Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add fusiform muscle #180

Merged
merged 7 commits into from
Jun 3, 2022
Merged

Add fusiform muscle #180

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
04bf1b5
Add fusiform muscle
elias-soltani Mar 10, 2022
772703e
Make different groups for elements along the cylinder. Add muscle and…
elias-soltani Mar 15, 2022
512c4ed
Merge branch 'main' into muscle/fusiform_muscle
elias-soltani Mar 20, 2022
b9f0fec
Make circle coordintes precise
elias-soltani Mar 20, 2022
9ac8cd2
Merge branch 'main' into muscle/fusiform_muscle
elias-soltani May 22, 2022
83840d4
Remove tendon and muscle groups. Add muscle annotaion terms in annota…
elias-soltani May 23, 2022
e468c70
Make arclength function more accurate
elias-soltani May 23, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
256 changes: 256 additions & 0 deletions src/scaffoldmaker/meshtypes/meshtype_3d_musclefusiform1.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,256 @@
"""
Generates a fusiform muscle with tendon and muscle groups using a CylinderMesh of all cube elements,
with variable numbers of elements in major, minor, shell and axial directions.
"""

from __future__ import division

import copy

from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
from opencmiss.zinc.node import Node
from scaffoldmaker.annotation.annotationgroup import AnnotationGroup
from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1
from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
from scaffoldmaker.scaffoldpackage import ScaffoldPackage
from scaffoldmaker.utils.cylindermesh import CylinderMesh, CylinderShape, CylinderEnds, CylinderCentralPath
from scaffoldmaker.utils.meshrefinement import MeshRefinement
from scaffoldmaker.utils.zinc_utils import exnodeStringFromNodeValues


class MeshType_3d_musclefusiform1(Scaffold_base):
"""
Generates a fusiform muscle using a CylinderMesh of all cube elements,
with variable numbers of elements in major, minor, shell and axial directions.
"""
centralPathDefaultScaffoldPackages = {
'Brachioradialis 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 3.0,
'Number of elements': 6
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3], [
[[-0.27, 0.44, 0.87], [6.61, 7.71, 43.82], [4.56, -1.02, -0.51], [-1.56, 0.44, 0.72], [0.29, 1.48, -0.30], [0.18, 0.93, 0.18]],
[[3.25, 5.21, 45.57], [0.37, 1.78, 45.29], [4.61, -0.73, -0.01], [1.66, 0.13, 0.29], [0.40, 2.58, -0.10], [0.04, 1.24, 0.22]],
[[0.46, 3.96, 90.94], [-0.69, -2.01, 59.61], [7.90, -0.75, 0.06], [5.17, -0.55, -0.35], [0.37, 3.97, 0.14], [0.20, 2.18, -0.21]],
[[3.28, 1.02, 164.51], [5.37, 7.23, 72.38], [16.12, -2.18, -0.99], [0.07, -0.49, -0.76], [0.95, 7.43, -0.81], [0.35, 1.21, -0.89]],
[[11.03, 18.03, 234.00], [11.41, 10.94, 50.55], [8.22, -1.76, -1.46], [-5.41, 0.42, 0.14], [1.09, 6.46, -1.64], [0.55, -0.34, 0.05]],
[[21.86, 23.91, 265.44], [9.61, 3.36, 33.13], [3.98, -1.33, -1.02], [-3.21, 0.42, 0.52], [1.83, 6.41, -1.18], [0.10, -1.87, 0.76]],
[[30.07, 24.60, 299.90], [6.77, -1.97, 35.60], [1.85, -0.92, -0.40], [-1.04, 0.40, 0.71], [1.27, 2.61, -0.09], [-1.23, -5.71, 1.40]]
])
}),
'Long head of right biceps femoris 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 3.0,
'Number of elements': 7
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3], [
[[1.11, 0.78, 0.89], [-17.32, 0.85, 44.44], [-2.04, 5.00, -0.89], [-0.58, 1.13, -0.73], [-3.62, -1.72, -1.38], [1.97, 0.30, 2.07]],
[[-10.89, 4.78, 45.89], [-6.48, 7.14, 45.04], [-2.06, 8.08, -1.58], [0.54, 5.02, -0.64], [-5.26, -1.44, -0.53], [-5.24, 0.26, -0.37]],
[[-11.89, 14.78, 89.89], [-7.65, 6.42, 47.75], [-0.97, 14.98, -2.17], [1.04, 8.35, 0.22], [-13.97, -1.21, -2.08], [-5.63, 0.61, -1.67]],
[[-26.89, 16.78, 139.89], [-11.94, 2.01, 49.14], [0.00, 25.00, -1.02], [-0.01, 5.35, 0.32], [-16.03, -0.16, -3.89], [-3.03, 0.13, -0.53]],
[[-35.89, 18.78, 187.89], [-8.02, 2.49, 49.02], [-0.92, 25.98, -1.47], [-0.47, -0.50, -0.79], [-19.97, -0.89, -3.22], [-1.57, -0.42, 0.72]],
[[-42.89, 21.78, 237.89], [-6.50, 5.06, 48.56], [-0.91, 23.94, -2.62], [-0.55, -6.63, -0.82], [-19.08, -0.99, -2.45], [3.07, -0.76, 1.14]],
[[-48.89, 28.78, 284.89], [-5.02, 10.53, 46.68], [-1.99, 12.97, -3.14], [-0.54, -9.05, 0.11], [-13.94, -2.37, -0.97], [5.44, -0.79, 1.45]],
[[-52.89, 42.78, 330.89], [-2.97, 17.41, 45.15], [-1.98, 5.86, -2.39], [0.55, -5.16, 1.38], [-8.19, -2.58, 0.46], [6.06, 0.38, 1.39]]
])
}),

