Vary inner radius and tenia coli width along colon length #59

mlin865 · 2019-09-27T03:37:41Z

No description provided.

…to path tangent

…art and end

rchristie

You've demonstrated that the bulk of the work to get proper variation across segments is working fine; I've not looked into that in details here.
The code around this needs some changes:
Colon-specific parameters are being passed to tubemesh; as described in the comments, anything specific to a particular segment profile needs to be supplied to and sampled by the profile, not tubemesh itself.
Best have a discussion with me; it might simplify things.
I'm also wondering about removing the 'simple mesentery' case and just consider it as being a colon with a single tenia coli and no extra thickness (i.e. no extra later of elements).

rchristie · 2019-09-29T21:26:31Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

+    xList = []
+    d1List = []
+    for i in range(len(lengthList)):
+        v = [lengthList[i], paramList[i], 0.0]


No need for 3rd component for v and d1 as smooth function handles n components.

rchristie · 2019-09-29T21:34:04Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

+        d1 = [(lengthList[i+1] - lengthList[i]) if i < len(lengthList)-1 else (lengthList[i] - lengthList[i-1]), 0.0, 0.0]
+        nx.append(v)
+        nd1.append(d1)
+    smoothd1 = interp.smoothCubicHermiteDerivativesLine(nx, nd1)


Alternatively, could have proximal, (mid) transverse and distal parameters and assume zero derivatives? That would make this function colon-specific. What are researchers likely to measure?

Discussed offline with Richard. Decided to keep things as they are now and will modify later when requirements change.

rchristie · 2019-09-29T21:35:03Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

@@ -350,3 +453,59 @@ def generateMesh(cls, region, options):
        meshrefinement = MeshRefinement(baseRegion, region, baseAnnotationGroups)
        meshrefinement.refineAllElementsCubeStandard3d(refineElementsCountAround, refineElementsCountAlong, refineElementsCountThroughWall)
        return meshrefinement.getAnnotationGroups()
+
+def sampleParameterAlongLength(paramList, lengthList, segmentCount):


As written this function is general purpose so could go in tubemesh? But read comments below first...
Update: sampling needs to be done in the tube mesh segment generator as described elsewhere.

rchristie · 2019-09-29T21:42:25Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

+
+    # Find parameter value at each segment
+    xTol = 1.0E-6
+    for n in range(segmentCount + 1):


Isn't this loop the same as interp.sampleCubicHermiteCurves (also interp.sampleCubicHermiteCurvesSmooth)? These would be more efficient than using getCubicHermiteCurvesPointsAtArcDistance...

interp.sampleCubicHermiteCurves will sample the curve describing how parameter changes along the centre line into equal arclength, but here I want to sample along the center line and get the parameter value along each of these points on the center line.

rchristie · 2019-09-29T21:44:57Z

scaffoldmaker/meshtypes/meshtype_3d_colonsegmentsimplemesentery1.py

-            'Inner radius': 0.2,
-            'Mesenteric zone width': 0.08,
+            'Start inner radius': 0.094,
+            'Start radius derivative': 0.0,


Start inner radius derivative, also End below

rchristie · 2019-09-29T21:48:22Z

scaffoldmaker/meshtypes/meshtype_3d_colonsegmentsimplemesentery1.py

+    """
+
+    def __init__(self, region, elementsCountAroundMZ, elementsCountAroundNonMZ,
+    elementsCountAlongSegment, segmentLength, wallThickness):


indent second row of arguments

rchristie · 2019-09-29T21:52:36Z

scaffoldmaker/meshtypes/meshtype_3d_colonsegmentsimplemesentery1.py

-    mzWidth, radius, segmentLength, wallThickness):
+class TubeMeshSegmentInnerPointsNoTeniaColi:
+    """
+    Generates a class object and function to pass the inner profile


Generates inner profile of a simple mesentery colon segment i.e. no tenia coli, for use by tubemesh.

