Lungs #101

zekh167 · 2020-11-17T23:49:23Z

No description provided.

rchristie

Remove lungs1 scaffold and keep only lung1.
If you copied lungs1 to lung1 with the operating system and not using 'git mv oldname newname' then it will have lost its history. Let me know if you want help getting it back.

rchristie · 2020-11-18T22:41:46Z

src/scaffoldmaker/meshtypes/meshtype_3d_lungs1.py

+from opencmiss.zinc.node import Node
+
+
+class MeshType_3d_lungs1(Scaffold_base):


Remove this file. You committed both lungs1 and lung1.
In future use:
git mv old_file_name new_file_name
to tell git to rename it.

rchristie · 2020-11-18T22:44:39Z

src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py

+    @classmethod
+    def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=None):
+        '''
+        :param parameterSetName:  Name of valid parameter set for option Scaffold, or None for default.
+        :return: ScaffoldPackage.
+        '''
+        if parameterSetName:
+            assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
+                'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + ' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
+        assert False, cls.__name__ + '.getOptionScaffoldPackage:  Option ' + optionName + ' is not a scaffold'


Remove as not using sub-scaffolds.

rchristie · 2020-11-18T22:47:09Z

src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py

+        :return: annotationGroups
+        '''
+        fm = region.getFieldmodule()
+        fm.beginChange()


Remove beginChange and later endChange as these are called by caller Scaffold_base.generateMesh.
Note if we ever need them we now call opencmiss.utils.general ChangeManager(fieldmodule) as this guarantees endChange is called even if an exception occurs.

rchristie · 2020-11-18T22:50:47Z

src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py

+        markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
+        nodeIdentifier += 1
+        cache.setNode(markerPoint)
+        markerName.assignString(cache, 'APEX')


This should be 'apex of left lung'. In the long run we want these to also be in interlex.

rchristie · 2020-11-19T00:46:57Z

src/scaffoldmaker/utils/eftfactory_tricubichermite.py

+        remapEftNodeValueLabel(eft, [1, 2, 5, 6], Node.VALUE_LABEL_D2_DS1DS2, [])
+        remapEftNodeValueLabel(eft, [1, 2, 5, 6], Node.VALUE_LABEL_D2_DS1DS3, [])
+        remapEftNodeValueLabel(eft, [1, 2, 5, 6], Node.VALUE_LABEL_D2_DS2DS3, [])
+        remapEftNodeValueLabel(eft, [1, 2, 5, 6], Node.VALUE_LABEL_D3_DS1DS2DS3, [])
+
+        ln_map = [1, 1, 2, 3, 4, 4, 5, 6]
+        remapEftLocalNodes(eft, 6, ln_map)
+        assert eft.validate(), 'eftfactory_tricubichermite.createEftWedgeCollapseXi1AtXi2Zero:  Failed to validate eft'
+        return eft
+
+    def createEftWedgeCollapseXi1AtXi2One(self):
+        '''
+        Create a tricubic hermite element field for a wedge element, where xi1 collapsed on xi2 = 1.
+        :return: Element field template
+        '''
+        eft = self.createEftBasic()
+
+        # remap parameters on xi2 = 1 before collapsing nodes
+        remapEftNodeValueLabel(eft, [3, 4, 7, 8], Node.VALUE_LABEL_D_DS1, [])
+        remapEftNodeValueLabel(eft, [3, 7], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])])
+
+        # zero cross derivative parameters
+        remapEftNodeValueLabel(eft, [3, 4, 7, 8], Node.VALUE_LABEL_D2_DS1DS2, [])
+        remapEftNodeValueLabel(eft, [3, 4, 7, 8], Node.VALUE_LABEL_D2_DS1DS3, [])
+        remapEftNodeValueLabel(eft, [3, 4, 7, 8], Node.VALUE_LABEL_D2_DS2DS3, [])
+        remapEftNodeValueLabel(eft, [3, 4, 7, 8], Node.VALUE_LABEL_D3_DS1DS2DS3, [])
+
+        ln_map = [1, 2, 3, 3, 4, 5, 6, 6]
+        remapEftLocalNodes(eft, 6, ln_map)
+        assert eft.validate(), 'eftfactory_tricubichermite.createEftWedgeCollapseXi1AtXi2One:  Failed to validate eft'
+        return eft
+
+    def createEftWedgeCollapseXi2RightAtXi3One(self):
+        '''
+        Create a tricubic hermite element field for a wedge element, where xi2 collapsed on xi3 = 1 creating the
+        wedge elements. Top right Nodes are collapsed.
+        :return: Element field template
+        '''
+        eft = self.createEftBasic()
+
+        # remap parameters on xi3 = 1 before collapsing nodes
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS2, [])
+        remapEftNodeValueLabel(eft, [5, 6], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [])])
+
+        # zero cross derivative parameters
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS2, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS2DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D3_DS1DS2DS3, [])
+
+        ln_map = [1, 2, 3, 4, 5, 6, 5, 6]
+        remapEftLocalNodes(eft, 6, ln_map)
+        assert eft.validate(), 'eftfactory_tricubichermite.createEftWedgeCollapseXi2RightAtXi3One:  Failed to validate eft'
+        return eft
+
+    def createEftWedgeCollapseXi2LeftAtXi3One(self):
+        '''
+        Create a tricubic hermite element field for a wedge element, where xi2 collapsed on xi3 = 1 creating the
+        wedge elements. Top left nodes are collapsed.
+        :return: Element field template
+        '''
+        eft = self.createEftBasic()
+        setEftScaleFactorIds(eft, [1], [])
+
+        # remap parameters on xi3 = 1 before collapsing nodes
+        remapEftNodeValueLabel(eft, [7, 8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [1])])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS2, [])
+
+        # zero cross derivative parameters
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS2, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS2DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D3_DS1DS2DS3, [])
+
+        ln_map = [1, 2, 3, 4, 5, 6, 5, 6]
+        remapEftLocalNodes(eft, 6, ln_map)
+        assert eft.validate(), 'eftfactory_tricubichermite.createEftWedgeCollapseXi2LeftAtXi3One:  Failed to validate eft'
+        return eft
+
+    def createEftWedgeCollapseXi1AtXi3One(self):
+        '''
+        Create a tricubic hermite element field for a wedge element, where xi1 collapsed on xi3 = 1.
+        :return: Element field template
+        '''
+        eft = self.createEftBasic()
+
+        # remap parameters on xi3 = 1 before collapsing nodes
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS1, [])
+        remapEftNodeValueLabel(eft, [5, 7], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [])])
+
+        # zero cross derivative parameters
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS2, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS2DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D3_DS1DS2DS3, [])
+
+        ln_map = [1, 2, 3, 4, 5, 5, 6, 6]
+        remapEftLocalNodes(eft, 6, ln_map)
+        assert eft.validate(), 'eftfactory_tricubichermite.createEftWedgeCollapseXi1AtXi3One:  Failed to validate eft'
+        return eft


