Source code for drizzlepac.stisData
"""
``stisData`` module provides classes used to import STIS specific instrument
data.
:Authors: Megan Sosey, Christopher Hanley, Mihai Cara
:License: :doc:`/LICENSE`
"""
from stsci.tools import fileutil
import numpy as np
from .imageObject import imageObject
[docs]
class STISInputImage (imageObject):
SEPARATOR = '_'
def __init__(self,filename=None, output=None, group=None):
super().__init__(filename, output=output, group=group)
# define the cosmic ray bits value to use in the dq array
self.cr_bits_value = 8192
self._effGain = 1.
self._instrument = self._image["PRIMARY"].header["INSTRUME"] # this just shows instrument, not detector, detector asigned by subclass
self.native_units = 'COUNTS'
[docs]
def getflat(self, chip):
"""
Method for retrieving a detector's flat field. For STIS there are three.
This method will return an array the same shape as the image.
"""
sci_chip = self._image[self.scienceExt,chip]
exten = self.errExt+','+str(chip)
# The keyword for STIS flat fields in the primary header of the flt
lflatfile = fileutil.osfn(self._image["PRIMARY"].header['LFLTFILE'])
pflatfile = fileutil.osfn(self._image["PRIMARY"].header['PFLTFILE'])
# Try to open the file in the location specified by LFLTFILE.
try:
handle = fileutil.openImage(lflatfile, mode='readonly', memmap=False)
hdu = fileutil.getExtn(handle,extn=exten)
lfltdata = hdu.data
if lfltdata.shape != self.full_shape:
lfltdata = expand_image(lfltdata, self.full_shape)
except IOError:
lfltdata = np.ones(self.full_shape, dtype=sci_chip.data.dtype)
print("Cannot find file '{:s}'. Treating flatfield constant value "
"of '1'.\n".format(lflatfile))
# Try to open the file in the location specified by PFLTFILE.
try:
handle = fileutil.openImage(pflatfile, mode='readonly', memmap=False)
hdu = fileutil.getExtn(handle,extn=exten)
pfltdata = hdu.data
except IOError:
pfltdata = np.ones(self.full_shape, dtype=sci_chip.data.dtype)
print("Cannot find file '{:s}'. Treating flatfield constant value "
"of '1'.\n".format(pflatfile))
flat = lfltdata * pfltdata
return flat
[docs]
def doUnitConversions(self):
"""Convert the data to electrons.
This converts all science data extensions and saves
the results back to disk. We need to make sure
the data inside the chips already in memory is altered as well.
"""
# Image information
_handle = fileutil.openImage(self._filename, mode='readonly', memmap=False)
for det in range(1,self._numchips+1,1):
chip=self._image[self.scienceExt,det]
if chip._gain is not None:
conversionFactor = chip._gain
chip._effGain = chip._gain #1.
chip._conversionFactor = conversionFactor #1.
else:
msg = "Invalid gain value for data, no conversion done"
print(msg)
raise ValueError(msg)
# Close the files and clean-up
_handle.close()
self._effGain = conversionFactor # 1.0
def _assignSignature(self, chip):
"""Assign a unique signature for the image based
on the instrument, detector, chip, and size
this will be used to uniquely identify the appropriate
static mask for the image.
This also records the filename for the static mask to the outputNames dictionary.
"""
sci_chip = self._image[self.scienceExt,chip]
ny=sci_chip._naxis1
nx=sci_chip._naxis2
detnum = sci_chip.detnum
sig=(self.outroot,(nx,ny),int(detnum)) #signature is a tuple
sci_chip.signature=sig #signature is a tuple
[docs]
class CCDInputImage(STISInputImage):
def __init__(self, filename=None, output=None, group=None):
super().__init__(filename, output=output, group=group)
self.full_shape = (1024, 1024)
self._detector=self._image["PRIMARY"].header["DETECTOR"]
for chip in range(1,self._numchips+1,1):
self._image[self.scienceExt,chip].cte_dir = 1
self._image[self.scienceExt,chip].darkcurrent = self.getdarkcurrent()
self.cte_dir = 1
[docs]
def getdarkcurrent(self):
"""
Returns the dark current for the STIS CCD chip.
Returns
-------
darkcurrent : float
Dark current value in **units of electrons** (or counts, if proc_unit=='native').
"""
darkcurrent = 0.009 #electrons/sec
if self.proc_unit == 'native':
return darkcurrent / self._gain()
return darkcurrent
[docs]
def getReadNoise(self):
"""
Method for returning the readnoise of a detector (in DN).
:units: DN
This should work on a chip, since different chips to be consistant with other
detector classes where different chips have different gains.
"""
if self.proc_unit == 'native':
return self._rdnoise / self._gain()
return self._rdnoise
[docs]
def setInstrumentParameters(self, instrpars):
""" This method overrides the superclass to set default values into
the parameter dictionary, in case empty entries are provided.
