Adding support for reading only chunks and various pieces of the H5Py lower level interface#5
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bnlawrence merged 29 commits intomasterfrom Jul 9, 2024
Merged
Adding support for reading only chunks and various pieces of the H5Py lower level interface#5bnlawrence merged 29 commits intomasterfrom
bnlawrence merged 29 commits intomasterfrom
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…ven't got any tests around this yet.
…changes to actually using the filter pipeline. At this point is failling test_reference.
…lso remove list definition which breaks references.
… a pseudo chunked read. Lots of things to do around optimising that read, but let's test this more widely first.
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first set of review comments @bnlawrence - mostly very minor stuff 😁 )review stopped at h5d.py)
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Done with the review @bnlawrence - really awesome stuff here! I think we should approach this in a structured manner:
- get this PR in your main fork's
master(after you've done whatever changes you think need be done from my review - I can also help with a re-review at the very end) - crack open a PR from your fork to the main Pyfive repo - provided that all tests pass, and we write a very descriptive PR note (that can also go in their docs - which they don't really have, but that would be a good start)
- offer me and/or you and/or @davidhassell as maintainers of their package - on conda-feedstock (so we get our men in the loop)
- offer you as Pyfive core dev (or whatever they call it, main developer etc)
- note that they may complain about the Zarr module we lift and shift - we ought to think about that
Cheers and have fun Swifting 🤣
| from .indexing import OrthogonalIndexer, ZarrArrayStub | ||
| from .btree import BTreeV1RawDataChunks | ||
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| StoreInfo = namedtuple('StoreInfo',"chunk_offset filter_mask byte_offset size") |
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| StoreInfo = namedtuple('StoreInfo',"chunk_offset filter_mask byte_offset size") | |
| StoreInfo = namedtuple('StoreInfo', "chunk_offset filter_mask byte_offset size") |
| if self.filter_pipeline is not None: | ||
| chunk_buffer = BTreeV1RawDataChunks._filter_chunk(chunk_buffer, filter_mask, self.filter_pipeline, self.dtype.itemsize) | ||
| chunk_data = np.frombuffer(chunk_buffer, dtype=self.dtype) | ||
| out[out_selection] = chunk_data.reshape(self._chunks, order=self._order)[chunk_selection] |
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this was giving us plenty of headaches in PyActive - I'd definitely encase it in a few try/excepts with plenty of descriptive exceptions
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I think this should be much safer in here. I'd like it to die very publicly if it does.
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The key changes are the introduction of a subclass of DataObjects which represents a singleton variable DataObject, and a new H5D class which provides the lower level chunk interface. Arguably these two classes could be combined.