Bladder coordinates #235

zekh167 · 2023-07-26T06:13:03Z

Hi Richard. I made the following changes based on our last discussion:

Changed the Material central path's coordinates and derivatives based on the magnitudes obtained from an ellipsoid with height 2.0 and diameter 1.0.
Changed the nodes to be made from outer surface toward the inner surface. The only thing I was thinking about is the name of "getCoordinatesFromInner" function in tubemesh.py which I suggest to be "getCoordinatesOffset" or "getTubeCoordinatesOffset" or something else since this function can be used to create both the "outer from inner" and the "inner from outer".
Changed the marker locations to put them on the inner surface as before.
Changed the wall thicknesses for different species.
Adjusted the test_bladder.py code.

…present an ellipsoid.

rchristie

I noticed serosa/lumen annotations were reversed, but the problem is caused by incorrect extrusion from outer surface (use Hermite through wall to see D3 is inward; I need to see why the element axes are not showing the problem). See comment in code for fixing - should be straightforward.
See also comment about hiding fixed ureter position option.
Please be very careful to check annotations and tests are fine.
Other than that I'm very happy with the material coordinates.

rchristie · 2023-08-06T23:41:48Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

@@ -1297,7 +1335,7 @@ def getBladderCoordinates(elementsCountAlongDome, elementsCountAlongNeck, elemen
            d3Inner.append(d3)

    # Create outer layers from the inner nodes
-    wallThicknessList = [wallThickness] * (elementsCountAlongBladder + 1)
+    wallThicknessList = [-wallThickness] * (elementsCountAlongBladder + 1)
    relativeThicknessList = []
    transitElementList = [0] * elementsCountAround
    xList, d1List, d2List, d3List, curvatureList = \


You can't just negate the wall thickness and pass to this function. What you're getting is elements with negative volume, with xi0 on the outside and xi1 on the inside. This also means your lumen/serosa annotations appear wrong.
Note the surface annotation code is correct: you need to fix this function to be able to create coordinates from outer properly.
I suggest you rename Mabelle's tubemesh function to extrudeSurfaceCoordinates() and have an additional option outward=True (you will supply False, which will internally use -wall thickness, but importantly must keep layer ordering from inside to out and d3 direction from inside to out. This should be a small change to this function; I don't want to see a whole copy of the code for the outward=False case, should just be a different sequence of inserting in the lists, e.g. list.insert(0, layer) for that case, where list.append(layer) is used for outward=True.
Please be careful to rename all variables so they say e.g. xSurf rather than xInner and ensure the function arguments are correctly documented.
Update comment to say 'create inner layers from outer' in bladder.
Please make sure all the tests pass and the annotations look correct. Check Colon etc. look correct and its annotations are correct. Be careful that all previous uses of getCoordinateFromInner call the new function.

I renamed Mabelle's tubemesh function and added the outward parameter to this function in all previous uses. Nothing else has been changed for the other scaffolds' code.

I also changed all variables in that function in tubemesh and documented the function arguments.

Changed the tubemesh function in order to create the nodes order from inner to outer, d3 pointing from inside to out while the bladder scaffold is created inward (outward=False). It also works properly for the outward=True in other scaffolds like colonsegment and esophagus.

Adjusted the markers location.

Checked the annotation to be true.

Bladder test has been updated. All tests pass.

rchristie · 2023-08-07T00:12:54Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

            options['Ureter position around'] = 0.67  # should be on the dorsal part (> 0.5)
        if 'Material' in parameterSetName:
            options['Number of elements along dome'] = 8
            options['Number of elements along neck'] = 4
            options['Number of elements around'] = 8
-            options['Wall thickness'] = 0.01
+            options['Wall thickness'] = 0.016  # an average of the wall thicknesses for above species
            options['Ureter position around'] = 0.67


Since we require the 'Ureter position around' to be the same for all variants, remove it from the per-species and material code. Add a comment explaining that it's a fixed material coordinate and thus not to be edited.
Remove this option from the visible options in getOrderedOptionNames() below.

Done as suggested above.

rchristie

Some minor fixes and code improvements.
Please eyeball changes and run tests again after changing.

rchristie · 2023-08-11T00:40:32Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

        markerList = []
        markerList.append({"group": apexGroup, "elementId": idx1, "xi": xi1})
        idx2 = elementsCountAlongDome * elementsCountAround * elementsCountThroughWall + ureterElementPositionAround + 1
-        xi2 = [ureter1Position.xi1, 0.0, 1.0]
+        xi2 = [ureter1Position.xi1, 0.0, 0.0]


This should have remained at 1.0 ? Want apex marker on the outside. Check it is correct and the bladder test still passes!

