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rchristierchristie
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Merge pull request ABI-Software#279 from rchristie/ellipsoid
Add ellipsoid scaffold
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‎src/scaffoldmaker/meshtypes/meshtype_3d_ellipsoid1.py‎

Lines changed: 174 additions & 0 deletions
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@@ -0,0 +1,174 @@
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"""
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Generates a solid ellipsoid of hexahedral elements.
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"""
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import math
5+
from cmlibs.utils.zinc.field import find_or_create_field_coordinates
6+
from scaffoldmaker.annotation.annotationgroup import AnnotationGroup
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from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
8+
from scaffoldmaker.utils.ellipsoidmesh import EllipsoidMesh, EllipsoidSurfaceD3Mode
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from scaffoldmaker.utils.meshrefinement import MeshRefinement
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11+
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class MeshType_3d_ellipsoid1(Scaffold_base):
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"""
14+
Generates a solid ellipsoid of hexahedral elements.
15+
"""
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@classmethod
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def getName(cls):
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return "3D Ellipsoid 1"
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@classmethod
22+
def getDefaultOptions(cls, parameterSetName='Default'):
23+
options = {
24+
"Number of elements across axis 1": 4,
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"Number of elements across axis 2": 6,
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"Number of elements across axis 3": 8,
27+
"2D surface only": False,
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"Number of transition elements": 1,
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"Axis length x": 1.0,
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"Axis length y": 1.5,
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"Axis length z": 2.0,
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"Axis 2 x-rotation degrees": 0.0,
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"Axis 3 x-rotation degrees": 90.0,
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"Advanced n-way derivative factor": 0.6,
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"Advanced surface D3 mode": EllipsoidSurfaceD3Mode.SURFACE_NORMAL.value,
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"Refine": False,
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"Refine number of elements": 4,
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}
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return options
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@classmethod
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def getOrderedOptionNames(cls):
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return [
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"Number of elements across axis 1",
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"Number of elements across axis 2",
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"Number of elements across axis 3",
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"Number of transition elements",
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"2D surface only",
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"Axis length x",
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"Axis length y",
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"Axis length z",
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"Axis 2 x-rotation degrees",
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"Axis 3 x-rotation degrees",
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"Advanced n-way derivative factor",
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"Advanced surface D3 mode",
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"Refine",
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"Refine number of elements"
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]
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@classmethod
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def checkOptions(cls, options):
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dependent_changes = False
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max_transition_count = None
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for key in [
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"Number of elements across axis 1",
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"Number of elements across axis 2",
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"Number of elements across axis 3"
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]:
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if options[key] < 4:
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options[key] = 4
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elif options[key] % 2:
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options[key] += 1
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transition_count = (options[key] // 2) - 1
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if (max_transition_count is None) or (transition_count < max_transition_count):
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max_transition_count = transition_count
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if options["Number of transition elements"] < 1:
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options["Number of transition elements"] = 1
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elif options["Number of transition elements"] > max_transition_count:
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options["Number of transition elements"] = max_transition_count
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dependent_changes = True
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for key in [
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"Axis length x",
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"Axis length y",
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"Axis length z"
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]:
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if options[key] <= 0.0:
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options[key] = 1.0
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if options["Advanced n-way derivative factor"] < 0.1:
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options["Advanced n-way derivative factor"] = 0.1
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elif options["Advanced n-way derivative factor"] > 1.0:
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options["Advanced n-way derivative factor"] = 1.0
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try:
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mode = EllipsoidSurfaceD3Mode(options["Advanced surface D3 mode"])
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except ValueError:
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options["Advanced surface D3 mode"] = EllipsoidSurfaceD3Mode.SURFACE_NORMAL.value
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for key in [
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"Refine number of elements"
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]:
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if options[key] < 1:
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options[key] = 1
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return dependent_changes
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@classmethod
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def generateBaseMesh(cls, region, options):
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"""
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Generate the base tricubic Hermite mesh. See also generateMesh().
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:param region: Zinc region to define model in. Must be empty.
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:param options: Dict containing options. See getDefaultOptions().
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:return: empty list of AnnotationGroup, None
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"""
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element_counts = [options[key] for key in [
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"Number of elements across axis 1", "Number of elements across axis 2", "Number of elements across axis 3"]]
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transition_element_count = options["Number of transition elements"]
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a = options["Axis length x"]
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b = options["Axis length y"]
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c = options["Axis length z"]
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axis2_x_rotation_radians = math.radians(options["Axis 2 x-rotation degrees"])
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axis3_x_rotation_radians = math.radians(options["Axis 3 x-rotation degrees"])
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surface_only = options["2D surface only"]
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nway_derivative_factor = options["Advanced n-way derivative factor"]
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surface_d3_mode = EllipsoidSurfaceD3Mode(options["Advanced surface D3 mode"])
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fieldmodule = region.getFieldmodule()
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coordinates = find_or_create_field_coordinates(fieldmodule)
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ellipsoid = EllipsoidMesh(a, b, c, element_counts, transition_element_count,
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axis2_x_rotation_radians, axis3_x_rotation_radians, surface_only)
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left_group = AnnotationGroup(region, ("left", ""))
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right_group = AnnotationGroup(region, ("right", ""))
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back_group = AnnotationGroup(region, ("back", ""))
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front_group = AnnotationGroup(region, ("front", ""))
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bottom_group = AnnotationGroup(region, ("bottom", ""))
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top_group = AnnotationGroup(region, ("top", ""))
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annotation_groups = [left_group, right_group, back_group, front_group, bottom_group, top_group]
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octant_group_lists = []
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for octant in range(8):
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octant_group_list = []
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octant_group_list.append((right_group if (octant & 1) else left_group).getGroup())
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octant_group_list.append((front_group if (octant & 2) else back_group).getGroup())
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octant_group_list.append((top_group if (octant & 4) else bottom_group).getGroup())
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octant_group_lists.append(octant_group_list)
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ellipsoid.set_octant_group_lists(octant_group_lists)
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if not surface_only:
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box_group = AnnotationGroup(region, ("box", ""))
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transition_group = AnnotationGroup(region, ("transition", ""))
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annotation_groups += [box_group, transition_group]
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ellipsoid.set_box_transition_groups(box_group.getGroup(), transition_group.getGroup())
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ellipsoid.set_nway_derivative_factor(nway_derivative_factor)
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ellipsoid.set_surface_d3_mode(surface_d3_mode)
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ellipsoid.build()
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ellipsoid.generate_mesh(fieldmodule, coordinates)
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return annotation_groups, None
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@classmethod
166+
def refineMesh(cls, meshRefinement, options):
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"""
168+
Refine source mesh into separate region, with change of basis.
169+
:param meshRefinement: MeshRefinement, which knows source and target region.
170+
:param options: Dict containing options. See getDefaultOptions().
171+
"""
172+
assert isinstance(meshRefinement, MeshRefinement)
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refineElementsCount = options["Refine number of elements"]
174+
meshRefinement.refineAllElementsCubeStandard3d(refineElementsCount, refineElementsCount, refineElementsCount)

