RM listActiveNode & reducedMass: (#112)

dquote> - old mechanism that is not used anymore, using new SOFA matrix assembly & solver replace this
dquote> - add utility fct to execute SOFA scene in batch and get if stdout has errors
dquote> - In sceneCreation fix if node we reduce has multiple parents

python/mor/gui/ui_mor.py

@@ -314,8 +314,7 @@ def checkPhases(self):
                         ["/debug/debug_scene.py","/debug/stateFile.state"],
                         ["/data/modes.txt"],
                         ["/debug/reducedFF_*","/debug/*_elmts.txt"], #["/debug/step2_stateFile.state",
-                        ["/data/*_RID.txt","/data/*_weight.txt","/data/*listActiveNodes.txt","/reduced_*"]
-                        # "/data/*_reduced.txt" search for reduced mass, remove it for the moment
+                        ["/data/*_RID.txt","/data/*_weight.txt","/reduced_*"]
                     ]
 
             def check(file,item):
@@ -850,4 +849,4 @@ def main():
     app.exec_()  # and execute the app
 
 if __name__ == '__main__':  # if we're running file directly and not importing it
-    main()  # run the main function
+    main()  # run the main function

python/mor/reduction/container/reductionParam.py

@@ -29,9 +29,6 @@ def __init__(self,tolModes,tolGIE,addRigidBodyModes,dataDir,saveVelocitySnapshot
         self.RIDFilesNames = []
         self.weightsFilesNames = [] 
         self.savedElementsFilesNames = []
-        self.listActiveNodesFilesNames = []
-        self.massName = ''
-
 
         self.nbrOfModes = -1
         self.periodSaveGIE = 6 #10
@@ -50,7 +47,7 @@ def setNbTrainingSet(self,rangeOfAction,incr):
 
         self.nbTrainingSet = int(rangeOfAction/incr)
 
-    def addParamWrapper(self ,nodeToReduce ,prepareECSW = True, paramForcefield = None ,paramMappedMatrixMapping = None ,paramMORMapping = None):
+    def addParamWrapper(self ,nodeToReduce ,prepareECSW = True, paramForcefield = None ,paramMORMapping = None):
         '''
         '''
         nodeToReduce = "".join(nodeToReduce)
@@ -67,15 +64,6 @@ def addParamWrapper(self ,nodeToReduce ,prepareECSW = True, paramForcefield = No
                 'paramMORMapping' : {
                     'input': '@../MechanicalObject',
                     'modesPath': self.dataDir+self.modesFileName},
-
-                'paramMappedMatrixMapping' : {
-                    'nodeToParse': nodeToParse,
-                    'template': 'Vec1d,Vec1d',
-                    'object1': '@./MechanicalObject',
-                    'object2': '@./MechanicalObject',
-                    'timeInvariantMapping1': True,
-                    'timeInvariantMapping2': True,
-                    'performECSW': False}
                 }
 
         defaultParamPerform = {
@@ -88,34 +76,20 @@ def addParamWrapper(self ,nodeToReduce ,prepareECSW = True, paramForcefield = No
                 'paramMORMapping' : {
                     'input': '@../MechanicalObject',
                     'modesPath': self.dataFolder+self.modesFileName},
-
-                'paramMappedMatrixMapping' : {
-                    'nodeToParse': nodeToParse,
-                    'template': 'Vec1d,Vec1d',
-                    'object1': '@./MechanicalObject',
-                    'object2': '@./MechanicalObject',
-                    'timeInvariantMapping1': True,
-                    'timeInvariantMapping2': True,
-                    'listActiveNodesPath' : self.dataFolder+'listActiveNodes.txt',
-                    'performECSW': True,
-                    'usePrecomputedMass': True,
-                    'precomputedMassPath': self.dataFolder+self.massName}
                 }
 