I moved the apex to outside surface and updated the test. Done.

rchristie · 2023-08-11T00:41:38Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

@@ -344,7 +344,7 @@ def getDefaultOptions(cls, parameterSetName='Default'):
            'Number of elements around': 8,
            'Number of elements through wall': 1,
            'Wall thickness': 0.016,


Default parameters use the cat central path but the material wall thickness - please change to make cat parameters the default. Just need to change wall thickness to 0.007 above.

rchristie · 2023-08-11T00:43:15Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

        if 'Rat 1' in parameterSetName:
            options['Wall thickness'] = 0.006  # was 0.3 * 2.0 / 110.40996641878101
-            options['Ureter position around'] = 0.67  # should be on the dorsal part (> 0.5)
        if 'Material' in parameterSetName:
            options['Number of elements along dome'] = 8
            options['Number of elements along neck'] = 4
            options['Number of elements around'] = 8
            options['Wall thickness'] = 0.016  # an average of the wall thicknesses for above species


Make the wall thickness in material coordinates 0.02 so it's a nice round number (and closer to half the human wall thickness). I'm still surprised by the variations here...

options['Wall thickness'] = 0.02 # an average of the wall thicknesses for above species, rounded

rchristie · 2023-08-11T00:45:16Z

src/scaffoldmaker/utils/tubemesh.py

+    :param xSurf: Coordinates on surface
+    :param d1Surf: Derivatives on surface around tube
+    :param d2Surf: Derivatives on surface along tube
+    :param d3Surf: Derivatives on surface through wall
    :param wallThicknessList: Wall thickness for each element along tube


Is this actually for each node along tube?

I think this represents the wallthickness for each layer of elements along tube.

The code says:

for n2 in range(elementsCountAlong + 1): wallThickness = wallThicknessList[n2]

which would make it nodes.

rchristie · 2023-08-11T00:46:15Z

src/scaffoldmaker/utils/tubemesh.py

    :param wallThicknessList: Wall thickness for each element along tube
    :param relativeThicknessList: Relative wall thickness for each element through wall
    :param elementsCountAround: Number of elements around tube
    :param elementsCountAlong: Number of elements along tube
    :param elementsCountThroughWall: Number of elements through tube wall
    :param transitElementList: stores true if element around is a transition
-    element that is between a big and a small element.


Restore this comment line.

rchristie · 2023-08-11T00:53:36Z

src/scaffoldmaker/utils/tubemesh.py

+        if outward:
+            wallThickness = wallThicknessList[n2]
+        else:
+            wallThickness = -wallThicknessList[n2]


The code below has several near identical cases for inward and outward which are different only because of the above sign. Don't modify the wallThickness, instead have a new variable:

wallOutwardDisplacement = wallThickness if outward else -wallThickness

Use it in the extrusion code below (see other comment).

rchristie · 2023-08-11T00:55:42Z

src/scaffoldmaker/utils/tubemesh.py

-            xOuter.append(x)
+            norm = d3Surf[n]
+            # Calculate extruded coordinates
+            x = [xSurf[n][i] + norm[i]*wallThickness for i in range(3)]


Use the signed wall displacement here only:

x = [xSurf[n][i] + norm[i]*wallOutwardDisplacement for i in range(3)]

rchristie · 2023-08-11T00:58:57Z

src/scaffoldmaker/utils/tubemesh.py

+                if outward:
+                    dWall = [wallThickness * c for c in norm]
+                    x = interp.interpolateCubicHermite(surfx, dWall, extrudedx, dWall, xi3)
+                else:
+                    dWall = [-wallThickness * c for c in norm]
+                    x = interp.interpolateCubicHermite(extrudedx, dWall, surfx, dWall, xi3)


Still need separate cases for x = ~, but dWall = should not depend on inward/outward.

