diff --git a/combine.py b/combine.py new file mode 100644 index 0000000000000000000000000000000000000000..753b50b01bcf6f83ec741b9cc753064165f047a6 --- /dev/null +++ b/combine.py @@ -0,0 +1,25 @@ +import dask.array as da +import os +from zarr_tools.convert import to_zarr +import fire + +def combine(BF_zarr_2D_path:str, TRITC_zarr_3D_path:str, out_zarr_path:str): + bd2d = da.from_zarr(os.path.join(BF_zarr_2D_path,'0/')) + print('Opened BF:', bd2d) + fd3d = da.from_zarr(os.path.join(TRITC_zarr_3D_path,'0/')) + print('Opened TRITC:', fd3d) + fd2d = fd3d.max(axis=1) + bd2d = da.stack([bd2d, fd2d], axis=1) + print('Resulting stack:', bd2d) + to_zarr( + bd2d, + path=out_zarr_path, + steps=4, + name=['BF','TRITC'], + colormap=['gray','orange'], + lut=((1000,30000),(440, 600)), + ) + +# combine(snakemake.input[0], snakemake.input[1], snakemake.output[0]) +if __name__ == "__main__": + fire.Fire(combine) \ No newline at end of file