Allow for repeat contours in neurolucida

slider/chart_reg.py

@@ -66,7 +66,12 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):
     img = jp2.read(rlevel=rlevel)
 
     # initial scaling based on boundng boxes
-    edge_crds = contour[boundary_key][:, :2] * [1, -1]
+    boundary_idx = np.where([f==boundary_key for f,_ in contour])[0]
+    if boundary_idx.size > 1:
+        raise RuntimeError(f'Repeated entries of boundary key in chart: {boundary_key}')
+    print(boundary_idx)
+
+    edge_crds = contour[boundary_idx[0]][1][:, :2] * [1, -1]
     init = _init_scale(img, slide_res, edge_crds, verbose=True)
     print(init)
     print(
@@ -95,9 +100,9 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):
 
     # apply opt-xfm to contours and cells and save
 
-    contour_xfm = {
-        k: _apply_xfm(opt, v[:, :2] * [1, -1]).tolist() for k, v in contour.items()
-    }
+    contour_xfm = [
+        (k, _apply_xfm(opt, v[:, :2] * [1, -1]).tolist()) for k, v in contour
+    ]
 
     if DO_PLOTS:
         fig, ax = plt.subplots(figsize=(10, 10))
@@ -105,7 +110,7 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):
         extent = np.array([0, img.shape[1], img.shape[0], 0]) * slide_res
         ax.imshow(img, extent=extent)
 
-        for name, coords in contour_xfm.items():
+        for name, coords in contour_xfm:
 
             coords = np.array(coords)
 

slider/external/neurolucida.py

@@ -180,14 +180,14 @@ def _flatten_subsection(subsection, _type, offset, parent):
 
 def _to_data(sections):
     cells    = []
-    contour = {}
+    contour = []
 
     xyz     = []
     for section in sections:
         if section[0] == 'Asterisk':  # Cell
             cells.append( np.asarray(section[2],dtype=np.float64) )           
         else:
-            contour[section[0].replace('"','')] = np.asarray(section[1:],dtype=np.float64)
+            contour.append((section[0].replace('"',''), np.asarray(section[1:],dtype=np.float64)))
 
     cells = np.asarray(cells)
 
@@ -195,7 +195,7 @@ def _to_data(sections):
         
 
 def read(file):
-    '''return a dict
+    '''return a list of tuples
     '''
 
     with open(file, encoding='utf-8', errors='replace') as fd: