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Set fitted human lung parameters #107

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Nov 29, 2020
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Set fitted human lung parameters #107

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94 changes: 89 additions & 5 deletions src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,78 @@ def generateBaseMesh(cls, region, options):
eftTetCollapseXi1Xi2_53 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(5, 3)

if isHuman:

#valueLabels = [ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D_DS3 ]
nodeFieldParameters = [
( 1, [ [ 204.214, 217.387, -341.252 ], [ -62.947, -35.911, 0.688 ], [ 25.814, -29.305, 29.820 ], [ -4.512, 17.903, 91.032 ] ] ),
( 2, [ [ 269.306, 209.072, -354.889 ], [ -20.103, -4.908, 79.411 ], [ 47.047, -49.139, -2.543 ], [ 0.175, 15.720, 89.961 ] ] ),
( 3, [ [ 223.341, 188.444, -308.232 ], [ -60.426, -24.274, -1.081 ], [ 20.503, -36.477, 21.902 ], [ 3.351, 18.019, 52.584 ] ] ),
( 4, [ [ 175.499, 161.680, -317.300 ], [ -27.384, -29.319, -26.704 ], [ 9.020, -29.937, 61.149 ], [ 2.480, 21.158, 82.660 ] ] ),
( 5, [ [ 292.990, 153.587, -341.674 ], [ -10.831, 26.074, 66.575 ], [ -10.247, -58.090, 17.240 ], [ 10.595, 29.035, 61.452 ] ] ),
( 6, [ [ 241.787, 149.543, -291.578 ], [ -78.934, -21.344, 11.789 ], [ 22.813, -35.233, 12.622 ], [ -6.632, 28.612, 43.054 ] ] ),
( 7, [ [ 159.624, 124.828, -273.695 ], [ -83.355, -36.289, 19.187 ], [ 42.385, -36.600, 4.581 ], [ 14.994, 29.267, 38.119 ] ] ),
( 8, [ [ 279.346, 98.455, -327.717 ], [ -21.666, 16.370, 35.485 ], [ -18.452, -43.354, 8.934 ], [ 18.541, 53.843, 54.860 ] ] ),
( 9, [ [ 251.887, 110.979, -294.259 ], [ -46.884, -0.667, 13.029 ], [ -6.640, -34.923, -9.542 ], [ -1.793, 34.831, 57.261 ] ] ),
( 10, [ [ 203.673, 108.786, -280.769 ], [ -46.008, -21.960, 13.143 ], [ 34.048, -17.679, -6.475 ], [ 5.003, 37.773, 28.793 ] ] ),
( 11, [ [ 256.681, 71.412, -322.006 ], [ -14.537, 11.023, 15.628 ], [ -7.850, -10.251, 25.280 ], [ 35.613, 35.978, 71.913 ] ] ),
( 12, [ [ 243.935, 80.999, -302.872 ], [ -16.394, 8.598, 18.165 ], [ -8.074, -19.651, -6.343 ], [ 10.839, 34.046, 66.123 ] ] ),
( 13, [ [ 226.628, 91.702, -285.892 ], [ -23.230, -0.285, 15.358 ], [ 7.839, -18.769, -11.448 ], [ 6.974, 29.647, 42.160 ] ] ),
( 14, [ [ 217.057, 233.615, -251.001 ], [ -56.387, -12.798, -2.074 ], [ 6.551, -32.468, 4.928 ], [ 7.180, 7.996, 92.202 ] ] ),
( 15, [ [ 267.567, 218.538, -268.608 ], [ -31.271, -28.559, 17.780 ], [ 28.703, -41.920, -22.876 ], [ -2.499, 2.835, 82.368 ] ] ),
( 16, [ [ 227.626, 202.773, -250.316 ], [ -46.421, -9.158, 11.317 ], [ 7.297, -31.033, 0.920 ], [ -0.016, 8.237, 63.668 ] ] ),
( 17, [ [ 178.790, 194.631, -246.555 ], [ -50.393, -5.414, -8.376 ], [ -22.308, -44.954, 12.222 ], [ 3.296, 11.647, 70.649 ] ] ),
( 18, [ [ 296.250, 178.154, -283.773 ], [ -52.959, -4.397, 27.035 ], [ 10.998, -43.061, -0.027 ], [ -2.037, 9.722, 56.957 ] ] ),
( 19, [ [ 240.706, 174.731, -251.298 ], [ -65.503, -16.663, 18.653 ], [ 12.413, -26.875, 3.862 ], [ -0.209, 7.605, 43.189 ] ] ),
