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display atlas images and meshes in pixel space #160

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Sep 30, 2024
Merged

display atlas images and meshes in pixel space #160

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15 changes: 8 additions & 7 deletions brainrender_napari/napari_atlas_representation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@

@dataclass
class NapariAtlasRepresentation:
"""Representation of a BG atlas as napari layers"""
"""Representation of a BG atlas as napari layers, in pixel space."""

bg_atlas: BrainGlobeAtlas
viewer: Viewer
Expand All @@ -39,37 +39,39 @@ def add_to_viewer(self):
"""
reference = self.viewer.add_image(
self.bg_atlas.reference,
scale=self.bg_atlas.resolution,
name=f"{self.bg_atlas.atlas_name}_reference",
visible=False,
)

annotation = self.viewer.add_labels(
self.bg_atlas.annotation,
scale=self.bg_atlas.resolution,
name=f"{self.bg_atlas.atlas_name}_annotation",
)

annotation.mouse_move_callbacks.append(self._on_mouse_move)
reference.mouse_move_callbacks.append(self._on_mouse_move)

def add_structure_to_viewer(self, structure_name: str):
"""Adds the mesh of a structure to the viewer
"""Adds the mesh of a structure to the viewer.
The mesh will be rescaled to pixel space.

structure_name: the id or acronym of the structure.
"""
mesh = self.bg_atlas.mesh_from_structure(structure_name)
scale = [1.0 / resolution for resolution in self.bg_atlas.resolution]
color = self.bg_atlas.structures[structure_name]["rgb_triplet"]
self._add_mesh(
mesh,
scale,
name=f"{self.bg_atlas.atlas_name}_{structure_name}_mesh",
color=color,
)

def _add_mesh(self, mesh: Mesh, name: str, color=None):
def _add_mesh(self, mesh: Mesh, scale: list, name: str, color=None):
"""Helper function to add a mesh as a surface layer to the viewer.

mesh: the mesh to add
scale: List of scaling factors for each axis
name: name for the surface layer
color: RGB values (0-255) as a list to colour mesh with
"""
Expand All @@ -85,15 +87,14 @@ def _add_mesh(self, mesh: Mesh, name: str, color=None):
viewer_kwargs["vertex_colors"] = np.repeat(
[[float(c) / 255 for c in color]], len(points), axis=0
)
self.viewer.add_surface((points, cells), **viewer_kwargs)
self.viewer.add_surface((points, cells), scale=scale, **viewer_kwargs)

def add_additional_reference(self, additional_reference_key: str):
"""Adds a given additional reference as a layer to the viewer.
and connects it to the mouse move callback to set tooltip.
"""
additional_reference = self.viewer.add_image(
self.bg_atlas.additional_references[additional_reference_key],
scale=self.bg_atlas.resolution,
name=f"{self.bg_atlas.atlas_name}_{additional_reference_key}_reference",
)
additional_reference.mouse_move_callbacks.append(self._on_mouse_move)
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