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Lung 2 scaffold #200

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merged 22 commits into from
Jul 6, 2022
Merged

Lung 2 scaffold #200

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bb8d2c9
Create a generic lung scaffold and its parameters for species
arti-sukasem May 17, 2022
9e85aad
Fix review and update parameters
arti-sukasem May 23, 2022
8be2034
Fix parameter names and update test_lung for lung2
arti-sukasem May 24, 2022
5358575
Add discontinuity to utils, test_lung, and lung terms
arti-sukasem Jun 9, 2022
be98974
Fix right lung and left lung annotation
arti-sukasem Jun 14, 2022
1ea6be0
Fix material parameters
arti-sukasem Jun 14, 2022
d1495cb
Fix the centre of the bendingAroundAxis and parameter sets
arti-sukasem Jun 14, 2022
ce6c03a
Add annotations and markers to right lung accessory lobe
arti-sukasem Jun 14, 2022
4fab444
Add ellipsoid polar/cartesian conversions
rchristie Jun 17, 2022
81e7084
Minimise displacement of lower lobe
arti-sukasem Jun 21, 2022
4183657
Improve lung2 curvature and adjust species' parameters
rchristie Jun 21, 2022
788304b
Improve pig lung spacing
rchristie Jun 21, 2022
5081093
Remove duplicate term
rchristie Jun 21, 2022
dda5734
Improve mouse, rat lung2 parameters
rchristie Jun 22, 2022
60a6f6e
Update lung test answers
rchristie Jun 22, 2022
40b0c4b
Fix surface of lobe groups for closed fissure case
rchristie Jun 22, 2022
7c98bed
Fix surface of lobe groups for open fissure case
rchristie Jun 22, 2022
e6056a8
Set pig number of left lung lobes to 2
rchristie Jun 22, 2022
434fec7
Improve lung2 conformance with ellipsoid
rchristie Jun 29, 2022
7ba29dd
Fix smoothing and creation of upper lobe nodes
rchristie Jul 1, 2022
a2be8f3
Fix ranges of lung material coordinates
rchristie Jul 2, 2022
715d283
Fix accessory lobe surface with open fissures
rchristie Jul 4, 2022
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58 changes: 56 additions & 2 deletions src/scaffoldmaker/annotation/lung_terms.py
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Expand Up @@ -4,30 +4,84 @@

# convention: preferred name, preferred id, followed by any other ids and alternative names
lung_terms = [
("apex of right lung accessory lobe", "ILX:0778119"),
("anterior border of left lung", "ILX:0793130"),
("anterior border of right lung", "ILX:0793129"),
("anterior mediastinum of left lung", "ILX:0793183"),
("anterior mediastinum of right lung", "ILX:0793184"),
("apex of left lung", "ILX:0778112"),
("apex of right lung", "ILX:0778113"),
("apex of right lung accessory lobe", "ILX:0778119"),
("base of left lung surface", "ILX:0793187"),
("base of lower lobe of left lung surface", "ILX:0793577"),
("base of upper lobe of left lung surface", "ILX:0793578"),
("base of right lung accessory lobe surface", "ILX:0793189"),
("base of right lung surface", "ILX:0793188"),
("base of lower lobe of right lung surface", "ILX:0793579"),
("base of middle lobe of right lung surface", "ILX:0793580"),
("dorsal apex of right lung accessory lobe", "ILX:0793603"),
("dorsal base of right lung accessory lobe", "ILX:0778125"),
("dorsal base of left lung", "ILX:0778126"),
("dorsal base of right lung", "ILX:0778127"),
("dorsal surface of right lung accessory lobe", "ILX:0793609"),
("horizontal fissure of right lung", "ILX:0746327"),
("horizontal fissure of lower lobe of right lung", "ILX:0793581"),
("horizontal fissure of middle lobe of right lung", "ILX:0793582"),
("horizontal fissure of upper lobe of right lung", "ILX:0793583"),
("laterodorsal tip of middle lobe of right lung", "ILX:0778124"),
("lateral surface of left lung", "ILX:0793601"),
("lateral surface of right lung", "ILX:0793602"),
("lateral surface of lower lobe of left lung", "ILX:0793584"),
("lateral surface of lower lobe of right lung", "ILX:0793585"),
("lateral surface of middle lobe of right lung", "ILX:0793586"),
("lateral surface of upper lobe of left lung", "ILX:0793587"),
("lateral surface of upper lobe of right lung", "ILX:0793588"),
("left dorsal base of right lung accessory lobe", "ILX:0793607"),
("left lung", "UBERON:0002168", "ILX:0733450"),
("left lung surface", "ILX:0793186"),
("left surface of right lung accessory lobe", "ILX:0793611"),
("left ventral base of right lung accessory lobe", "ILX:0793605"),
("lower lobe of left lung", "UBERON:0008953", "ILX:0735534"),
("lower lobe of left lung surface", "ILX:0793192"),
("lower lobe of right lung", "UBERON:0002171", "ILX:0725712"),
("lower lobe of right lung surface", "ILX:0793191"),
("lung", "UBERON:0002048", "ILX:0726937"),
("medial surface of left lung", "ILX:0793599"),
("medial surface of right lung", "ILX:0793600"),
("medial surface of lower lobe of left lung", "ILX:0793589"),
("medial surface of lower lobe of right lung", "ILX:0793590"),
("medial surface of middle lobe of right lung", "ILX:0793591"),
("medial surface of upper lobe of left lung", "ILX:0793592"),
("medial surface of upper lobe of right lung", "ILX:0793593"),
("middle lobe of right lung", "UBERON:0002174", "ILX:0733737"),
("middle lobe of right lung surface", "ILX:0793193"),
("medial base of left lung", "ILX:0778120"),
("medial base of right lung", "ILX:0778121"),
("anterior mediastinum of left lung", "UBERON:0008820", "ILX:0725455"),
("anterior mediastinum of right lung", "UBERON:0008820", "ILX:0725455"),
("oblique fissure of left lung", "ILX:0778115"),
("oblique fissure of lower lobe of left lung", "ILX:0793594"),
("oblique fissure of upper lobe of left lung", "ILX:0793595"),
("oblique fissure of right lung", "ILX:0778114"),
("oblique fissure of lower lobe of right lung", "ILX:0793596"),
("oblique fissure of middle lobe of right lung", "ILX:0793597"),
("oblique fissure of upper lobe of right lung", "ILX:0793598"),
("right dorsal base of right lung accessory lobe", "ILX:0793608"),
("right lung", "UBERON:0002167", "ILX:0729582"),
("right lung surface", "ILX:0793185"),
("right lung accessory lobe", "UBERON:0004890", "ILX:0728696"),
("right lung accessory lobe surface", "ILX:0793190"),
("right surface of right lung accessory lobe", "ILX:0793612"),
("right ventral base of right lung accessory lobe", "ILX:0793606"),
("upper lobe of left lung", "UBERON:0008952", "ILX:0735339"),
("upper lobe of left lung surface", "ILX:0793194"),
("upper lobe of right lung", "UBERON:0002170", "ILX:0728821"),
("upper lobe of right lung surface", "ILX:0793195"),
("ventral apex of right lung accessory lobe", "ILX:0793604"),
("ventral base of right lung accessory lobe", "ILX:0778123"),
("ventral base of left lung", "ILX:0778118"),
("ventral base of right lung", "ILX:0778122")
("ventral base of right lung", "ILX:0778122"),
("ventral surface of right lung accessory lobe", "ILX:0793610")

]

def get_lung_term(name : str):
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