rchristie · 2019-09-29T21:55:05Z

scaffoldmaker/meshtypes/meshtype_3d_colonsegmentteniacoli1.py

-    cornerInnerRadiusFactor, haustrumInnerRadiusFactor, segmentLengthEndDerivativeFactor, segmentLengthMidDerivativeFactor, segmentLength, wallThickness):
+class TubeMeshSegmentInnerPointsTeniaColi:
+    """
+    Generates a class object and function to pass the inner profile


Improve description - see simple mesentery comment

rchristie · 2019-09-29T22:01:30Z

scaffoldmaker/utils/tubemesh.py

-    xInner, d1Inner, d2Inner, wallThickness,
-    segmentAxis, segmentLength,
+    innerRadiusList, dInnerRadiusList,
+    tcWidthList, dTCWidthList,


Can't pass colon-specific parameters in this way as it takes away the generic-ness of tubemesh.
All varying properties need to be passed to the segment generator, including radius and TC width. This makes sense as they are specific to that generator.
Tubemesh will supply distance along when it calls the segment generator which can use it to sample the varying properties.

rchristie · 2019-09-29T22:11:20Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

-            annotationGroups, annotationArray, transitElementList, uList, arcLengthOuterMidLength)
+        annotationGroups, nextNodeIdentifier, nextElementIdentifier, xList, d1List, d2List, d3List, sx, curvatureAlong, factorList, uList, relaxedLengthList, tubeTCWidthList = tubemesh.generatetubemesh(region,
+           elementsCountAround, elementsCountAlongSegment, elementsCountThroughWall, segmentCount, cx, cd1, cd2, cd12, innerRadiusSegmentList, dInnerRadiusSegmentList,
+           tcWidthSegmentList, dTCWidthSegmentList, tubeMeshSegmentInnerPoints, wallThickness, segmentLength, useCrossDerivatives, useCubicHermiteThroughWall)


Can't pass TC width here - see comments on tubemesh class.

…htype

mlin865 · 2019-10-01T01:04:54Z

I've made the changes as per request, please review. Thanks!

rchristie

There are values returned by tubemesh (tubeTCWidthList etc.) which it shouldn't know about, making it not generic... see comments.
Also request change to parameter sampling code - should be equally spaced along length.

rchristie · 2019-10-01T01:20:46Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

-            elementsCountAround, elementsCountAlongSegment, elementsCountThroughWall, segmentCount, cx, cd1, cd2, cd12,
-            xInner, d1Inner, d2Inner, wallThickness, segmentAxis, segmentLength, useCrossDerivatives, useCubicHermiteThroughWall,
-            annotationGroups, annotationArray, transitElementList, uList, arcLengthOuterMidLength)
+        annotationGroups, nextNodeIdentifier, nextElementIdentifier, xList, d1List, d2List, d3List, sx, curvatureAlong, factorList, uList, relaxedLengthList, tubeTCWidthList = tubemesh.generatetubemesh(region,


Can't return anything specific to a segment profile from this function either (relaxedLengthList, tubeTCWidthList; not sure what ulist is). Probable solution is to store these in the tubeMeshSegmentInnerPoints? Alternative is to return a generic map of names to lists of values.

rchristie · 2019-10-01T01:24:11Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py


        # Generate tenia coli
-        if segmentScaffoldType == MeshType_3d_colonsegmentteniacoli1:
+        if tcCount > 1:


Use a boolean flag setting control whether these are made, or zero thickness.

rchristie · 2019-10-01T01:25:36Z

scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py

-           useCrossDerivatives, useCubicHermiteThroughWall, xList, d1List, d2List, d3List,
-           elementsCountAroundTC, elementsCountAroundHaustrum, elementsCountAlongSegment, elementsCountThroughWall, wallThickness,
-           tcWidth, tcThickness, sx, curvatureAlong, factorList, uList, arcLengthOuterMidLength, segmentLength, tcCount)
+        if tcCount > 1:


See previous comment for colon 1. Replace with flag or zero thickness.

rchristie · 2019-10-01T01:26:46Z

scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py

-    Generates a 3-D colon segment mesh with two or three tenia coli with variable
+
+    def __init__(self, region, elementsCountAroundTC, elementsCountAroundHaustrum,
+    elementsCountAlongSegment, tcCount, segmentLengthEndDerivativeFactor,


indent argument lines 2 onwards with 8 spaces (2*4). See second accepted example at https://www.python.org/dev/peps/pep-0008/#code-lay-out.

