Skel source (#38)

* start adding skel source

* add skeleton source and shader options

src/nglui/easyviewer/ev_base/base.py

@@ -58,6 +58,18 @@ def add_segmentation_layer(self, layer_name, source, **kwargs):
         with self.txn() as s:
             s.layers[layer_name] = self._SegmentationLayer(source=source, **kwargs)
 
+    @abstractmethod
+    def append_source_to_segmentation_layer(self, layer_name, source):
+        pass
+
+    @abstractmethod
+    def add_skeleton_source(self, layer_name, source, shader_text=None):
+        pass
+
+    @abstractmethod
+    def set_skeleton_shader(self, layer_name, shader_text=None):
+        pass
+
     def add_image_layer(self, layer_name, source, contrast_range=None, **kwargs):
         """Add segmentation layer to viewer instance.
 

src/nglui/easyviewer/ev_base/mainline.py

@@ -18,6 +18,11 @@
 from . import utils
 from .base import SEGMENTATION_LAYER_TYPES, EasyViewerBase
 
+DEFAULT_SKELETON_SHADER = """void main() {
+  emitDefault();
+}
+"""
+
 
 def nanometer_dimension(resolution):
     return neuroglancer.CoordinateSpace(
@@ -185,7 +190,7 @@ def append_source_to_segmentation_layer(self, layer_name, source):
         layer_name : str
             Name of an existing layer
         source : str or list of str
-            Source or sources to add to the layer
+            Source or sources to add to the layer. Can be segment properties or skeleton sources, for example.
         """
         if isinstance(source, str):
             source = [source]
@@ -195,6 +200,19 @@ def append_source_to_segmentation_layer(self, layer_name, source):
             for src in source:
                 s.layers[layer_name].source.append({"url": src})
 
+    def add_skeleton_source(self, layer_name, source, shader_text=None):
+        if shader_text is None:
+            shader_text = DEFAULT_SKELETON_SHADER
+        with self.txn() as s:
+            s.layers[layer_name].source.append({"url": source})
+            s.layers[layer_name].skeletonShader = shader_text
+
+    def set_skeleton_shader(self, layer_name, shader_text=None):
+        if shader_text is None:
+            shader_text = DEFAULT_SKELETON_SHADER
+        with self.txn() as s:
+            s.layers[layer_name].skeletonShader = shader_text
+
     def set_view_options(
         self,
         show_slices: Optional[bool] = None,

src/nglui/easyviewer/ev_base/seunglab.py

@@ -59,6 +59,15 @@ def add_segmentation_layer(self, layer_name, source, **kwargs):
             warn("Only using first source in list for seung-lab segmentation layer")
         super().add_segmentation_layer(layer_name, source, **kwargs)
 
+    def append_source_to_segmentation_layer(self, layer_name, source):
+        warn("Additional segment source is not supported in Seung-lab viewer")
+
+    def add_skeleton_source(self, layer_name, source, shader_text=None):
+        warn("Skeleton sources are not supported in Seung-lab viewer")
+
+    def set_skeleton_shader(self, layer_name, shader_text=None):
+        warn("Skeleton shaders are not supported in Seung-lab viewer")
+
     def add_annotation_layer(
         self,
         layer_name=None,

src/nglui/statebuilder/layers.py

@@ -217,6 +217,10 @@ class SegmentationLayerConfig(LayerConfigBase):
         Name of the mapping set, the key in the data dictionary for statebuilder. Optional, default is None.
     segment_properties: str, optional
         Location of a segment properties file. Optional, default is None.
+    skeleton_source: str, optional
+        Location of a skeleton source. Optional, default is None.
+    skeleton_shader: str, optional
+        Shader function for rendering skeletons, if set with `skeleton_source`. Optional, default is None.
     """
 
     def __init__(
@@ -237,6 +241,8 @@ def __init__(
         data_resolution=None,
         mapping_set=None,
         segment_properties=None,
+        skeleton_source=None,
+        skeleton_shader=None,
     ):
         if name is None:
             name = DEFAULT_SEG_LAYER
@@ -246,6 +252,8 @@ def __init__(
         )
         self._config["data_resolution"] = data_resolution
         self._config["segment_properties"] = segment_properties
+        self._config["skeleton_source"] = skeleton_source
+        self._config["skeleton_shader"] = skeleton_shader
 
         if selected_ids_column is not None or fixed_ids is not None:
             self._selection_map = SelectionMapper(
@@ -305,6 +313,14 @@ def source(self):
         else:
             return out
 
+    @property
+    def skeleton_source(self):
+        return self._config.get("skeleton_source", None)
+
+    @property
+    def skeleton_shader(self):
+        return self._config.get("skeleton_shader", None)
+
     def add_segment_propeties(
         self,
         segment_property: str,
@@ -447,6 +463,10 @@ def add_selection_map(
 
     def _add_layer(self, viewer):
         viewer.add_segmentation_layer(self.name, self.source)
+        if self.skeleton_source is not None:
+            viewer.add_skeleton_source(
+                self.name, self.skeleton_source, self.skeleton_shader
+            )
 
     def _specific_rendering(
         self,

tests/test_statebuilder.py

@@ -37,6 +37,16 @@ def anno_layer_basic():
     return anno_layer
 
 
+@pytest.fixture
+def skel_source():
+    return "precomputed://https://skeleton-source/"
+
+
+@pytest.fixture
+def skel_shader_text():
+    return "void main() { emitRGB(vec3(1.0, 0.0, 0.0)); }"
+
+
 def test_basic(image_layer, seg_layer_basic, anno_layer_basic):
     sb = StateBuilder(
         [image_layer, seg_layer_basic, anno_layer_basic], target_site="seunglab"
@@ -355,3 +365,18 @@ def test_timestamp(seg_path_graphene, target_site):
     else:
         # Not implemented yet in cave-explorer
         assert True
+
+
+@pytest.mark.parametrize("target_site", [None, "seunglab", "cave-explorer"])
+def test_skeleton_source(seg_path_graphene, skel_source, target_site, skel_shader_text):
+    seg = SegmentationLayerConfig(
+        seg_path_graphene, skeleton_source=skel_source, skeleton_shader=skel_shader_text
+    )
+    sb = StateBuilder([seg], target_site=target_site)
+    state = sb.render_state(return_as="dict")
+    if target_site == "cave-explorer":
+        assert state["layers"][0]["source"][1]["url"] == skel_source
+        assert state["layers"][0]["skeletonRendering"]["shader"] == skel_shader_text
+    else:
+        # Not implemented in older versions
+        assert True