def set_arrays(filename, args, fields=None, ascii=True, clobber=False):
if os.path.isfile(filename) and not clobber:
raise IOErr("filefound", filename)
if not numpy.iterable(args) or len(args) == 0:
raise IOErr('noarrayswrite')
if not numpy.iterable(args[0]):
raise IOErr('noarrayswrite')
size = len(args[0])
for arg in args:
if not numpy.iterable(arg):
raise IOErr('noarrayswrite')
elif len(arg) != size:
raise IOErr('arraysnoteq')
if ascii and '[' not in filename and ']' not in filename:
filename += "[opt kernel=text/simple]"
tbl = pycrates.TABLECrate()
if fields is None:
fields = ['col%i' % (ii+1) for ii in range(len(args))]
if len(args) != len(fields):
raise IOErr('toomanycols', str(len(fields)), str(len(args)))
for val, name in izip(args, fields):
_set_column(tbl, name, val)
pycrates.write_file(tbl, filename, clobber=True)
close_crate_dataset(tbl.get_dataset())
def set_arrays(filename, args, fields=None, ascii=True, clobber=False):
if os.path.isfile(filename) and not clobber:
raise IOErr("filefound", filename)
if not numpy.iterable(args) or len(args) == 0:
raise IOErr('noarrayswrite')
if not numpy.iterable(args[0]):
raise IOErr('noarrayswrite')
size = len(args[0])
for arg in args:
if not numpy.iterable(arg):
raise IOErr('noarrayswrite')
elif len(arg) != size:
raise IOErr('arraysnoteq')
if ascii and '[' not in filename and ']' not in filename:
filename += "[opt kernel=text/simple]"
tbl = pycrates.TABLECrate()
if fields is None:
fields = ['col%i' % (ii + 1) for ii in range(len(args))]
if len(args) != len(fields):
raise IOErr('toomanycols', str(len(fields)), str(len(args)))
for val, name in izip(args, fields):
_set_column(tbl, name, val)
pycrates.write_file(tbl, filename, clobber=True)
close_crate_dataset(tbl.get_dataset())
def set_table_data(filename, data, col_names, hdr=None, hdrnames=None,
ascii=False, clobber=False, packup=False):
if not packup and os.path.isfile(filename) and not clobber:
raise IOErr("filefound", filename)
tbl = pycrates.TABLECrate()
col_names = [name for name in col_names if data[name] != None]
col_names.remove('name')
try:
cols = [pycrates.CrateData() for i in range(len(col_names))]
for name, col in izip(col_names, cols):
if data[name] is None:
continue
_set_column( tbl, col, name, data[name] )
finally:
if packup:
return tbl
if ascii and '[' not in filename and ']' not in filename:
filename += "[opt kernel=text/simple]"
pycrates.write_file(tbl, filename)
def noise(infits,outimage,mask=None): """ Module to add poisson noise to the image data Input: Fits image Output: Fits image - An image with possion randon noise """ ctimg = pycrates.read_file(infits) img = ctimg.get_image() pix = img.values noiseimg = poisson(pix) if mask != None: bla = pycrates.read_file(mask) msk_values = bla.get_image().values msk = msk_values == 0 noiseimg[msk] = msk_values[msk] img.values = noiseimg pycrates.write_file(ctimg,outimage,clobber=True)
def set_image_data(filename, data, header, ascii=False, clobber=False,
packup=False):
if not packup and os.path.isfile(filename) and not clobber:
raise IOErr('filefound', filename)
img = pycrates.IMAGECrate()
# Write Image Header Keys
for key in header.keys():
if header[key] is None:
continue
_set_key(img, pycrates.CrateKey(), key, header[key])
# Write Image WCS Header Keys
if data['eqpos'] is not None:
cdeltw = data['eqpos'].cdelt
crvalw = data['eqpos'].crval
crpixw = data['eqpos'].crpix
equin = data['eqpos'].equinox
if data['sky'] is not None:
cdeltp = data['sky'].cdelt
crvalp = data['sky'].crval
crpixp = data['sky'].crpix