‎src/scaffoldmaker/scaffolds.py‎

Lines changed: 2 additions & 0 deletions
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@@ -22,6 +22,7 @@
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from scaffoldmaker.meshtypes.meshtype_3d_cecum1 import MeshType_3d_cecum1
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from scaffoldmaker.meshtypes.meshtype_3d_colon1 import MeshType_3d_colon1
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from scaffoldmaker.meshtypes.meshtype_3d_colonsegment1 import MeshType_3d_colonsegment1
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from scaffoldmaker.meshtypes.meshtype_3d_ellipsoid1 import MeshType_3d_ellipsoid1
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from scaffoldmaker.meshtypes.meshtype_3d_esophagus1 import MeshType_3d_esophagus1
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from scaffoldmaker.meshtypes.meshtype_3d_gastrointestinaltract1 import MeshType_3d_gastrointestinaltract1
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from scaffoldmaker.meshtypes.meshtype_3d_heart1 import MeshType_3d_heart1
@@ -88,6 +89,7 @@ def __init__(self):
8889
MeshType_3d_cecum1,
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MeshType_3d_colon1,
9091
MeshType_3d_colonsegment1,
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MeshType_3d_ellipsoid1,
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MeshType_3d_esophagus1,
9294
MeshType_3d_gastrointestinaltract1,
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MeshType_3d_heart1,