-        if paramForcefield and paramMappedMatrixMapping and paramMORMapping :
+        if paramForcefield and paramMORMapping :
             pass
         else:
             if prepareECSW:
                 self.paramWrapper = (   (nodeToReduce ,
                                        {'paramForcefield': defaultParamPrepare['paramForcefield'].copy(),
-                                        'paramMORMapping': defaultParamPrepare['paramMORMapping'].copy(),
-                                        'paramMappedMatrixMapping': defaultParamPrepare['paramMappedMatrixMapping'].copy()} ) )
+                                        'paramMORMapping': defaultParamPrepare['paramMORMapping'].copy()} ) )
 
             else :
                 self.paramWrapper = (   (nodeToReduce ,
                                        {'paramForcefield': defaultParamPerform['paramForcefield'].copy(),
-                                        'paramMORMapping': defaultParamPerform['paramMORMapping'].copy(),
-                                        'paramMappedMatrixMapping': defaultParamPerform['paramMappedMatrixMapping'].copy()} ) )
+                                        'paramMORMapping': defaultParamPerform['paramMORMapping'].copy()} ) )
 
         return self.paramWrapper
 
@@ -129,4 +103,3 @@ def setFilesName(self):
         self.RIDFilesNames.append('RID_'+nodeName+'.txt')
         self.weightsFilesNames.append('weight_'+nodeName+'.txt')
         self.savedElementsFilesNames.append('elmts_'+nodeName+'.txt')
-        self.listActiveNodesFilesNames.append('listActiveNodes_'+nodeName+'.txt')

python/mor/reduction/reduceModel.py

@@ -131,12 +131,13 @@ def __init__(self,
         self.activesNodesLists = []
         self.listSofaScene = []
 
-        strInfo = 'periodSaveGIE : '+str(self.reductionParam.periodSaveGIE)+' | '
-        strInfo += 'nbTrainingSet : '+str(self.reductionParam.nbTrainingSet)+' | '
-        strInfo += 'nbIterations : '+str(self.reductionAnimations.nbIterations)+'\n'
-        # strInfo += "List of phase :"+str(self.reductionAnimations.phaseNumClass)+'\n'
-        strInfo += "##################################################"
-        print(strInfo)
+        if (verbose):
+            strInfo = 'periodSaveGIE : '+str(self.reductionParam.periodSaveGIE)+' | '
+            strInfo += 'nbTrainingSet : '+str(self.reductionParam.nbTrainingSet)+' | '
+            strInfo += 'nbIterations : '+str(self.reductionAnimations.nbIterations)+'\n'
+            # strInfo += "List of phase :"+str(self.reductionAnimations.phaseNumClass)+'\n'
+            strInfo += "##################################################"
+            print(strInfo)
 
     def setListSofaScene(self,phasesToExecute=None,phase=None):
         """
@@ -388,13 +389,6 @@ def phase3(self,phasesToExecute=None,nbrOfModes=None):
 
         for fileName in self.reductionParam.savedElementsFilesNames :
             u.copyFileIntoAnother(results[self.phaseToSaveIndex]["directory"]+slash+fileName,self.packageBuilder.debugDir+fileName)
-
-        ### commented out waiting for change in c++ code
-        # optimization done in MMM but now removed
-        # self.reductionParam.massName = glob.glob(results[self.phaseToSaveIndex]["directory"]+slash+"*_reduced.txt")[0]
-        # # print("massName -----------------------> ",self.reductionParam.massName)
-        # u.copy(self.reductionParam.massName,self.reductionParam.dataDir)
-        #####
 
         files = glob.glob(results[self.phaseToSaveIndex]["directory"]+slash+"*_Gie.txt")
         if files: 
@@ -427,7 +421,6 @@ def phase4(self,nbrOfModes=None):
         Final step :
 
             - compute the RID and Weigts with :py:mod:`.ReadGieFileAndComputeRIDandWeights`
-            - compute the Active Nodes with :py:mod:`.ConvertRIDinActiveNodes`
             - finalize the package
             - add it to the plugin library if option activated
 
@@ -475,51 +468,24 @@ def phase4(self,nbrOfModes=None):
                     self.reductionParam.savedElementsFilesNames[j] = self.reductionParam.savedElementsFilesNames[i]
                     self.reductionParam.savedElementsFilesNames[i] = tmp
 
