I am using n5-zarr 1.5.1 which is zarr v2.
I have an image series, xyzct and I am writing chunks (w, h, d, 1, 1). I save an image, (32, 32, 32, 2, 2) to a new zarr but translated in 2 time steps in the time frame, then the result is a broken zarr. When I load it with fiji : file->import->n5/zarr I get a (32, 32, 32, 2, 2) image, but it is all zeros.
However, if I save a second (32, 32, 32, 2, 2) image translated 4 steps then it works correctly. When I import it I get an image (32, 32, 32, 2, 6) the first two frames are empty. The next four frames have the expected data.
What appears to be happening, in the .zarray file the shape is recorded as 2, 2, 32, 32, 32 when it should be (4, 2, 32, 32, 32). If I edit the file and make that change then when I load the image it works as expected. The first two time points are black and the 3 and 4 time points are the values I assigned.
I can make a complete example, but maybe this has already been fixed. Also, for my use case I write more than one time and then the shape is calculated correctly.
Cheers.
I am using n5-zarr 1.5.1 which is zarr v2.
I have an image series, xyzct and I am writing chunks (w, h, d, 1, 1). I save an image, (32, 32, 32, 2, 2) to a new zarr but translated in 2 time steps in the time frame, then the result is a broken zarr. When I load it with fiji : file->import->n5/zarr I get a (32, 32, 32, 2, 2) image, but it is all zeros.
However, if I save a second (32, 32, 32, 2, 2) image translated 4 steps then it works correctly. When I import it I get an image (32, 32, 32, 2, 6) the first two frames are empty. The next four frames have the expected data.
What appears to be happening, in the .zarray file the shape is recorded as 2, 2, 32, 32, 32 when it should be (4, 2, 32, 32, 32). If I edit the file and make that change then when I load the image it works as expected. The first two time points are black and the 3 and 4 time points are the values I assigned.
I can make a complete example, but maybe this has already been fixed. Also, for my use case I write more than one time and then the shape is calculated correctly.
Cheers.