def get_measurements(self, pipeline, object_name, category):
if object_name == cpmeas.IMAGE and category == cpmeas.C_METADATA:
keys = self.get_metadata_keys()
if needs_well_metadata(keys):
keys = list(keys) + [cpmeas.FTR_WELL]
return keys
return []
def get_measurements(self, pipeline, object_name, category):
if object_name == cpmeas.IMAGE and category == cpmeas.C_METADATA:
keys = self.get_metadata_keys()
if needs_well_metadata(keys):
keys = list(keys) + [cpmeas.FTR_WELL]
return keys
return []
def get_measurement_columns(self, pipeline):
"""Get the metadata measurements collected by this module"""
keys = self.get_metadata_keys()
result = [(cpmeas.IMAGE, "_".join((cpmeas.C_METADATA, key)), cpmeas.COLTYPE_VARCHAR_FILE_NAME) for key in keys]
if needs_well_metadata(keys):
result.append((cpmeas.IMAGE, cpmeas.M_WELL, cpmeas.COLTYPE_VARCHAR_FORMAT % 4))
return result
def get_measurement_columns(self, pipeline):
'''Get the metadata measurements collected by this module'''
keys = self.get_metadata_keys()
result = [(cpmeas.IMAGE, '_'.join(
(cpmeas.C_METADATA, key)), cpmeas.COLTYPE_VARCHAR_FILE_NAME)
for key in keys]
if needs_well_metadata(keys):
result.append((cpmeas.IMAGE, cpmeas.M_WELL,
cpmeas.COLTYPE_VARCHAR_FORMAT % 4))
return result
def manually_extract_metadata(self, group, ipd):
if group.source == XM_FILE_NAME:
text = os.path.split(ipd.path)[1]
pattern = group.file_regexp.value
elif group.source == XM_FOLDER_NAME:
text = os.path.split(ipd.path)[0]
pattern = group.folder_regexp.value
else:
return {}
match = re.search(pattern, text)
if match is None:
return {}
result = match.groupdict()
tokens = result.keys()
if needs_well_metadata(tokens):
well_row_token, well_column_token = well_metadata_tokens(tokens)
result[cpmeas.FTR_WELL] = result[well_row_token] + result[well_column_token]
return result
def manually_extract_metadata(self, group, ipd):
if group.source == XM_FILE_NAME:
text = os.path.split(ipd.path)[1]
pattern = group.file_regexp.value
elif group.source == XM_FOLDER_NAME:
text = os.path.split(ipd.path)[0]
pattern = group.folder_regexp.value
else:
return {}
match = re.search(pattern, text)
if match is None:
return {}
result = match.groupdict()
tokens = result.keys()
if needs_well_metadata(tokens):
well_row_token, well_column_token = well_metadata_tokens(tokens)
result[cpmeas.FTR_WELL] = \
result[well_row_token] + result[well_column_token]
return result