}

@staticmethod
def getName():
return '3D Muscle Fusiform 1'

@staticmethod
def getParameterSetNames():
return [
'Default',
'Brachioradialis 1',
'Long head of right biceps femoris 1',
rchristie marked this conversation as resolved.
Show resolved Hide resolved
]

@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
if parameterSetName == 'Default':
parameterSetName = 'Brachioradialis 1'

if 'Brachioradialis 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Brachioradialis 1']
elif 'Long head of right biceps femoris 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Long head of right biceps femoris 1']

options = {
'Central path': copy.deepcopy(centralPathOption),
'Number of elements across major': 4,
'Number of elements across minor': 4,
'Number of elements across shell': 0,
'Number of elements across transition': 1,
'Number of elements along': 6,
'Number of tendon elements': [0, 0],
'Shell element thickness proportion': 1.0,
'Use cross derivatives': False,
'Refine': False,
'Refine number of elements across': 4,
'Refine number of elements along': 4
}
return options

@staticmethod
def getOrderedOptionNames():
return [
'Central path',
'Number of elements across major',
'Number of elements across minor',
'Number of elements across shell',
'Number of elements across transition',
'Number of elements along',
'Number of tendon elements',
'Shell element thickness proportion',
'Refine',
'Refine number of elements across',
'Refine number of elements along'
]

@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Central path':
return [MeshType_1d_path1]
return []

@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Central path':
return list(cls.centralPathDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), \
cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()

@classmethod
def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + \
' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(cls.centralPathDefaultScaffoldPackages[parameterSetName])
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'

@classmethod
def checkOptions(cls, options):
if not options['Central path'].getScaffoldType() in cls.getOptionValidScaffoldTypes('Central path'):
options['Central path'] = cls.getOptionScaffoldPackage('Central path', MeshType_1d_path1)
dependentChanges = False

if options['Number of elements across major'] < 4:
options['Number of elements across major'] = 4
if options['Number of elements across major'] % 2:
options['Number of elements across major'] += 1

if options['Number of elements across minor'] < 4:
options['Number of elements across minor'] = 4
if options['Number of elements across minor'] % 2:
options['Number of elements across minor'] += 1
if options['Number of elements along'] < 1:
options['Number of elements along'] = 1
if options['Number of elements across transition'] < 1:
options['Number of elements across transition'] = 1
Rcrit = min(options['Number of elements across major']-4, options['Number of elements across minor']-4)//2
if options['Number of elements across shell'] + options['Number of elements across transition'] - 1 > Rcrit:
dependentChanges = True
options['Number of elements across shell'] = Rcrit
options['Number of elements across transition'] = 1

