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Integrate fastcore functions #150

Merged
merged 34 commits into from
Aug 15, 2024
Merged

Integrate fastcore functions #150

merged 34 commits into from
Aug 15, 2024

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schlegelp
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@schlegelp schlegelp commented Jul 8, 2024 •
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This is a work-in-progress PR to integrate functions re-implemented in Rust via navis-fastcore.

List of functions that will now use fastcore under-the-hood if available:

  • geodesic_matrix(): 20x faster (note that this will also speed up a number of downstream functions such as longest_neurite)
  • prune_twigs(): 4x faster
  • strahler_index(): 20x faster
  • synapse_flow_centrality(): 4.5x faster (but importantly much more memory efficient)
  • segments_to_coords(): 3.5x faster (this function is a major bottleneck during plotting)
  • TreeNeuron.cable_length property: 2x faster
  • _connected_components(): 1.4x faster

Potential TODOs:

  • skeletonization (bigger project)
  • NBLAST (protoype working but oddly still slower than implementation in navis)
  • pin fastcore version

Misc:

  • this PR also fixes a couple bugs encountered in the progress:
    • fixed synblast multiprocessing (pickling) issue
    • fixed issue with ax.add_collection3d in plot2d (introduced with in recent matplotlib version)
    • single disconnected nodes will now be ignored during plotting when radius=True (caused error previously)
    • neuPrint interface: fetch_mesh_neuron() will now ignore lod parameter if not supported by mesh source (e.g. for legacy meshes); previously this caused an error
  • fixed a bunch of deprecation warnings e.g. from numpy, igraph and matplotlib
  • subset_neuron now sets ._soma to None if the soma is lost during subsetting

schlegelp added 30 commits July 7, 2024 10:39
@schlegelp
use navis-fastcore when available:
4e5f8cd 
- _generate_segments() and _break_segments()
- _connected_components() if input is skeleton
- skeletons.cable_length (via new cable_length() function)
- geodesic_matrix()
- prune_twigs() when precise=False
- segments_to_coords
- synapse_flow_centrality()
@schlegelp
add missing import
fc73768
@schlegelp
add fastcore tests
5f2242c
@schlegelp
add navis-fastcore as extra requirement
14c034c
@schlegelp
plot2d: avoid issue with numpy 1.26.4 and matplotlib 3.9.1
64c8464
@schlegelp
use fastcore in navis.strahler_index(); important note:
bd7f657 
- this also changes how the "greedy" method works
@schlegelp
docs: add fastcore descriptions
4c79f31
@schlegelp
strahler_index: remove superfluous print statements
006dd59
@schlegelp
docs: fix typo in mirror_brain docstring
bc1dcb9
@schlegelp
requirements: pin navis-fastcore==0.0.3
d799006
@schlegelp
remove a few unnecessary imports
a9794cc
@schlegelp
requirements: bump minimum navis-fastcore version to 0.0.4
3a18bc6
@schlegelp
doctests: exclude '/scripts' path
5c9de87
@schlegelp
to_adjacency: avoid setting on copy warning
579f72a
@schlegelp
pandas: avoid future issues with mismatching dtypes when updating values
36cef59
@schlegelp
resample_skeleton: fix issue when segments is array, not list (fastcore)
a3a7b5d
@schlegelp
plot2d: replace depcrecated mpl proj_points function
143d74b
@schlegelp
synblast: avoid issue with pykdtree's KDTree being unpickable
46e9977
@schlegelp
MovingLeastSquaresTransform: fix doctests; important note:
20e3652 
no clue why that passed previously - I did investigate but did not find
a reason
@schlegelp
replace deprecated alias: numpy.product -> numpy.prod
df709b4
@schlegelp
pd.read_json: avoid deprecation warning by wrapping string in StringIO
c1612d1
@schlegelp
update transforms README
01f42c7
@schlegelp
replace deprecated igraph shortest_paths() -> distances()
5b9ea64
@schlegelp
node_label_sorting: avoid issues if segment list if array not list
5471610
@schlegelp
fix issue with parsing vertex colors for mesh neurons:
7bde4f7 
- eval_color: make sure numpy arrays are not converted to lists
- prepare_colormap: not sure why this was wrong but it was
- mesh2plotly: deal with rgb vs rgba colors
@schlegelp
fix synblast:
26f4fa9 
- remove accidental return
- fix single query target
@schlegelp
fix morph analysis notebook
acfbc17
@schlegelp
subset_neuron (skeletons): drop soma if not part of neuron anymore
52f2004
@schlegelp
prepare_colormap: fix issue with numpy array of colors
173de40
@schlegelp
some formatting in various files
241658f
@schlegelp schlegelp changed the title [WIP] Integrate fastcore functions Integrate fastcore functions Aug 15, 2024
@schlegelp
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There is one remaining failing test: strangely, MovingLeastSquaresTransform.xform return different values depending on whether I run it locally on my machine or whether it runs on Github. Since this problem is unrelated to this PR, I will ignore it and go ahead with the merge.

@schlegelp schlegelp merged commit 5d21d13 into master Aug 15, 2024
13 of 25 checks passed
@schlegelp schlegelp deleted the fastcore branch August 15, 2024 18:29
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@schlegelp