API to load detector data with mask #518
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| @@ -1102,6 +1191,12 @@ | |||
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| return arr | |||
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| class XtdfMaskedKeyData(DetectorMaskedKeyData, XtdfImageMultimodKeyData): | |||
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Code scanning / CodeQL
Missing call to `__init__` during object initialization Error
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I believe this is a false positive caused by CodeQL not fully understanding super() with multiple inheritance. The __init__ method is inherited from DetectorMaskedKeyData, which does call super().__init__(...). That calls the next __init__ in the method resolution order - not just the parent class - so when it's creating an XtdfMaskedKeyData, it will find XtdfImageMultimodKeyData.__init__().
In [2]: XtdfMaskedKeyData.__mro__
Out[2]:
(extra_data.components.XtdfMaskedKeyData,
extra_data.components.DetectorMaskedKeyData,
extra_data.components.XtdfImageMultimodKeyData,
extra_data.components.MultimodKeyData,
object)
I usually avoid multiple inheritance because even if it works, it's a pain to think about stuff like this. In this instance, I started writing the masked KeyData classes as wrappers around the existing classes (has-a relationships rather than is-a), but it was going to be several times more code to provide the same methods and attributes again. So I decided using inheritance was the lesser of two evils.
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| return out | |||
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| def xarray(self, *, fill_value=None, roi=(), astype=None): | |||
| def _wrap_xarray(self, arr): | |||
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Code scanning / CodeQL
Mismatch between signature and use of an overridden method Note
takluyver
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| @@ -176,6 +177,31 @@ def __init__(self, data: DataCollection, detector_name=None, modules=None, | |||
| def __getitem__(self, item): | |||
| return MultimodKeyData(self, item) | |||
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| def masked_data(self, key=None, *, mask_bits=None, masked_value=np.nan): | |||
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Since bit logic is not generally intuitive for pragmatic programmers, allowing to pass bad pixel bits by iterable may be nice here as well.
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That makes sense. I guess we should also expose the bad pixel flags somewhere - I don't think we have those at the moment. Maybe they belong in extra.calibration ?
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Definitely, EXtra was the intended target for some time now. extra.calibration makes sense given it's used in calibration data.
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Just to record here, I opened European-XFEL/EXtra#172 to do that.
extra_data/components.py
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| The replacement value to use for masked data. By default this is NaN. | ||
| """ | ||
| key = key or self._main_data_key | ||
| self[self._mask_data_key] # Check that the mask is there |
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I would maybe raise a more explicit error message here if that happens.
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This continues the KeyData pattern, so you can do:
Which is equivalent to: