def make_rn_dist(det_save_path):
"""
Draw random samples from distribution to create read
noise values.
Inputs:
det_save_path - Directory to save rn distribution to
"""
if det_save_path == "None":
det_save_path = detpath
# First look to see if detectors already made
if os.path.exists(det_save_path + 'HARMONI_dets.fits'):
logging.info('- found existing HARMONI detectors')
if config_data['systematics']['force_new'] == False:
logging.info('- using existing detectors')
hdulist = fits.open(det_save_path + 'HARMONI_dets.fits')
rn_vals = hdulist[0].data
return rn_vals
else:
logging.info('- overwriting exisiting detectors')
logging.info('- no exisiting HARMONI detectors found')
logging.info('- creating new detectors')
rn_path = path_setup('../../' + config_data["data_dir"] + 'detectors/')
rn_file = rn_path + config_data['systematics']['rn_file']
if os.path.isfile(rn_file) is False:
logging.error('There was an error finding rn_file. \
Check config.py to ensure filename is correct')
return
hdu = fits.open(rn_file)
rn_data = hdu[0].data
side_len, N_det = config_data['side_length'], config_data['N_IR_det']
N = (side_len**2) * N_det
rands = np.random.random(N)
rands_sort = np.sort(rands)
rn_vals = interp(rn_data.flatten())(rands_sort)
np.random.shuffle(rn_vals)
rn_vals = np.reshape(rn_vals, (N_det, side_len, side_len))
#Saving detectors for future use
fits.writeto(det_save_path + 'HARMONI_dets.fits', rn_vals, overwrite=True)
return rn_vals
and computes the ADR if requested
'''
import os
import logging
import numpy as np
from astropy.convolution import Gaussian1DKernel
from src.config import *
from src.modules.misc_utils import path_setup
from src.modules.rebin import *
from src.modules.adr import apply_adr
import matplotlib.pyplot as plt
bgpath = path_setup('../../' + config_data["data_dir"] + 'sky/')
def convolve_1d_spectrum(input_lambda, input_flux, output_spec_res):
'''Function that convolves a sky spectrum with a Gaussian to
match the input cube spectral resolution.
Inputs:
input_lambda: input sky spectrum lambda
input_flux: input sky spectrum flux
output_spec_res: Spectral resolution of the convolved sky spectrum output
Outputs:
convolved sky spectrum
'''
import os
import logging
import numpy as np
import scipy.constants as sp
from scipy.interpolate import UnivariateSpline
from scipy import integrate
from astropy.convolution import Gaussian1DKernel
from astropy.io import fits
from src.modules.misc_utils import path_setup
from src.config import *
from src.modules import nghxrg as ng
from src.modules.em_model import *
detpath = path_setup('../../' + config_data["data_dir"] + 'detectors/')
#Detector throughput curve generated just using wavelength array.
def detector_QE_curve(wavels, grating, debug_plots, output_file):
'''Function that generates a detector QE curve.
Current detector data taken from Detector Reference
table.
Inputs:
wavels: array of wavelengths for datacube
grating: grating choice to set detector
Outputs:
cube_det_qe: array of detector QE values for
each wavelength in array
'''
import getopt
import sys
import os
import numpy as n
import multiprocessing as mp
from src.JSIM_main import main
import commands
from src.modules.misc_utils import path_setup
if __name__ == "__main__":
#Get version number
try:
verpath = path_setup('../../')
verinfo = open(verpath + 'PKG-INFO')
ver = verinfo.readlines()[2][:-1].split('Version: ')[1]
print 'VERSION = ', ver
verinfo.close()
except:
ver = str(
commands.getoutput(
"svnversion -c ./ | sed -e 's/[MS]//g' -e 's/^[[:digit:]]*://'"
))
optlist, args = getopt.getopt(sys.argv[1:], 'hcp:o:',
['help', 'cline', 'proc', 'odir'])
for o, a in optlist:
if o in ("-h", "--help"):
def InitUI(self):
panel = wx.Panel(self)
titlefont = wx.Font(18, wx.DEFAULT, wx.NORMAL, wx.BOLD)
# Set up the menu.
filemenu = wx.Menu()
menuAbout = filemenu.Append(
wx.ID_ABOUT, "&About",
" Information about this program")
menuExit = filemenu.Append(wx.ID_EXIT, "&Exit",
" Terminate the program")
# Creating the menubar.
menuBar = wx.MenuBar()
menuBar.Append(
filemenu,
"&File") # Adding the "filemenu" to the MenuBar
self.SetMenuBar(
menuBar) # Adding the MenuBar to the Frame content.