I've had a think about how to manage all the permutations of these functions and ease of identifying which one to use.
I think these should be divided into just 3 functions based on which xi is collapsed, and pass the 2 local nodes which are 'rotated' 90 degrees on to their neighbours to use derivatives mapped to the next 'quadrant':
createEftWedgeCollapseXi1Quadrant(self, collapseNodes)
e.g.
eft = tricubicfactory.createEftWedgeCollapseXi1Quadrant([1, 5]) would do the same as createEftWedgeCollapseXi1AtXi2Zero
Inside the function it would look like:

eft = self.createEftBasic() if (collapseNodes == [1,5]) or (collapseNodes == [2,6]): # remap nodes # & do common code such as zero derivatives on face, which is same for both these cases. elif ...: else: assert False, 'eftfactory_tricubichermite.createEftWedgeCollapseXiQuadrant not implemented for nodes ' + str(rotateNodes) eft = None return eft

We don't have to implement all cases now, but there will be an obvious place to put them when we need them.

I think we need both"createEftWedgeCollapseXi1QuadrantAtXi2Zero(self, collapseNodes)" and "createEftWedgeCollapseXi1QuadrantAtXi2One(self, collapseNodes)" since they have different node numbering and mapping. So, I decided to define one function named "createEftWedgeCollapseXi1QuadrantAtXi2Plane(self, collapseNodes, Xi2=None)" which include 4 cases:

Xi2=0 and collapseNodes = [1, 5]

Xi2=0 and collapseNodes = [2, 6]

Xi2=1 and collapseNodes = [3, 7]

Xi2=1 and collapseNodes = [4, 8]

I'm also defining "createEftWedgeCollapseXi2QuadrantAtXi3Plane(self, collapseNodes, Xi3=None)" which includes following cases:

Xi3=0 and collapseNodes = [1, 2]

Xi3=0 and collapseNodes = [3, 4]

Xi3=1 and collapseNodes = [5, 6]

Xi3=1 and collapseNodes = [7, 8]

and the third one as : "createEftWedgeCollapseXi1QuadrantAtXi3Plane"

So, now I replaced 3 functions for creating wedge elements which cover 12 cases.

I don't think you need to mention AtXi3Plane, it's Xi2 which is being collapsed and the list of nodes say where.

