From dac567699497d0d33b07666c88273c20793697b6 Mon Sep 17 00:00:00 2001
From: Maciej Wielgosz <maciej.wielgosz@nibio.no>
Date: Thu, 10 Aug 2023 11:24:49 +0200
Subject: [PATCH] fix in fsct/point2trees.py to solve convex hull 2D problem in
the cube function
---
fsct/points2trees.py | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/fsct/points2trees.py b/fsct/points2trees.py
index 93e3785..311b89b 100644
--- a/fsct/points2trees.py
+++ b/fsct/points2trees.py
@@ -5,6 +5,7 @@ import argparse
import numpy as np
import pandas as pd
from tqdm.auto import tqdm
+import scipy
from sklearn.neighbors import NearestNeighbors
from sklearn.cluster import DBSCAN
@@ -65,16 +66,18 @@ def generate_path(samples, origins, n_neighbours=200, max_length=0):
return paths
-
def cube(pc):
-
if len(pc) > 5:
- vertices = ConvexHull(pc[['x', 'y', 'z']]).vertices
- idx = np.random.choice(vertices, size=len(vertices), replace=False)
- return pc.loc[pc.index[idx]]
+ try:
+ vertices = ConvexHull(pc[['x', 'y', 'z']]).vertices
+ idx = np.random.choice(vertices, size=len(vertices), replace=False)
+ return pc.loc[pc.index[idx]]
+ except scipy.spatial.qhull.QhullError as e:
+ print(f"Error computing convex hull for group with {len(pc)} points: {e}")
+ # Handle the special case as needed, e.g., return the input or a default value
+ return pc
else:
- return pc
-
+ return pc
if __name__ == '__main__':
@@ -199,11 +202,13 @@ if __name__ == '__main__':
# group skeleton points
grouped = stem_pc.loc[stem_pc.clstr != -1].groupby('clstr')
+
if params.verbose: print('fitting convex hulls to clusters')
if params.pandarallel:
chull = grouped.parallel_apply(cube) # parallel_apply only works witn pd < 1.3
else:
chull = grouped.apply(cube) # don't think works with Jasmin or parallel_apply only works witn pd < 1.3
+
chull = chull.reset_index(drop=True)
### identify possible stems ###
--
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