-        ### commented out waiting for change in c++ code
-        # optimization done in MMM but now removed
-        # tmp = glob.glob(self.packageBuilder.dataDir+"*_reduced.txt")[0]
-        # tmp = os.path.normpath(tmp)
-        # self.reductionParam.massName = tmp.split(slash)[-1]
-        ####
-
         self.reductionParam.RIDFilesNames = []
         self.reductionParam.weightsFilesNames = []
-        self.reductionParam.listActiveNodesFilesNames = []
         for fileName in self.reductionParam.gieFilesNames :
             if not os.path.isfile(self.packageBuilder.debugDir+fileName):
                 raise IOError("There is no GIE file at "+self.packageBuilder.debugDir+fileName\
                     +"\nPlease give one at this location or indicate the correct location or re-generate one with phase 3")
 
             self.reductionParam.RIDFilesNames.append(fileName.replace('_Gie','_RID'))
             self.reductionParam.weightsFilesNames.append(fileName.replace('_Gie','_weight'))
-            self.reductionParam.listActiveNodesFilesNames.append(fileName.replace('_Gie','_listActiveNodes'))
 
 
-        self.listActiveNodesFilesNames = []
         for i , fileName in enumerate(self.reductionParam.gieFilesNames) :
 
-            # index = self.reductionParam.gieFilesNames.index(fileName)
             script.readGieFileAndComputeRIDandWeights( self.packageBuilder.debugDir+fileName,
                                                 self.packageBuilder.dataDir+self.reductionParam.RIDFilesNames[i],
                                                 self.packageBuilder.dataDir+self.reductionParam.weightsFilesNames[i],
                                                 self.reductionParam.tolGIE,
                                                 verbose= self.verbose)
-            # print(index)
-            # print(len(self.reductionParam.savedElementsFilesNames))
-            # if index-1 < len(self.reductionParam.savedElementsFilesNames):
-            self.activesNodesLists.append(  script.convertRIDinActiveNodes(self.packageBuilder.dataDir+self.reductionParam.RIDFilesNames[i],
-                                                                    self.packageBuilder.debugDir+self.reductionParam.savedElementsFilesNames[i],
-                                                                    self.packageBuilder.dataDir+self.reductionParam.listActiveNodesFilesNames[i],
-                                                                    verbose= self.verbose))
-
-        finalListActiveNodes = []
-        for activeNodes in self.activesNodesLists:
-                finalListActiveNodes = list(set().union(finalListActiveNodes,activeNodes))
-        finalListActiveNodes = sorted(finalListActiveNodes)
-        with open(self.packageBuilder.dataDir+'listActiveNodes.txt', "w") as file:
-            for item in finalListActiveNodes:
-              file.write("%i\n" % item)
-        file.close()
 
         filename = "phase3_performECSW.py"
         filesandtemplates = [(open(pathToTemplate+filename).read(), filename)]

python/mor/reduction/script/ConvertRIDinActiveNodes.py

@@ -47,11 +47,6 @@ def convertRIDinActiveNodes(RIDFileName,connectivityFileName,listActiveNodesFile
     dimension = len(lineSplit)
     listActiveNodes = []
     for i in RIDlist:
-        #if verbose :
-            # print "#######################"
-            # print "elem number: ", i
-            # for coordIndex in range(dimension):
-            #     print connecList[i][coordIndex]
         lenStart = len(listActiveNodes)
         for coordIndex in range(dimension):
             if connecList[i][coordIndex] not in listActiveNodes:

python/mor/reduction/template/phase2_prepareECSW.py

@@ -27,7 +27,6 @@
 nbrOfModes = $NBROFMODES
 periodSaveGIE = $PERIODSAVEGIE
 paramWrapper = $PARAMWRAPPER
-phaseToSave = $PHASETOSAVE
 
 path, param = paramWrapper
 param['nbrOfModes'] = $NBROFMODES
@@ -48,12 +47,6 @@ def createScene(rootNode):
     # Add MOR plugin if not found
     #u.addPlugin(rootNode,"ModelOrderReduction")
 