( 20, [ [ 170.036, 151.299, -240.510 ], [ -77.888, -18.667, 9.104 ], [ 21.815, -36.197, 2.313 ], [ 11.396, 18.147, 30.385 ] ] ),
( 21, [ [ 297.502, 143.355, -275.679 ], [ -48.044, 9.944, 32.993 ], [ -5.929, -36.823, 16.652 ], [ -0.988, 42.077, 47.842 ] ] ),
( 22, [ [ 250.978, 148.431, -247.195 ], [ -50.687, 1.846, 9.041 ], [ 9.032, -28.662, 9.417 ], [ -4.776, 32.784, 41.932 ] ] ),
( 23, [ [ 204.680, 141.636, -246.513 ], [ -35.493, -20.244, 16.094 ], [ 31.013, -11.624, 3.008 ], [ -11.195, 25.677, 39.181 ] ] ),
( 24, [ [ 287.464, 106.726, -251.655 ], [ -25.621, 6.219, 23.134 ], [ -19.294, -29.795, 27.926 ], [ 17.692, 37.852, 69.883 ] ] ),
( 25, [ [ 257.922, 116.607, -238.393 ], [ -31.830, 9.651, 4.808 ], [ -9.432, -33.031, 3.881 ], [ -10.300, 42.470, 62.047 ] ] ),
( 26, [ [ 228.110, 129.472, -238.391 ], [ -30.191, 5.166, -9.731 ], [ 19.291, -27.684, 5.002 ], [ -37.186, 41.031, 47.384 ] ] ),
( 27, [ [ 219.598, 234.911, -158.376 ], [ -59.865, -18.569, -15.474 ], [ 6.365, -34.542, -21.886 ], [ -2.376, -5.948, 82.683 ] ] ),
( 28, [ [ 271.479, 212.598, -191.075 ], [ -45.292, -11.794, 7.859 ], [ 30.495, -31.862, -46.294 ], [ 1.874, -12.175, 77.537 ] ] ),
( 29, [ [ 226.886, 201.943, -182.154 ], [ -46.036, -0.006, 5.281 ], [ 5.759, -30.320, -27.476 ], [ 4.237, -12.188, 64.641 ] ] ),
( 30, [ [ 181.157, 202.415, -182.448 ], [ -45.198, -1.262, 0.548 ], [ -3.376, -48.006, -27.616 ], [ -1.725, -4.852, 66.277 ] ] ),
( 31, [ [ 291.428, 178.268, -232.360 ], [ -43.644, -20.853, 24.989 ], [ 9.889, -35.193, -43.486 ], [ 4.353, -16.910, 50.697 ] ] ),
( 32, [ [ 237.268, 175.712, -212.165 ], [ -56.954, -16.756, 10.424 ], [ 13.032, -26.067, -32.916 ], [ 0.506, -11.344, 40.699 ] ] ),
( 33, [ [ 177.122, 161.633, -212.853 ], [ -60.962, -16.488, -9.264 ], [ 19.400, -26.292, -38.189 ], [ 2.855, 9.850, 36.322 ] ] ),
( 34, [ [ 219.695, 225.898, -85.992 ], [ -73.383, -7.270, 0.075 ], [ 9.466, -34.972, -20.253 ], [ -0.443, -16.457, 58.378 ] ] ),
( 35, [ [ 276.870, 199.241, -113.455 ], [ -50.589, -4.004, 2.780 ], [ 27.986, -43.217, -64.463 ], [ -2.551, -14.345, 71.169 ] ] ),
( 36, [ [ 228.512, 190.564, -119.932 ], [ -48.632, -2.241, 2.901 ], [ 10.553, -37.072, -44.027 ], [ -7.211, -10.078, 60.219 ] ] ),
( 37, [ [ 181.214, 185.829, -116.571 ], [ -45.024, -10.633, 6.490 ], [ 36.691, -40.359, -41.741 ], [ -7.404, -14.171, 56.958 ] ] ),
( 38, [ [ 294.618, 150.473, -187.485 ], [ -61.912, 3.854, 13.211 ], [ -7.435, -61.052, 31.811 ], [ 4.313, 46.520, 70.475 ] ] ),
( 39, [ [ 237.513, 155.974, -176.526 ], [ -52.879, 5.296, 5.774 ], [ -7.421, -52.768, 1.120 ], [ -9.440, 39.508, 59.010 ] ] ),
( 40, [ [ 189.392, 160.334, -172.880 ], [ -42.801, 6.979, 3.264 ], [ 21.841, -37.859, 28.056 ], [ -6.732, 20.365, 70.432 ] ] ),
( 41, [ [ 247.653, 64.318, -306.449 ], [ -7.559, 4.781, 7.258 ], [ -10.993, -6.381, 15.496 ], [ 30.221, 28.933, 71.221 ] ] ),
( 42, [ [ 239.325, 70.695, -300.571 ], [ -8.415, 6.741, 6.479 ], [ -7.094, -9.314, 3.351 ], [ 10.779, 13.380, 72.272 ] ] ),
( 43, [ [ 231.513, 77.178, -292.656 ], [ -12.525, 4.255, 3.319 ], [ -0.928, -16.243, -4.197 ], [ 11.706, 13.532, 59.617 ] ] ),
