tiledbsoma.io.get_experiment_shapes¶

tiledbsoma.io.get_experiment_shapes(uri: str, *, context: SOMATileDBContext | None = None) → dict[str, Any]¶

Returns the current shapes of the elements in the Experiment.

Similar to show_experiment_shapes but returns a nested Python dict.

Returns the non_empty_domain, domain, and maxdomain of dataframes and the non_empty_domain, shape, and maxshape of arrays as a dictionary. This method is applied to the following elements inside the SOMA Experiment:

The shapes of the following elements are output:

the obs dataframe in the experiment,

and for each measurement:

the var dataframe,

all X arrays,

all obsm arrays,

all varm arrays,

all obsp arrays,

all varm arrays,

all varp arrays.

Example:

>>> tiledbsoma.io.get_experiment_shapes('pbmc3k_unprocessed')

{
    "obs": {
        "uri": "exp/obs",
        "type": "DataFrame",
        "count": 2700,
        "non_empty_domain": ((0, 2699),),
        "domain": ((0, 2699),),
        "maxdomain": ((0, 2147483646),),
        "upgraded": False,
    },
    "ms": {
        "RNA": {
            "var": {
                "uri": "exp/ms/RNA/var",
                "type": "DataFrame",
                "count": 13714,
                "non_empty_domain": ((0, 13713),),
                "domain": ((0, 13713),),
                "maxdomain": ((0, 2147483646),),
                "upgraded": False,
            },
            "X": {
                "data": {
                    "uri": "exp/ms/RNA/X/data",
                    "type": "SparseNDArray",
                    "non_empty_domain": ((0, 2699), (0, 13713)),
                    "shape": (2700, 13714),
                    "maxshape": (2147483646, 2147483646),
                    "upgraded": False,
                }
            },
        }
    },
}

Parameters:

uri – The URI of a SOMA Experiment.
context – Optional SOMATileDBContext.
output_handle – The handle to print the output to.

Returns: a nested Python dict.