def __init__(self,
naxis1=None,
naxis2=None,
naxis3=None,
n_out=None,
dt=None,
nroh=None,
nfoh=None,
nfoh_pix=None,
dark_file=None,
bias_file=None,
verbose=False,
reverse_scan_direction=False,
reference_pixel_border_width=None,
wind_mode='FULL',
x0=0,
y0=0,
det_size=None,
use_fftw=False,
ncores=None):
# pyFFTW usage
self.use_fftw = True if (use_fftw and pyfftw_available) else False
# By default, use 50% of available cores for FFTW parallelization
self.ncores = mp.cpu_count() // 2 if ncores is None else int(ncores)
# ======================================================================
#
# 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?
if wind_mode is None:
wind_mode = 'FULL'
if det_size is None:
det_size = 2048
wind_mode = wind_mode.upper()
modes = ['FULL', 'STRIPE', 'WINDOW']
if wind_mode not in modes:
_log.warning('%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 = 2048 if naxis1 is None else int(naxis1)
self.naxis2 = 2048 if naxis2 is None else int(naxis2)
self.naxis3 = 1 if naxis3 is None else int(naxis3)
self.n_out = 4 if n_out is None else int(n_out)
self.dt = 10e-6 if dt is None else dt
self.nroh = 12 if nroh is None else int(nroh)
self.nfoh = 1 if nfoh is None else int(nfoh)
self.nfoh_pix = 0 #if nfoh_pix is None else int(nfoh_pix)
self.reference_pixel_border_width = 4 if reference_pixel_border_width is None \
else int(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.warning(
'NAXIS1 %s greater than det_size %s! Returning...' %
(self.naxis1, det_size))
os.sys.exit()
if (self.naxis2 > det_size):
_log.warning(
'NAXIS2 %s greater than det_size %s! Returning...' %
(self.naxis1, det_size))
os.sys.exit()
# Initialize PCA-zero file and make sure that it exists and is a file
#self.bias_file = os.getenv('NGHXRG_HOME')+'/sca_images/nirspec_pca0.fits' if \
# bias_file is None else bias_file
#self.bias_file = 'nirspec_pca0.fits' if bias_file is None else bias_file
self.bias_file = bias_file
if bias_file is not None:
if os.path.isfile(self.bias_file) is False:
raise ValueError(
'There was an error finding bias_file {}'.format(
bias_file))
print('There was an error finding bias_file!')
print(bias_file)
#os.sys.exit()
# print('There was an error finding bias_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()
# Add in dark current file (JML)
self.dark_file = dark_file
if dark_file is not None:
if os.path.isfile(self.dark_file) is False:
raise ValueError(
'There was an error finding dark_file {}'.format(
dark_file))
#print('There was an error finding dark_file!')
#print(dark_file)
#os.sys.exit()
# ======================================================================
# Configure Subarray
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_frame = (self.xsize + self.nroh) * (
self.naxis2 + self.nfoh) + self.nfoh_pix
self.nstep = self.nstep_frame * self.naxis3
# Pad nsteps to a power of 2, which is much faster
self.nstep2 = int(2**np.ceil(np.log2(self.nstep)))
# Compute frame time and ramp time
self.tframe = self.nstep_frame * self.dt
self.inttime = self.tframe * self.naxis3
# 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
self.f3 = np.fft.rfftfreq(2 * self.naxis3)
# 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_filter3 = np.sqrt(self.f3**self.alpha)
self.p_filter1[0] = 0.
self.p_filter2[0] = 0.
self.p_filter3[0] = 0.
# Initialize pca0. This includes scaling to the correct size,
# zero offsetting, and renormalization. We use robust statistics
# because pca0 is real data
if self.bias_file is None:
h = fits.PrimaryHDU(np.zeros([det_size, det_size]))
hdu = fits.HDUList([h])
else:
hdu = fits.open(self.bias_file)
nx_pca0 = hdu[0].header['naxis1']
ny_pca0 = hdu[0].header['naxis2']
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
#print(zoom_factor)
if zoom_factor != 1:
data = zoom(data, zoom_factor, order=1, mode='wrap')
# Copy data to save as bias pattern
bias_image = data.copy()
# Renormalize for PCA0 noise stuff
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
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.warning(
'Specified window size does not fit within detector array!')
