Reaching maximum recursion depth while loading zarr file
FIrgolitsch opened this issue · 9 comments
Hello,
I've created a zarr file where I stored a 4D image (2-channel 3D image) and written a label inside the zarr file using the write_labels function. Afterwards when I try to load the image, and list its nodes, I get an error message saying it has reached maximum recursion depth. When I look at the nodes that are in the reader object I find the final two entries to be this:
<path>/S23.zarr/labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/ [zgroup]
<path>/S23.zarr/labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/ [zgroup]
It seems that when it reaches the mask node, it tries to go back to the original image path using ../../ which I set in the metadata using the source property as per the example in section 2.6 of the NGFF specification. What could be causing this recursion issue? I have had it working before and I am unsure why it would start to recursively load the same nodes.
This is the metadata of the labels file:
{
"image-label": {
"colors": [
{
"label-value": 0,
"rgba": [
0,
0,
0,
0
]
},
{
"label-value": 1,
"rgba": [
0,
255,
0,
64
]
}
],
"source": {
"image": "../../"
},
"version": "0.4"
},
"multiscales": [
{
"axes": [
{
"name": "z",
"type": "space",
"unit": "micrometer"
},
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
],
"datasets": [
{
"coordinateTransformations": [
{
"scale": [
6.5,
6.5,
6.5
],
"type": "scale"
}
],
"path": "0"
},
{
"coordinateTransformations": [
{
"scale": [
13.0,
13.0,
13.0
],
"type": "scale"
}
],
"path": "1"
},
{
"coordinateTransformations": [
{
"scale": [
26.0,
26.0,
26.0
],
"type": "scale"
}
],
"path": "2"
},
{
"coordinateTransformations": [
{
"scale": [
52.0,
52.0,
52.0
],
"type": "scale"
}
],
"path": "3"
},
{
"coordinateTransformations": [
{
"scale": [
104.0,
104.0,
104.0
],
"type": "scale"
}
],
"path": "4"
}
],
"name": "mask",
"version": "0.4"
}
]
}
And the metadata of the image itself:
{
"multiscales": [
{
"axes": [
{
"name": "c",
"type": "channel"
},
{
"name": "z",
"type": "space",
"unit": "micrometer"
},
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
],
"datasets": [
{
"coordinateTransformations": [
{
"scale": [
1,
6.5,
6.5,
6.5
],
"type": "scale"
}
],
"path": "0"
},
{
"coordinateTransformations": [
{
"scale": [
1,
13.0,
13.0,
13.0
],
"type": "scale"
}
],
"path": "1"
},
{
"coordinateTransformations": [
{
"scale": [
1,
26.0,
26.0,
26.0
],
"type": "scale"
}
],
"path": "2"
},
{
"coordinateTransformations": [
{
"scale": [
1,
52.0,
52.0,
52.0
],
"type": "scale"
}
],
"path": "3"
},
{
"coordinateTransformations": [
{
"scale": [
1,
104.0,
104.0,
104.0
],
"type": "scale"
}
],
"path": "4"
}
],
"name": "/",
"version": "0.4"
}
]
}
After some further testing, I've noticed that it seems to be a problem introduced in version 0.8.3. When I downgraded the package to 0.8.2 I just got the three nodes for the root group, the labels group and the mask group and no recursive paths.
Hello, is there any update on this?
I've noticed that builds are failing at https://github.com/ome/ome_zarr_test_suite/actions/workflows/main.yml with the same error.
Presumably if you remove the source attribute from the label, then this avoids the recursion?
"source": {
"image": "../../"
},
I'll try to reproduce...
@will-moore : #342 might have been related.
As described at #339 (comment) it seems that I didn't see the recursion issue with fsspec==2023.6.0 (as was pinned before #342) but I did see it with more recent fsspec==2023.12.1.
I just tried with fsspec-2024.3.1 and I didn't see any recursion issue testing as at #339 with coinsdata.
I'm not able to reproduce the recursion error testing with current master branch of ome-zarr:
$ pip freeze | grep fs
fsspec==2023.12.1
s3fs==2023.12.1
>>> url = "coinsdata"
>>> from ome_zarr.io import parse_url
>>> from ome_zarr.reader import Reader
>>> store = parse_url(url, mode="r").store
>>> reader = Reader(parse_url(url))
>>> nodes = list(reader())
>>> print(nodes)
[/Users/wmoore/Desktop/ZARR/data/coinsdata [zgroup], /Users/wmoore/Desktop/ZARR/data/coinsdata/labels [zgroup] (hidden), /Users/wmoore/Desktop/ZARR/data/coinsdata/labels/coins [zgroup] (hidden)]
Other related versions:
$ pip freeze | grep zarr
napari-ome-zarr==0.5.2
-e git+ssh://git@github.com/ome/ome-zarr-py.git@e33f736cb7591b7ab9cb2bdd8568dc0e01a853b8#egg=ome_zarr
-e git+ssh://git@github.com/ome/omero-cli-zarr.git@75ab185a184410aa408772e12315ba9cbf209b36#egg=omero_cli_zarr
-e git+ssh://git@github.com/ome/omero-web-zarr.git@38e91255c80bfb04b814ef37056b355d692c2c96#egg=omero_web_zarr
vizarr==0.0.1
zarr==2.14.2
If I uninstall and reinstall:
pip uninstall ome_zarr
pip install ome-zarr
Now I don't see the recursion error, but I get a very long list of nodes!
>>> print(len(nodes))
154
@FIrgolitsch can you test with the latest master branch of ome-zarr-py... That helps for me:
cd ome-zarr-py/
git checkout origin/master
pip install -e .
Thanks for the response! I finally had some time today to test things. I retested with the current version available on pip (0.8.3) and still got the recursion problem:
OSError: [Errno 63] File name too long: '/Users/<uname>/docker_data/LSFM/S19/S19.zarr/labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/atlas/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/../../labels/mask/0/.zarray'Since it returns an OS error, the specific path length might be MacOS limiting the maximum path length.
I retried after with the version currently on the master branch (0.8.4.dev0), and everything seems to work correctly there. I'll be waiting for the full release of 0.8.4!
As for fsspec, I have version 2024.3.1 installed.
@will-moore and I believe that this is now (more?) fixed with 0.9.0