Api qc

def qc(adata,**kwargs):
    '''
    qc
    '''


    if settings.mode == 'gpu':
        print('GPU mode activated')
        return qc_gpu(adata,**kwargs)
    else:
        print('CPU mode activated')
        return qc_cpu(adata,**kwargs)

def store_layers(adata,layers='counts'):
    """
    Store the X of adata in adata.uns['layers_{}'.format(layers)]

    Arguments:
        adata: AnnData
        layers: the layers name to store, default 'counts'
    """


    if issparse(adata.X) and not isspmatrix_csr(adata.X):
        adata.uns['layers_{}'.format(layers)]=anndata.AnnData(csr_matrix(adata.X.copy()),
                                           obs=pd.DataFrame(index=adata.obs.index),
                                          var=pd.DataFrame(index=adata.var.index),)
    elif issparse(adata.X):
        adata.uns['layers_{}'.format(layers)]=anndata.AnnData(adata.X.copy(),
                                           obs=pd.DataFrame(index=adata.obs.index),
                                           var=pd.DataFrame(index=adata.var.index),)
    else:
        adata.uns['layers_{}'.format(layers)]=anndata.AnnData(csr_matrix(adata.X.copy()),
                                           obs=pd.DataFrame(index=adata.obs.index),
                                          var=pd.DataFrame(index=adata.var.index),)
    print('......The X of adata have been stored in {}'.format(layers))

def retrieve_layers(adata,layers='counts'):
    """
    Retrieve the X of adata from adata.uns['layers_{}'.format(layers)]

    Arguments:
        adata: AnnData
        layers: the layers name to retrieve, default 'counts'

    """

    adata_test=adata.uns['layers_{}'.format(layers)].copy()
    adata_test=adata_test[adata.obs.index,adata.var.index]

    if issparse(adata.X) and not isspmatrix_csr(adata.X):
        adata.uns['layers_raw'.format(layers)]=anndata.AnnData(csr_matrix(adata.X.copy()),
                                           obs=pd.DataFrame(index=adata.obs.index),
                                          var=pd.DataFrame(index=adata.var.index),)
    elif issparse(adata.X):
        adata.uns['layers_raw'.format(layers)]=anndata.AnnData(adata.X.copy(),
                                           obs=pd.DataFrame(index=adata.obs.index),
                                           var=pd.DataFrame(index=adata.var.index),)
    else:
        adata.uns['layers_raw'.format(layers)]=anndata.AnnData(csr_matrix(adata.X.copy()),
                                           obs=pd.DataFrame(index=adata.obs.index),
                                          var=pd.DataFrame(index=adata.var.index),)
    print('......The X of adata have been stored in raw')
    adata.X=adata_test.X.copy()
    print('......The layers {} of adata have been retreved'.format(layers))
    del adata_test

def anndata_sparse(adata):
    """
    Set adata.X to csr_matrix

    Arguments:
        adata: AnnData

    Returns:
        adata: AnnData

    """

    from scipy.sparse import csr_matrix
    x = csr_matrix(adata.X.copy())
    adata.X=x
    return adata