def fits_subset_mask_importer(filename):
if not is_fits(filename):
raise IOError("File {0} is not a valid FITS file".format(filename))
masks = OrderedDict()
label = os.path.basename(filename).rpartition('.')[0]
with fits.open(filename) as hdulist:
for ihdu, hdu in enumerate(hdulist):
if hdu.data is not None and hdu.data.dtype.kind == 'i':
if not hdu.name:
name = '{0}[{1}]'.format(label, ihdu)
elif ihdu == 0:
name = label
else:
name = hdu.name
masks[name] = hdu.data > 0
if len(masks) == 0:
raise ValueError('No HDUs with integer values (which would normally indicate a mask) were found in file')
return masks
def fits_subset_mask_importer(filename):
if not is_fits(filename):
raise IOError("File {0} is not a valid FITS file".format(filename))
masks = OrderedDict()
label = os.path.basename(filename).rpartition('.')[0]
with fits.open(filename) as hdulist:
for ihdu, hdu in enumerate(hdulist):
if hdu.data is not None and hdu.data.dtype.kind == 'i':
if not hdu.name:
name = '{0}[{1}]'.format(label, ihdu)
elif ihdu == 0:
name = label
else:
name = hdu.name
masks[name] = hdu.data > 0
if len(masks) == 0:
raise ValueError('No HDUs with integer values (which would normally indicate a mask) were found in file')
return masks
def is_dendro(file, **kwargs):
if is_hdf5(file):
import h5py
f = h5py.File(file, 'r')
return 'data' in f and 'index_map' in f and 'newick' in f
elif is_fits(file):
from astropy.io import fits
with fits.open(file, ignore_missing_end=True) as hdulist:
# For recent versions of astrodendro the HDUs have a recongnizable
# set of names.
if 'DATA' in hdulist and 'INDEX_MAP' in hdulist and 'NEWICK' in hdulist:
return True
# For older versions of astrodendro, the HDUs did not have names
# Here we use heuristics to figure out if this is likely to be a
# dendrogram. Specifically, there should be three HDU extensions.
# The primary HDU should be empty, HDU 1 and HDU 2 should have
# matching shapes, and HDU 3 should have a 1D array. Also, if the
# HDUs do have names then this is not a dendrogram since the old
# files did not have names
# This branch can be removed once we think most dendrogram files
# will have HDU names.
if len(hdulist) != 4:
return False
if hdulist[1].name != '' or hdulist[2].name != '' or hdulist[
3].name != '':
return False
if hdulist[0].data is not None:
return False
if hdulist[1].data is None or hdulist[2].data is None or hdulist[
3].data is None:
return False
if hdulist[1].data.shape != hdulist[2].data.shape:
return False
if hdulist[3].data.ndim != 1:
return False
# We're probably ok, so return True
return True
else:
return False
def is_gridded_data(filename, **kwargs):
if is_hdf5(filename):
return True
if is_fits(filename):
from astropy.io import fits
with fits.open(filename) as hdulist:
return is_image_hdu(hdulist[0])
return False
def is_gridded_data(filename, **kwargs):
if is_hdf5(filename):
return True
if is_fits(filename):
from astropy.io import fits
with fits.open(filename) as hdulist:
return is_image_hdu(hdulist[0])
return False
def identify_file_format(filename):
if os.path.isdir(filename):
if os.path.exists(os.path.join(filename, 'table.f0')):
return 'casa_image'
else:
return None
else:
if is_fits(filename):
return 'fits'
else:
return None
def is_spectral_cube(filename, **kwargs):
"""
Check that the file is a 3D or 4D FITS spectral cube
"""
if not is_fits(filename):
return False
try:
StokesSpectralCube.read(filename)
except Exception:
return False
else:
return True
def gridded_data(filename, format='auto', **kwargs):
result = Data()
# Try and automatically find the format if not specified
if format == 'auto':
format = file_format(filename)
# Read in the data
if is_fits(filename):
from astropy.io import fits
arrays = extract_data_fits(filename, **kwargs)
header = fits.getheader(filename)
result.coords = coordinates_from_header(header)
elif is_hdf5(filename):
arrays = extract_data_hdf5(filename, **kwargs)
else:
raise Exception("Unkonwn format: %s" % format)
for component_name in arrays:
comp = Component.autotyped(arrays[component_name])
result.add_component(comp, component_name)
return result
def gridded_data(filename, format='auto', **kwargs):
result = Data()
# Try and automatically find the format if not specified
if format == 'auto':
format = file_format(filename)
# Read in the data
if is_fits(filename):
from astropy.io import fits
arrays = extract_data_fits(filename, **kwargs)
header = fits.getheader(filename)
result.coords = coordinates_from_header(header)
elif is_hdf5(filename):
arrays = extract_data_hdf5(filename, **kwargs)
else:
raise Exception("Unkonwn format: %s" % format)
for component_name in arrays:
comp = Component.autotyped(arrays[component_name])
result.add_component(comp, component_name)
return result
def is_dendro(file, **kwargs):
if is_hdf5(file):
import h5py
f = h5py.File(file, 'r')
return 'data' in f and 'index_map' in f and 'newick' in f
elif is_fits(file):
from astropy.io import fits
hdulist = fits.open(file, ignore_missing_end=True)
# In recent versions of Astropy, we could do 'DATA' in hdulist etc. but
# this doesn't work with Astropy 0.3, so we use the following method
# instead:
try:
hdulist['DATA']
hdulist['INDEX_MAP']
hdulist['NEWICK']
except KeyError:
pass # continue
else:
return True
# For older versions of astrodendro, the HDUs did not have names
# Here we use heuristics to figure out if this is likely to be a
# dendrogram. Specifically, there should be three HDU extensions.
# The primary HDU should be empty, HDU 1 and HDU 2 should have
# matching shapes, and HDU 3 should have a 1D array. Also, if the
# HDUs do have names then this is not a dendrogram since the old
# files did not have names
# This branch can be removed once we think most dendrogram files
# will have HDU names.
if len(hdulist) != 4:
return False
if hdulist[1].name != '' or hdulist[2].name != '' or hdulist[3].name != '':
return False
if hdulist[0].data is not None:
return False
if hdulist[1].data is None or hdulist[2].data is None or hdulist[3].data is None:
return False
if hdulist[1].data.shape != hdulist[2].data.shape:
return False
if hdulist[3].data.ndim != 1:
return False
# We're probably ok, so return True
return True
else:
return False