Source code for pacfish.qualitycontrol.CompletenessChecker
# SPDX-FileCopyrightText: 2021 International Photoacoustics Standardisation Consortium (IPASC)
# SPDX-FileCopyrightText: 2021 Janek Gröhl
# SPDX-FileCopyrightText: 2021 Lina Hacker
# SPDX-License-Identifier: BSD 3-Clause License
from pacfish import MetadataAcquisitionTags
from pacfish import MetadataDeviceTags
from pacfish import MetaDatum
[docs]class CompletenessChecker:
"""
Tests a given AcquisitionMetadata dictionary or a given DeviceMetadata dictionary
for completeness.
For these purposes, the check_acquisition_meta_data and check_device_meta_data methods can be used::
pa_data = #TODO load pa_data here
cc = CompletenessChecker(verbose=True)
acquisition_metadata_complete = cc.check_acquisition_meta_data(pa_data.meta_data_acquisition)
device_metadata_complete = cc.check_device_meta_data(pa_data.meta_data_device)
"""
def __init__(self, verbose: bool = False, log_file_path: str = None):
"""
Parameters
----------
verbose: bool
A flag to indicate whether the log should be printed to the console.
log_file_path: str
A string with the path to where the log file should be written to.
If 'None', then no log file is written.
"""
self.save_file_name = "logfile.md"
self.verbose = verbose
self.log_file_path = log_file_path
[docs] def check_acquisition_meta_data(self, meta_data_dictionary: dict) -> bool:
"""
This function will evaluate the completeness of the given acquisition metadata.
It can be used to generate a report to the console by setting `verbose`
to True. When setting a file path to log_file, it will also save the
report as a txt file in the designated path.
Parameters
----------
meta_data_dictionary: dict
A dictionary containing all acquisition meta data.
Raises
------
ValueError:
if meta_data_dictionary was None
TypeError:
if one of the arguments ws not of the correct type
Return
------
bool
True, if the meta_data_dictionary is complete
"""
# Input data validation
if meta_data_dictionary is None:
raise ValueError("the field meta_data_dictionary must not be None!")
if not isinstance(meta_data_dictionary, dict):
raise TypeError("The field meta_data_dictionary was not of " +
"type dict")
# Creation of the completenes report
incompletenes_count = 0
log_string = "#Completeness Report\n\n"
log_string += "##Acquisition Meta Data\n\n"
for metadatum in MetadataAcquisitionTags.TAGS:
[log, count] = CompletenessChecker.check_metadatum_from_dict(meta_data_dictionary, metadatum)
incompletenes_count += count
log_string += log
log_string += "## Result\n\n"
log_string += (str(incompletenes_count) + " metadata fields were "
"found to be incomplete or missing.\n\n")
if incompletenes_count > 0:
log_string += "The metadata dictionary is incomplete\n"
else:
log_string += "The metadata dictionary is complete\n"
# Reporting of the results
if self.verbose:
print(log_string)
if self.log_file_path is not None:
with open(self.log_file_path + self.save_file_name, "a") as log_file_handle:
log_file_handle.writelines(log_string)
return incompletenes_count == 0
[docs] def check_device_meta_data(self, device_meta_data: dict):
"""
This function will evaluate the completeness of the given device metadata.
It can be used to generate a report to the console by setting `verbose`
to True. When setting a file path to log_file, it will also save the
report as a txt file in the designated path.
Parameters
----------
device_meta_data: dict
A dictionary containing all device meta data.
Raises
------
ValueError:
if meta_data_dictionary was None
TypeError:
if one of the arguments ws not of the correct type
Return
------
bool
True, if the meta_data_dictionary is complete
"""
incompletenes_count = 0
# Input data validation
if device_meta_data is None:
raise ValueError("the field device_meta_data must not be None!")
