Material coordinates by 0huitzil · Pull Request #295 · ABI-Software/scaffoldmaker

0huitzil · 2026-07-29T03:35:21Z

Whole-body scaffold is in need of a material coordinates field. This pull request includes the following changes to the wholebody2 scaffold:

Added a material coordinates field into the scaffold (body coordinates). This is done by calling the tube generator one more time, with default settings.
Changes the default proportions of the 1d-network-layout scaffold to be more consistent to those of a "default" human
Created a script which automatically generated the network layout of the body (util/human_network_layout)
Subdivided arms into brachium/antebrachium
Subdivided legs into upper/lower leg
Added skin groups for hand and foot

rchristie

Not really a full review as this is a larger change than I expected (which was just to add material coordinates). For a larger change including upper/lower limbs etc. I will need to look at when I'm back from Mon 17.
There are some comments about unnecessary formatting changes, but little real substance due to the following:
For some reason the meshtype_3d_wholebody2 scaffold diff is unable to be rendered in the github interface. Has it caught up to the tube mesh dome changes?
I'll need you to walk me through the changes now they're a bit larger.

rchristie · 2026-08-06T21:56:26Z

    _allScaffoldTypes = [
        MeshType_1d_bifurcationtree1,
        MeshType_1d_uterus_network_layout1,
+        MeshType_1d_human_body_network_layout1,


This shouldn't be committed to the public scaffold list.
I don't expect any change to this whole file -- can you revert it?

rchristie · 2026-08-06T22:00:23Z

+    AnnotationGroup,
+    findOrCreateAnnotationGroupForTerm,
+    getAnnotationGroupForTerm,
+)


Don't needlessly change style like this. I don't want one line per imported function as we can get dozens from some utilities.

rchristie · 2026-08-06T22:02:30Z

+import math
+


math was already being imported below -- don't change unlesss we agree on a new standard for ordering, and the current approach is that python system libraries are imported last after our own sources.

rchristie · 2026-08-06T22:03:15Z

-    computeCubicHermiteEndDerivative, getCubicHermiteArcLength, interpolateLagrangeHermiteDerivative,
-    sampleCubicHermiteCurvesSmooth, smoothCubicHermiteDerivativesLine)
+    computeCubicHermiteEndDerivative,
+    getCubicHermiteArcLength,
+    interpolateLagrangeHermiteDerivative,
+    sampleCubicHermiteCurvesSmooth,
+    smoothCubicHermiteDerivativesLine,
+)
 from scaffoldmaker.utils.networkmesh import NetworkMesh
-from scaffoldmaker.utils.tubenetworkmesh import BodyTubeNetworkMeshBuilder, TubeNetworkMeshGenerateData
-import math
+from scaffoldmaker.utils.tubenetworkmesh import (
+    BodyTubeNetworkMeshBuilder,
+    TubeNetworkMeshGenerateData,
+)


Revert these unnecessary changes.

rchristie · 2026-08-06T22:06:19Z

    ("abdominopelvic cavity", "UBERON:0035819"),
    ("upper limb", "UBERON:0001460"),
    ("left upper limb", "UBERON:8300002", "FMA:7186"),
+    ("left shoulder", ""),


Do any of these new terms have ILX or UBERON ids?
Look up on interlex...

rchristie · 2026-08-06T22:07:30Z

    ("head core", ""),
    ("diaphragm", "UBERON:0001103", "ILX:0103194"),
    ("hand", "ILX:0104885", "FMA:9712"),
+    ("hip", ""),


Does hip have a real anatomical definition? Perhaps needs to be a more focused term for the level of the top of the pelvis?

rchristie · 2026-08-06T22:08:55Z

@@ -0,0 +1,139 @@
+#%%


I wouldn't have started a new utility that is used in one place, but it's OK.
However, need to have header text explaining what it is for.

rchristie · 2026-08-06T22:09:27Z

+    'footElementsCount': 2
+}
+
+def create_segment_layout(nodeCount:int, nodeIdentifier:int,


This is a very generic name. Is the function able to be used for other scaffolds?
It seems like it should be a method of a class that maintains the next node identifier...

rchristie · 2026-08-06T22:20:25Z

+
+    :param nodeCount: Number of nodes to add.
+
+    :param networkLayout: String containing the current network layout.


