MRC parsing bug in cryodrgn_utils invert_contrast and flip_hand

[zhonge]

$ cryodrgn_utils flip_hand vol_000.mrc -o tmp.mrc
Traceback (most recent call last):
  File "/Users/zhonge/anaconda3/envs/cryodrgn/bin/cryodrgn_utils", line 8, in <module>
    sys.exit(util_commands())
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/command_line.py", line 53, in util_commands
    _get_commands(os.path.join(os.path.dirname(__file__), "commands_utils"))
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/command_line.py", line 43, in _get_commands
    args.func(args)
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/commands_utils/flip_hand.py", line 24, in main
    MRCFile.write(
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/mrc.py", line 260, in write
    header = MRCHeader.make_default_header(
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/mrc.py", line 142, in make_default_header
    dmin, dmax, dmean, rms = data.min(), data.max(), data.mean(), data.std()
AttributeError: 'MRCFileSource' object has no attribute 'min'

$ cryodrgn_utils invert_contrast vol_000.mrc -o tmp.mrc
Traceback (most recent call last):
  File "/Users/zhonge/anaconda3/envs/cryodrgn/bin/cryodrgn_utils", line 8, in <module>
    sys.exit(util_commands())
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/command_line.py", line 53, in util_commands
    _get_commands(os.path.join(os.path.dirname(__file__), "commands_utils"))
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/command_line.py", line 43, in _get_commands
    args.func(args)
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/commands_utils/invert_contrast.py", line 22, in main
    MRCFile.write(args.o, src, transform_fn=lambda data, indices: -data)
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/mrc.py", line 260, in write
    header = MRCHeader.make_default_header(
  File "/Users/zhonge/dev/cryodrgn/cryodrgn/mrc.py", line 142, in make_default_header
    dmin, dmax, dmean, rms = data.min(), data.max(), data.mean(), data.std()
AttributeError: 'MRCFileSource' object has no attribute 'min'

[michal-g]

I was able to reproduce these errors with an MRCFile volume generated by abinit_homo, and both commands worked fine with the ImageSource volumes currently used for testing. This suggests we need to do some deeper cleaning of the MRCFile and ImageSource classes and the code where they are used, but for now I have fixed the behavior in mrc.make_default_header that was causing this behaviour:

        if is_vol:
            if data is None:
                raise ValueError("If is_vol=True, data array must be specified")

            if isinstance(data, (np.ndarray, torch.Tensor)):
                dmin, dmax, dmean, rms = data.min(), data.max(), data.mean(), data.std()
            elif isinstance(data, ImageSource):
                imgdata = data.images()
                dmin = imgdata.min().item()
                dmax = imgdata.max().item()
                dmean = imgdata.mean().item()
                rms = imgdata.std().item()
            else:
                raise TypeError(f"Unrecognized type of data: `{type(data).__name__}`!")

        else:  # use undefined values for image stacks
            dmin, dmax, dmean, rms = -1, -2, -3, -1

I've also added more cases to test_flip_hand and test_invert_contrast that specifically cover this example!

[michal-g]

Aforementioned fixes were included in the v3.2.0 release!