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Error using images2zarr.convert_all #6

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nosound2 opened this issue Aug 19, 2019 · 0 comments
Open

Error using images2zarr.convert_all #6

nosound2 opened this issue Aug 19, 2019 · 0 comments

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@nosound2
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Can't figure out how to use images2zarr conversion. I get the following error, I guess it is related to packages versions but I am not sure what is required

dask==2.3.0
zarr==2.3.2


TypeError Traceback (most recent call last)
in
----> 1 images2zarr.convert_all(str(PATH), str(Path('D:/recursion')), str(PATH))

C:\StudioProjects\Recursion\rxrx1-utils\rxrx\preprocess\images2zarr.py in convert_all(raw_images, dest_path, metadata)
43 sites = metadata_df[['dataset', 'experiment', 'plate', 'well', 'site']].to_dict(orient='rows')
44 bag = dask.bag.from_sequence(sites)
---> 45 bag.map(convert_to_zarr(raw_images, dest_path)).compute()
46
47

~\Anaconda3\envs\fastai\lib\site-packages\dask\base.py in compute(self, **kwargs)
154 This turns a lazy Dask collection into its in-memory equivalent.
155 For example a Dask.array turns into a :func:numpy.array and a Dask.dataframe
--> 156 turns into a Pandas dataframe. The entire dataset must fit into memory
157 before calling this operation.
158

~\Anaconda3\envs\fastai\lib\site-packages\dask\base.py in compute(*args, **kwargs)
393
394 Parameters
--> 395 ----------
396 args : object
397 Any number of objects. If it is a dask object, it's computed and the

~\Anaconda3\envs\fastai\lib\site-packages\dask\multiprocessing.py in get(dsk, keys, num_workers, func_loads, func_dumps, optimize_graph, **kwargs)
189 loads = func_loads or config.get("func_loads", None) or _loads
190 dumps = func_dumps or config.get("func_dumps", None) or _dumps
--> 191
192 # Note former versions used a multiprocessing Manager to share
193 # a Queue between parent and workers, but this is fragile on Windows

~\Anaconda3\envs\fastai\lib\site-packages\dask\local.py in get_async(apply_async, num_workers, dsk, result, cache, get_id, rerun_exceptions_locally, pack_exception, raise_exception, callbacks, dumps, loads, **kwargs)
492 res, worker_id = loads(res_info)
493 state["cache"][key] = res
--> 494 finish_task(dsk, key, state, results, keyorder.get)
495 for f in posttask_cbs:
496 f(key, res, dsk, state, worker_id)

TypeError: init() missing 3 required positional arguments: 'node_def', 'op', and 'message'

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