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added laterodorsal tip of the middle lobe to rat and mouse mesh #143

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merged 3 commits into from
May 20, 2021
Merged

added laterodorsal tip of the middle lobe to rat and mouse mesh #143

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6028d9a
added laterodorsal tip of the middle lobe to rat and mouse mesh
arti-sukasem May 19, 2021
2db9698
add fissures to the rat lung
arti-sukasem May 20, 2021
3678cf5
Updated accessory lobe parameter
arti-sukasem May 20, 2021
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21 changes: 12 additions & 9 deletions src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,8 @@ def generateBaseMesh(cls, region, options):
get_lung_term("ventral base of left lung"))
rightVentralGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
get_lung_term("ventral base of right lung"))
rightLateralGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
get_lung_term("laterodorsal tip of middle lobe of right lung"))

if isHuman:
# Annotation groups
Expand All @@ -146,9 +148,6 @@ def generateBaseMesh(cls, region, options):
get_lung_term("medial base of left lung"))
rightMedialGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
get_lung_term("medial base of right lung"))
rightLateralGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
get_lung_term(
"laterodorsal tip of middle lobe of right lung"))

elif isMouse or isRat:
# Annotation groups
Expand Down Expand Up @@ -719,11 +718,11 @@ def generateBaseMesh(cls, region, options):
( 122, [ [-36.05698,47.08828,-57.59312], [-0.33087, 6.49415,-1.52348], [-4.22413,-0.19610, 2.45611], [ 0.86437, 0.11917, 2.42078] ] ),
( 123, [ [-39.45486,46.70341,-55.90009], [-0.52891, 2.95603,-0.83710], [-3.83060,-1.56861, 1.91682], [ 0.75162, 0.23938, 5.48570] ] ),
( 124, [ [-43.26144,43.67862,-54.30818], [-2.11455, 1.11413,-0.62146], [-3.58216,-5.45812,-1.65953], [-1.38549, 1.91028, 7.94585] ] ),
( 125, [ [-27.14882,42.63985,-72.83542], [-2.39908,-2.21192,-1.83394], [ 2.66008,-2.38403,-0.11581], [-0.62274,-0.65278, 1.68398] ] ),
( 125, [ [-27.80895,42.29657,-71.76398], [-2.39908,-2.21192,-1.83394], [ 2.66008,-2.38403,-0.11581], [-0.62274,-0.65278, 1.68398] ] ),
( 126, [ [-29.57739,40.41327,-74.41851], [-2.32766, 0.20361,-0.92860], [ 1.02254,-1.40708, 0.12967], [-0.89774, 0.95716, 2.98675] ] ),
( 127, [ [-31.53743,42.08706,-74.75581], [-1.79202, 1.61708,-0.20859], [-0.60802,-2.71699,-0.55044], [ 0.13308,-1.13913, 2.56261] ] ),
( 128, [ [-33.07261,43.56021,-74.84381], [-1.27451, 1.32523, 0.03249], [-1.23146, 1.13905,-0.20501], [ 0.18233,-1.49460, 3.76854] ] ),
( 129, [ [-25.73953,41.37681,-72.89677], [-2.14750,-3.12098,-0.43623], [ 0.15850,-0.14205,-0.00690], [-2.25880,-0.11247, 3.10309] ] ),
( 129, [ [-26.34498,40.88118,-71.47592], [-2.83460,-3.50334,-1.51836], [ 0.15850,-0.14205,-0.00690], [-2.30608,-0.42110, 3.09443] ] ),
( 130, [ [-28.15167,38.16528,-73.75299], [-4.45232,-0.20121,-2.45714], [-2.21565,-2.76126,-1.15169], [-1.71227, 0.39194, 1.70072] ] ),
( 131, [ [-32.51213,39.59458,-75.66792], [-3.86135, 3.07822,-1.14798], [-1.32468,-2.19335,-1.25866], [-0.27050,-0.64795, 1.67969] ] ),
( 132, [ [-35.18203,43.76194,-75.84548], [-1.35322, 4.81128, 0.72570], [-2.48689,-1.19853,-1.71501], [-0.02335,-3.92115, 1.96130] ] ),
Expand All @@ -739,11 +738,11 @@ def generateBaseMesh(cls, region, options):
( 142, [ [-35.29802,31.56232,-84.03479], [-2.52798, 1.97099, 0.19535], [-0.51301, 0.28231,-2.87352], [-5.42833, 3.79002, 1.00935] ] ),
( 143, [ [-37.50222,33.66238,-83.76215], [-1.86147, 2.21435, 0.34847], [-1.02924,-1.11071,-2.17874], [-2.49882, 2.04923, 1.65780] ] ),
( 144, [ [-39.01443,35.93252,-83.35268], [-1.15121, 2.30243, 0.46572], [-0.24273,-0.69371,-0.78924], [-0.59296, 0.43710, 2.01947] ] ),
( 145, [ [-28.26507,42.20700,-70.31010], [-2.65658,-1.46782,-1.04197], [ 0.60494,-1.76289, 0.79032], [-1.59622,-0.19873, 3.33003] ] ),
( 145, [ [-28.89715,42.05184,-69.19026], [-2.65658,-1.46782,-1.04197], [ 0.60494,-1.76289, 0.79032], [-1.29990, 0.10470, 3.01137] ] ),
( 146, [ [-30.43873,41.36221,-71.17016], [-1.64770,-0.19798,-0.66127], [ 0.81326,-3.40475,-1.08727], [-0.84583, 0.92548, 3.49209] ] ),
( 147, [ [-31.39295,41.49878,-71.55841], [-1.21593, 0.56347,-0.02935], [-0.47735,-2.67446,-1.28525], [ 0.15131, 0.00171, 3.74414] ] ),
( 148, [ [-32.51085,42.47326,-71.03994], [-0.94278, 1.28077, 0.98569], [-1.80398,-2.44667,-1.84750], [ 0.93880,-0.65971, 3.78979] ] ),
( 149, [ [-27.85799,41.02071,-69.77828], [-1.74206,-2.73513,-1.70182], [ 0.20922,-0.60969, 0.27333], [-1.97005,-0.59933, 3.12281] ] ),
( 149, [ [-28.07969,40.55486,-69.18155], [-1.74206,-2.73513,-1.70182], [ 0.20922,-0.60969, 0.27333], [-1.35261,-0.13534, 2.53856] ] ),
( 150, [ [-29.90161,38.37547,-71.60989], [-2.57835,-0.04563,-2.18332], [-2.35314,-2.43925,-1.99758], [-1.79146, 0.12567, 2.52558] ] ),
( 151, [ [-32.44716,38.92879,-73.09666], [-2.35217, 1.05436,-0.62351], [-1.61858,-2.39556,-1.75762], [ 0.40667,-0.66871, 3.42414] ] ),
( 152, [ [-34.26246,40.22361,-72.97721], [-1.13101, 1.35825, 0.76297], [-1.69543,-2.04746,-2.02314], [ 1.86391,-2.91723, 3.65605] ] ),
Expand All @@ -761,7 +760,7 @@ def generateBaseMesh(cls, region, options):
( 164, [ [-39.67552,36.17645,-81.02003], [-0.09632, 0.95562, 0.42229], [-0.92690,-0.49432,-2.39307], [-0.72528, 0.04786, 2.63242] ] ),
( 165, [ [-30.36982,42.42619,-66.24109], [-1.10379,-0.21005,-1.50004], [ 1.39510,-4.44932,-0.86350], [-2.60222, 0.63441, 4.78763] ] ),
( 166, [ [-31.24582,42.25949,-67.43156], [-0.64821,-0.12335,-0.88090], [ 0.77823,-4.30120,-0.53797], [ 0.14073, 1.49608, 4.43944] ] ),
( 167, [ [-29.66838,40.18912,-66.67525], [-3.42687,-3.30561,-3.99791], [ 0.00778,-0.02482,-0.00482], [-1.64436,-1.05975, 3.07134] ] ),
( 167, [ [-29.64218,40.14305,-66.66589], [-3.42687,-3.30561,-3.99791], [ 0.00778,-0.02482,-0.00482], [-1.17406,-0.66008, 2.60229] ] ),
( 168, [ [-31.54090,38.36864,-68.89869], [-0.34167,-0.32959,-0.39861], [-1.46530,-3.06898,-2.29517], [-0.84087,-0.24505, 1.92152] ] ),
( 169, [ [-33.64994,36.50360,-71.44255], [-0.39332, 0.82355,-0.16046], [-2.19761,-1.36920,-2.46011], [-0.41980,-0.16235, 1.39866] ] ),
( 170, [ [-35.94629,35.83690,-73.80384], [-0.33050, 1.22614,-0.12953], [-2.27997,-0.51240,-2.29570], [-0.93819, 0.15378, 1.43130] ] ),
Expand Down Expand Up @@ -939,6 +938,9 @@ def generateBaseMesh(cls, region, options):
idx = leftLungElementsCount + (lElementsCount1 // 2)
markerList.append({"group": rightDorsalGroup, "elementId": idx, "xi": [0.0, 0.0, 0.0]})

