Open labels in https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr
will-moore opened this issue · 2 comments
will-moore commented
We only have a single public example of labels at https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr
e.g. wanted to provide this as a response to https://twitter.com/jm_mightypirate/status/1447486365252399108
But can't get it working...
Starting with recent releases:
napari-0.4.11
napari-ome-zarr==0.2.0
ome-zarr==0.1.0
zarr==2.9.5
$ napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr -vvv
Opens the image (2 channels) but No labels channel.
Labels seen in verbose logging...
10:53:09 DEBUG open(ZarrLocation(https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels))
10:53:09 DEBUG https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels
10:53:09 DEBUG Created legacy flat FSStore(https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels, r)
10:53:09 DEBUG https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels/.zarray
10:53:09 DEBUG https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels/.zgroup
10:53:10 WARNING version mismatch: detected:FormatV03, requested:FormatV01
10:53:10 DEBUG https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels
10:53:10 DEBUG Created nested FSStore(https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels, r, {'dimension_separator': '/', 'normalize_keys': True})
10:53:10 DEBUG https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels/.zarray
10:53:10 DEBUG https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/labels/.zgroup
but nothing after that...
TODO: try more versions...
will-moore commented
With ome/ome-zarr-py#111 in ome-zarr-0.1.1 now I'm seeing...
napari==0.4.11
napari-ome-zarr==0.2.0
zarr==2.10.1
ome-zarr-0.1.1
$ napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr -vvv
12:00:23 DEBUG https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr/2/0.1.0.0.0
Traceback (most recent call last):
File "/opt/anaconda3/envs/ome_ngff/bin/napari", line 8, in <module>
sys.exit(main())
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/__main__.py", line 424, in main
_run()
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/__main__.py", line 308, in _run
viewer = view_path( # noqa: F841
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/view_layers.py", line 169, in view_path
return _make_viewer_then('open', args, kwargs)
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/view_layers.py", line 119, in _make_viewer_then
method(*args, **kwargs)
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/components/viewer_model.py", line 914, in open
self._add_layers_with_plugins(
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/components/viewer_model.py", line 987, in _add_layers_with_plugins
added.extend(self._add_layer_from_data(*_data))
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/components/viewer_model.py", line 1064, in _add_layer_from_data
raise exc
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/components/viewer_model.py", line 1061, in _add_layer_from_data
layer = add_method(data, **(meta or {}))
File "<string>", line 4, in add_labels
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/layers/labels/labels.py", line 243, in __init__
data = self._ensure_int_labels(data)
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/layers/labels/labels.py", line 534, in _ensure_int_labels
raise TypeError(
TypeError: Only integer types are supported for Labels layers, but data contains float64.
will-moore commented
Tried to convert 'float' data with this diff:
$ git diff
diff --git a/napari_ome_zarr/_reader.py b/napari_ome_zarr/_reader.py
index c7fdc48..09d306c 100644
--- a/napari_ome_zarr/_reader.py
+++ b/napari_ome_zarr/_reader.py
@@ -9,6 +9,7 @@ import warnings
from typing import Any, Callable, Dict, Iterator, List, Optional
from vispy.color import Colormap
+import numpy as np
from ome_zarr.data import CHANNEL_DIMENSION
from ome_zarr.io import parse_url
@@ -101,6 +102,12 @@ def transform(nodes: Iterator[Node]) -> Optional[ReaderFunction]:
for x in METADATA_KEYS:
if x in node.metadata:
metadata[x] = node.metadata[x]
+ # need to ensure dtype is integer not float
+ print("DTYPE", data[0].dtype.str, data[0].itemsize)
+ if data[0].itemsize == 8 or 'f' in data[0].dtype.str:
+ # convert to something napari can handle
+ data = [data[0].astype(np.dtype('i4'))]
+ print('data', data[0])
else:
channel_axis = None
if "axes" in node.metadata:
But that crashes (and even causes Python to crash):
$ napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr
/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/napari/_qt/__init__.py:54: UserWarning:
napari was tested with QT library `>=5.12.3`.
The version installed is 5.9.7. Please report any issues with
this specific QT version at https://github.com/Napari/napari/issues.
warn(message=warn_message)
12:36:45 WARNING version mismatch: detected:FormatV01, requested:FormatV03
12:36:46 WARNING version mismatch: detected:FormatV03, requested:FormatV01
12:36:47 WARNING version mismatch: detected:FormatV01, requested:FormatV03
12:36:48 WARNING version mismatch: detected:FormatV03, requested:FormatV01
DTYPE <i8 8
data dask.array<astype, shape=(1, 1, 257, 210, 253), dtype=int32, chunksize=(1, 1, 33, 53, 64), chunktype=numpy.ndarray>
WARNING: Traceback (most recent call last):
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/vispy/app/backends/_qt.py", line 897, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/vispy/util/event.py", line 451, in __call__
raise RuntimeError('EventEmitter loop detected!')
RuntimeError: EventEmitter loop detected!
12:36:50 WARNING Traceback (most recent call last):
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/vispy/app/backends/_qt.py", line 897, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/opt/anaconda3/envs/ome_ngff/lib/python3.9/site-packages/vispy/util/event.py", line 451, in __call__
raise RuntimeError('EventEmitter loop detected!')
RuntimeError: EventEmitter loop detected!
Abort trap: 6
(ome_ngff) LS30778:napari-ome-zarr wmoore$ /opt/anaconda3/envs/ome_ngff/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '