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 process(self, metadata):
"""
Perform the main work of the task and return the results as a Python data structure.
This method overrides JWST_ObsCoreCalcTask method to use iRods file access.
"""
if (self._DEBUG):
print("({}.process): ARGS={}".format(self.TOOL_NAME, self.args),
file=sys.stderr)
# use the specified HDU of the FITS file to compute the WCS information
which_hdu = self.args.get('which_hdu', 0)
# get the iRods file path argument of the file to be opened
irff_path = self.args.get('irods_fits_file')
try:
# get the FITS file at the specified path
irff = self.irods.getf(irff_path, absolute=True)
# sanity check on the given FITS file
if (irff.size < FITS_BLOCK_SIZE):
errMsg = "Skipping file too small to be a valid FITS file: '{}'".format(
irff_path)
raise errors.UnsupportedType(errMsg)
if (self._DEBUG):
print("({}): Reading iRods FITS file '{}'.".format(
self.TOOL_NAME, irff_path),
file=sys.stderr)
# try to get the specified header and read WCS info from it
header = self.irods.get_header(irff, which_hdu)
if (header):
wcs_info = self.irods.get_WCS(header)
else: # unable to read the specified header
errMsg = "Unable to find or read HDU {} of FITS file '{}'.".format(
which_hdu, irff_path)
raise errors.ProcessingError(errMsg)
except DataObjectDoesNotExist as dodne:
errMsg = "Unable to find the specified iRods FITS file '{}'.".format(
irff_path)
raise errors.ProcessingError(errMsg)
except OSError as oserr:
errMsg = "Unable to read WCS info from iRods FITS file '{}': {}.".format(
irff_path, oserr)
raise errors.ProcessingError(errMsg)
# check that we got the WCS information from the file
if (wcs_info is None):
errMsg = "No WCS info found in iRods FITS file '{}'.".format(
irff_path)
raise errors.ProcessingError(errMsg)
# try to produce values for each of the desired result fields
calculated = self.calculate_results(wcs_info, metadata)
metadata['calculated'] = calculated # add calculations to metadata
return metadata # return the results of processing
def test_ute_code(self):
ute = xcpt.UnsupportedType(self.EMSG, self.ECODE)
print(ute)
print(type(ute))
assert ute.error_code == self.ECODE
utedict = ute.to_dict()
assert 'message' in utedict
assert 'error_code' in utedict
assert utedict.get('message') == self.EMSG
assert utedict.get('error_code') == self.ECODE
utetup = ute.to_tuple()
assert utetup[0] == self.EMSG
assert utetup[1] == self.ECODE
def test_ute(self):
ute = xcpt.UnsupportedType(self.EMSG)
print(ute)
print(type(ute))
assert ute.error_code == xcpt.UnsupportedType.ERROR_CODE
utedict = ute.to_dict()
assert 'message' in utedict
assert 'error_code' in utedict
assert utedict.get('message') == self.EMSG
assert utedict.get('error_code') == xcpt.UnsupportedType.ERROR_CODE
utetup = ute.to_tuple()
assert utetup[0] == self.EMSG
assert utetup[1] == xcpt.UnsupportedType.ERROR_CODE
utestr = str(ute)
print(utestr)
assert str(xcpt.UnsupportedType.ERROR_CODE) in utestr
assert 'wrong' in utestr
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 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)
# get the selection and filtering arguments
which_hdu = self.args.get('which_hdu', 0)
ignore_list = self.args.get(
'ignore_list') or fits_utils.FITS_IGNORE_KEYS
# get the iRods file path argument of the file to be opened
irff_path = self.args.get('irods_fits_file')
try:
# get the FITS file at the specified path
irff = self.irods.getf(irff_path, absolute=True)
# sanity check on the given FITS file
if (irff.size < FITS_BLOCK_SIZE):
errMsg = "Skipping file too small to be a valid FITS file: '{}'".format(
irff_path)
raise errors.UnsupportedType(errMsg)
# actually read the file to get the specified header
header = self.irods.get_header(irff, which_hdu)
if (header):
if (not self.irods.is_image_header(header)):
errMsg = "HDU {} is not an image header. Skipping FITS file '{}'.".format(
which_hdu, irff_path)
raise errors.ProcessingError(errMsg)
# get and save some common file information
file_info = self.irods.get_irods_file_info(irff)
# get additional metadata ABOUT the iRods file itself
irods_metadata = self.irods.get_irods_metadata(irff)
# get any content metadata attached to the file
content_metadata = self.irods.get_content_metadata(irff)
# now try to read the FITS header from the FITS file
hdrs = fits_utils.get_fields_from_header(header, ignore_list)
else: # unable to read the specified header
errMsg = "Unable to read image metadata from HDU {} of FITS file '{}'.".format(
which_hdu, irff_path)
raise errors.ProcessingError(errMsg)
except DataObjectDoesNotExist as dodne:
errMsg = "Unable to find the specified iRods FITS file '{}'.".format(
irff_path)
raise errors.ProcessingError(errMsg)
except OSError as oserr:
errMsg = "Unable to read image metadata from iRods FITS file '{}': {}.".format(
irff_path, oserr)
raise errors.ProcessingError(errMsg)
metadata = dict() # create overall metadata structure
metadata[
'file_info'] = file_info # add previously gathered remote file information
metadata['irods_metadata'] = irods_metadata
metadata['content_metadata'] = content_metadata
if (hdrs is not None):
metadata['headers'] = hdrs # add the headers to the metadata
return metadata # return the results of processing