rchristie · 2020-11-19T01:05:30Z

src/scaffoldmaker/utils/eftfactory_tricubichermite.py

+    def createEftTetrahedronCollapseXi1Xi2AtXi3OneXi1AtXi2Zero(self):
+        '''
+        Create a tricubic hermite element field for a tetrahedron element, where xi1 and xi2 are collapsed on xi3 = 1
+        , and then, xi1 for nodes on both xi2 = 0 and  xi3 = 0 is collapsed.
+        :return: Element field template
+        '''
+        eft = self.createEftBasic()
+        setEftScaleFactorIds(eft, [1], [])
+
+        # remap parameters on xi3 = 1 before collapsing nodes
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS1, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS2, [])
+        remapEftNodeValueLabel(eft, [5, 6], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [])])
+        remapEftNodeValueLabel(eft, [7], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [])])
+
+        # remap parameters on xi2 = 0 before collapsing nodes
+        remapEftNodeValueLabel(eft, [1, 2], Node.VALUE_LABEL_D_DS1, [])
+        remapEftNodeValueLabel(eft, [1], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1])])
+
+        # zero cross derivative parameters
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS2, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS2DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D3_DS1DS2DS3, [])
+
+        ln_map = [1, 1, 2, 3, 4, 4, 4, 4]
+        remapEftLocalNodes(eft, 4, ln_map)
+        assert eft.validate(), 'eftfactory_tricubichermite.createEftTetrahedronCollapseXi1Xi2AtXi3OneXi1AtXi2Zero:  Failed to validate eft'
+        return eft
+
+    def createEftTetrahedronCollapseXi1Xi2AtXi3OneXi1AtXi2One(self):
+        '''
+        Create a tricubic hermite element field for a tetrahedron element, where xi1 and xi2 are collapsed on xi3 = 1
+        , and then, xi1 for nodes on both xi2 = 1 and xi3 = 0 is collapsed.
+        :return: Element field template
+        '''
+        eft = self.createEftBasic()
+        setEftScaleFactorIds(eft, [1], [])
+
+        # remap parameters on xi3 = 1 before collapsing nodes
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS1, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS2, [])
+        remapEftNodeValueLabel(eft, [7, 8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [1])])
+        remapEftNodeValueLabel(eft, [5], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [])])
+
+        # remap parameters on xi2 = 1 before collapsing nodes
+        remapEftNodeValueLabel(eft, [3, 4], Node.VALUE_LABEL_D_DS1, [])
+        remapEftNodeValueLabel(eft, [3], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])])
+
+        # zero cross derivative parameters
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS2, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS1DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D2_DS2DS3, [])
+        remapEftNodeValueLabel(eft, [5, 6, 7, 8], Node.VALUE_LABEL_D3_DS1DS2DS3, [])
+
+        ln_map = [1, 2, 3, 3, 4, 4, 4, 4]
+        remapEftLocalNodes(eft, 4, ln_map)
+        assert eft.validate(), 'eftfactory_tricubichermite.createEftTetrahedronCollapseXi1Xi2AtXi3OneXi1AtXi2One:  Failed to validate eft'
+        return eft


Similar to the wedge, need a naming scheme to manage all these permutations, suggest for all tetrahedra collapsed in xi1xi2:
createEftTetrahedronCollapseXi1Xi2Quadrant(self, peakNode, sideNode)
where peakNode is the localNode where the whole of xi1, xi2 is collapsed on to (on either xi3=0 or xi3=1), and sideNode is the node at the other end of xi3 which has another node collapsed onto it.
e.g.
eft = tricubicfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(8, 2) would do the same as createEftTetrahedronCollapseXi1Xi2AtXi3OneXi1AtXi2Zero

I defined one function named "createEftTetrahedronCollapseXi1Xi2QuadrantAtXi3One" which create four types of tetrahedron. Later, other cases can be added.

…eir peak node is on xi3=1.

…elements.

rchristie

Great thanks.

zekh167 added 13 commits November 13, 2020 17:50

Added lungs meshtypes.

eda7f10

Created regular elements for the left lung.

4fc2e2f

Created the back and front wedge elements.

6e8f67a

Added different wedge element templates.

4a35705

Added new wedge and tetrahedron element templates.

e78f794

Created tetrahedron elements at the top.

e13480b

Changed the lung meshtype name.

e808a18

Added lung terms.

6bb756c

Added annotation groups and marker point.

d531c3d

Changes two functions names.

5a6d473

Added definition for the new element field templates.

3cb481e

Minor change.

3c16be2

Changed names.

a1fbe9a

rchristie requested changes Nov 19, 2020

View reviewed changes

zekh167 added 10 commits November 19, 2020 14:08

delet meshtype_3d_lungs1

5a2c4c6

Deleted "getOptionScaffoldPackage".

dfbf190

Deleted "beginChange" and "endChange".

49fb6e9

Renamed the apex.

18d0499

Added new wedge and tetrahedron element templates.

73d3a1c

Replaced new wedge element templates.

7982bde

Replaced 1 function to create 4 cases of tetrahedron elements that th…

337f95a

…eir peak node is on xi3=1.

Converted eft6 and eft7 to the new one.

0e03132

Used the renamed functions.

b6e6086

Merged different functions and have only 3 for wedge and tetrahedron …

73995cc

…elements.

rchristie approved these changes Nov 20, 2020

View reviewed changes

rchristie merged commit b5f578c into ABI-Software:master Nov 20, 2020

zekh167 deleted the lungs branch November 20, 2020 03:40

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		from opencmiss.zinc.node import Node


		class MeshType_3d_lungs1(Scaffold_base):

Lungs #101

Lungs #101

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zekh167 commented Nov 17, 2020

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