def addDQ(self, rc):
"""
This primitive is used to add a DQ extension to the input AstroData
object. The value of a pixel in the DQ extension will be the sum of the
following: (0=good, 1=bad pixel (found in bad pixel mask), 2=pixel is
in the non-linear regime, 4=pixel is saturated). This primitive will
trim the BPM to match the input AstroData object(s).
:param bpm: The file name, including the full path, of the BPM(s) to be
used to flag bad pixels in the DQ extension. If only one
BPM is provided, that BPM will be used to flag bad pixels
in the DQ extension for all input AstroData object(s). If
more than one BPM is provided, the number of BPMs must
match the number of input AstroData objects. If no BPM is
provided, the primitive will attempt to determine an
appropriate BPM.
:type bpm: string or list of strings
"""
# Instantiate the log
log = logutils.get_logger(__name__)
# Log the standard "starting primitive" debug message
log.debug(gt.log_message("primitive", "addDQ", "starting"))
# Define the keyword to be used for the time stamp for this primitive
timestamp_key = self.timestamp_keys["addDQ"]
# Initialize the list of output AstroData objects
adoutput_list = []
# Set the data type of the data quality array
# It can be uint8 for now, it will get converted up as we assign higher bit values
# shouldn't need to force it up to 16bpp yet.
dq_dtype = np.dtype(np.uint8)
#dq_dtype = np.dtype(np.uint16)
# Get the input AstroData objects
adinput = rc.get_inputs_as_astrodata()
# Loop over each input AstroData object in the input list
for ad in adinput:
# Check whether the addDQ primitive has been run previously
if ad.phu_get_key_value(timestamp_key):
log.warning("No changes will be made to %s, since it has "
"already been processed by addDQ" % ad.filename)
# Append the input AstroData object to the list of output
# AstroData objects without further processing
adoutput_list.append(ad)
continue
# Parameters specified on the command line to reduce are converted
# to strings, including None
##M What about if a user doesn't want to add a BPM at all?
##M Are None's not converted to Nonetype from the command line?
if rc["bpm"] and rc["bpm"] != "None":
# The user supplied an input to the bpm parameter
bpm = rc["bpm"]
else:
# The user did not supply an input to the bpm parameter, so try
# to find an appropriate one. Get the dictionary containing the
# list of BPMs for all instruments and modes.
all_bpm_dict = Lookups.get_lookup_table("Gemini/BPMDict",
"bpm_dict")
# Call the _get_bpm_key helper function to get the key for the
# lookup table
key = self._get_bpm_key(ad)
# Get the appropriate BPM from the look up table
if key in all_bpm_dict:
bpm = lookup_path(all_bpm_dict[key])
else:
bpm = None
log.warning("No BPM found for %s, no BPM will be "
"included" % ad.filename)
# Ensure that the BPMs are AstroData objects
bpm_ad = None
if bpm is not None:
log.fullinfo("Using %s as BPM" % str(bpm))
if isinstance(bpm, AstroData):
bpm_ad = bpm
else:
bpm_ad = AstroData(bpm)
##M Do we want to fail here depending on context?
if bpm_ad is None:
log.warning("Cannot convert %s into an AstroData "
"object, no BPM will be added" % bpm)
final_bpm = None
if bpm_ad is not None:
# Clip the BPM data to match the size of the input AstroData
# object science and pad with overscan region, if necessary
final_bpm = gt.clip_auxiliary_data(adinput=ad, aux=bpm_ad,
aux_type="bpm")[0]
# Get the non-linear level and the saturation level using the
# appropriate descriptors - Individual values get checked in the
# next loop
non_linear_level_dv = ad.non_linear_level()
saturation_level_dv = ad.saturation_level()
# Loop over each science extension in each input AstroData object
for ext in ad[SCI]:
# Retrieve the extension number for this extension
extver = ext.extver()
# Check whether an extension with the same name as the DQ
# AstroData object already exists in the input AstroData object
if ad[DQ, extver]:
log.warning("A [%s,%d] extension already exists in %s"
% (DQ, extver, ad.filename))
continue
# Get the non-linear level and the saturation level for this
# extension
non_linear_level = non_linear_level_dv.get_value(extver=extver)
saturation_level = saturation_level_dv.get_value(extver=extver)
# To store individual arrays created for each of the DQ bit
# types
dq_bit_arrays = []
# Create an array that contains pixels that have a value of 2
# when that pixel is in the non-linear regime in the input
# science extension
if non_linear_level is not None:
non_linear_array = None
if saturation_level is not None:
