pythonwarningssimpleitk

How to catch SimpleITK warnings?


I am loading a volume from a dicom folder

import SimpleITK as sitk
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(input_dir)
reader.SetFileNames(dicom_names)
image = reader.Execute()

, and I am getting the following warning. Is it possible to catch this warning?

WARNING: In d:\a\1\work\b\itk-prefix\include\itk-5.1\itkImageSeriesReader.hxx, line 480
ImageSeriesReader (000002C665417450): Non uniform sampling or missing slices detected,  maximum nonuniformity:292.521

I have tried the solutions from this question and it does not work. Is it because the warning message is coming from the C code?


Solution

  • As the warning generated from C++ code cannot be caught in python, I came up with a workaround/hack, which does not depend on a warning object. The solution is based on redirecting sys.stderr of the code that can generate a warning to a file and checking the file for the "warning" keyword.

    The context manager code based on this answer.

    import sys
    from contextlib import contextmanager
    
    def flush(stream):
        try:
            libc.fflush(None)
            stream.flush()
        except (AttributeError, ValueError, IOError):
            pass  # unsupported
    
    
    def fileno(file_or_fd):
        fd = getattr(file_or_fd, 'fileno', lambda: file_or_fd)()
        if not isinstance(fd, int):
            raise ValueError("Expected a file (`.fileno()`) or a file descriptor")
        return fd
    
    
    @contextmanager
    def stdout_redirected(to=os.devnull, stdout=None):
        if stdout is None:
           stdout = sys.stdout
    
        stdout_fd = fileno(stdout)
        # copy stdout_fd before it is overwritten
        # Note: `copied` is inheritable on Windows when duplicating a standard stream
        with os.fdopen(os.dup(stdout_fd), 'wb') as copied:
            # stdout.flush()  # flush library buffers that dup2 knows nothing about
            # stdout.flush() does not flush C stdio buffers on Python 3 where I/O is
            # implemented directly on read()/write() system calls. To flush all open C stdio
            # output streams, you could call libc.fflush(None) explicitly if some C extension uses stdio-based I/O:
            flush(stdout)
            try:
                os.dup2(fileno(to), stdout_fd)  # $ exec >&to
            except ValueError:  # filename
                with open(to, 'wb') as to_file:
                    os.dup2(to_file.fileno(), stdout_fd)  # $ exec > to
            try:
                yield stdout  # allow code to be run with the redirected stdout
            finally:
                # restore stdout to its previous value
                # Note: dup2 makes stdout_fd inheritable unconditionally
                # stdout.flush()
                flush(stdout)
                os.dup2(copied.fileno(), stdout_fd)  # $ exec >&copied
    

    Detecting warning generated by the C++ code:

    import SimpleITK as sitk
    
    with open('output.txt', 'w') as f, stdout_redirected(f, stdout=sys.stderr):
        reader = sitk.ImageSeriesReader()
        dicom_names = reader.GetGDCMSeriesFileNames(input_dir)
        reader.SetFileNames(dicom_names)
        image = reader.Execute()
    
    with open('output.txt') as f:
        content = f.read()
    if "warning" in content.lower():
        raise RuntimeError('SimpleITK Warning!')