Merge pull request #70 from rchristie/fiducial

Improve annotations, refinement and VTK export

src/scaffoldmaker/annotation/annotationgroup.py

@@ -9,35 +9,41 @@ class AnnotationGroup(object):
     Describes subdomains of a scaffold with attached names and terms.
     '''
 
-    def __init__(self, region, name, FMANumber, lyphID):
+    def __init__(self, region, term):
         '''
         :param region: The Zinc region the AnnotationGroup is to be made for.
-        :param name: The name of an annotation group e.g. common medical term.
-        :param FMANumber: The FMA Number of the group.
-        :param lyphID: The Apinatomy Lyph ID for the group.
+        :param term: Identifier for anatomical term, currently a tuple of name, id.
+        e.g. ("heart", "FMA:7088")
         '''
-        self._name = name
-        self._FMANumber = FMANumber
-        self._lyphID = lyphID
+        self._name = term[0]
+        self._id = term[1]
         fm = region.getFieldmodule()
-        field = fm.findFieldByName(name)
+        field = fm.findFieldByName(self._name)
         if field.isValid():
             self._group = field.castGroup()
-            assert self._group.isValid(), 'AnnotationGroup found existing non-group field called ' + name
+            assert self._group.isValid(), 'AnnotationGroup found existing non-group field called ' + self._name
         else:
             # assume client is calling between fm.begin/endChange()
             self._group = fm.createFieldGroup()
-            self._group.setName(name)
+            self._group.setName(self._name)
             self._group.setManaged(True)
 
     def getName(self):
         return self._name
 
+    def getId(self):
+        return self._id
+
     def getFMANumber(self):
-        return self._FMANumber
+        """
+        :return: Integer FMA number or None.
+        """
+        if self._id and (self.id[:4] == "FMA:"):
+            return int(self._id[4:])
+        return None
 
-    def getLyphID(self):
-        return self._lyphID
+    def getTerm(self):
+        return ( self._name, self._id )
 
     def getGroup(self):
         return self._group
@@ -69,13 +75,29 @@ def getMeshGroup(self, mesh):
         '''
         return self.getFieldElementGroup(mesh).getMeshGroup()
 
+    def hasMeshGroup(self, mesh):
+        '''
+        :param mesh: The Zinc mesh to query a sub group of.
+        :return: True if MeshGroup for mesh exists and is not empty, otherwise False.
+        '''
+        elementGroup = self._group.getFieldElementGroup(mesh)
+        return elementGroup.isValid() and (elementGroup.getMeshGroup().getSize() > 0)
+
     def getNodesetGroup(self, nodeset):
         '''
         :param nodeset: The Zinc nodeset to manage a sub group of.
         :return: The Zinc nodesetGroup for adding nodes from nodeset in this AnnotationGroup.
         '''
         return self.getFieldNodeGroup(nodeset).getNodesetGroup()
 
+    def hasNodesetGroup(self, nodeset):
+        '''
+        :param nodeset: The Zinc nodeset to query a sub group of.
+        :return: True if NodesetGroup for nodeset exists and is not empty, otherwise False.
+        '''
+        nodeGroup = self._group.getFieldNodeGroup(nodeset)
+        return nodeGroup.isValid() and (nodeGroup.getNodesetGroup().getSize() > 0)
+
     def addSubelements(self):
         '''
         Call after group is complete and faces have been defined to add faces and
@@ -92,13 +114,64 @@ def addSubelements(self):
                 meshGroup.addElementsConditional(elementGroup)  # use FieldElementGroup as conditional field
 