if options['Shell element thickness proportion'] < 0.15:
options['Shell element thickness proportion'] = 1.0

if sum(options['Number of tendon elements']) > options['Number of elements along']:
options['Number of tendon elements'] = [0, 0]

if any(c < 0 for c in options['Number of tendon elements']):
options['Number of tendon elements'] = [0, 0]

return dependentChanges

@staticmethod
def generateBaseMesh(region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: None
"""

centralPath = options['Central path']
full = True
elementsCountAcrossMajor = options['Number of elements across major']
if not full:
elementsCountAcrossMajor //= 2
elementsCountAcrossMinor = options['Number of elements across minor']
elementsCountAcrossShell = options['Number of elements across shell']
elementsCountAcrossTransition = options['Number of elements across transition']
elementsCountAlong = options['Number of elements along']
shellProportion = options['Shell element thickness proportion']
numberOftendonElements = options['Number of tendon elements']
useCrossDerivatives = options['Use cross derivatives']

meshGroupsElementsAlong = [numberOftendonElements[0], elementsCountAlong - sum(numberOftendonElements),
numberOftendonElements[1]]

fm = region.getFieldmodule()
coordinates = findOrCreateFieldCoordinates(fm)

mesh = fm.findMeshByDimension(3)
tendonGroup1 = AnnotationGroup(region, ("tendon group 1", ""))
tendonMeshGroup1 = tendonGroup1.getMeshGroup(mesh)
muscleGroup = AnnotationGroup(region, ("muscle group", ""))
muscleMeshGroup = muscleGroup.getMeshGroup(mesh)
tendonGroup2 = AnnotationGroup(region, ("tendon group 2", ""))
tendonMeshGroup2 = tendonGroup2.getMeshGroup(mesh)
meshGroups = [tendonMeshGroup1, muscleMeshGroup, tendonMeshGroup2]
annotationGroups = [tendonGroup1, muscleGroup, tendonGroup2]

cylinderCentralPath = CylinderCentralPath(region, centralPath, elementsCountAlong)

cylinderShape = CylinderShape.CYLINDER_SHAPE_FULL if full else CylinderShape.CYLINDER_SHAPE_LOWER_HALF

base = CylinderEnds(elementsCountAcrossMajor, elementsCountAcrossMinor, elementsCountAcrossShell,
elementsCountAcrossTransition,
shellProportion,
[0.0, 0.0, 0.0], cylinderCentralPath.alongAxis[0], cylinderCentralPath.majorAxis[0],
cylinderCentralPath.minorRadii[0])
cylinder1 = CylinderMesh(fm, coordinates, elementsCountAlong, base,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath, useCrossDerivatives=False,
meshGroupsElementsAlong=meshGroupsElementsAlong, meshGroups=meshGroups)

