Consistent null particle addition and sorting

magdalenat · Apr 12, 2018 · c61a162 · c61a162
1 parent c33c3c9
commit c61a162
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Showing 4 changed files with 12 additions and 18 deletions.
diff --git a/trackpy/linking/find_link.py b/trackpy/linking/find_link.py
@@ -475,8 +475,10 @@ def assign_links(self):
             else:
                 new_cands = set()
 
-            for sp in source_set:
-                sp.forward_cands.sort(key=lambda x: x[1])
+            # sort candidates and add in penalty for not linking
+            for _s in source_set:
+                _s.forward_cands.sort(key=lambda x: x[1])
+                _s.forward_cands.append((None, self.search_range))
 
             # link
             sn_spl, sn_dpl = self.subnet_linker(source_set, dest_set,

diff --git a/trackpy/linking/linking.py b/trackpy/linking/linking.py
@@ -500,8 +500,11 @@ def next_level(self, coords, t, extra_data=None):
     def assign_links(self):
         spl, dpl = [], []
         for source_set, dest_set in self.subnets:
-            for sp in source_set:
-                sp.forward_cands.sort(key=lambda x: x[1])
+            # sort candidates and add in penalty for not linking before the
+            # subnetlinker, preventing repeats occuring during adaptive linking
+            for _s in source_set:
+                _s.forward_cands.sort(key=lambda x: x[1])
+                _s.forward_cands.append((None, self.search_range))
 
             sn_spl, sn_dpl = self.subnet_linker(source_set, dest_set,
                                                 self.search_range)

diff --git a/trackpy/linking/subnet.py b/trackpy/linking/subnet.py
@@ -294,6 +294,9 @@ def split_subnet(source, dest, new_range):
             # if dp is None:
             #     continue
             assign_subnet(sp, dp, subnets=subnets)
+
+        # the null particle was removed: re-add it here
+        sp.forward_cands.append((None, new_range))
     return (subnets[key] for key in subnets)
 
 

diff --git a/trackpy/linking/subnetlinker.py b/trackpy/linking/subnetlinker.py
@@ -386,11 +386,6 @@ def subnet_linker_recursive(source_set, dest_set, search_range, **kwargs):
         # particle is lost. Not possible with default Linker implementation.
         return [source_set.pop()], [None]
 
-    # sort candidates and add in penalty for not linking
-    for _s in source_set:
-        _s.forward_cands.sort(key=lambda x: x[1])
-        _s.forward_cands.append((None, search_range))
-
     snl = SubnetLinker(source_set, len(dest_set), search_range, **kwargs)
     sn_spl, sn_dpl = [list(particles) for particles in zip(*snl.best_pairs)]
 
@@ -413,11 +408,6 @@ def subnet_linker_nonrecursive(source_set, dest_set, search_range, **kwargs):
         # particle is lost. Not possible with default Linker implementation.
         return [source_set.pop()], [None]
 
-    # sort candidates and add in penalty for not linking
-    for _s in source_set:
-        _s.forward_cands.sort(key=lambda x: x[1])
-        _s.forward_cands.append((None, search_range))
-
     sn_spl, sn_dpl = nonrecursive_link(source_set, len(dest_set), search_range, **kwargs)
 
     for dp in dest_set - set(sn_dpl):
@@ -453,10 +443,6 @@ def subnet_linker_numba(source_set, dest_set, search_range,
         # particle is lost. Not possible with default Linker implementation.
         return [source_set.pop()], [None]
 
-    # Forward candidates were already sorted by Linker.assign_links()
-    for _s in source_set:
-        _s.forward_cands.append((None, search_range))
-
     # Shortcut for small subnets, because the numba linker has significant overhead
     if (lds == 1 or lss == 1 or (lds <= 3 and lss <= 3)) and hybrid:
         sn_spl, sn_dpl = recursive_linker_obj(source_set, lds, search_range, **kwargs)