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Integrate fastcore functions #150

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merged 34 commits into from
Aug 15, 2024
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4e5f8cd
use navis-fastcore when available:
schlegelp Jul 7, 2024
fc73768
add missing import
schlegelp Jul 7, 2024
5f2242c
add fastcore tests
schlegelp Jul 7, 2024
14c034c
add navis-fastcore as extra requirement
schlegelp Jul 7, 2024
64c8464
plot2d: avoid issue with numpy 1.26.4 and matplotlib 3.9.1
schlegelp Jul 8, 2024
bd7f657
use fastcore in navis.strahler_index(); important note:
schlegelp Jul 8, 2024
4c79f31
docs: add fastcore descriptions
schlegelp Jul 8, 2024
006dd59
strahler_index: remove superfluous print statements
schlegelp Jul 8, 2024
bc1dcb9
docs: fix typo in `mirror_brain` docstring
schlegelp Jul 25, 2024
d799006
requirements: pin navis-fastcore==0.0.3
schlegelp Jul 25, 2024
a9794cc
remove a few unnecessary imports
schlegelp Jul 25, 2024
3a18bc6
requirements: bump minimum navis-fastcore version to 0.0.4
schlegelp Jul 25, 2024
5c9de87
doctests: exclude '/scripts' path
schlegelp Jul 28, 2024
579f72a
to_adjacency: avoid setting on copy warning
schlegelp Jul 28, 2024
36cef59
pandas: avoid future issues with mismatching dtypes when updating values
schlegelp Jul 28, 2024
a3a7b5d
resample_skeleton: fix issue when segments is array, not list (fastcore)
schlegelp Jul 28, 2024
143d74b
plot2d: replace depcrecated mpl proj_points function
schlegelp Jul 28, 2024
46e9977
synblast: avoid issue with pykdtree's KDTree being unpickable
schlegelp Jul 28, 2024
20e3652
MovingLeastSquaresTransform: fix doctests; important note:
schlegelp Jul 28, 2024
df709b4
replace deprecated alias: numpy.product -> numpy.prod
schlegelp Jul 28, 2024
c1612d1
pd.read_json: avoid deprecation warning by wrapping string in StringIO
schlegelp Jul 28, 2024
01f42c7
update transforms README
schlegelp Jul 29, 2024
5b9ea64
replace deprecated igraph shortest_paths() -> distances()
schlegelp Jul 29, 2024
5471610
node_label_sorting: avoid issues if segment list if array not list
schlegelp Jul 29, 2024
7bde4f7
fix issue with parsing vertex colors for mesh neurons:
schlegelp Jul 30, 2024
26f4fa9
fix synblast:
schlegelp Jul 30, 2024
acfbc17
fix morph analysis notebook
schlegelp Jul 30, 2024
52f2004
subset_neuron (skeletons): drop soma if not part of neuron anymore
schlegelp Jul 30, 2024
173de40
prepare_colormap: fix issue with numpy array of colors
schlegelp Jul 30, 2024
241658f
some formatting in various files
schlegelp Aug 2, 2024
d7aa6fd
small fixes in transforms README
schlegelp Aug 2, 2024
63fe8f0
parse_objects: return pygfx objects as visuals
schlegelp Aug 2, 2024
73ca674
small fixes in neuPrint interface:
schlegelp Aug 2, 2024
7dc5011
make_tube: skip single point branches
schlegelp Aug 11, 2024
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make_tube: skip single point branches
schlegelp committed Aug 11, 2024
commit 7dc50111457f408b2169933be68b63e73a4d2009
4 changes: 4 additions & 0 deletions navis/plotting/plot_utils.py
Original file line number Diff line number Diff line change
@@ -200,6 +200,10 @@ def make_tube(segments, radii=1.0, tube_points=8, use_normals=True):
# Need to make sure points are floats
points = np.array(points).astype(float)

# Skip single points
if len(points) < 2:
continue

if use_normals:
tangents, normals, binormals = _frenet_frames(points)
else: