first working version

pyproject.toml

@@ -25,7 +25,11 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "numpy",
+    "qtpy",
+    "pandas",
+    "fsspec",
+    "napari-ome-zarr",
+    "tifffile",
 ]
 
 [project.optional-dependencies]

src/napari_royerlab_data/__init__.py

@@ -1,4 +1,5 @@
 __version__ = "0.0.1"
-from ._sample_data import make_sample_data
 
-__all__ = ("make_sample_data",)
+from napari_royerlab_data._widget import DataLoaderWidget
+
+__all__ = ("DataLoaderWidget",)

src/napari_royerlab_data/_widget.py

@@ -0,0 +1,141 @@
+import urllib
+import urllib.parse
+from typing import TYPE_CHECKING, Dict, List, Literal, Tuple
+
+import fsspec
+import pandas as pd
+from magicgui.widgets import ComboBox, Container, PushButton
+from ome_zarr.io import parse_url
+from ome_zarr.reader import Reader
+
+if TYPE_CHECKING:
+    import napari
+
+
+class DataLoaderWidget(Container):
+
+    ROYERLAB_DATA_URL = "https://public.czbiohub.org/royerlab"
+
+    def __init__(self, viewer: "napari.viewer.Viewer"):
+        super().__init__()
+        # Create an HTTP file system
+        self._viewer: napari.Viewer = viewer
+        self._fs = fsspec.filesystem("http")
+
+        self._images_url: Dict[str, str] = {}
+        self._tracks_url: Dict[str, str] = {}
+
+        self._fill_urls()
+
+        self._images_combobox = ComboBox(
+            name="Image",
+            choices=sorted(self._images_url.keys()),
+        )
+        self.append(self._images_combobox)
+
+        self._images_btn = PushButton(
+            name="Load Image",
+        )
+        self._images_btn.changed.connect(self._on_image_btn_click)
+        self.append(self._images_btn)
+
+        self._tracks_combobox = ComboBox(
+            name="Tracks",
+            choices=sorted(self._tracks_url.keys()),
+        )
+        self.append(self._tracks_combobox)
+
+        self._tracks_btn = PushButton(
+            name="Load Tracks",
+        )
+        self._tracks_btn.changed.connect(self._on_tracks_btn_click)
+        self.append(self._tracks_btn)
+
+    @staticmethod
+    def _parse_url(path: str) -> Tuple[str, str]:
+        if path.endswith("/"):
+            path = path[:-1]
+        basename = urllib.parse.urlparse(path).path.split("/")[-1]
+        try:
+            stem, ext = basename.split(".", 1)
+        except ValueError:
+            stem, ext = basename, ""
+        return stem, ext.lower()
+
+    def _fill_urls(self) -> None:
+
+        queue = [self.ROYERLAB_DATA_URL]
+
+        while queue:
+            path = queue.pop(0)
+            dirs = self._iter_children(path, "directory")
+            files = self._iter_children(path, "file")
+
+            for f in files:
+                stem, ext = self._parse_url(f)
+                if ext == "csv":
+                    self._tracks_url[stem] = f
+
+            for d in dirs:
+                if ".zarr" in d:
+                    if self._is_ome_zarr(d):
+                        stem, ext = self._parse_url(d)
+                        self._images_url[stem] = urllib.parse.urljoin(path, d)
+                elif ".." in d:
+                    pass
+                else:
+                    queue.append(d)
+
+    def _is_ome_zarr(self, path: str) -> bool:
+        url = parse_url(path)
+        if url is None:
+            return False
+        reader = Reader(url)
+        try:
+            node = next(reader())
+        except StopIteration:
+            return False
+        return len(node.metadata) > 0
+
+    def _on_image_btn_click(self) -> None:
+        if self._images_combobox.value is None:
+            return
+
+        url = self._images_url[self._images_combobox.value]
+
+        self._viewer.open(
+            url,
+            plugin="napari-ome-zarr",
+        )
+
+    def _on_tracks_btn_click(self) -> None:
+        if self._tracks_combobox.value is None:
+            return
+
+        tracks_df = pd.read_csv(self._tracks_url[self._tracks_combobox.value])
+
+        track_id_col = "track_id"
+        if track_id_col not in tracks_df.columns:
+            track_id_col = "TrackID"
+
+        if "z" in tracks_df.columns:
+            spatial_cols = ["z", "y", "x"]
+        else:
+            spatial_cols = ["y", "x"]
+
+        self._viewer.add_tracks(
+            tracks_df[[track_id_col, "t", *spatial_cols]],
+            name=self._tracks_combobox.value,
+        )
+
+    def _iter_children(
+        self,
+        path: str,
+        path_type: Literal["file", "directory"],
+    ) -> List[str]:
+
+        return [
+            child["name"]
+            for child in self._fs.ls(path)
+            if child["type"] == path_type
+        ]

src/napari_royerlab_data/napari.yaml

@@ -2,14 +2,12 @@ name: napari-royerlab-data
 display_name: RoyerLab Data
 # use 'hidden' to remove plugin from napari hub search results
 visibility: public
-# see https://napari.org/stable/plugins/manifest.html for valid categories
-categories: ["Annotation", "Segmentation", "Acquisition"]
+categories: ["Dataset"]
 contributions:
   commands:
-    - id: napari-royerlab-data.make_sample_data
-      python_name: napari_royerlab_data._sample_data:make_sample_data
-      title: Load sample data from RoyerLab Data
-  sample_data:
-    - command: napari-royerlab-data.make_sample_data
-      display_name: RoyerLab Data
-      key: unique_id.1
+    - id: napari-royerlab-data.data_loader
+      python_name: napari_royerlab_data:DataLoaderWidget
+      title: RoyerLab's data loader
+  widgets:
+    - command: napari-royerlab-data.data_loader
+      display_name: RoyerLab's data loader