rchristie · 2019-10-01T01:49:55Z

scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py

+        endTCWidth = self._tcWidthSegmentList[nSegment+1]
+        endTCWidthDerivative = self._dTCWidthSegmentList[nSegment+1]
+
+        return getColonSegmentInnerPoints(self._region, self._elementsCountAroundTC,


Expect some of the return values from this call to be held here and not returned to tubemesh, e.g. TC widths.

rchristie · 2019-10-01T01:55:04Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

+        innerRadiusSegmentList, dInnerRadiusSegmentList = interp.sampleParameterAlongCenterLine(innerRadiusList, lengthList, segmentCount)
+
+        tcWidthList = [proximalTCWidth, proximalTransverseTCWidth, transverseDistalTCWidth, distalTCWidth]
+        tcWidthSegmentList, dTCWidthSegmentList = interp.sampleParameterAlongCenterLine(tcWidthList, lengthList, segmentCount)


I had expected the sampling to be done within the TubeMeshSegmentInnerPoints, but I see you instead pass the segment number when calling it. I'm happy with this.

rchristie · 2019-10-01T02:15:37Z

scaffoldmaker/utils/interpolation.py

@@ -787,3 +787,61 @@ def getDoubleCubicHermiteCurvesMidDerivative(ax, ad1, mx, bx, bd1):
    magb = vector.magnitude(bd1)
    magm = arcLengtha + arcLengthb - 0.5*(maga + magb)
    return vector.setMagnitude(md1, magm)
+
+def sampleParameterAlongCenterLine(paramList, lengthList, outputElementsCount):


Remove 'Center' from name as redundant (I try to avoid using names where there are US spelling differences anyway). I would pass the lengthList as first argument because it is the reference onto which the parameters are mapped (the x to the y).

rchristie · 2019-10-01T02:41:53Z

scaffoldmaker/utils/interpolation.py

+        nd1.append(d1)
+    smoothd1 = smoothCubicHermiteDerivativesLine(nx, nd1)
+
+    # Get total arclength


I think this should be sampling at equal distances along the lengths, not including the parameter as a component of coordinates (it may after all be used for a non-spatial value). It would look increasingly wrong if there was a lot of variation of the parameter at one end vs. the other.
I think we need a special smoothing function to get derivatives of parameter p with linearly varying x lengths.
The arc length should just be the total length of the line (last x - first x). Find xi in the original elements at sample lengths, then evaluate p, dp/dxi, dx/dxi and use chain rule to get dp/dx. Divide by outputElementsCount to get derivatives for the segment length?
Probably easier to describe on paper.

…oordinates

rchristie

Minor changes now. A rename and a new flag option.

rchristie · 2019-11-03T19:57:33Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

+
+        relaxedLengthList, xiList = tubeMeshSegmentInnerPoints.getRelaxedLengthAndXiList()
+
+        if tcCount != 1:


This should test a separate setting e.g. a boolean flag indicating extra tenia thickness (or possibly if that thickness > 0). Should be possible to make 2, 3 tenia without extra thickening. Just as importantly, it means the code is self-documenting.

rchristie · 2019-11-03T21:04:23Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

+        tubeMeshSegmentInnerPoints = TubeMeshSegmentInnerPoints(
+            region, elementsCountAroundTC, elementsCountAroundHaustrum, elementsCountAlongSegment,
+            tcCount, segmentLengthEndDerivativeFactor, segmentLengthMidDerivativeFactor,
+            segmentLength, wallThickness, cornerInnerRadiusFactor, haustrumInnerRadiusFactor,
+            innerRadiusSegmentList, dInnerRadiusSegmentList, tcWidthSegmentList, dTCWidthSegmentList)


This object has a generic name but takes TC arguments?

