Bladder urethra #85

zekh167 · 2020-08-18T02:12:24Z

No description provided.

rchristie

First the straightforward fixes:
There are some minor fixes in names and individual lines of code.
The separate utility functions need polishing (I'm quite careful about these).
While I think in the medium term I'd want the bladder in a separate scaffold for re-use, I think it's more important right now to update this code to use a common central path for the bladder and urethra with annotation groups marking where one stops and the other begins. We can generalise 1d path utility function extractPathParametersFromRegion to take an optional group and otherwise use it as before.

rchristie · 2020-08-18T21:05:13Z

src/scaffoldmaker/utils/geometry.py

@@ -242,3 +242,31 @@ def getSurfaceProjectionAxes(ax, ad1, ad2, ad3, angle1radians, angle2radians, le
    bd1 = vector.crossproduct3(ad2, bd3)
    bd2 = vector.crossproduct3(bd3, bd1)
    return bx, bd1, bd2, bd3
+
+def createEllipsePoints(cx, radian, axis1, axis2, elementsCountAround, startRadians = 0.0):


This function is useful but it should be changed to give even spaced points in physical distance rather than radians.
Change to use:

getApproximateEllipsePerimeter to get total distance around ellipse, to divide by elementsCountAround to get constant element length.

updateEllipseAngleByArcLength to move the constant element length around the ellipse from the initial radians.
Have a look at createEllipsoidPoints() for example use of the latter.

I still want createEllipsePoints changed as described above.

src/scaffoldmaker/utils/annulusmesh.py

rchristie · 2020-08-18T21:08:33Z

src/scaffoldmaker/utils/annulusmesh.py

+        for i in range(len(deleteElementIdentifier)):
+            elementIdentifier = deleteElementIdentifier[i]


These two lines are more elegantly written in python as:

for elementIdentifier in deleteElementIdentifiers:

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

rchristie · 2020-08-18T22:48:05Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+            'Neck diameter 1': 5.0,
+            'Neck diameter 2': 3.0,
+            'Bladder wall thickness': 0.5,
+            'Neck angle': 45,


Rename: Neck angle degrees

rchristie · 2020-08-18T22:49:47Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+        bladderWallThickness = options['Bladder wall thickness']
+        useCrossDerivatives = options['Use cross derivatives']
+        useCubicHermiteThroughWall = not(options['Use linear through wall'])
+        neckAngle_radian = math.pi * options['Neck angle'] / 180


Cleaner to use this standard function:
neckAngleRadians = math.radians(options['Neck angle degrees'])
I'd also prefer to keep CamelCase rather than mix underscore style for variable names.

rchristie · 2020-08-18T22:53:30Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+            'Central path LUT': copy.deepcopy(centralPathOption_LUT),
+            'Central path bladder': copy.deepcopy(centralPathOption_bladder),


We need to have a discussion about how these are being used; I thought we'd have just a single path and use annotation groups to separate bladder and urethra?

rchristie · 2020-08-18T22:55:01Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+            'Urethra diameter 1': 1.5,
+            'Urethra diameter 2': 1.0,
+            'Urethra wall thickness': 0.5,
+            'Length factor': 0.5,


Length factor is not self-explanatory. Perhaps will be replaced by annotation groups on central path?

I changed it to "Urethra length proportion to central path". This parameter is used to identify the urethra length and also the bladder length along the central path.

rchristie · 2020-08-18T23:00:21Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+            'Minor diameter': 25.0,
+            'Neck diameter 1': 5.0,
+            'Neck diameter 2': 3.0,
+            'Bladder wall thickness': 0.5,


This is where not having sub-scaffolds for bladder and urethra is becoming problematic since you have to be clear about which part the parameter belongs to. Perhaps make it a rule that since this is 'Bladder with Urethra', bladder-only parameters don't need to be qualified, but you need to put 'Urethra' in front of urethra-specific parameters.