Done. Kept the dWall the same, but different x.

zekh167 · 2023-08-15T00:46:20Z

All above comments applied and updated the bladder, bladderurethra, cecum, colon, colonsegment, esophagus and smallintestine tests.

rchristie

d1 calculation is incorrect in extrusion.
Fix comment.
cecum, colon, colon segment, esophagus and small intestine test answers should not have changed - please restore them.

rchristie · 2023-08-15T01:03:28Z

src/scaffoldmaker/utils/tubemesh.py

+    :param xSurf: Coordinates on surface
+    :param d1Surf: Derivatives on surface around tube
+    :param d2Surf: Derivatives on surface along tube
+    :param d3Surf: Derivatives on surface through wall
    :param wallThicknessList: Wall thickness for each element along tube


The code says:

for n2 in range(elementsCountAlong + 1): wallThickness = wallThicknessList[n2]

which would make it nodes.

rchristie · 2023-08-15T02:12:18Z

src/scaffoldmaker/utils/tubemesh.py

                xList.append(x)

                # dx_ds1
-                factor = 1.0 + wallThickness*xi3 * curvatureAroundInner[n]
-                d1 = [ factor*c for c in d1Inner[n]]
+                factor = 1.0 - wallOutwardDisplacement * xi3 * curvatureAroundSurf[n]


The old code was correct (except for rename of Inner -> Surf):

factor = 1.0 + wallThickness * xi3 * curvatureAroundSurf[n]

rchristie

Fix d3 in tubemesh

rchristie · 2023-08-15T03:29:52Z

src/scaffoldmaker/utils/tubemesh.py

                d2List.append(d2)
                curvatureList.append(curvature)

                #dx_ds3
-                d3 = [c * wallThickness * (relativeThicknessList[n3] if relativeThicknessList else 1.0/elementsCountThroughWall) for c in norm]
+                d3 = [c * -wallOutwardDisplacement * (relativeThicknessList[n3] if relativeThicknessList else 1.0 / elementsCountThroughWall) for c in norm]


Old code was fine. Use wallThickness not -wallOutwardDisplacement which was reversing colon d3.

rchristie

Looking great now.

zekh167 added 6 commits July 24, 2023 12:33

Changed the wall thickness amounts.

19bc323

Changed the material central path's coordinates and derivatives to re…

16946f1

…present an ellipsoid.

Making the nodes from outer surface to inner surface.

a5c6efc

Put the markers on inner surface.

5e3dde1

Changed the wall thicknesses.

daec000

changed the test for bladder.

7b954e2

rchristie requested changes Aug 7, 2023

View reviewed changes

zekh167 added 13 commits August 8, 2023 13:41

Changed the function to get the right coordinates and derivatives.

e0e6792

Changed the function name and added the outward parameter.

d9ee349

Changed the function name and added the outward parameter.

a35fd20

Changed the function name and added the outward parameter.

888d585

Changed the function name and added the outward parameter.

899d888

Changed the function name and added the outward parameter.

d3feb2a

Changed the function name and added the outward parameter.

d0ff653

Changed the function name and made the required changes to apex.

fca492f

Updated the bladder test.

7355186

Removed the 'Ureter position around' from the visible options.

13e8ac2

Fixed the issues with Hermite through wall for material coordinates.

e2b7eac

Fixed the markers location.

690bbd6

Updated the bladder test.

81f60f3

rchristie requested changes Aug 11, 2023

View reviewed changes

zekh167 added 9 commits August 15, 2023 12:13

Moved the apex to outside surface.

0902725

Updated bladder test.

0145808

Changed two parameters for Cat and Material.

9d2386d

Changed the material wall thickness.

b6ba03c

Updated.

fedb407

Updated cecum test.

2a703c5

Updated colon test.

3cef73e

Updated colon segment test.

8d05ff8

Updated esophagus test.

8aa67dc

zekh167 added 2 commits August 15, 2023 12:42

Updated small intestine test.

181202d

Updated the extrudeSurfaceCoordinates function.

56e932e

Updated the colonsegment test.

b6c49d0

rchristie requested changes Aug 15, 2023

View reviewed changes

Fixed the d1.

165064e

rchristie requested changes Aug 15, 2023

View reviewed changes

zekh167 added 8 commits August 15, 2023 15:38

Fixed d3.

f89c5d9

Updated bladderurethra test with main branch.

0bbbe97

Updated cecum test with main branch.

86b3538

Updated colon test with main branch.

ddc85dd

Updated colonsegment test with main branch.

ea67b23

Updated esophagus test with main branch.

ee141f1

Updated small intestine test with main branch.

101c355

Minor change.

ab7cd5c

rchristie approved these changes Aug 15, 2023

View reviewed changes

rchristie merged commit c71519d into ABI-Software:main Aug 15, 2023

zekh167 deleted the bladder_coordinates branch August 15, 2023 22:05

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Bladder coordinates #235

Bladder coordinates #235

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Bladder coordinates #235

Bladder coordinates #235

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