( 44, [ [ 230.978, 62.444, -297.245 ], [ -14.698, 11.188, -2.359 ], [ -8.962, -8.354, 1.170 ], [ 0.931, 7.312, 54.971 ] ] ),
( 45, [ [ 258.329, 78.766, -234.210 ], [ -8.603, 4.498, 0.874 ], [ -37.867, -20.422, 2.056 ], [ 3.424, 4.618, 67.449 ] ] ),
( 46, [ [ 248.799, 84.344, -233.104 ], [ -10.725, 6.321, 0.445 ], [ -24.858, -21.841, -4.453 ], [ -12.855, -3.519, 64.769 ] ] ),
( 47, [ [ 238.275, 93.157, -232.136 ], [ -12.861, 7.971, -1.034 ], [ -9.789, -33.602, -12.451 ], [ -9.411, 14.946, 61.906 ] ] ),
( 48, [ [ 223.573, 66.187, -240.080 ], [ -19.654, 31.273, -7.973 ], [ -20.558, -22.685, -0.982 ], [ -25.963, -0.396, 55.488 ] ] ),
( 49, [ [ 253.968, 82.516, -174.339 ], [ -21.821, 14.346, -0.313 ], [ -70.819, -36.828, -4.473 ], [ -6.474, 1.765, 58.654 ] ] ),
( 50, [ [ 232.669, 96.602, -174.812 ], [ -20.714, 13.936, 0.272 ], [ -45.067, -35.411, -8.030 ], [ -18.872, 10.884, 54.020 ] ] ),
( 51, [ [ 211.888, 109.358, -175.186 ], [ -20.256, 12.504, 0.821 ], [ -16.313, -50.413, -13.321 ], [ -35.462, 14.924, 45.481 ] ] ),
( 52, [ [ 187.821, 69.713, -187.140 ], [ -13.187, 61.646, 5.702 ], [ -34.715, -33.733, -12.517 ], [ -31.504, 10.855, 49.018 ] ] ),
( 53, [ [ 213.425, 207.382, -42.148 ], [ -56.500, 0.342, -5.827 ], [ 6.048, -18.275, -16.938 ], [ -5.756, -22.958, 37.324 ] ] ),
( 54, [ [ 258.130, 182.777, -53.571 ], [ -32.759, -3.828, -5.952 ], [ 46.842, -36.257, -14.249 ], [ -42.970, -18.327, 45.780 ] ] ),
( 55, [ [ 221.272, 179.757, -61.791 ], [ -41.743, -3.435, -5.875 ], [ 10.486, -36.897, -21.690 ], [ -5.754, -11.017, 49.078 ] ] ),
( 56, [ [ 175.167, 176.300, -67.698 ], [ -50.920, -3.892, 0.663 ], [ -2.971, -33.698, -41.085 ], [ -2.018, -13.036, 51.511 ] ] ),
( 57, [ [ 270.017, 129.272, -88.096 ], [ -48.699, 18.376, -7.516 ], [ -17.418, -51.841, -36.718 ], [ -50.518, -29.109, 80.611 ] ] ),
( 58, [ [ 224.626, 141.720, -98.406 ], [ -43.872, 3.149, -4.298 ], [ -5.587, -42.256, -31.773 ], [ 2.711, -18.020, 68.031 ] ] ),
( 59, [ [ 185.274, 147.077, -102.145 ], [ -35.411, -3.106, -4.228 ], [ 15.191, -29.940, -31.756 ], [ -14.714, -1.454, 64.340 ] ] ),
( 60, [ [ 236.417, 87.160, -119.825 ], [ -26.717, 14.046, -6.516 ], [ -56.297, -42.646, -20.424 ], [ -33.135, 2.045, 67.489 ] ] ),
( 61, [ [ 209.605, 101.124, -126.121 ], [ -27.728, 12.727, -4.885 ], [ -42.756, -25.066, -21.644 ], [ -36.638, 1.272, 45.800 ] ] ),
( 62, [ [ 181.792, 113.536, -131.292 ], [ -27.851, 13.168, -2.607 ], [ -10.444, -42.179, -14.896 ], [ -23.513, 15.200, 47.902 ] ] ),
( 63, [ [ 162.311, 78.408, -140.383 ], [ -34.319, 54.554, -5.830 ], [ -48.917, -26.754, 6.663 ], [ -11.741, 16.148, 53.528 ] ] ),
( 64, [ [ 203.028, 174.619, -25.286 ], [ -60.155, -2.415, -3.955 ], [ -17.934, -44.396, 2.254 ], [ -5.864, 0.361, 32.179 ] ] ),
( 65, [ [ 189.331, 131.538, -54.161 ], [ -73.019, 16.272, -14.723 ], [ -17.980, -26.665, -45.176 ], [ -2.116, -19.030, 46.007 ] ] ),
( 66, [ [ 159.408, 102.276, -88.784 ], [ -38.581, 50.234, -40.028 ], [ -29.507, -44.106, -22.230 ], [ -56.230, -1.913, 36.555 ] ] )
]
generateParameters = False