if not isinstance(device_meta_data, dict):
raise TypeError("The field device_meta_data was not of type dict")
log_string = "#Device Metadata Completeness Report\n\n"
log_string += "##General information\n\n"
general_tags = [MetadataDeviceTags.UNIQUE_IDENTIFIER, MetadataDeviceTags.FIELD_OF_VIEW]
if MetadataDeviceTags.GENERAL.tag not in device_meta_data:
log_string += "General device meta data is missing!\n\n"
incompletenes_count += len(general_tags)
else:
for general_meta_datum in general_tags:
[log, count] = CompletenessChecker.check_metadatum_from_dict(
device_meta_data[MetadataDeviceTags.GENERAL.tag], general_meta_datum)
log_string += log
incompletenes_count += count
log_string += "##Detection Elements\n\n"
detection_tags = [MetadataDeviceTags.DETECTOR_GEOMETRY, MetadataDeviceTags.DETECTOR_ORIENTATION,
MetadataDeviceTags.DETECTOR_POSITION, MetadataDeviceTags.FREQUENCY_RESPONSE,
MetadataDeviceTags.ANGULAR_RESPONSE]
if MetadataDeviceTags.DETECTORS.tag not in device_meta_data:
log_string += "Detection elements data is missing!\n\n"
incompletenes_count += len(detection_tags)
else:
log_string += ("Found " + str(len(device_meta_data[MetadataDeviceTags.DETECTORS.tag])) +
" detection elements.\n\n")
for detector_dict in device_meta_data[MetadataDeviceTags.DETECTORS.tag]:
log_string += ("Now analyzing detector element \"" +
detector_dict + "\"\n\n")
for detector_meta_datum in detection_tags:
[log, count] = CompletenessChecker.check_metadatum_from_dict(
device_meta_data[MetadataDeviceTags.DETECTORS.tag][detector_dict], detector_meta_datum)
log_string += log
incompletenes_count += count
log_string += "##Illumination Elements\n\n"
illumination_tags = [MetadataDeviceTags.ILLUMINATOR_GEOMETRY, MetadataDeviceTags.ILLUMINATOR_ORIENTATION,
MetadataDeviceTags.ILLUMINATOR_POSITION, MetadataDeviceTags.WAVELENGTH_RANGE,
MetadataDeviceTags.BEAM_ENERGY_PROFILE, MetadataDeviceTags.PULSE_WIDTH,
MetadataDeviceTags.BEAM_STABILITY_PROFILE, MetadataDeviceTags.BEAM_INTENSITY_PROFILE,
MetadataDeviceTags.BEAM_DIVERGENCE_ANGLES]
if MetadataDeviceTags.ILLUMINATORS.tag not in device_meta_data:
log_string += "Illumination elements data is missing!\n\n"
incompletenes_count += len(illumination_tags)
else:
log_string += ("Found " + str(len(device_meta_data[MetadataDeviceTags.ILLUMINATORS.tag])) +
" illumination elements.\n\n")
for illuminator_dict in device_meta_data[MetadataDeviceTags.ILLUMINATORS.tag]:
log_string += ("Now analyzing illumination element \"" +
illuminator_dict + "\"\n\n")
for illuminator_meta_datum in illumination_tags:
[log, count] = CompletenessChecker.check_metadatum_from_dict(
device_meta_data[MetadataDeviceTags.ILLUMINATORS.tag][illuminator_dict], illuminator_meta_datum)
log_string += log
incompletenes_count += count
log_string += "## Result\n\n"
log_string += (str(incompletenes_count) + " metadata fields were "
"found to be incomplete or missing.\n\n")
if incompletenes_count > 0:
log_string += "The metadata dictionary is incomplete!\n"
else:
log_string += "The metadata dictionary is complete.\n"
if self.verbose:
print(log_string)
if self.log_file_path is not None:
with open(self.log_file_path + self.save_file_name, "a") as log_file_handle:
log_file_handle.writelines(log_string)
return incompletenes_count == 0
[docs] @staticmethod
def check_metadatum_from_dict(dictionary: dict, metadatum: MetaDatum):
"""
Internal method to systematically test a metadata field.
Parameters
----------
dictionary: dict
The dictionary supposedly containing the metadatum at the top level
metadatum: MetaDatum
The metadatum to test
Return
------
(str, int)
A tuple with the log string and an integer that is 0 if everything was fine and
1 if there was an error.
"""
log_string = ""
count = 0
if metadatum.tag not in dictionary:
log_string += "* missing entry \"" + metadatum.tag + "\"\n"
log_string += " * metadatum not found in dictionary\n\n"
count += 1
elif dictionary[metadatum.tag] is None:
log_string += "* missing entry \"" + metadatum.tag + "\"\n"
log_string += " * metadatum found in dictionary\n"
log_string += " * but the mapped field was None\n\n"
count += 1
elif not isinstance(dictionary[metadatum.tag], metadatum.dtype):
log_string += "* corrupt entry \"" + metadatum.tag + "\"\n"
log_string += " * metadatum found in dictionary\n"
log_string += " * and the mapped field was not None\n"
log_string += (" * but the mapped field was not of type " +
str(metadatum.dtype) + "\n\n")
count += 1
return [log_string, count]