gerlichlab / looptrace

Fork (from EMBL Gitlab) of the looptrace project: https://git.embl.de/grp-ellenberg/looptrace
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Pass nothing for the `images_folder` for the `ImageHandler` creation for bead ROI generation #219

Open vreuter opened 5 months ago

vreuter commented 5 months ago

All that's gotten from ImageHandler is the path for the bead ROIs folder and the number of timepoints (by the length of the frame_name list from the config file. Instead, for each FOV, this length could be gotten from the array that's the value of the "shape" key in a .zarray file (1 for each FOV). Example:

P0001.zarr/0/.zarray
{
    "chunks": [
        1,
        1,
        1,
        2044,
        2048
    ],
    "compressor": {
        "blocksize": 0,
        "clevel": 5,
        "cname": "zstd",
        "id": "blosc",
        "shuffle": 2
    },
    "dimension_separator": "/",
    "dtype": "<u2",
    "fill_value": 0,
    "filters": null,
    "order": "C",
    "shape": [
        61,
        2,
        38,
        2044,
        2048
    ],
    "zarr_format": 2
}
vreuter commented 5 months ago

Note also that this metadata is available for each FOV, and therefore would work nicely even if we ultimately entirely parallelise across FOV (#75 )