def __init__(self,
init_data=False,
init_mask=False,
init_weight=False,
shape=(4096, 2048),
sourcefile=None):
"""Create a new DESImage
Create an empty DESImage
In mast cases, DESImage.create or DESImage.load will be safer
and more covenient.
"""
super().__init__(
data=np.zeros(shape, dtype=data_dtype) if init_data else None,
sourcefile=sourcefile)
#self.data = np.zeros(shape, dtype=data_dtype) if init_data else None
self.mask = None
if init_mask:
self.init_mask()
self.weight = None
if init_weight:
self.init_weight()
self.variance = None
#self.header = FITSHDR({})
#self.pri_hdr = self.header
self.mask_hdr = FITSHDR({})
self.weight_hdr = FITSHDR({})
class DESSingleImage:
def __init__(self):
self.header = FITSHDR({})
self.pri_hdr = FITSHDR({})
# If we index this object, assume we are after keywords in the header
def __getitem__(self, key):
if key in self.header:
return self.header[key]
return self.pri_hdr[key]
def __setitem__(self, key, value):
self.header[key] = value
def write_key(self, key, value, comment=None):
"""
Add or alter a header keyword/value pair, with optional comment field
"""
if comment is None:
self.header[key] = value
else:
self.header.add_record({
'name': key,
'value': value,
'comment': comment
})
def __init__(self, data, header={}, pri_hdr=None, sourcefile=None):
"""Create a new DESDataImage
:Parameters:
- `data`: the numpy data array
- `header`: the header
- `pri_hdr`: the primary header of the FITS file
"""
super().__init__()
self.data = data
self.sourcefile = sourcefile
if getattr(header, "add_record", None) is None:
self.header = FITSHDR(header)
else:
self.header = header
if pri_hdr is None:
self.pri_hdr = self.header
if getattr(pri_hdr, "add_record", None) is None:
self.pri_hdr = FITSHDR(pri_hdr)
else:
self.pri_hdr = pri_hdr
def __init__(self,tim, gain=4.0, seed=None, folding_threshold=1.e-5):
"""Initialize the BuildStamp object with the CCD-level properties we need."""
self.band = tim.band.strip().upper()
# GSParams should be used when galsim object is initialized
self.gsparams = galsim.GSParams(maximum_fft_size=2L**30L,\
folding_threshold=folding_threshold)
#print('FIX ME!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
self.gsdeviate = galsim.BaseDeviate()
#if seed is None:
# self.gsdeviate = galsim.BaseDeviate()
#else:
# self.gsdeviate = galsim.BaseDeviate(seed)
self.wcs = tim.getWcs()
self.psf = tim.getPsf()
# Tractor wcs object -> galsim wcs object
temp_hdr = FITSHDR()
subwcs = tim.wcs.wcs.get_subimage(tim.wcs.x0, tim.wcs.y0,
int(tim.wcs.wcs.get_width())-tim.wcs.x0,
int(tim.wcs.wcs.get_height())-tim.wcs.y0)
subwcs.add_to_header(temp_hdr)
# Galsim uses astropy header, not fitsio
hdr = fits.Header()
for key in temp_hdr.keys(): hdr[key]=temp_hdr[key]
self.galsim_wcs = galsim.GSFitsWCS(header=hdr)
del subwcs,temp_hdr,hdr
# zpscale equivalent to magzpt = self.t.ccdzpt+2.5*np.log10(self.t.exptime)
self.zpscale = tim.zpscale # nanomaggies-->ADU conversion factor
self.nano2e = self.zpscale*gain # nanomaggies-->electrons conversion factor
def new_header(og_header: FITSHDR) -> FITSHDR:
"""
Modifies an existing XMM Newton fits image header, removes some elements, and adds a little extra
information. The new header is then used for PSF corrected fits image files.
:param og_header: The header from the fits image that has been PSF corrected.
:return: The new, modified, fits header.
:rtype: FITSHDR
"""
# These are nuisance entries that I want gone
remove_list = ["CREATOR", "CONTINUE", "XPROC0", "XDAL0"]
# FITSHDR takes a dictionary as its main content argument
new_header_info = {}
# We want to copy most of the original header
for e in og_header:
# But those that are in the remove list aren't copied over.
if e not in remove_list:
new_header_info[e] = og_header[e]
# Also change the creator entry for a little self serving brand placement
elif e == "CREATOR":
new_header_info[e] = "XGA"
# Setting some new headers for further information
new_header_info["COMMENT"] = "THIS IMAGE HAS BEEN PSF CORRECTED BY XGA"
new_header_info["PSFBins"] = bins
new_header_info["PSFAlgorithm"] = "Richardson-Lucy"
new_header_info["PSFAlgorithmIterations"] = iterations
new_header_info["PSFModel"] = psf_model
return FITSHDR(new_header_info)
def __init__(self, bpm, header={}, pri_hdr=None, sourcefile=None):
"""Create a new DESBPMImage
:Parameters:
- `bpm`: the numpy data array
- `header`: the header
- `pri_hdr`: the primary header of the FITS file
"""
self.mask = bpm
self.sourcefile = sourcefile
if getattr(header, "add_record", None) is None:
self.header = FITSHDR(header)
else:
self.header = header
if pri_hdr is None:
self.pri_hdr = self.header
if getattr(pri_hdr, "add_record", None) is None:
self.pri_hdr = FITSHDR(pri_hdr)
else:
self.pri_hdr = pri_hdr
def __init__(self):
self.header = FITSHDR({})
self.pri_hdr = FITSHDR({})
# Read in the read noise from a fits file generated with Bernie's ngxhrg
# noisemode 'last' uses one realization because the full one takes
# a long time to create
if noisemode == 'last':
noise = fitsio.read(noisefile)
data_cube_Q[-1, :, :] += noise # Adding to only the final time
elif noisemode == 'full':
noise = fitsio.read(noisefile)
data_cube_Q += noise # Adding the noise at all reads
# Convert charge to signal, clipping values<0 and >2**16
data_cube_S = np.array(np.clip(data_cube_Q / gain, 0, 65535), dtype=np.uint16)
# Write simple header, todo: add more thorough comments
hdr = FITSHDR()
hdr['GAIN'] = gain
hdr['ILLUMIN'] = I
hdr['QE'] = QE
hdr['RNGSEED'] = rngseed
if (lipcmode == 'true'):
hdr['LINIPC'] = lipc_alpha[0]
if (nlmode == 'quadratic'):
hdr['BETA'] = nlbeta
if (nlmode == 'quartic'):
hdr['NLCOEFFS_c2'] = nlcoeffs_arr[0]
hdr['NLCOEFFS_c3'] = nlcoeffs_arr[1]
hdr['NLCOEFFS_c4'] = nlcoeffs_arr[2]
if (bfemode == 'true'):
hdr['BFE_A00'] = a_coeff[2][2] # Hard-coded to expect 5x5 a coeffs
def write_catalog(fname,
x,
y,
z,
w,
type="DATA",
format="fits",
coord="PSEUDO_EQUATORIAL"):
if format == "txt":
np.savetxt(fname, np.transpose([x, y, z, w]))
elif format == "fits":
# current DM supported
DM_VERSION = "2.5.0"
# Extracted from AsciiToFits.py written by Daniele Tavagnacco
if coord == "PSEUDO_EQUATORIAL":
columns = [['SOURCE_ID', -1, 'f8'], ['RA', x, 'f8'],
['DEC', y, 'f8'], ['REDSHIFT', z, 'f8'],
['WEIGHT', -1, 'f8'], ['DENSITY', w, 'f8']]
elif coord == "CARTESIAN":
columns = [['SOURCE_ID', -1, 'f8'], ['COMOV_X', x, 'f8'],
['COMOV_Y', y, 'f8'], ['COMOV_Z', z, 'f8'],
['WEIGHT', -1, 'f8'], ['DENSITY', w, 'f8']]
header_keywords = {
"TELESCOP": "EUCLID",
"INSTRUME": "LE3GC-MOCKS",
"FILENAME": fname,
"CAT_ID": "MOCK",
"COORD": coord,
"ANGLE": "DEGREES"
}
# fname_nodir = fname[[pos for pos, char in enumerate(fname) if char == '/'][-1]+1:]
# zshell = fname[fname.find('zshell'):-5]
# header_keywords = {'TELESCOP' : 'EUCLID ',
# 'INSTRUME' : 'LE3IDSELID',
# 'FILENAME' : fname_nodir,
# 'CAT_TYPE' : type,
# 'CAT_NAME' : 'MOCK-LE3GC',
# 'CAT_NOBJ' : x.size,
# 'COORD ' : 'EQUATORIAL',
# 'ANGLE ' : 'DEG ',
# 'COMPLETE' : 1.0,
# 'PURITY ' : 1.0,
# 'SELECT ' : zshell}
extension = "CATALOG"
xmlKeys = {
"pf": "PK_LE3_GC_WindowMultipoles",
"instr": "LE3_GC_MOCKS",
"id": "MOCK",
"coord": coord
}
print("Preparing FITS structure")
types = []
