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Open labels in https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr #11

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will-moore opened this issue Sep 17, 2021 · 3 comments
Open

Open labels in https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr #11

will-moore opened this issue Sep 17, 2021 · 3 comments

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@will-moore
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will-moore commented Sep 17, 2021 •
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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
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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 will-moore changed the title Labels v0.3 investigation Open labels in https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr Oct 11, 2021
@will-moore
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will-moore commented Oct 11, 2021 •
edited
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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 '

@joshmoore joshmoore mentioned this issue Feb 14, 2024
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@psobolewskiPhD
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This is still not working:
napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr
ome-zarr: 0.9.0
napari: 0.5.0
napari-ome-zarr: 0.6.1

╰─ napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr(napari-050) ─╯
Traceback (most recent call last):
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/_qt/qt_viewer.py", line 986, in _qt_open
    self.viewer.open(
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/components/viewer_model.py", line 1215, in open
    layers = self._open_or_raise_error(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/components/viewer_model.py", line 1335, in _open_or_raise_error
    raise MultipleReaderError(
napari.errors.reader_errors.MultipleReaderError: Multiple plugins found capable of reading https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr. Select plugin from {'napari': 'napari builtins', 'napari-ome-zarr': 'napari-ome-zarr'} and pass to reading function e.g. `viewer.open(..., plugin=...)`.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/bin/napari", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/__main__.py", line 584, in main
    _run()
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/__main__.py", line 348, in _run
    viewer._window._qt_viewer._qt_open(
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/_qt/qt_viewer.py", line 1004, in _qt_open
    handle_gui_reading(filenames, self, stack, **kwargs)
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/_qt/dialogs/qt_reader_dialog.py", line 201, in handle_gui_reading
    open_with_dialog_choices(
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/_qt/dialogs/qt_reader_dialog.py", line 294, in open_with_dialog_choices
    qt_viewer.viewer.open(paths, stack=stack, plugin=plugin_name, **kwargs)
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/components/viewer_model.py", line 1205, in open
    self._add_layers_with_plugins(
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/components/viewer_model.py", line 1405, in _add_layers_with_plugins
    layer_data, hookimpl = read_data_with_plugins(
                           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/plugins/io.py", line 78, in read_data_with_plugins
    res = _npe2.read(paths, plugin, stack=stack)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/napari/plugins/_npe2.py", line 57, in read
    layer_data, reader = io_utils.read_get_reader(
                         ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/npe2/io_utils.py", line 66, in read_get_reader
    return _read(
           ^^^^^^
  File "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-050/lib/python3.12/site-packages/npe2/io_utils.py", line 176, in _read
    raise ValueError(
ValueError: Reader 'napari-ome-zarr' was selected to open ['https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001247.zarr'], but returned no data.

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@will-moore @psobolewskiPhD