# Events.
self.Bind(wx.EVT_MENU, self.OnExit, menuExit)
self.Bind(wx.EVT_MENU, self.OnAbout, menuAbout)
hbox = wx.BoxSizer(wx.HORIZONTAL)
fg = wx.FlexGridSizer(8, 2, 15, 10)
#Instrument parameters
inst = wx.StaticText(panel, label='Instrument')
inst.SetFont(titlefont)
subinst = wx.StaticText(panel, label=' ')
INPUTCUBE = wx.StaticText(panel, label="Input Cube")
self.INPUTCUBEVAL = wx.FilePickerCtrl(panel, path="")
DIT = wx.StaticText(panel, label="DIT [s]")
self.DITVAL = wx.TextCtrl(panel, value='900')
NDIT = wx.StaticText(panel, label="NINT")
self.NDITVAL = wx.TextCtrl(panel, value='1')
PHOTOBAND = wx.StaticText(panel, label='Grating')
self.PHOTOBANDVAL = wx.Choice(
panel,
choices=[
'F070-G140M [0.7-1.2 um] (R=1000)',
'F100-G140M [1.0-1.8 um] (R=1000)',
'G235M [1.7-3.0 um] (R=1000)',
'G395M [2.9-5.0 um] (R=1000)',
'F070-G140H [0.7-1.2 um] (R=2700)',
'F100-G140H [1.0-1.8 um] (R=2700)',
'G235H [1.7-3.0 um] (R=2700)',
'G395H [2.9-5.0 um] (R=2700)',
'Prism [0.6-5.0 um] (R~100)'
])
IGNORESPEC = wx.StaticText(panel,
label='Ignore LSF convolution')
self.IGNORESPECVAL = wx.CheckBox(panel)
DRIZZLE = wx.StaticText(panel,
label='Drizzle (50 mas sampling)')
self.DRIZZLEVAL = wx.CheckBox(panel)
DIR = wx.StaticText(panel, label='Output Dir')
self.DIRVAL = wx.DirPickerCtrl(
panel, path=path_setup('../../Output_cubes/'))
fg.AddMany([(inst), (subinst), (INPUTCUBE),
(self.INPUTCUBEVAL, 1, wx.EXPAND), (DIR),
(self.DIRVAL, 1, wx.EXPAND), (DIT),
(self.DITVAL, 1, wx.EXPAND), (NDIT),
(self.NDITVAL, 1, wx.EXPAND), (PHOTOBAND),
(self.PHOTOBANDVAL, 1, wx.EXPAND),
(IGNORESPEC),
(self.IGNORESPECVAL, 1, wx.EXPAND), (DRIZZLE),
(self.DRIZZLEVAL, 1, wx.EXPAND)])
fg.AddGrowableCol(1, 1)
hbox.Add(fg,
proportion=1,
flag=wx.ALL | wx.EXPAND,
border=10)
# #Telescope parameters
# fgs = wx.FlexGridSizer(2, 2, 15, 10)
# tele = wx.StaticText(panel, label='Telescope')
# tele.SetFont(titlefont)
# subtele = wx.StaticText(panel, label=' ')
# # SITETEMP = wx.StaticText(panel, label="Temperature [K]:")
# # self.SITETEMPVAL = wx.TextCtrl(panel, value='3.0')
# fgs.AddMany([(tele), (subtele),
# (USERPSF), (self.USERPSFVAL, 1, wx.EXPAND)])
# # (SITETEMP), (self.SITETEMPVAL, 1, wx.EXPAND)])
# fgs.AddGrowableCol(1,1)
# hbox.Add(fgs, proportion=1, flag=wx.ALL|wx.EXPAND, border=10)
#Misc. parameters
fgss = wx.FlexGridSizer(9, 2, 15, 10)
misc = wx.StaticText(panel, label="Miscellaneous")
misc.SetFont(titlefont)
submisc = wx.StaticText(panel, label=' ')
REMOVE_BG = wx.StaticText(panel,
label='Subtract Background')
self.REMOVE_BGVAL = wx.CheckBox(panel)
OUTPUT_OB = wx.StaticText(panel,
label='Return Object Cube')
self.OUTPUT_OBVAL = wx.CheckBox(panel)
OUTPUT_TS = wx.StaticText(panel,
label='Return Transmission Cube')
self.OUTPUT_TSVAL = wx.CheckBox(panel)
gapaa = wx.StaticText(panel, label=' ------------ ')
gapbb = wx.StaticText(panel, label=' ')
NOISESEED = wx.StaticText(panel, label="Noise Seed")
self.NOISESEEDVAL = wx.Choice(panel,
choices=['Random', '1', '2'])
SETR = wx.StaticText(panel, label="Set Spec Samp [A/pix]")
self.SETRVAL = wx.TextCtrl(panel)
N_PROC = wx.StaticText(panel,
label='No. of processors (1-' +
str(mp.cpu_count()) + ')')
self.N_PROCVAL = wx.TextCtrl(panel, value=str(1))
RESJIT = wx.StaticText(panel,
label="Additional PSF Blur [mas]:")
self.RESJITVAL = wx.TextCtrl(panel, value='0')
fgss.AddMany([
(misc), (submisc), (REMOVE_BG),
(self.REMOVE_BGVAL, 1, wx.EXPAND), (OUTPUT_OB),
(self.OUTPUT_OBVAL, 1, wx.EXPAND), (OUTPUT_TS),
(self.OUTPUT_TSVAL, 1, wx.EXPAND), (gapaa), (gapbb),
(N_PROC), (self.N_PROCVAL, 1, wx.EXPAND), (NOISESEED),
(self.NOISESEEDVAL, 1, wx.EXPAND), (SETR),
(self.SETRVAL, 1, wx.EXPAND), (RESJIT),
(self.RESJITVAL, 1, wx.EXPAND)
])
fgss.AddGrowableCol(1, 1)
hbox.Add(fgss,
proportion=1,
flag=wx.ALL | wx.EXPAND,
border=10)
panel.SetSizer(hbox)
# A button
button = wx.Button(panel, 10, "Commence Simulation",
wx.Point(360, 325))
wx.EVT_BUTTON(panel, 10, self.OnClick)
import getopt
import sys
import os
import numpy as n
import multiprocessing as mp
from src.TheSimulator import main
import commands
from src.modules.misc_utils import path_setup
if __name__=="__main__":
#Get version number
try:
verpath = path_setup('../../')
verinfo = open(verpath+'PKG-INFO')
ver = verinfo.readlines()[2][:-1].split('Version: ')[1]
print 'VERSION = ', ver
verinfo.close()
except:
ver = str(commands.getoutput("svnversion -c ./ | sed -e 's/[MS]//g' -e 's/^[[:digit:]]*://'"))
optlist, args = getopt.getopt(sys.argv[1:], 'hcp:o:', ['help', 'cline', 'proc', 'odir'])
for o, a in optlist:
if o in ("-h", "--help"):
print""
print ' -------- '
print 'HARMONI Simulator'
def InitUI(self):
panel = wx.Panel(self)
titlefont = wx.Font(18, wx.DEFAULT, wx.NORMAL, wx.BOLD)
# Set up the menu.
filemenu = wx.Menu()
menuAbout = filemenu.Append(wx.ID_ABOUT, "&About"," Information about this program")
menuExit = filemenu.Append(wx.ID_EXIT,"&Exit"," Terminate the program")
# Creating the menubar.
menuBar = wx.MenuBar()
menuBar.Append(filemenu,"&File") # Adding the "filemenu" to the MenuBar
self.SetMenuBar(menuBar) # Adding the MenuBar to the Frame content.
