def main():
"""Entry point for the check_model script.
Returns
-------
:class:`int`
An integer suitable for passing to :func:`sys.exit`.
"""
from sys import argv
from argparse import ArgumentParser
desc = """Check actual files against the data model for validity.
"""
parser = ArgumentParser(description=desc, prog=os.path.basename(argv[0]))
parser.add_argument('-d', '--datamodel-dir', dest='desidatamodel',
metavar='DIR',
help='Override the value of DESIDATAMODEL.')
parser.add_argument('-F', '--compare-files', dest='files',
action='store_true',
help='Compare an individual data model to an individual file.')
parser.add_argument('-W', '--warning-is-error', dest='error',
action='store_true',
help='Data model warnings raise exceptions.')
parser.add_argument('-v', '--verbose', dest='verbose', action='store_true',
help='Set log level to DEBUG.')
parser.add_argument('section', metavar='DIR or FILE',
help='Section of the data model or individual model file.')
parser.add_argument('directory', metavar='DIR or FILE',
help='Check files in this top-level directory, or one individual file.')
options = parser.parse_args()
if options.verbose:
log.setLevel(DEBUG)
if 'DESIDATAMODEL' in os.environ:
data_model_root = os.environ['DESIDATAMODEL']
else:
if options.desidatamodel is not None:
data_model_root = options.desidatamodel
else:
log.critical(("DESIDATAMODEL is not defined. " +
"Cannot find data model files!"))
return 1
log.debug("DESIDATAMODEL=%s", data_model_root)
if options.files:
filename = os.path.join(data_model_root, 'doc', options.section)
section = os.path.join(data_model_root, 'doc', options.section.split('/')[0])
log.info("Loading individual data model: %s.", filename)
files = [DataModel(filename, section)]
log.info("Skipping regular expression processing.")
# files[0].get_regexp(options.directory, error=options.error)
log.info("Setting prototype file for %s to %s.", filename, options.directory)
files[0].prototype = options.directory
else:
section = os.path.join(data_model_root, 'doc', options.section)
log.info("Loading data model file in %s.", section)
files = scan_model(section)
log.info("Searching for data files in %s.", options.directory)
files_to_regexp(options.directory, files, error=options.error)
log.info("Identifying prototype files in %s.", options.directory)
collect_files(options.directory, files)
validate_prototypes(files, error=options.error)
return 0
def columns(self, hdu, error=False):
"""Describe the columns of a BINTABLE HDU.
Parameters
----------
hdu : :class:`int`
The HDU number (zero-indexed).
error : :class:`bool`, optional
If ``True``, failure to extract certain required metadata raises an
exception.
Returns
-------
:class:`list`
The rows of the table.
Raises
------
:exc:`~desidatamodel.DataModelError`
If the BINTABLE is actually a compressed image.
:exc:`ValueError`
If `error` and a ``TUNIT`` value does not have FITS-standard
units.
"""
hdr = self.headers[hdu]
if 'ZBITPIX' in hdr:
raise DataModelError(
"HDU{0:d} is actually a compressed image!".format(hdu))
ncol = hdr['TFIELDS']
c = list()
c.append(self.columns_header)
for j in range(ncol):
jj = '{0:d}'.format(j + 1)
name = hdr['TTYPE' + jj].strip()
ttype = fits_column_format(hdr['TFORM' + jj].strip())
tunit = 'TUNIT' + jj
if tunit in hdr:
units = hdr[tunit].strip()
bad_unit = self.check_unit(units, error=error)
if bad_unit:
log.debug(
"Non-standard (but acceptable) unit %s detected for column %s in HDU %d of %s.",
bad_unit, j, hdu, self.filename)
else:
units = ''
# Check TCOMMnn keyword, otherwise use TTYPE comment
# for description.
commkey = 'TCOMM' + jj
if commkey in hdr:
description = escape(hdr[commkey].strip())
else:
description = escape(hdr.comments['TTYPE' + jj])
c.append((name, ttype, units, description))
return c
def columns(self, hdu, error=False):
"""Describe the columns of a BINTABLE HDU.
Parameters
----------
hdu : :class:`int`
The HDU number (zero-indexed).
error : :class:`bool`, optional
If ``True``, failure to extract certain required metadata raises an
exception.
Returns
-------
:class:`list`
The rows of the table.
Raises
------
:exc:`~desidatamodel.DataModelError`
If the BINTABLE is actually a compressed image.
:exc:`ValueError`
If `error` and a ``TUNIT`` value does not have FITS-standard
units.
"""
hdr = self.headers[hdu]
if 'ZBITPIX' in hdr:
raise DataModelError("HDU{0:d} is actually a compressed image!".format(hdu))
ncol = hdr['TFIELDS']
c = list()
c.append(self.columns_header)
for j in range(ncol):
jj = '{0:d}'.format(j+1)
name = hdr['TTYPE'+jj].strip()
ttype = fits_column_format(hdr['TFORM'+jj].strip())
tunit = 'TUNIT'+jj
if tunit in hdr:
units = hdr[tunit].strip()
bad_unit = self.check_unit(units, error=error)
if bad_unit:
log.debug("Non-standard (but acceptable) unit %s detected for column %s in HDU %d of %s.",
bad_unit, j, hdu, self.filename)
else:
units = ''
# Check TCOMMnn keyword, otherwise use TTYPE comment
# for description.
commkey = 'TCOMM'+jj
if commkey in hdr:
description = escape(hdr[commkey].strip())
else:
description = escape(hdr.comments['TTYPE'+jj])
c.append((name, ttype, units, description))
return c
def image_format(self, hdr):
"""Obtain format of an image HDU.
Parameters
----------
hdr : :class:`~astropy.io.fits.Header`
The header to parse.
Returns
-------
:class:`str`
A string describing the image format.
Raises
------
:exc:`~desidatamodel.DataModelError`
If ``self.error`` is set a `BUNIT` header with units that do not
follow the FITS standard is detected.
"""
n = hdr['NAXIS']
if n == 0:
return 'Empty HDU.'
bitmap = {
8: 'char',
16: 'int16',
32: 'int32',
64: 'int64',
-32: 'float32',
-64: 'float64'
}
if 'ZBITPIX' in hdr:
n = hdr['ZNAXIS']
dims = [str(hdr['ZNAXIS{0:d}'.format(k + 1)]) for k in range(n)]
try:
datatype = bitmap[hdr['ZBITPIX']] + ' (compressed)'
except KeyError:
datatype = 'BITPIX={0} (compressed)'.format(hdr['ZBITPIX'])
else:
dims = [str(hdr['NAXIS{0:d}'.format(k + 1)]) for k in range(n)]
try:
datatype = bitmap[hdr['BITPIX']]
except KeyError:
datatype = 'BITPIX={}'.format(hdr['BITPIX'])
if 'BUNIT' in hdr:
log.debug("BUNIT = '%s'", hdr['BUNIT'])
bad_unit = self.check_unit(hdr['BUNIT'], error=self.error)
if bad_unit:
log.debug(
"Non-standard (but acceptable) unit %s detected in %s.",
bad_unit, self.filename)
return 'Data: FITS image [{0}, {1}]'.format(datatype, 'x'.join(dims))
def image_format(self, hdr):
"""Obtain format of an image HDU.
Parameters
----------
hdr : :class:`~astropy.io.fits.Header`
The header to parse.
Returns
-------
:class:`str`
A string describing the image format.
Raises
------
:exc:`~desidatamodel.DataModelError`
If ``self.error`` is set a `BUNIT` header with units that do not
follow the FITS standard is detected.
"""
n = hdr['NAXIS']
if n == 0:
return 'Empty HDU.'
bitmap = {8: 'char', 16: 'int16', 32: 'int32', 64: 'int64',
-32: 'float32', -64: 'float64'}
if 'ZBITPIX' in hdr:
n = hdr['ZNAXIS']
dims = [str(hdr['ZNAXIS{0:d}'.format(k+1)]) for k in range(n)]
try:
datatype = bitmap[hdr['ZBITPIX']] + ' (compressed)'
except KeyError:
datatype = 'BITPIX={0} (compressed)'.format(hdr['ZBITPIX'])
else:
dims = [str(hdr['NAXIS{0:d}'.format(k+1)]) for k in range(n)]
try:
datatype = bitmap[hdr['BITPIX']]
except KeyError:
datatype = 'BITPIX={}'.format(hdr['BITPIX'])
if 'BUNIT' in hdr:
log.debug("BUNIT = '%s'", hdr['BUNIT'])
bad_unit = self.check_unit(hdr['BUNIT'], error=self.error)
if bad_unit:
log.debug("Non-standard (but acceptable) unit %s detected in %s.",
bad_unit, self.filename)
return 'Data: FITS image [{0}, {1}]'.format(datatype, 'x'.join(dims))
def get_regexp(self, root, error=False):
"""Obtain the regular expression used to match files on disk.
Parameters
----------
root : :class:`str`
Path to real files on disk.
error : :class:`bool`, optional
If ``True``, failure to find a regular expression raises an
exception instead of just a warning.
Returns
-------
regular expression
The regular expression found, or ``None`` if not found.
The regular expression is also stored internally.
Raises
------
:exc:`~desimodel.DataModelError`
If `error` is set and problems with the data model file are
detected.
"""
with open(self.filename) as dm:
for line in dm.readlines():
if line.startswith('See :doc:'):
self.ref = self._cross_reference(line)
log.debug("Cross reference detected %s -> %s.",
self.filename, self.ref)
break
if self._regexpline.match(line) is not None:
d = os.path.dirname(self.filename).replace(
self.section, root)
for k in self._d2r:
d = d.replace(k, self._d2r[k])
r = line.strip().split()[1].replace('``', '')
self.regexp = re.compile(os.path.join(d, r))
break
if self.regexp is None and self.ref is not None:
with open(self.ref) as dm:
for line in dm.readlines():
#
# Hopefully cross-references are not nested.
#
# if line.startswith('See :doc:'):
# self.ref = self._cross_reference(line)
# break
if self._regexpline.match(line) is not None:
d = os.path.dirname(self.filename).replace(
self.section, root)
for k in self._d2r:
d = d.replace(k, self._d2r[k])
r = line.strip().split()[1].replace('``', '')
self.regexp = re.compile(os.path.join(d, r))
break
if self.regexp is None:
m = "%s has no file regexp!"
if error:
log.critical(m, self.filename)
raise DataModelError(m % self.filename)
else:
log.warning(m, self.filename)
return self.regexp
def main():
"""Entry point for the check_model script.