return annotationGroups

@classmethod
def refineMesh(cls, meshRefinement, options):
"""
Refine source mesh into separate region, with change of basis.
:param meshRefinement: MeshRefinement, which knows source and target region.
:param options: Dict containing options. See getDefaultOptions().
"""
assert isinstance(meshRefinement, MeshRefinement)
refineElementsCountAcross = options['Refine number of elements across']
refineElementsCountAlong = options['Refine number of elements along']
meshRefinement.refineAllElementsCubeStandard3d(refineElementsCountAcross, refineElementsCountAlong, refineElementsCountAcross)
11 changes: 4 additions & 7 deletions src/scaffoldmaker/meshtypes/meshtype_3d_wholebody1.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -405,11 +405,10 @@ def generateBaseMesh(region, options):
rightUreterJunctionWithBladder = bladder_terms.get_bladder_term('right ureter junction with bladder')
urethraJunctionWithBladderDorsal = bladder_terms.get_bladder_term('urethra junction of dorsal bladder neck')
urethraJunctionWithBladderVentral = bladder_terms.get_bladder_term('urethra junction of ventral bladder neck')
gastroesophagalJunctionOnLesserCurvature = stomach_terms.get_stomach_term('gastro-esophagal junction on lesser curvature')
limitingRidgeOnGreaterCurvature = stomach_terms.get_stomach_term('limiting ridge on greater curvature')
pylorusOnGreaterCurvature = stomach_terms.get_stomach_term('pylorus on greater curvature')
duodenumOnGreaterCurvature = stomach_terms.get_stomach_term('duodenum on greater curvature')
junctionBetweenFundusAndBodyOnGreaterCurvature = stomach_terms.get_stomach_term("junction between fundus and body on greater curvature")
gastroesophagalJunctionOnLesserCurvature = stomach_terms.get_stomach_term('esophagogastric junction along the lesser curvature on serosa')
limitingRidgeOnGreaterCurvature = stomach_terms.get_stomach_term('limiting ridge at the greater curvature on serosa')
pylorusOnGreaterCurvature = stomach_terms.get_stomach_term('gastroduodenal junction along the greater curvature on serosa')
junctionBetweenFundusAndBodyOnGreaterCurvature = stomach_terms.get_stomach_term("fundus-body junction along the greater curvature on serosa")
apexOfLeftLung = lung_terms.get_lung_term('apex of left lung')
ventralBaseOfLeftLung = lung_terms.get_lung_term('ventral base of left lung')
dorsalBaseOfLeftLung = lung_terms.get_lung_term('dorsal base of left lung')
Expand Down Expand Up @@ -463,7 +462,6 @@ def generateBaseMesh(region, options):
{"group": gastroesophagalJunctionOnLesserCurvature, "x": [0.12, 0.009, 1.446]},
{"group": limitingRidgeOnGreaterCurvature, "x": [0.318, 0.097, 1.406]},
{"group": pylorusOnGreaterCurvature, "x": [0.08, -0.111, 1.443]},
{"group": duodenumOnGreaterCurvature, "x": [0.029, -0.138, 1.481]},
]
elif isHuman:
bodyMarkerPoints = [
Expand All @@ -490,7 +488,6 @@ def generateBaseMesh(region, options):
{"group": dorsalBaseOfRightLung, "x": [0.0369, -0.2524, 0.912]},
{"group": gastroesophagalJunctionOnLesserCurvature, "x": [-0.0062, -0.3259, 0.8586]},
{"group": pylorusOnGreaterCurvature, "x": [-0.0761, -0.3189, 0.8663]},
{"group": duodenumOnGreaterCurvature, "x": [-0.1599, 0.1601, 1.1939]},
{"group": junctionBetweenFundusAndBodyOnGreaterCurvature, "x": [0.1884, -0.1839, 0.9639]},
]

Expand Down
2 changes: 2 additions & 0 deletions src/scaffoldmaker/scaffolds.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
from scaffoldmaker.meshtypes.meshtype_3d_heartventriclesbase2 import MeshType_3d_heartventriclesbase2
from scaffoldmaker.meshtypes.meshtype_3d_lens1 import MeshType_3d_lens1
from scaffoldmaker.meshtypes.meshtype_3d_lung1 import MeshType_3d_lung1
from scaffoldmaker.meshtypes.meshtype_3d_musclefusiform1 import MeshType_3d_musclefusiform1
from scaffoldmaker.meshtypes.meshtype_3d_ostium1 import MeshType_3d_ostium1
from scaffoldmaker.meshtypes.meshtype_3d_smallintestine1 import MeshType_3d_smallintestine1
from scaffoldmaker.meshtypes.meshtype_3d_solidcylinder1 import MeshType_3d_solidcylinder1
Expand Down Expand Up @@ -83,6 +84,7 @@ def __init__(self):
MeshType_3d_heartventriclesbase2,
MeshType_3d_lens1,
MeshType_3d_lung1,
MeshType_3d_musclefusiform1,
MeshType_3d_ostium1,
MeshType_3d_smallintestine1,
MeshType_3d_solidcylinder1,
Expand Down
Loading