
self._getChipRowCol() self._getChipRowCol()
# Set the relavent specs for FGS detectors # Set the relavent specs for detectors
# [TODO]
try: try:
with pkg_resources.files('ObservationSim.Instrument.data.ccd').joinpath("chip_definition.json") as chip_definition: with pkg_resources.files('ObservationSim.Instrument.data.ccd').joinpath("chip_definition.json") as chip_definition:
with open(chip_definition, "r") as f: with open(chip_definition, "r") as f:
...@@ -58,6 +53,7 @@ class Chip(FocalPlane): ...@@ -58,6 +53,7 @@ class Chip(FocalPlane):
chip_dict = json.load(f)[str(self.chipID)] chip_dict = json.load(f)[str(self.chipID)]
for key in chip_dict: for key in chip_dict:
setattr(self, key, chip_dict[key]) setattr(self, key, chip_dict[key])
if self.filter_type == "FGS": if self.filter_type == "FGS":
if ("field_dist" in config) and (config["ins_effects"]["field_dist"]) == False: if ("field_dist" in config) and (config["ins_effects"]["field_dist"]) == False:
self.fdModel = None self.fdModel = None
...@@ -77,7 +73,6 @@ class Chip(FocalPlane): ...@@ -77,7 +73,6 @@ class Chip(FocalPlane):
self.fdModel = None self.fdModel = None
else: else:
try: try:
# with pkg_resources.files('ObservationSim.Instrument.data.field_distortion').joinpath("FieldDistModelGlobal_mainFP_v1.0.pickle") as field_distortion:
with pkg_resources.files('ObservationSim.Instrument.data.field_distortion').joinpath("FieldDistModel_v2.0.pickle") as field_distortion: with pkg_resources.files('ObservationSim.Instrument.data.field_distortion').joinpath("FieldDistModel_v2.0.pickle") as field_distortion:
with open(field_distortion, "rb") as f: with open(field_distortion, "rb") as f:
self.fdModel = pickle.load(f) self.fdModel = pickle.load(f)
...@@ -88,9 +83,11 @@ class Chip(FocalPlane): ...@@ -88,9 +83,11 @@ class Chip(FocalPlane):
# Get boundary (in pix) # Get boundary (in pix)
self.bound = self.getChipLim() self.bound = self.getChipLim()
self.ccdEffCurve_dir = ccdEffCurve_dir self.ccdEffCurve_dir = ccdEffCurve_dir
self.CRdata_dir = CRdata_dir self.CRdata_dir = CRdata_dir
slsconfs = self.getChipSLSConf()
slsconfs = chip_utils.getChipSLSConf(chipID=self.chipID)
if np.size(slsconfs) == 1: if np.size(slsconfs) == 1:
try: try:
with pkg_resources.files('ObservationSim.Instrument.data.sls_conf').joinpath(slsconfs) as conf_path: with pkg_resources.files('ObservationSim.Instrument.data.sls_conf').joinpath(slsconfs) as conf_path:
...@@ -157,13 +154,6 @@ class Chip(FocalPlane): ...@@ -157,13 +154,6 @@ class Chip(FocalPlane):
if filter_type in ['NUV', 'u', 'GU']: filename = 'UV0.txt' if filter_type in ['NUV', 'u', 'GU']: filename = 'UV0.txt'
if filter_type in ['g', 'r', 'GV', 'FGS']: filename = 'Astro_MB.txt' # TODO, need to switch to the right efficiency curvey for FGS CMOS if filter_type in ['g', 'r', 'GV', 'FGS']: filename = 'Astro_MB.txt' # TODO, need to switch to the right efficiency curvey for FGS CMOS
if filter_type in ['i', 'z', 'y', 'GI']: filename = 'Basic_NIR.txt' if filter_type in ['i', 'z', 'y', 'GI']: filename = 'Basic_NIR.txt'
# Mirror efficiency:
# if filter_type == 'NUV': mirror_eff = 0.54
# if filter_type == 'u': mirror_eff = 0.68
# if filter_type in ['g', 'r', 'i', 'z', 'y']: mirror_eff = 0.8
# if filter_type in ['GU', 'GV', 'GI']: mirror_eff = 1. # Not sure if this is right
# path = os.path.join(self.ccdEffCurve_dir, filename)
# table = Table.read(path, format='ascii')
try: try:
with pkg_resources.files('ObservationSim.Instrument.data.ccd').joinpath(filename) as ccd_path: with pkg_resources.files('ObservationSim.Instrument.data.ccd').joinpath(filename) as ccd_path:
table = Table.read(ccd_path, format='ascii') table = Table.read(ccd_path, format='ascii')
...@@ -181,13 +171,26 @@ class Chip(FocalPlane): ...@@ -181,13 +171,26 @@ class Chip(FocalPlane):
except AttributeError: except AttributeError:
with pkg_resources.path('ObservationSim.Instrument.data', "wfc-cr-attachpixel.dat") as cr_path: with pkg_resources.path('ObservationSim.Instrument.data', "wfc-cr-attachpixel.dat") as cr_path:
self.attachedSizes = np.loadtxt(cr_path) self.attachedSizes = np.loadtxt(cr_path)
def loadSLSFLATCUBE(self, flat_fn='flat_cube.fits'):
try:
with pkg_resources.files('ObservationSim.Instrument.data').joinpath(flat_fn) as data_path:
flat_fits = fits.open(data_path, ignore_missing_simple=True)
except AttributeError:
with pkg_resources.path('ObservationSim.Instrument.data', flat_fn) as data_path:
flat_fits = fits.open(data_path, ignore_missing_simple=True)
fl = len(flat_fits)
fl_sh = flat_fits[0].data.shape
assert fl == 4, 'FLAT Field Cube is Not 4 layess!!!!!!!'
self.flat_cube = np.zeros([fl, fl_sh[0], fl_sh[1]])
for i in np.arange(0, fl, 1):
self.flat_cube[i] = flat_fits[i].data
def getChipFilter(self, chipID=None, filter_layout=None): def getChipFilter(self, chipID=None):
"""Return the filter index and type for a given chip #(chipID) """Return the filter index and type for a given chip #(chipID)
""" """
filter_type_list = ["NUV","u", "g", "r", "i","z","y","GU", "GV", "GI", "FGS"] filter_type_list = ["NUV","u", "g", "r", "i","z","y","GU", "GV", "GI", "FGS"]
if filter_layout is not None:
return filter_layout[chipID][0], filter_layout[chipID][1]
if chipID == None: if chipID == None:
chipID = self.chipID chipID = self.chipID
...@@ -217,45 +220,18 @@ class Chip(FocalPlane): ...@@ -217,45 +220,18 @@ class Chip(FocalPlane):
Returns: Returns:
A galsim BoundsD object A galsim BoundsD object
""" """
if ((chipID is not None) and (int(chipID) <= 30)) or (self.chipID <= 30): xmin, xmax, ymin, ymax = 1e10, -1e10, 1e10, -1e10
# [TODO] xcen = self.x_cen / self.pix_size
if chipID == None: ycen = self.y_cen / self.pix_size
chipID = self.chipID sign_x = [-1., 1., -1., 1.]
rowID, colID = self.rowID, self.colID sign_y = [-1., -1., 1., 1.]
else: for i in range(4):
rowID, colID = self.getChipRowCol(chipID) x = xcen + sign_x[i] * self.npix_x / 2.
gx1, gx2 = self.npix_gap_x y = ycen + sign_y[i] * self.npix_y / 2.
gy = self.npix_gap_y x, y = rotate_conterclockwise(x0=xcen, y0=ycen, x=x, y=y, angle=self.rotate_angle)
xmin, xmax = min(xmin, x), max(xmax, x)
# xlim of a given CCD chip ymin, ymax = min(ymin, y), max(ymax, y)
xrem = 2*(colID - 1) - (self.nchip_x - 1) return galsim.BoundsD(xmin, xmax, ymin, ymax)
xcen = (self.npix_x//2 + gx1//2) * xrem
if chipID >= 26 or chipID == 21:
xcen = (self.npix_x//2 + gx1//2) * xrem - (gx2-gx1)
if chipID <= 5 or chipID == 10:
xcen = (self.npix_x//2 + gx1//2) * xrem + (gx2-gx1)
nx0 = xcen - self.npix_x//2 + 1
nx1 = xcen + self.npix_x//2
# ylim of a given CCD chip
yrem = (rowID - 1) - self.nchip_y // 2
ycen = (self.npix_y + gy) * yrem
ny0 = ycen - self.npix_y//2 + 1
ny1 = ycen + self.npix_y//2
return galsim.BoundsD(nx0-1, nx1-1, ny0-1, ny1-1)
else:
xmin, xmax, ymin, ymax = 1e10, -1e10, 1e10, -1e10
xcen = self.x_cen / self.pix_size
ycen = self.y_cen / self.pix_size
sign_x = [-1., 1., -1., 1.]
sign_y = [-1., -1., 1., 1.]
for i in range(4):
x = xcen + sign_x[i] * self.npix_x / 2.
y = ycen + sign_y[i] * self.npix_y / 2.
x, y = rotate_conterclockwise(x0=xcen, y0=ycen, x=x, y=y, angle=self.rotate_angle)
xmin, xmax = min(xmin, x), max(xmax, x)
ymin, ymax = min(ymin, y), max(ymax, y)
return galsim.BoundsD(xmin, xmax, ymin, ymax)
...@@ -291,83 +267,8 @@ class Chip(FocalPlane): ...@@ -291,83 +267,8 @@ class Chip(FocalPlane):
noise = self.dark_noise * exptime + self.read_noise**2 noise = self.dark_noise * exptime + self.read_noise**2
return noise return noise
def getChipSLSConf(self):
confFile = ''
if self.chipID == 1: confFile = ['CSST_GI2.conf', 'CSST_GI1.conf']
if self.chipID == 2: confFile = ['CSST_GV4.conf', 'CSST_GV3.conf']
if self.chipID == 3: confFile = ['CSST_GU2.conf', 'CSST_GU1.conf']
if self.chipID == 4: confFile = ['CSST_GU4.conf', 'CSST_GU3.conf']
if self.chipID == 5: confFile = ['CSST_GV2.conf', 'CSST_GV1.conf']
if self.chipID == 10: confFile = ['CSST_GI4.conf', 'CSST_GI3.conf']
if self.chipID == 21: confFile = ['CSST_GI6.conf', 'CSST_GI5.conf']
if self.chipID == 26: confFile = ['CSST_GV8.conf', 'CSST_GV7.conf']
if self.chipID == 27: confFile = ['CSST_GU6.conf', 'CSST_GU5.conf']
if self.chipID == 28: confFile = ['CSST_GU8.conf', 'CSST_GU7.conf']
if self.chipID == 29: confFile = ['CSST_GV6.conf', 'CSST_GV5.conf']
if self.chipID == 30: confFile = ['CSST_GI8.conf', 'CSST_GI7.conf']
return confFile
def generateHeader(self, ra_cen, dec_cen, img_rot, im_type, pointing_ID, exptime=150., timestamp = 1621915200):
datetime_obs = datetime.utcfromtimestamp(timestamp)
date_obs = datetime_obs.strftime("%y%m%d")
time_obs = datetime_obs.strftime("%H%M%S")
h_prim = generatePrimaryHeader(
xlen=self.npix_x,
ylen=self.npix_y,
pointNum = str(pointing_ID),
ra=ra_cen,
dec=dec_cen,
pixel_scale=self.pix_scale,
date=date_obs,
time_obs=time_obs,
im_type = im_type,
exptime=exptime,
chip_name=str(self.chipID).rjust(2, '0')
)
h_ext = generateExtensionHeader(
chip=self,
xlen=self.npix_x,
ylen=self.npix_y,
ra=ra_cen,
dec=dec_cen,
pa=img_rot.deg,
gain=self.gain,
readout=self.read_noise,
dark=self.dark_noise,
saturation=90000,
pixel_scale=self.pix_scale,
pixel_size=self.pix_size,
xcen=self.x_cen,
ycen=self.y_cen,
extName='SCI',
timestamp = timestamp,
exptime = exptime,
readoutTime = 40.)
return h_prim, h_ext
def outputCal(self, img, ra_cen, dec_cen, img_rot, im_type, pointing_ID, output_dir, exptime=150., timestamp = 1621915200):
h_prim, h_ext = self.generateHeader(
ra_cen=ra_cen,
dec_cen=dec_cen,
img_rot=img_rot,
im_type=im_type,
pointing_ID=pointing_ID,
exptime=exptime,
timestamp = timestamp)
hdu1 = fits.PrimaryHDU(header=h_prim)
hdu1.add_checksum()
hdu1.header.comments['CHECKSUM'] = 'HDU checksum'
hdu1.header.comments['DATASUM'] = 'data unit checksum'
hdu2 = fits.ImageHDU(img.array, header=h_ext)
hdu2.add_checksum()
hdu2.header.comments['XTENSION'] = 'extension type'
hdu2.header.comments['CHECKSUM'] = 'HDU checksum'
hdu2.header.comments['DATASUM'] = 'data unit checksum'
hdu1 = fits.HDUList([hdu1, hdu2])
fname = os.path.join(output_dir, h_prim['FILENAME']+'.fits')
hdu1.writeto(fname, output_verify='ignore', overwrite=True)
def addEffects(self, config, img, chip_output, filt, ra_cen, dec_cen, img_rot, exptime=150., pointing_ID=0, timestamp_obs=1621915200, pointing_type='MS', sky_map=None, tel=None, logger=None): def addEffects(self, config, img, chip_output, filt, ra_cen, dec_cen, img_rot, exptime=150., pointing_ID=0, timestamp_obs=1621915200, pointing_type='MS', sky_map=None, tel=None, logger=None):
# Set random seeds
SeedGainNonuni=int(config["random_seeds"]["seed_gainNonUniform"]) SeedGainNonuni=int(config["random_seeds"]["seed_gainNonUniform"])
SeedBiasNonuni=int(config["random_seeds"]["seed_biasNonUniform"]) SeedBiasNonuni=int(config["random_seeds"]["seed_biasNonUniform"])
SeedRnNonuni = int(config["random_seeds"]["seed_rnNonUniform"]) SeedRnNonuni = int(config["random_seeds"]["seed_rnNonUniform"])
...@@ -386,42 +287,19 @@ class Chip(FocalPlane): ...@@ -386,42 +287,19 @@ class Chip(FocalPlane):
self.logger = logger self.logger = logger
# Get Poisson noise generator # Get Poisson noise generator
seed = int(config["random_seeds"]["seed_poisson"]) + pointing_ID*30 + self.chipID rng_poisson, poisson_noise = chip_utils.get_poisson(
rng_poisson = galsim.BaseDeviate(seed) seed=int(config["random_seeds"]["seed_poisson"]) + pointing_ID*30 + self.chipID, sky_level=0.)
poisson_noise = galsim.PoissonNoise(rng_poisson, sky_level=0.)
