def _init_as_astrodata(self):
"""
Initialize parameters to be used by as_astrodata.
Creates a WCS object (pywcs) from the SCI header and
form the output AD object with the PHU and MDF from
the input AD. We are adding the TRACEFP extension as well
for later use on the spectral reduction process.
Input:
self.ad: AD object.
Output:
adout: Output AD object with AD phu and MDF
"""
ad = self.ad
# Start output AD with the original phu and the MDF extension.
adout = AstroData(phu=ad.phu)
adout.append(ad['MDF'])
adout.append(ad['TRACEFP'])
# Get wcs information. It is in the PHU
try:
self.wcs = pywcs.WCS(ad.phu.header)
if not hasattr(self.wcs.wcs, 'cd'):
self.wcs = None
except: # Something wrong with WCS, set it to None
self.wcs = None
return adout
def runappend(f1=None, f2=None, auto=False):
ad = AstroData(f1)
md = AstroData(f2)
pstr = "\n\n >>>>>>> AD <<<<<<<<\n"
pstr += str(ad.infostr())
pstr += "\n\n >>>>>>> AD APPEND <<<<<<<<\n"
pstr += str(md.infostr())
ad.append(moredata=md, auto_number=auto)
pstr +="\n\n >>>>>>> NEW AD <<<<<<<<\n"
pstr += str(ad.infostr())
print(pstr)
return ad
def test_method_append_8():
ad = AstroData(TESTFILE)
ad.append(header=header1, data=data1, extname='TESTH', extver=2)
assert ad[3].header['EXTVER'] == 2
def test_method_append_6():
ad = AstroData(TESTFILE)
initial_len = len(ad)
ad.append(header=header1, data=data1, auto_number=True)
def test_method_append_5():
ad = AstroData(TESTFILE)
ad.append(moredata=hdu1, auto_number=True)
assert ad.hdulist[-1] == hdu1
def test_method_append_4():
ad = AstroData(TESTFILE)
initial_len = len(ad)
ad.append(moredata=hdu1, auto_number=True)
assert len(ad) == initial_len + 1
def test_method_append_2():
ad = AstroData(TESTFILE)
ad2 = AstroData(TESTFILE2)
with pytest.raises(AstroDataError):
ad.append(moredata=ad2)
def test_method_append_9():
ad = AstroData(TESTFILE)
ad.append(header=header1, data=data1, extname='TESTH', extver=1)
assert ad[('TESTH', 1)]
def test_method_close_2():
ad = AstroData(TESTFILE)
ad.close()
with pytest.raises(AstroDataError):
ad.append(moredata=hdu1)
def test_method_append_6():
ad = AstroData(TESTFILE)
initial_len = len(ad)
ad.append(header=header1, data=data1, auto_number=True)
def test_method_append_8():
ad = AstroData(TESTFILE)
ad.append(header=header1, data=data1, extname='TESTH', extver=2)
assert ad[3].header['EXTVER'] == 2
def test_method_append_5():
ad = AstroData(TESTFILE)
ad.append(moredata=hdu1, auto_number=True)
assert ad.hdulist[-1] == hdu1
def test_method_append_4():
ad = AstroData(TESTFILE)
initial_len = len(ad)
ad.append(moredata=hdu1, auto_number=True)
assert len(ad) == initial_len + 1
def test_method_append_2():
ad = AstroData(TESTFILE)
ad2 = AstroData(TESTFILE2)
with pytest.raises(AstroDataError):
ad.append(moredata=ad2)
def test_method_append_9():
ad = AstroData(TESTFILE)
ad.append(header=header1, data=data1, extname='TESTH', extver=1)
assert ad[('TESTH', 1)]
def makeFringeFrame(self,rc):
# Instantiate the log
log = gemLog.getGeminiLog(logType=rc["logType"],
logLevel=rc["logLevel"])
# Log the standard "starting primitive" debug message
log.debug(gt.log_message("primitive", "makeFringeFrame",
"starting"))
# Initialize the list of output AstroData objects
adoutput_list = []
# Check for at least 3 input frames
adinput = rc.get_inputs_as_astrodata()
if len(adinput)<3:
log.stdinfo('Fewer than 3 frames provided as input. ' +
'Not making fringe frame.')
# Report the empty list to the reduction context
rc.report_output(adoutput_list)
else:
rc.run("correctBackgroundToReferenceImage"\
"(remove_zero_level=True)")
# If needed, do a rough median on all frames, subtract,
# and then redetect to help distinguish sources from fringes
sub_med = rc["subtract_median_image"]
if sub_med:
adinput = rc.get_inputs_as_astrodata()
# Get data by science extension
data = {}
for ad in adinput:
for sciext in ad["SCI"]:
key = (sciext.extname(),sciext.extver())
if data.has_key(key):
data[key].append(sciext.data)
else:
data[key] = [sciext.data]
# Make a median image for each extension
import pyfits as pf
median_ad = AstroData()
median_ad.filename = gt.filename_updater(
adinput=adinput[0], suffix="_stack_median", strip=True)
for key in data:
med_data = np.median(np.dstack(data[key]),axis=2)
hdr = pf.Header()
ext = AstroData(data=med_data, header=hdr)
ext.rename_ext(key)
median_ad.append(ext)
# Subtract the median image
rc["operand"] = median_ad
rc.run("subtract")
# Redetect to get a good object mask
rc.run("detectSources")
# Add the median image back in to the input
rc.run("add")
# Add the object mask into the DQ plane
rc.run("addObjectMaskToDQ")
# Stack frames with masking from DQ plane
rc.run("stackFrames(operation=%s)" % rc["operation"])
yield rc
def test_method_close_2():
ad = AstroData(TESTFILE)
ad.close()
with pytest.raises(AstroDataError):
ad.append(moredata=hdu1)
def as_astrodata(self, extname=None, tile=False, block=None, return_ROI=True,
return_associated_bintables=True, return_non_associations=True,
update_catalog_method='wcs'):
"""
Returns an AstroData object containing by default the mosaiced
IMAGE extensions, the merged associated BINTABLEs and all other
non-associated extensions of any other type. WCS information in
the headers of the IMAGE extensions and any pixel coordinates in
BINTABLEs will be updated appropriately.
