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Stomach #236

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Aug 24, 2023
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c55b30f
Update derivatives at apex and Richard's suggestions
mlin865 Jul 5, 2023
b7a20c3
Add points along fundus on central path
mlin865 Jul 6, 2023
6bcc1a9
Correct typo to gastro-esophageal
mlin865 Jul 6, 2023
5fbdd1c
Pre-calculate how to spread out elements along
mlin865 Jul 6, 2023
128c06a
Remove return of elementCountGroupList
mlin865 Jul 6, 2023
fa3c272
Remove unused code
mlin865 Jul 7, 2023
5e36d44
Merge remote-tracking branch 'abi/main' into stomach
mlin865 Jul 7, 2023
ad756cb
Update antrum to 0.3, fundus to 0.7 in material coordinates
mlin865 Jul 18, 2023
c008203
Implement hemisphere and cubic hermite functions for material coordin…
mlin865 Jul 19, 2023
67c6296
Update central paths to make smooth track surfaces
mlin865 Jul 21, 2023
564b028
Update central path unit scale and align axis origin to fundus-body i…
mlin865 Jul 21, 2023
f9860ef
Update human 1 central path
mlin865 Jul 21, 2023
855c7bc
Update generateMesh for track surface
mlin865 Jul 31, 2023
887de79
Make d1 at apex zero for track surface
mlin865 Jul 31, 2023
dcc3e4b
Distribute elements along each region equally using track surface
mlin865 Aug 8, 2023
ececfe2
Remove use of elements between fundus apex to cardia and cardia to du…
mlin865 Aug 9, 2023
c67e1d3
Allow variable elements around esophagus
mlin865 Aug 10, 2023
06630ec
Clean up code
mlin865 Aug 10, 2023
140fa60
Fix linear mapping at corners around annulus
mlin865 Aug 11, 2023
42a17aa
Make smooth curves from apex to annulus and annulus to body
mlin865 Aug 11, 2023
02d81a6
Allow refinement of cardia surface elements
mlin865 Aug 14, 2023
8457280
Allow number of elements along stomach
mlin865 Aug 14, 2023
43f94ff
Update mouse central path for apex and flatter duodenum
mlin865 Aug 15, 2023
1aad953
Update number of elements for parameter sets
mlin865 Aug 15, 2023
d112608
Update unit tests
mlin865 Aug 15, 2023
6aa3cea
Merge remote-tracking branch 'abi/main' into stomach
mlin865 Aug 15, 2023
e6ba9fd
Merge remote-tracking branch 'abi/main' into stomach
mlin865 Aug 15, 2023
bdd69df
Fix problem with large number of elements around duodenum
mlin865 Aug 22, 2023
2a30ea8
Make derivatives around annulus in correct direction and magnitude
mlin865 Aug 23, 2023
b65e498
Set minimum elements in fundus and pylorus
mlin865 Aug 24, 2023
5704223
Update mouse and rat central paths
mlin865 Aug 24, 2023
6ca1bbb
Update curvature for derivatives around annulus
mlin865 Aug 24, 2023
fe3d331
Update unit tests
mlin865 Aug 24, 2023
0be9130
Merge remote-tracking branch 'abi/main' into stomach
mlin865 Aug 24, 2023
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12 changes: 9 additions & 3 deletions docs/scaffolds/stomach.rst
Original file line number Diff line number Diff line change
Expand Up @@ -60,9 +60,15 @@ which is intended to be fitted to actual data for a specimen.

The material coordinates field ``stomach coordinates`` defines a highly idealized coordinate system to give permanent
locations for embedding structures in the stomach. It is defined by a capsule-shaped structure with an inlet cylindrical
tube representing the esophagus and another outlet tube representing the duodenum. This can be viewed by
visualising this field in the *Display* tab of **Scaffold Creator** or by switching to the special ``Material``
parameter set.
tube representing the esophagus and another outlet tube representing the duodenum. In this coordinate field, the stomach
has a unit length of 2.0. The length of the fundus region is 0.7 unit. It is represented by a hemisphere with
unit length diameter along the first 0.5 unit length and a cylindrical tube with a uniform unit diameter along the next
0.2 unit along its length. The body continues as a cylindrical tube with a uniform unit diameter along its 0.6 unit
length. The antrum is a cylindrical tube of 0.3 unit length and the rate of change of its diameter along its length is
described by a cubic hermite function, decreasing at a rate of 0.75 unit/unit length. The pylorus and duodenum are both
described by cylindrical tube with a uniform diameter of 0.4 unit and a length of 0.2 unit. The material coordinates
field can be viewed by visualising this field in the *Display* tab of **Scaffold Creator** or by switching to the
special ``Material`` parameter set.

The stomach scaffold supports limited refinement/resampling by checking *Refine* (set parameter to ``true``) with chosen
*Refine number of elements* parameters. Be aware that only the ``coordinates`` field is currently defined on the refined
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