# Add sky background # Add sky background
if sky_map is None:
sky_map = filt.getSkyNoise(exptime=exptime)
sky_map = sky_map * np.ones_like(img.array)
sky_map = galsim.Image(array=sky_map)
# Apply Poisson noise to the sky map
# (NOTE): only for photometric chips
# since it utilize the photon shooting
# to draw stamps
if self.survey_type == "photometric":
sky_map.addNoise(poisson_noise)
elif img.array.shape != sky_map.shape:
raise ValueError("The shape img and sky_map must be equal.")
elif tel is not None: # If sky_map is given in flux
sky_map = sky_map * tel.pupil_area * exptime
if config["ins_effects"]["add_back"] == True: if config["ins_effects"]["add_back"] == True:
img += sky_map img, sky_map = chip_utils.add_sky_background(img=img, filt=filt, exptime=exptime, sky_map=sky_map, tel=tel)
del sky_map del sky_map
# Apply flat-field large scale structure for one chip # Apply flat-field large scale structure for one chip
if config["ins_effects"]["flat_fielding"] == True: if config["ins_effects"]["flat_fielding"] == True:
if self.logger is not None: chip_utils.log_info(msg=" Creating and applying Flat-Fielding", logger=self.logger)
self.logger.info(" Creating and applying Flat-Fielding") chip_utils.log_info(msg=str(img.bounds), logger=self.logger)
msg = str(img.bounds) flat_img, flat_normal = chip_utils.get_flat(img=img, seed=int(config["random_seeds"]["seed_flat"]))
self.logger.info(msg)
else:
print(" Creating and applying Flat-Fielding", flush=True)
print(img.bounds, flush=True)
flat_img = effects.MakeFlatSmooth(
img.bounds,
int(config["random_seeds"]["seed_flat"]))
flat_normal = flat_img / np.mean(flat_img.array)
if self.survey_type == "photometric": if self.survey_type == "photometric":
img *= flat_normal img *= flat_normal
del flat_normal del flat_normal
...@@ -430,10 +308,7 @@ class Chip(FocalPlane): ...@@ -430,10 +308,7 @@ class Chip(FocalPlane):
# Apply Shutter-effect for one chip # Apply Shutter-effect for one chip
if config["ins_effects"]["shutter_effect"] == True: if config["ins_effects"]["shutter_effect"] == True:
if self.logger is not None: chip_utils.log_info(msg=" Apply shutter effect", logger=self.logger)
self.logger.info(" Apply shutter effect")
else:
print(" Apply shutter effect", flush=True)
shuttimg = effects.ShutterEffectArr(img, t_shutter=1.3, dist_bearing=735, dt=1E-3) # shutter effect normalized image for this chip shuttimg = effects.ShutterEffectArr(img, t_shutter=1.3, dist_bearing=735, dt=1E-3) # shutter effect normalized image for this chip
if self.survey_type == "photometric": if self.survey_type == "photometric":
img *= shuttimg img *= shuttimg
...@@ -443,36 +318,19 @@ class Chip(FocalPlane): ...@@ -443,36 +318,19 @@ class Chip(FocalPlane):
del shutt_gsimg del shutt_gsimg
del shuttimg del shuttimg
# Add Poisson noise to the resulting images # # Add Poisson noise to the resulting images
# (NOTE): this can only applied to the slitless image # # (NOTE): this can only applied to the slitless image
# since it dose not use photon shooting to draw stamps # # since it dose not use photon shooting to draw stamps
if self.survey_type == "spectroscopic": # if self.survey_type == "spectroscopic":
img.addNoise(poisson_noise) # img.addNoise(poisson_noise)
# Add cosmic-rays # Add cosmic-rays
if config["ins_effects"]["cosmic_ray"] == True and pointing_type=='MS': if config["ins_effects"]["cosmic_ray"] == True and pointing_type=='MS':
if self.logger is not None: chip_utils.log_info(msg=" Adding Cosmic-Ray", logger=self.logger)
self.logger.info((" Adding Cosmic-Ray")) img, crmap_gsimg, cr_event_num = chip_utils.add_cosmic_rays(img=img, chip=self, exptime=exptime,
else: seed=SeedCosmicRay+pointing_ID*30+self.chipID)
print(" Adding Cosmic-Ray", flush=True) chip_utils.outputCal(
cr_map, cr_event_num = effects.produceCR_Map( chip=self,
xLen=self.npix_x, yLen=self.npix_y,
exTime=exptime+0.5*self.readout_time,
cr_pixelRatio=0.003*(exptime+0.5*self.readout_time)/600.,
gain=self.gain,
attachedSizes=self.attachedSizes,
seed=SeedCosmicRay+pointing_ID*30+self.chipID) # seed: obj-imaging:+0; bias:+1; dark:+2; flat:+3;
img += cr_map
cr_map[cr_map > 65535] = 65535
cr_map[cr_map < 0] = 0
crmap_gsimg = galsim.Image(cr_map, dtype=np.uint16)
del cr_map
# crmap_gsimg.write("%s/CosmicRay_%s_1.fits" % (chip_output.subdir, self.chipID))
# crmap_gsimg.write("%s/CosmicRay_%s.fits" % (chip_output.subdir, self.chipID))
# datetime_obs = datetime.utcfromtimestamp(timestamp_obs)
# date_obs = datetime_obs.strftime("%y%m%d")
# time_obs = datetime_obs.strftime("%H%M%S")
self.outputCal(
img=crmap_gsimg, img=crmap_gsimg,
ra_cen=ra_cen, ra_cen=ra_cen,
dec_cen=dec_cen, dec_cen=dec_cen,
...@@ -486,25 +344,28 @@ class Chip(FocalPlane): ...@@ -486,25 +344,28 @@ class Chip(FocalPlane):
# Apply PRNU effect and output PRNU flat file: # Apply PRNU effect and output PRNU flat file:
if config["ins_effects"]["prnu_effect"] == True: if config["ins_effects"]["prnu_effect"] == True:
if self.logger is not None: chip_utils.log_info(msg=" Applying PRNU effect", logger=self.logger)
self.logger.info(" Applying PRNU effect") img, prnu_img = chip_utils.add_PRNU(img=img, chip=self,
else: seed=int(config["random_seeds"]["seed_prnu"]+self.chipID))
print(" Applying PRNU effect", flush=True)
prnu_img = effects.PRNU_Img(
xsize=self.npix_x,
ysize=self.npix_y,
sigma=0.01,
seed=int(config["random_seeds"]["seed_prnu"]+self.chipID))
img *= prnu_img
if config["output_setting"]["prnu_output"] == True: if config["output_setting"]["prnu_output"] == True:
prnu_img.write("%s/FlatImg_PRNU_%s.fits" % (chip_output.subdir,self.chipID)) prnu_img.write("%s/FlatImg_PRNU_%s.fits" % (chip_output.subdir,self.chipID))
if config["output_setting"]["flat_output"] == False: if config["output_setting"]["flat_output"] == False:
del prnu_img del prnu_img
# Add dark current # # Add dark current
# if config["ins_effects"]["add_dark"] == True:
# dark_noise = galsim.DeviateNoise(galsim.PoissonDeviate(rng_poisson, self.dark_noise*(exptime+0.5*self.readout_time)))
# img.addNoise(dark_noise)
# Add dark current & Poisson noise
if config["ins_effects"]["add_dark"] == True: if config["ins_effects"]["add_dark"] == True:
dark_noise = galsim.DeviateNoise(galsim.PoissonDeviate(rng_poisson, self.dark_noise*(exptime+0.5*self.readout_time))) img, _ = chip_utils.add_poisson(img=img, chip=self, exptime=exptime, poisson_noise=poisson_noise)
img.addNoise(dark_noise) else:
img, _ = chip_utils.add_poisson(img=img, chip=self, exptime=exptime, poisson_noise=poisson_noise, dark_noise=0.)
# Add diffusion & brighter-fatter effects
if config["ins_effects"]["bright_fatter"] == True:
img = chip_utils.add_brighter_fatter(img=img)
# Add Hot Pixels or/and Dead Pixels # Add Hot Pixels or/and Dead Pixels
rgbadpix = Generator(PCG64(int(SeedDefective+self.chipID))) rgbadpix = Generator(PCG64(int(SeedDefective+self.chipID)))
...@@ -517,34 +378,22 @@ class Chip(FocalPlane): ...@@ -517,34 +378,22 @@ class Chip(FocalPlane):
# Apply Nonlinearity on the chip image # Apply Nonlinearity on the chip image
if config["ins_effects"]["non_linear"] == True: if config["ins_effects"]["non_linear"] == True:
if self.logger is not None: chip_utils.log_info(msg=" Applying Non-Linearity on the chip image", logger=self.logger)
self.logger.info(" Applying Non-Linearity on the chip image")
else:
print(" Applying Non-Linearity on the chip image", flush=True)
img = effects.NonLinearity(GSImage=img, beta1=5.e-7, beta2=0) img = effects.NonLinearity(GSImage=img, beta1=5.e-7, beta2=0)
# Apply CCD Saturation & Blooming # Apply CCD Saturation & Blooming
if config["ins_effects"]["saturbloom"] == True: if config["ins_effects"]["saturbloom"] == True:
if self.logger is not None: chip_utils.log_info(msg=" Applying CCD Saturation & Blooming", logger=self.logger)
self.logger.info(" Applying CCD Saturation & Blooming")
else:
print(" Applying CCD Saturation & Blooming")
img = effects.SaturBloom(GSImage=img, nsect_x=1, nsect_y=1, fullwell=fullwell) img = effects.SaturBloom(GSImage=img, nsect_x=1, nsect_y=1, fullwell=fullwell)
# Apply CTE Effect # Apply CTE Effect
if config["ins_effects"]["cte_trail"] == True: if config["ins_effects"]["cte_trail"] == True:
if self.logger is not None: chip_utils.log_info(msg=" Apply CTE Effect", logger=self.logger)
self.logger.info(" Apply CTE Effect")
else:
print(" Apply CTE Effect")
img = effects.CTE_Effect(GSImage=img, threshold=27) img = effects.CTE_Effect(GSImage=img, threshold=27)
# Add Bias level # Add Bias level
if config["ins_effects"]["add_bias"] == True: if config["ins_effects"]["add_bias"] == True:
if self.logger is not None: chip_utils.log_info(msg=" Adding Bias level and 16-channel non-uniformity", logger=self.logger)
self.logger.info(" Adding Bias level and 16-channel non-uniformity")
else:
print(" Adding Bias level and 16-channel non-uniformity")
if config["ins_effects"]["bias_16channel"] == True: if config["ins_effects"]["bias_16channel"] == True:
img = effects.AddBiasNonUniform16(img, img = effects.AddBiasNonUniform16(img,
bias_level=float(self.bias_level), bias_level=float(self.bias_level),
...@@ -562,10 +411,7 @@ class Chip(FocalPlane): ...@@ -562,10 +411,7 @@ class Chip(FocalPlane):
img.addNoise(readout_noise) img.addNoise(readout_noise)
# Apply Gain & Quantization # Apply Gain & Quantization
if self.logger is not None: chip_utils.log_info(msg=" Applying Gain (and 16 channel non-uniformity) & Quantization", logger=self.logger)
self.logger.info(" Applying Gain (and 16 channel non-uniformity) & Quantization")
else:
print(" Applying Gain (and 16 channel non-uniformity) & Quantization", flush=True)
if config["ins_effects"]["gain_16channel"] == True: if config["ins_effects"]["gain_16channel"] == True:
img, self.gain_channel = effects.ApplyGainNonUniform16( img, self.gain_channel = effects.ApplyGainNonUniform16(
img, gain=self.gain, img, gain=self.gain,
...@@ -633,12 +479,9 @@ class Chip(FocalPlane): ...@@ -633,12 +479,9 @@ class Chip(FocalPlane):
BiasCombImg.replaceNegative(replace_value=0) BiasCombImg.replaceNegative(replace_value=0)
BiasCombImg.quantize() BiasCombImg.quantize()
BiasCombImg = galsim.ImageUS(BiasCombImg) BiasCombImg = galsim.ImageUS(BiasCombImg)
# BiasCombImg.write("%s/BiasImg_%s_%s_%s.fits" % (chip_output.subdir, BiasTag, self.chipID, i+1))
# datetime_obs = datetime.utcfromtimestamp(timestamp_obs)
# date_obs = datetime_obs.strftime("%y%m%d")
# time_obs = datetime_obs.strftime("%H%M%S")
timestamp_obs += 10 * 60 timestamp_obs += 10 * 60
self.outputCal( chip_utils.outputCal(
chip=self,
img=BiasCombImg, img=BiasCombImg,
ra_cen=ra_cen, ra_cen=ra_cen,
dec_cen=dec_cen, dec_cen=dec_cen,
...@@ -736,12 +579,9 @@ class Chip(FocalPlane): ...@@ -736,12 +579,9 @@ class Chip(FocalPlane):
FlatCombImg.replaceNegative(replace_value=0) FlatCombImg.replaceNegative(replace_value=0)
FlatCombImg.quantize() FlatCombImg.quantize()
FlatCombImg = galsim.ImageUS(FlatCombImg) FlatCombImg = galsim.ImageUS(FlatCombImg)
# FlatCombImg.write("%s/FlatImg_%s_%s_%s.fits" % (chip_output.subdir, FlatTag, self.chipID, i+1))
# datetime_obs = datetime.utcfromtimestamp(timestamp_obs)
# date_obs = datetime_obs.strftime("%y%m%d")
# time_obs = datetime_obs.strftime("%H%M%S")
timestamp_obs += 10 * 60 timestamp_obs += 10 * 60
self.outputCal( chip_utils.outputCal(
chip=self,
img=FlatCombImg, img=FlatCombImg,
ra_cen=ra_cen, ra_cen=ra_cen,
dec_cen=dec_cen, dec_cen=dec_cen,
...@@ -793,10 +633,8 @@ class Chip(FocalPlane): ...@@ -793,10 +633,8 @@ class Chip(FocalPlane):
cr_map[cr_map < 0] = 0 cr_map[cr_map < 0] = 0
crmap_gsimg = galsim.Image(cr_map, dtype=np.uint16) crmap_gsimg = galsim.Image(cr_map, dtype=np.uint16)
del cr_map del cr_map
# datetime_obs = datetime.utcfromtimestamp(timestamp_obs) chip_utils.outputCal(
# date_obs = datetime_obs.strftime("%y%m%d") chip=self,
# time_obs = datetime_obs.strftime("%H%M%S")
self.outputCal(
img=crmap_gsimg, img=crmap_gsimg,
ra_cen=ra_cen, ra_cen=ra_cen,
dec_cen=dec_cen, dec_cen=dec_cen,
...@@ -860,12 +698,9 @@ class Chip(FocalPlane): ...@@ -860,12 +698,9 @@ class Chip(FocalPlane):
DarkCombImg.replaceNegative(replace_value=0) DarkCombImg.replaceNegative(replace_value=0)
DarkCombImg.quantize() DarkCombImg.quantize()
DarkCombImg = galsim.ImageUS(DarkCombImg) DarkCombImg = galsim.ImageUS(DarkCombImg)
# DarkCombImg.write("%s/DarkImg_%s_%s_%s.fits" % (chip_output.subdir, DarkTag, self.chipID, i+1))
# datetime_obs = datetime.utcfromtimestamp(timestamp_obs)
# date_obs = datetime_obs.strftime("%y%m%d")
# time_obs = datetime_obs.strftime("%H%M%S")
timestamp_obs += 10 * 60 timestamp_obs += 10 * 60
self.outputCal( chip_utils.outputCal(
chip=chip,
img=DarkCombImg, img=DarkCombImg,
ra_cen=ra_cen, ra_cen=ra_cen,
dec_cen=dec_cen, dec_cen=dec_cen,
...@@ -894,19 +729,3 @@ class Chip(FocalPlane): ...@@ -894,19 +729,3 @@ class Chip(FocalPlane):
# del sub_img # del sub_img
return img return img
def loadSLSFLATCUBE(self, flat_fn='flat_cube.fits'):
from astropy.io import fits
try:
with pkg_resources.files('ObservationSim.Instrument.data').joinpath(flat_fn) as data_path:
flat_fits = fits.open(data_path, ignore_missing_simple=True)
except AttributeError:
with pkg_resources.path('ObservationSim.Instrument.data', flat_fn) as data_path:
flat_fits = fits.open(data_path, ignore_missing_simple=True)
fl = len(flat_fits)
fl_sh = flat_fits[0].data.shape
assert fl == 4, 'FLAT Field Cube is Not 4 layess!!!!!!!'