rchristie · 2019-11-03T21:09:18Z

scaffoldmaker/meshtypes/meshtype_3d_colon1.py

@@ -6,13 +6,13 @@

 import copy
 from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion
-from scaffoldmaker.meshtypes.meshtype_3d_colonsegmentsimplemesentery1 import MeshType_3d_colonsegmentsimplemesentery1, getColonSegmentInnerPointsNoTeniaColi
-from scaffoldmaker.meshtypes.meshtype_3d_colonsegmentteniacoli1 import MeshType_3d_colonsegmentteniacoli1, getColonSegmentInnerPointsTeniaColi, getTeniaColi
+from scaffoldmaker.meshtypes.meshtype_3d_colonsegment1 import MeshType_3d_colonsegment1, TubeMeshSegmentInnerPoints, getTeniaColi, createFlatAndTextureCoordinatesTeniaColi, createNodesAndElementsTeniaColi


TubeMeshSegmentInnerPoints name is too generic; should be renamed to describe that it's for colon only. Probably want to rename the original class in this case, but worth knowing you can always rename something on import:
from scaffoldmaker.meshtypes.meshtype_3d_colonsegment1 import TubeMeshSegmentInnerPoints as ColonSegmentTubeMeshSegmentInnerPoints
This is often needed to disambiguate objects with the same name in two sources.

mlin865 added 8 commits July 10, 2019 13:41

Modify mouse centre to correct length

568578d

Modify default parameters for mouse segment profile

bd936d1

Merge remote-tracking branch 'abi/master' into mouseData

a4eb98b

Add mouse2 and correct code for cases where segment axis is parallel …

cece0cb

…to path tangent

Scale segment profile based on diameter along colon length

5b583bb

Create colon segment class object for passing to tubemesh

0fd56c6

Vary radius and tenia coli width using parameter and derivative at st…

e55561b

…art and end

Remove import math

90e45e8

rchristie requested changes Sep 29, 2019

View reviewed changes

mlin865 added 6 commits September 30, 2019 13:49

Remove 3rd component for v and d1

1ae7c8f

Change parameter name to start inner radius derivative, also end

52d654a

Improve description for TubeMeshSegmentInnerPoints

73029a6

Integrate simple mesentery case as one tenia coli in colonsegment mes…

c44a641

…htype

Remove passing of colon specific parameters to tubemesh

97a65b5

Rename and move sampleParameterAlongLength to interpolation.py

b1a5935

rchristie requested changes Oct 1, 2019

View reviewed changes

mlin865 added 10 commits October 1, 2019 16:45

Indent argument lines 2 onwards with 8 spaces

b12d266

Use a boolean flag to control whether tenia coli are made

00fc7e2

Remove 'Center' from function name and re-order function argument

3e48b5e

Store tubeTCWidthList in tubeMeshSegmentInnerPoints

a1d183b

Reorganise to keep tubemesh generic and reorder nodes and elements

7fa7545

Modify sampling function to not include parameter as a component of c…

4e38e01

…oordinates

Convert cm to mm

9fa3beb

Smooth d2 for nodes between segments

5156eb9

Scale outer d2 using curvature along inner surface

8d9427c

Update parameters for human colon with literature values

975f39a

rchristie requested changes Nov 3, 2019

View reviewed changes

mlin865 added 2 commits November 4, 2019 10:29

Modify flag option

f6b4d55

Rename TubeMeshSegmentInnerPoints to ColonSegmentTubeMeshInnerPoints

912800b

mlin865 added 2 commits November 4, 2019 12:19

Modify flag to read in annotation groups for human colon

8c6db49

Update parameters for pig colon

e8a9300

rchristie approved these changes Nov 7, 2019

View reviewed changes

rchristie merged commit 28e7cc7 into ABI-Software:master Nov 7, 2019

mlin865 deleted the mouseData branch November 7, 2019 00:43

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Vary inner radius and tenia coli width along colon length #59

Vary inner radius and tenia coli width along colon length #59

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		relaxedLengthList, xiList = tubeMeshSegmentInnerPoints.getRelaxedLengthAndXiList()

		if tcCount != 1:

Vary inner radius and tenia coli width along colon length #59

Vary inner radius and tenia coli width along colon length #59

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mlin865 commented Sep 27, 2019

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