Add solid core to tubenetwork mesh #262
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oneway1225
commented
Jul 29, 2024
oneway1225
commented
- Add solid core component to tubenetwork mesh.
- Add 3D whole body scaffold
| if self._isCore and self._elementsCountTransition > 1: | ||
| self._elementsCountAround = (elementsCountAround - 8 * (self._elementsCountTransition - 1)) |
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This should be checked and adjusted in the scaffolds' checkOptions method.
Elements count around should be satisfied first and transition/across major adjusted to fit.
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The reason why I had this in the tubenetworkmesh instead of the scaffolds' checkOptions is because I couldn't figure out a nice way of switching between one transition element case and multiple transition elements case.
For example, if I had an initial elementsCountAround of 16 in the UI, and I change elementsCountTransition to 2, then the new elementsCountAround would be 8. If this change was made in the UI, then the values that get sent to tubenetworkmesh would be 8 and 2. Now, if I change the elementsCountTransition back to 1, then the values that get sent to tubenetworkmesh would be 8 and 1, which is different to the initial elementsCountAround of 16.
Any suggestions?
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Just need a priority e.g. number around > transition > across major.
I think it's best to make the number around guaranteed, then work with the transition ensuring its possible for the number around or reducing to 1, then fix the across-major number to work in with the others.
| P0 = x[self._elementsCountAround // 4] | ||
| P1 = x[self._elementsCountAround // 4 * 3] |
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Requires multiple of 4 around. Safer to do mean of all points around.
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| coreCentres, arcCentres = [], [] | ||
| for i in range(self._elementsCountAround): | ||
| tol = 1e-10 # tolerance to avoid float division zero |
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Tolerances should not be absolute values. Can determine max range from outer coordinates and take 1.e-10 x that.
| OP = magnitude(sub(ox[i], cp[0])) | ||
| IP = magnitude(sub(ix[i], cp[1])) | ||
| distBetweenOuterAndInner = magnitude(sub(cp[1], cp[0])) | ||
| distBetweenOuterAndInner = tol if distBetweenOuterAndInner == 0 else distBetweenOuterAndInner |
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Would be more logical to use max(tol, distanceBetweenOuterAndInner).
| IP = magnitude(sub(ix[i], cp[1])) | ||
| distBetweenOuterAndInner = magnitude(sub(cp[1], cp[0])) | ||
| distBetweenOuterAndInner = tol if distBetweenOuterAndInner == 0 else distBetweenOuterAndInner | ||
| outerBase = (OP ** 2 - IP ** 2 - distBetweenOuterAndInner ** 2) / (2 * distBetweenOuterAndInner) |
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The algorithm is non-obvious, so I'd want a comment explaining it in plain english.
tests/test_wholebody2.py
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| region = context.getDefaultRegion() | ||
| self.assertTrue(region.isValid()) | ||
| annotationGroups = scaffold.generateMesh(region, options)[0] | ||
| self.assertEqual(5, len(annotationGroups)) # Needs updating as we add more annotation groups |
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Needs fixing, see new comments.
| cbx, cbd1, cd2, cbd3, ctx, ctd1, ctd2, ctd3 = [], [], [], [], [], [], [], [] | ||
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| for i in range(m): | ||
| for lst in (cbx, cbd1, cd2, cbd3): | ||
| lst.append([[0, 0, 0] for _ in range(n)]) |
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cd2 misnamed and not used, ctd2 not used
| tmdd3 = id3[startIndex] | ||
| rcx = [tmdxStart, tmdxEnd] | ||
| mag = -1 if n == 0 else 1 | ||
| rcd3 = [set_magnitude(tmdd3, mag), set_magnitude(tmdd3, mag)] |
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The middle derivative should surely be closer to difference between end and start coordinates.
Result with this code will be a symmetric cubic wave with a peak in the middle. Can't see how the current geometry is created with this.
This replacement code fixes boundary glitches caused by the above issue:
tmdd3Delta = sub(ix[n2z], ix[n2a])
for n in range(2):
startIndex = [n2a, n2z][n]
tmdxStart = ix[startIndex] if n == 0 else centre
tmdxEnd = centre if n == 0 else ix[startIndex]
rcx = [tmdxStart, tmdxEnd]
tmdd3Start = [-d for d in id3[startIndex]] if n == 0 else tmdd3Delta
tmdd3End = tmdd3Delta if n == 0 else id3[startIndex]
rcd3 = [normalize(tmdd3Start), normalize(tmdd3End)]
Note the issue only affected the first and last box values on the minor rows as the remaining values are resampled for the major columns.
| for n1 in range(self._elementsCountAround // 4 * 3 - nSkip, | ||
| self._elementsCountAround // 4 * 3 + nSkip + 1): |
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Define separate skip number for the major axis:
oSkip = self._elementsCountAcrossMajor // 2 - (1 + self._elementsCountTransition)
Need to use that to fix the other direction; logically that should have happened in _sampleCoreNodesAlongMinorAxis.
for n1 in range(self._elementsCountAround // 4 * 3 - oSkip,
self._elementsCountAround // 4 * 3 + oSkip + 1):