# Events.
self.Bind(wx.EVT_MENU, self.OnExit, menuExit)
self.Bind(wx.EVT_MENU, self.OnAbout, menuAbout)
hbox = wx.BoxSizer(wx.HORIZONTAL)
fg = wx.FlexGridSizer(8, 2, 15, 10)
#Instrument parameters
inst = wx.StaticText(panel, label='Instrument')
inst.SetFont(titlefont)
subinst = wx.StaticText(panel, label=' ')
INPUTCUBE = wx.StaticText(panel, label="Input Cube")
self.INPUTCUBEVAL = wx.FilePickerCtrl(panel, path="")
DIT = wx.StaticText(panel, label="DIT [s]")
self.DITVAL = wx.TextCtrl(panel, value='900')
NDIT = wx.StaticText(panel, label="NINT")
self.NDITVAL = wx.TextCtrl(panel, value='1')
XSPAX = wx.StaticText(panel, label="X Scale [mas]")
self.XSPAXVAL = wx.TextCtrl(panel, value='20')
YSPAX = wx.StaticText(panel, label="Y Scale [mas]")
self.YSPAXVAL = wx.TextCtrl(panel, value='20')
PHOTOBAND = wx.StaticText(panel, label='Grating')
self.PHOTOBANDVAL = wx.Choice(panel, choices=['V+R [0.47-0.81 um] (R=3500)', 'Iz+J [0.8-1.36 um] (R=3500)', 'H+K [1.45-2.45 um] (R=3500)',
'V [0.5-0.63 um] (R=7500)', 'R [0.63-0.79 um] (R=7500)', 'Iz [0.82-1.03 um] (R=7500)',
'J [1.08-1.36 um] (R=7500)', 'H [1.46-1.83 um] (R=7500)', 'K [1.95-2.45 um] (R=7500)',
'V-high [0.53-0.59 um] (R=20000)', 'R-high [0.61-0.68 um] (R=20000)', 'z [0.82-0.91 um] (R=20000)',
'J-high [1.17-1.29 um] (R=20000)','H-high [1.545-1.715 um] (R=20000)','K-high [2.09-2.32 um] (R=20000)',
'None'])
DIR = wx.StaticText(panel, label='Output Dir')
self.DIRVAL = wx.DirPickerCtrl(panel, path=path_setup('../../Output_cubes/'))
fg.AddMany([(inst), (subinst), (INPUTCUBE),
(self.INPUTCUBEVAL, 1, wx.EXPAND),
(DIR), (self.DIRVAL, 1, wx.EXPAND),
(DIT), (self.DITVAL, 1, wx.EXPAND),
(NDIT), (self.NDITVAL, 1, wx.EXPAND),
(XSPAX), (self.XSPAXVAL, 1, wx.EXPAND),
(YSPAX), (self.YSPAXVAL, 1, wx.EXPAND),
(PHOTOBAND), (self.PHOTOBANDVAL, 1, wx.EXPAND),])
fg.AddGrowableCol(1,1)
hbox.Add(fg, proportion=1, flag=wx.ALL|wx.EXPAND, border=10)
#Telescope parameters(AO mode, seeing, zenith angle etc):
fgs = wx.FlexGridSizer(8, 2, 15, 10)
tele = wx.StaticText(panel, label='Telescope')
tele.SetFont(titlefont)
subtele = wx.StaticText(panel, label=' ')
TELESCOPE = wx.StaticText(panel, label="Telescope:")
self.TELESCOPEVAL = wx.Choice(panel, choices=['E-ELT', 'VLT'])
AOMODE = wx.StaticText(panel, label="AO Mode:")
self.AOMODEVAL = wx.Choice(panel, choices=['LTAO', 'SCAO', 'Gaussian'])
SEEING = wx.StaticText(panel, label="Zenith Seeing [arcsec]:")
self.SEEINGVAL = wx.TextCtrl(panel, value='0.67')
ZENITHA = wx.StaticText(panel, label="Zenith Angle [deg]")
self.ZENITHAVAL = wx.TextCtrl(panel, value='0')
USERPSF = wx.StaticText(panel, label='User PSF (replaces AO choice)')
self.USERPSFVAL = wx.FilePickerCtrl(panel, path="None")
gapa = wx.StaticText(panel, label=' ------------ ')
gapb = wx.StaticText(panel, label=' ')
SITETEMP = wx.StaticText(panel, label="Telescope Temperature [K]:")
self.SITETEMPVAL = wx.TextCtrl(panel, value='280.5')
fgs.AddMany([(tele), (subtele), (TELESCOPE),
(self.TELESCOPEVAL, 1, wx.EXPAND),
(AOMODE), (self.AOMODEVAL, 1, wx.EXPAND),
(SEEING), (self.SEEINGVAL, 1, wx.EXPAND),
(ZENITHA), (self.ZENITHAVAL, 1, wx.EXPAND),
(gapa), (gapb),
(USERPSF), (self.USERPSFVAL, 1, wx.EXPAND),
(SITETEMP), (self.SITETEMPVAL, 1, wx.EXPAND)])
fgs.AddGrowableCol(1,1)
hbox.Add(fgs, proportion=1, flag=wx.ALL|wx.EXPAND, border=10)
#Misc. parameters
fgss = wx.FlexGridSizer(10, 2, 15, 10)
misc = wx.StaticText(panel, label="Miscellaneous")
misc.SetFont(titlefont)
submisc = wx.StaticText(panel, label=' ')
REMOVE_BG = wx.StaticText(panel, label='Subtract Background')
self.REMOVE_BGVAL = wx.CheckBox(panel)
OUTPUT_OB = wx.StaticText(panel, label='Return Object Cube')
self.OUTPUT_OBVAL = wx.CheckBox(panel)
OUTPUT_TS = wx.StaticText(panel, label='Return Transmission Cube')
self.OUTPUT_TSVAL = wx.CheckBox(panel)
gapaa = wx.StaticText(panel, label=' ------------ ')
gapbb = wx.StaticText(panel, label=' ')
NOISESEED = wx.StaticText(panel, label="Noise Seed")
