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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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30 changes: 23 additions & 7 deletions src/sparc/client/zinchelper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,9 @@
import os
import re

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.exporter.vtk import ArgonSceneExporter as VTKExporter
from cmlibs.utils.zinc.field import field_exists, get_group_list
from cmlibs.zinc.context import Context
from cmlibs.zinc.result import RESULT_OK
from mbfxml2ex.app import read_xml
Expand Down Expand Up @@ -129,9 +129,9 @@ def _get_scaffold(self, dataset_id):
sm = scaffolds.Scaffolds_decodeJSON(c["scaffold_settings"]["scaffoldPackage"])
sm.generate(self._region)

def get_scaffold_vtk(self, dataset_id, output_location=None):
def get_scaffold_as_vtk(self, dataset_id, output_location=None):
"""
Generates a VTK file for the scaffold settings of a dataset.
Generates a VTK file from the scaffold settings defined in a dataset.

Args:
dataset_id (int): The ID of the dataset to generate the VTK file for.
Expand All @@ -146,9 +146,9 @@ def get_scaffold_vtk(self, dataset_id, output_location=None):
ex = VTKExporter(output_location, "scaffold")
ex.export_vtk_from_scene(self._region.getScene())

def get_scaffold_stl(self, dataset_id, output_location=None):
def get_scaffold_as_stl(self, dataset_id, output_location=None):
"""
Generates an STL file for the scaffold settings of a dataset.
Generates an STL file from the scaffold settings defined in a dataset.

Args:
dataset_id (int): The ID of the dataset to generate the STL file for.
Expand All @@ -161,7 +161,23 @@ 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: /
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Shape. Dimension=0
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0.000000000000000e+00 1.500000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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Shape. Dimension=3, line*line*line
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#Nodes=8
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x. c.Hermite*c.Hermite*c.Hermite, no modify, standard node based.
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Value labels: value d/ds1 d/ds2
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Value labels: zero zero zero
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Value labels: value d/ds1 d/ds2
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Value labels: zero
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Value labels: zero zero zero
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Value labels: zero
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Value labels: d/ds3
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Value labels: zero zero zero
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Value labels: value d/ds1 d/ds2
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Value labels: zero
6. #Values=1
Value labels: d/ds3
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Value labels: zero zero zero
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Value labels: zero
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Value labels: zero zero zero
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Value labels: value d/ds1 d/ds2
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Value labels: zero
8. #Values=1
Value labels: d/ds3
0. #Values=3
Value labels: zero zero zero
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#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
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Value labels: value d/ds1 d/ds2
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Value labels: zero
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Value labels: d/ds3
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Value labels: zero zero zero
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Value labels: value d/ds1 d/ds2
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Value labels: zero
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Value labels: value d/ds1 d/ds2
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Value labels: d/ds3
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Value labels: zero zero zero
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Value labels: value d/ds1 d/ds2
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Value labels: zero
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Value labels: d/ds3
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Value labels: value d/ds1 d/ds2
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Value labels: value d/ds1 d/ds2
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Value labels: zero
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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
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