# keep just wanted columns ...bad but..
for c in columns:
types.append((c[0], c[2]))
hdr = FITSHDR()
print("+ Add keywords")
for k in header_keywords:
hdr[k] = header_keywords[k]
keep_table = {}
for c in columns:
# if required but not existing (-1) fill with ones
if (c[1] is -1):
# add tmp column with correct name and position, bu only ones
print(str("+ -Col '%s' filled" % c[0]))
keep_table[c[0]] = np.ones_like(columns[1][1],
dtype=np.float64)
else:
# keep column with requested position in the input file
print(str("+ -Col '%s' from '%s'" % (c[0], c[1])))
keep_table[c[0]] = c[1].astype(np.float64)
fullsize = len(keep_table) * len(c[1]) * 8 / 1024 / 1024.
print(str("+ ~%.2f MB in memory" % fullsize))
# now write some data
print(str("+ Write FITS: %s" % fname))
fits = FITS(fname, 'rw', clobber=True)
fits.write_table(data=keep_table, header=hdr, extname=extension)
fits.close()
print("+ Preparing XML product")
with open(fname.replace(input.cat4le3_format, "xml"), "w+") as f:
f.write(
'''<?xml version="1.0" encoding="UTF-8" standalone="no" ?>\n'''
)
if (type == "RANDOM"):
f.write(
'''<p1:DpdLE3gcInputRandCat xmlns:p1="http://euclid.esa.org/schema/dpd/le3/gc/inp/catrandin">\n'''
)
else:
f.write(
'''<p1:DpdLE3gcInputDataCat xmlns:p1="http://euclid.esa.org/schema/dpd/le3/gc/inp/catdatain">\n'''
)
f.write(''' <Header>\n''')
f.write(
str(''' <ProductId>%s</ProductId>\n''' %
header_keywords["FILENAME"].split('.')[0]))
f.write(
''' <ProductType>dpdLE3gcInputRandCat</ProductType>\n''')
f.write(''' <SoftwareName>LE3_GC_test</SoftwareName>\n''')
f.write(''' <SoftwareRelease>1.0</SoftwareRelease>\n''')
f.write(
''' <ManualValidationStatus>UNKNOWN</ManualValidationStatus>\n'''
)
f.write(''' <PipelineRun>LE3_GC_Test_Inputs</PipelineRun>\n''')
f.write(''' <ExitStatusCode>OK</ExitStatusCode>\n''')
f.write(
str(''' <DataModelVersion>%s</DataModelVersion>\n''' %
DM_VERSION))
f.write(
str(''' <MinDataModelVersion>%s</MinDataModelVersion>\n''' %
DM_VERSION))
f.write(''' <ScientificCustodian>LE3</ScientificCustodian>\n''')
f.write(''' <AccessRights>\n''')
f.write(
''' <EuclidConsortiumRead>true</EuclidConsortiumRead>\n'''
)
f.write(
''' <EuclidConsortiumWrite>true</EuclidConsortiumWrite>\n'''
)
f.write(
''' <ScientificGroupRead>true</ScientificGroupRead>\n''')
f.write(
''' <ScientificGroupWrite>true</ScientificGroupWrite>\n'''
)
f.write(''' </AccessRights>\n''')
f.write(''' <Curator>\n''')
f.write(''' <Name>SDC-IT</Name>\n''')
f.write(''' </Curator>\n''')
f.write(str(''' <Creator>%s</Creator>\n''' % xmlKeys["pf"]))
f.write(
''' <CreationDate>2019-10-31T12:12:12Z</CreationDate>\n''')
f.write(''' </Header>\n''')
f.write(''' <Data>\n''')
f.write(
str(''' <Instrument>%s</Instrument>\n''' % xmlKeys["instr"]))
f.write(str(''' <Catalog_ID>%s</Catalog_ID>\n''' % xmlKeys["id"]))
f.write(str(''' <CoordType>%s</CoordType>\n''' %
xmlKeys["coord"]))
f.write(''' <Catalog format="le3.gc.cat.test" version="0.2">\n''')
f.write(''' <DataContainer filestatus="PROPOSED">\n''')
f.write(str(''' <FileName>%s.fits</FileName>\n''' % fname))
f.write(''' </DataContainer>\n''')
f.write(''' </Catalog>\n''')
f.write(''' </Data>\n''')
if (type == "RANDOM"):
f.write('''</p1:DpdLE3gcInputRandCat>\n''')
else:
f.write('''</p1:DpdLE3gcInputDataCat>\n''')
f.close()
print("files %s and %s written" %
(fname, fname.replace(input.cat4le3_format, "xml")))
else:
print("ERROR: unrecognized format in write_catalog")
sys.exit(-1)