:param extname: If None mosaic all IMAGE extensions. Otherwise
only the given extname. This becomes the ref_extname.
:type extname: (string). Default is None
:param tile: (boolean). If True, the mosaics returned are not
corrected for shifting and rotation.
:param block: See description below in method 'mosaic_image_data'.
:param return_ROI: (True). Returns the minimum frame size calculated
from the location of the amplifiers in a given block. If False uses
the blocksize value.
:param return_associated_bintables: (True). If a bintable is associated
to the ref_extname then is returned as a merged table in the
output AD. If False, they are not returned in the output AD.
:param return_non_associations (True). Specifies whether to return
extensions that are not deemed to be associated with the ref_extname.
:param update_catalog_method: ('wcs'). Specifies if the X
and Y pixel coordinates of any source positions in the BINTABLEs
are to be recalculated using the output WCS and the sources R.A.
and Dec. values within the table. If set to 'transform' the updated X
and Y pixel coordinates will be determined using the transformations
used to mosaic the pixel data. In the case of tiling, a shift is
technically being applied and therefore update_catalog_method='wcs'
should be set internally (Not yet implemented).
:type update_catalog_method: (string). Possible values are
'wcs' or 'transform'.
"""
# If extname is None create mosaics of all image data in ad, merge
# the bintables if they are associated with the image extensions
# and append to adout all non_associatiated extensions. Appending
# these extensions to the output AD is controlled by
# return_associated_bintables and return_non_associations.
# Make blank ('') same as None; i.e. handle all extensions.
if extname == '': extname = None
if (extname != None) and (extname not in self.extnames):
raise ValueError("as_astrodata: Extname '"+extname+\
"' not found in AD object.")
adin = self.ad # alias
# Load input data if data_list attribute is not defined.
#if not hasattr(self, "data_list"):
# self.data_list = self.get_data_list(extname)
adout = AstroData() # Prepare output AD
adout.phu = adin.phu.copy() # Use input AD phu as output phu
adout.phu.header.update('TILED', ['FALSE', 'TRUE'][tile],
'False: Image Mosaicked, True: tiled')
# Set up extname lists with all the extension names that are going to
# be mosaiced and table extension names to associate.
#
if extname is None: # Let's work through all extensions
if self.associated_im_extns:
extname_list = self.associated_im_extns
else:
extname_list = self.im_extnames
else:
self.ref_extname = extname # Redefine reference extname
if extname in self.associated_im_extns:
self.associated_im_extns = [extname] # We need this extname only
extname_list = [extname]
elif extname in self.non_associated_extns:
# Extname is not in associated lists; so clear these lists.
extname_list = []
self.associated_im_extns = []
self.associated_tab_extns = []
elif extname in self.associated_tab_extns:
# Extname is an associated bintable.
extname_list = []
self.associated_im_extns = []
self.associated_tab_extns = [extname]
else:
extname_list = [extname]
# ------ Create mosaic ndarrays, update the output WCS, create an
# AstroData object and append to the output list.
# Make the list to have the order 'sci','var','dq'
svdq = [k for k in ['SCI','VAR','DQ'] if k in extname_list]
# add the rest of the extension names.
extname_list = svdq + list(set(extname_list)-set(svdq))
for extn in extname_list:
# Mosaic the IMAGE extensions now
mosarray = self.mosaic_image_data(extn,tile=tile,block=block,
return_ROI=return_ROI)
# Create the mosaic FITS header using the reference
# extension header.
header = self.mosaic_header(mosarray.shape,block,tile)
# Generate WCS object to be used in the merging the object
# catalog table for updating the objects pixel coordinates
# w/r to the new crpix1,2.
ref_wcs = pywcs.WCS(header)
# Setup output AD
new_ext = AstroData(data=mosarray,header=header)
# Reset extver to 1.
new_ext.rename_ext(name=extn,ver=1)
adout.append(new_ext)
if return_associated_bintables:
# If we have associated bintables with image extensions, then
# merge the tables.
for tab_extn in self.associated_tab_extns:
# adout will get the merge table
new_tab = self.merge_table_data(ref_wcs, tile, tab_extn, block,
update_catalog_method)
adout.append(new_tab[0])
# If we have a list of extension names that have not tables extension
# names associated, then mosaic them.
#
if return_non_associations:
for extn in self.non_associated_extns:
# Now get the list of extver to append
if extn in self.im_extnames: # Image extensions
# We need to mosaic image extensions having more
# than one extver.
#
if adin.count_exts(extn) > 1:
mosarray = self.mosaic_image_data(extn,
tile=tile,block=block,
return_ROI=return_ROI)
# Get reference extension header
header = self.mosaic_header(mosarray.shape,block,tile)
new_ext = AstroData(data=mosarray,header=header)
# Reset extver to 1.
new_ext.rename_ext(name=extn,ver=1)
adout.append(new_ext)
else:
self.log.warning("as_astrodata: extension '"+extn+\
"' has 1 extension.")
adout.append(adin[extn])
if extn in self.tab_extnames: # We have a list of extvers
for extv in self.tab_extnames[extn]:
adout.append(adin[extn,extv])
# rediscover classifications.
adout.refresh_types()
return adout