add xml viewer widget napari plugin

.pre-commit-config.yaml

@@ -23,4 +23,4 @@ repos:
     rev: "v0.902"
     hooks:
       - id: mypy
-        exclude: ^testing|^docs
+        exclude: ^testing|^docs|_napari_plugin

setup.cfg

@@ -19,6 +19,7 @@ classifiers =
     Programming Language :: Python :: 3 :: Only
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
 
 [options]
 zip_safe = False
@@ -32,6 +33,10 @@ install_requires =
     xmlschema==1.4.1
     Pint>=0.15
 
+[options.entry_points]
+napari.plugin =
+    ome-types = ome_types._napari_plugin
+
 [options.package_data]
 * = *.xsd
 ome_types = py.typed

src/ome_types/_napari_plugin.py

@@ -0,0 +1,111 @@
+import warnings
+from typing import Union
+
+from napari_plugin_engine import napari_hook_implementation
+from qtpy.QtCore import QMimeData, Qt
+from qtpy.QtWidgets import QTreeWidget, QTreeWidgetItem
+
+from ome_types import OME
+
+
+@napari_hook_implementation
+def napari_experimental_provide_dock_widget():
+    return OMETree, {"name": "OME Metadata Viewer"}
+
+
+@napari_hook_implementation
+def napari_get_reader(path):
+    """Show OME XML if an ome.xml file is dropped on the viewer."""
+    if isinstance(path, str) and path.endswith("ome.xml"):
+        return view_ome_xml
+
+
+def view_ome_xml(path):
+    from napari._qt.qt_main_window import _QtMainWindow
+
+    # close your eyes, or look away...
+    # there is nothing worth looking at here!
+    window = _QtMainWindow.current()
+    if not window:
+        return
+    viewer = window.qt_viewer.viewer
+    dw, widget = viewer.window.add_plugin_dock_widget("ome-types")
+    widget.update(path)
+
+    return [(None,)]  # sentinel
+
+
+class OMETree(QTreeWidget):
+    """A Widget that can show OME XML"""
+
+    def __init__(self, ome_dict: dict = None, parent=None) -> None:
+        super().__init__(parent=parent)
+        self.setAcceptDrops(True)
+        self.setDropIndicatorShown(True)
+        self.setHeaderHidden(True)
+        self.update(ome_dict)
+
+    def update(self, ome: Union[OME, str]):
+        if not ome:
+            return
+        if isinstance(ome, str):
+            try:
+                if ome.endswith(".xml"):
+                    ome = OME.from_xml(ome)
+                elif ome.lower().endswith((".tif", ".tiff")):
+                    ome = OME.from_tiff(ome)
+                else:
+                    warnings.warn(f"Unrecognized file type: {ome}")
+                    return
+            except Exception as e:
+                warnings.warn(f"Could not parse OME metadata from {ome}: {e}")
+                return
+
+        self._fill_item(ome.dict(exclude_unset=True))
+
+    def _fill_item(self, obj, item: QTreeWidgetItem = None):
+        if item is None:
+            self.clear()
+            item = self.invisibleRootItem()
+        if isinstance(obj, dict):
+            for key, val in sorted(obj.items()):
+                child = QTreeWidgetItem([key])
+                item.addChild(child)
+                self._fill_item(val, child)
+        elif isinstance(obj, (list, tuple)):
+            for n, val in enumerate(obj):
+                text = val.get("id", n) if hasattr(val, "get") else n
+                child = QTreeWidgetItem([str(text)])
+                item.addChild(child)
+                self._fill_item(val, child)
+        else:
+            t = getattr(obj, "value", str(obj))
+            item.setText(0, f"{item.text(0)}: {t}")
+
+    def dropMimeData(
+        self, parent: QTreeWidgetItem, index: int, data: QMimeData, a
+    ) -> bool:
+        if data.hasUrls():
+            for url in data.urls():
+                lf = url.toLocalFile()
+                if lf.endswith((".xml", ".tiff", ".tif")):
+                    self.update(lf)
+                    return True
+        return False
+
+    def mimeTypes(self):
+        return ["text/uri-list"]
+
+    def supportedDropActions(self):
+        return Qt.CopyAction
+
+
+if __name__ == "__main__":
+    from qtpy.QtWidgets import QApplication
+
+    app = QApplication([])
+
+    widget = OMETree()
+    widget.show()
+
+    app.exec()

testing/test_widget.py

@@ -0,0 +1,14 @@
+from pathlib import Path
+
+import pytest
+
+nplg = pytest.importorskip("ome_types._napari_plugin")
+
+DATA = Path(__file__).parent / "data"
+
+
+@pytest.mark.parametrize("fname", DATA.iterdir(), ids=lambda x: x.stem)
+def test_widget(fname, qtbot):
+    if fname.stem in ("bad.ome", "timestampannotation.ome"):
+        pytest.xfail()
+    nplg.OMETree(str(fname))