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Update heart terms, improve epicardium, add docs #195

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Jun 9, 2022
Merged

Update heart terms, improve epicardium, add docs #195

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7d86488
Improve epicardial fat layer
rchristie May 11, 2022
f344de2
Use UBERON terms for heart
rchristie May 24, 2022
f95a5ce
Make all heart parameter sets unit scale
rchristie Jun 2, 2022
4478f9a
Update heart annotation group terms
rchristie Jun 8, 2022
193ac6f
Merge branch 'main' into fatpad2
rchristie Jun 8, 2022
880aadf
Add heart scaffold documentation
rchristie Jun 9, 2022
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139 changes: 86 additions & 53 deletions src/scaffoldmaker/annotation/heart_terms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,60 +4,93 @@

# convention: preferred name, preferred id, followed by any other ids and alternative names
heart_terms = [
( "heart", "UBERON:0000948", "FMA:7088" ),
# ventricles
( "left ventricle myocardium", "FMA:9558" ),
( "right ventricle myocardium", "FMA:9535" ),
( "interventricular septum", "FMA:7133" ),
( "endocardium of left ventricle", "FMA:9559" ),
( "endocardium of right ventricle", "FMA:9536" ),
( "epicardial fat", "UBERON:0015129"),
( "epicardium", "FMA:9461", "UBERON:0002348"),
#( "epicardium of ventricle", "FMA:12150", "UBERON:0001082" ),
# ventricles with base
( "conus arteriosus", "UBERON:0003983" ),
( "left fibrous ring", "FMA:77124" ),
( "right fibrous ring", "FMA:77125" ),
# atria
( "left atrium myocardium", "FMA:7285" ),
( "right atrium myocardium", "FMA:7282" ),
( "endocardium of left atrium", "FMA:7286", "UBERON:0034903" ),
( "endocardium of right atrium", "FMA:7281", "UBERON:0009129" ),
( "interatrial septum", "FMA:7108" ),
( "fossa ovalis", "FMA:9246" ),
( "left auricle", "FMA:7219", "UBERON:0006630" ), # uncertain if just the tissue like myocardium
( "right auricle", "FMA:7218", "UBERON:0006631" ), # uncertain if just the tissue like myocardium
( "endocardium of left auricle", "FMA:13236", "UBERON:0011006" ),
( "endocardium of right auricle", "FMA:13235", "UBERON:0011007" ),
( "epicardium of left auricle", "FMA:13233" ),
( "epicardium of right auricle", "FMA:13232" ),
( "pulmonary vein", "FMA:66643", "UBERON:0002016" ),
( "left pulmonary vein", "UBERON:0009030" ),
( "left inferior pulmonary vein", "FMA:49913" ),
( "left superior pulmonary vein", "FMA:49916" ),
( "middle pulmonary vein", "ILX:0739222" ), # in mouse, rat, rabbit
( "right pulmonary vein", "UBERON:0009032" ),
( "right inferior pulmonary vein", "FMA:49911" ),
( "right superior pulmonary vein", "FMA:49914" ),
( "inferior vena cava", "FMA:10951", "UBERON:0001072", "posterior vena cava" ),
( "inferior vena cava inlet", "ILX:0738358" ),
( "superior vena cava", "FMA:4720", "UBERON:0001585", "anterior vena cava" ),
( "superior vena cava inlet", "ILX:0738367" ),
# arterial root
( "root of aorta", "FMA:3740" ),
( "posterior cusp of aortic valve", "FMA:7253" ),
( "right cusp of aortic valve", "FMA:7252" ),
( "left cusp of aortic valve", "FMA:7251" ),
( "root of pulmonary trunk", "FMA:8612" ),
( "right cusp of pulmonary valve", "FMA:7250" ),
( "anterior cusp of pulmonary valve", "FMA:7249" ),
( "left cusp of pulmonary valve", "FMA:7247" ),
# heart - volume terms
("heart", "UBERON:0000948", "FMA:7088"), # group of the entire heart
("epicardial fat", "UBERON:0015129"), # not used
("epicardium", "UBERON:0002348", "FMA:9461"), # volumetric layer outside myocardium to pericardial cavity
# heart - surface terms
("outer surface of epicardium", "ILX:0793548"),
("outer surface of myocardium", "ILX:0793530"),

# ventricles - volume terms
("conus arteriosus", "UBERON:0003983"),
("endocardium of left ventricle", "UBERON:0009713", "FMA:9559"),
("endocardium of right ventricle", "UBERON:0009712", "FMA:9536"),
("heart left ventricle", "UBERON:0002084"), # the whole left ventricle
("heart right ventricle", "UBERON:0002080"), # the whole right ventricle
("interventricular septum", "UBERON:0002094", "FMA:7133"),
("left fibrous ring", "FMA:77124"),
("left ventricle myocardium", "UBERON:0006566", "FMA:9558"),
("right fibrous ring", "FMA:77125"),
("right ventricle myocardium", "UBERON:0006567", "FMA:9535"),
# ventricles - surface terms
("luminal surface of left ventricle", "ILX:0793537"),
("luminal surface of right ventricle", "ILX:0793538"),
("outer surface of myocardium of left ventricle", "ILX:0793533"),
("outer surface of myocardium of right ventricle", "ILX:0793534"),

# atria - volume terms
("left atrium endocardium", "UBERON:0034903", "FMA:7286"),
("endocardium of left auricle", "UBERON:0011006", "FMA:13236"),
("right atrium endocardium", "UBERON:0009129", "FMA:7281"),
("endocardium of right auricle", "UBERON:0011007", "FMA:13235"),
("epicardium of left auricle", "FMA:13233"),
("epicardium of right auricle", "FMA:13232"),
("fossa ovalis", "UBERON:0003369", "FMA:9246"),
("inferior vena cava", "UBERON:0001072", "FMA:10951", "posterior vena cava"),
("inferior vena cava inlet", "ILX:0738358"),
("interatrial septum", "UBERON:0002085", "FMA:7108"),
("left atrium myocardium", "FMA:7285"),
("left auricle", "UBERON:0006630", "FMA:7219"),
("left cardiac atrium", "UBERON:0002079"), # the whole left atrium
("left inferior pulmonary vein", "FMA:49913"),
("left pulmonary vein", "UBERON:0009030"),
("left superior pulmonary vein", "FMA:49916"),
("middle pulmonary vein", "ILX:0739222"), # in mouse, rat, rabbit
("pulmonary vein", "UBERON:0002016", "FMA:66643"),
("right atrium myocardium", "FMA:7282"),
("right auricle", "UBERON:0006631", "FMA:7218"),
("right cardiac atrium", "UBERON:0002078"), # the whole right atrium
("right inferior pulmonary vein", "FMA:49911"),
("right pulmonary vein", "UBERON:0009032"),
("right superior pulmonary vein", "FMA:49914"),
("superior vena cava", "UBERON:0001585", "FMA:4720", "anterior vena cava"),
("superior vena cava inlet", "ILX:0738367"),
# atria - surface terms
("luminal surface of left atrium", "ILX:0793535"),
("luminal surface of right atrium", "ILX:0793536"),
("luminal surface of inferior vena cava", "ILX:0793542"),
("luminal surface of left pulmonary vein", "ILX:0793539"),
("luminal surface of middle pulmonary vein", "ILX:0793540"),
("luminal surface of right pulmonary vein", "ILX:0793541"),
("luminal surface of superior vena cava", "ILX:0793543"),
("outer surface of myocardium of left atrium", "ILX:0793531"),
("outer surface of myocardium of right atrium", "ILX:0793532"),

# arterial valves and great vessels - volume terms
("root of aorta", "FMA:3740"),
("posterior cusp of aortic valve", "FMA:7253"),
("right cusp of aortic valve", "FMA:7252"),
("left cusp of aortic valve", "FMA:7251"),
("root of pulmonary trunk", "FMA:8612"),
("right cusp of pulmonary valve", "FMA:7250"),
("anterior cusp of pulmonary valve", "FMA:7249"),
("left cusp of pulmonary valve", "FMA:7247"),
# arterial valves and great vessels - surface terms
("luminal surface of aorta", "ILX:0793544"),
("luminal surface of pulmonary trunk", "ILX:0793546"),
("luminal surface of root of aorta", "ILX:0793545"),
("luminal surface of root of pulmonary trunk", "ILX:0793547"),

# fiducial markers
( "apex of heart", "UBERON:0002098", "FMA:7164"),
( "crux of heart", "ILX:0777104", "FMA:7220" ), # point on posterior surface where the four chambers meet on interventricular, atrio-ventricular and interatrial sulci
( "left atrium epicardium venous midpoint", "ILX:0778116"), # point at centre of pulmonary vein ostia on left atrium epicardium, on anterior/ventral side for rodents
( "right atrium epicardium venous midpoint", "ILX:0778117") # point at centre of inferior & superior vena cavae on right atrium epicardium
]
("apex of heart", "UBERON:0002098", "FMA:7164"),
# point on posterior surface where the four chambers meet on interventricular, A-V and interatrial sulci
("crux cordis", "ILX:0777104", "FMA:7220"),
# point at centre of pulmonary vein ostia on left atrium epicardium, on anterior/ventral side for rodents
("left atrium epicardium venous midpoint", "ILX:0778116"),
# point at centre of inferior & superior vena cavae on right atrium epicardium
("right atrium epicardium venous midpoint", "ILX:0778117")
]

def get_heart_term(name : str):
"""
Expand Down
38 changes: 10 additions & 28 deletions src/scaffoldmaker/meshtypes/meshtype_3d_heart1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,11 +36,7 @@ def getParameterSetNames():
'Human 1',
'Mouse 1',
'Pig 1',
'Rat 1',
'Unit Human 1',
'Unit Mouse 1',
'Unit Pig 1',
'Unit Rat 1']
'Rat 1']

@staticmethod
def getDefaultOptions(parameterSetName='Default'):
Expand Down Expand Up @@ -83,7 +79,7 @@ def getOrderedOptionNames():
'Refine number of elements surface',
'Refine number of elements through LV wall',
'Refine number of elements through wall',
'Refine number of elements through epicardial fat layer']:
'Refine number of elements through epicardium layer']:
optionNames.remove(optionName)
optionNames.append(optionName)
return optionNames
Expand Down Expand Up @@ -133,32 +129,20 @@ def generateBaseMesh(cls, region, options):
coordinates = findOrCreateFieldCoordinates(fm)
cache = fm.createFieldcache()

mesh = fm.findMeshByDimension(3)

# generate heartventriclesbase1 model and put atria1 on it
ventriclesAnnotationGroups = MeshType_3d_heartventriclesbase1.generateBaseMesh(region, options)
atriaAnnotationGroups = MeshType_3d_heartatria1.generateBaseMesh(region, options)
annotationGroups = mergeAnnotationGroups(ventriclesAnnotationGroups, atriaAnnotationGroups)
heartGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("heart"))
cruxGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("crux of heart"))
cruxGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("crux cordis"))
lFibrousRingGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("left fibrous ring"))
rFibrousRingGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("right fibrous ring"))

# annotation fiducial points
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(fm, mesh, name="marker_location")

nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup, nodes).getNodesetGroup()
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)

##############
# Create nodes
##############

nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodeIdentifier = max(1, getMaximumNodeIdentifier(nodes) + 1)

# discover left and right fibrous ring nodes from ventricles and atria
Expand Down Expand Up @@ -219,6 +203,7 @@ def generateBaseMesh(cls, region, options):
# Create elements
#################

mesh = fm.findMeshByDimension(3)
heartMeshGroup = heartGroup.getMeshGroup(mesh)
lFibrousRingMeshGroup = lFibrousRingGroup.getMeshGroup(mesh)
rFibrousRingMeshGroup = rFibrousRingGroup.getMeshGroup(mesh)
Expand Down Expand Up @@ -397,16 +382,13 @@ def generateBaseMesh(cls, region, options):
for meshGroup in meshGroups:
meshGroup.addElement(element)

# annotation fiducial points
# crux cordis annotation point
cruxElement = mesh.findElementByIdentifier(cruxElementId)
cruxXi = [ 0.5, 0.5, 1.0 ]
markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
nodeIdentifier += 1
cache.setNode(markerPoint)
markerName.assignString(cache, cruxGroup.getName())
markerLocation.assignMeshLocation(cache, cruxElement, cruxXi)
for group in [ heartGroup, cruxGroup ]:
group.getNodesetGroup(nodes).addNode(markerPoint)
markerNode = cruxGroup.createMarkerNode(nodeIdentifier, element=cruxElement, xi=cruxXi)
nodeIdentifier = markerNode.getIdentifier() + 1
for group in [ heartGroup ]:
group.getNodesetGroup(nodes).addNode(markerNode)

return annotationGroups

Expand Down
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