U mdb@sdZddlZddlZddlZddlZddlmZddlm Z ddl m Z ddl m Z ddlmZmZddlmZmZdd lmZmZmZmZmZmZmZddlZdd lmZdd lm Z dd l!m"Z"m#Z$dd l%m&Z&ddl'm(Z(ddl)m*Z*ddl+m,Z,ddl-m.Z/ddl0m1Z1GdddeZ2e2j3Z4ede5ej6fZ7dZ8ddZ9eee:fee;dddZdbee;d#d$d%Z?ee;d#d&d'Z@d(d)ZAd*d+ZBe"edeCfeCd,d-d.ZDdcd/d0ZEddd1d2ZFdee"e;e;e,d5eGee5d6d7d8ZHd9d:ZIdfdd?ZKd@dAZLejMe5dBdCdDZNdgee;efee;efee;efdEdFdGZOeejMe jPfdHdIdJZQdhdMdNZRdidOdPZSdjejMe5e5eejMejMfdQdRdSZTdkejMe5e5eejMejMfdTdUdVZUe dWdXdYZVdZd[ZWd\d]ZXGd^d_d_ZYd`daZZdS)lzUtility functions and classes This file largely consists of the old _utils.py file. Over time, these functions should be moved of this file. N)Enum)Path)WeakSet) namedtuple)partialwraps) ModuleType MethodType)UnionCallableOptionalMappingAnyDictTuple)random)sparse)AnnData __version__)dedent)version)settings)Literal)logging) is_constantc@seZdZdZdS)EmptyrN)__name__ __module__ __qualname__tokenr"r"O/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/_utils/__init__.pyr srgV瞯=0.6.10, not z). 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Parameters ---------- adata prediction Field name of adata.obs. reference Field name of adata.obs. normalization Whether to normalize with respect to the predicted groups or the reference groups. threshold Do not consider associations whose overlap is below this fraction. max_n_names Control how many reference names you want to be associated with per predicted name. Set to `None`, if you want all. 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T)Z return_countscs g|]\}}||qSr"r"r@rn) pred_dictsub_pred_countsr"r#rx|sz#identify_groups..cs g|]\}}|qSr"r"r)ref_dict ref_labelrr"r#rxsr)ZaxisNrc)runiquedictrrZc_minr)Z ref_labelsZ pred_labelsZreturn_overlapsZ ref_uniqueZ ref_countsZ pred_uniqueZ pred_countsZassociated_predictionsZassociated_overlapsZsub_pred_uniqueZrelative_overlaps_predZrelative_overlaps_refZrelative_overlapsZrelative_overlaps_minZpred_best_indexr")rrrrr#identify_groupsas2    rcCs |dS)z-Transform string annotations to categoricals.N) _sanitizer|r"r"r#rsrcCs&|jr"tjddd||dS)Nz-Received a view of an AnnData. Making a copy.r)rR)Zis_viewrSrWZ_init_as_actualrrr"r"r#view_to_actuals r)arcCsDtj|td}||d|d| ||d<||dd|S)a-Moving average over one-dimensional array. Parameters ---------- a One-dimensional array. n Number of entries to average over. n=2 means averaging over the currrent the previous entry. 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Returns ------- Xsampled Subsampled X. rows Indices of rows that are stored in Xsampled. rzn must be greater 0F)rreplace)rrrrrchoice)rrrrrr"r"r#rbs $r)rcCs"|sddlm}|||dS)z,Check if file is present otherwise download.r) _downloadN)is_fileZ readwriter)rZ backup_urlrr"r"r#check_presence_downloads rcCsZz tj|WStk rTtj|}tj|}tj|j}| ||YSXdS)uDImports a module in a way that it’s only executed on member accessN) rmodulesr importlibutil find_specmodule_from_spec LazyLoaderloader exec_module)Z full_namespecmodulerr"r"r# lazy_imports    rcCs8|dkr||kr||}|dkr0||kr0||}||fSror")dctZconnsdistsZ conns_keyZ dists_keyr"r"r#_fallback_to_unss r c@s*eZdZdZd ddZddZddZdS) NeighborsViewaConvenience class for accessing neighbors graph representations. Allows to access neighbors distances, connectivities and settings dictionary in a uniform manner. Parameters ---------- adata AnnData object. key This defines where to look for neighbors dictionary, connectivities, distances. neigh = NeighborsView(adata, key) neigh['distances'] neigh['connectivities'] neigh['params'] 'connectivities' in neigh 'params' in neigh is the same as adata.obsp[adata.uns[key]['distances_key']] adata.obsp[adata.uns[key]['connectivities_key']] adata.uns[key]['params'] adata.uns[key]['connectivities_key'] in adata.obsp 'params' in adata.uns[key] NcCsd|_d|_|dks|dkrHd|jkr.td|jd|_d|_d|_n>||jkrbtd|d|j||_|jd|_|jd|_|j|jkr|j|j|_|j|jkr|j|j|_t|j|j|j|j|j\|_|_dS) N neighborszNo "neighbors" in .unsconnectivities distancesNo "z " in .unsZconnectivities_keyZ distances_key) _connectivities _distancesrr_neighbors_dict _conns_key _dists_keyobspr )selfr|rr"r"r#r1s0        zNeighborsView.__init__cCs^|dkr(d|kr"td|jd|jS|dkrPd|krJtd|jd|jS|j|SdS)Nrrz " in .obspr )rrrrrrrrr"r"r# __getitem__szNeighborsView.__getitem__cCs2|dkr|jdk S|dkr$|jdk S||jkSdS)Nrr )rrrrr"r"r# __contains__s   zNeighborsView.__contains__)N)rrr r0r1rrr"r"r"r#r s  r cCsP|dk r|dk rtd|dk r*|j|St||}d|krDtd|dSdS)zs    $        $      Y 3    , .  +  S