Merge pull request #6 from panel-extensions/refactor

Refactoring and renaming of Neuroglancer component

README.md

@@ -1,9 +1,12 @@
-# `panel-neuroglancer` 
+# `panel-neuroglancer`
+
 Use HoloViz [`Panel`](https://panel.holoviz.org/) to integrate [Neuroglancer](https://www.github.com/google/neuroglancer) into Jupyter notebook workflows and applications for scientifically contextualized, reproducible, and extensible workflows involving large volumetric datasets, such as those from electron and fluorescent microscopy. See the [Overview](#overview) below for more explanation.
 
 ## Usage
+
 ### Option 1 - Load from a neuroglancer url:
-Either use `NeuroglancerNB(source=<URL>)` or just run `NeuroglancerNB()` and input the URL in the GUI:
+
+Either use `Neuroglancer(source=<URL>)` or just run `Neuroglancer()` and input the URL in the GUI:
 ![](assets/demo_fromurl.png)
 
 
@@ -21,8 +24,9 @@ with viewer.txn() as s:
     s.layers["segmentation"] = neuroglancer.SegmentationLayer(
         source="precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.1/segmentation",
     )
-NeuroglancerNB(source=viewer, show_state=True)
+Neuroglancer(source=viewer, show_state=True)
 ```
+
 ![](assets/demo_fromviewer.png)
 
 ## Overview

src/panel_neuroglancer/__init__.py

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

src/panel_neuroglancer/neuroglancer.py

@@ -0,0 +1,165 @@
+from __future__ import annotations
+
+import neuroglancer
+import panel as pn
+import param
+
+from neuroglancer.viewer import Viewer
+from panel.custom import PyComponent
+
+
+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"
+
+
+class Neuroglancer(PyComponent):
+    """
+    Neuroglancer is a Panel component for visualizing and interacting with a Neuroglancer Viewer.
+
+    The component can be initialized from a URL or a `neuroglancer.viewer.Viewer` instance.
+    """
+
+    show_state = param.Boolean(default=False, doc="""
+        Provides a collapsible card widget under the viewer that displays the viewer's state.""")
+
+    url = param.String(default=None, doc="""
+        The URL public URL of the Neuroglancer Viewer.""")
+
+    def __init__(
+        self,
+        source=None,
+        load_demo=False,
+        **params,
+    ):
+        viewer = None
+        if isinstance(source, str):
+            params['url'] = source
+        elif isinstance(source, Viewer):
+            params['url'] = source.get_viewer_url()
+            viewer = source
+        elif source is not None:
+            raise ValueError('Neuroglancer source must be a URL or neuroglancer Viewer instance')
+        self._source_not_provided = source is None
+        super().__init__(**params)
+        if viewer is None:
+            viewer = neuroglancer.Viewer()
+        self.viewer = viewer
+
+        self._setup_ui_components()
+        self._configure_viewer()
+        self._setup_callbacks()
+
+        if isinstance(source, str):
+            self._load_state_from_url(source)
+        if load_demo:
+            self._load_demo()
+
+    def _setup_ui_components(self):
+        self.url_input = pn.widgets.TextInput.from_param(
+            self.param.url,
+            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", sizing_mode='stretch_both'
+        )
+
+        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=self.param.aspect_ratio,
+            margin=0,
+            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._load_url)
+        self.demo_button.on_click(self._load_demo)
+        self.viewer.shared_state.add_changed_callback(self._on_viewer_state_changed)
+
+    def _load_demo(self, event=None):
+        self.url = DEMO_URL
+        self._load_state_from_url(self.url)
+
+    def _load_url(self, event=None):
+        self._load_state_from_url(self.url)
+
+    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):
+        self.url = 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):
+        controls = pn.Column(
+            pn.Row(self.demo_button, self.load_button, visible=self._source_not_provided),
+            pn.Row(self.url_input, visible=self._source_not_provided),
+            self.local_url_pane,
+            self.shareable_url_pane
+        )
+        state_widget = pn.Card(
+            self.json_pane,
+            title="State",
+            collapsed=False,
+            visible=self.param.show_state,
+            styles={"background": "WhiteSmoke"},
+            max_width=350
+        )
+        return pn.Column(
+            controls,
+            pn.Row(state_widget, self.iframe),
+        )