mirror of
https://github.com/chanzuckerberg/cellxgene.git
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711f3b7048
* initial cut at backed mode * make flask multithreading conditional on debug flag * update X access to support backed mode * lint * improve help message for backed mode * fix tests * add MatrixProxy to normalize supported matrix types * add FAQ entry for --backed * remove use of matrix.T * clean up * add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user * fix tests * do not print diffexp speed warning if diffexp is disabled * tweak wording of diffexp speed messages * add FAQ entry on --disable-diffexp * revise heuristic for warning about slow diffexp * use quick tooltip delay on diffexp button
43 lines
1.4 KiB
Python
43 lines
1.4 KiB
Python
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from server.app.util.matrix_proxy import MatrixProxyView, ArrayProxyView
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"""
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AnnData/h5py are inconsistent in the API supported by various types of
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X matrices. Sometimes you get a fully ndarray, sometims a Scipy sparse
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matrix, sometimes h5py proxies with a subset of our needed interfaces.
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This glue code paves over all of that, providing the core set of methods
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that the cellxgene ScanPy driver assumes are in existance. Put another
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way, all of the non-portable assumptions are here.
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"""
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class ArrayProxyView_anndata_h5py(ArrayProxyView):
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"""
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override to handle sparse getitem semantics, which differ
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from numpy.
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"""
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def toarray(self):
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""" sadly, sparse indexing doesn't drop dimensions like numpy! """
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arr = self.m[self._index[0], self._index[1]]
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if self._vdim == 0:
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arr = arr.transpose()
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return arr.toarray()[0]
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class MatrixProxy_anndata_h5py(MatrixProxyView):
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"""
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AnnData sparse array stored in H5AD, or proxies for backed data.
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None of these handle indexing very well, so we plop a proxy on top.
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"""
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@classmethod
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def __supports__(cls):
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return ("anndata.h5py.h5sparse.SparseDataset",
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"anndata.h5py.h5sparse.backed_csc_matrix",
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"anndata.h5py.h5sparse.backed_csr_matrix",
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"h5py._hl.dataset.Dataset")
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@classmethod
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def create_array(cls, *args, **kwargs):
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return ArrayProxyView_anndata_h5py(*args, **kwargs)
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