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Created parameters for rat and human #146

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merged 10 commits into from
Jun 9, 2021
Merged

Created parameters for rat and human #146

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a2b3c3d
Created parameters for rat and human
arti-sukasem Jun 3, 2021
c4b85be
added ILX to Geometric markers
arti-sukasem Jun 3, 2021
5407ecf
Fixed CylinderCentralPath since it crashed the whole body mesh
arti-sukasem Jun 3, 2021
24fb80f
reviewed change requests
arti-sukasem Jun 4, 2021
39f234d
Updated marker_brainstem_coordinates and exterior
arti-sukasem Jun 7, 2021
b079ae5
reviewed minor changes
arti-sukasem Jun 7, 2021
d98441b
annotated interface, updated parameters
arti-sukasem Jun 8, 2021
d806b01
smoothened side derivatives
arti-sukasem Jun 8, 2021
0990679
smoothened side derivatives
arti-sukasem Jun 8, 2021
45bf6e8
Reverted cylinderMesh.py and minor fixes
arti-sukasem Jun 9, 2021
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29 changes: 22 additions & 7 deletions src/scaffoldmaker/annotation/brainstem_terms.py
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Expand Up @@ -3,15 +3,30 @@
"""

# convention: preferred name, preferred id, followed by any other ids and alternative names
brainstem_terms = [
("medulla oblongata", "UBERON:0001896"),
("pons", "UBERON:0000988"),
("midbrain", "UBERON:0001891"),
("diencephalon", "UBERON:0001894"),
("brainstem", "UBERON:0002298")
brainstem_terms = [ # Landmarks and groups
("brainstem", "UBERON:0002298", "ILX:0101444"),
("central canal of spinal cord", "UBERON:0002291", "ILX:0724457"),
("cerebral aqueduct", "UBERON:0002289", "ILX:0101977"),
("diencephalon", "UBERON:0001894", "ILX:0103217"),
("foramen caecum of medulla oblongata", "ILX:0746371"),
("medulla oblongata", "UBERON:0001896", "ILX:0106736"),
("midbrain", "UBERON:0001891", "ILX:0106935"),
("middle cerebellar peduncle", "UBERON:0002152", "ILX:0106956"),
("obex", "ILX:0107862"),
("pons", "UBERON:0000988", "ILX:0109019"),

# Geometric markers
("brainstem dorsal midline caudal point", "None"),
("brainstem ventral midline caudal point", "None"),
("brainstem dorsal midline cranial point", "None"),
("brainstem ventral midline cranial point", "None"),
("brainstem dorsal midline pons-medulla junction", "None"),
("brainstem ventral midline pons-medulla junction", "None"),
("brainstem dorsal midline midbrain-pons junction", "None"),
("brainstem ventral midline midbrain-pons junction", "None")
]

def get_brainstem_annotation_term(name : str):
def get_brainstem_term(name : str):
"""
Find term by matching name to any identifier held for a term.
Raise exception if name not found.
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