_set_key(img, pycrates.CrateKey(), 'MTYPE1', 'sky ')
_set_key(img, pycrates.CrateKey(), 'MFORM1', 'x,y ')
_set_key(img, pycrates.CrateKey(), 'CTYPE1P','x ')
_set_key(img, pycrates.CrateKey(), 'CTYPE2P','y ')
_set_key(img, pycrates.CrateKey(), 'WCSNAMEP','PHYSICAL')
_set_key(img, pycrates.CrateKey(), 'CDELT1P', cdeltp[0])
_set_key(img, pycrates.CrateKey(), 'CDELT2P', cdeltp[1])
_set_key(img, pycrates.CrateKey(), 'CRPIX1P', crpixp[0])
_set_key(img, pycrates.CrateKey(), 'CRPIX2P', crpixp[1])
_set_key(img, pycrates.CrateKey(), 'CRVAL1P', crvalp[0])
_set_key(img, pycrates.CrateKey(), 'CRVAL2P', crvalp[1])
if data['eqpos'] is not None:
# Simply the inverse of read transformations in get_image_data
cdeltw = cdeltw * cdeltp
crpixw = ((crpixw - crvalp) / cdeltp + crpixp )
if data['eqpos'] is not None:
_set_key(img, pycrates.CrateKey(), 'MTYPE2', 'EQPOS ')
_set_key(img, pycrates.CrateKey(), 'MFORM2', 'RA,DEC ')
_set_key(img, pycrates.CrateKey(), 'CTYPE1', 'RA---TAN')
_set_key(img, pycrates.CrateKey(), 'CTYPE2', 'DEC--TAN')
_set_key(img, pycrates.CrateKey(), 'CDELT1', cdeltw[0])
_set_key(img, pycrates.CrateKey(), 'CDELT2', cdeltw[1])
_set_key(img, pycrates.CrateKey(), 'CRPIX1', crpixw[0])
_set_key(img, pycrates.CrateKey(), 'CRPIX2', crpixw[1])
_set_key(img, pycrates.CrateKey(), 'CRVAL1', crvalw[0])
_set_key(img, pycrates.CrateKey(), 'CRVAL2', crvalw[1])
_set_key(img, pycrates.CrateKey(), 'EQUINOX', equin)
# Write Image pixel values
shape = data['pixels'].shape
pix_col = pycrates.CrateData()
pix_col.set_dimarr( shape, len(shape) )
pix_col.set_nsets(1)
pix_col.set_values( data['pixels'].ravel() )
pycrates.add_piximg(img, pix_col)
if packup:
return img
if ascii and '[' not in filename and ']' not in filename:
#filename += "[opt kernel=text/simple]"
raise IOErr('writenoimg')
pycrates.write_file(img, filename)
def write_draws(draws, outfile, params=None, format="ascii"):
"""Writes the draws (except for iteration number 0) to the file outfile.
Over-writes the file if it exists. If params is given then it
should be the output of get_parameter_info and is used to
add extra information to the output file (well, it will do,
for now it does not).
The output format is determined by the format parameter; it
can be one of
"fits" - FITS binary table
"ascii" - simple ASCII table (two comment lines then data)
"dtf" - ASCII file in CIAO TEXT/DTF format (CIAO tools can
treat it similarly to a FITS table)
None - let Crates determine, probably because you have
specified an option within the outfile name
(specialised use only)
"""
formats = {"ascii": "text/simple", "dtf": "text/dtf", "fits": "fits"}
if format != None and not formats.has_key(format.lower()):
raise RuntimeError, "Unknown output format '%s'" % format
# Use crates to create the output file.
#
cr = crates.TABLECrate()
# We need to store the crate data objects so that they are not
# garbage collected until after the write_file() call.
#
store = {}
def create_col(cname, cval):
store[cname] = crates.CrateData()
store[cname].name = cname
if 1 != store[cname].load(cval, 1):
raise RuntimeError, "Unable to add column %s to the Crate Data object." % cname
if 1 != crates.add_col(cr, store[cname]):
raise RuntimeError, "Unable to add column %s to the Crates." % cname
def create_key(kname, kval, desc=None):
store[kname] = crates.CrateKey()
store[kname].name = kname
if desc != None:
store[kname].desc = desc
if 1 != store[kname].load(kval):
raise RuntimeError, "Unable to set key %s to %g" % (name, kval)
if 1 != crates.add_key(cr, store[kname]):
