Create 3D Slicer subject hierarchy from BodyParts3D

create-partof-hierarchy.py

# Source data can be obtained from http://lifesciencedb.jp/bp3d/ (tested with partof_BP3D_4.0_obj_99)
# These input file must be loaded into the scene:
# - partof_inclusion_relation_list.txt and partof_element_parts.txt (loaded as Table nodes)
# - OBJ files

shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
sceneItemID = shNode.GetSceneItemID()

def getItemParentsFmaIds(shNode, itemShItemId):
    existingParentShItemId = shNode.GetItemParent(itemShItemId)
    existingParentFmaIds = []
    while existingParentShItemId != sceneItemID:
        existingParentFmaIds.append(shNode.GetItemUID(existingParentShItemId, "FMA"))
        existingParentShItemId = shNode.GetItemParent(existingParentShItemId)
    return existingParentFmaIds

# Create partof hierarchy
inclusionListTable = getNode('partof_inclusion_relation_list').GetTable()
parentIdArray = inclusionListTable.GetColumnByName('parent id')
parentNameArray = inclusionListTable.GetColumnByName('parent name')
childIdArray = inclusionListTable.GetColumnByName('child id')
childNameArray = inclusionListTable.GetColumnByName('child name')
for i in range(inclusionListTable.GetNumberOfRows()):
    parentFmaId = parentIdArray.GetValue(i)
    parentShItemId = shNode.GetItemByUID("FMA", parentFmaId)
    if not parentShItemId:
        parentShItemId = shNode.CreateFolderItem(sceneItemID, parentNameArray.GetValue(i))
        shNode.SetItemUID(parentShItemId, "FMA", parentFmaId)
    childFmaId = childIdArray.GetValue(i)
    childShItemId = shNode.GetItemByUID("FMA", childFmaId)
    if not childShItemId:
        childShItemId = shNode.CreateFolderItem(sceneItemID, childNameArray.GetValue(i))
        shNode.SetItemUID(childShItemId, "FMA", childFmaId)
    existingParentFmaIds = getItemParentsFmaIds(shNode, childShItemId)
    if parentFmaId in existingParentFmaIds:
        # this parent is already a parent of the current item
        continue
    shNode.SetItemParent(childShItemId,parentShItemId)


# Update part list with names and FMA IDs
partsListTable = getNode('partof_element_parts').GetTable()
fmaIdArray = partsListTable.GetColumnByName('concept id')
filenameArray = partsListTable.GetColumnByName('element file id')
for i in range(partsListTable.GetNumberOfRows()):
    partNode = slicer.mrmlScene.GetFirstNodeByName(filenameArray.GetValue(i))
    if not partNode:
      continue
    parentFmaId = fmaIdArray.GetValue(i)
    parentShItemId = shNode.GetItemByUID("FMA", parentFmaId)
    if not parentShItemId:
        # this hierarchy is not found in the SH tree
        continue
    itemShItemId = shNode.GetItemByDataNode(partNode)
    existingParentFmaIds = getItemParentsFmaIds(shNode, itemShItemId)
    newParentFmaIds = getItemParentsFmaIds(shNode, parentShItemId)
    if len(newParentFmaIds)>len(existingParentFmaIds):
        # New parent is more specific than the current (parent has more nesting levels)
        shNode.SetItemParent(itemShItemId, parentShItemId)


# systemFmaIds = ['FMA7152', 'FMA7157', 'FMA7158', 'FMA7159', 'FMA7161', 'FMA7482', 'FMA9668', 'FMA7160', 'FMA72979']
# nonSystemFmaIds = ['FMA7154','FMA7184','FMA7185','FMA7186','FMA7187','FMA7188','FMA74657','FMA79063','FMA228642','FMA231424']
# for fmaId in systemFmaIds:
#     shNode.RemoveItem(shNode.GetItemByUID("FMA", fmaId))

# Limitation: this terminology is not a tree, therefore it is not possible to build a tree without loss of data or duplication of data
#
# Example: some structures are not part of any "system"
#
# FMA20394	human body	FJ1294
#     FMA7154	head	FJ1294
#         FMA24728	face	FJ1294
#             FMA54450	left eye	FJ1294
#                 FMA49051	left inferior oblique	FJ1294

# Example: some structures are part of multiple non-system branches
#
# FMA20394	human body [FJ2810]
#     FMA72979	integumentary system [FJ2810]
#     FMA74657	integument [FJ2810]
#         FMA7163	skin [FJ2810]

# Example: some structures are part of multiple system branches
#
# FMA20394	human body	FJ1737
#     FMA7157	nervous system	FJ1737
#         FMA55675	neuraxis	FJ1737
#             FMA7647	spinal cord	FJ1737
#                 FMA78497	central canal of spinal cord	FJ1737
#             FMA242675	ventricular system of neuraxis	FJ1737
#                 FMA75007	cavity of neuraxis	FJ1737

# FMA20394	human body	FJ2593
#     FMA7152	alimentary system	FJ2593
#         FMA71132	gastrointestinal tract	FJ2593
#             FMA7200	small intestine	FJ2593
#                 FMA7208	ileum	FJ2593
#                     FMA14966	distal part of ileum	FJ2593
#             FMA49179	lower gastrointestinal tract	FJ2593