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Replace heart atria, improve parameters for all species #56

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merged 27 commits into from
Jul 6, 2019
Merged

Replace heart atria, improve parameters for all species #56

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b8342cd
Add utility functions
rchristie Jun 17, 2019
635a246
Add new heart atria1 with ostium subscaffolds
rchristie Jun 17, 2019
f0d9534
Fix left atrium curves
rchristie Jun 21, 2019
0b5519e
Merge remote-tracking branch 'abi/master' into atria
rchristie Jun 21, 2019
e774a7c
Make proper crista terminalis curve
rchristie Jun 23, 2019
6e01d8f
Fix left atrium curves, LPV position
rchristie Jun 25, 2019
860319e
Fix element conformance near cfb
rchristie Jun 25, 2019
9204791
Increase interatrial groove depth
rchristie Jun 25, 2019
a9d8932
Separate annulus mesh, support bicubic-linear
rchristie Jun 26, 2019
b0095cc
Add left atrial appendage
rchristie Jun 28, 2019
2c52875
Add right atrial appendage
rchristie Jun 28, 2019
f80d60b
Improve right atrial appendage
rchristie Jun 30, 2019
825ac42
Improve right atria top derivatives
rchristie Jun 30, 2019
405fe20
Add appendage axial rotation, customise
rchristie Jul 1, 2019
d9c9141
Support up to 3 vessels in ostium
rchristie Jul 3, 2019
ad1313c
Merge remote-tracking branch 'abi/master' into atria
rchristie Jul 3, 2019
72e8557
Fix derivative smoothing between ostium vessels
rchristie Jul 4, 2019
992cc17
Add rat atria, tidy ostia code
rchristie Jul 4, 2019
885a97d
Rename coronary sinus to vestibule
rchristie Jul 4, 2019
fecea98
Fix editing atria sub-scaffolds on heart
rchristie Jul 4, 2019
0c510cb
Make appendages project horizontally
rchristie Jul 4, 2019
ccd15f2
Close rat atria
rchristie Jul 5, 2019
216b27f
Customise rat heart
rchristie Jul 6, 2019
2d615ee
Customise mouse heart
rchristie Jul 6, 2019
25ffc02
Customise human heart
rchristie Jul 6, 2019
dc94952
Customise pig heart
rchristie Jul 6, 2019
7f6bcd6
Merge remote-tracking branch 'abi/master' into atria
rchristie Jul 6, 2019
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167 changes: 93 additions & 74 deletions scaffoldmaker/meshtypes/meshtype_3d_heart1.py
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5,058 changes: 3,441 additions & 1,617 deletions scaffoldmaker/meshtypes/meshtype_3d_heartatria1.py
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99 changes: 61 additions & 38 deletions scaffoldmaker/meshtypes/meshtype_3d_heartventricles1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,53 +43,76 @@ def getParameterSetNames():

@staticmethod
def getDefaultOptions(parameterSetName='Default'):
options = {
'Number of elements around LV free wall' : 5,
'Number of elements around RV free wall' : 7,
'Number of elements up LV apex' : 1,
'Number of elements up RV' : 4,
'Unit scale' : 1.0,
'Interventricular sulcus derivative factor' : 0.5,
'LV outer height' : 1.0,
'LV outer diameter' : 1.0,
'LV free wall thickness' : 0.12,
'LV apex thickness' : 0.06,
'RV inner height fraction' : 0.85,
'RV arc around degrees' : 155.0,
'RV arc apex fraction' : 0.6,
'RV free wall thickness' : 0.05,
'RV width' : 0.4,
'RV width growth factor' : 0.7,
'RV side extension' : 0.12,
'RV side extension growth factor' : 0.5,
'Ventricular septum thickness' : 0.1,
'Ventricular septum base radial displacement' : 0.05,
'Use cross derivatives' : False,
'Refine' : False,
'Refine number of elements surface' : 4,
'Refine number of elements through LV wall' : 1,
'Refine number of elements through wall' : 1
}
if 'Human' in parameterSetName:
isHuman = 'Human' in parameterSetName
isMouse = 'Mouse' in parameterSetName
isPig = 'Pig' in parameterSetName
isRat = 'Rat' in parameterSetName
notUnitScale = 'Unit' not in parameterSetName
options = {}
options['Number of elements around LV free wall'] = 5
options['Number of elements around RV free wall'] = 7
options['Number of elements up LV apex'] = 1
options['Number of elements up RV'] = 3
options['Unit scale'] = 1.0
options['Interventricular sulcus derivative factor'] = 0.5
options['LV outer height'] = 1.0
options['LV outer diameter'] = 0.95
options['LV free wall thickness'] = 0.14
options['LV apex thickness'] = 0.08
options['RV inner height fraction'] = 0.85
options['RV arc around degrees'] = 145.0
options['RV arc apex fraction'] = 0.5
options['RV free wall thickness'] = 0.05
options['RV width'] = 0.3
options['RV width growth factor'] = 0.7
options['RV side extension'] = 0.12
options['RV side extension growth factor'] = 0.5
options['Ventricular septum thickness'] = 0.12
options['Ventricular septum base radial displacement'] = 0.1
options['Use cross derivatives'] = False
options['Refine'] = False
options['Refine number of elements surface'] = 4
options['Refine number of elements through LV wall'] = 1
options['Refine number of elements through wall'] = 1
if isHuman:
if 'Unit' not in parameterSetName:
options['Unit scale'] = 80.0
options['LV outer height'] = 0.9
elif 'Mouse' in parameterSetName:
if 'Unit' not in parameterSetName:
options['Unit scale'] = 5.0
elif isMouse or isRat:
if notUnitScale:
options['Unit scale'] = 5.0 if isMouse else 12.0
#options['Interventricular sulcus derivative factor'] = 0.5
options['LV outer height'] = 0.95
options['LV outer diameter'] = 0.95
options['LV free wall thickness'] = 0.15
options['LV apex thickness'] = 0.08
options['RV width'] = 0.35
elif 'Pig' in parameterSetName:
options['Number of elements up LV apex'] = 2
if isMouse:
options['RV inner height fraction'] = 0.9
else:
options['RV inner height fraction'] = 0.85
options['RV arc around degrees'] = 140.0
#options['RV arc apex fraction'] = 0.6
options['RV free wall thickness'] = 0.07
options['RV width'] = 0.25
options['RV width growth factor'] = 0.8
options['RV side extension'] = 0.05
options['RV side extension growth factor'] = 0.8
options['Ventricular septum thickness'] = 0.12
options['Ventricular septum base radial displacement'] = 0.08
elif isPig:
options['Number of elements up LV apex'] = 1
options['Number of elements up RV'] = 3
if 'Unit' not in parameterSetName:
options['Unit scale'] = 80.0
options['LV outer height'] = 0.9
options['LV free wall thickness'] = 0.15
options['LV free wall thickness'] = 0.17
options['LV apex thickness'] = 0.07
options['RV inner height fraction'] = 0.65
options['RV width growth factor'] = 0.65
options['Ventricular septum thickness'] = 0.12
options['RV arc around degrees'] = 140.0
options['RV free wall thickness'] = 0.06
options['RV width growth factor'] = 0.4
options['RV side extension'] = 0.1
options['RV side extension growth factor'] = 0.4
options['Ventricular septum thickness'] = 0.13
elif 'Rat' in parameterSetName:
if 'Unit' not in parameterSetName:
options['Unit scale'] = 12.0
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