Merge pull request #29 from rchristie/heart1

Add new heart1 scaffold

scaffoldmaker/annotation/annotationgroup.py

@@ -45,20 +45,37 @@ def getGroup(self):
     def getFieldElementGroup(self, mesh):
         '''
         :param mesh: The Zinc mesh to manage a sub group of.
-        :return: The Zinc meshGroup for adding elements of mesh in this AnnotationGroup.
+        :return: The Zinc element group field for mesh in this AnnotationGroup.
         '''
         elementGroup = self._group.getFieldElementGroup(mesh)
         if not elementGroup.isValid():
             elementGroup = self._group.createFieldElementGroup(mesh)
         return elementGroup
 
+    def getFieldNodeGroup(self, nodeset):
+        '''
+        :param nodeset: The Zinc nodeset to manage a sub group of.
+        :return: The Zinc node group field for nodeset in this AnnotationGroup.
+        '''
+        nodeGroup = self._group.getFieldNodeGroup(nodeset)
+        if not nodeGroup.isValid():
+            nodeGroup = self._group.createFieldNodeGroup(nodeset)
+        return nodeGroup
+
     def getMeshGroup(self, mesh):
         '''
         :param mesh: The Zinc mesh to manage a sub group of.
         :return: The Zinc meshGroup for adding elements of mesh in this AnnotationGroup.
         '''
         return self.getFieldElementGroup(mesh).getMeshGroup()
 
+    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 addSubelements(self):
         '''
         Call after group is complete and faces have been defined to add faces and

scaffoldmaker/meshtypes/meshtype_3d_heart2.py

@@ -56,12 +56,13 @@ def getOrderedOptionNames():
 
     @staticmethod
     def checkOptions(options):
-        MeshType_3d_heartventriclesbase2.checkOptions(options)
-        MeshType_3d_heartatria2.checkOptions(options)
+        dependentChanges = MeshType_3d_heartventriclesbase2.checkOptions(options) \
+            or MeshType_3d_heartatria2.checkOptions(options)
         # only works with particular numbers of elements around
         options['Number of elements around atrial septum'] = 2
         # set dependent outer diameter used in atria2
         options['LV outlet outer diameter'] = options['LV outlet inner diameter'] + 2.0*options['LV outlet wall thickness']
+        return dependentChanges
 
     @classmethod
     def generateBaseMesh(cls, region, options):

scaffoldmaker/meshtypes/meshtype_3d_heartatria2.py

@@ -89,6 +89,14 @@ def getOrderedOptionNames():
 
     @staticmethod
     def checkOptions(options):
+        '''
+        :return:  True if dependent options changed, otherwise False. This
+        happens where two or more options must change together to be valid.
+        Here the number of elements around atrial free wall must be an even number,
+        but the parameter is number of elements around atria, which depends on
+        number of elements around atrial septum.
+        '''
+        dependentChanges = False
         if options['Number of elements around atria'] < 6:
             options['Number of elements around atria'] = 6
         if options['Number of elements around atrial septum'] < 1:
@@ -98,6 +106,7 @@ def checkOptions(options):
         # need even number of elements around free wall
         if ((options['Number of elements around atria'] - options['Number of elements around atrial septum']) % 2) == 1:
             options['Number of elements around atria'] += 1
+            dependentChanges = True
         if options['Number of elements up atria'] < 3:
             options['Number of elements up atria'] = 3
         for key in [
@@ -138,6 +147,7 @@ def checkOptions(options):
             'Refine number of elements through atrial wall']:
             if options[key] < 1:
                 options[key] = 1
+        return dependentChanges
 
     @classmethod
     def generateBaseMesh(cls, region, options):

scaffoldmaker/meshtypes/meshtype_3d_heartventricles2.py

@@ -77,6 +77,10 @@ def getOrderedOptionNames():
 
     @staticmethod
     def checkOptions(options):
+        '''
+        :return:  True if dependent options changed, otherwise False.
+        '''
+        dependentChanges = False
         for key in [
             'Refine number of elements surface',
             'Refine number of elements through LV wall',
@@ -112,6 +116,7 @@ def checkOptions(options):
             options['RV arc around degrees'] = 45.0
         elif options['RV arc around degrees'] > 270.0:
             options['RV arc around degrees'] = 270.0
+        return dependentChanges
 
     @classmethod
     def generateBaseMesh(cls, region, options):

scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase2.py

@@ -38,6 +38,7 @@ def getDefaultOptions():
         options['Number of elements around LV free wall'] = 5
         options['Number of elements around ventricular septum'] = 7
         options['Number of elements around atria'] = 8
+        options['Number of elements around atrial septum'] = 2
         # works best with particular numbers of elements up
         options['Number of elements up LV apex'] = 1
         options['Number of elements up ventricular septum'] = 4
@@ -64,6 +65,7 @@ def getDefaultOptions():
     def getOrderedOptionNames():
         optionNames = MeshType_3d_heartventricles2.getOrderedOptionNames()
         optionNames.insert(4, 'Number of elements around atria')
+        optionNames.insert(5, 'Number of elements around atrial septum')
         optionNames += [
             'Atria base inner major axis length',
             'Atria base inner minor axis length',
@@ -93,11 +95,15 @@ def getOrderedOptionNames():
 
     @staticmethod
     def checkOptions(options):
-        MeshType_3d_heartventricles2.checkOptions(options)
+        '''
+        :return:  True if dependent options changed, otherwise False.
+        '''
+        dependentChanges = MeshType_3d_heartventricles2.checkOptions(options)
         # only works with particular numbers of elements around
         options['Number of elements around LV free wall'] = 5
         options['Number of elements around ventricular septum'] = 7
         options['Number of elements around atria'] = 8
+        options['Number of elements around atrial septum'] = 2
         for key in [
             'Atria base inner major axis length',
             'Atria base inner minor axis length',
@@ -119,6 +125,7 @@ def checkOptions(options):
             options['Atria major axis rotation degrees'] = -75.0
         elif options['Atria major axis rotation degrees'] > 75.0:
             options['Atria major axis rotation degrees'] = 75.0
+        return dependentChanges
 
     @classmethod
     def generateBaseMesh(cls, region, options):
@@ -136,8 +143,8 @@ def generateBaseMesh(cls, region, options):
         elementsCountUpLV = elementsCountUpLVApex + elementsCountUpVSeptum
         elementsCountUpRV = elementsCountUpVSeptum + 1
         elementsCountAroundRV = elementsCountAroundVSeptum + 2
-        elementsCountAtrialSeptum = 2  # elementsCountAroundVSeptum - 5
         elementsCountAroundAtria = options['Number of elements around atria']
+        elementsCountAtrialSeptum = options['Number of elements around atrial septum']
         lvOuterHeight = options['LV outer height']
         lvOuterRadius = options['LV outer radius']
         lvFreeWallThickness = options['LV free wall thickness']

scaffoldmaker/scaffolds.py

@@ -9,6 +9,7 @@
 from scaffoldmaker.meshtypes.meshtype_3d_box1 import MeshType_3d_box1
 from scaffoldmaker.meshtypes.meshtype_3d_boxhole1 import MeshType_3d_boxhole1
 from scaffoldmaker.meshtypes.meshtype_3d_centrallinetube1 import MeshType_3d_centrallinetube1
+from scaffoldmaker.meshtypes.meshtype_3d_heart1 import MeshType_3d_heart1
 from scaffoldmaker.meshtypes.meshtype_3d_heart2 import MeshType_3d_heart2
 from scaffoldmaker.meshtypes.meshtype_3d_heartatria1 import MeshType_3d_heartatria1
 from scaffoldmaker.meshtypes.meshtype_3d_heartatria2 import MeshType_3d_heartatria2
@@ -35,6 +36,7 @@ def __init__(self):
             MeshType_3d_box1,
             MeshType_3d_boxhole1,
             MeshType_3d_centrallinetube1,
+            MeshType_3d_heart1,
             MeshType_3d_heart2,
             MeshType_3d_heartatria1,
             MeshType_3d_heartatria2,