 
-def findAnnotationGroupByName(annotationGroups, name):
+def findAnnotationGroupByName(annotationGroups: list, name: str):
     '''
+    Find existing annotation group for name.
     :param annotationGroups: list(AnnotationGroup)
     :param name: Name of group.
-    :return: AnnotationGroup or None.
+    :return: AnnotationGroup or None if not found.
     '''
     for annotationGroup in annotationGroups:
         if annotationGroup._name == name:
             return annotationGroup
     return None
+
+
+def findOrCreateAnnotationGroupForTerm(annotationGroups: list, region, term) -> AnnotationGroup:
+    '''
+    Find existing annotation group for term, or create it for region if not found.
+    If annotation group created here, append it to annotationGroups.
+    :param annotationGroups: list(AnnotationGroup)
+    :param region: Zinc region to create group for.
+    :param term: Identifier for anatomical term, currently a tuple of name, id.
+    :return: AnnotationGroup.
+    '''
+    name = term[0]
+    annotationGroup = findAnnotationGroupByName(annotationGroups, name)
+    if annotationGroup:
+        assert annotationGroup._id == term[1], "Annotation group '" + name + "' id '" + term[1] + "' does not match existing id '" + annotationGroup._id + "'"
+    else:
+        annotationGroup = AnnotationGroup(region, term)
+        annotationGroups.append(annotationGroup)
+    return annotationGroup
+
+
+def getAnnotationGroupForTerm(annotationGroups: list, term) -> AnnotationGroup:
+    '''
+    Get existing annotation group for term. Raise exception if not found.
+    :param annotationGroups: list(AnnotationGroup)
+    :param term: Identifier for anatomical term, currently a tuple of name, id.
+    :return: AnnotationGroup.
+    '''
+    name = term[0]
+    annotationGroup = findAnnotationGroupByName(annotationGroups, name)
+    if annotationGroup:
+        assert annotationGroup._id == term[1], "Annotation group '" + name + "' id '" + term[1] + "' does not match existing id '" + annotationGroup._id + "'"
+        return annotationGroup
+    raise NameError("Annotation group '" + name + "' not found.")
+
+
+def mergeAnnotationGroups(*annotationGroupsIn):
+    '''
+    Merge the supplied sequence of list(annotationGroups) to a single list,
+    without duplicates.
+    :param annotationGroupsIn: Variable number of list(AnnotationGroup) to merge.
+     Groups must be for the same region.
+    :return: Merged list(AnnotationGroup)
+    '''
+    annotationGroups = []
+    for agroups in annotationGroupsIn:
+        for agroup in agroups:
+            if not findAnnotationGroupByName(annotationGroups, agroup._name):
+                annotationGroups.append(agroup)
+    return annotationGroups

src/scaffoldmaker/annotation/bladder_terms.py

@@ -0,0 +1,21 @@
+"""
+Common resource for bladder annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+bladder_terms = [
+    ( "urinary bladder", "FMA:15900", "UBERON:0001255" ),
+    ( "neck of urinary bladder", "FMA:15912", "UBERON:0001258"),
+    ( "body of urinary bladder", None)  # needs to be replaced with an actual term e.g. urinary bladder (which includes neck)
+   ]
+
+def get_bladder_term(name : str):
+    """
+    Find term by matching name to any identifier held for a term.
+    Raise exception if name not found.
+    :return ( preferred name, preferred id )
+    """
+    for term in bladder_terms:
+        if name in term:
+            return ( term[0], term[1] )
+    raise NameError("Bladder annotation term '" + name + "' not found.")

src/scaffoldmaker/annotation/colon_terms.py

@@ -0,0 +1,25 @@
+"""
+Common resource for colon annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+colon_terms = [
+    ( "colon", "UBERON:0001155", "FMA:14543" ),
+    ( "mesenteric zone", None ),
+    ( "non-mesenteric zone", None ),
+    ( "taenia coli", "UBERON:0012419", "FMA:15041" ),
+    ( "tenia libera", None ),
+    ( "tenia mesocolica", None ),
+    ( "tenia omentalis", None )
+    ]
+
+def get_colon_term(name : str):
+    """
+    Find term by matching name to any identifier held for a term.
+    Raise exception if name not found.
+    :return ( preferred name, preferred id )
+    """
+    for term in colon_terms:
+        if name in term:
+            return ( term[0], term[1] )
+    raise NameError("Colon annotation term '" + name + "' not found.")