self.flat_cube = np.zeros([fl, fl_sh[0], fl_sh[1]])
for i in np.arange(0, fl, 1):
self.flat_cube[i] = flat_fits[i].data
ObservationSim/Instrument/Chip/ChipUtils.py 0 → 100644
View file @ a6664237
import os
import galsim
import ctypes
import numpy as np
from astropy.io import fits
from datetime import datetime
from ObservationSim.Instrument.Chip import Effects as effects
from ObservationSim.Config.Header import generatePrimaryHeader, generateExtensionHeader
try:
import importlib.resources as pkg_resources
except ImportError:
# Try backported to PY<37 'importlib_resources'
import importlib_resources as pkg_resources
def log_info(msg, logger=None):
if logger:
logger.info(msg)
else:
print(msg, flush=True)
def getChipSLSConf(chipID):
confFile = ''
if chipID == 1: confFile = ['CSST_GI2.conf', 'CSST_GI1.conf']
if chipID == 2: confFile = ['CSST_GV4.conf', 'CSST_GV3.conf']
if chipID == 3: confFile = ['CSST_GU2.conf', 'CSST_GU1.conf']
if chipID == 4: confFile = ['CSST_GU4.conf', 'CSST_GU3.conf']
if chipID == 5: confFile = ['CSST_GV2.conf', 'CSST_GV1.conf']
if chipID == 10: confFile = ['CSST_GI4.conf', 'CSST_GI3.conf']
if chipID == 21: confFile = ['CSST_GI6.conf', 'CSST_GI5.conf']
if chipID == 26: confFile = ['CSST_GV8.conf', 'CSST_GV7.conf']
if chipID == 27: confFile = ['CSST_GU6.conf', 'CSST_GU5.conf']
if chipID == 28: confFile = ['CSST_GU8.conf', 'CSST_GU7.conf']
if chipID == 29: confFile = ['CSST_GV6.conf', 'CSST_GV5.conf']
if chipID == 30: confFile = ['CSST_GI8.conf', 'CSST_GI7.conf']
return confFile
def generateHeader(chip, ra_cen, dec_cen, img_rot, im_type, pointing_ID, exptime=150., timestamp = 1621915200):
datetime_obs = datetime.utcfromtimestamp(timestamp)
date_obs = datetime_obs.strftime("%y%m%d")
time_obs = datetime_obs.strftime("%H%M%S")
h_prim = generatePrimaryHeader(
xlen=chip.npix_x,
ylen=chip.npix_y,
pointNum = str(pointing_ID),
ra=ra_cen,
dec=dec_cen,
pixel_scale=chip.pix_scale,
date=date_obs,
time_obs=time_obs,
im_type = im_type,
exptime=exptime,
chip_name=str(chip.chipID).rjust(2, '0')
)
h_ext = generateExtensionHeader(
chip=chip,
xlen=chip.npix_x,
ylen=chip.npix_y,
ra=ra_cen,
dec=dec_cen,
pa=img_rot.deg,
gain=chip.gain,
readout=chip.read_noise,
dark=chip.dark_noise,
saturation=90000,
pixel_scale=chip.pix_scale,
pixel_size=chip.pix_size,
xcen=chip.x_cen,
ycen=chip.y_cen,
extName='SCI',
timestamp = timestamp,
exptime = exptime,
readoutTime = chip.readout_time)
return h_prim, h_ext
def outputCal(chip, img, ra_cen, dec_cen, img_rot, im_type, pointing_ID, output_dir, exptime=150., timestamp = 1621915200):
h_prim, h_ext = generateHeader(
chip=chip,
ra_cen=ra_cen,
dec_cen=dec_cen,
img_rot=img_rot,
im_type=im_type,
pointing_ID=pointing_ID,
exptime=exptime,
timestamp=timestamp)
hdu1 = fits.PrimaryHDU(header=h_prim)
hdu1.add_checksum()
hdu1.header.comments['CHECKSUM'] = 'HDU checksum'
hdu1.header.comments['DATASUM'] = 'data unit checksum'
hdu2 = fits.ImageHDU(img.array, header=h_ext)
hdu2.add_checksum()
hdu2.header.comments['XTENSION'] = 'extension type'
hdu2.header.comments['CHECKSUM'] = 'HDU checksum'
hdu2.header.comments['DATASUM'] = 'data unit checksum'
hdu1 = fits.HDUList([hdu1, hdu2])
fname = os.path.join(output_dir, h_prim['FILENAME']+'.fits')
hdu1.writeto(fname, output_verify='ignore', overwrite=True)
def add_sky_background(img, filt, exptime, sky_map=None, tel=None):
# Add sky background
if sky_map is None:
sky_map = filt.getSkyNoise(exptime=exptime)
sky_map = sky_map * np.ones_like(img.array)
sky_map = galsim.Image(array=sky_map)
# Apply Poisson noise to the sky map
# # (NOTE): only for photometric chips if it utilizes the photon shooting to draw stamps
# if self.survey_type == "photometric":
# sky_map.addNoise(poisson_noise)
elif img.array.shape != sky_map.shape:
raise ValueError("The shape img and sky_map must be equal.")
elif tel is not None: # If sky_map is given in flux
sky_map = sky_map * tel.pupil_area * exptime
img += sky_map
return img, sky_map
def get_flat(img, seed):
flat_img = effects.MakeFlatSmooth(
GSBounds=img.bounds,
seed=seed)
flat_normal = flat_img / np.mean(flat_img.array)
return flat_img, flat_normal
def add_cosmic_rays(img, chip, exptime=150, seed=0):
cr_map, cr_event_num = effects.produceCR_Map(
xLen=chip.npix_x, yLen=chip.npix_y,
exTime=exptime+0.5*chip.readout_time,
cr_pixelRatio=0.003*(exptime+0.5*chip.readout_time)/600.,
gain=chip.gain,
attachedSizes=chip.attachedSizes,
seed=seed) # seed: obj-imaging:+0; bias:+1; dark:+2; flat:+3;
img += cr_map
cr_map[cr_map > 65535] = 65535
cr_map[cr_map < 0] = 0
crmap_gsimg = galsim.Image(cr_map, dtype=np.uint16)
del cr_map
return img, crmap_gsimg, cr_event_num
def add_PRNU(img, chip, seed=0):
prnu_img = effects.PRNU_Img(
xsize=chip.npix_x,
ysize=chip.npix_y,
sigma=0.01,
seed=seed)
img *= prnu_img
return img, prnu_img
def get_poisson(seed=0, sky_level=0.):
rng_poisson = galsim.BaseDeviate(seed)
poisson_noise = galsim.PoissonNoise(rng_poisson, sky_level=sky_level)
return rng_poisson, poisson_noise
def get_base_img(img, read_noise, readout_time, dark_noise, exptime=150.):
base_level = read_noise**2 + dark_noise*(exptime+0.5*readout_time)
base_img = base_level * np.ones_like(img.array)
return base_img
def add_poisson(img, chip, exptime=150., seed=0, sky_level=0., poisson_noise=None, dark_noise=None):
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, read_noise=read_noise, readout_time=chip.readout_time, dark_noise=dark_noise, exptime=exptime)
img += base_img
img.addNoise(poisson_noise)
img -= read_noise**2
return img, base_img
def add_brighter_fatter(img):
#Inital dynamic lib
try:
with pkg_resources.files('ObservationSim.Instrument.Chip.lib_bf').joinpath("libmoduleBF.so") as lib_path:
lib_bf = ctypes.CDLL(lib_path)
except AttributeError:
with pkg_resources.path('ObservationSim.Instrument.Chip.lib_bf', "libmoduleBF.so") as lib_path:
lib_bf = ctypes.CDLL(lib_path)
lib_bf.addEffects.argtypes = [ctypes.c_int, ctypes.c_int, ctypes.POINTER(ctypes.c_float), ctypes.POINTER(ctypes.c_float), ctypes.c_int]
# Set bit flag
bit_flag = 1
bit_flag = bit_flag | (1 << 2)
nx, ny = img.array.shape
nn = nx * ny
arr_ima= (ctypes.c_float*nn)()
arr_imc= (ctypes.c_float*nn)()
arr_ima[:]= img.array.reshape(nn)
arr_imc[:]= np.zeros(nn)
lib_bf.addEffects(nx, ny, arr_ima, arr_imc, bit_flag)
img.array[:, :] = np.array(arr_imc[:]).reshape([nx, ny])
del arr_ima, arr_imc
return img
\ No newline at end of file
ObservationSim/Instrument/Chip/lib_bf/diffusion_X1.c 0 → 100644
View file @ a6664237
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "nrutil.h"
#define ISSETBITFLAG(x,b) ((x) & (1 << (b)))
#define ADD_DIFFUSION 1
#define ADD_BF_FILTER 2
float linearInterp(float xp, float x0, float y0, float x1, float y1);
void addEffects(int ngx_ima, int ngy_ima, float *arr_ima, float *arr_imc, int bit_flag)
{
int nx, ny, i,j,k,ks;
int it,jt,itt,jtt;
int diffuidx[26][2],diffuN,ilow,ih,im,dim[3];
float diffua[5][5],cdiffu[26],**bfa;
double mvar,mcov,tmp,ma,mb,mc;
char fname[100];
nx = ngx_ima; //input-image size
ny = ngy_ima;
//0. init. original image with an input array (arr_ima)
//1. Adding diffusion effect.
