From a348bc3c04c56fb3ca6662a49330541a51a91aa1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Mon, 5 Jul 2021 21:28:55 +0100
Subject: [PATCH] bugfixed and add npairs function
Former-commit-id: e14a74604bb44168ab2212ea787a9d4095a9f3c0
---
core/io/base.py | 23 +++++++++++++++++++----
1 file changed, 19 insertions(+), 4 deletions(-)
diff --git a/core/io/base.py b/core/io/base.py
index cb771ced..181f23b0 100644
--- a/core/io/base.py
+++ b/core/io/base.py
@@ -49,9 +49,11 @@ class BridgeH5:
] # get indices of consecutive elements
return where_consec
- def get_npairs(self, nstepsback=2):
- tree = b.cell_tree
- consecutive = b.get_consecutives(tree, nstepsback=nstepsback)
+ def get_npairs(self, nstepsback=2, tree=None):
+ if tree is None:
+ tree = self.cell_tree
+
+ consecutive = self.get_consecutives(tree, nstepsback=nstepsback)
flat_tree = flatten(tree)
n_predictions = 0
@@ -59,10 +61,23 @@ class BridgeH5:
flat = list(chain(*[product([k], list(v)) for k, v in d.items()]))
pairs = [(f, (f[0], f[1] + i)) for f in flat]
for p in pairs:
- n_predictions += len(flat_tree[p[0]]) * len(flat_tree[p[1]])
+ n_predictions += len(flat_tree.get(p[0], [])) * len(
+ flat_tree.get(p[1], [])
+ )
return n_predictions
+ def get_npairs_over_time(self, nstepsback=2):
+ tree = self.cell_tree
+ npairs = []
+ for t in self._hdf["cell_info"]["processed_timepoints"][()]:
+ tmp_tree = {
+ k: {k2: v2 for k2, v2 in v.items() if k2 <= t} for k, v in tree.items()
+ }
+ npairs.append(self.get_npairs(tree=tmp_tree))
+
+ return np.diff(npairs)
+
def get_info_tree(
self, fields: Union[tuple, list] = ("trap", "timepoint", "cell_label")
):
--
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