Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Create a generic lung scaffold and its parameters for species #196

Closed
wants to merge 11 commits into from
Closed

Create a generic lung scaffold and its parameters for species #196

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
7be30a6
Create a generic lung scaffold and its parameters for species
arti-sukasem May 17, 2022
c4dae5f
Fix review and update parameters
arti-sukasem May 23, 2022
00e298e
Fix parameter names and update test_lung for lung2
arti-sukasem May 24, 2022
a7f9cf0
Add discontinuity to utils, test_lung, and lung terms
arti-sukasem Jun 9, 2022
9cff049
Fix right lung and left lung annotation
arti-sukasem Jun 14, 2022
f14ca2c
Fix material parameters
arti-sukasem Jun 14, 2022
e916903
Fix the centre of the bendingAroundAxis and parameter sets
arti-sukasem Jun 14, 2022
f34b6f5
Add annotations and markers to right lung accessory lobe
arti-sukasem Jun 14, 2022
474a315
Add ellipsoid polar/cartesian conversions
rchristie Jun 17, 2022
e2210ea
Merge pull request #2 from rchristie/ellipsoid
arti-sukasem Jun 19, 2022
df43ddc
Minimise displacement of lower lobe
arti-sukasem Jun 21, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
58 changes: 56 additions & 2 deletions src/scaffoldmaker/annotation/lung_terms.py
View file
Open in desktop
Original file line number Diff line number Diff line change
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):
Expand Down
Loading