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Bladder ilx #148

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merged 2 commits into from
Jun 15, 2021
Merged

Bladder ilx #148

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2c13b22
updated new terms with ILX.
zekh167 Jun 14, 2021
37e54f0
Changed some annotation terms.
zekh167 Jun 14, 2021
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16 changes: 8 additions & 8 deletions src/scaffoldmaker/annotation/bladder_terms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@
bladder_terms = [
("bladder lumen", "UBERON:0009958"),
("dome of the bladder", "ILX:0738433"),
("dorsal part of bladder lumen", "None"),
("dorsal part of urinary bladder lumen", "ILX:0777128"),
("dorsal part of lumen of body of urinary bladder", "ILX:0739250"),
("dorsal part of lumen of neck of urinary bladder", "ILX:0739255"),
("dorsal part of lumen of urethra", "ILX:0739260"),
("dorsal part of bladder", "None"),
("dorsal part of bladder", "ILX:0778155"),
("dorsal part of urethra", "ILX:0739258"),
("dorsal part of serosa of body of urinary bladder", "ILX:0739278"),
("dorsal part of serosa of neck of urinary bladder", "ILX:0739280"),
Expand All @@ -27,21 +27,21 @@
("ureter", "UBERON:0000056", "ILX:0728080"),
("urethra", "UBERON:0000057", "ILX:0733022"),
("urinary bladder", "UBERON:0001255", "FMA:15900"),
("ventral part of bladder lumen", "None"),
("ventral part of urinary bladder lumen", "ILX:0777129"),
("ventral part of lumen of body of urinary bladder", "ILX:0739251"),
("ventral part of lumen of neck of urinary bladder", "ILX:0739257"),
("ventral part of lumen of urethra", "ILX:0739261"),
("ventral part of serosa of body of urinary bladder", "ILX:0739279"),
("ventral part of serosa of neck of urinary bladder", "ILX:0739281"),
("ventral part of serosa of urethra", "ILX:0739306"),
("ventral part of serosa of urinary bladder", "ILX:0739249"),
("ventral part of bladder", "None"),
("ventral part of bladder", "ILX:0778156 "),
("ventral part of urethra", "ILX:0739259"),
("apex of urinary bladder", "ILX:0774405"),
("left ureter junction with bladder", "None"),
("right ureter junction with bladder", "None"),
("urethra junction with bladder dorsal", "None"),
("urethra junction with bladder ventral", "None")
("left ureter junction with bladder", "ILX:0778142"),
("right ureter junction with bladder", "ILX:0778143"),
("urethra junction of dorsal bladder neck", "ILX:0778154"),
("urethra junction of ventral bladder neck", "ILX:0738410")
]

def get_bladder_term(name : str):
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8 changes: 4 additions & 4 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
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Expand Up @@ -896,8 +896,8 @@ def generateBaseMesh(cls, region, options):
apexGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("apex of urinary bladder"))
leftUreterGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("left ureter junction with bladder"))
rightUreterGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("right ureter junction with bladder"))
dorsalUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction with bladder dorsal"))
ventralUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction with bladder ventral"))
dorsalUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction of dorsal bladder neck"))
ventralUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction of ventral bladder neck"))

idx1 = 1
xi1 = [0.0, 0.0, 0.0]
Expand Down Expand Up @@ -1017,11 +1017,11 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
serosaOfBladder_ventral.getMeshGroup(mesh2d).addElementsConditional(is_bladder_serosa_ventral)

is_bladder_lumen_dorsal = fm.createFieldAnd(is_urinaryBladder_lumen, is_dorsal_bladder)
lumenOfBladder_dorsal = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("dorsal part of bladder lumen"))
lumenOfBladder_dorsal = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("dorsal part of urinary bladder lumen"))
lumenOfBladder_dorsal.getMeshGroup(mesh2d).addElementsConditional(is_bladder_lumen_dorsal)

is_bladder_lumen_ventral = fm.createFieldAnd(is_urinaryBladder_lumen, is_ventral_bladder)
lumenOfBladder_ventral = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("ventral part of bladder lumen"))
lumenOfBladder_ventral = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("ventral part of urinary bladder lumen"))
lumenOfBladder_ventral.getMeshGroup(mesh2d).addElementsConditional(is_bladder_lumen_ventral)

is_body_serosa_dorsal = fm.createFieldAnd(is_body_serosa, is_dorsal_bladder)
Expand Down