Returns
-------
:class:`int`
An integer suitable for passing to :func:`sys.exit`.
"""
from sys import argv
from argparse import ArgumentParser
desc = """Check actual files against the data model for validity.
"""
parser = ArgumentParser(description=desc, prog=os.path.basename(argv[0]))
parser.add_argument('-d',
'--datamodel-dir',
dest='desidatamodel',
metavar='DIR',
help='Override the value of DESIDATAMODEL.')
parser.add_argument(
'-F',
'--compare-files',
dest='files',
action='store_true',
help='Compare an individual data model to an individual file.')
parser.add_argument('-W',
'--warning-is-error',
dest='error',
action='store_true',
help='Data model warnings raise exceptions.')
parser.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
help='Set log level to DEBUG.')
parser.add_argument(
'section',
metavar='DIR or FILE',
help='Section of the data model or individual model file.')
parser.add_argument(
'directory',
metavar='DIR or FILE',
help='Check files in this top-level directory, or one individual file.'
)
options = parser.parse_args()
if options.verbose:
log.setLevel(DEBUG)
if 'DESIDATAMODEL' in os.environ:
data_model_root = os.environ['DESIDATAMODEL']
else:
if options.desidatamodel is not None:
data_model_root = options.desidatamodel
else:
log.critical(("DESIDATAMODEL is not defined. " +
"Cannot find data model files!"))
return 1
log.debug("DESIDATAMODEL=%s", data_model_root)
if options.files:
filename = os.path.join(data_model_root, 'doc', options.section)
section = os.path.join(data_model_root, 'doc',
options.section.split('/')[0])
log.info("Loading individual data model: %s.", filename)
files = [DataModel(filename, section)]
log.info("Skipping regular expression processing.")
# files[0].get_regexp(options.directory, error=options.error)
log.info("Setting prototype file for %s to %s.", filename,
options.directory)
files[0].prototype = options.directory
else:
section = os.path.join(data_model_root, 'doc', options.section)
log.info("Loading data model file in %s.", section)
files = scan_model(section)
log.info("Searching for data files in %s.", options.directory)
files_to_regexp(options.directory, files, error=options.error)
log.info("Identifying prototype files in %s.", options.directory)
collect_files(options.directory, files)
validate_prototypes(files, error=options.error)
return 0
def extract_metadata(self, error=False):
"""Extract metadata from a data model file.
Parameters
----------
error : :class:`bool`, optional
If ``True``, failure to extract certain required metadata raises an
exception.
Returns
-------
:class:`list`
Metadata in a form similar to :class:`~desidatamodel.stub.Stub`
metadata.
Raises
------
:exc:`~desidatamodel.DataModelError`
If `error` is set and the HDU has no `EXTNAME` keyword.
"""
metafile = self.filename
if self.ref is not None:
metafile = self.ref
if self._metafile_data is None:
with open(metafile) as f:
self._metafile_data = f.read()
lines = self._metafile_data.split('\n')
hdu_sections = [
i for i, l in enumerate(lines)
if (self._hduline.match(l) is not None
or self._hduspan.match(l) is not None)
]
self.hdumeta = list()
for k in range(len(hdu_sections)):
try:
section = lines[hdu_sections[k]:hdu_sections[k + 1]]
except IndexError:
section = lines[hdu_sections[k]:]
m = self._hduspan.match(section[0])
if m is not None:
#
# Detected HDU span.
#
g = m.groups()
spanstart = int(g[0])
spanend = int(g[1])
log.debug('Detected range specification from HDU %d to HDU %d',
spanstart, spanend)
spanref = [l for l in section if l.startswith('Data:')][0]
spanext = spanref[spanref.lower().index('see') + 4:].replace(
'.', '')
spanmeta = [
m for m in self.hdumeta if m['extname'] == spanext
][0]
spanname = [
l.split('=')[1].strip() for l in section
if l.startswith('EXTNAME = ')
][0]
extnames = [p.strip() for p in spanname.split(',')]
if len(range(spanstart, spanend + 1)) == len(extnames):
for i, l in enumerate(range(spanstart, spanend + 1)):
meta = dict()
meta['title'] = 'HDU{0:d}'.format(l)
meta['extname'] = extnames[i]
meta['extension'] = spanmeta['extension']
meta['format'] = spanmeta['format']
meta['keywords'] = spanmeta['keywords']
self.hdumeta.append(meta)
else:
log.warning(
('Range specification from HDU %d to HDU %d ' +
'does not have a matching EXTNAME specification'),
spanstart, spanend)
continue
meta = dict()
meta['title'] = section[0]
if 'Empty HDU.' in section:
meta['extension'] = 'IMAGE'
meta['format'] = 'Empty HDU.'
image_data = [l for l in section if l.startswith('Data:')]
if image_data:
meta['extension'] = 'IMAGE'
meta['format'] = image_data[0]
try:
rdtc = section.index('Required Data Table Columns')
except ValueError:
rdtc = None
if rdtc is not None:
meta['extension'] = 'BINTABLE'
table = [
i for i, l in enumerate(section[rdtc:])
if self._tableboundary.match(l) is not None
][1:3]
columns = list(map(len, section[rdtc:][table[0]].split()))
table_lines = section[rdtc:][table[0] + 1:table[1]]
meta['format'] = [
self._extract_columns(t, columns) for t in table_lines
]
for mk in meta['format']:
if not mk[1]:
m = "Missing type for column %s in HDU %d of %s!"
