add known channels + lower tol step

Author: quentinblampey

spatialdata_xenium_explorer/_constants.py

@@ -13,7 +13,7 @@ class ExplorerConstants:
     MICRONS_TO_PIXELS = 4.705882
 
     COLORS = [400, 500, 550, 600, 650, 700]
-    KNOWN_CHANNELS = {"DAPI": 400}
+    KNOWN_CHANNELS = {"DAPI": 400, "DNA1": 400, "DAPI (000)": 400}
 
 
 class Versions:

spatialdata_xenium_explorer/core/shapes.py

@@ -12,8 +12,12 @@
 
 log = logging.getLogger(__name__)
 
+TOLERANCE_STEP = 0.5
 
-def pad_polygon(polygon: Polygon, max_vertices: int, tolerance: float = 1) -> np.ndarray:
+
+def pad_polygon(
+    polygon: Polygon, max_vertices: int, tolerance: float = TOLERANCE_STEP
+) -> np.ndarray:
     """Transform the polygon to have the desired number of vertices
 
     Args:
@@ -37,7 +41,7 @@ def pad_polygon(polygon: Polygon, max_vertices: int, tolerance: float = 1) -> np
 
     # TODO: improve it: how to choose the right tolerance?
     polygon = polygon.simplify(tolerance=tolerance)
-    return pad_polygon(polygon, max_vertices, tolerance + 1)
+    return pad_polygon(polygon, max_vertices, tolerance + TOLERANCE_STEP)
 
 
 def write_polygons(