Merge pull request #3 from panel-extensions/migrate_app

Migrating NeuroglancerNB class to dedicated repo

README.md

@@ -1,3 +1,26 @@
 # `panel-neuroglancer` 
-Use [`panel`](https://panel.holoviz.org/) to embed [neuroglancer](https://www.github.com/google/neuroglancer) in Jupyter notebooks 
+Use [`panel`](https://panel.holoviz.org/) to embed [neuroglancer](https://www.github.com/google/neuroglancer) in Jupyter notebooks.
 
+## Usage
+### Option 1 - Load from a neuroglancer url:
+Either use `NeuroglancerNB(source=<URL>)` or just run `NeuroglancerNB()` and input the URL in the GUI:
+![](assets/demo_fromurl.png)
+
+
+### Option 2 - Load from `neuroglancer.Viewer` instance:
+
+```python
+viewer = neuroglancer.Viewer()
+
+with viewer.txn() as s:
+    # Add an image layer from a precomputed data source
+    s.layers["image"] = neuroglancer.ImageLayer(
+        source="precomputed://gs://neuroglancer-janelia-flyem-hemibrain/emdata/clahe_yz/jpeg",
+    )
+    # Add a segmentation layer
+    s.layers["segmentation"] = neuroglancer.SegmentationLayer(
+        source="precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.1/segmentation",
+    )
+NeuroglancerNB(source=viewer, show_state=True)
+```
+![](assets/demo_fromviewer.png)

src/panel_neuroglancer/__init__.py

@@ -1,3 +1,3 @@
-from panel_neuroglancer.neuroglancer_nbv import NeuroglancerNbViewer
+from panel_neuroglancer.neuroglancer_nb import NeuroglancerNb
 
-__all__ = ["NeuroglancerNbViewer"]
+__all__ = ["NeuroglancerNb"]

