U vId3 @s^ddlZddlmZddlmZddlmZddlmZddl m Z m Z m Z m Z mZddl mZmZmZddlZddlZddlZddlmZd d lmZd d lmZd d lmZd d lm Z m!Z!m"Z"d dl#m$Z$ddl%m&Z&m'Z'm(Z(m)Z)m*Z*ddl+m,Z,m-Z-ddl.m/Z/e dZ0deide ee1feee1eddddZ2e(eifddZ3e e1efededddZ4d8dej5dd e e1efe ede6dfee1e ej7e8ed!d"d#Z9d9d$d%e ej:efee1e ej;gej7fee1ed)d*d+Z?ej>d)d,d-Z@e'ej;d.d/d0ZAe'ej;ej7e8d1d2d3ZBd:d4d5ZCd;d6d7ZDdS)<N)partial)warn)Path)MappingProxyType)CallableTypeTypeVarUnionLiteral) CollectionSequenceMapping)sparse) SparseDataset)AnnDataFileManager)AnnData)_from_fixed_length_strings_decode_structured_array _clean_uns)read_dispatched)H5PY_V3report_read_key_on_errorreport_write_key_on_erroridx_chunks_along_axis_read_legacy_raw) read_elem write_elem)OldFormatWarningT)as_densedataset_kwargs)filepathadatar"r#returnc Ksddlm}t|tr|g}d|kr:t|}d||d<tdd|DrTtdd|krn|jdkrnt d| |jdk r| |jj ||}t |}|j rd nd }|j r|jt||}|d }|jd d |jddd|kr"t|jtjtfr"t|d|j|dn.|j r>t |jt |ksPt|d|j|dd|krt|jjtjtfrt|d|jj|dt|d|jj |dt|dt|jj|dn|jdk rt|d|j|dt|d|j|dt|d|j |dt|dt|j|dt|dt|j|dt|dt|j|dt|dt|j |dt|dt|j!|dt|dt|j"|dW5QRXdS)Nr)write_dispatchedraw.Xraw/Xcss|]}|dkVqdS)Xr)Nr!).0valr!r!I/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/anndata/_io/h5ad.py 3szwrite_h5ad..zBCurrently, only `X` and `raw/X` are supported values in `as_dense`u>Cannot specify writing `raw/X` to dense if it doesn’t exist.aw/ encoding-typeanndatazencoding-versionz0.1.0r+)r#zraw/varzraw/varmrawobsvarobsmvarmobspvarplayersuns)#Zanndata.experimentalr' isinstancestrlistindexanyNotImplementedErrorr5 ValueErrorZstrings_to_categoricalsr7rZisbackedfilecloseh5pyFileattrs setdefaultr+rspmatrixrwrite_sparse_as_densefilenamerdictr9r6r8r:r;r<r=)r$r%r"r#kwargsr'modefr!r!r. write_h5ad$sn       rRcCsd}||krPt|tjtjtfrJ|jj|jjkrJ|}tdd| d}n||=|j |f|j |j d|}t t|tj}t|j |dD]}||||<q|dk r||=||||<||=dS)Nz(.*)(\w(?!.*/))z\1_\2r2)shapedtypei)r>rGGroupDatasetrrErMresubrstripZcreate_datasetrSrTintr csc_matrixrZtoarray)rQkeyvaluer#Zreal_keyZdsetZcompressed_axisidxr!r!r.rLfs" rL)rr+)rMrPr&cst||d}t||ddddddg}dd g}d jkrF||n"|D]}|krJt|||<qJ|fd d |Dtd dhd |d<tf|}t dtj rt ||S)N)rMfilemoder8r9r:r;r=r<r6r7r3cs"i|]}|kr|t|qSr!)rr,krQr!r. sz$read_h5ad_backed..rIr5) rNrGrHrIextendread_dataframeupdate _read_rawrr>rVr)rMrPd attributesZ df_attributesrcr%r!rdr.read_h5ad_backed}s     rmp) as_sparse as_sparse_fmt chunk_size)rMbackedrorprqr&c s.|dkr.|}|dkrd}|dks$tt||S|tjtjfkrFtdttrXgntt t D].}|dkrd|<ql|dkrltd qlt t ||d t |d ntd fd d td}dkrtft}|j|_||_tdt jr t|W5QRX|S)ad Read `.h5ad`-formatted hdf5 file. Parameters ---------- filename File name of data file. backed If `'r'`, load :class:`~anndata.AnnData` in `backed` mode instead of fully loading it into memory (`memory` mode). If you want to modify backed attributes of the AnnData object, you need to choose `'r+'`. Currently, `backed` only support updates to `X`. That means any changes to other slots like `obs` will not be written to disk in `backed` mode. If you would like save changes made to these slots of a `backed` :class:`~anndata.AnnData`, write them to a new file (see :meth:`~anndata.AnnData.write`). For an example, see [here] (https://anndata-tutorials.readthedocs.io/en/latest/getting-started.html#Partial-reading-of-large-data). as_sparse If an array was saved as dense, passing its name here will read it as a sparse_matrix, by chunk of size `chunk_size`. as_sparse_fmt Sparse format class to read elements from `as_sparse` in as. chunk_size Used only when loading sparse dataset that is stored as dense. 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