if(ISSETBITFLAG(bit_flag, ADD_DIFFUSION))
{
printf("adding diffusion.....\n");
printf("ERR: no diffusion filter ...");
exit(0);
}
//2. Adding BF effect
if(ISSETBITFLAG(bit_flag, ADD_BF_FILTER))
{
printf("Adding BF effect...\n");
//setup BF correlation fliter
float neX;
float neP1 = 50000;
float bfaP1[9]={0.9707182, 0.002143905, 0.004131103, 0.001149542, 0.0005501739, 0.0005469659, 0.0003726081, 0.0003795207, 0.0001633302};
float neP2 = 10000;
float bfaP2[9]={0.9945288, 0.0003041936, 0.0007539311, 0.0002424675, 0.0001226098, 0.00009308617, 0.00008027447, 0.00006309676, 0.00006400052};
bfa=matrix(-2,2,-2,2);
// smooth with the BF filter
for(i=0;i<nx;i++)for(j=0;j<ny;j++) arr_imc[j+i*ny]=0;
for(i=0;i<nx;i++)
{
for(j=0;j<ny;j++)
{
//rescale BF filter with the local pix value
neX = arr_ima[j+i*ny];
if(neX >= 10000)
{
bfa[0][0]=0; //linearInterp(neX, neP1, bfaP1[0], neP2, bfaP2[0]); //0;
bfa[0][1]=bfa[0][-1]=linearInterp(neX, neP1, bfaP1[1], neP2, bfaP2[1]); //0.01575;
bfa[-1][0]=bfa[1][0]=linearInterp(neX, neP1, bfaP1[2], neP2, bfaP2[2]); //0.00652;
bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=linearInterp(neX, neP1, bfaP1[3], neP2, bfaP2[3]); //0.00335;
bfa[0][-2]=bfa[0][2]=linearInterp(neX, neP1, bfaP1[4], neP2, bfaP2[4]);
bfa[-2][0]=bfa[2][0]=linearInterp(neX, neP1, bfaP1[5], neP2, bfaP2[5]); //0.00118;
bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=linearInterp(neX, neP1, bfaP1[6], neP2, bfaP2[6]);
bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=linearInterp(neX, neP1, bfaP1[7], neP2, bfaP2[7]); //0.00083;
bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=linearInterp(neX, neP1, bfaP1[8], neP2, bfaP2[8]); //0.00043;
}
else
{
neX=10000;
bfa[0][0]=0;
bfa[0][1]=bfa[0][-1]=bfaP2[1];
bfa[-1][0]=bfa[1][0]=bfaP2[2];
bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=bfaP2[3];
bfa[0][-2]=bfa[0][2]=bfaP2[4];
bfa[-2][0]=bfa[2][0]=bfaP2[5];
bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=bfaP2[6];
bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=bfaP2[7];
bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=bfaP2[8];
}
tmp = 0;
for(it=-2;it<=2;it++)
for(jt=-2;jt<=2;jt++)
{
bfa[it][jt] = bfa[it][jt]/neX*arr_ima[j+i*ny];
tmp += bfa[it][jt];
}
bfa[0][0]=1.-tmp;
// assign electrons according to the BF filter bfat
for(it=-2;it<=2;it++)
{
for(jt=-2;jt<=2;jt++)
{
itt=i+it;
jtt=j+jt;
if(itt>=0 && jtt>=0 && itt<nx && jtt<ny)
//c0[itt][jtt]+=bfa[it][jt]*b[i][j];
arr_imc[jtt+itt*ny] += bfa[it][jt]*arr_ima[j+i*ny];
}
}
}
}
free_matrix(bfa,-2,2,-2,2);
}
else
{
for(i=0;i<nx;i++) for(j=0;j<ny;j++) arr_imc[j+i*ny]=arr_ima[j+i*ny]; ////for ADD_BF False
}
}
float linearInterp(float xp, float x0, float y0, float x1, float y1)
{
float yp;
yp = y0 + ((y1-y0)/(x1-x0)) * (xp - x0);
return yp;
}
ObservationSim/Instrument/Chip/lib_bf/nrutil.c 0 → 100644
View file @ a6664237
#if defined(__STDC__) || defined(ANSI) || defined(NRANSI) /* ANSI */
#include <stdio.h>
#include <stddef.h>
#include <stdlib.h>
#define NR_END 1
#define FREE_ARG char*
void nrerror(char error_text[])
/* Numerical Recipes standard error handler */
{
fprintf(stderr,"Numerical Recipes run-time error...\n");
fprintf(stderr,"%s\n",error_text);
fprintf(stderr,"...now exiting to system...\n");
exit(1);
}
float *vector(long nl, long nh)
/* allocate a float vector with subscript range v[nl..nh] */
{
float *v;
v=(float *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(float)));
if (!v) nrerror("allocation failure in vector()");
return v-nl+NR_END;
}
int *ivector(long nl, long nh)
/* allocate an int vector with subscript range v[nl..nh] */
{
int *v;
v=(int *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(int)));
if (!v) nrerror("allocation failure in ivector()");
return v-nl+NR_END;
}
unsigned char *cvector(long nl, long nh)
/* allocate an unsigned char vector with subscript range v[nl..nh] */
{
unsigned char *v;
v=(unsigned char *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(unsigned char)));
if (!v) nrerror("allocation failure in cvector()");
return v-nl+NR_END;
}
long *lvector(long nl, long nh)
/* allocate an long vector with subscript range v[nl..nh] */
{
long *v;
v=(long *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(long)));
if (!v) nrerror("allocation failure in lvector()");
return v-nl+NR_END;
}
double *dvector(long nl, long nh)
/* allocate a double vector with subscript range v[nl..nh] */
{
double *v;
v=(double *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(double)));
if (!v) nrerror("allocation failure in dvector()");
return v-nl+NR_END;
}
float **matrix(long nrl, long nrh, long ncl, long nch)
/* allocate a float matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
float **m;
/* allocate pointers to rows */
m=(float **) malloc((size_t)((nrow+NR_END)*sizeof(float*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(float *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(float)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
double **dmatrix(long nrl, long nrh, long ncl, long nch)
/* allocate a double matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
double **m;
/* allocate pointers to rows */
m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
int **imatrix(long nrl, long nrh, long ncl, long nch)
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
int **m;
/* allocate pointers to rows */
m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
float **submatrix(float **a, long oldrl, long oldrh, long oldcl, long oldch,
long newrl, long newcl)
/* point a submatrix [newrl..][newcl..] to a[oldrl..oldrh][oldcl..oldch] */
{
long i,j,nrow=oldrh-oldrl+1,ncol=oldcl-newcl;
float **m;
/* allocate array of pointers to rows */
m=(float **) malloc((size_t) ((nrow+NR_END)*sizeof(float*)));
if (!m) nrerror("allocation failure in submatrix()");
m += NR_END;
m -= newrl;
/* set pointers to rows */
for(i=oldrl,j=newrl;i<=oldrh;i++,j++) m[j]=a[i]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
float **convert_matrix(float *a, long nrl, long nrh, long ncl, long nch)
/* allocate a float matrix m[nrl..nrh][ncl..nch] that points to the matrix
declared in the standard C manner as a[nrow][ncol], where nrow=nrh-nrl+1
and ncol=nch-ncl+1. The routine should be called with the address
&a[0][0] as the first argument. */
{
long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1;
float **m;
/* allocate pointers to rows */
m=(float **) malloc((size_t) ((nrow+NR_END)*sizeof(float*)));
if (!m) nrerror("allocation failure in convert_matrix()");
m += NR_END;
m -= nrl;
/* set pointers to rows */
m[nrl]=a-ncl;
for(i=1,j=nrl+1;i<nrow;i++,j++) m[j]=m[j-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
float ***f3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh)
/* allocate a float 3tensor with range t[nrl..nrh][ncl..nch][ndl..ndh] */
{
long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1,ndep=ndh-ndl+1;
float ***t;
/* allocate pointers to pointers to rows */
t=(float ***) malloc((size_t)((nrow+NR_END)*sizeof(float**)));
if (!t) nrerror("allocation failure 1 in f3tensor()");
t += NR_END;
t -= nrl;
/* allocate pointers to rows and set pointers to them */
t[nrl]=(float **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(float*)));
if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
t[nrl] += NR_END;
t[nrl] -= ncl;
/* allocate rows and set pointers to them */
t[nrl][ncl]=(float *) malloc((size_t)((nrow*ncol*ndep+NR_END)*sizeof(float)));
if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
t[nrl][ncl] += NR_END;
t[nrl][ncl] -= ndl;
for(j=ncl+1;j<=nch;j++) t[nrl][j]=t[nrl][j-1]+ndep;
for(i=nrl+1;i<=nrh;i++) {
t[i]=t[i-1]+ncol;
t[i][ncl]=t[i-1][ncl]+ncol*ndep;
for(j=ncl+1;j<=nch;j++) t[i][j]=t[i][j-1]+ndep;
}
/* return pointer to array of pointers to rows */
return t;
}
double ***d3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh)
/* allocate a double 3tensor with range t[nrl..nrh][ncl..nch][ndl..ndh] */
{
long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1,ndep=ndh-ndl+1;
double ***t;
/* allocate pointers to pointers to rows */
t=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double**)));
if (!t) nrerror("allocation failure 1 in f3tensor()");
t += NR_END;
t -= nrl;
/* allocate pointers to rows and set pointers to them */
t[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double*)));
if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
t[nrl] += NR_END;
t[nrl] -= ncl;
/* allocate rows and set pointers to them */
t[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*ndep+NR_END)*sizeof(double)));
if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
t[nrl][ncl] += NR_END;
t[nrl][ncl] -= ndl;
for(j=ncl+1;j<=nch;j++) t[nrl][j]=t[nrl][j-1]+ndep;
for(i=nrl+1;i<=nrh;i++) {
t[i]=t[i-1]+ncol;
t[i][ncl]=t[i-1][ncl]+ncol*ndep;
for(j=ncl+1;j<=nch;j++) t[i][j]=t[i][j-1]+ndep;
}
/* return pointer to array of pointers to rows */
return t;
}
char **cmatrix(long nrl, long nrh, long ncl, long nch)
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
char **m;
/* allocate pointers to rows */
m=(char **) malloc((size_t)((nrow+NR_END)*sizeof(char*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(char *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(char)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
void free_vector(float *v, long nl, long nh)
/* free a float vector allocated with vector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_ivector(int *v, long nl, long nh)
/* free an int vector allocated with ivector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_cvector(unsigned char *v, long nl, long nh)
/* free an unsigned char vector allocated with cvector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_lvector(long *v, long nl, long nh)
/* free an long vector allocated with lvector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_dvector(double *v, long nl, long nh)
/* free a double vector allocated with dvector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_matrix(float **m, long nrl, long nrh, long ncl, long nch)
/* free a float matrix allocated by matrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch)
/* free a double matrix allocated by dmatrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
void free_imatrix(int **m, long nrl, long nrh, long ncl, long nch)
/* free an int matrix allocated by imatrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
void free_submatrix(float **b, long nrl, long nrh, long ncl, long nch)
/* free a submatrix allocated by submatrix() */
{
free((FREE_ARG) (b+nrl-NR_END));
}
void free_convert_matrix(float **b, long nrl, long nrh, long ncl, long nch)
/* free a matrix allocated by convert_matrix() */
{
free((FREE_ARG) (b+nrl-NR_END));
}
void free_f3tensor(float ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh)
/* free a float f3tensor allocated by f3tensor() */
{
free((FREE_ARG) (t[nrl][ncl]+ndl-NR_END));
free((FREE_ARG) (t[nrl]+ncl-NR_END));
free((FREE_ARG) (t+nrl-NR_END));
}
void free_d3tensor(double ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh)
/* free a double f3tensor allocated by f3tensor() */
{
free((FREE_ARG) (t[nrl][ncl]+ndl-NR_END));
free((FREE_ARG) (t[nrl]+ncl-NR_END));
free((FREE_ARG) (t+nrl-NR_END));
}
void free_cmatrix(char **m, long nrl, long nrh, long ncl, long nch)
/* free a character matrix allocated by matrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
#else /* ANSI */
/* traditional - K&R */
#include <stdio.h>
#define NR_END 1
#define FREE_ARG char*
void nrerror(error_text)
char error_text[];
/* Numerical Recipes standard error handler */
{
void exit();
fprintf(stderr,"Numerical Recipes run-time error...\n");
fprintf(stderr,"%s\n",error_text);
fprintf(stderr,"...now exiting to system...\n");
exit(1);
}
float *vector(nl,nh)
long nh,nl;
/* allocate a float vector with subscript range v[nl..nh] */
{
float *v;
v=(float *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(float)));
if (!v) nrerror("allocation failure in vector()");
return v-nl+NR_END;
}
int *ivector(nl,nh)
long nh,nl;
/* allocate an int vector with subscript range v[nl..nh] */
{
int *v;
v=(int *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(int)));
if (!v) nrerror("allocation failure in ivector()");
return v-nl+NR_END;
}
unsigned char *cvector(nl,nh)
long nh,nl;
/* allocate an unsigned char vector with subscript range v[nl..nh] */
{
unsigned char *v;
v=(unsigned char *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(unsigned char)));
if (!v) nrerror("allocation failure in cvector()");
return v-nl+NR_END;
}
long *lvector(nl,nh)
long nh,nl;
/* allocate an unsigned long vector with subscript range v[nl..nh] */
{
long *v;
v=(long *)malloc((int) ((nh-nl+1+NR_END)*sizeof(long)));
if (!v) nrerror("allocation failure in lvector()");
return v-nl+NR_END;
}
double *dvector(nl,nh)
long nh,nl;
/* allocate a double vector with subscript range v[nl..nh] */
{
double *v;
v=(double *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(double)));
if (!v) nrerror("allocation failure in dvector()");
return v-nl+NR_END;
}
float **matrix(nrl,nrh,ncl,nch)
long nch,ncl,nrh,nrl;
/* allocate a float matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
float **m;
/* allocate pointers to rows */
m=(float **) malloc((unsigned int)((nrow+NR_END)*sizeof(float*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(float *) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(float)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
double **dmatrix(nrl,nrh,ncl,nch)
long nch,ncl,nrh,nrl;
/* allocate a double matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
double **m;
/* allocate pointers to rows */
m=(double **) malloc((unsigned int)((nrow+NR_END)*sizeof(double*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(double *) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(double)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
int **imatrix(nrl,nrh,ncl,nch)
long nch,ncl,nrh,nrl;
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
int **m;
/* allocate pointers to rows */
m=(int **) malloc((unsigned int)((nrow+NR_END)*sizeof(int*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(int *) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(int)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
float **submatrix(a,oldrl,oldrh,oldcl,oldch,newrl,newcl)
float **a;
long newcl,newrl,oldch,oldcl,oldrh,oldrl;
/* point a submatrix [newrl..][newcl..] to a[oldrl..oldrh][oldcl..oldch] */
{
long i,j,nrow=oldrh-oldrl+1,ncol=oldcl-newcl;
float **m;
/* allocate array of pointers to rows */
m=(float **) malloc((unsigned int) ((nrow+NR_END)*sizeof(float*)));
if (!m) nrerror("allocation failure in submatrix()");
m += NR_END;
m -= newrl;
/* set pointers to rows */
for(i=oldrl,j=newrl;i<=oldrh;i++,j++) m[j]=a[i]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
float **convert_matrix(a,nrl,nrh,ncl,nch)
float *a;
long nch,ncl,nrh,nrl;
/* allocate a float matrix m[nrl..nrh][ncl..nch] that points to the matrix
declared in the standard C manner as a[nrow][ncol], where nrow=nrh-nrl+1
and ncol=nch-ncl+1. The routine should be called with the address
&a[0][0] as the first argument. */
{
long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1;
float **m;
/* allocate pointers to rows */
m=(float **) malloc((unsigned int) ((nrow+NR_END)*sizeof(float*)));
if (!m) nrerror("allocation failure in convert_matrix()");
m += NR_END;
m -= nrl;
/* set pointers to rows */
m[nrl]=a-ncl;
for(i=1,j=nrl+1;i<nrow;i++,j++) m[j]=m[j-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
double ***d3tensor(nrl,nrh,ncl,nch,ndl,ndh)
long nch,ncl,ndh,ndl,nrh,nrl;
/* allocate a float 3tensor with range t[nrl..nrh][ncl..nch][ndl..ndh] */
{
long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1,ndep=ndh-ndl+1;
double ***t;
/* allocate pointers to pointers to rows */
t=(double ***) malloc((unsigned int)((nrow+NR_END)*sizeof(double**)));
if (!t) nrerror("allocation failure 1 in f3tensor()");
t += NR_END;
t -= nrl;
/* allocate pointers to rows and set pointers to them */
t[nrl]=(double **) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(double*)));
if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
t[nrl] += NR_END;
t[nrl] -= ncl;
/* allocate rows and set pointers to them */
t[nrl][ncl]=(double *) malloc((unsigned int)((nrow*ncol*ndep+NR_END)*sizeof(double)));
if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
t[nrl][ncl] += NR_END;
t[nrl][ncl] -= ndl;
for(j=ncl+1;j<=nch;j++) t[nrl][j]=t[nrl][j-1]+ndep;
for(i=nrl+1;i<=nrh;i++) {
t[i]=t[i-1]+ncol;
t[i][ncl]=t[i-1][ncl]+ncol*ndep;
for(j=ncl+1;j<=nch;j++) t[i][j]=t[i][j-1]+ndep;
}
/* return pointer to array of pointers to rows */
return t;
}
float ***f3tensor(nrl,nrh,ncl,nch,ndl,ndh)
long nch,ncl,ndh,ndl,nrh,nrl;
/* allocate a float 3tensor with range t[nrl..nrh][ncl..nch][ndl..ndh] */
{
long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1,ndep=ndh-ndl+1;
float ***t;
/* allocate pointers to pointers to rows */
t=(float ***) malloc((unsigned int)((nrow+NR_END)*sizeof(float**)));
if (!t) nrerror("allocation failure 1 in f3tensor()");
t += NR_END;
t -= nrl;
/* allocate pointers to rows and set pointers to them */
t[nrl]=(float **) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(float*)));
if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
t[nrl] += NR_END;
t[nrl] -= ncl;
/* allocate rows and set pointers to them */
t[nrl][ncl]=(float *) malloc((unsigned int)((nrow*ncol*ndep+NR_END)*sizeof(float)));
if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
t[nrl][ncl] += NR_END;
t[nrl][ncl] -= ndl;
for(j=ncl+1;j<=nch;j++) t[nrl][j]=t[nrl][j-1]+ndep;
for(i=nrl+1;i<=nrh;i++) {
t[i]=t[i-1]+ncol;
t[i][ncl]=t[i-1][ncl]+ncol*ndep;
for(j=ncl+1;j<=nch;j++) t[i][j]=t[i][j-1]+ndep;
}
/* return pointer to array of pointers to rows */
return t;
}
char **cmatrix(nrl,nrh,ncl,nch)
long nch,ncl,nrh,nrl;
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
char **m;
/* allocate pointers to rows */
m=(char **) malloc((unsigned int)((nrow+NR_END)*sizeof(char*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(char *) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(char)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
void free_vector(v,nl,nh)
float *v;
long nh,nl;
/* free a float vector allocated with vector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_ivector(v,nl,nh)
int *v;
long nh,nl;
/* free an int vector allocated with ivector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_cvector(v,nl,nh)
long nh,nl;
unsigned char *v;
/* free an unsigned char vector allocated with cvector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_lvector(v,nl,nh)
long nh,nl;
long *v;
/* free an long vector allocated with lvector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_dvector(v,nl,nh)
double *v;
long nh,nl;
/* free a double vector allocated with dvector() */
{
free((FREE_ARG) (v+nl-NR_END));
}
void free_matrix(m,nrl,nrh,ncl,nch)
float **m;
long nch,ncl,nrh,nrl;
/* free a float matrix allocated by matrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
void free_dmatrix(m,nrl,nrh,ncl,nch)
double **m;
long nch,ncl,nrh,nrl;
/* free a double matrix allocated by dmatrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
void free_imatrix(m,nrl,nrh,ncl,nch)
int **m;
long nch,ncl,nrh,nrl;
/* free an int matrix allocated by imatrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
void free_submatrix(b,nrl,nrh,ncl,nch)
float **b;
long nch,ncl,nrh,nrl;
/* free a submatrix allocated by submatrix() */
{
free((FREE_ARG) (b+nrl-NR_END));
}
void free_convert_matrix(b,nrl,nrh,ncl,nch)
float **b;
long nch,ncl,nrh,nrl;
/* free a matrix allocated by convert_matrix() */
{
free((FREE_ARG) (b+nrl-NR_END));
}
void free_f3tensor(t,nrl,nrh,ncl,nch,ndl,ndh)
float ***t;
long nch,ncl,ndh,ndl,nrh,nrl;
/* free a float f3tensor allocated by f3tensor() */
{
free((FREE_ARG) (t[nrl][ncl]+ndl-NR_END));
free((FREE_ARG) (t[nrl]+ncl-NR_END));
free((FREE_ARG) (t+nrl-NR_END));
}
void free_d3tensor(t,nrl,nrh,ncl,nch,ndl,ndh)
double ***t;
long nch,ncl,ndh,ndl,nrh,nrl;
/* free a float f3tensor allocated by f3tensor() */
{
free((FREE_ARG) (t[nrl][ncl]+ndl-NR_END));
free((FREE_ARG) (t[nrl]+ncl-NR_END));
free((FREE_ARG) (t+nrl-NR_END));
}
void free_cmatrix(m,nrl,nrh,ncl,nch)
char **m;
long nch,ncl,nrh,nrl;
/* free a double matrix allocated by dmatrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
#endif /* ANSI */
ObservationSim/Instrument/Chip/lib_bf/nrutil.h 0 → 100644
View file @ a6664237
/* CAUTION: This is the ANSI C (only) version of the Numerical Recipes
utility file nrutil.h. Do not confuse this file with the same-named
file nrutil.h that may be supplied in a 'misc' subdirectory.
*That* file is the one from the book, and contains both ANSI and
traditional K&R versions, along with #ifdef macros to select the
correct version. *This* file contains only ANSI C. */
#ifndef _NR_UTILS_H_
#define _NR_UTILS_H_
static float sqrarg;
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 : sqrarg*sqrarg)
static double dsqrarg;
#define DSQR(a) ((dsqrarg=(a)) == 0.0 ? 0.0 : dsqrarg*dsqrarg)
static double dmaxarg1,dmaxarg2;
#define DMAX(a,b) (dmaxarg1=(a),dmaxarg2=(b),(dmaxarg1) > (dmaxarg2) ?\
(dmaxarg1) : (dmaxarg2))
static double dminarg1,dminarg2;
#define DMIN(a,b) (dminarg1=(a),dminarg2=(b),(dminarg1) < (dminarg2) ?\
(dminarg1) : (dminarg2))
static float maxarg1,maxarg2;
#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ?\
(maxarg1) : (maxarg2))
static float minarg1,minarg2;
#define FMIN(a,b) (minarg1=(a),minarg2=(b),(minarg1) < (minarg2) ?\
(minarg1) : (minarg2))
static long lmaxarg1,lmaxarg2;
#define LMAX(a,b) (lmaxarg1=(a),lmaxarg2=(b),(lmaxarg1) > (lmaxarg2) ?\
(lmaxarg1) : (lmaxarg2))
static long lminarg1,lminarg2;
#define LMIN(a,b) (lminarg1=(a),lminarg2=(b),(lminarg1) < (lminarg2) ?\
(lminarg1) : (lminarg2))
static int imaxarg1,imaxarg2;
#define IMAX(a,b) (imaxarg1=(a),imaxarg2=(b),(imaxarg1) > (imaxarg2) ?\
(imaxarg1) : (imaxarg2))
static int iminarg1,iminarg2;
#define IMIN(a,b) (iminarg1=(a),iminarg2=(b),(iminarg1) < (iminarg2) ?\
(iminarg1) : (iminarg2))
#define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
void nrerror(char error_text[]);
float *vector(long nl, long nh);
int *ivector(long nl, long nh);
unsigned char *cvector(long nl, long nh);
long *lvector(long nl, long nh);
double *dvector(long nl, long nh);
float **matrix(long nrl, long nrh, long ncl, long nch);
double **dmatrix(long nrl, long nrh, long ncl, long nch);
int **imatrix(long nrl, long nrh, long ncl, long nch);
float **submatrix(float **a, long oldrl, long oldrh, long oldcl, long oldch,
long newrl, long newcl);
float **convert_matrix(float *a, long nrl, long nrh, long ncl, long nch);
float ***f3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
void free_vector(float *v, long nl, long nh);
void free_ivector(int *v, long nl, long nh);
void free_cvector(unsigned char *v, long nl, long nh);
void free_lvector(long *v, long nl, long nh);
void free_dvector(double *v, long nl, long nh);
void free_matrix(float **m, long nrl, long nrh, long ncl, long nch);
void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch);
void free_imatrix(int **m, long nrl, long nrh, long ncl, long nch);
void free_submatrix(float **b, long nrl, long nrh, long ncl, long nch);
void free_convert_matrix(float **b, long nrl, long nrh, long ncl, long nch);
void free_f3tensor(float ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh);
int ***i3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
void free_i3tensor(int ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh);
unsigned char ***b3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
void free_b3tensor(unsigned char ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh);
double ***d3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
void free_d3tensor(double ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh);
char **cmatrix(long nrl, long nrh, long ncl, long nch);
void free_cmatrix(char **m, long nrl, long nrh, long ncl, long nch);
#endif /* _NR_UTILS_H_ */
ObservationSim/MockObject/Galaxy.py
View file @ a6664237
...@@ -14,18 +14,6 @@ from ObservationSim.MockObject.MockObject import MockObject ...@@ -14,18 +14,6 @@ from ObservationSim.MockObject.MockObject import MockObject
class Galaxy(MockObject): class Galaxy(MockObject):
def __init__(self, param, logger=None): def __init__(self, param, logger=None):
super().__init__(param, logger=logger) super().__init__(param, logger=logger)
# self.thetaR = self.param["theta"]
# self.bfrac = self.param["bfrac"]
# self.hlr_disk = self.param["hlr_disk"]
# self.hlr_bulge = self.param["hlr_bulge"]
# Extract ellipticity components
# self.e_disk = galsim.Shear(g=self.param["ell_disk"], beta=self.thetaR*galsim.degrees)
# self.e_bulge = galsim.Shear(g=self.param["ell_bulge"], beta=self.thetaR*galsim.degrees)
# self.e_total = galsim.Shear(g=self.param["ell_tot"], beta=self.thetaR*galsim.degrees)
# self.e1_disk, self.e2_disk = self.e_disk.g1, self.e_disk.g2
# self.e1_bulge, self.e2_bulge = self.e_bulge.g1, self.e_bulge.g2
# self.e1_total, self.e2_total = self.e_total.g1, self.e_total.g2
if not hasattr(self, "disk_sersic_idx"): if not hasattr(self, "disk_sersic_idx"):
self.disk_sersic_idx = 1. self.disk_sersic_idx = 1.
