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Fix empty STL export and CI failure issues #34

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merged 7 commits into from
Dec 7, 2023
Merged

Fix empty STL export and CI failure issues #34

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4064aac
Fix empty STL export
Kayvv Dec 5, 2023
a6727e4
Add more test case and rename the functions
Kayvv Dec 5, 2023
9b1fbe8
Remove unnecessary test case
Kayvv Dec 7, 2023
fa8d0f8
Merge branch 'nih-sparc:main' into zinchelper
Kayvv Dec 7, 2023
036c1cc
Fix reviewdog format
Kayvv Dec 7, 2023
79ccd4b
Merge remote-tracking branch 'origin/zinchelper' into zinchelper
Kayvv Dec 7, 2023
7e4cb7a
Reviewdog fix
Kayvv Dec 7, 2023
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Fix empty STL export
  • Loading branch information
@Kayvv
Kayvv committed Dec 5, 2023
commit 4064aac52c8bacee0a1ad1f93198faa7b7067211
18 changes: 16 additions & 2 deletions src/sparc/client/zinchelper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

from cmlibs.exporter.vtk import ArgonSceneExporter as VTKExporter
from cmlibs.exporter.stl import ArgonSceneExporter as STLExporter
from cmlibs.utils.zinc.field import get_group_list
from cmlibs.utils.zinc.field import get_group_list, field_exists
from cmlibs.zinc.context import Context
from cmlibs.zinc.result import RESULT_OK
from mbfxml2ex.app import read_xml
Expand Down Expand Up @@ -161,7 +161,21 @@ def get_scaffold_stl(self, dataset_id, output_location=None):
output_location = "."

ex = STLExporter(output_location, "scaffold")
ex.export_stl_from_scene(self._region.getScene())
scene = self._region.getScene()
surfaces = scene.createGraphicsSurfaces()
surfaces.setBoundaryMode(surfaces.BOUNDARY_MODE_BOUNDARY)
fm = self._region.getFieldmodule()
coordinates = fm.findFieldByName("coordinates")
if not coordinates.isValid():
field_iterator = fm.createFielditerator()
field = field_iterator.next()
while field.isValid() and not coordinates.isValid():
if field_exists(fm, field.getName(), 'FiniteElement', 3):
coordinates = field
field = field_iterator.next()

surfaces.setCoordinateField(coordinates)
ex.export_stl_from_scene(scene)

def get_mbf_vtk(self, dataset_id, dataset_file, output_file=None):
"""
Expand Down
290 changes: 290 additions & 0 deletions tests/resources/cube.exf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,290 @@
EX Version: 2
Region: /
!#nodeset nodes
Shape. Dimension=0
#Fields=1
1) notcoordinates, coordinate, rectangular cartesian, real, #Components=3
x. #Values=4 (value,d/ds1,d/ds2,d/ds3)
y. #Values=4 (value,d/ds1,d/ds2,d/ds3)
z. #Values=4 (value,d/ds1,d/ds2,d/ds3)
Node: 1
0.000000000000000e+00 1.500000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
Node: 2
1.500000000000000e+00 1.499999999876600e+00 0.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
Node: 3
0.000000000000000e+00 1.500000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00 0.000000000000000e+00 9.999999999732445e-01 0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
Node: 4
1.500000000000000e+00 1.499999999876600e+00 0.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00 0.000000000000000e+00 9.999999999732445e-01 0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
Node: 5
0.000000000000000e+00 1.500000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999999732445e-01
Node: 6
1.500000000000000e+00 1.499999999876600e+00 0.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999999732445e-01
Node: 7
0.000000000000000e+00 1.500000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00 0.000000000000000e+00 9.999999999732445e-01 0.000000000000000e+00
1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999999732445e-01
Node: 8
1.500000000000000e+00 1.499999999876600e+00 0.000000000000000e+00 0.000000000000000e+00
1.000000000000000e+00 0.000000000000000e+00 9.999999999732445e-01 0.000000000000000e+00
1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999999732445e-01
!#mesh mesh1d, dimension=1, nodeset=nodes
Shape. Dimension=1, line
#Scale factor sets=0
#Nodes=0
#Fields=0
Element: 1
Element: 2
Element: 3
Element: 4
Element: 5
Element: 6
Element: 7
Element: 8
Element: 9
Element: 10
Element: 11
Element: 12
!#mesh mesh2d, dimension=2, face mesh=mesh1d, nodeset=nodes
Shape. Dimension=2, line*line
#Scale factor sets=0
#Nodes=0
#Fields=0
Element: 1
Faces:
1 2 3 4
Element: 2
Faces:
5 6 7 8
Element: 3
Faces:
9 10 1 5
Element: 4
Faces:
11 12 2 6
Element: 5
Faces:
3 7 9 11
Element: 6
Faces:
4 8 10 12
!#mesh mesh3d, dimension=3, face mesh=mesh2d, nodeset=nodes
Shape. Dimension=3, line*line*line
#Scale factor sets=0
#Nodes=8
#Fields=1
1) notcoordinates, coordinate, rectangular cartesian, real, #Components=3
x. c.Hermite*c.Hermite*c.Hermite, no modify, standard node based.
#Nodes=8
1. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
1. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
2. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
2. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
3. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
3. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
4. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
4. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
5. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
5. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
6. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
6. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
7. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
7. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
8. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
8. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
y. c.Hermite*c.Hermite*c.Hermite, no modify, standard node based.
#Nodes=8
1. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
1. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
2. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
2. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
3. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
3. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
4. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
4. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
5. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
5. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
6. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
6. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
7. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
7. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
8. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
8. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
z. c.Hermite*c.Hermite*c.Hermite, no modify, standard node based.
#Nodes=8
1. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
1. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
2. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
2. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
3. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
3. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
4. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
4. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
5. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
5. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
6. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
6. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
7. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
7. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
8. #Values=3
Value labels: value d/ds1 d/ds2
0. #Values=1
Value labels: zero
8. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
Element: 1
Faces:
1 2 3 4 5 6
Nodes:
1 2 3 4 5 6 7 8
26 changes: 25 additions & 1 deletion tests/test_zinc.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,31 @@ def test_export_scaffold_into_stl_format(zinc):
with pytest.raises(AssertionError):
zinc.get_scaffold_stl(dataset_id, output_location)

# ensure the function generates a VTK file with valid content
# ensure the function generates an STL file with valid content
dataset_id = 292
zinc.get_scaffold_stl(dataset_id, output_location)

output_file = os.path.join(output_location, "scaffold_zinc_graphics.stl")
assert os.path.exists(output_file)
assert os.path.getsize(output_file) > 0

# Clean up the temporary output file
os.remove(output_file)


def _mock_get_scaffold(self, dataset_id):
self._region.readFile(os.path.join(os.path.dirname(__file__), "resources", "cube.exf"))


def test_export_scaffold_into_stl_format_non_default_coordinates(zinc):
# create a temporary output file
output_location = os.path.abspath(
os.path.join(os.path.dirname(__file__), "resources/")
)

zinc._get_scaffold = _mock_get_scaffold.__get__(zinc)

# ensure the function generates an STL file with valid content
dataset_id = 292
zinc.get_scaffold_stl(dataset_id, output_location)

Expand Down