self.NOISESEEDVAL = wx.Choice(panel, choices=['Random', '1', '2'])
SETR = wx.StaticText(panel, label="Set Spec Samp [A/pix]")
self.SETRVAL = wx.TextCtrl(panel)
N_PROC = wx.StaticText(panel, label='No. of processors (1-'+str(mp.cpu_count())+')')
self.N_PROCVAL = wx.TextCtrl(panel, value=str(mp.cpu_count()-1))
RESJIT = wx.StaticText(panel, label="Additional PSF Blur [mas]:")
self.RESJITVAL = wx.TextCtrl(panel, value='0')
ADR = wx.StaticText(panel, label="Turn off ADR")
self.ADRVAL = wx.CheckBox(panel)
fgss.AddMany([(misc), (submisc),
(REMOVE_BG), (self.REMOVE_BGVAL, 1, wx.EXPAND),
(OUTPUT_OB), (self.OUTPUT_OBVAL, 1, wx.EXPAND),
(OUTPUT_TS), (self.OUTPUT_TSVAL, 1, wx.EXPAND),
(gapaa), (gapbb),
(N_PROC), (self.N_PROCVAL, 1, wx.EXPAND),
(NOISESEED), (self.NOISESEEDVAL, 1, wx.EXPAND),
(SETR), (self.SETRVAL, 1, wx.EXPAND),
(RESJIT), (self.RESJITVAL, 1, wx.EXPAND),
(ADR), (self.ADRVAL, 1, wx.EXPAND)])
fgss.AddGrowableCol(1,1)
hbox.Add(fgss, proportion=1, flag=wx.ALL|wx.EXPAND, border=10)
panel.SetSizer(hbox)
# A button
button =wx.Button(panel, 10, "Commence Simulation", wx.Point(465, 325))
wx.EVT_BUTTON(panel, 10, self.OnClick)
def InitUI(self):
panel = wx.Panel(self)
titlefont = wx.Font(18, wx.DEFAULT, wx.NORMAL, wx.BOLD)
# Set up the menu.
filemenu = wx.Menu()
menuAbout = filemenu.Append(
wx.ID_ABOUT, "&About",
" Information about this program")
menuExit = filemenu.Append(wx.ID_EXIT, "&Exit",
" Terminate the program")
# Creating the menubar.
menuBar = wx.MenuBar()
menuBar.Append(
filemenu,
"&File") # Adding the "filemenu" to the MenuBar
self.SetMenuBar(
menuBar) # Adding the MenuBar to the Frame content.
# Events.
self.Bind(wx.EVT_MENU, self.OnExit, menuExit)
self.Bind(wx.EVT_MENU, self.OnAbout, menuAbout)
hbox = wx.BoxSizer(wx.HORIZONTAL)
fg = wx.FlexGridSizer(8, 2, 15, 10)
#Instrument parameters
inst = wx.StaticText(panel, label='Instrument')
inst.SetFont(titlefont)
subinst = wx.StaticText(panel, label=' ')
INPUTCUBE = wx.StaticText(panel, label="Input Cube")
self.INPUTCUBEVAL = wx.FilePickerCtrl(panel, path="")
DIT = wx.StaticText(panel, label="DIT [s]")
self.DITVAL = wx.TextCtrl(panel, value='900')
NDIT = wx.StaticText(panel, label="NINT")
self.NDITVAL = wx.TextCtrl(panel, value='1')
XSPAX = wx.StaticText(panel, label="X Scale [mas]")
self.XSPAXVAL = wx.TextCtrl(panel, value='20')
YSPAX = wx.StaticText(panel, label="Y Scale [mas]")
self.YSPAXVAL = wx.TextCtrl(panel, value='20')
PHOTOBAND = wx.StaticText(panel, label='Grating')
self.PHOTOBANDVAL = wx.Choice(
panel,
choices=[
'V+R [0.47-0.81 um] (R=3500)',
'Iz+J [0.8-1.36 um] (R=3500)',
'H+K [1.45-2.45 um] (R=3500)',
'V [0.5-0.63 um] (R=7500)',
'R [0.63-0.79 um] (R=7500)',
'Iz [0.82-1.03 um] (R=7500)',
'J [1.08-1.36 um] (R=7500)',
'H [1.46-1.83 um] (R=7500)',
'K [1.95-2.45 um] (R=7500)',
'V-high [0.53-0.59 um] (R=20000)',
'R-high [0.61-0.68 um] (R=20000)',
'z [0.82-0.91 um] (R=20000)',
'J-high [1.17-1.29 um] (R=20000)',
'H-high [1.545-1.715 um] (R=20000)',
'K-high [2.09-2.32 um] (R=20000)', 'None'
])
DIR = wx.StaticText(panel, label='Output Dir')
self.DIRVAL = wx.DirPickerCtrl(
panel, path=path_setup('../../Output_cubes/'))
fg.AddMany([
(inst),
(subinst),
(INPUTCUBE),
(self.INPUTCUBEVAL, 1, wx.EXPAND),
(DIR),
(self.DIRVAL, 1, wx.EXPAND),
(DIT),
(self.DITVAL, 1, wx.EXPAND),
(NDIT),
(self.NDITVAL, 1, wx.EXPAND),
(XSPAX),
(self.XSPAXVAL, 1, wx.EXPAND),
(YSPAX),
(self.YSPAXVAL, 1, wx.EXPAND),
(PHOTOBAND),
(self.PHOTOBANDVAL, 1, wx.EXPAND),
])
fg.AddGrowableCol(1, 1)
hbox.Add(fg,
proportion=1,
flag=wx.ALL | wx.EXPAND,
border=10)
#Telescope parameters(AO mode, seeing, zenith angle etc):
fgs = wx.FlexGridSizer(8, 2, 15, 10)
tele = wx.StaticText(panel, label='Telescope')
tele.SetFont(titlefont)
subtele = wx.StaticText(panel, label=' ')
TELESCOPE = wx.StaticText(panel, label="Telescope:")
self.TELESCOPEVAL = wx.Choice(panel,
choices=['E-ELT', 'VLT'])
AOMODE = wx.StaticText(panel, label="AO Mode:")
self.AOMODEVAL = wx.Choice(
panel, choices=['LTAO', 'SCAO', 'Gaussian'])
SEEING = wx.StaticText(panel,
label="Zenith Seeing [arcsec]:")
self.SEEINGVAL = wx.TextCtrl(panel, value='0.67')
ZENITHA = wx.StaticText(panel, label="Zenith Angle [deg]")
self.ZENITHAVAL = wx.TextCtrl(panel, value='0')
USERPSF = wx.StaticText(
panel, label='User PSF (replaces AO choice)')
self.USERPSFVAL = wx.FilePickerCtrl(panel, path="None")
gapa = wx.StaticText(panel, label=' ------------ ')
gapb = wx.StaticText(panel, label=' ')
SITETEMP = wx.StaticText(
panel, label="Telescope Temperature [K]:")
self.SITETEMPVAL = wx.TextCtrl(panel, value='280.5')
fgs.AddMany([(tele), (subtele), (TELESCOPE),
(self.TELESCOPEVAL, 1, wx.EXPAND), (AOMODE),
(self.AOMODEVAL, 1, wx.EXPAND), (SEEING),
(self.SEEINGVAL, 1, wx.EXPAND), (ZENITHA),
(self.ZENITHAVAL, 1, wx.EXPAND), (gapa),
(gapb), (USERPSF),
(self.USERPSFVAL, 1, wx.EXPAND), (SITETEMP),
(self.SITETEMPVAL, 1, wx.EXPAND)])
fgs.AddGrowableCol(1, 1)
hbox.Add(fgs,
proportion=1,
flag=wx.ALL | wx.EXPAND,
border=10)
#Misc. parameters
fgss = wx.FlexGridSizer(10, 2, 15, 10)
misc = wx.StaticText(panel, label="Miscellaneous")
misc.SetFont(titlefont)
submisc = wx.StaticText(panel, label=' ')
REMOVE_BG = wx.StaticText(panel,
label='Subtract Background')
self.REMOVE_BGVAL = wx.CheckBox(panel)
OUTPUT_OB = wx.StaticText(panel,
label='Return Object Cube')
self.OUTPUT_OBVAL = wx.CheckBox(panel)
OUTPUT_TS = wx.StaticText(panel,
label='Return Transmission Cube')
self.OUTPUT_TSVAL = wx.CheckBox(panel)
gapaa = wx.StaticText(panel, label=' ------------ ')
gapbb = wx.StaticText(panel, label=' ')
NOISESEED = wx.StaticText(panel, label="Noise Seed")
self.NOISESEEDVAL = wx.Choice(panel,
choices=['Random', '1', '2'])
SETR = wx.StaticText(panel, label="Set Spec Samp [A/pix]")
self.SETRVAL = wx.TextCtrl(panel)
N_PROC = wx.StaticText(panel,
label='No. of processors (1-' +
str(mp.cpu_count()) + ')')
self.N_PROCVAL = wx.TextCtrl(panel,
value=str(mp.cpu_count() - 1))
RESJIT = wx.StaticText(panel,
label="Additional PSF Blur [mas]:")
self.RESJITVAL = wx.TextCtrl(panel, value='0')
ADR = wx.StaticText(panel, label="Turn off ADR")
self.ADRVAL = wx.CheckBox(panel)
fgss.AddMany([
(misc), (submisc), (REMOVE_BG),
(self.REMOVE_BGVAL, 1, wx.EXPAND), (OUTPUT_OB),
(self.OUTPUT_OBVAL, 1, wx.EXPAND), (OUTPUT_TS),
(self.OUTPUT_TSVAL, 1, wx.EXPAND), (gapaa), (gapbb),
(N_PROC), (self.N_PROCVAL, 1, wx.EXPAND), (NOISESEED),
(self.NOISESEEDVAL, 1, wx.EXPAND), (SETR),
(self.SETRVAL, 1, wx.EXPAND), (RESJIT),
(self.RESJITVAL, 1, wx.EXPAND), (ADR),
(self.ADRVAL, 1, wx.EXPAND)
])
fgss.AddGrowableCol(1, 1)
hbox.Add(fgss,
proportion=1,
flag=wx.ALL | wx.EXPAND,
border=10)
panel.SetSizer(hbox)
# A button
button = wx.Button(panel, 10, "Commence Simulation",
wx.Point(465, 325))
wx.EVT_BUTTON(panel, 10, self.OnClick)
'''
Calculates LSF, instrument background and transmission
'''
import logging
import numpy as np
from scipy.interpolate import interp1d, interp2d
import scipy.constants as sp
from astropy.convolution import Gaussian1DKernel
from astropy.io import fits
from src.config import *
from src.modules.misc_utils import path_setup
from src.modules.em_model import *
tppath = path_setup('../../' + config_data["data_dir"] + 'throughput/')
hc_path = path_setup('../../' + config_data["data_dir"] + 'HC/')
class InstrumentPart:
substrate = "Suprasil3001_50mm_Emissivity.txt"
mirror = "QuantumFS500_Emissivity.txt"
edust = 0.5 # Grey Dust covering on some optics
mindustfrac = 0.005 # 0.5% dust on optical surfaces - won't be perfectly clean
def __init__(self,
name,
temp,
area,
n_mirrors=0,
n_lenses=0,
def __init__(self,
naxis1=None,
naxis2=None,
naxis3=None,
n_out=None,
dt=None,
nroh=None,
nfoh=None,
pca0_file=None,
verbose=False,
reverse_scan_direction=False,
reference_pixel_border_width=None,
wind_mode='FULL',
x0=0,
y0=0,
det_size=None,
rn_file=None):
"""
Simulate Teledyne HxRG+SIDECAR ASIC system noise.