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

rchristie

I want you to change to annotate the central path and have explained how in the comments.
It's really much better as user can make a path of any length provided they make appropriate groups for 'urinary bladder' and 'urethra', and can guarantee have a node on the junction. Remove the length/proportion.
Note: I have just made some necessary fixes to scaffoldmaker and meshgeneratorstep so you'll need to update the codes first.
Remember to also check that your bladder test passes - may already have mismatches in numbers of annotation groups. May want to test the subscaffold annotation groups exists too?

rchristie · 2020-08-31T02:54:28Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

@@ -491,7 +454,9 @@ def generateBaseMesh(cls, region, options):
                    d2 = [segmentLength, 0.0, 0.0]
                elif n1 == elementsCountAlongBladder:
                    if not includeUrethra:
-                        d2 = [0.0, 0.0, segmentLength]
+                        badderSegmentLength = (1 - lengthFactor) * length / elementsCountAlongBladder


Typo: badder

rchristie · 2020-09-01T23:56:56Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+                    [[0.3, 3.2, 75.2], [0.5, 1.5, 12.7], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
+                    [[0.6, 5.6, 90.2], [0.5, 1.8, 13.2], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
+                    [[1.0, 8.7, 105.0], [0.7, 3.7, 12.9], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
+                    [[1.7, 13.9, 119.2], [0.9, 5.5, 13.3], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]]])


I'm wanting you to add user annotation groups demarking which part of the path is bladder and which is urethra, for both cat and rat.
Add a comma after the above line and add (though not perfectly elegant with double calls to get_bladder_term):

'userAnnotationGroups': [ { '_AnnotationGroup': True, 'dimension': 1, 'identifierRanges': '1-4', 'name': get_bladder_term('urinary bladder')[0], 'ontId': get_bladder_term('urinary bladder')[1] }, { '_AnnotationGroup': True, 'dimension': 1, 'identifierRanges': '5-8', 'name': get_bladder_term('urethra')[0], 'ontId': get_bladder_term('urethra')[1] } ]

To use these we'll add an optional group name parameter to extractPathParametersFromRegion in meshtype_1d_path1.py:

def extractPathParametersFromRegion(region, groupName = None): ''' :param groupName: Optional name of group to get node parameters from, otherwise all nodes are used. '''' # at the appropriate point after: nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES) if groupName: group = fm.findFieldByName(groupName).castGroup() nodes = group.getFieldNodeGroup(nodes).getNodesetGroup() assert nodes.isValid() # in case invalid or not found

You'll need to update the bladder with urethra to get parameters from the path with the appropriate group name matching the annotation group for bladder or urethra as we added earlier (from bladder terms).

rchristie · 2020-09-01T23:59:46Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+            'Urethra diameter 1',
+            'Urethra diameter 2',
+            'Urethra wall thickness',
+            'Urethra length proportion to central path',


This length proportion is no longer needed with an annotated central path.

After deleting the "Urethra length proportion to central path", Should I delete the "Number of elements Along" from options and instead add "Number of elements Along Bladder" and "Number of elements Along Urethra", which are independent?
Then, the segmentLength will be different in bladder and urethra parts, right?

Yes, you'll have independent numbers of elements along bladder and urethra, but you need to make the element size transition properly between them. Either the urethra fits to the bladder or vice versa.

rchristie · 2020-09-02T00:01:38Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+        # Central path
+        tmpRegion = region.createRegion()
+        centralPath.generate(tmpRegion)
+        cx, cd1, cd2, cd12 = extractPathParametersFromRegion(tmpRegion)


This will be called twice to extract parameters for bladder and urethra separately, passing the group name. See comment earlier.

Should I change the following part, too? Because the segmentLength will be different after deleting the "urethraLengthPortion".

# Find arcLength length = 0.0 elementsCountIn = len(cx) - 1 sd1 = interp.smoothCubicHermiteDerivativesLine(cx, cd1, fixAllDirections=True, magnitudeScalingMode=interp.DerivativeScalingMode.HARMONIC_MEAN) for e in range(elementsCountIn): arcLength = interp.getCubicHermiteArcLength(cx[e], sd1[e], cx[e + 1], sd1[e + 1]) length += arcLength segmentLength = length / elementsCountAlong

Shouldn't need to smooth the central path. (Separately we need to find a way for the user to smooth the 1D path as needed; on the to-do list.)
You should have a separate cx, cd1 for bladder and urethra. Can have a fixed segment length for one or the other, but not both:
If it is the bladder, the first element of the urethra needs to transition from the derivatives supplied by the end of the bladder. If it is the urethra, the last element of the bladder needs to transition to fit the first urethra derivatives.

