Catching SITK Warnings

[c-winder]

Hi,

I'm trying to catch warnings thrown by SITK while using tio.ScalarImage(DICOM_DIRECTORY) to read a DICOM series.

The warnings are as follows:
WARNING: In D:\a\1\sitk-build\ITK-prefix\include\ITK-5.3\itkImageSeriesReader.hxx, line 478 ImageSeriesReader (0000016B8C6D7180): Non uniform sampling or missing slices detected, maximum nonuniformity:1112.44

I believe these are thrown by corrupt scans in my dataset, and I would like to catch these warnings so that I can filter such scans from my dataset. Unfortunately this is not as simple as using warnings.filterwarnings("error"), as the error is thrown by C code in SITK and not recognised by Python. Is there a way around this?

[fepegar]

Hi, @c-winder. This is not a TorchIO issue but a SimpleITK issue, but I think you can solve it like this:

import SimpleITK as sitk

sitk.ProcessObject_SetGlobalWarningDisplay(False)
tio.ScalarImage(DICOM_DIRECTORY)
sitk.ProcessObject_SetGlobalWarningDisplay(True)

I guess you could create a context manager:

@contextmanager
def suppress_sitk_warnings():
    display_sitk_warnings = sitk.ProcessObject_GetGlobalWarningDisplay()
    sitk.ProcessObject_SetGlobalWarningDisplay(False)
    yield
    sitk.ProcessObject_SetGlobalWarningDisplay(display_sitk_warnings)

Does that help?

[c-winder]

Hi @fepegar .

Thanks for the suggestion, unfortunately this isn't what I need. I want to catch SimpleITK warnings rather than suppress them.

I managed to get the following working although for some reason it only works if I directly load the image in SimpleITK and later convert it to tio.ScalarImage, which is a bit clunky. Do you know of a better solution?

import pathlib
import torchio as tio
import SimpleITK as sitk
import logging

# from https://simpleitk.readthedocs.io/en/release/link_Logging_docs.html
class SimpleITKLogger(sitk.LoggerBase):
    def __init__(
        self, logger: logging.Logger = logging.getLogger("SimpleITK")
    ):
        """
        Initializes with a Logger object to handle the messages emitted from
        SimpleITK/ITK.
        """
        super(SimpleITKLogger, self).__init__()
        self._logger = logger

    @property
    def logger(self):
        return self._logger

    @logger.setter
    def logger(self, logger):
        self._logger = logger

    def __enter__(self):
        self._old_logger = self.SetAsGlobalITKLogger()
        return self

    def __exit__(self, exc_type, exc_val, exc_tb):
        self._old_logger.SetAsGlobalITKLogger()
        del self._old_logger

    def DisplayText(self, s):
        # Remove newline endings from SimpleITK/ITK messages since the Python
        # logger adds during output.
        self._logger.info(s.rstrip())

    def DisplayErrorText(self, s):
        self._logger.error(s.rstrip())

    def DisplayWarningText(self, s):
        self._logger.warning(s.rstrip())

    def DisplayGenericOutputText(self, s):
        self._logger.info(s.rstrip())

    def DisplayDebugText(self, s):
        self._logger.debug(s.rstrip())

# adapted from https://stackoverflow.com/questions/3290292/read-from-a-log-file-as-its-being-written-using-python  
class SimpleITKLogHandler(logging.Handler):
   """ Class to redistribute python logging data """

    def __init__(
            self,
    ):

        # Initialize the Handler
        logging.Handler.__init__(self)

        # Construct a SimpleITK logger to Python Logger adaptor
        self.sitkLogger = SimpleITKLogger()

        # Configure ITK to use the logger adaptor
        self.sitkLogger.SetAsGlobalITKLogger()

        # make the logger send data to this class
        self.sitkLogger.logger.addHandler(self)

        # initialise empty record
        self.record = None

    def emit(self, record):
        """ Overload of logging.Handler method """
        self.record = record

    def clear_record(self):
        """ Clear existing record """
        self.record = None


# log handler to log warnings from sitk
log_handler = SimpleITKLogHandler()

print('Loading with torchio and attempting to catch warning')

# read scan
tio_scan = tio.ScalarImage(DICOM_DIR)

# check for warning
# if no warning occurred, process scan as usual
if log_handler.record is None:
    print('Scan loaded successfully')
# otherwise, log scan as error
else:
    print('SITK warning occurred')
    print(log_handler.record)
    log_handler.clear_record()

print('------------------')
print('Loading with SITK and attempting to catch warning')
reader = sitk.ImageSeriesReader()

reader.SetFileNames(
    reader.GetGDCMSeriesFileNames(
        str(DICOM_DIR)
    )
)

sitk_scan = reader.Execute()
if log_handler.record is None:
    print('Scan loaded successfully')
# otherwise, log scan as error
else:
    print('SITK warning occurred')
    print(log_handler.record)
    log_handler.clear_record()
    tio_scan = tio.ScalarImage.from_sitk(sitk_scan)

Output:

Loading with torchio and attempting to catch warning
Scan loaded successfully
------------------
Loading with SITK and attempting to catch warning
SITK warning occurred
<LogRecord: SimpleITK, 30, F:\body-comp\Playground\test.py, 53, "WARNING: In D:\a\1\sitk-build\ITK-prefix\include\ITK-5.3\itkImageSeriesReader.hxx, line 478
ImageSeriesReader (00000145F6FA73D0): Non uniform sampling or missing slices detected,  maximum nonuniformity:515.789">