New build system

README.rst

@@ -10,16 +10,17 @@ Building the example
 Instructions on how to configure and build with CMake::
 
   git clone https://github.com/OpenCMISS-Examples/left_ventricle_inflation.git
+  cd left_ventricle_inflation
   mkdir build
-  cmake -DOpenCMISSLibs_DIR=/path/to/opencmisslib/install ../left_ventricle_inflation
+  cd build
+  cmake -DOpenCMISS_INSTALL_ROOT=/path/to/opencmiss/install ../.
   make  # cmake --build . will also work here and is much more platform agnostic.
 
 Running the example
 ===================
 
 Explain how the example is run::
 
-  cd build
   ./src/fortran/left_ventricle_inflation.F90
 
 or maybe it is a Python only example::

src/python/exfile.py

@@ -127,7 +127,7 @@ def _read_element(self, f):
         try:
             indices = map(int, element_line.split(':')[1].split())
         except:
-            print element_line
+            print(element_line)
             raise
         if indices[1] == 0 and indices[2] == 0:
             #raise ExfileError(f, "Face or line elements not supported")
@@ -292,12 +292,13 @@ def _read_node(self, f):
         while read < self.num_node_values:
             line = f.readline()
             try:
-                new_values = map(float, line.split())
+                new_values = list(map(float, line.split()))
             except ValueError:
                 raise ExfileError(f, "Expecting node values, got: %s" % line.strip())
-            if read + len(new_values) > self.num_node_values:
+            if read + len(list(new_values)) > self.num_node_values:
                 raise ExfileError(f, "Got more node values than expected.")
-            values[read:read + len(new_values)] = new_values
+            for nodeIndex in (0,len(new_values)-1):
+                 values[read+nodeIndex] = new_values[nodeIndex]
             read += len(new_values)
 
         self.nodes.append(ExnodeNode(number, values))
@@ -462,7 +463,7 @@ def _read_element(self, f):
         element_line = f.readline()
         if element_line == "":
             raise EOFError
-        indices = map(int, element_line.split(':')[1].split())
+        indices = list(map(int, element_line.split(':')[1].split()))
         if indices[1] == 0 and indices[2] == 0:
             # raise ExfileError(f, "Face or line elements not supported")
             values = []

src/python/left_ventricle_inflation.py

@@ -26,7 +26,7 @@
 #> of Oxford are Copyright (C) 2007 by the University of Auckland and
 #> the University of Oxford. All Rights Reserved.
 #>
-#> Contributor(s): Sander Land
+#> Contributor(s): Zhinuo Jenny Wang, Sander Land
 #>
 #> Alternatively, the contents of this file may be used under the terms of
 #> either the GNU General Public License Version 2 or later (the "GPL"), or
@@ -77,13 +77,15 @@
 cellMLOption = [False]
 
 ### Set arbitrary user numbers which are unique to each object.
-(coordinateSystemUserNumber,
+(contextUserNumber,
+ coordinateSystemUserNumber,
  regionUserNumber,
  linearBasisUserNumber,
  cubicBasisUserNumber,
  generatedMeshUserNumber,
  meshUserNumber,
  decompositionUserNumber,
+ decomposerUserNumber,
  geometricFieldUserNumber,
  equationsSetUserNumber,
  equationsSetFieldUserNumber,
@@ -96,7 +98,7 @@
  cellMLUserNumber,
  cellMLModelsFieldUserNumber,
  cellMLParametersFieldUserNumber,
- cellMLIntermediateFieldUserNumber) = range(1, 21)
+ cellMLIntermediateFieldUserNumber) = range(1, 23)
 
 # Set up geometric model
 # longitudinal elements, circumferential elements, transmural elements
@@ -116,31 +118,38 @@
     apex_elems.append([start, end])
 
 # Set up region and CS
-[numOfCompNodes, compNodeNum, CS, region] = BasicSetUp(regionUserNumber, coordinateSystemUserNumber)
+[context, worldWorkGroup, numOfCompNodes, compNodeNum, CS, region] = BasicSetUp(contextUserNumber, regionUserNumber, coordinateSystemUserNumber)
+
+# Set the OpenCMISS random seed so that we can test this example by using the
+# same parallel decomposition
+numberOfRandomSeeds = context.RandomSeedsSizeGet()
+randomSeeds = [0]*numberOfRandomSeeds
+randomSeeds[0] = 100
+context.RandomSeedsSet(randomSeeds)
 
 # Set up tricubic Hermite basis functions
-[linearBasis, colBasis] = BasisFunction(linearBasisUserNumber, numOfXi, option, collapsed=True)
+[linearBasis, colBasis] = BasisFunction(context, linearBasisUserNumber, numOfXi, option, collapsed=True)
 
 # Set up mesh
-mesh = iron.Mesh()
+mesh = oc.Mesh()
 mesh.CreateStart(meshUserNumber, region, numOfXi)
 mesh.NumberOfComponentsSet(1)
 mesh.NumberOfElementsSet(inputElems.num_elements)
 