_log.warning(
'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()
# Save as properties
self.pca0 = data[y1:y2, x1:x2]
self.bias_image = bias_image[y1:y2, x1:x2]
# Open dark current file (ADU/sec/pixel)
if self.dark_file is not None:
dark_hdu = fits.open(self.dark_file)
dark_image = dark_hdu[0].data
self.dark_image = dark_image[y1:y2, x1:x2]
# Dark current distributions are very wide because of uncertainties
# This causes certain pixels to fall below 0.
# We can assume all pixels within 5-sigma have the same dark current
# as well as those with negative values.
# Those with large dark currents are likely real.
sig = 1.4826 * mad(dark_image)
med = np.median(dark_image)
l1 = med - 5 * sig
l2 = med + 5 * sig
self.dark_image[(self.dark_image > l1)
& (self.dark_image < l2)] = med
# Set negative values to median
self.dark_image[self.dark_image < 0] = med
# Set negative values to median
#self.dark_image[self.dark_image<0] = np.median(self.dark_image)
#self.dark_image[self.dark_image<0.005] = 0.001
else:
self.dark_image = None
# 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
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):
"""
Simulate Teledyne HxRG+SIDECAR ASIC system noise.
Parameters
----------
naxis1 : int
X-dimension of the FITS cube
naxis2 : int
Y-dimension of the FITS cube
naxis3 : int
Z-dimension of the FITS cube (number of up-the-ramp samples)
n_out : int
Number of detector outputs
nfoh : int
New frame overhead in rows. This allows for a short wait at the end
of a frame before starting the next one.
nroh : int
New row overhead in pixels. This allows for a short
wait at the end of a row before starting the next one.
dt : int
Pixel dwell time in seconds
pca0_file : str
Name of a FITS file that contains PCA-zero
verbose : bool
Enable this to provide status reporting
reference_pixel_border_width : int
Width of reference pixel border around image area
reverse_scan_direction : bool
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.
#
# ======================================================================
# Default clocking pattern is JWST NIRSpec
self.naxis1 = 2048 if naxis1 is None else int(naxis1)
self.naxis2 = 2048 if naxis2 is None else int(naxis2)
self.naxis3 = 1 if naxis3 is None else int(naxis3)
self.n_out = 4 if n_out is None else int(n_out)
self.dt = 1.e-5 if dt is None else dt
self.nroh = 12 if nroh is None else int(nroh)
self.nfoh = 1 if nfoh is None else int(nfoh)
self.reference_pixel_border_width = 4 \
if reference_pixel_border_width is \
None else reference_pixel_border_width
# 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
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 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
# 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.nstep) # Frequencies for nstep elements
self.f2 = np.fft.rfftfreq(2 * self.nstep) # ... 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)
naxis1 = hdu[0].header['naxis1']
naxis2 = hdu[0].header['naxis2']
if (naxis1 != self.naxis1 or naxis2 != self.naxis2):
zoom_factor = self.naxis1 / naxis1
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
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):
"""
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
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 = 2048
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 = 2048 if naxis1 is None else naxis1
self.naxis2 = 2048 if naxis2 is None else naxis2
self.naxis3 = 1 if naxis3 is None else naxis3
self.n_out = 4 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()
# Initialize PCA-zero file and make sure that it exists and is a file
path = os.getenv('NIRISS_NOISE_HOME')
if path is None:
path = '.'
self.pca0_file = path + '/niriss_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 NIRISS_NOISE_HOME shell environment')
print('variable is set correctly and that the')
print('$NIRISS_NOISE_HOME/ directory contains the desired PCA0')
print('file. The default is niriss_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
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):
"""
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
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 = 2048
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 = 2048 if naxis1 is None else naxis1
self.naxis2 = 2048 if naxis2 is None else naxis2
self.naxis3 = 1 if naxis3 is None else naxis3
self.n_out = 4 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()
# 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
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