...@@ -101,10 +89,6 @@ class Galaxy(MockObject): ...@@ -101,10 +89,6 @@ class Galaxy(MockObject):
if self.logger: if self.logger:
self.logger.error(e) self.logger.error(e)
return 2, None return 2, None
nphotons_sum = 0
photons_list = []
xmax, ymax = 0, 0
# # [C6 TEST] # # [C6 TEST]
# print('hlr_disk = %.4f, hlr_bulge = %.4f'%(self.hlr_disk, self.hlr_bulge)) # print('hlr_disk = %.4f, hlr_bulge = %.4f'%(self.hlr_disk, self.hlr_bulge))
...@@ -114,7 +98,7 @@ class Galaxy(MockObject): ...@@ -114,7 +98,7 @@ class Galaxy(MockObject):
if self.hlr_disk > 3.0 or self.hlr_bulge > 3.0: # Very big galaxy if self.hlr_disk > 3.0 or self.hlr_bulge > 3.0: # Very big galaxy
big_galaxy = True big_galaxy = True
# (TEST) Galsim Parameters # Set Galsim Parameters
if self.getMagFilter(filt) <= 15 and (not big_galaxy): if self.getMagFilter(filt) <= 15 and (not big_galaxy):
folding_threshold = 5.e-4 folding_threshold = 5.e-4
else: else:
...@@ -122,7 +106,7 @@ class Galaxy(MockObject): ...@@ -122,7 +106,7 @@ class Galaxy(MockObject):
gsp = galsim.GSParams(folding_threshold=folding_threshold) gsp = galsim.GSParams(folding_threshold=folding_threshold)
self.real_pos = self.getRealPos(chip.img, global_x=self.posImg.x, global_y=self.posImg.y, self.real_pos = self.getRealPos(chip.img, global_x=self.posImg.x, global_y=self.posImg.y,
img_real_wcs=self.real_wcs) img_real_wcs=self.chip_wcs)
x, y = self.real_pos.x + 0.5, self.real_pos.y + 0.5 x, y = self.real_pos.x + 0.5, self.real_pos.y + 0.5
x_nominal = int(np.floor(x + 0.5)) x_nominal = int(np.floor(x + 0.5))
...@@ -130,9 +114,11 @@ class Galaxy(MockObject): ...@@ -130,9 +114,11 @@ class Galaxy(MockObject):
dx = x - x_nominal dx = x - x_nominal
dy = y - y_nominal dy = y - y_nominal
offset = galsim.PositionD(dx, dy) offset = galsim.PositionD(dx, dy)
# Get real local wcs of object (deal with chip rotation w.r.t its center)
chip_wcs_local = self.chip_wcs.local(self.real_pos)
is_updated = 0
real_wcs_local = self.real_wcs.local(self.real_pos) # Model the galaxy as disk + bulge
disk = galsim.Sersic(n=self.disk_sersic_idx, half_light_radius=self.hlr_disk, flux=1.0, gsparams=gsp) disk = galsim.Sersic(n=self.disk_sersic_idx, half_light_radius=self.hlr_disk, flux=1.0, gsparams=gsp)
disk_shape = galsim.Shear(g1=self.e1_disk, g2=self.e2_disk) disk_shape = galsim.Shear(g1=self.e1_disk, g2=self.e2_disk)
disk = disk.shear(disk_shape) disk = disk.shear(disk_shape)
...@@ -140,33 +126,33 @@ class Galaxy(MockObject): ...@@ -140,33 +126,33 @@ class Galaxy(MockObject):
bulge_shape = galsim.Shear(g1=self.e1_bulge, g2=self.e2_bulge) bulge_shape = galsim.Shear(g1=self.e1_bulge, g2=self.e2_bulge)
bulge = bulge.shear(bulge_shape) bulge = bulge.shear(bulge_shape)
# Get shear and deal with shear induced by field distortion
if fd_shear: if fd_shear:
g1 += fd_shear.g1 g1 += fd_shear.g1
g2 += fd_shear.g2 g2 += fd_shear.g2
gal_shear = galsim.Shear(g1=g1, g2=g2) gal_shear = galsim.Shear(g1=g1, g2=g2)
# Loop over all sub-bandpasses
for i in range(len(bandpass_list)): for i in range(len(bandpass_list)):
bandpass = bandpass_list[i] bandpass = bandpass_list[i]
try: try:
sub = integrate_sed_bandpass(sed=self.sed, bandpass=bandpass) sub = integrate_sed_bandpass(sed=self.sed, bandpass=bandpass)
except Exception as e: except Exception as e:
print(e) print(e)
if self.logger: if self.logger:
self.logger.error(e) self.logger.error(e)
# return False
continue continue
ratio = sub/full ratio = sub/full
if not (ratio == -1 or (ratio != ratio)): if not (ratio == -1 or (ratio != ratio)):
nphotons = ratio * nphotons_tot nphotons = ratio * nphotons_tot
else: else:
continue continue
nphotons_sum += nphotons
# nphotons_sum += nphotons
# # [C6 TEST] # # [C6 TEST]
# print("nphotons_sub-band_%d = %.2f"%(i, nphotons)) # print("nphotons_sub-band_%d = %.2f"%(i, nphotons))
# Get PSF model
psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img, bandpass=bandpass, folding_threshold=folding_threshold) psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img, bandpass=bandpass, folding_threshold=folding_threshold)
gal_temp = self.bfrac * bulge + (1.0 - self.bfrac) * disk gal_temp = self.bfrac * bulge + (1.0 - self.bfrac) * disk
...@@ -194,39 +180,21 @@ class Galaxy(MockObject): ...@@ -194,39 +180,21 @@ class Galaxy(MockObject):
# for stat in top_stats[:10]: # for stat in top_stats[:10]:
# print(stat) # print(stat)
stamp = gal.drawImage(wcs=real_wcs_local, method='phot', offset=offset, save_photons=True) # stamp = gal.drawImage(wcs=chip_wcs_local, method='phot', offset=offset, save_photons=True)
photons = stamp.photons stamp = gal.drawImage(wcs=chip_wcs_local, offset=offset)
photons.x += x_nominal if np.sum(np.isnan(stamp.array)) > 0:
photons.y += y_nominal # ERROR happens
photons_list.append(photons) return 2, pos_shear
stamp.wcs = real_wcs_local
stamp.setCenter(x_nominal, y_nominal) stamp.setCenter(x_nominal, y_nominal)
bounds = stamp.bounds & galsim.BoundsI(0, chip.npix_x - 1, 0, chip.npix_y - 1) bounds = stamp.bounds & galsim.BoundsI(0, chip.npix_x - 1, 0, chip.npix_y - 1)
if bounds.area() > 0: if bounds.area() > 0:
chip.img.setOrigin(0, 0) chip.img.setOrigin(0, 0)
stamp[bounds] = chip.img[bounds] chip.img[bounds] += stamp[bounds]
is_updated = 1
if not big_galaxy:
for i in range(len(photons_list)):
if i == 0:
chip.sensor.accumulate(photons_list[i], stamp)
else:
chip.sensor.accumulate(photons_list[i], stamp, resume=True)
else:
sensor = galsim.Sensor()
for i in range(len(photons_list)):
if i == 0:
sensor.accumulate(photons_list[i], stamp)
else:
sensor.accumulate(photons_list[i], stamp, resume=True)
del sensor
chip.img[bounds] = stamp[bounds]
chip.img.setOrigin(chip.bound.xmin, chip.bound.ymin) chip.img.setOrigin(chip.bound.xmin, chip.bound.ymin)
else: del stamp
if is_updated == 0:
# Return code 0: object photons missed this detector # Return code 0: object photons missed this detector
print("obj %s missed"%(self.id)) print("obj %s missed"%(self.id))
if self.logger: if self.logger:
...@@ -235,8 +203,6 @@ class Galaxy(MockObject): ...@@ -235,8 +203,6 @@ class Galaxy(MockObject):
# # [C6 TEST] # # [C6 TEST]
# print("nphotons_sum = ", nphotons_sum) # print("nphotons_sum = ", nphotons_sum)
del photons_list
del stamp
return 1, pos_shear return 1, pos_shear
def drawObj_slitless(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0, def drawObj_slitless(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0,
...@@ -255,7 +221,7 @@ class Galaxy(MockObject): ...@@ -255,7 +221,7 @@ class Galaxy(MockObject):
names=('WAVELENGTH', 'FLUX')) names=('WAVELENGTH', 'FLUX'))
self.real_pos = self.getRealPos(chip.img, global_x=self.posImg.x, global_y=self.posImg.y, self.real_pos = self.getRealPos(chip.img, global_x=self.posImg.x, global_y=self.posImg.y,
img_real_wcs=self.real_wcs) img_real_wcs=self.chip_wcs)
x, y = self.real_pos.x + 0.5, self.real_pos.y + 0.5 x, y = self.real_pos.x + 0.5, self.real_pos.y + 0.5
x_nominal = int(np.floor(x + 0.5)) x_nominal = int(np.floor(x + 0.5))
...@@ -264,7 +230,7 @@ class Galaxy(MockObject): ...@@ -264,7 +230,7 @@ class Galaxy(MockObject):
dy = y - y_nominal dy = y - y_nominal
offset = galsim.PositionD(dx, dy) offset = galsim.PositionD(dx, dy)
real_wcs_local = self.real_wcs.local(self.real_pos) chip_wcs_local = self.chip_wcs.local(self.real_pos)
big_galaxy = False big_galaxy = False
...@@ -313,7 +279,7 @@ class Galaxy(MockObject): ...@@ -313,7 +279,7 @@ class Galaxy(MockObject):
# if fd_shear is not None: # if fd_shear is not None:
# gal = gal.shear(fd_shear) # gal = gal.shear(fd_shear)
starImg = gal.drawImage(wcs=real_wcs_local, offset=offset) starImg = gal.drawImage(wcs=chip_wcs_local, offset=offset)
origin_star = [y_nominal - (starImg.center.y - starImg.ymin), origin_star = [y_nominal - (starImg.center.y - starImg.ymin),
x_nominal - (starImg.center.x - starImg.xmin)] x_nominal - (starImg.center.x - starImg.xmin)]
...@@ -340,7 +306,7 @@ class Galaxy(MockObject): ...@@ -340,7 +306,7 @@ class Galaxy(MockObject):
isAlongY=0, isAlongY=0,
flat_cube=flat_cube) flat_cube=flat_cube)
self.addSLStoChipImage(sdp=sdp_p1, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=real_wcs_local) self.addSLStoChipImage(sdp=sdp_p1, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=chip_wcs_local)
subImg_p2 = starImg.array[:, subSlitPos+1:starImg.array.shape[1]] subImg_p2 = starImg.array[:, subSlitPos+1:starImg.array.shape[1]]
star_p2 = galsim.Image(subImg_p2) star_p2 = galsim.Image(subImg_p2)
...@@ -357,7 +323,7 @@ class Galaxy(MockObject): ...@@ -357,7 +323,7 @@ class Galaxy(MockObject):
isAlongY=0, isAlongY=0,
flat_cube=flat_cube) flat_cube=flat_cube)
self.addSLStoChipImage(sdp=sdp_p2, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=real_wcs_local) self.addSLStoChipImage(sdp=sdp_p2, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=chip_wcs_local)
del sdp_p1 del sdp_p1
del sdp_p2 del sdp_p2
...@@ -369,7 +335,7 @@ class Galaxy(MockObject): ...@@ -369,7 +335,7 @@ class Galaxy(MockObject):
conf=chip.sls_conf[1], conf=chip.sls_conf[1],
isAlongY=0, isAlongY=0,
flat_cube=flat_cube) flat_cube=flat_cube)
self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=real_wcs_local) self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=chip_wcs_local)
del sdp del sdp
elif grating_split_pos_chip>=gal_end[1]: elif grating_split_pos_chip>=gal_end[1]:
sdp = SpecDisperser(orig_img=starImg, xcenter=x_nominal - 0, sdp = SpecDisperser(orig_img=starImg, xcenter=x_nominal - 0,
...@@ -379,7 +345,7 @@ class Galaxy(MockObject): ...@@ -379,7 +345,7 @@ class Galaxy(MockObject):
conf=chip.sls_conf[0], conf=chip.sls_conf[0],
isAlongY=0, isAlongY=0,
flat_cube=flat_cube) flat_cube=flat_cube)
self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=real_wcs_local) self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=chip_wcs_local)
del sdp del sdp
# print(self.y_nominal, starImg.center.y, starImg.ymin) # print(self.y_nominal, starImg.center.y, starImg.ymin)
...@@ -404,46 +370,6 @@ class Galaxy(MockObject): ...@@ -404,46 +370,6 @@ class Galaxy(MockObject):
final = galsim.Convolve(psf, gal) final = galsim.Convolve(psf, gal)
return final return final
def drawObject(self, img, final, noise_level=0.0, flux=None, filt=None, tel=None, exptime=150.):
""" Override the method in parent class
Need to constrain the size of image stamp for extended objects
"""
isUpdated = True
if flux == None:
flux = self.getElectronFluxFilt(filt, tel, exptime)
stamp = final.drawImage(wcs=self.localWCS, offset=self.offset)
stamp_arr = stamp.array
mask = (stamp_arr >= 0.001*noise_level) # why 0.001?
err = int(np.sqrt(mask.sum()))
if np.mod(err, 2) == 1:
err += 1
# if err == 1:
if err == 0:
subSize = 16 # why 16?