if error:
log.critical(m, mk[0], k, metafile)
raise DataModelError(m % (mk[0], k, metafile))
else:
log.warning(m, mk[0], k, metafile)
if mk[2]:
bad_unit = self.check_unit(mk[2], error=error)
if bad_unit:
log.debug(
"Non-standard (but acceptable) unit %s detected for column %s in HDU %d of %s.",
bad_unit, mk[0], k, metafile)
try:
rhk = section.index('Required Header Keywords')
except ValueError:
meta['keywords'] = []
else:
table = [
i for i, l in enumerate(section[rhk:])
if self._tableboundary.match(l) is not None
][1:3]
columns = list(map(len, section[rhk:][table[0]].split()))
table_lines = section[rhk:][table[0] + 1:table[1]]
meta['keywords'] = [
self._extract_columns(t, columns) for t in table_lines
]
for mk in meta['keywords']:
if not mk[2]:
m = "Missing type for keyword %s in HDU %d of %s!"
if error:
log.critical(m, mk[0], k, metafile)
raise DataModelError(m % (mk[0], k, metafile))
else:
log.warning(m, mk[0], k, metafile)
if mk[0] == 'BUNIT':
bad_unit = self.check_unit(mk[1], error=error)
if bad_unit:
log.debug(
"Non-standard (but acceptable) unit %s detected for column %s in HDU %d of %s.",
bad_unit, mk[0], k, metafile)
#
# Need to know the format by this point!
#
try:
foo = meta['format']
except KeyError:
m = "Unable to determine format for HDU %d in %s!"
log.critical(m, k, metafile)
raise DataModelError(m % (k, metafile))
#
# See https://github.com/desihub/desidatamodel/issues/69 for
# the detailed policy on EXTNAME.
#
try:
meta['extname'] = [
l.split()[2] for l in section if l.startswith('EXTNAME = ')
][0]
except IndexError:
meta['extname'] = ''
if (k > 0 or (k == 0 and meta['format'] != 'Empty HDU.')):
m = "HDU %d in %s has no EXTNAME!"
if error:
log.critical(m, k, metafile)
raise DataModelError(m % (k, metafile))
else:
log.warning(m, k, metafile)
else:
if k == 0 and meta['format'] == 'Empty HDU.':
if len(meta['keywords']) > 0:
m = "HDU %d in %s should have EXTNAME = 'PRIMARY'."
log.warning(m, k, metafile)
else:
#
# If we reach here, meta['extname'] *is* defined.
#
if k == 0:
if meta['format'] == 'Empty HDU.':
if len(meta['keywords']
) > 0 and meta['extname'] != 'PRIMARY':
m = "HDU %d in %s has acceptable alternative EXTNAME = '%d'."
log.debug(m, k, metafile, meta['extname'])
else:
if meta['extname'] == 'PRIMARY':
m = "HDU %d in %s should have a more meaningful EXTNAME than 'PRIMARY'."
log.warning(m, k, metafile)
self.hdumeta.append(meta)
return self.hdumeta
def get_regexp(self, root, error=False):
"""Obtain the regular expression used to match files on disk.
Parameters
----------
root : :class:`str`
Path to real files on disk.
error : :class:`bool`, optional
If ``True``, failure to find a regular expression raises an
exception instead of just a warning.
Returns
-------
regular expression
The regular expression found, or ``None`` if not found.
The regular expression is also stored internally.
Raises
------
:exc:`~desimodel.DataModelError`
If `error` is set and problems with the data model file are
detected.
"""
with open(self.filename) as dm:
for line in dm.readlines():
if line.startswith('See :doc:'):
self.ref = self._cross_reference(line)
log.debug("Cross reference detected %s -> %s.",
self.filename, self.ref)
break
if self._regexpline.match(line) is not None:
d = os.path.dirname(self.filename).replace(self.section,
root)
for k in self._d2r:
d = d.replace(k, self._d2r[k])
r = line.strip().split()[1].replace('``', '')
self.regexp = re.compile(os.path.join(d, r))
break
if self.regexp is None and self.ref is not None:
with open(self.ref) as dm:
for line in dm.readlines():
#
# Hopefully cross-references are not nested.
#
# if line.startswith('See :doc:'):
# self.ref = self._cross_reference(line)
# break
if self._regexpline.match(line) is not None:
d = os.path.dirname(self.filename).replace(self.section,
root)
for k in self._d2r:
d = d.replace(k, self._d2r[k])
r = line.strip().split()[1].replace('``', '')
self.regexp = re.compile(os.path.join(d, r))
break
if self.regexp is None:
m = "%s has no file regexp!"
if error:
log.critical(m, self.filename)
raise DataModelError(m % self.filename)
else:
log.warning(m, self.filename)
return self.regexp
def extract_metadata(self, error=False):
"""Extract metadata from a data model file.
Parameters
----------
error : :class:`bool`, optional
If ``True``, failure to extract certain required metadata raises an
exception.
Returns
-------
:class:`list`
Metadata in a form similar to :class:`~desidatamodel.stub.Stub`
metadata.
Raises
------
:exc:`~desidatamodel.DataModelError`
If `error` is set and the HDU has no `EXTNAME` keyword.
"""
metafile = self.filename
if self.ref is not None:
metafile = self.ref
if self._metafile_data is None:
with open(metafile) as f:
self._metafile_data = f.read()
lines = self._metafile_data.split('\n')
hdu_sections = [i for i, l in enumerate(lines)
if (self._hduline.match(l) is not None or
self._hduspan.match(l) is not None)]
self.hdumeta = list()
for k in range(len(hdu_sections)):
try:
section = lines[hdu_sections[k]:hdu_sections[k+1]]
except IndexError:
section = lines[hdu_sections[k]:]
m = self._hduspan.match(section[0])
if m is not None:
#
# Detected HDU span.
#
g = m.groups()
spanstart = int(g[0])
spanend = int(g[1])
log.debug('Detected range specification from HDU %d to HDU %d',
spanstart, spanend)
spanref = [l for l in section if l.startswith('Data:')][0]
spanext = spanref[spanref.lower().index('see') + 4:].replace('.', '')
spanmeta = [m for m in self.hdumeta if m['extname'] == spanext][0]
spanname = [l.split('=')[1].strip() for l in section
if l.startswith('EXTNAME = ')][0]
extnames = [p.strip() for p in spanname.split(',')]
if len(range(spanstart, spanend+1)) == len(extnames):
for i, l in enumerate(range(spanstart, spanend+1)):
meta = dict()
meta['title'] = 'HDU{0:d}'.format(l)
meta['extname'] = extnames[i]
meta['extension'] = spanmeta['extension']
meta['format'] = spanmeta['format']
meta['keywords'] = spanmeta['keywords']
self.hdumeta.append(meta)
else:
log.warning(('Range specification from HDU %d to HDU %d ' +
'does not have a matching EXTNAME specification'),
spanstart, spanend)
continue
meta = dict()
meta['title'] = section[0]
if 'Empty HDU.' in section:
meta['extension'] = 'IMAGE'
meta['format'] = 'Empty HDU.'
image_data = [l for l in section if l.startswith('Data:')]
if image_data:
meta['extension'] = 'IMAGE'
meta['format'] = image_data[0]
try:
rdtc = section.index('Required Data Table Columns')
except ValueError:
rdtc = None
if rdtc is not None:
meta['extension'] = 'BINTABLE'
table = [i for i, l in enumerate(section[rdtc:])
if self._tableboundary.match(l) is not None][1:3]
columns = list(map(len, section[rdtc:][table[0]].split()))
table_lines = section[rdtc:][table[0]+1:table[1]]
meta['format'] = [self._extract_columns(t, columns)
for t in table_lines]
for mk in meta['format']:
if not mk[1]:
m = "Missing type for column %s in HDU %d of %s!"
if error:
log.critical(m, mk[0], k, metafile)
raise DataModelError(m % (mk[0], k, metafile))
else:
log.warning(m, mk[0], k, metafile)
if mk[2]:
bad_unit = self.check_unit(mk[2], error=error)
if bad_unit:
log.debug("Non-standard (but acceptable) unit %s detected for column %s in HDU %d of %s.",
bad_unit, mk[0], k, metafile)
try:
rhk = section.index('Required Header Keywords')
except ValueError:
meta['keywords'] = []
else:
table = [i for i, l in enumerate(section[rhk:])
if self._tableboundary.match(l) is not None][1:3]
columns = list(map(len, section[rhk:][table[0]].split()))
table_lines = section[rhk:][table[0]+1:table[1]]
meta['keywords'] = [self._extract_columns(t, columns)
for t in table_lines]
for mk in meta['keywords']:
if not mk[2]:
m = "Missing type for keyword %s in HDU %d of %s!"
if error:
log.critical(m, mk[0], k, metafile)
raise DataModelError(m % (mk[0], k, metafile))
else:
log.warning(m, mk[0], k, metafile)
if mk[0] == 'BUNIT':
bad_unit = self.check_unit(mk[1], error=error)
if bad_unit:
log.debug("Non-standard (but acceptable) unit %s detected for column %s in HDU %d of %s.",
bad_unit, mk[0], k, metafile)
#
# Need to know the format by this point!
#
try:
foo = meta['format']
except KeyError:
m = "Unable to determine format for HDU %d in %s!"
log.critical(m, k, metafile)
raise DataModelError(m % (k, metafile))
#
# See https://github.com/desihub/desidatamodel/issues/69 for
# the detailed policy on EXTNAME.
#
try:
meta['extname'] = [l.split()[2] for l in section
if l.startswith('EXTNAME = ')][0]
except IndexError:
meta['extname'] = ''
if (k > 0 or (k == 0 and meta['format'] != 'Empty HDU.')):
m = "HDU %d in %s has no EXTNAME!"
if error:
log.critical(m, k, metafile)
raise DataModelError(m % (k, metafile))
else:
log.warning(m, k, metafile)
else:
if k == 0 and meta['format'] == 'Empty HDU.':
if len(meta['keywords']) > 0:
m = "HDU %d in %s should have EXTNAME = 'PRIMARY'."
log.warning(m, k, metafile)
else:
if k == 0:
if meta['format'] == 'Empty HDU.':
if len(meta['keywords']) > 0:
m = "HDU %d in %s should have EXTNAME = 'PRIMARY'."
log.warning(m, k, metafile)
else:
if meta['extname'] == 'PRIMARY':
m = "HDU %d in %s should have a more meaningful EXTNAME than 'PRIMARY'."
log.warning(m, k, metafile)
self.hdumeta.append(meta)
return self.hdumeta
def load_zbest(datapath=None, hdu='ZBEST', q3c=False):
"""Load zbest files into the zcat table.
