def check_regular_expression(cls, regex):
'''Checks whether a named regular expression has all required fields.
Parameters
----------
regex: str
regular expression
Raises
------
tmlib.erros.RegexError
when a provided field is not supported
'''
if not regex:
raise RegexError('No regular expression provided.')
provided_fields = re.findall(r'\(\?P\<(\w+)\>', regex)
for name in provided_fields:
if name not in _SUPPORTED__FIELDS:
raise RegexError(
'"%s" is not a supported regular expression field.\n'
'Supported are "%s"' %
(name, '", "'.join(_SUPPORTED__FIELDS)))
for name in _SUPPORTED__FIELDS:
if name not in provided_fields and name in _FIELD_DEFAULTS:
logger.warning(
'regular expression field "%s" not provided, defaults to %s',
name, str(_FIELD_DEFAULTS[name]))
def extract_fields_from_filename(cls, regex, filename, defaults=True):
'''Extracts fields from image filenames using a regular expression.
Parameters
----------
regex: str
regular expression
filename: str
name of a microscope image file
defaults: bool, optional
whether default values should be used
Returns
-------
tmlib.workflow.metaconfig.base.MetadataFields
named tuple with extracted values
'''
r = re.compile(regex)
match = r.search(str(filename))
if match is None:
raise RegexError('Metadata attributes could not be retrieved from '
'filename "%s" using regular expression "%s"' %
(filename, regex))
captures = match.groupdict()
for k in _SUPPORTED__FIELDS:
v = captures.get(k, None)
if v is None:
if defaults:
captures[k] = str(_FIELD_DEFAULTS[k])
else:
captures[k] = v
return MetadataFields(**captures)
def get_bit_depth(pixel_type):
r = re.compile(r'(\d+)$')
m = r.search(pixel_type)
if not m:
raise RegexError(
'Bit depth could not be determined from pixel type.')
return int(m.group(1))
def get_image_ix(image_id):
'''
Get the index of an image within the OMEXML metadata object given the
ID of the image.
Parameters
----------
image_id: str
image identifier in the format ``Image:\d+``
Returns
-------
int
zero-based index number
'''
match = re.search(r'^Image:(\d+)$', image_id)
if not match:
RegexError('Index of image could not be determined from image ID.')
return int(match.group(1))