src/scaffoldmaker/annotation/heart_terms.py

@@ -0,0 +1,67 @@
+"""
+Common resource for heart annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+heart_terms = [
+    ( "heart", "FMA:7088", "UBERON:0000948" ),
+    # ventricles
+    ( "left ventricle myocardium", "FMA:9558" ),
+    ( "right ventricle myocardium", "FMA:9535" ),
+    ( "interventricular septum", "FMA:7133" ),
+    ( "endocardium of left ventricle", "FMA:9559" ),
+    ( "endocardium of right ventricle", "FMA:9536" ),
+    ( "epicardium", "FMA:9461", "UBERON:0002348"),
+    #( "epicardium of ventricle", "FMA:12150", "UBERON:0001082" ),
+    # ventricles with base
+    ( "conus arteriosus", "UBERON:0003983" ),
+    ( "left fibrous ring", "FMA:77124" ),
+    ( "right fibrous ring", "FMA:77125" ),
+    # atria
+    ( "left atrium myocardium", "FMA:7285" ),
+    ( "right atrium myocardium", "FMA:7282" ),
+    ( "endocardium of left atrium", "FMA:7286", "UBERON:0034903" ),
+    ( "endocardium of right atrium", "FMA:7281", "UBERON:0009129" ),
+    ( "interatrial septum", "FMA:7108" ),
+    ( "fossa ovalis", "FMA:9246" ),
+    ( "left auricle", "FMA:7219", "UBERON:0006630" ),  # uncertain if just the tissue like myocardium
+    ( "right auricle", "FMA:7218", "UBERON:0006631" ),  # uncertain if just the tissue like myocardium
+    ( "endocardium of left auricle", "FMA:13236", "UBERON:0011006" ),
+    ( "endocardium of right auricle", "FMA:13235", "UBERON:0011007" ),
+    ( "epicardium of left auricle", "FMA:13233" ),
+    ( "epicardium of right auricle", "FMA:13232" ),
+    ( "pulmonary vein", "FMA:66643", "UBERON:0002016" ),
+    ( "left pulmonary vein", "UBERON:0009030" ),
+    ( "left inferior pulmonary vein", "FMA:49913" ),
+    ( "left superior pulmonary vein", "FMA:49916" ),
+    ( "middle pulmonary vein", "ILX:0739222" ),  # in mouse, rat, rabbit
+    ( "right pulmonary vein", "UBERON:0009032" ),
+    ( "right inferior pulmonary vein", "FMA:49911" ),
+    ( "right superior pulmonary vein", "FMA:49914" ),
+    ( "inferior vena cava", "FMA:10951", "UBERON:0001072", "posterior vena cava" ),
+    ( "inferior vena cava inlet", "ILX:0738358" ),
+    ( "superior vena cava", "FMA:4720", "UBERON:0001585", "anterior vena cava" ),
+    ( "superior vena cava inlet", "ILX:0738367" ),
+    # arterial root
+    ( "root of aorta", "FMA:3740" ),
+    ( "posterior cusp of aortic valve", "FMA:7253" ),
+    ( "right cusp of aortic valve", "FMA:7252" ),
+    ( "left cusp of aortic valve", "FMA:7251" ),
+    ( "root of pulmonary trunk", "FMA:8612" ),
+    ( "right cusp of pulmonary valve", "FMA:7250" ),
+    ( "anterior cusp of pulmonary valve", "FMA:7249" ),
+    ( "left cusp of pulmonary valve", "FMA:7247" ),
+    # future: fiducial markers
+    ( "apex of heart", "FMA:7164", "UBERON:0002098")
+    ]
+
+def get_heart_term(name : str):
+    """
+    Find term by matching name to any identifier held for a term.
+    Raise exception if name not found.
+    :return ( preferred name, preferred id )
+    """
+    for term in heart_terms:
+        if name in term:
+            return ( term[0], term[1] )
+    raise NameError("Heart annotation term '" + name + "' not found.")

