From 3462dff2c2766cadf32a1003d37cbd93e21a7245 Mon Sep 17 00:00:00 2001
From: mattminder <myfiles@Mattus-MacBook-Pro.local>
Date: Fri, 8 May 2020 15:35:53 +0200
Subject: [PATCH] Bugfix for error when running tracking on a frame with no
preceding frame
---
unet/hungarian.py | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/unet/hungarian.py b/unet/hungarian.py
index 45069e7..13d7284 100644
--- a/unet/hungarian.py
+++ b/unet/hungarian.py
@@ -40,6 +40,12 @@ def hungarian_align(m1, m2):
value is -1.
"""
dist, ix1, ix2 = cell_distance(m1, m2)
+
+ # If dist couldn't be calculated, return dictionary from cells to themselves
+ if dist is None:
+ unique_m2 = np.unique(m2)
+ return dict(zip(unique_m2, unique_m2))
+
solver = Munkres()
indexes = solver.compute(make_square(dist))
@@ -62,18 +68,12 @@ def cell_to_features(im, c, nsamples=None, time=None):
com = sampled.mean(axis=0)
- # roundness, principal direction
- dev = sampled - com
- cov = dev.T @ dev
- evals, evecs = np.linalg.eig(cov)
- roundness = min(evals)/max(evals)
return {'cell': c,
'time': time,
'sqrtarea': np.sqrt(area),
'area': area,
'com_x': com[0],
- 'com_y': com[1],
- 'roundness': roundness}
+ 'com_y': com[1]}
def cell_distance(m1, m2, weight_com=3):
@@ -97,6 +97,11 @@ def cell_distance(m1, m2, weight_com=3):
# Create df, rescale
feat1, ix_to_cell1 = get_features(m1, 1)
feat2, ix_to_cell2 = get_features(m2, 2)
+
+ # Check if one of matrices doesn't contain cells
+ if len(feat1)==0 or len(feat2)==0:
+ return None, None, None
+
df = pd.concat((feat1, feat2))
df[cols] = scale(df[cols])
--
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