Parameters:
naxis1 - X-dimension of the FITS cube
naxis2 - Y-dimension of the FITS cube
naxis3 - Z-dimension of the FITS cube
(number of up-the-ramp samples)
n_out - Number of detector outputs
nfoh - New frame overhead in rows. This allows for a short
wait at the end of a frame before starting the next
one.
nroh - New row overhead in pixels. This allows for a short
wait at the end of a row before starting the next one.
dt - Pixel dwell time in seconds
pca0_file - Name of a FITS file that contains PCA-zero
rn_file - Name of a FITS file that contains read noisepca
verbose - Enable this to provide status reporting
wind_mode - 'FULL', 'STRIPE', or 'WINDOW' (JML)
x0/y0 - Pixel positions of subarray mode (JML)
det_size - Pixel dimension of full detector (square), used only
for WINDOW mode (JML)
reference_pixel_border_width - Width of reference pixel border
around image area
reverse_scan_direction - Enable this to reverse the fast scanner
readout directions. This
capability was added to support
Teledyne's programmable fast scan
readout directions. The default
setting =False corresponds to
what HxRG detectors default to
upon power up.
"""
# ======================================================================
#
# DEFAULT CLOCKING PARAMETERS
#
# The following parameters define the default HxRG clocking pattern. The
# parameters that define the default noise model are defined in the
# mknoise() method.
#
# ======================================================================
# Subarray Mode? (JML)
if wind_mode is None:
wind_mode = 'FULL'
if det_size is None:
det_size = 4096
wind_mode = wind_mode.upper()
modes = ['FULL', 'STRIPE', 'WINDOW']
if wind_mode not in modes:
_log.warn('%s not a valid window readout mode! Returning...' %
inst_params['wind_mode'])
os.sys.exit()
if wind_mode == 'WINDOW':
n_out = 1
if wind_mode == 'FULL':
x0 = 0
y0 = 0
if wind_mode == 'STRIPE':
x0 = 0
# Default clocking pattern is JWST NIRSpec
self.naxis1 = 4096 if naxis1 is None else naxis1
self.naxis2 = 4096 if naxis2 is None else naxis2
self.naxis3 = 1 if naxis3 is None else naxis3
self.n_out = 64 if n_out is None else n_out
self.dt = 1.e-5 if dt is None else dt
self.nroh = 12 if nroh is None else nroh
self.nfoh = 1 if nfoh is None else nfoh
self.reference_pixel_border_width = 4 if reference_pixel_border_width is None \
else reference_pixel_border_width
# Check that det_size is greater than self.naxis1 and self.naxis2 in WINDOW mode (JML)
if wind_mode == 'WINDOW':
if (self.naxis1 > det_size):
_log.warn('NAXIS1 %s greater than det_size %s! Returning...' %
(self.naxis1, det_size))
os.sys.exit()
if (self.naxis2 > det_size):
_log.warn('NAXIS2 %s greater than det_size %s! Returning...' %
(self.naxis1, det_size))
os.sys.exit()
NGHXRG_HOME = path_setup('../../' + config_data["data_dir"] +
'detectors/')
# Initialize PCA-zero file and make sure that it exists and is a file
#self.pca0_file = os.getenv('NGHXRG_HOME')+'/nirspec_pca0.fits' if \
# pca0_file is None else pca0_file
self.pca0_file = NGHXRG_HOME+'/nirspec_pca0.fits' if \
pca0_file is None else pca0_file
if os.path.isfile(self.pca0_file) is False:
print('There was an error finding pca0_file! Check to be')
print('sure that the NGHXRG_HOME shell environment')
print('variable is set correctly and that the')
print('$NGHXRG_HOME/ directory contains the desired PCA0')
print('file. The default is nirspec_pca0.fits.')
os.sys.exit()
# ======================================================================
# Configure Subarray (JML)
self.wind_mode = wind_mode
self.det_size = det_size
self.x0 = x0
self.y0 = y0
# Configure status reporting
self.verbose = verbose
# Configure readout direction
self.reverse_scan_direction = reverse_scan_direction
# Compute the number of pixels in the fast-scan direction per
# output
self.xsize = self.naxis1 // self.n_out
# Compute the number of time steps per integration, per
# output
self.nstep = (self.xsize + self.nroh) * (self.naxis2 +
self.nfoh) * self.naxis3
# Pad nsteps to a power of 2, which is much faster (JML)
self.nstep2 = int(2**np.ceil(np.log2(self.nstep)))
# For adding in ACN, it is handy to have masks of the even
# and odd pixels on one output neglecting any gaps
self.m_even = np.zeros((self.naxis3, self.naxis2, self.xsize))
self.m_odd = np.zeros_like(self.m_even)
for x in np.arange(0, self.xsize, 2):
self.m_even[:, :self.naxis2, x] = 1
self.m_odd[:, :self.naxis2, x + 1] = 1
self.m_even = np.reshape(self.m_even, np.size(self.m_even))
self.m_odd = np.reshape(self.m_odd, np.size(self.m_odd))
# Also for adding in ACN, we need a mask that point to just
# the real pixels in ordered vectors of just the even or odd
# pixels
self.m_short = np.zeros((self.naxis3, self.naxis2+self.nfoh, \
(self.xsize+self.nroh)//2))
self.m_short[:, :self.naxis2, :self.xsize // 2] = 1
self.m_short = np.reshape(self.m_short, np.size(self.m_short))