No such argument. A NetworkLayout is a specific class. This would logically be what we call a structure string.

rchristie · 2026-08-06T22:23:06Z

@@ -0,0 +1,139 @@
+#%%
+# Number of elements per segment. Used to calculate the number of nodes per segment.
+human_network_element_counts = {


This might be better done as a members of a class?
The generate function would then be a method on that class?

0huitzil · 2026-08-14T00:16:30Z

On a second look, the limb subdivision changes are definitely undercooked. And, given the usefulness of the material coordinates to the other projects we are working on, I decided to move the other limb subdivision changes to a separate branch, and just keep the following changes:

Added material coordinates to the scaffold
Updated default lengths of the 1d network
Updated the test to the new default parameters

rchristie

Can we change to the following default sizes in the body coordinates branch:

"Abdomen length": 3.0,
"Hand length": 2.0,
"Head length": 2.5,
"Neck length": 1.0,
"Shoulder width": 4.5,
"Thorax length": 2.5,

We'll tweak this again in subsequent stuff, but I think these will be better.
Can you make these changes, update test answers, commit and remove 'draft' from the PR.

Restore previous torso depth and update test answers.

Fix trimming errors at armpits

rchristie

Minor fixes

rchristie · 2026-09-18T04:12:39Z

+    ("right hand", "ILX:"),
+    ("left hand", "ILX:"),
+    ("right hand skin epidermis outer surface", "ILX:"),
+    ("left hand skin epidermis outer surface", "ILX:"),


If there is not term ID use "" (empty quotes)

rchristie · 2026-09-18T04:13:10Z

+    ("right foot", "ILX:"),
+    ("left foot", "ILX:"),
+    ("right foot skin epidermis outer surface", "ILX:"),
+    ("left foot skin epidermis outer surface", "ILX:"),


Use blank id""

rchristie

Looks good.

rchristie requested changes Aug 6, 2026

View reviewed changes

0huitzil force-pushed the material-coordinates branch 2 times, most recently from 21f0b41 to fbd6d4e Compare August 12, 2026 22:28

Added material coordinates to scaffold

709d608

0huitzil force-pushed the material-coordinates branch from fbd6d4e to 709d608 Compare August 12, 2026 22:32

Changed default 1d network lengths

1379fa9

0huitzil force-pushed the material-coordinates branch from d26e0c3 to 1379fa9 Compare August 13, 2026 00:26

Updated tests to new default parameters

b091f7c

Added new terms for hands and feet. Minor proportion changes.

4082541

rchristie requested changes Sep 7, 2026

View reviewed changes

Updated some default lengths and corrected tests

d541bcd

0huitzil marked this pull request as ready for review September 8, 2026 01:30

rchristie and others added 2 commits September 18, 2026 12:25

Fix trimming errors at armpits

0081e7f

Restore previous torso depth and update test answers.

Merge pull request #1 from rchristie/material-coordinates-fix

8943ad4

Fix trimming errors at armpits

rchristie requested changes Sep 18, 2026

View reviewed changes

Update body terms with empty identifiers

c23ceb4

rchristie approved these changes Sep 28, 2026

View reviewed changes

rchristie merged commit e7a3ca2 into ABI-Software:main Sep 28, 2026
9 checks passed

0huitzil deleted the material-coordinates branch September 29, 2026 01:46


		:param nodeCount: Number of nodes to add.

		:param networkLayout: String containing the current network layout.

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0huitzil commented Jul 29, 2026

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0huitzil commented Aug 14, 2026

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