"""
pri_header = self._image[0].header
if self._isNotValid (instrpars['gain'], instrpars['gnkeyword']):
instrpars['gnkeyword'] = 'ATODGAIN'
if self._isNotValid (instrpars['rdnoise'], instrpars['rnkeyword']):
instrpars['rnkeyword'] = 'READNSE'
if self._isNotValid (instrpars['exptime'], instrpars['expkeyword']):
instrpars['expkeyword'] = 'EXPTIME'
for chip in self.returnAllChips(extname=self.scienceExt):
chip._gain = self.getInstrParameter(instrpars['gain'], pri_header,
instrpars['gnkeyword'])
chip._rdnoise = self.getInstrParameter(instrpars['rdnoise'], pri_header,
instrpars['rnkeyword'])
chip._exptime = self.getInstrParameter(instrpars['exptime'], chip.header,
instrpars['expkeyword'])
if chip._gain is None or chip._rdnoise is None or chip._exptime is None:
print('ERROR: invalid instrument task parameter')
raise ValueError
chip._effGain = chip._gain
self._assignSignature(chip._chip) #this is used in the static mask
self.doUnitConversions()
[docs]
class NUVInputImage(STISInputImage):
def __init__(self, filename, output=None, group=None):
self.effGain = 1.0
super().__init__(filename, output=output, group=group)
self._detector=self._image["PRIMARY"].header["DETECTOR"]
# no cte correction for STIS/NUV-MAMA so set cte_dir=0.
print('WARNING: No cte correction will be made for this STIS/NUV-MAMA data.')
for chip in range(1,self._numchips+1,1):
self._image[self.scienceExt,chip].cte_dir = 0
self._image[self.scienceExt,chip].darkcurrent = self.getdarkcurrent()
[docs]
def setInstrumentParameters(self, instrpars):
""" This method overrides the superclass to set default values into
the parameter dictionary, in case empty entries are provided.
"""
pri_header = self._image[0].header
if self._isNotValid (instrpars['gain'], instrpars['gnkeyword']):
instrpars['gnkeyword'] = None
if self._isNotValid (instrpars['rdnoise'], instrpars['rnkeyword']):
instrpars['rnkeyword'] = None
if self._isNotValid (instrpars['exptime'], instrpars['expkeyword']):
instrpars['expkeyword'] = 'EXPTIME'
# We need to determine if the user has used the default readnoise/gain value
# since if not, they will need to supply a gain/readnoise value as well
usingDefaultGain = instrpars['gnkeyword'] is None
usingDefaultReadnoise = instrpars['rnkeyword'] is None
for chip in self.returnAllChips(extname=self.scienceExt):
#pri_header=chip.header
chip.cte_dir=0
# We need to treat Read Noise and Gain as a special case since it is
# not populated in the STIS primary header for the MAMAs
if instrpars['rnkeyword'] is not None:
chip._rdnoise = self.getInstrParameter(
instrpars['rdnoise'], pri_header, instrpars['rnkeyword']
)
else:
chip._rdnoise = None
if instrpars['gnkeyword'] is not None:
chip._gain = self.getInstrParameter(
instrpars['gain'], pri_header, instrpars['gnkeyword']
)
else:
chip._gain = None
# Set the default readnoise or gain values based upon the amount of user input given.
if usingDefaultReadnoise:
chip._rdnoise= self._setMAMADefaultReadnoise()
if usingDefaultGain:
chip._gain = self._setMAMADefaultGain()
self._assignSignature(chip._chip) #this is used in the static mask
chip._exptime = self.getInstrParameter(instrpars['exptime'], chip.header,
instrpars['expkeyword'])
if chip._exptime is None:
print('ERROR: invalid instrument task parameter')
raise ValueError
# Convert the science data to electrons if specified by the user.
self.doUnitConversions()
def _setMAMAchippars(self):
self._setMAMADefaultGain()
self._setMAMADefaultReadnoise()
def _setMAMADefaultGain(self):
self._gain = 1
self.effGain = 1
return self._gain
def _setMAMADefaultReadnoise(self):
self._rdnoise = 0
return self._rdnoise
[docs]
def getdarkcurrent(self):
"""
Returns the dark current for the STIS NUV detector.
Returns
-------
darkcurrent : float
Dark current value in **units of electrons** (or counts, if proc_unit=='native').
"""
darkcurrent = 0.0013 #electrons/sec
if self.proc_unit == 'native':
return darkcurrent / self._gain()
return darkcurrent
[docs]
def doUnitConversions(self):
"""Convert the data to electrons.
This converts all science data extensions and saves
the results back to disk. We need to make sure
the data inside the chips already in memory is altered as well.
"""
for det in range(1,self._numchips+1,1):
chip=self._image[self.scienceExt,det]
conversionFactor = self.effGain
chip._gain = self.effGain #1.
chip.effGain = self.effGain
chip._conversionFactor = conversionFactor #1.
[docs]
class FUVInputImage(STISInputImage):
def __init__(self, filename=None, output=None, group=None):
self.effGain=1.0
super().__init__(filename, output=output, group=group)
self._detector=self._image["PRIMARY"].header["DETECTOR"]
# no cte correction for STIS/FUV-MAMA so set cte_dir=0.
print('WARNING: No cte correction will be made for this STIS/FUV-MAMA data.')
for chip in range(1,self._numchips+1,1):
self._image[self.scienceExt,chip].cte_dir = 0
self._image[self.scienceExt,chip].darkcurrent = self.getdarkcurrent()
[docs]
def setInstrumentParameters(self, instrpars):
""" This method overrides the superclass to set default values into
the parameter dictionary, in case empty entries are provided.
"""
pri_header = self._image[0].header
usingDefaultGain = False
usingDefaultReadnoise = False
if self._isNotValid (instrpars['gain'], instrpars['gnkeyword']):
instrpars['gnkeyword'] = None
if self._isNotValid (instrpars['rdnoise'], instrpars['rnkeyword']):
instrpars['rnkeyword'] = None
if self._isNotValid (instrpars['exptime'], instrpars['expkeyword']):
instrpars['expkeyword'] = 'EXPTIME'
for chip in self.returnAllChips(extname=self.scienceExt):
#pri_header=chip.header #stis stores stuff in the science data header
chip.cte_dir=0
chip._exptime = self.getInstrParameter(
instrpars['exptime'], chip.header, instrpars['expkeyword']
)
if chip._exptime is None:
print('ERROR: invalid instrument task parameter')
raise ValueError
if instrpars['rnkeyword'] is not None:
chip._rdnoise = self.getInstrParameter(
instrpars['rdnoise'], pri_header, instrpars['rnkeyword']
)
else:
chip._rdnoise = None
usingDefaultReadnoise = True
if instrpars['gnkeyword'] is not None:
chip._gain = self.getInstrParameter(
instrpars['gain'], pri_header, instrpars['gnkeyword']
)
else:
chip._gain = None
usingDefaultGain = True
if chip._exptime is None:
print('ERROR: invalid instrument task parameter')
raise ValueError
# We need to determine if the user has used the default readnoise/gain value
# since if not, they will need to supply a gain/readnoise value as well
if usingDefaultReadnoise:
chip._rdnoise= self._setMAMADefaultReadnoise()
if usingDefaultGain:
chip._gain = self._setMAMADefaultGain()
self._assignSignature(chip._chip) #this is used in the static mask
chip._effGain=chip._gain
# Convert the science data to electrons if specified by the user.
self.doUnitConversions()
[docs]
def getdarkcurrent(self):
"""
Returns the dark current for the STIS FUV detector.
Returns
-------
darkcurrent : float
Dark current value in **units of electrons** (or counts, if proc_unit=='native').
"""
darkcurrent = 0.07 #electrons/sec
if self.proc_unit == 'native':
return darkcurrent / self._gain()
return darkcurrent
def _setMAMADefaultGain(self):
return 1
def _setMAMADefaultReadnoise(self):
return 0
[docs]
def doUnitConversions(self):
"""Convert the data to electrons.
This converts all science data extensions and saves
the results back to disk. We need to make sure
the data inside the chips already in memory is altered as well.
"""
for det in range(1,self._numchips+1,1):
chip=self._image[self.scienceExt,det]
conversionFactor = self.effGain
chip._gain = self.effGain #1.
chip.effGain = self.effGain
chip._conversionFactor = conversionFactor #1.
def expand_image(image, shape):
""" Expand image from original shape to requested shape. Output shape
must be an integer multiple of input image shape for each axis. """
if (shape[0] % image.shape[0]) or (shape[1] % image.shape[1]):
raise ValueError("Output shape must be an integer multiple of input "
"image shape.")
sx = shape[1] // image.shape[1]
sy = shape[0] // image.shape[0]
ox = (sx - 1.0) / (2.0 * sx)
oy = (sy - 1.0) / (2.0 * sy)
# generate output coordinates:
y, x = np.indices(shape, dtype=float)
x = x / sx - ox
y = y / sy - oy
# interpolate:
return bilinear_interp(image, x, y)
def bilinear_interp(data, x, y):
""" Interpolate input ``data`` at "pixel" coordinates ``x`` and ``y``. """
x = np.asarray(x)
y = np.asarray(y)
if x.shape != y.shape:
raise ValueError("X- and Y-coordinates must have identical shapes.")
out_shape = x.shape
out_size = x.size
x = x.ravel()
y = y.ravel()
x0 = np.empty(out_size, dtype=int)
y0 = np.empty(out_size, dtype=int)
np.clip(x, 0, data.shape[1] - 2, out=x0)
np.clip(y, 0, data.shape[0] - 2, out=y0)
x1 = x0 + 1
y1 = y0 + 1
f00 = data[(y0, x0)]
f10 = data[(y1, x0)]
f01 = data[(y0, x1)]
f11 = data[(y1, x1)]
w00 = (x1 - x) * (y1 - y)
w10 = (x1 - x) * (y - y0)
w01 = (x - x0) * (y1 - y)
w11 = (x - x0) * (y - y0)
interp = w00 * f00 + w10 * f10 + w01 * f01 + w11 * f11
return interp.reshape(out_shape).astype(data.dtype.type)