Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Make projection task work with zyx data #840

Open
jluethi opened this issue Sep 17, 2024 · 1 comment
Open

Make projection task work with zyx data #840

jluethi opened this issue Sep 17, 2024 · 1 comment

Comments

@jluethi
Copy link
Collaborator

jluethi commented Sep 17, 2024

Currently, the projection task fails when it's given zyx data (e.g. from FAIM-IPA converter) instead of czyx data:

fractal_server.app.runner.exceptions.TaskExecutionError: 2024-09-17 12:09:57,810; INFO; START projection task
2024-09-17 12:09:57,810; INFO; init_args.origin_url='/path/to/001_240815-SB-020-AAB/MD-4x/240815-SB-040-AAB-Reg-10WntCM_out-FractalWeb/240815-SB-040-AAB-Reg-10WntCM_out.zarr/E/04/0'
2024-09-17 12:09:57,810; INFO; zarr_url='/path/to/001_240815-SB-020-AAB/MD-4x/240815-SB-040-AAB-Reg-10WntCM_out-FractalWeb/240815-SB-040-AAB-Reg-10WntCM_out_minip.zarr/E/04/0'
2024-09-17 12:09:57,810; INFO; method=<DaskProjectionMethod.MINIP: 'minip'>
2024-09-17 12:10:00,203; INFO; num_channels=10
2024-09-17 12:10:00,203; INFO; chunksize_y=2048
2024-09-17 12:10:00,203; INFO; chunksize_x=2048
2024-09-17 12:10:02,140; INFO; [build_pyramid] High-resolution path: /path/to/001_240815-SB-020-AAB/MD-4x/240815-SB-040-AAB-Reg-10WntCM_out-FractalWeb/240815-SB-040-AAB-Reg-10WntCM_out_minip.zarr/E/04/0/0
2024-09-17 12:10:02,146; INFO; [build_pyramid] High-resolution data: dask.array<from-zarr, shape=(10, 1, 2048), dtype=uint16, chunksize=(1, 1, 2048), chunktype=numpy.ndarray>
Traceback (most recent call last):
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.3.0/venv/lib/python3.10/site-packages/fractal_tasks_core/tasks/projection.py", line 190, in <module>
    run_fractal_task(
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.3.0/venv/lib/python3.10/site-packages/fractal_tasks_core/tasks/_utils.py", line 79, in run_fractal_task
    metadata_update = task_function(**pars)
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.3.0/venv/lib/python3.10/site-packages/pydantic/validate_call_decorator.py", line 60, in wrapper_function
    return validate_call_wrapper(*args, **kwargs)
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.3.0/venv/lib/python3.10/site-packages/pydantic/_internal/_validate_call.py", line 96, in __call__
    res = self.__pydantic_validator__.validate_python(pydantic_core.ArgsKwargs(args, kwargs))
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.3.0/venv/lib/python3.10/site-packages/fractal_tasks_core/tasks/projection.py", line 113, in projection
    build_pyramid(
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.3.0/venv/lib/python3.10/site-packages/fractal_tasks_core/pyramids.py", line 80, in build_pyramid
    raise ValueError(

cc @silvbarb

@jluethi
Copy link
Collaborator Author

jluethi commented Sep 17, 2024

The multiscales metadata of the corresponding images contains this:

    "multiscales": [
        {
            "axes": [
                {
                    "name": "z",
                    "type": "space",
                    "unit": "micrometer"
                },
                {
                    "name": "y",
                    "type": "space",
                    "unit": "micrometer"
                },
                {
                    "name": "x",
                    "type": "space",
                    "unit": "micrometer"
                }
            ],

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
Development

No branches or pull requests

1 participant