Fix a bug of parsing channel validity #59
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nd2reader/raw_metadata.py
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| @@ -139,11 +139,15 @@ def _process_channels_metadata(self, metadata): | |||
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| def _get_channel_validity_list(self, metadata): | |||
| try: | |||
| validity = self.image_metadata[six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][0][ | |||
| six.b('ppNextLevelEx')][six.b('')][0][six.b('pItemValid')] | |||
| validity = self.image_metadata[six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][ | |||
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Identical blocks of code found in 2 locations. Consider refactoring.
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I am not sure if it makes sense to refactor it. Please advise me if I need to try to remove this duplication. For readability, it may make sense to keep the current state.
nd2reader/raw_metadata.py
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| # If none of the channels have been deleted, there is no validity list, so we just make one | ||
| validity = [True for _ in metadata] | ||
| try: | ||
| validity = self.image_metadata[six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][0][ |
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Identical blocks of code found in 2 locations. Consider refactoring.
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Hej Hayato, thanks for the PR. I'm only a contributor here and I am thus unable to approve or merge PRs. @rbnvrw would be the best for that :) |
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Hi, thank you so much for the PR. This package is no longer actively developed because I'm no longer working in this field and due to various personal reasons, I can't properly maintain it any longer. If you'd like to help and become a maintainer, please reach out to me @ggirelli @hayatoikoma |
This PR fixes the bug of parsing channel validity and also adds a support of another (probably, newer) metadata format.
The sample nd2 data downloaded from OME in the unit test was not correctly parsed, and the
_get_channel_validity_listwas returning[True, True, True, True, True, True, True]although the data has only 5 channels. Additionally, the metadata didn't have the unnecessary array format in the metadata, which made it falling back to theexceptstatement much earlier than it should. This bug actually didn't allow us to read an image with more than 7 channels. I assumed that the unnecessary array format was used in older nd2 files, and I kept the original try statement.I wasn't sure how you are assuring the order of
validityis alined withsorted(metadata[six.b('sPlaneNew')].items()in_process_channels_metadata. As you have some comments for this sorting, I left as it is. Would you advise me if I need to touch here?I didn't add a unit test for this fix because most unit tests seems to be using an artificially generated nd2 data. I can try to add something in
test_parser.pyif necessary.Thanks for making this awesome library!