raise RuntimeError, "Unable to add key %s to Crates." % kname
# Column data, and then keywords.
# Note that we do not write out any iteration numbered 0 as this is
# assumed to be the "best-fit" position.
#
idx = draws["iteration"] > 0
for cname in ["iteration", "accept", "statistic"]:
create_col(cname, draws[cname][idx])
for cname in draws["parnames"]:
create_col(cname, draws[cname][idx])
if params == None:
create_key("statmin", draws["statistic"][0], "statistic at best-fit location")
for k in draws["parnames"]:
create_key("P_%s" % k, draws[k][0], "best-fit value")
else:
create_key("statmin", params["statval"], "statistic at best-fit location")
create_key("sigma", params["sigma"], "sigma value for lower/upper limits")
for (k, v, l, h) in zip(params["parnames"], params["parvals"], params["parmins"], params["parmaxes"]):
create_key("p_%s" % k, v, "best-fit value")
create_key("dl_%s" % k, l, "best-fit lower limit")
create_key("dh_%s" % k, h, "best-fit upper limit")
# Write out the file
#
if format == None:
outname = outfile
else:
outname = outfile + "[opt kernel=%s]" % formats[format.lower()]
if 1 != crates.write_file(cr, outname):
raise IOError, "Unable to write data out to '%s'" % outname
print "Created: %s" % outfile
def write_draws(draws, outfile, params=None, format="ascii"):
"""Writes the draws (except for iteration number 0) to the file outfile.
Over-writes the file if it exists. If params is given then it
should be the output of get_parameter_info and is used to
add extra information to the output file (well, it will do,
for now it does not).
The output format is determined by the format parameter; it
can be one of
"fits" - FITS binary table
"ascii" - simple ASCII table (two comment lines then data)
"dtf" - ASCII file in CIAO TEXT/DTF format (CIAO tools can
treat it similarly to a FITS table)
None - let Crates determine, probably because you have
specified an option within the outfile name
(specialised use only)
"""
formats = {"ascii": "text/simple", "dtf": "text/dtf", "fits": "fits"}
if format != None and not formats.has_key(format.lower()):
raise RuntimeError, "Unknown output format '%s'" % format
# Use crates to create the output file.
#
cr = crates.TABLECrate()
# We need to store the crate data objects so that they are not
# garbage collected until after the write_file() call.
#
store = {}
def create_col(cname, cval):
store[cname] = crates.CrateData()
store[cname].name = cname
if 1 != store[cname].load(cval, 1):
raise RuntimeError, "Unable to add column %s to the Crate Data object." % cname
if 1 != crates.add_col(cr, store[cname]):
raise RuntimeError, "Unable to add column %s to the Crates." % cname
def create_key(kname, kval, desc=None):
store[kname] = crates.CrateKey()
store[kname].name = kname
if desc != None:
store[kname].desc = desc
if 1 != store[kname].load(kval):
raise RuntimeError, "Unable to set key %s to %g" % (name, kval)
if 1 != crates.add_key(cr, store[kname]):
raise RuntimeError, "Unable to add key %s to Crates." % kname
# Column data, and then keywords.
# Note that we do not write out any iteration numbered 0 as this is
# assumed to be the "best-fit" position.
#
idx = draws["iteration"] > 0
for cname in ["iteration", "accept", "statistic", "alphas"]:
create_col(cname, draws[cname][idx])
for cname in draws["parnames"]:
create_col(cname, draws[cname][idx])
if params == None:
create_key("statmin", draws["statistic"][0],
"statistic at best-fit location")
for k in draws["parnames"]:
create_key("P_%s" % k, draws[k][0], "best-fit value")
else:
create_key("statmin", params["statval"],
"statistic at best-fit location")
create_key("sigma", params["sigma"],
"sigma value for lower/upper limits")
for (k, v, l, h) in zip(params["parnames"], params["parvals"],
params["parmins"], params["parmaxes"]):
create_key("p_%s" % k, v, "best-fit value")
create_key("dl_%s" % k, l, "best-fit lower limit")
create_key("dh_%s" % k, h, "best-fit upper limit")
# Write out the file
#
if format == None:
outname = outfile
else:
outname = outfile + "[opt kernel=%s]" % formats[format.lower()]
if 1 != crates.write_file(cr, outname):
raise IOError, "Unable to write data out to '%s'" % outname
print "Created: %s" % outfile