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Add support for label properties in zattrs and plugin #61

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merged 8 commits into from
Nov 30, 2020
Merged

Add support for label properties in zattrs and plugin #61

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7e77cf9
Read properties from zattrs and pass to napari reader
Nov 16, 2020
d1d8373
Resolving comments
Nov 17, 2020
d99ae0a
Fix formatting
Nov 17, 2020
59c031e
Fix precommit issues
Nov 17, 2020
a4b5a3e
More precommit issues
joshmoore Nov 17, 2020
d1b8e37
Update setup-miniconda action
joshmoore Nov 17, 2020
391545c
Add test for label properties
Nov 20, 2020
309d1fe
Merge branch 'add-label-properties' of https://github.com/DragaDoncil…
Nov 20, 2020
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18 changes: 18 additions & 0 deletions ome_zarr/napari.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,24 @@ def f(*args: Any, **kwargs: Any) -> List[LayerData]:
layer_type = "labels"
if "colormap" in metadata:
del metadata["colormap"]
if "properties" in metadata:
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props = metadata["properties"]
reader_props = {}
label_indices = list(props.keys())
reader_props["index"] = label_indices

# properties may be ragged, so we need to know all possible properties
all_keys = set()
for index in label_indices:
all_keys = all_keys.union(set(props[index].keys()))

# napari expects lists of equal length so we must fill with None
for prop_key in all_keys:
reader_props[prop_key] = [
props[i][prop_key] if prop_key in props[i] else "None"
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This can probably be an actual None value here instead of a string "None" (unless it has to be a string for some reason). Since if some code is testing for the value being None, then the string won't be recognised as None.

for i in label_indices
]
metadata['properties'] = reader_props

elif shape[CHANNEL_DIMENSION] > 1:
metadata["channel_axis"] = CHANNEL_DIMENSION
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9 changes: 9 additions & 0 deletions ome_zarr/reader.py
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Expand Up @@ -216,13 +216,22 @@ def __init__(self, node: Node) -> None:
except Exception as e:
LOGGER.error(f"invalid color - {color}: {e}")

properties: Dict[int, Dict[str, str]] = {}
props_list = image_label.get('properties', [])
if props_list:
for props in props_list:
label_val = props['label-value']
del props['label-value']
properties[label_val] = props
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Could you explain what's happening here? We'll need to check whether the underlying dictionary is a deep-copy of the original, or whether it returns a reference which means this may update the properties seen by other code.

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Yes, if I do image_label.get('properties', []) after this for loop, I get the properties without the label-values so you probably should create a copy of the props before editing.
This seems to work:

                properties[label_val] = dict(props)
                del properties[label_val]['label-value']


# TODO: a metadata transform should be provided by specific impls.
name = self.zarr.basename()
node.metadata.update(
{
"visible": node.visible,
"name": name,
"color": colors,
"properties": properties,
"metadata": {"image": self.lookup("image", {}), "path": name},
}
)
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