# Define frequency arrays
self.f1 = np.fft.rfftfreq(
self.nstep2) # Frequencies for nstep elements
self.f2 = np.fft.rfftfreq(2 * self.nstep2) # ... for 2*nstep elements
# Define pinkening filters. F1 and p_filter1 are used to
# generate ACN. F2 and p_filter2 are used to generate 1/f noise.
self.alpha = -1 # Hard code for 1/f noise until proven otherwise
self.p_filter1 = np.sqrt(self.f1**self.alpha)
self.p_filter2 = np.sqrt(self.f2**self.alpha)
self.p_filter1[0] = 0.
self.p_filter2[0] = 0.
# Initialize pca0. This includes scaling to the correct size,
# zero offsetting, and renormalization. We use robust statistics
# because pca0 is real data
hdu = fits.open(self.pca0_file)
nx_pca0 = hdu[0].header['naxis1']
ny_pca0 = hdu[0].header['naxis2']
# Do this slightly differently, taking into account the
# different types of readout modes (JML)
#if (nx_pca0 != self.naxis1 or naxis2 != self.naxis2):
# zoom_factor = self.naxis1 / nx_pca0
# self.pca0 = zoom(hdu[0].data, zoom_factor, order=1, mode='wrap')
#else:
# self.pca0 = hdu[0].data
#self.pca0 -= np.median(self.pca0) # Zero offset
#self.pca0 /= (1.4826*mad(self.pca0)) # Renormalize
data = hdu[0].data
# Make sure the real PCA image is correctly scaled to size of fake data (JML)
# Depends if we're FULL, STRIPE, or WINDOW
if wind_mode == 'FULL':
scale1 = self.naxis1 / nx_pca0
scale2 = self.naxis2 / ny_pca0
zoom_factor = np.max([scale1, scale2])
if wind_mode == 'STRIPE':
zoom_factor = self.naxis1 / nx_pca0
if wind_mode == 'WINDOW':
# Scale based on det_size
scale1 = self.det_size / nx_pca0
scale2 = self.det_size / ny_pca0
zoom_factor = np.max([scale1, scale2])
# Resize PCA0 data
if zoom_factor != 1:
data = zoom(data, zoom_factor, order=1, mode='wrap')
data -= np.median(data) # Zero offset
data /= (1.4826 * mad(data)) # Renormalize
# Select region of pca0 associated with window position
if self.wind_mode == 'WINDOW':
x1 = self.x0
y1 = self.y0
elif self.wind_mode == 'STRIPE':
x1 = 0
y1 = self.y0
else:
x1 = 0
y1 = 0
# print(y1, self.naxis2) This appears to be a stub
x2 = x1 + self.naxis1
y2 = y1 + self.naxis2
# Make sure x2 and y2 are valid
if (x2 > data.shape[0] or y2 > data.shape[1]):
_log.warn(
'Specified window size does not fit within detector array!')
_log.warn(
'X indices: [%s,%s]; Y indices: [%s,%s]; XY Size: [%s, %s]' %
(x1, x2, y1, y2, data.shape[0], data.shape[1]))
os.sys.exit()
self.pca0 = data[y1:y2, x1:x2]
# How many reference pixels on each border?
w = self.reference_pixel_border_width # Easier to work with
lower = w - y1
upper = w - (det_size - y2)
left = w - x1
right = w - (det_size - x2)
ref_all = np.array([lower, upper, left, right])
ref_all[ref_all < 0] = 0
self.ref_all = ref_all
from scipy.interpolate import interp2d
from astropy.convolution import Gaussian2DKernel
try:
from ..config import *
except:
from config import *
try:
from src.modules.misc_utils import path_setup
from src.modules.rebin import *
except:
from modules.misc_utils import path_setup
from modules.rebin import *
psf_path = path_setup('../../' + config_data["data_dir"] + 'PSF/')
hc_path = path_setup('../../' + config_data["data_dir"] + 'HC/')
# Thierry FUSCO 18/12/17 17:42
# SIMUL_PSF_DataPackage.zip
#Programme pour prendre en compte la multi-analyse les geometries
#d'etoiles et la postion de la galaxie
def psd_to_psf(psd,
pup,
D,
phase_static=None,
samp=None,
fov=None,
lamb=2.2 * 1.e-6,
jitter=0.):
def InitUI(self):
panel = wx.Panel(self)
titlefont = wx.Font(18, wx.DEFAULT, wx.NORMAL, wx.BOLD)
# Set up the menu.
filemenu = wx.Menu()
menuAbout = filemenu.Append(wx.ID_ABOUT, "&About"," Information about this program")
menuExit = filemenu.Append(wx.ID_EXIT,"&Exit"," Terminate the program")
# Creating the menubar.
menuBar = wx.MenuBar()
menuBar.Append(filemenu,"&File") # Adding the "filemenu" to the MenuBar
self.SetMenuBar(menuBar) # Adding the MenuBar to the Frame content.
# Events.
self.Bind(wx.EVT_MENU, self.OnExit, menuExit)
self.Bind(wx.EVT_MENU, self.OnAbout, menuAbout)
hbox = wx.BoxSizer(wx.HORIZONTAL)
fg = wx.FlexGridSizer(8, 2, 15, 10)
#Instrument parameters
inst = wx.StaticText(panel, label='Instrument')
inst.SetFont(titlefont)
subinst = wx.StaticText(panel, label=' ')
INPUTCUBE = wx.StaticText(panel, label="Input Cube")
self.INPUTCUBEVAL = wx.FilePickerCtrl(panel, path="")
DIT = wx.StaticText(panel, label="DIT [s]")
self.DITVAL = wx.TextCtrl(panel, value='900')
NDIT = wx.StaticText(panel, label="NINT")
self.NDITVAL = wx.TextCtrl(panel, value='1')
PHOTOBAND = wx.StaticText(panel, label='Grating')
self.PHOTOBANDVAL = wx.Choice(panel, choices=['F070-G140M [0.7-1.2 um] (R=1000)','F100-G140M [1.0-1.8 um] (R=1000)',
'G235M [1.7-3.0 um] (R=1000)', 'G395M [2.9-5.0 um] (R=1000)',
'F070-G140H [0.7-1.2 um] (R=2700)', 'F100-G140H [1.0-1.8 um] (R=2700)',
'G235H [1.7-3.0 um] (R=2700)', 'G395H [2.9-5.0 um] (R=2700)',
'Prism [0.6-5.0 um] (R~100)'])
IGNORESPEC = wx.StaticText(panel, label='Ignore LSF convolution')
self.IGNORESPECVAL = wx.CheckBox(panel)
DRIZZLE = wx.StaticText(panel, label='Drizzle (50 mas sampling)')
self.DRIZZLEVAL = wx.CheckBox(panel)
DIR = wx.StaticText(panel, label='Output Dir')
self.DIRVAL = wx.DirPickerCtrl(panel, path=path_setup('../../Output_cubes/'))
fg.AddMany([(inst), (subinst), (INPUTCUBE),
(self.INPUTCUBEVAL, 1, wx.EXPAND),
(DIR), (self.DIRVAL, 1, wx.EXPAND),
(DIT), (self.DITVAL, 1, wx.EXPAND),
(NDIT), (self.NDITVAL, 1, wx.EXPAND),
(PHOTOBAND), (self.PHOTOBANDVAL, 1, wx.EXPAND),
(IGNORESPEC), (self.IGNORESPECVAL, 1, wx.EXPAND),
(DRIZZLE), (self.DRIZZLEVAL, 1, wx.EXPAND)])
fg.AddGrowableCol(1,1)
hbox.Add(fg, proportion=1, flag=wx.ALL|wx.EXPAND, border=10)
# #Telescope parameters
# fgs = wx.FlexGridSizer(2, 2, 15, 10)
# tele = wx.StaticText(panel, label='Telescope')
# tele.SetFont(titlefont)
# subtele = wx.StaticText(panel, label=' ')
# # SITETEMP = wx.StaticText(panel, label="Temperature [K]:")
# # self.SITETEMPVAL = wx.TextCtrl(panel, value='3.0')
# fgs.AddMany([(tele), (subtele),
# (USERPSF), (self.USERPSFVAL, 1, wx.EXPAND)])
# # (SITETEMP), (self.SITETEMPVAL, 1, wx.EXPAND)])
# fgs.AddGrowableCol(1,1)
# hbox.Add(fgs, proportion=1, flag=wx.ALL|wx.EXPAND, border=10)
#Misc. parameters
fgss = wx.FlexGridSizer(9, 2, 15, 10)
misc = wx.StaticText(panel, label="Miscellaneous")
misc.SetFont(titlefont)
submisc = wx.StaticText(panel, label=' ')
REMOVE_BG = wx.StaticText(panel, label='Subtract Background')
self.REMOVE_BGVAL = wx.CheckBox(panel)
OUTPUT_OB = wx.StaticText(panel, label='Return Object Cube')
self.OUTPUT_OBVAL = wx.CheckBox(panel)
OUTPUT_TS = wx.StaticText(panel, label='Return Transmission Cube')
self.OUTPUT_TSVAL = wx.CheckBox(panel)
gapaa = wx.StaticText(panel, label=' ------------ ')
gapbb = wx.StaticText(panel, label=' ')
NOISESEED = wx.StaticText(panel, label="Noise Seed")
self.NOISESEEDVAL = wx.Choice(panel, choices=['Random', '1', '2'])
SETR = wx.StaticText(panel, label="Set Spec Samp [A/pix]")
self.SETRVAL = wx.TextCtrl(panel)
N_PROC = wx.StaticText(panel, label='No. of processors (1-'+str(mp.cpu_count())+')')
self.N_PROCVAL = wx.TextCtrl(panel, value=str(1))
RESJIT = wx.StaticText(panel, label="Additional PSF Blur [mas]:")
self.RESJITVAL = wx.TextCtrl(panel, value='0')
fgss.AddMany([(misc), (submisc),
(REMOVE_BG), (self.REMOVE_BGVAL, 1, wx.EXPAND),
(OUTPUT_OB), (self.OUTPUT_OBVAL, 1, wx.EXPAND),
(OUTPUT_TS), (self.OUTPUT_TSVAL, 1, wx.EXPAND),
(gapaa), (gapbb),
(N_PROC), (self.N_PROCVAL, 1, wx.EXPAND),
(NOISESEED), (self.NOISESEEDVAL, 1, wx.EXPAND),
(SETR), (self.SETRVAL, 1, wx.EXPAND),
(RESJIT), (self.RESJITVAL, 1, wx.EXPAND)])
fgss.AddGrowableCol(1,1)
hbox.Add(fgss, proportion=1, flag=wx.ALL|wx.EXPAND, border=10)
panel.SetSizer(hbox)
# A button
button =wx.Button(panel, 10, "Commence Simulation", wx.Point(360, 325))
wx.EVT_BUTTON(panel, 10, self.OnClick)