This function is deprecated since there should now be a single
redshift catalog file.
Parameters
----------
datapath : :class:`str`
Full path to the directory containing zbest files.
hdu : :class:`int` or :class:`str`, optional
Read a data table from this HDU (default 'ZBEST').
q3c : :class:`bool`, optional
If set, create q3c index on the table.
"""
if datapath is None:
datapath = specprod_root()
zbestpath = os.path.join(datapath, 'spectra-64', '*', '*',
'zbest-64-*.fits')
log.info("Using zbest file search path: %s.", zbestpath)
zbest_files = glob.glob(zbestpath)
if len(zbest_files) == 0:
log.error("No zbest files found!")
return
log.info("Found %d zbest files.", len(zbest_files))
#
# Read the identified zbest files.
#
for f in zbest_files:
brickname = os.path.basename(os.path.dirname(f))
with fits.open(f) as hdulist:
data = hdulist[hdu].data
log.info("Read data from %s HDU %s.", f, hdu)
good_targetids = ((data['TARGETID'] != 0) & (data['TARGETID'] != -1))
#
# If there are too many targetids, the in_ clause will blow up.
# Disabling this test, and crossing fingers.
#
# q = dbSession.query(ZCat).filter(ZCat.targetid.in_(data['TARGETID'].tolist())).all()
# if len(q) != 0:
# log.warning("Duplicate TARGETID found in %s.", f)
# for z in q:
# log.warning("Duplicate TARGETID = %d.", z.targetid)
# good_targetids = good_targetids & (data['TARGETID'] != z.targetid)
data_list = [data[col][good_targetids].tolist() for col in data.names]
data_names = [col.lower() for col in data.names]
log.info("Initial column conversion complete on brick = %s.",
brickname)
#
# Expand COEFF
#
col = 'COEFF'
expand = (
'coeff_0',
'coeff_1',
'coeff_2',
'coeff_3',
'coeff_4',
'coeff_5',
'coeff_6',
'coeff_7',
'coeff_8',
'coeff_9',
)
i = data_names.index(col.lower())
del data_names[i]
del data_list[i]
for j, n in enumerate(expand):
log.debug("Expanding column %d of %s (at index %d) to %s.", j, col,
i, n)
data_names.insert(i + j, n)
data_list.insert(i + j, data[col][:, j].tolist())
log.debug(data_names)
#
# zbest files don't contain the same columns as zcatalog.
#
for col in ZCat.__table__.columns:
if col.name not in data_names:
data_names.append(col.name)
data_list.append([0] * len(data_list[0]))
data_rows = list(zip(*data_list))
log.info("Converted columns into rows on brick = %s.", brickname)
try:
dbSession.bulk_insert_mappings(
ZCat, [dict(zip(data_names, row)) for row in data_rows])
except IntegrityError as e:
log.error("Integrity Error detected!")
log.error(e)
dbSession.rollback()
else:
log.info("Inserted %d rows in %s for brick = %s.", len(data_rows),
ZCat.__tablename__, brickname)
dbSession.commit()
if q3c:
q3c_index('zcat')
return
def load_file(filepath,
tcls,
hdu=1,
expand=None,
convert=None,
index=None,
rowfilter=None,
q3c=False,
chunksize=50000,
maxrows=0):
"""Load a data file into the database, assuming that column names map
to database column names with no surprises.
Parameters
----------
filepath : :class:`str`
Full path to the data file.
tcls : :class:`sqlalchemy.ext.declarative.api.DeclarativeMeta`
The table to load, represented by its class.
hdu : :class:`int` or :class:`str`, optional
Read a data table from this HDU (default 1).
expand : :class:`dict`, optional
If set, map FITS column names to one or more alternative column names.
convert : :class:`dict`, optional
If set, convert the data for a named (database) column using the
supplied function.
index : :class:`str`, optional
If set, add a column that just counts the number of rows.
rowfilter : callable, optional
If set, apply this filter to the rows to be loaded. The function
should return :class:`bool`, with ``True`` meaning a good row.
q3c : :class:`bool`, optional
If set, create q3c index on the table.
chunksize : :class:`int`, optional
If set, load database `chunksize` rows at a time (default 50000).
maxrows : :class:`int`, optional
If set, stop loading after `maxrows` are loaded. Alteratively,
set `maxrows` to zero (0) to load all rows.