src/panel_neuroglancer/neuroglancer_nb.py

@@ -0,0 +1,174 @@
+import panel as pn
+import neuroglancer
+
+pn.extension()
+class NeuroglancerNB(pn.viewable.Viewer):
+    """
+    A HoloViz Panel app for visualizing and interacting with Neuroglancer viewers
+    within a Jupyter Notebook.
+
+    This app supports loading from a parameterized Neuroglancer URL or an existing
+    `neuroglancer.viewer.Viewer` instance.
+    """
+
+    DEMO_URL = "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%7B%22x%22%3A%5B6.000000000000001e-9%2C%22m%22%5D%2C%22y%22%3A%5B6.000000000000001e-9%2C%22m%22%5D%2C%22z%22%3A%5B3.0000000000000004e-8%2C%22m%22%5D%7D%2C%22position%22%3A%5B5029.42333984375%2C6217.5849609375%2C1182.5%5D%2C%22crossSectionScale%22%3A3.7621853549999242%2C%22projectionOrientation%22%3A%5B-0.05179581791162491%2C-0.8017329573631287%2C0.0831851214170456%2C-0.5895944833755493%5D%2C%22projectionScale%22%3A4699.372698097029%2C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%2C%22source%22%3A%22precomputed%3A%2F%2Fgs%3A%2F%2Fneuroglancer-public-data%2Fkasthuri2011%2Fimage%22%2C%22tab%22%3A%22source%22%2C%22name%22%3A%22original-image%22%7D%2C%7B%22type%22%3A%22image%22%2C%22source%22%3A%22precomputed%3A%2F%2Fgs%3A%2F%2Fneuroglancer-public-data%2Fkasthuri2011%2Fimage_color_corrected%22%2C%22tab%22%3A%22source%22%2C%22name%22%3A%22corrected-image%22%7D%2C%7B%22type%22%3A%22segmentation%22%2C%22source%22%3A%22precomputed%3A%2F%2Fgs%3A%2F%2Fneuroglancer-public-data%2Fkasthuri2011%2Fground_truth%22%2C%22tab%22%3A%22source%22%2C%22selectedAlpha%22%3A0.63%2C%22notSelectedAlpha%22%3A0.14%2C%22segments%22%3A%5B%223208%22%2C%224901%22%2C%2213%22%2C%224965%22%2C%224651%22%2C%222282%22%2C%223189%22%2C%223758%22%2C%2215%22%2C%224027%22%2C%223228%22%2C%22444%22%2C%223207%22%2C%223224%22%2C%223710%22%5D%2C%22name%22%3A%22ground_truth%22%7D%5D%2C%22layout%22%3A%224panel%22%7D"
+
+    def __init__(
+        self,
+        source=None,
+        aspect_ratio=2.75,
+        show_state=False,
+        load_demo=False,
+        **params,
+    ):
+        """
+        Initializes the NeuroglancerNB app.
+
+        Parameters
+        ----------
+        source : str or neuroglancer.viewer.Viewer, optional
+            Source for the initial state of the viewer, which can be a URL string or an existing `neuroglancer.viewer.Viewer` instance.
+            If None, a new viewer will be initialized without a predefined state.
+        aspect_ratio : float, optional
+            The width-to-height ratio for the window-responsive Neuroglancer viewer. Default is 2.75.
+        show_state : bool, optional
+            Provides a collapsible card widget under the viewer that displays the viewer's state.
+            Useful for debugging. Default is False.
+        load_demo : bool, optional
+            If True, loads the demo dataset upon initialization. Default is False.
+        **params
+            Additional parameters passed to the parent class.
+        """
+        super().__init__(**params)
+        self.source_not_provided = False if source else True
+        self.show_state = show_state
+        self.viewer = (
+            source
+            if isinstance(source, neuroglancer.viewer.Viewer)
+            else neuroglancer.Viewer()
+        )
+
+        self._setup_ui_components(aspect_ratio=aspect_ratio)
+        self._configure_viewer()
+        self._setup_callbacks()
+
+        if source and not isinstance(source, neuroglancer.viewer.Viewer):
+            self._initialize_viewer_from_url(source)
+
+        if load_demo:
+            self.demo_button.clicks += 1
+
+    def _initialize_viewer_from_url(self, source: str):
+        self.url_input.value = source
+        self._load_state_from_url(source)
+
+    def _setup_ui_components(self, aspect_ratio):
+        self.url_input = pn.widgets.TextInput(
+            placeholder="Enter a Neuroglancer URL and click Load",
+            name="Input URL",
+            width=700,
+        )
+
+        self.load_button = pn.widgets.Button(
+            name="Load", button_type="primary", width=75
+        )
+        self.demo_button = pn.widgets.Button(
+            name="Demo", button_type="warning", width=75
+        )
+
+        self.json_pane = pn.pane.JSON(
+            {}, theme="light", depth=2, name="Viewer State", height=800, width=350
+        )
+
+        self.shareable_url_pane = pn.pane.Markdown("**Shareable URL:**")
+        self.local_url_pane = pn.pane.Markdown("**Local URL:**")
+
+        self.iframe = pn.pane.HTML(
+            sizing_mode="stretch_both",
+            aspect_ratio=aspect_ratio,
+            min_height=800,
+            styles={"resize": "both", "overflow": "hidden"},
+        )
+
+    def _configure_viewer(self):
+        self._update_local_url()
+        self._update_iframe_with_local_url()
+
+    def _setup_callbacks(self):
+        self.load_button.on_click(self._on_load_button_clicked)
+        self.demo_button.on_click(self._on_demo_button_clicked)
+        self.viewer.shared_state.add_changed_callback(self._on_viewer_state_changed)
+
+    def _on_demo_button_clicked(self, event):
+        self.url_input.value = self.DEMO_URL
+        self._load_state_from_url(self.url_input.value)
+
+    def _on_load_button_clicked(self, event):
+        self._load_state_from_url(self.url_input.value)
+
+    def _load_state_from_url(self, url):
+        try:
+            new_state = self._parse_state_from_url(url)
+            self.viewer.set_state(new_state)
+        except Exception as e:
+            print(f"Error loading Neuroglancer state: {e}")
+
+    def _parse_state_from_url(self, url):
+        return neuroglancer.parse_url(url)
+
+    def _on_viewer_state_changed(self):
+        self._update_shareable_url()
+        self._update_json_pane()
+
+    def _update_shareable_url(self):
+        shareable_url = neuroglancer.to_url(self.viewer.state)
+        self.shareable_url_pane.object = self._generate_dropdown_markup(
+            "Shareable URL", shareable_url
+        )
+
+    def _update_local_url(self):
+        self.local_url_pane.object = self._generate_dropdown_markup(
+            "Local URL", self.viewer.get_viewer_url()
+        )
+
+    def _update_iframe_with_local_url(self):
+        iframe_style = (
+            'frameborder="0" scrolling="no" marginheight="0" marginwidth="0" '
+            'style="width:100%; height:100%; min-width:500px; min-height:500px;"'
+        )
+        self.iframe.object = (
+            f'<iframe src="{self.viewer.get_viewer_url()}" {iframe_style}></iframe>'
+        )
+
+    def _update_json_pane(self):
+        self.json_pane.object = self.viewer.state.to_json()
+
+    def _generate_dropdown_markup(self, title, url):
+        return f"""
+            <details>
+                <summary><b>{title}:</b></summary>
+                <a href="{url}" target="_blank">{url}</a>
+            </details>
+        """
+
+    def __panel__(self):
+        # only visible if no source is provided
+        controls_layout = pn.Column(
+            pn.Row(self.demo_button, self.load_button),
+            pn.Row(self.url_input),
+            visible=self.source_not_provided,
+        )
+        links_layout = pn.Column(self.local_url_pane, self.shareable_url_pane)
+
+        state_widget = pn.Card(
+                self.json_pane,
+                title="State",
+                collapsed=False,
+                visible=self.show_state,
+                styles={"background": "WhiteSmoke"},
+                max_width=350
+            )
+        return pn.Column(
+            controls_layout,
+            links_layout,
+            pn.Row(state_widget, self.iframe))