else:
subSize = max([err, 16])
fluxRatio = flux / stamp_arr[mask].sum()
final = final.withScaledFlux(fluxRatio)
imgSub = galsim.ImageF(subSize, subSize)
# Draw with FFT
# stamp = final.drawImage(image=imgSub, wcs=self.localWCS, offset=self.offset)
# Draw with Photon Shoot
stamp = final.drawImage(image=imgSub, wcs=self.localWCS, method='phot', offset=self.offset)
stamp.setCenter(self.x_nominal, self.y_nominal)
if np.sum(np.isnan(stamp.array)) >= 1:
stamp.setZero()
bounds = stamp.bounds & img.bounds
if bounds.area() == 0:
isUpdated = False
else:
img[bounds] += stamp[bounds]
return img, stamp, isUpdated
def getObservedEll(self, g1=0, g2=0): def getObservedEll(self, g1=0, g2=0):
e1_obs, e2_obs, e_obs, theta = eObs(self.e1_total, self.e2_total, g1, g2) e1_obs, e2_obs, e_obs, theta = eObs(self.e1_total, self.e2_total, g1, g2)
return self.e1_total, self.e2_total, g1, g2, e1_obs, e2_obs return self.e1_total, self.e2_total, g1, g2, e1_obs, e2_obs
ObservationSim/MockObject/MockObject.py
View file @ a6664237
...@@ -13,7 +13,6 @@ from ObservationSim.MockObject.SpecDisperser import SpecDisperser ...@@ -13,7 +13,6 @@ from ObservationSim.MockObject.SpecDisperser import SpecDisperser
class MockObject(object): class MockObject(object):
def __init__(self, param, logger=None): def __init__(self, param, logger=None):
self.param = param self.param = param
for key in self.param: for key in self.param:
setattr(self, key, self.param[key]) setattr(self, key, self.param[key])
...@@ -27,14 +26,10 @@ class MockObject(object): ...@@ -27,14 +26,10 @@ class MockObject(object):
elif self.param["star"] == 3: elif self.param["star"] == 3:
self.type = "stamp" self.type = "stamp"
###mock_stamp_END ###mock_stamp_END
self.sed = None self.sed = None
self.fd_shear = None
# Place holder for outputs # Place holder for outputs
self.additional_output_str = "" self.additional_output_str = ""
self.fd_shear = None
self.logger = logger self.logger = logger
def getMagFilter(self, filt): def getMagFilter(self, filt):
...@@ -65,6 +60,7 @@ class MockObject(object): ...@@ -65,6 +60,7 @@ class MockObject(object):
def getPosImg_Offset_WCS(self, img, fdmodel=None, chip=None, verbose=True, chip_wcs=None, img_header=None): def getPosImg_Offset_WCS(self, img, fdmodel=None, chip=None, verbose=True, chip_wcs=None, img_header=None):
self.posImg = img.wcs.toImage(self.getPosWorld()) self.posImg = img.wcs.toImage(self.getPosWorld())
self.localWCS = img.wcs.local(self.posImg) self.localWCS = img.wcs.local(self.posImg)
# Apply field distortion model
if (fdmodel is not None) and (chip is not None): if (fdmodel is not None) and (chip is not None):
if verbose: if verbose:
print("\n") print("\n")
...@@ -74,6 +70,7 @@ class MockObject(object): ...@@ -74,6 +70,7 @@ class MockObject(object):
if verbose: if verbose:
print("After field distortion:\n") print("After field distortion:\n")
print("x = %.2f, y = %.2f\n" % (self.posImg.x, self.posImg.y), flush=True) print("x = %.2f, y = %.2f\n" % (self.posImg.x, self.posImg.y), flush=True)
x, y = self.posImg.x + 0.5, self.posImg.y + 0.5 x, y = self.posImg.x + 0.5, self.posImg.y + 0.5
self.x_nominal = int(np.floor(x + 0.5)) self.x_nominal = int(np.floor(x + 0.5))
self.y_nominal = int(np.floor(y + 0.5)) self.y_nominal = int(np.floor(y + 0.5))
...@@ -81,50 +78,22 @@ class MockObject(object): ...@@ -81,50 +78,22 @@ class MockObject(object):
dy = y - self.y_nominal dy = y - self.y_nominal
self.offset = galsim.PositionD(dx, dy) self.offset = galsim.PositionD(dx, dy)
# Deal with chip rotation
if chip_wcs is not None: if chip_wcs is not None:
self.real_wcs = chip_wcs self.chip_wcs = chip_wcs
elif img_header is not None: elif img_header is not None:
self.real_wcs = galsim.FitsWCS(header=img_header) self.chip_wcs = galsim.FitsWCS(header=img_header)
else: else:
self.real_wcs = None self.chip_wcs = None
return self.posImg, self.offset, self.localWCS, self.real_wcs, self.fd_shear return self.posImg, self.offset, self.localWCS, self.chip_wcs, self.fd_shear
def getRealPos(self, img, global_x=0., global_y=0., img_real_wcs=None): def getRealPos(self, img, global_x=0., global_y=0., img_real_wcs=None):
img_global_pos = galsim.PositionD(global_x, global_y) img_global_pos = galsim.PositionD(global_x, global_y)
cel_pos = img.wcs.toWorld(img_global_pos) cel_pos = img.wcs.toWorld(img_global_pos)
realPos = img_real_wcs.toImage(cel_pos) realPos = img_real_wcs.toImage(cel_pos)
return realPos return realPos
def drawObject(self, img, final, flux=None, filt=None, tel=None, exptime=150.):
""" Draw (point like) object on img.
Should be overided for extended source, e.g. galaxy...
Paramter:
img: the "canvas"
final: final (after shear, PSF etc.) GSObject
Return:
img: the image with the GSObject added (or discarded)
isUpdated: is the "canvas" been updated? (a flag for updating statistcs)
"""
isUpdated = True
# Draw with FFT
# stamp = final.drawImage(wcs=self.localWCS, offset=self.offset)
# Draw with Photon Shoot
stamp = final.drawImage(wcs=self.localWCS, method='phot', offset=self.offset)
stamp.setCenter(self.x_nominal, self.y_nominal)
if np.sum(np.isnan(stamp.array)) >= 1:
stamp.setZero()
bounds = stamp.bounds & img.bounds
if bounds.area() == 0:
isUpdated = False
else:
img[bounds] += stamp[bounds]
return img, stamp, isUpdated
def drawObj_multiband(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0, def drawObj_multiband(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0,
exptime=150., fd_shear=None): exptime=150., fd_shear=None):
if nphotons_tot == None: if nphotons_tot == None:
...@@ -139,29 +108,27 @@ class MockObject(object): ...@@ -139,29 +108,27 @@ class MockObject(object):
self.logger.error(e) self.logger.error(e)
return 2, None return 2, None
nphotons_sum = 0 # Set Galsim Parameters
photons_list = []
xmax, ymax = 0, 0
# (TEST) Galsim Parameters
if self.getMagFilter(filt) <= 15: if self.getMagFilter(filt) <= 15:
folding_threshold = 5.e-4 folding_threshold = 5.e-4
else: else:
folding_threshold = 5.e-3 folding_threshold = 5.e-3
gsp = galsim.GSParams(folding_threshold=folding_threshold) gsp = galsim.GSParams(folding_threshold=folding_threshold)
# Get real image position of object (deal with chip rotation w.r.t its center)
self.real_pos = self.getRealPos(chip.img, global_x=self.posImg.x, global_y=self.posImg.y, self.real_pos = self.getRealPos(chip.img, global_x=self.posImg.x, global_y=self.posImg.y,
img_real_wcs=self.real_wcs) img_real_wcs=self.chip_wcs)
x, y = self.real_pos.x + 0.5, self.real_pos.y + 0.5 x, y = self.real_pos.x + 0.5, self.real_pos.y + 0.5
x_nominal = int(np.floor(x + 0.5)) x_nominal = int(np.floor(x + 0.5))
y_nominal = int(np.floor(y + 0.5)) y_nominal = int(np.floor(y + 0.5))
dx = x - x_nominal dx = x - x_nominal
dy = y - y_nominal dy = y - y_nominal
offset = galsim.PositionD(dx, dy) offset = galsim.PositionD(dx, dy)
# Get real local wcs of object (deal with chip rotation w.r.t its center)
chip_wcs_local = self.chip_wcs.local(self.real_pos)
is_updated = 0
real_wcs_local = self.real_wcs.local(self.real_pos) # Loop over all sub-bandpasses
for i in range(len(bandpass_list)): for i in range(len(bandpass_list)):
bandpass = bandpass_list[i] bandpass = bandpass_list[i]
try: try:
...@@ -170,61 +137,41 @@ class MockObject(object): ...@@ -170,61 +137,41 @@ class MockObject(object):
print(e) print(e)
if self.logger: if self.logger:
self.logger.error(e) self.logger.error(e)
# return False
continue continue
ratio = sub / full ratio = sub / full
if not (ratio == -1 or (ratio != ratio)): if not (ratio == -1 or (ratio != ratio)):
nphotons = ratio * nphotons_tot nphotons = ratio * nphotons_tot
else: else:
# return False
continue continue
nphotons_sum += nphotons
# nphotons_sum += nphotons
# print("nphotons_sub-band_%d = %.2f"%(i, nphotons)) # print("nphotons_sub-band_%d = %.2f"%(i, nphotons))
# Get PSF model
psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img, bandpass=bandpass, psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img, bandpass=bandpass,
folding_threshold=folding_threshold) folding_threshold=folding_threshold)
star = galsim.DeltaFunction(gsparams=gsp) star = galsim.DeltaFunction(gsparams=gsp)
star = star.withFlux(nphotons) star = star.withFlux(nphotons)
star = galsim.Convolve(psf, star) star = galsim.Convolve(psf, star)
stamp = star.drawImage(wcs=real_wcs_local, method='phot', offset=offset, save_photons=True) stamp = star.drawImage(wcs=chip_wcs_local, offset=offset)
xmax = max(xmax, stamp.xmax) if np.sum(np.isnan(stamp.array)) > 0:
ymax = max(ymax, stamp.ymax) continue
photons = stamp.photons stamp.setCenter(x_nominal, y_nominal)
photons.x += x_nominal bounds = stamp.bounds & galsim.BoundsI(0, chip.npix_x - 1, 0, chip.npix_y - 1)
photons.y += y_nominal if bounds.area() > 0:
photons_list.append(photons) chip.img.setOrigin(0, 0)
chip.img[bounds] += stamp[bounds]
stamp = galsim.ImageF(int(xmax * 1.1), int(ymax * 1.1)) is_updated = 1
stamp.wcs = real_wcs_local chip.img.setOrigin(chip.bound.xmin, chip.bound.ymin)
stamp.setCenter(x_nominal, y_nominal) del stamp
bounds = stamp.bounds & galsim.BoundsI(0, chip.npix_x - 1, 0, chip.npix_y - 1)
# # (DEBUG) if is_updated == 0:
# print("stamp bounds: ", stamp.bounds) # Return code 0: object has missed this detector
# print(bounds)
if bounds.area() > 0:
chip.img.setOrigin(0, 0)
stamp[bounds] = chip.img[bounds]
for i in range(len(photons_list)):
if i == 0:
chip.sensor.accumulate(photons_list[i], stamp)
else:
chip.sensor.accumulate(photons_list[i], stamp, resume=True)
chip.img[bounds] = stamp[bounds]
chip.img.setOrigin(chip.bound.xmin, chip.bound.ymin)
else:
# Return code 0: object photons missed this detector
print("obj %s missed"%(self.id)) print("obj %s missed"%(self.id))
if self.logger: if self.logger:
self.logger.info("obj %s missed"%(self.id)) self.logger.info("obj %s missed"%(self.id))
return 0, pos_shear return 0, pos_shear
del photons_list
del stamp
return 1, pos_shear # Return code 1: draw sucesss return 1, pos_shear # Return code 1: draw sucesss
def addSLStoChipImage(self, sdp=None, chip=None, xOrderSigPlus=None, local_wcs=None): def addSLStoChipImage(self, sdp=None, chip=None, xOrderSigPlus=None, local_wcs=None):
...@@ -299,7 +246,7 @@ class MockObject(object): ...@@ -299,7 +246,7 @@ class MockObject(object):
names=('WAVELENGTH', 'FLUX')) names=('WAVELENGTH', 'FLUX'))
self.real_pos = self.getRealPos(chip.img, global_x=self.posImg.x, global_y=self.posImg.y, self.real_pos = self.getRealPos(chip.img, global_x=self.posImg.x, global_y=self.posImg.y,
img_real_wcs=self.real_wcs) img_real_wcs=self.chip_wcs)
x, y = self.real_pos.x + 0.5, self.real_pos.y + 0.5 x, y = self.real_pos.x + 0.5, self.real_pos.y + 0.5
x_nominal = int(np.floor(x + 0.5)) x_nominal = int(np.floor(x + 0.5))
...@@ -308,7 +255,7 @@ class MockObject(object): ...@@ -308,7 +255,7 @@ class MockObject(object):
dy = y - y_nominal dy = y - y_nominal
offset = galsim.PositionD(dx, dy) offset = galsim.PositionD(dx, dy)
real_wcs_local = self.real_wcs.local(self.real_pos) chip_wcs_local = self.chip_wcs.local(self.real_pos)
flat_cube = chip.flat_cube flat_cube = chip.flat_cube
...@@ -323,7 +270,7 @@ class MockObject(object): ...@@ -323,7 +270,7 @@ class MockObject(object):
star = star.withFlux(tel.pupil_area * exptime) star = star.withFlux(tel.pupil_area * exptime)
star = galsim.Convolve(psf, star) star = galsim.Convolve(psf, star)
starImg = star.drawImage(nx=100, ny=100, wcs=real_wcs_local, offset=offset) starImg = star.drawImage(nx=100, ny=100, wcs=chip_wcs_local, offset=offset)
origin_star = [y_nominal - (starImg.center.y - starImg.ymin), origin_star = [y_nominal - (starImg.center.y - starImg.ymin),
x_nominal - (starImg.center.x - starImg.xmin)] x_nominal - (starImg.center.x - starImg.xmin)]
...@@ -350,7 +297,7 @@ class MockObject(object): ...@@ -350,7 +297,7 @@ class MockObject(object):
isAlongY=0, isAlongY=0,
flat_cube=flat_cube) flat_cube=flat_cube)
self.addSLStoChipImage(sdp=sdp_p1, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=real_wcs_local) self.addSLStoChipImage(sdp=sdp_p1, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
subImg_p2 = starImg.array[:, subSlitPos + 1:starImg.array.shape[1]] subImg_p2 = starImg.array[:, subSlitPos + 1:starImg.array.shape[1]]
star_p2 = galsim.Image(subImg_p2) star_p2 = galsim.Image(subImg_p2)
...@@ -367,7 +314,7 @@ class MockObject(object): ...@@ -367,7 +314,7 @@ class MockObject(object):
isAlongY=0, isAlongY=0,
flat_cube=flat_cube) flat_cube=flat_cube)
self.addSLStoChipImage(sdp=sdp_p2, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=real_wcs_local) self.addSLStoChipImage(sdp=sdp_p2, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
del sdp_p1 del sdp_p1
del sdp_p2 del sdp_p2
...@@ -379,7 +326,7 @@ class MockObject(object): ...@@ -379,7 +326,7 @@ class MockObject(object):
conf=chip.sls_conf[1], conf=chip.sls_conf[1],
isAlongY=0, isAlongY=0,
flat_cube=flat_cube) flat_cube=flat_cube)
self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=real_wcs_local) self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
del sdp del sdp
elif grating_split_pos_chip >= gal_end[1]: elif grating_split_pos_chip >= gal_end[1]:
sdp = SpecDisperser(orig_img=starImg, xcenter=x_nominal - 0, sdp = SpecDisperser(orig_img=starImg, xcenter=x_nominal - 0,
...@@ -389,7 +336,7 @@ class MockObject(object): ...@@ -389,7 +336,7 @@ class MockObject(object):
conf=chip.sls_conf[0], conf=chip.sls_conf[0],
isAlongY=0, isAlongY=0,
flat_cube=flat_cube) flat_cube=flat_cube)
self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=real_wcs_local) self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
del sdp del sdp
del psf del psf
return 1, pos_shear return 1, pos_shear
......