"""
tn = tcls.__tablename__
if filepath.endswith('.fits'):
with fits.open(filepath) as hdulist:
data = hdulist[hdu].data
elif filepath.endswith('.ecsv'):
data = Table.read(filepath, format='ascii.ecsv')
else:
log.error("Unrecognized data file, %s!", filepath)
return
if maxrows == 0:
maxrows = len(data)
log.info("Read data from %s HDU %s", filepath, hdu)
try:
colnames = data.names
except AttributeError:
colnames = data.colnames
for col in colnames:
if data[col].dtype.kind == 'f':
bad = np.isnan(data[col][0:maxrows])
if np.any(bad):
nbad = bad.sum()
log.warning(
"%d rows of bad data detected in column " + "%s of %s.",
nbad, col, filepath)
#
# Temporary workaround for bad flux values, see
# https://github.com/desihub/desitarget/issues/397
#
if col in ('FLUX_R', 'FIBERFLUX_R', 'FIBERTOTFLUX_R'):
data[col][0:maxrows][bad] = -9999.0
log.info("Integrity check complete on %s.", tn)
if rowfilter is None:
good_rows = np.ones((maxrows, ), dtype=np.bool)
else:
good_rows = rowfilter(data[0:maxrows])
data_list = [data[col][0:maxrows][good_rows].tolist() for col in colnames]
data_names = [col.lower() for col in colnames]
finalrows = len(data_list[0])
log.info("Initial column conversion complete on %s.", tn)
if expand is not None:
for col in expand:
i = data_names.index(col.lower())
if isinstance(expand[col], str):
#
# Just rename a column.
#
log.debug("Renaming column %s (at index %d) to %s.",
data_names[i], i, expand[col])
data_names[i] = expand[col]
else:
#
# Assume this is an expansion of an array-valued column
# into individual columns.
#
del data_names[i]
del data_list[i]
for j, n in enumerate(expand[col]):
log.debug("Expanding column %d of %s (at index %d) to %s.",
j, col, i, n)
data_names.insert(i + j, n)
data_list.insert(i + j, data[col][:, j].tolist())
log.debug(data_names)
log.info("Column expansion complete on %s.", tn)
del data
if convert is not None:
for col in convert:
i = data_names.index(col)
data_list[i] = [convert[col](x) for x in data_list[i]]
log.info("Column conversion complete on %s.", tn)
if index is not None:
data_list.insert(0, list(range(1, finalrows + 1)))
data_names.insert(0, index)
log.info("Added index column '%s'.", index)
data_rows = list(zip(*data_list))
del data_list
log.info("Converted columns into rows on %s.", tn)
for k in range(finalrows // chunksize + 1):
data_chunk = [
dict(zip(data_names, row))
for row in data_rows[k * chunksize:(k + 1) * chunksize]
]
if len(data_chunk) > 0:
engine.execute(tcls.__table__.insert(), data_chunk)
log.info("Inserted %d rows in %s.",
min((k + 1) * chunksize, finalrows), tn)
# for k in range(finalrows//chunksize + 1):
# data_insert = [dict([(col, data_list[i].pop(0))
# for i, col in enumerate(data_names)])
# for j in range(chunksize)]
# session.bulk_insert_mappings(tcls, data_insert)
# log.info("Inserted %d rows in %s..",
# min((k+1)*chunksize, finalrows), tn)
# session.commit()
# dbSession.commit()
if q3c:
q3c_index(tn)
return
def load_zbest(datapath=None, hdu='ZBEST', q3c=False):
"""Load zbest files into the zcat table.
This function is deprecated since there should now be a single
redshift catalog file.
Parameters
----------
datapath : :class:`str`
Full path to the directory containing zbest files.
hdu : :class:`int` or :class:`str`, optional
Read a data table from this HDU (default 'ZBEST').
q3c : :class:`bool`, optional
If set, create q3c index on the table.
"""
if datapath is None:
datapath = specprod_root()
zbestpath = os.path.join(datapath, 'spectra-64', '*', '*', 'zbest-64-*.fits')
log.info("Using zbest file search path: %s.", zbestpath)
zbest_files = glob.glob(zbestpath)
if len(zbest_files) == 0:
log.error("No zbest files found!")
return
log.info("Found %d zbest files.", len(zbest_files))
#
# Read the identified zbest files.
#
for f in zbest_files:
brickname = os.path.basename(os.path.dirname(f))
with fits.open(f) as hdulist:
data = hdulist[hdu].data
log.info("Read data from %s HDU %s.", f, hdu)
good_targetids = ((data['TARGETID'] != 0) & (data['TARGETID'] != -1))
#
# If there are too many targetids, the in_ clause will blow up.
# Disabling this test, and crossing fingers.
#
# q = dbSession.query(ZCat).filter(ZCat.targetid.in_(data['TARGETID'].tolist())).all()
# if len(q) != 0:
# log.warning("Duplicate TARGETID found in %s.", f)
# for z in q:
# log.warning("Duplicate TARGETID = %d.", z.targetid)
# good_targetids = good_targetids & (data['TARGETID'] != z.targetid)
data_list = [data[col][good_targetids].tolist()
for col in data.names]
data_names = [col.lower() for col in data.names]
log.info("Initial column conversion complete on brick = %s.", brickname)
#
# Expand COEFF
#
col = 'COEFF'
expand = ('coeff_0', 'coeff_1', 'coeff_2', 'coeff_3', 'coeff_4',
'coeff_5', 'coeff_6', 'coeff_7', 'coeff_8', 'coeff_9',)
i = data_names.index(col.lower())
del data_names[i]
del data_list[i]
for j, n in enumerate(expand):
log.debug("Expanding column %d of %s (at index %d) to %s.", j, col, i, n)
data_names.insert(i + j, n)
data_list.insert(i + j, data[col][:, j].tolist())
log.debug(data_names)
#
# zbest files don't contain the same columns as zcatalog.
#
for col in ZCat.__table__.columns:
if col.name not in data_names:
data_names.append(col.name)
data_list.append([0]*len(data_list[0]))
data_rows = list(zip(*data_list))
log.info("Converted columns into rows on brick = %s.", brickname)
try:
dbSession.bulk_insert_mappings(ZCat, [dict(zip(data_names, row))
for row in data_rows])
except IntegrityError as e:
log.error("Integrity Error detected!")
