debug graph cut

ecut/base_types.py

@@ -89,7 +89,7 @@ def export_swc(self, partition=True):
             frag_node = self._fragment_trees[frag.source][frag_id]
             nodes = self._fragment[frag_id].nodes
             if not frag_node.reverse:
-                nodes = reversed(nodes)
+                nodes = nodes[::-1]
             par_frag_id = frag_node.parent
             if par_frag_id == -1:
                 last_id = -1, 1
@@ -126,10 +126,9 @@ def _linear_programming(self):
         # finding variables for fragment/soma pairs that require solving
         scores = {}      # var_i_s, i: fragment id, s: soma id
         for i, frag in self._fragment.items():
-            if len(frag.traversed) > 1:  # mixed sources
-                scores[i] = {}
-                for s in frag.traversed:
-                    scores[i][s] = pulp.LpVariable(f'Score_{i}_{s}', 0)        # non-negative
+            scores[i] = {}
+            for s in frag.traversed:
+                scores[i][s] = pulp.LpVariable(f'Score_{i}_{s}', 0)        # non-negative
 
         # objective func: cost * score
         self._problem += pulp.lpSum(

example/app2_processing.py

@@ -8,15 +8,17 @@
 
 
 if __name__ == '__main__':
-    tree = swc_handler.parse_swc('../test/data/gcut_input.swc_sorted.swc')
+    # tree = swc_handler.parse_swc('../test/data/gcut_input.swc_sorted.swc')
+    tree = swc_handler.parse_swc(r'D:\rectify\my_app2\18452_26569_3425_5509.swc')
+
+    # detect soma
+    d = DetectTracingMask(5)
+    soma = d.predict(tree, [.3, .3, 1.])
 
     # anneal
     a = MorphAnneal(tree)
     tree = a.run()
 
-    # detect soma
-    d = DetectTracingMask(2.5, 100)
-    soma = d.predict(tree, [.25, .25, 1.])
     kd = KDTree([t[2:5] for t in tree])
     inds = kd.query(soma, return_distance=False)
     inds = [tree[i[0]][0] for i in inds]

example/batch_1891.py

@@ -58,6 +58,6 @@ def main(args):
     files = sorted(indir.glob('*.swc'))
     outfiles = [outdir / f.name for f in files]
     arglist = [*zip(files, outfiles)]
-    with Pool(16) as p:
+    with Pool(12) as p:
         for i in tqdm(p.imap(main, arglist), total=len(arglist)):
             pass