# Test the saturation level against non_linear level
# They can be the same or the saturation level can be
# greater than but not less than the non-linear level.
# If they are the same then only flag saturated pixels
# below. This just means not creating an unneccessary
# intermediate array.
if saturation_level > non_linear_level:
log.fullinfo("Flagging pixels in the DQ extension "
"corresponding to non linear pixels "
"in %s[%s,%d] using non linear "
"level = %.2f" % (ad.filename, SCI,
extver,
non_linear_level))
non_linear_array = np.where(
((ext.data >= non_linear_level) &
(ext.data < saturation_level)), 2, 0)
elif saturation_level < non_linear_level:
log.warning("%s[%s,%d] saturation_level value is"
"less than the non_linear_level not"
"flagging non linear pixels" %
(ad.filname, SCI, extver))
else:
log.fullinfo("Saturation and non-linear values "
"for %s[%s,%d] are the same. Only "
"flagging saturated pixels."
% (ad.filename, SCI, extver))
else:
log.fullinfo("Flagging pixels in the DQ extension "
"corresponding to non linear pixels "
"in %s[%s,%d] using non linear "
"level = %.2f" % (ad.filename, SCI, extver,
non_linear_level))
non_linear_array = np.where(
(ext.data >= non_linear_level), 2, 0)
dq_bit_arrays.append(non_linear_array)
# Create an array that contains pixels that have a value of 4
# when that pixel is saturated in the input science extension
if saturation_level is not None:
saturation_array = None
log.fullinfo("Flagging pixels in the DQ extension "
"corresponding to saturated pixels in "
"%s[%s,%d] using saturation level = %.2f" %
(ad.filename, SCI, extver, saturation_level))
saturation_array = np.where(
ext.data >= saturation_level, 4, 0)
dq_bit_arrays.append(saturation_array)
# BPMs have an EXTNAME equal to DQ
bpmname = None
if final_bpm is not None:
bpm_array = None
bpmname = os.path.basename(final_bpm.filename)
log.fullinfo("Flagging pixels in the DQ extension "
"corresponding to bad pixels in %s[%s,%d] "
"using the BPM %s[%s,%d]" %
(ad.filename, SCI, extver, bpmname, DQ, extver))
bpm_array = final_bpm[DQ, extver].data
dq_bit_arrays.append(bpm_array)
# Create a single DQ extension from the three arrays (BPM,
# non-linear and saturated)
if not dq_bit_arrays:
# The BPM, non-linear and saturated arrays were not
# created. Create a single DQ array with all pixels set
# equal to 0
log.fullinfo("The BPM, non-linear and saturated arrays "
"were not created. Creating a single DQ "
"array with all the pixels set equal to zero")
final_dq_array = np.zeros(ext.data.shape).astype(dq_dtype)
else:
final_dq_array = self._bitwise_OR_list(dq_bit_arrays)
final_dq_array = final_dq_array.astype(dq_dtype)
# Create a data quality AstroData object
dq = AstroData(data=final_dq_array)
dq.rename_ext(DQ, ver=extver)
dq.filename = ad.filename
# Call the _update_dq_header helper function to update the
# header of the data quality extension with some useful
# keywords
dq = self._update_dq_header(sci=ext, dq=dq, bpmname=bpmname)
# Append the DQ AstroData object to the input AstroData object
log.fullinfo("Adding extension [%s,%d] to %s"
% (DQ, extver, ad.filename))
ad.append(moredata=dq)
# Add the appropriate time stamps to the PHU
gt.mark_history(adinput=ad, keyword=timestamp_key)
# Change the filename
ad.filename = gt.filename_updater(adinput=ad, suffix=rc["suffix"],
strip=True)
# Append the output AstroData object to the list of output
# AstroData objects
adoutput_list.append(ad)
# Report the list of output AstroData objects to the reduction context
rc.report_output(adoutput_list)
yield rc
def addMDF(self, rc):
"""
This primitive is used to add an MDF extension to the input AstroData
object. If only one MDF is provided, that MDF will be add to all input
AstroData object(s). If more than one MDF is provided, the number of
MDF AstroData objects must match the number of input AstroData objects.
If no MDF is provided, the primitive will attempt to determine an
appropriate MDF.
:param mdf: The file name of the MDF(s) to be added to the input(s)
:type mdf: string
"""
# Instantiate the log
log = logutils.get_logger(__name__)
# Log the standard "starting primitive" debug message
log.debug(gt.log_message("primitive", "addMDF", "starting"))
# Define the keyword to be used for the time stamp for this primitive
timestamp_key = self.timestamp_keys["addMDF"]
# Initialize the list of output AstroData objects
adoutput_list = []
# Get the input AstroData objects
adinput = rc.get_inputs_as_astrodata()
# Loop over each input AstroData object in the input list
for ad in adinput:
# Check whether the addMDF primitive has been run previously
if ad.phu_get_key_value(timestamp_key):
log.warning("No changes will be made to %s, since it has "
"already been processed by addMDF" % ad.filename)
# Append the input AstroData object to the list of output
# AstroData objects without further processing
adoutput_list.append(ad)
continue
# Check whether the input is spectroscopic data
if "SPECT" not in ad.types:
log.stdinfo("%s is not spectroscopic data, so no MDF will be "
"added" % ad.filename)
# Append the input AstroData object to the list of output
# AstroData objects without further processing
adoutput_list.append(ad)
continue
# Check whether an MDF extension already exists in the input
# AstroData object
if ad["MDF"]:
log.warning("An MDF extension already exists in %s, so no MDF "
"will be added" % ad.filename)
# Append the input AstroData object to the list of output
# AstroData objects without further processing
adoutput_list.append(ad)
continue
# Parameters specified on the command line to reduce are converted
# to strings, including None
if rc["mdf"] and rc["mdf"] != "None":
# The user supplied an input to the mdf parameter
mdf = rc["mdf"]
else:
# The user did not supply an input to the mdf parameter, so try
# to find an appropriate one. Get the dictionary containing the
# list of MDFs for all instruments and modes.
all_mdf_dict = Lookups.get_lookup_table("Gemini/MDFDict",
"mdf_dict")
# The MDFs are keyed by the instrument and the MASKNAME. Get
# the instrument and the MASKNAME values using the appropriate
# descriptors
instrument = ad.instrument()
mask_name = ad.phu_get_key_value("MASKNAME")
# Create the key for the lookup table
if instrument is None or mask_name is None:
log.warning("Unable to create the key for the lookup "
"table (%s), so no MDF will be added"
% ad.exception_info)
# Append the input AstroData object to the list of output
# AstroData objects without further processing
adoutput_list.append(ad)
continue
key = "%s_%s" % (instrument, mask_name)
# Get the appropriate MDF from the look up table
if key in all_mdf_dict:
mdf = lookup_path(all_mdf_dict[key])
else:
# The MASKNAME keyword defines the actual name of an MDF
if not mask_name.endswith(".fits"):
mdf = "%s.fits" % mask_name
else:
mdf = str(mask_name)
# Check if the MDF exists in the current working directory
if not os.path.exists(mdf):
log.warning("The MDF %s was not found in the current "
"working directory, so no MDF will be "
"added" % mdf)
# Append the input AstroData object to the list of output
# AstroData objects without further processing
adoutput_list.append(ad)
continue
# Ensure that the MDFs are AstroData objects
if not isinstance(mdf, AstroData):
mdf_ad = AstroData(mdf)
if mdf_ad is None:
log.warning("Cannot convert %s into an AstroData object, so "
"no MDF will be added" % mdf)
# Append the input AstroData object to the list of output
# AstroData objects without further processing
adoutput_list.append(ad)
continue
# Check if the MDF is a single extension fits file
if len(mdf_ad) > 1:
log.warning("The MDF %s is not a single extension fits file, "
"so no MDF will be added" % mdf)
# Append the input AstroData object to the list of output
# AstroData objects without further processing
adoutput_list.append(ad)
continue
# Name the extension appropriately
mdf_ad.rename_ext("MDF", 1)
# Append the MDF AstroData object to the input AstroData object
log.fullinfo("Adding the MDF %s to the input AstroData object "
"%s" % (mdf_ad.filename, ad.filename))
ad.append(moredata=mdf_ad)
# Add the appropriate time stamps to the PHU
gt.mark_history(adinput=ad, keyword=timestamp_key)
# Change the filename
ad.filename = gt.filename_updater(adinput=ad, suffix=rc["suffix"],
strip=True)
# Append the output AstroData object to the list of output
# AstroData objects
adoutput_list.append(ad)
# Report the list of output AstroData objects to the reduction context
rc.report_output(adoutput_list)
yield rc
