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Issue 174 #175

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merged 10 commits into from
Dec 15, 2024
Merged

Issue 174 #175

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e038c89
replicate error in pytest
floesche Dec 9, 2024
259be83
potential fix for #174
floesche Dec 9, 2024
94ec009
Issue 174 ci (#1)
floesche Dec 10, 2024
b006dc3
restart CI
floesche Dec 11, 2024
09c7a15
reset to original
floesche Dec 11, 2024
50c552a
move blender
floesche Dec 11, 2024
eb96d7e
create symlink
floesche Dec 11, 2024
05a5d6e
modify env
floesche Dec 11, 2024
3b25166
Merge branch 'issue_174' into issue_174_ci2
floesche Dec 11, 2024
196a3cd
Merge pull request #2 from floesche/issue_174_ci2
floesche Dec 11, 2024
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10 changes: 10 additions & 0 deletions navis/meshes/b3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,9 +37,19 @@
simp
Simplified mesh object.

Examples
--------
>>> import navis
>>> n = navis.example_neurons(1, kind="mesh")
>>> n_sm = simplify_mesh_blender(n,
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I think it's a good idea to provide some example here. Currently, this will cause an error during doctests because Blender is not installed on the Github worker.

You can either edit test-package.yml to install Blender before running pytest, or add the # doctest: +SKIP directive to exclude this line from the tests (see other such examples throughout the codebase). In theory, the former should be pretty straight forward: wget the linux distribution, unzip somewhere and add to PATH. In practice, Github Actions can be a pain in the neck to debug.

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Thanks, that's a great idea.

I had issue with the current installation with some mesa related libraries and removed graphviz-dev and mesa-vulkan-drivers from my test-package.yml. I also added the latest blender-LTS via moguri/setup-blender@v1 action.

I did not see the tests finish, but in at least one of the runs I saw the test from b3d pass. Let me know if this could work for you?

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I updated the solution to keeping the ubuntu libraries as they were before and installing the blender directly via wget, not relying on an external and potentially unnecessary complex action. The simplify_mesh_blender seems to pass more reliably now, the comparison between basic types and numpy types still fails, so the overall tests currently still fail.

Let me know if I should change anything else?

... F=0.2,
... inplace=False)
>>> n.n_vertices > n_sm.n_vertices
True

"""
if not tm.interfaces.blender.exists:
raise ModuleNotFoundError('No Blender 3D unavailable (executable not found).')

Check failure on line 52 in navis/meshes/b3d.py

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GitHub Actions / build (3.9) 

No Blender 3D unavailable (executable not found).
_blender_executable = tm.interfaces.blender._blender_executable

if F > 1 or F < 0:
Expand Down
34 changes: 23 additions & 11 deletions navis/meshes/templates/blender_decimate.py.template
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Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,29 @@ import os
if __name__ == '__main__':
# clear scene of default box
bpy.ops.wm.read_homefile()
try:
bpy.ops.object.mode_set(mode='OBJECT')
except BaseException:
pass
bpy.ops.object.select_all(action='SELECT')
bpy.ops.object.delete(use_global=True)
if bpy.app.version > (3, 2, 0):
objs = [bpy.context.scene.objects['Camera'], bpy.context.scene.objects['Cube'], bpy.context.scene.objects['Light']]
with bpy.context.temp_override(selected_objects=objs):
bpy.ops.object.delete()
else:
try:
bpy.ops.object.mode_set(mode='OBJECT')
except BaseException:
pass
bpy.ops.object.select_all(action='SELECT')
bpy.ops.object.delete(use_global=True)

# get temporary files from templated locations
mesh_pre = $MESH_PRE
mesh_post = os.path.abspath(r'$MESH_POST')

for filename in mesh_pre: # use data.objects instead of context.scene.objects
bpy.ops.import_mesh.stl(filepath=os.path.abspath(filename))

if bpy.app.version > (4, 0, 0):
bpy.ops.wm.stl_import(filepath=os.path.abspath(filename))
else:
bpy.ops.import_mesh.stl(filepath=os.path.abspath(filename))
mesh = bpy.data.objects[0]

# Make sure mesh is the active object
try:
# earlier than blender <2.8
Expand All @@ -29,13 +37,17 @@ if __name__ == '__main__':
bpy.context.view_layer.objects.active = mesh

# add decimate modifier

mod = mesh.modifiers.new('decimate', 'DECIMATE')
mod.decimate_type = 'COLLAPSE'
mod.ratio = $RATIO
mod.use_collapse_triangulate = True

bpy.ops.object.modifier_apply(modifier=mod.name)

bpy.ops.export_mesh.stl(
filepath=mesh_post,
use_mesh_modifiers=True)
if bpy.app.version > (4, 0, 0):
bpy.ops.wm.stl_export(filepath=mesh_post, apply_modifiers=True)
else:
bpy.ops.export_mesh.stl(
filepath=mesh_post,
use_mesh_modifiers=True)
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