lElementsCount1 = 2
lElementsCount2 = 4
lElementsCount3 = 3
Expand All @@ -156,7 +228,7 @@ def generateBaseMesh(cls, region, options):
d1 = [1.0, 0.0, 0.0]
d2 = [0.0, 1.0, 0.0]
d3 = [0.0, 0.0, 1.0]

nodeIndex = 0
# Lower lobe nodes
for n3 in range(lElementsCount3 + 1):
lNodeIds.append([])
Expand All @@ -171,7 +243,13 @@ def generateBaseMesh(cls, region, options):

node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
x = [1.0 * (n1 - 1), 1.0 * (n2 - 1), 1.0 * n3]
if generateParameters:
x = [1.0 * (n1 - 1), 1.0 * (n2 - 1), 1.0 * n3]
else:
nodeParameters = nodeFieldParameters[nodeIndex]
nodeIndex += 1
assert nodeIdentifier == nodeParameters[0]
x, d1, d2, d3 = nodeParameters[1]
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, x)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, d1)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, d2)
Expand All @@ -198,16 +276,22 @@ def generateBaseMesh(cls, region, options):
# Oblique fissure nodes
if (n2 == (uElementsCount2 - 2)) and (n3 < (uElementsCount3 - 2)):
uNodeIds[n3][n2][n1] = lNodeIds[n3][lElementsCount2][n1]
print('uNodeIds', uNodeIds[n3][n2][n1])
#print('uNodeIds', uNodeIds[n3][n2][n1])
continue
elif (n2 < (uElementsCount2 - 1)) and (n3 == (uElementsCount3 - 2)):
uNodeIds[n3][n2][n1] = lNodeIds[lElementsCount3][n2][n1]
print('uNodeIds', uNodeIds[n3][n2][n1])
#print('uNodeIds', uNodeIds[n3][n2][n1])
continue

node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
x = [1.0 * (n1 - 1), 1.0 * (n2 - 1) + 2.5, 1.0 * n3 + 2.0]
if generateParameters:
x = [1.0 * (n1 - 1), 1.0 * (n2 - 1) + 2.5, 1.0 * n3 + 2.0]
else:
nodeParameters = nodeFieldParameters[nodeIndex]
nodeIndex += 1
assert nodeIdentifier == nodeParameters[0]
x, d1, d2, d3 = nodeParameters[1]
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, x)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, d1)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, d2)
Expand Down