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

@@ -10,6 +10,7 @@
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup
+from scaffoldmaker.annotation.bladder_terms import get_bladder_term
 from scaffoldmaker.meshtypes.meshtype_3d_ostium1 import MeshType_3d_ostium1, generateOstiumMesh
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.scaffoldpackage import ScaffoldPackage
@@ -264,8 +265,8 @@ def generateBaseMesh(region, options):
 
         cache = fm.createFieldcache()
 
-        neckGroup = AnnotationGroup(region, 'neck of bladder', FMANumber='unknown', lyphID='unknown')
-        bodyGroup = AnnotationGroup(region, 'body of bladder', FMANumber='unknown', lyphID='unknown')
+        neckGroup = AnnotationGroup(region, get_bladder_term("neck of urinary bladder"))
+        bodyGroup = AnnotationGroup(region, get_bladder_term("body of urinary bladder"))
         annotationGroups = [neckGroup, bodyGroup]
 
         neckMeshGroup = neckGroup.getMeshGroup(mesh)

src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py

@@ -12,6 +12,7 @@
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup
+from scaffoldmaker.annotation.colon_terms import get_colon_term
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.eftfactory_bicubichermitelinear import eftfactory_bicubichermitelinear
 from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite
@@ -537,8 +538,8 @@ def getColonSegmentInnerPoints(region, elementsCountAroundTC,
                 d2Final.append(d2Raw[n1][n2])
 
         # Create annotation groups for mouse colon
-        mzGroup = AnnotationGroup(region, 'mesenteric zone', FMANumber = 'FMANumber unknown', lyphID = 'Lyph ID unknown')
-        nonmzGroup = AnnotationGroup(region, 'non-mesenteric zone', FMANumber = 'FMANumber unknown', lyphID = 'Lyph ID unknown')
+        mzGroup = AnnotationGroup(region, get_colon_term("mesenteric zone"))
+        nonmzGroup = AnnotationGroup(region, get_colon_term("non-mesenteric zone"))
         annotationGroups = [mzGroup, nonmzGroup]
         annotationArray = (['mesenteric zone']*int(elementsCountAroundTC*0.5) +
                            ['non-mesenteric zone']*elementsCountAroundHaustrum +
@@ -1288,14 +1289,14 @@ def getTeniaColi(region, xList, d1List, d2List, d3List, curvatureList,
 
     # Update annotation groups
     if tcCount == 3:
-        tlGroup = AnnotationGroup(region, 'tenia libera', FMANumber = 'FMANumber unknown', lyphID = 'Lyph ID unknown')
-        tmGroup = AnnotationGroup(region, 'tenia mesocolica', FMANumber = 'FMANumber unknown', lyphID = 'Lyph ID unknown')
-        toGroup = AnnotationGroup(region, 'tenia omentalis', FMANumber = 'FMANumber unknown', lyphID = 'Lyph ID unknown')
+        tlGroup = AnnotationGroup(region, get_colon_term("tenia libera"))
+        tmGroup = AnnotationGroup(region, get_colon_term("tenia mesocolica"))
+        toGroup = AnnotationGroup(region, get_colon_term("tenia omentalis"))
         annotationGroupsTC = [tlGroup, tmGroup, toGroup]
-        annotationArrayTC = (['tenia omentalis']*int(elementsCountAroundTC*0.5) +
+        annotationArrayTC = (['tenia omentalis']*(elementsCountAroundTC//2) +
                              ['tenia libera']*elementsCountAroundTC +
                              ['tenia mesocolica']*elementsCountAroundTC +
-                             ['tenia omentalis']*int(elementsCountAroundTC*0.5))
+                             ['tenia omentalis']*(elementsCountAroundTC//2))
         annotationGroups += annotationGroupsTC
         annotationArray += annotationArrayTC