log.error(e)
dbSession.rollback()
else:
log.info("Inserted %d rows in %s for brick = %s.",
len(data_rows), ZCat.__tablename__, brickname)
dbSession.commit()
if q3c:
q3c_index('zcat')
return
def load_file(filepath, tcls, hdu=1, expand=None, convert=None, index=None,
rowfilter=None, q3c=False, chunksize=50000, maxrows=0):
"""Load a data file into the database, assuming that column names map
to database column names with no surprises.
Parameters
----------
filepath : :class:`str`
Full path to the data file.
tcls : :class:`sqlalchemy.ext.declarative.api.DeclarativeMeta`
The table to load, represented by its class.
hdu : :class:`int` or :class:`str`, optional
Read a data table from this HDU (default 1).
expand : :class:`dict`, optional
If set, map FITS column names to one or more alternative column names.
convert : :class:`dict`, optional
If set, convert the data for a named (database) column using the
supplied function.
index : :class:`str`, optional
If set, add a column that just counts the number of rows.
rowfilter : callable, optional
If set, apply this filter to the rows to be loaded. The function
should return :class:`bool`, with ``True`` meaning a good row.
q3c : :class:`bool`, optional
If set, create q3c index on the table.
chunksize : :class:`int`, optional
If set, load database `chunksize` rows at a time (default 50000).
maxrows : :class:`int`, optional
If set, stop loading after `maxrows` are loaded. Alteratively,
set `maxrows` to zero (0) to load all rows.
"""
tn = tcls.__tablename__
if filepath.endswith('.fits'):
with fits.open(filepath) as hdulist:
data = hdulist[hdu].data
elif filepath.endswith('.ecsv'):
data = Table.read(filepath, format='ascii.ecsv')
else:
log.error("Unrecognized data file, %s!", filepath)
return
if maxrows == 0:
maxrows = len(data)
log.info("Read data from %s HDU %s", filepath, hdu)
try:
colnames = data.names
except AttributeError:
colnames = data.colnames
for col in colnames:
if data[col].dtype.kind == 'f':
bad = np.isnan(data[col][0:maxrows])
if np.any(bad):
nbad = bad.sum()
log.warning("%d rows of bad data detected in column " +
"%s of %s.", nbad, col, filepath)
#
# Temporary workaround for bad flux values, see
# https://github.com/desihub/desitarget/issues/397
#
if col in ('FLUX_R', 'FIBERFLUX_R', 'FIBERTOTFLUX_R'):
data[col][0:maxrows][bad] = -9999.0
log.info("Integrity check complete on %s.", tn)
if rowfilter is None:
good_rows = np.ones((maxrows,), dtype=np.bool)
else:
good_rows = rowfilter(data[0:maxrows])
data_list = [data[col][0:maxrows][good_rows].tolist() for col in colnames]
data_names = [col.lower() for col in colnames]
finalrows = len(data_list[0])
log.info("Initial column conversion complete on %s.", tn)
if expand is not None:
for col in expand:
i = data_names.index(col.lower())
if isinstance(expand[col], str):
#
# Just rename a column.
#
log.debug("Renaming column %s (at index %d) to %s.", data_names[i], i, expand[col])
data_names[i] = expand[col]
else:
#
# Assume this is an expansion of an array-valued column
# into individual columns.
#
del data_names[i]
del data_list[i]
for j, n in enumerate(expand[col]):
log.debug("Expanding column %d of %s (at index %d) to %s.", j, col, i, n)
data_names.insert(i + j, n)
data_list.insert(i + j, data[col][:, j].tolist())
log.debug(data_names)
log.info("Column expansion complete on %s.", tn)
del data
if convert is not None:
for col in convert:
i = data_names.index(col)
data_list[i] = [convert[col](x) for x in data_list[i]]
log.info("Column conversion complete on %s.", tn)
if index is not None:
data_list.insert(0, list(range(1, finalrows+1)))
data_names.insert(0, index)
log.info("Added index column '%s'.", index)
data_rows = list(zip(*data_list))
del data_list
log.info("Converted columns into rows on %s.", tn)
for k in range(finalrows//chunksize + 1):
data_chunk = [dict(zip(data_names, row))
for row in data_rows[k*chunksize:(k+1)*chunksize]]
if len(data_chunk) > 0:
engine.execute(tcls.__table__.insert(), data_chunk)
log.info("Inserted %d rows in %s.",
min((k+1)*chunksize, finalrows), tn)
# for k in range(finalrows//chunksize + 1):
# data_insert = [dict([(col, data_list[i].pop(0))
# for i, col in enumerate(data_names)])
# for j in range(chunksize)]
# session.bulk_insert_mappings(tcls, data_insert)
# log.info("Inserted %d rows in %s..",
# min((k+1)*chunksize, finalrows), tn)
# session.commit()
# dbSession.commit()
if q3c:
q3c_index(tn)
return