ObservationSim/ObservationSim.py
View file @ a6664237
...@@ -186,7 +186,7 @@ class Observation(object): ...@@ -186,7 +186,7 @@ class Observation(object):
extName='SCI', extName='SCI',
timestamp = pointing.timestamp, timestamp = pointing.timestamp,
exptime = pointing.exp_time, exptime = pointing.exp_time,
readoutTime = 40.) readoutTime = chip.readout_time)
chip_wcs = galsim.FitsWCS(header=h_ext) chip_wcs = galsim.FitsWCS(header=h_ext)
...@@ -382,7 +382,7 @@ class Observation(object): ...@@ -382,7 +382,7 @@ class Observation(object):
extName='SCI', extName='SCI',
timestamp=pointing.timestamp, timestamp=pointing.timestamp,
exptime=pointing.exp_time, exptime=pointing.exp_time,
readoutTime=40.) readoutTime=chip.readout_time)
chip.img = galsim.Image(chip.img.array, dtype=np.uint16) chip.img = galsim.Image(chip.img.array, dtype=np.uint16)
hdu1 = fits.PrimaryHDU(header=h_prim) hdu1 = fits.PrimaryHDU(header=h_prim)
......
config/config_50sqdeg.yaml
View file @ a6664237
...@@ -9,9 +9,9 @@ ...@@ -9,9 +9,9 @@
# Base diretories and naming setup # Base diretories and naming setup
# Can add some of the command-line arguments here as well; # Can add some of the command-line arguments here as well;
# OK to pass either way or both, as long as they are consistent # OK to pass either way or both, as long as they are consistent
work_dir: "/share/home/fangyuedong/csst-simulation/workplace/" work_dir: "/share/home/fangyuedong/new_sim/workplace/"
data_dir: "/share/simudata/CSSOSDataProductsSims/data/" data_dir: "/share/simudata/CSSOSDataProductsSims/data/"
run_name: "rotate_0" run_name: "test_new_sim"
# Whether to use MPI # Whether to use MPI
run_option: run_option:
...@@ -45,10 +45,10 @@ catalog_options: ...@@ -45,10 +45,10 @@ catalog_options:
# AGN_SED_WAVE: "wave_ross13.npy" # AGN_SED_WAVE: "wave_ross13.npy"
# Only simulate stars? # Only simulate stars?
star_only: NO star_only: YES
# Only simulate galaxies? # Only simulate galaxies?
galaxy_only: YES galaxy_only: NO
# rotate galaxy ellipticity # rotate galaxy ellipticity
rotateEll: 0. # [degree] rotateEll: 0. # [degree]
...@@ -171,7 +171,7 @@ ins_effects: ...@@ -171,7 +171,7 @@ ins_effects:
non_linear: ON # Whether to add non-linearity non_linear: ON # Whether to add non-linearity
cosmic_ray: ON # Whether to add cosmic-ray cosmic_ray: ON # Whether to add cosmic-ray
cray_differ: ON # Whether to generate different cosmic ray maps CAL and MS output cray_differ: ON # Whether to generate different cosmic ray maps CAL and MS output
cte_trail: ON # Whether to simulate CTE trails cte_trail: OFF # Whether to simulate CTE trails
saturbloom: ON # Whether to simulate Saturation & Blooming saturbloom: ON # Whether to simulate Saturation & Blooming
add_badcolumns: ON # Whether to add bad columns add_badcolumns: ON # Whether to add bad columns
add_hotpixels: ON # Whether to add hot pixels add_hotpixels: ON # Whether to add hot pixels
......
libmoduleDfBF/diffusion_X1.c 0 → 100644
View file @ a6664237
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "nrutil.h"
#define ISSETBITFLAG(x,b) ((x) & (1 << (b)))
#define ADD_DIFFUSION 1
#define ADD_BF_FILTER 2
float linearInterp(float xp, float x0, float y0, float x1, float y1);
void addEffects(int ngx_ima, int ngy_ima, float *arr_ima, float *arr_imc, int bit_flag)
{
int nx, ny, i,j,k,ks;
int it,jt,itt,jtt;
int diffuidx[26][2],diffuN,ilow,ih,im,dim[3];
float diffua[5][5],cdiffu[26],**bfa;
double mvar,mcov,tmp,ma,mb,mc;
char fname[100];
nx = ngx_ima; //input-image size
ny = ngy_ima;
//0. init. original image with an input array (arr_ima)
//1. Adding diffusion effect.
if(ISSETBITFLAG(bit_flag, ADD_DIFFUSION))
{
printf("adding diffusion.....\n");
printf("ERR: no diffusion filter ...");
exit(0);
}
//2. Adding BF effect
if(ISSETBITFLAG(bit_flag, ADD_BF_FILTER))
{
printf("Adding BF effect...\n");
//setup BF correlation fliter
float neX;
float neP1 = 50000;
float bfaP1[9]={0.9707182, 0.002143905, 0.004131103, 0.001149542, 0.0005501739, 0.0005469659, 0.0003726081, 0.0003795207, 0.0001633302};
float neP2 = 10000;
float bfaP2[9]={0.9945288, 0.0003041936, 0.0007539311, 0.0002424675, 0.0001226098, 0.00009308617, 0.00008027447, 0.00006309676, 0.00006400052};
bfa=matrix(-2,2,-2,2);
// smooth with the BF filter
for(i=0;i<nx;i++)for(j=0;j<ny;j++) arr_imc[j+i*ny]=0;
for(i=0;i<nx;i++)
{
for(j=0;j<ny;j++)
{
//rescale BF filter with the local pix value
neX = arr_ima[j+i*ny];
if(neX >= 10000)
{
bfa[0][0]=0; //linearInterp(neX, neP1, bfaP1[0], neP2, bfaP2[0]); //0;
bfa[0][1]=bfa[0][-1]=linearInterp(neX, neP1, bfaP1[1], neP2, bfaP2[1]); //0.01575;
bfa[-1][0]=bfa[1][0]=linearInterp(neX, neP1, bfaP1[2], neP2, bfaP2[2]); //0.00652;
bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=linearInterp(neX, neP1, bfaP1[3], neP2, bfaP2[3]); //0.00335;
bfa[0][-2]=bfa[0][2]=linearInterp(neX, neP1, bfaP1[4], neP2, bfaP2[4]);
bfa[-2][0]=bfa[2][0]=linearInterp(neX, neP1, bfaP1[5], neP2, bfaP2[5]); //0.00118;
bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=linearInterp(neX, neP1, bfaP1[6], neP2, bfaP2[6]);
bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=linearInterp(neX, neP1, bfaP1[7], neP2, bfaP2[7]); //0.00083;
bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=linearInterp(neX, neP1, bfaP1[8], neP2, bfaP2[8]); //0.00043;
}
else
{
neX=10000;
bfa[0][0]=0;
bfa[0][1]=bfa[0][-1]=bfaP2[1];
bfa[-1][0]=bfa[1][0]=bfaP2[2];
bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=bfaP2[3];
bfa[0][-2]=bfa[0][2]=bfaP2[4];
bfa[-2][0]=bfa[2][0]=bfaP2[5];
bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=bfaP2[6];
bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=bfaP2[7];
bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=bfaP2[8];
}
tmp = 0;
for(it=-2;it<=2;it++)
for(jt=-2;jt<=2;jt++)
{
bfa[it][jt] = bfa[it][jt]/neX*arr_ima[j+i*ny];
tmp += bfa[it][jt];
}
bfa[0][0]=1.-tmp;
// assign electrons according to the BF filter bfat
for(it=-2;it<=2;it++)
{
for(jt=-2;jt<=2;jt++)
{
itt=i+it;
jtt=j+jt;
if(itt>=0 && jtt>=0 && itt<nx && jtt<ny)
//c0[itt][jtt]+=bfa[it][jt]*b[i][j];
arr_imc[jtt+itt*ny] += bfa[it][jt]*arr_ima[j+i*ny];
}
}
}
}
free_matrix(bfa,-2,2,-2,2);
}
else
{
for(i=0;i<nx;i++) for(j=0;j<ny;j++) arr_imc[j+i*ny]=arr_ima[j+i*ny]; ////for ADD_BF False
}
}
float linearInterp(float xp, float x0, float y0, float x1, float y1)
{
float yp;
yp = y0 + ((y1-y0)/(x1-x0)) * (xp - x0);
return yp;
}
profile_C6.sh
View file @ a6664237
...@@ -2,13 +2,12 @@ ...@@ -2,13 +2,12 @@
date date
python -m cProfile -o C6_profiler_test.pstats /share/home/fangyuedong/csst-simulation/run_sim.py \ python -m cProfile -o C6_profiler_test.pstats /share/home/fangyuedong/new_sim/csst-simulation/run_sim.py \
--config_file config_fgs.yaml \ --config_file config_50sqdeg.yaml \
--catalog FGS_Catalog \ --catalog C6_50sqdeg \
-c /share/home/fangyuedong/csst-simulation/config -c /share/home/fangyuedong/new_sim/csst-simulation/config
# --config_file config_fgs.yaml \
# --config_file config_50sqdeg.yaml \ # --catalog FGS_Catalog \
# --catalog C6_50sqdeg \
# -c /share/home/fangyuedong/csst-simulation/config # -c /share/home/fangyuedong/csst-simulation/config
# --config_file config_C6.yaml \ # --config_file config_C6.yaml \
......
run_C6.pbs
View file @ a6664237
...@@ -12,10 +12,10 @@ NP=96 ...@@ -12,10 +12,10 @@ NP=96
hostfile=wcl-1,wcl-2 hostfile=wcl-1,wcl-2
date date
mpirun --oversubscribe -H $hostfile -np $NP python /share/home/fangyuedong/csst-simulation/run_sim.py \ mpirun --oversubscribe -H $hostfile -np $NP python /share/home/fangyuedong/new_sim/csst-simulation/run_sim.py \
--config_file config_50sqdeg.yaml \ --config_file config_50sqdeg.yaml \
--catalog C6_50sqdeg \ --catalog C6_50sqdeg \
-c /share/home/fangyuedong/csst-simulation/config -c /share/home/fangyuedong/new_sim/csst-simulation/config
# --config_file config_C6.yaml \ # --config_file config_C6.yaml \
# --catalog C6_Catalog \ # --catalog C6_Catalog \
# -c /share/home/fangyuedong/csst-simulation/config # -c /share/home/fangyuedong/csst-simulation/config
......
setup.py
View file @ a6664237
...@@ -2,11 +2,30 @@ from setuptools import setup, find_packages ...@@ -2,11 +2,30 @@ from setuptools import setup, find_packages
from setuptools.extension import Extension from setuptools.extension import Extension
from setuptools.config import read_configuration from setuptools.config import read_configuration
from distutils.command.build_ext import build_ext
from Cython.Build import cythonize from Cython.Build import cythonize
import numpy import numpy
class CTypes(Extension): pass
class build_ext(build_ext):
def build_extension(self, ext):
self._ctypes = isinstance(ext, CTypes)
return super().build_extension(ext)
def get_export_symbols(self, ext):
if self._ctypes:
return ext.export_symbols
return super().get_export_symbols(ext)
def get_ext_filename(self, ext_name):
if self._ctypes:
return ext_name + '.so'
return super().get_ext_filename(ext_name)
extensions = [ extensions = [
Extension("ObservationSim.MockObject.SpecDisperser.disperse_c.interp", ["ObservationSim/MockObject/SpecDisperser/disperse_c/interp.pyx"], Extension("ObservationSim.MockObject.SpecDisperser.disperse_c.interp", ["ObservationSim/MockObject/SpecDisperser/disperse_c/interp.pyx"],
include_dirs = [numpy.get_include()], include_dirs = [numpy.get_include()],
...@@ -17,14 +36,17 @@ extensions = [ ...@@ -17,14 +36,17 @@ extensions = [
libraries=["m"]), libraries=["m"]),
] ]
df_module = [CTypes('ObservationSim.Instrument.Chip.lib_bf.libmoduleBF',
['ObservationSim/Instrument/Chip/lib_bf/diffusion_X1.c', 'ObservationSim/Instrument/Chip/lib_bf/nrutil.c'],
include_dirs=['ObservationSim/Instrument/Chip/lib_df_bf/', '/usr/include']
)]
# setup( # setup(
# name = "slssim_disperse", # name = "slssim_disperse",
# ext_modules = cythonize(extensions), # ext_modules = cythonize(extensions),
# ) # )
setup(name='CSSTSim', setup(name='CSSTSim',
version='2.1.0', version='2.1.0',
packages=find_packages(), packages=find_packages(),
...@@ -43,6 +65,7 @@ setup(name='CSSTSim', ...@@ -43,6 +65,7 @@ setup(name='CSSTSim',
], ],
package_data = { package_data = {
'ObservationSim.Astrometry.lib': ['libshao.so'], 'ObservationSim.Astrometry.lib': ['libshao.so'],
'ObservationSim.Instrument.Chip.lib_bf': ['libmoduleBF.so'],
'ObservationSim.MockObject.data': ['*.dat'], 'ObservationSim.MockObject.data': ['*.dat'],
'ObservationSim.Instrument.data': ['*.txt', '*.dat', '*.json'], 'ObservationSim.Instrument.data': ['*.txt', '*.dat', '*.json'],
'ObservationSim.Instrument.data.field_distortion': ['*.pickle'], 'ObservationSim.Instrument.data.field_distortion': ['*.pickle'],
...@@ -57,5 +80,6 @@ setup(name='CSSTSim', ...@@ -57,5 +80,6 @@ setup(name='CSSTSim',
'ObservationSim.Straylight.data.sky': ['*.dat'], 'ObservationSim.Straylight.data.sky': ['*.dat'],
'ObservationSim.Straylight.lib': ['*'], 'ObservationSim.Straylight.lib': ['*'],
}, },
ext_modules = cythonize(extensions), ext_modules = cythonize(extensions) + df_module,
cmdclass={'build_ext': build_ext}
) )
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