rchristie · 2020-09-02T00:01:58Z

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

+        # Sample central path
+        # sx, sd1, se, sxi, ssf = interp.sampleCubicHermiteCurves(cx, cd1, elementsCountAlong)
+        # sd2, sd12 = interp.interpolateSampleCubicHermite(cd2, cd12, se, sxi, ssf)
+        if includeUrethra:
+            sx, sd1, se, sxi, ssf = interp.sampleCubicHermiteCurves(cx, cd1, elementsCountAlong)
+            sd2, sd12 = interp.interpolateSampleCubicHermite(cd2, cd12, se, sxi, ssf)
+        else:
+            m = int((1 - urethraproportion) * len(cx))
+            cx = cx[:m+1]
+            cd1 = cd1[:m+1]
+            cd2 = cd2[:m+1]
+            cd12 = cd12[:m+1]
+            sx, sd1, se, sxi, ssf = interp.sampleCubicHermiteCurves(cx, cd1, elementsCountAlongBladder)
+            sd2, sd12 = interp.interpolateSampleCubicHermite(cd2, cd12, se, sxi, ssf)


Not needed with annotated central path.

If I delete this part, how I can run the following part?

# Project reference point for warping onto central path sxRefList, sd1RefList, sd2ProjectedListRef, zRefList = \ tubemesh.getPlaneProjectionOnCentralPath(innerNodes_x, elementsCountAround, elementsCountAlong, length, sx, sd1, sd2, sd12)

You can still do this on each respective sets of cx, cd1 for the bladder and urethra.

rchristie · 2020-09-02T22:27:13Z

src/scaffoldmaker/utils/annulusmesh.py

+from opencmiss.utils.zinc.general import ChangeManager
 from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
+from opencmiss.zinc.field import Field, FieldGroup
 from opencmiss.zinc.node import Node


Remove the remnants to your changes to annulus mesh since you've moved element/node deletion code elsewhere.

rchristie

Good.
At some future point we may want to use some of the new smoothing/normal functions of 1d path to improve default central paths.

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

zekh167 added 9 commits August 11, 2020 14:12

Created bladder&urethra based on central path.

4e3a502

Added urethra annotations.

376ef1b

Added bladderurethra1 meshtype.

3bc9a40

Moved a function to annulusmesh.py.

7db69df

Added deleteElementAndNodes function.

af4234e

Added createEllipsePoints function.

cb9a823

moved 2 functions to annulusmesh.py and geometry.py.

2d97e3f

Changed options order.

7be75b6

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

e30d2d0

rchristie requested changes Aug 18, 2020

View reviewed changes

zekh167 added 9 commits August 20, 2020 12:21

Changed some names and used radian function.

e8e1aad

Removed "deleteElementsAndNodesUnderAnnulusMesh" function.

0e4d6bc

Added a new function to delete elements.

6660243

Changed the function for deleting elements under ostium.

6565626

Changed the function for deleting the elements under ostiums.

739d52b

Used a common central path.

a3f728b

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

b9ab94c

Removed bladder from "Bladder wall thickness".

6f0f1df

Changed "lengthFactor".

54cc4e2

rchristie requested changes Sep 2, 2020

View reviewed changes

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

6b1eb6b

rchristie reviewed Sep 2, 2020

View reviewed changes

zekh167 added 8 commits September 9, 2020 09:38

Added userAnnotationGroup.

1265b95

Added group name to the function.

5ea4eb0

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

83d0c13

Added transit elements and cleaned the code.

4866ec8

Modified transition derivatives.

798ea7b

Removed extra parts.

47295c9

Removed groupName from 1d path.

5155467

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

8dd0ebf

zekh167 added 4 commits September 15, 2020 14:57

Removed smoothing the central path.

a040483

Modified createEllipsePionts function.

802bd26

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

f776de2

Applied changes to 1d path.

1db6764

rchristie approved these changes Sep 25, 2020

View reviewed changes

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py Show resolved Hide resolved

rchristie merged commit b49717d into ABI-Software:master Sep 25, 2020

zekh167 deleted the bladder_urethra branch September 27, 2020 21:55

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		for i in range(len(deleteElementIdentifier)):
		elementIdentifier = deleteElementIdentifier[i]

		'Central path LUT': copy.deepcopy(centralPathOption_LUT),
		'Central path bladder': copy.deepcopy(centralPathOption_bladder),

Bladder urethra #85

Bladder urethra #85

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zekh167 commented Aug 18, 2020

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