Source code for ibllib.atlas.genes

import logging
from pathlib import Path

import numpy as np
import pandas as pd

from import md5
import as aws

from ibllib.atlas.atlas import AllenAtlas

_logger = logging.getLogger(__name__)

[docs]def allen_gene_expression(filename='gene-expression.pqt', folder_cache=None): """ Reads in the Allen gene expression experiments binary data. :param filename: :param folder_cache: :return: a dataframe of experiments, where each record correspond to a single gene expression and a memmap of all experiments volumes, size (4345, 58, 41, 67) corresponding to (nexperiments, ml, dv, ap). The spacing between slices is 200 um """ OLD_MD5 = [] DIM_EXP = (4345, 58, 41, 67) folder_cache = folder_cache or AllenAtlas._get_cache_dir().joinpath(filename) file_parquet = Path(folder_cache).joinpath('gene-expression.pqt') file_bin = file_parquet.with_suffix(".bin") if not file_parquet.exists() or md5(file_parquet) in OLD_MD5: file_parquet.parent.mkdir(exist_ok=True, parents=True)'downloading gene expression data from {aws.S3_BUCKET_IBL} s3 bucket...') aws.s3_download_file(f'atlas/{}', file_parquet) aws.s3_download_file(f'atlas/{}', file_bin) df_genes = pd.read_parquet(file_parquet) gexp_all = np.memmap(file_bin, dtype=np.float16, mode='r', offset=0, shape=DIM_EXP) return df_genes, gexp_all