debug LP

ecut/base_types.py

@@ -192,6 +192,8 @@ def _linear_programming(self):
             frag.source = dict.fromkeys(frag.traversed, 1)
 
         for variable in self._problem.variables():
+            if 'dummy' in variable.name:
+                continue
             frag_id, src = variable.name.split('_')[1:]
             frag_id, src = int(frag_id), int(src)
             frag = self._fragment[frag_id]

example/app2_processing.py

@@ -9,13 +9,14 @@
 
 if __name__ == '__main__':
     # tree = swc_handler.parse_swc('../test/data/gcut_input.swc_sorted.swc')
-    tree = swc_handler.parse_swc(r'D:\rectify\my_app2\17302_14358_42117_2799.swc')
+    # tree = swc_handler.parse_swc(r'D:\rectify\my_app2\17302_14358_42117_2799.swc')
+    tree = swc_handler.parse_swc(r"C:\Users\zzh\Downloads\2965_9868_7229.swc")
     tree = [t for t in tree if not (t[1] == t[2] == t[3] == 0)]
     # tree = swc_handler.parse_swc(r'D:\rectify\my_app2\15257_16445_16836_4489.swc')
-
-    maxr = max([t[5] for t in tree]) * .3
-    rad = max(maxr * .5, 5.)
-    centers = DetectTracingMask(rad, 20.).predict(tree, [.3, .3, 1])
+    res = .23
+    maxr = max([t[5] for t in tree]) * res
+    rad = max(maxr * .5, 3.)
+    centers = DetectTracingMask(rad, 20.).predict(tree, [res, res, 1])
     # anneal
     a = MorphAnneal(tree)
     tree = a.run()
@@ -26,15 +27,14 @@
     kd = KDTree([t[2:5] for t in tree])
     inds = kd.query(centers, return_distance=False)
     inds = [tree[i[0]][0] for i in inds]
-    print(inds)
+    print(inds, centers)
     e = ECut(tree, inds)
     e.run()
     trees = e.export_swc()
-
     # pruning
     for k, v in trees.items():
         v = swc_handler.sort_swc(v)
-        p = ErrorPruning([.3,.3,1], anchor_dist=20., soma_radius=10.)
+        p = ErrorPruning([res,res,1], anchor_dist=20., soma_radius=10.)
         morph = Morphology(v)
         a = p.branch_prune(morph, 60, 1.5)
         b = p.crossover_prune(morph, 2, 60, 90, short_tips_thr=10., no_multi=False)