idx = leftLungElementsCount + + (lElementsCount1 * lElementsCount2 * lElementsCount3) + lElementsCount1
markerList.append({"group": rightLateralGroup, "elementId": idx, "xi": [1.0, 0.0, 1.0]})

upperRightLungElementsCount = (uElementsCount1 - 1) * uElementsCount2 * (uElementsCount3 + 1)
rightLungElementsCount = lowerRightLungElementsCount + upperRightLungElementsCount

Expand Down Expand Up @@ -992,6 +994,7 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
parameterSetName = options['Base parameter set']
isMouse = 'Mouse 1' in parameterSetName
isHuman = 'Human 1' in parameterSetName
isRat = 'Rat 1' in parameterSetName

# create fissure groups
fm = region.getFieldmodule()
Expand All @@ -1008,7 +1011,7 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
obliqueLeftGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_lung_term("oblique fissure of left lung"))
obliqueLeftGroup.getMeshGroup(mesh2d).addElementsConditional(is_obliqueLeftGroup)

if isHuman or isMouse:
if isHuman or isMouse or isRat:
upperRightGroup = getAnnotationGroupForTerm(annotationGroups, get_lung_term("upper lobe of right lung"))
middleRightGroup = getAnnotationGroupForTerm(annotationGroups, get_lung_term("middle lobe of right lung"))
lowerRightGroup = getAnnotationGroupForTerm(annotationGroups, get_lung_term("lower lobe of right lung"))
Expand Down