‎src/scaffoldmaker/utils/eft_utils.py‎

Lines changed: 70 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -687,6 +687,38 @@ def __init__(self):
687687
[[1.0, 0.0, 0.0], [1.0, 1.0, 0.0], [0.0, 1.0, 0.0], [-1.0, 1.0, 0.0],
688688
[-1.0, 0.0, 0.0], [-1.0, -1.0, 0.0], [0.0, -1.0, 0.0], [1.0, -1.0, 0.0],
689689
[0.0, 0.0, -1.0], [0.0, 0.0, 1.0]])
690+
self._nodeLayoutTriplePoint2DQ1 = HermiteNodeLayout(
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[[-1.0, 0.0], [0.0, -1.0], [1.0, 1.0]])
692+
self._nodeLayoutTriplePoint2DQ2 = HermiteNodeLayout(
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[[0.0, -1.0], [1.0, 0.0], [-1.0, 1.0]])
694+
self._nodeLayoutTriplePoint2DQ3 = HermiteNodeLayout(
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[[1.0, 0.0], [0.0, 1.0], [-1.0, -1.0]])
696+
self._nodeLayoutTriplePoint2DQ4 = HermiteNodeLayout(
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[[0.0, 1.0], [-1.0, 0.0], [1.0, -1.0]])
698+
self._nodeLayout3WayPoints12 = [
699+
HermiteNodeLayout([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [-1.0, -1.0, 0.0], [0.0, 0.0, -1.0], [0.0, 0.0, 1.0]]),
700+
HermiteNodeLayout([[-1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, -1.0, 0.0], [0.0, 0.0, -1.0], [0.0, 0.0, 1.0]]),
701+
HermiteNodeLayout([[1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [-1.0, 1.0, 0.0], [0.0, 0.0, -1.0], [0.0, 0.0, 1.0]]),
702+
HermiteNodeLayout([[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [1.0, 1.0, 0.0], [0.0, 0.0, -1.0], [0.0, 0.0, 1.0]])]
703+
self._nodeLayout3WayPoints13 = [
704+
HermiteNodeLayout([[-1.0, 0.0, 0.0], [0.0, 0.0, -1.0], [1.0, 0.0, 1.0], [0.0, -1.0, 0.0], [0.0, 1.0, 0.0]]),
705+
HermiteNodeLayout([[1.0, 0.0, 0.0], [0.0, 0.0, -1.0], [-1.0, 0.0, 1.0], [0.0, -1.0, 0.0], [0.0, 1.0, 0.0]]),
706+
HermiteNodeLayout([[1.0, 0.0, 0.0], [0.0, 0.0, -1.0], [-1.0, 0.0, 1.0], [0.0, -1.0, 0.0], [0.0, 1.0, 0.0]]),
707+
HermiteNodeLayout([[-1.0, 0.0, 0.0], [0.0, 0.0, -1.0], [1.0, 0.0, 1.0], [0.0, -1.0, 0.0], [0.0, 1.0, 0.0]])]
708+
self._nodeLayout3WayPoints23 = [
709+
HermiteNodeLayout([[0.0, 1.0, 0.0], [0.0, 0.0, -1.0], [0.0, -1.0, 1.0], [-1.0, 0.0, 0.0], [1.0, 0.0, 0.0]]),
710+
HermiteNodeLayout([[0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [0.0, 1.0, 1.0], [-1.0, 0.0, 0.0], [1.0, 0.0, 0.0]]),
711+
HermiteNodeLayout([[0.0, 1.0, 0.0], [0.0, 0.0, -1.0], [0.0, -1.0, 1.0], [-1.0, 0.0, 0.0], [1.0, 0.0, 0.0]]),
712+
HermiteNodeLayout([[0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [0.0, 1.0, 1.0], [-1.0, 0.0, 0.0], [1.0, 0.0, 0.0]])]
713+
self._nodeLayout4WayPoints = [
714+
HermiteNodeLayout([[-1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, -1.0], [1.0, -1.0, 1.0]]),
715+
HermiteNodeLayout([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, -1.0], [-1.0, -1.0, 1.0]]),
716+
HermiteNodeLayout([[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [1.0, 1.0, 1.0]]),
717+
HermiteNodeLayout([[1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [-1.0, 1.0, 1.0]]),
718+
HermiteNodeLayout([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, -1.0], [-1.0, -1.0, 1.0]]),
719+
HermiteNodeLayout([[-1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, -1.0], [1.0, -1.0, 1.0]]),
720+
HermiteNodeLayout([[1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [-1.0, 1.0, 1.0]]),
721+
HermiteNodeLayout([[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [1.0, 1.0, 1.0]])]
690722
self._nodeLayoutTriplePointTopLeft = HermiteNodeLayout(
691723
[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [-1.0, 0.0, 1.0]])
692724
self._nodeLayoutTriplePointTopRight = HermiteNodeLayout(
@@ -772,11 +804,48 @@ def getNodeLayoutTriplePoint23Back(self):
772804

773805
return nodeLayout
774806

807+
def getNodeLayoutTriplePoint2D(self):
808+
"""
809+
Get node layout for triple-point corners of 2D quadrants.
810+
:return: List of 4 HermiteNodeLayout.
811+
"""
812+
nodeLayouts = [self._nodeLayoutTriplePoint2DQ1, self._nodeLayoutTriplePoint2DQ2,
813+
self._nodeLayoutTriplePoint2DQ3, self._nodeLayoutTriplePoint2DQ4]
814+
return nodeLayouts
815+
816+
def getNodeLayout3WayPoints12(self):
817+
"""
818+
Get 3-way node layouts for quadrants 12 = NN, NP, PN, PP.
819+
:return: List of 4 HermiteNodeLayout.
820+
"""
821+
return self._nodeLayout3WayPoints12
822+
823+
def getNodeLayout3WayPoints13(self):
824+
"""
825+
Get 3-way node layouts for quadrants 13 = NN, NP, PN, PP.
826+
:return: List of 4 HermiteNodeLayout.
827+
"""
828+
return self._nodeLayout3WayPoints13
829+
830+
def getNodeLayout3WayPoints23(self):
831+
"""
832+
Get 3-way node layouts for quadrants 23 = NN, NP, PN, PP.
833+
:return: List of 4 HermiteNodeLayout.
834+
"""
835+
return self._nodeLayout3WayPoints23
836+
837+
def getNodeLayout4WayPoints(self):
838+
"""
839+
Get node layouts from a regular core for octants 123: NNN, NNP, NPN, NPP, PNN, PNP, PPN, PPP.
840+
:return: List of 8 HermiteNodeLayout.
841+
"""
842+
return self._nodeLayout4WayPoints
843+
775844
def getNodeLayoutTriplePoint(self):
776845
"""
777846
Get node layout for triple-point corners of core box elements. There are four corners (Top Left, Top Right,
778847
Bottom Left, and Bottom Right) each with its specific node layout.
779-
:return: HermiteNodeLayout.
848+
:return: List of 4 HermiteNodeLayout.
780849
"""
781850
nodeLayouts = [self._nodeLayoutTriplePointTopLeft, self._nodeLayoutTriplePointTopRight,
782851
self._nodeLayoutTriplePointBottomLeft, self._nodeLayoutTriplePointBottomRight]

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