Stomach #132
Stomach #132
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Very good, but some fixes needed as in review comments.
Note the human stomach has uneven bunching up of elements on the lesser curvature. Rat stomach has some nodes in non-ideal positions on cardia limiting ridge adjacent to 6-way point on lesser curvature. I'll accept this PR without these fixes, but we need to fix them soon.
Note when I properly smoothed the human central path (as requested in review comment), the bunching was almost gone, so this may be enough.
tests/test_stomach.py
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| self.assertAlmostEqual(surfaceArea, 2436.4955183926895, delta=1.0E-6) | ||
| result, volume = volumeField.evaluateReal(fieldcache, 1) | ||
| self.assertEqual(result, RESULT_OK) | ||
| self.assertAlmostEqual(volume, 1168.9418891341106, delta=1.0E-6) |
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Would be good to test number of annotation groups, checking numbers of elements in each of them. See test_heart.py
| def createEftWedgeCollapseXi2(self, collapseNodes): | ||
| ''' | ||
| Create a tricubic hermite element field for a wedge element, where xi2 collapsed on xi1 = 1. | ||
| :return: Element field template |
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Describe argument collapseNodes, for this and other functions, with an example.
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| def createEftWedgeCollapseXi2(self, collapseNodes): | ||
| ''' | ||
| Create a tricubic hermite element field for a wedge element, where xi2 collapsed on xi1 = 1. |
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Change to "Create a tricubic hermite element field for a wedge element collapsed in xi2."
... it can be collapsed in xi2 at all other ends of xi1 and xi3 depending on collapseNodes and future implementations; describe this with param collapseNodes.
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| def createEftWedgeCollapseXi2(self, collapseNodes): | ||
| ''' | ||
| Create a bicubic hermite linear element field for a wedge element, where xi2 collapsed on xi1 = 1. |
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Note just xi1 = 1. see my comments for bicubic linear function.
| @@ -249,6 +249,70 @@ def createEftWedgeXi1Zero(self): | |||
| assert eft.validate(), 'eftfactory_tricubichermite.createEftWedgeXi1Zero: Failed to validate eft' | |||
| return eft | |||
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| def createEftWedgeCollapseXi1Quadrant(self, collapseNodes): | |||
| ''' | |||
| Create a bicubic hermite linear element field for a wedge element, where xi1 collapsed on xi3 = 0 or xi3 = 1. | |||
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Not limited to xi3 = 0 or xi3 = 1. Can also be xi2 = 0 and xi2 = 1 depending on collapseNodes. Document param collapseNodes (see my later comments).
| [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], [ | ||
| [ [ 70.8, 72.3, 0.0 ], [ -15.1, -43.8, 0.0 ], [ 37.3, -18.7, 0.0 ], [ 2.2, 7.2, 0.0 ], [ 0.0, 0.0, 38.7 ], [ 0.0, 0.0, 4.5 ] ], | ||
| [ [ 51.1, 30.7, 0.0 ], [ -21.4, -33.7, 0.0 ], [ 33.9, -17.5, 0.0 ], [ -9.0, -4.8, 0.0 ], [ 0.0, 0.0, 41.4 ], [ 0.0, 0.0, 0.9 ] ], | ||
| [ [ 27.8, 2.7, 0.0 ], [ -27.7, -18.4, 0.0 ], [ 20.5, -27.0, 0.0 ], [-17.1, -3.5, 0.0 ], [ 0.0, 0.0, 40.9 ], [ 0.0, 0.0, -5.0 ] ], | ||
| [ [ -0.3, -5.8, 0.0 ], [ -28.0, -2.6, 0.0 ], [ 0.4, -25.7, 0.0 ], [-12.6, 3.7, 0.0 ], [ 0.0, 0.0, 32.3 ], [ 0.0, 0.0, -9.4 ] ], | ||
| [ [ -26.5, -2.9, 0.0 ], [ -20.6, 8.0, 0.0 ], [ -5.4, -19.9, 0.0 ], [ -5.6, 7.7, 0.0 ], [ 0.0, 0.0, 22.1 ], [ 0.0, 0.0, -6.8 ] ], | ||
| [ [ -40.6, 7.4, 0.0 ], [ -11.0, 12.5, 0.0 ], [ -10.9, -10.9, 0.0 ], [ -1.3, 7.9, 0.0 ], [ 0.0, 0.0, 17.6 ], [ 0.0, 0.0, -5.9 ] ], | ||
| [ [ -48.1, 21.0, 0.0 ], [ -6.4, 15.7, 0.0 ], [ -8.4, -4.0, 0.0 ], [ 0.1, 4.9, 0.0 ], [ 0.0, 0.0, 10.5 ], [ 0.0, 0.0, -3.1 ] ], | ||
| [ [ -52.9, 38.6, 0.0 ], [ -3.2, 19.3, 0.0 ], [ -11.2, -1.5, 0.0 ], [ -5.7, 0.1, 0.0 ], [ 0.0, 0.0, 12.0 ], [ 0.0, 0.0, 6.1 ] ] ] ), |
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These haven't been been fully smoothed - please do all the smoothing tools before committing central path parameters incl. update directions, side axes, side derivatives UNLESS you have a need for particular values or they have been fitted.
Same for rat.
| 'Gastro-esophagal junction position along factor': 0.35, | ||
| 'Annulus derivative factor': 1.0, | ||
| 'Use cross derivatives': False, | ||
| 'Use linear through wall' : False, |
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When I use this option I get:
AssertionError: eftfactory_bicubichermitelinear.createEftWedgeCollapseXi1Quadrant: Failed to validate eft
It even crashed when tried with multiple elements through the wall ... investigate.
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Could be due to the missing "setEftScaleFactorIds(eft, [1], []) " in a section which requires scale factor -1. I have updated eftfactory_bicubichermitelinear.createEftWedgeCollapseXi1Quadrant to reflect that. I am able to generate the the scaffold with linear through wall with multiple elements through wall. Can you please try on your mchine and let me know if this is not resolved?
| 'Number of elements around esophagus': 8, | ||
| 'Number of elements around duodenum': 12, | ||
| 'Number of elements between annulus and duodenum': 6, | ||
| 'Number of elements through wall': 1, |
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The annulus is not also supporting multiple elements through the wall. Do you want to update it to do so?
May be best to remove it until you're ready. There are issues of transitioning to fewer elements at each end which will be tricky.
| 'Refine number of elements around': 1, | ||
| 'Refine number of elements along': 1, |
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Merge these to Refine number of elements surface as they must be the same when you have tricky general linear maps.
| 'Number of elements around duodenum': 12, | ||
| 'Number of elements between annulus and duodenum': 6, | ||
| 'Number of elements through wall': 1, | ||
| 'Number of radial elements in annulus': 1, |
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When set to 2 this does some funny stuff on the lesser curvature for the rat ... can you look into. May be an issue in annulus mesh which can be fixed later. May want to add an issue on github for it?
Should this be Number of elements across cardia? User doesn't know which annulus you're referring to.
…ple elements through annulus wall
…m triple point to 6pt junction
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