-nodes = iron.Nodes()
+nodes = oc.Nodes()
 nodes.CreateStart(region, inputNodes.num_nodes)
 nodes.CreateFinish()
 
 # Linear lagrange component
-linearElem = iron.MeshElements()
+linearElem = oc.MeshElements()
 linearElem.CreateStart(mesh, 1, linearBasis)
 for elem in inputElems.elements:
     for i in range(1, elems[2]+1):
         if (elem.number >= (i-1)*elems[1]*elems[0]) & (elem.number <= i*elems[1]*elems[0]):
             if (elem.number >= apex_elems[i-1][0]) & (elem.number <= apex_elems[i-1][1]):
                 linearElem.BasisSet(elem.number, colBasis)
                 nodes = list(OrderedDict.fromkeys(elem.nodes))
-                nodes = map(int, nodes)
+                nodes = list(map(int, nodes))
                 linearElem.NodesSet(elem.number, nodes)
             else:
                 linearElem.NodesSet(elem.number, elem.nodes)
@@ -149,13 +158,16 @@
 mesh.CreateFinish()
 
 # Set up decomposition for the mesh.
-decomposition = DecompositionSetUp(decompositionUserNumber, mesh, numOfCompNodes)
+decomposition = DecompositionSetUp(decompositionUserNumber, mesh)
+
+# Decompose
+decomposer = DecomposerSetUp(decomposerUserNumber, region, worldWorkGroup, decomposition)
 
 # Set up geometric field.
 geometricField = GeometricFieldSetUp(geometricFieldUserNumber, region, decomposition, option)
 
 # Update the geometric field parameters manually
-geometricField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES)
+geometricField.ParameterSetUpdateStart(oc.FieldVariableTypes.U,oc.FieldParameterSetTypes.VALUES)
 
 def ExtractNodeCoords(nodes, field_name):
     coords = []
@@ -178,7 +190,7 @@ def ExtractNodeCoords(nodes, field_name):
     coord = []
     for component in [1,2,3]:
         value = all_nodes[node_num-1][component-1]
-        geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, 1,
+        geometricField.ParameterSetUpdateNodeDP(oc.FieldVariableTypes.U, oc.FieldParameterSetTypes.VALUES, 1, 1,
                                                 node_num, component, value)
     coord = all_nodes[node_num-1]
     if coord[2] >= 5:
@@ -222,7 +234,7 @@ def ExtractNodeCoords(nodes, field_name):
         eval_node_num.append(i+1)
 #print eval_node_num
 
-geometricField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,iron.FieldParameterSetTypes.VALUES)
+geometricField.ParameterSetUpdateFinish(oc.FieldVariableTypes.U,oc.FieldParameterSetTypes.VALUES)
 
 # Export undeformed geometry.
 GeometricFieldExport(region, "LVInflation_trilinear_undeformed_"+str(elems[2])+"-"+str(elems[1])+"-"+str(elems[0]))
@@ -237,15 +249,15 @@ def ExtractNodeCoords(nodes, field_name):
                                    cellMLOption)
 
 # Set up equations set
-equationsSetField = iron.Field()  # Equations are also in a field
-equationsSet = iron.EquationsSet()  # Initialise an equation set.
-equationsSetSpecification = [iron.EquationsSetClasses.ELASTICITY,
-                             iron.EquationsSetTypes.FINITE_ELASTICITY, 
-                             iron.EquationsSetSubtypes.TRANSVERSE_ISOTROPIC_GUCCIONE]
+equationsSetField = oc.Field()  # Equations are also in a field
+equationsSet = oc.EquationsSet()  # Initialise an equation set.
+equationsSetSpecification = [oc.EquationsSetClasses.ELASTICITY,
+                             oc.EquationsSetTypes.FINITE_ELASTICITY, 
+                             oc.EquationsSetSubtypes.TRANSVERSE_ISOTROPIC_GUCCIONE]
 equationsSet.CreateStart(equationsSetUserNumber, region, fibreField, equationsSetSpecification,
                          equationsSetFieldUserNumber, equationsSetField)
 equationsSet.CreateFinish()
-print "----> Set up equations set <---\n"
+print("----> Set up equations set <---\n")
 
 # Set up material field in equations set.
 equationsSet.MaterialsCreateStart(materialFieldUserNumber, materialField)
@@ -270,9 +282,9 @@ def ExtractNodeCoords(nodes, field_name):
         increm = pressure_increments[i]
         p = p + increm
         tol = tolerances[i]
-        print 'Applying pressure increment of: ', increm, ' using ', iters, ' iterations'
-        print 'Current pressure is: ', p
-        [problem, solverEquations] = ProblemSolverSetup(equationsSet, problemUserNumber, iters, tol, cellMLOption)
+        print('Applying pressure increment of: ', increm, ' using ', iters, ' iterations')
+        print('Current pressure is: ', p)
+        [problem, solverEquations] = ProblemSolverSetup(context, equationsSet, problemUserNumber, iters, tol, cellMLOption)
         BCEndoPressure(solverEquations, dependentField, endocardial_nodes, increm, basal_nodes, option)
 
         # Solve Problem