def process(self, _):
"""
Perform the main work of the task and return the results as a Python data structure.
"""
if (self._DEBUG):
print("({}.process): ARGS={}".format(self.TOOL_NAME, self.args),
file=sys.stderr)
# process the given, already validated FITS file
fits_file = self.args.get('fits_file')
ignore_list = self.args.get(
'ignore_list') or fits_utils.FITS_IGNORE_KEYS
which_hdu = self.args.get('which_hdu', 0)
try:
with fits.open(fits_file) as hdus_list:
if (not fits_utils.has_image_data(hdus_list)):
errMsg = f"Skipping FITS file '{fits_file}': no image data in primary HDU"
raise errors.UnsupportedType(errMsg)
hdrs = fits_utils.get_header_fields(hdus_list, which_hdu,
ignore_list)
except OSError as oserr:
errMsg = "Unable to read image metadata from FITS file '{}': {}.".format(
fits_file, oserr)
raise errors.ProcessingError(errMsg)
metadata = dict() # create overall metadata structure
finfo = gather_file_info(fits_file)
if (finfo is not None): # add common file information
metadata['file_info'] = finfo
if (hdrs is not None): # add the headers to the metadata
metadata['headers'] = hdrs
return metadata # return the results of processing
def test_get_header_fields_ignore_empty(self):
hdrs = None
with fits.open(self.m13_tstfyl) as hdus:
hdrs = utils.get_header_fields(hdus, ignore=[])
print(hdrs)
assert hdrs is not None
assert len(hdrs) > 0
assert len(hdrs) == 19 # really 25 but duplicates elided
assert 'CTYPE1' in hdrs
assert 'SIMPLE' in hdrs
assert 'COMMENT' in hdrs # should not be removed
def test_get_header_fields_default(self):
hdrs = None
with fits.open(self.m13_tstfyl) as hdus:
hdrs = utils.get_header_fields(hdus)
print(hdrs)
assert hdrs is not None
assert len(hdrs) > 0
assert len(
hdrs) == 18 # really 25 but duplicates elided, comments removed
assert 'CTYPE1' in hdrs
assert 'SIMPLE' in hdrs
assert 'COMMENT' not in hdrs # removed by default
def process(self, _):
"""
Perform the main work of the task and return the results as a Python data structure.
"""
if (self._DEBUG):
print("({}.process): ARGS={}".format(self.TOOL_NAME, self.args),
file=sys.stderr)
# process the given, already validated FITS file
fits_file = self.args.get('fits_file')
ignore_list = self.args.get(
'ignore_list') or fits_utils.FITS_IGNORE_KEYS
catalog_hdu = self.args.get('catalog_hdu', 1)
try:
with fits.open(fits_file) as hdus_list:
if (not fits_utils.has_catalog_data(hdus_list)):
errMsg = f"Skipping FITS file '{fits_file}': no catalog in HDU 1"
raise errors.UnsupportedType(errMsg)
hdrs = fits_utils.get_header_fields(hdus_list, catalog_hdu,
ignore_list)
cinfo = fits_utils.get_column_info(hdus_list, catalog_hdu)
fits_rec = hdus_list[catalog_hdu].data
data = fits_utils.rows_from_data(fits_rec)
table = Table.read(hdus_list, hdu=catalog_hdu)
meta = fits_utils.get_table_meta_attribute(table)
except OSError as oserr:
errMsg = "Unable to read catalog data from FITS file '{}': {}.".format(
fits_file, oserr)
raise errors.ProcessingError(errMsg)
outdata = dict() # create overall ouput structure
finfo = gather_file_info(fits_file)
if (finfo is not None): # add common file information
outdata['file_info'] = finfo
if (hdrs is not None): # add the headers to the output
outdata['headers'] = hdrs
if (cinfo is not None): # add column metadata to the output
outdata['column_info'] = cinfo
outdata['meta'] = meta # add extra table metadata to the output
outdata['data'] = data # add the data table to the output
return outdata # return the results of processing
def test_get_header_fields_badindex(self):
hdrs = None
with fits.open(self.m13_tstfyl) as hdus:
hdrs = utils.get_header_fields(hdus, 1) # no HDU at index 1
assert hdrs is None