-    # Save connectivity list that will allow us after work only on the necessary elements
-
-    if phase == phaseToSave:
-        u.saveElements(rootNode,rootNode.dt,replaceAndSave.forcefield)
-        param['paramMappedMatrixMapping']['saveReducedMass'] = True
-
     # Modify the scene to perform hyper-reduction according
     # to the informations collected by the wrapper
 
@@ -64,4 +57,4 @@ def createScene(rootNode):
     for path , item in replaceAndSave.pathToUpdate.items():
         data , newValue = item
         obj = get(rootNode,path)
-        setattr(obj,data,newValue)
+        setattr(obj,data,newValue)

python/mor/utility/sceneCreation.py

@@ -37,6 +37,9 @@
                             'HyperReducedRestShapeSpringsForceField':'points'
                         }
 
+import Sofa
+import numpy as np
+
 tmp = 0
 
 
@@ -320,17 +323,22 @@ def modifyGraphScene(node,nbrOfModes,newParam):
     try :
         currentNode = get(node,pathTmp[1:])
         solver = getNodeSolver(currentNode)
+        print("SOLVER",solver)
         if currentNode.getPathName() == pathTmp:
-            if 'paramMappedMatrixMapping' in param:
+            if 'prepareECSW' in param['paramForcefield'] or 'performECSW' in param['paramForcefield'] :
                 print('Create new child modelMOR and move node in it')
-                myParent = list(currentNode.parents)
-                modelMOR = myParent[0].addChild(currentNode.name.value+'_MOR')
-                myParent[0].removeChild(currentNode)
+                myParents = list(currentNode.parents)
+                modelMOR = Sofa.Core.Node(currentNode.name.value+'_MOR')
+                for parent in myParents:
+                    parent.removeChild(currentNode)
+                    parent.addChild(modelMOR)
+
                 modelMOR.addChild(currentNode)
 
-                for obj in solver:
-                    currentNode.removeObject(obj)
-                    modelMOR.addObject(obj)
+                if len(solver)>0:
+                    for obj in solver:
+                        currentNode.removeObject(obj)
+                        modelMOR.addObject(obj)
 
                 modelMOR.addObject('MechanicalObject', **argMecha)
 
@@ -349,55 +357,6 @@ def modifyGraphScene(node,nbrOfModes,newParam):
     except :
         print("[ERROR]    In modifyGraphScene , cannot modify scene from path : "+pathTmp[1:])
 
-def saveElements(node,dt,forcefield):
-    '''
-    **Depending on the forcefield will go search for the right kind
-    of elements (tetrahedron/triangles...) to save**
-
-    +------------+---------------------------------+----------------------------------------------------+
-    | argument   | type                            | definition                                         |
-    +============+=================================+====================================================+
-    | node       | :class:`sofaPy3:Sofa.Core.Node` | from which node will search to save elements       |
-    +------------+---------------------------------+----------------------------------------------------+
-    | dt         | sc                              | time step of our SOFA scene                        |
-    +------------+---------------------------------+----------------------------------------------------+
-    | forcefield | list(str)                       || list of path to the forcefield working on the     |
-    |            |                                 || elements we want to save see :py:obj:`.forcefield`|
-    +------------+---------------------------------+----------------------------------------------------+
-
-    After determining what to save we will add an animation with a *duration* of 0 that will
-    be executed only once when the scene is launched saving the elements.
-
-    To do that we use :func:`stlib:splib.animation.animate`
-
-    :return: None
-    '''
-
-    import numpy as np
-    def save(node,container,valueType, **param):
-        global tmp
-        elements = container.findData(valueType).value
-        np.savetxt('reducedFF_'+ node.name.value + '_' + str(tmp)+'_'+valueType+'_elmts.txt', elements,fmt='%i')
-        tmp += 1
-        print('save : '+'elmts_'+node.name.value+' from '+container.name.value+' with value Type '+valueType)
-
-    for objPath in forcefield:
-        nodePath = '/'.join(objPath.split('/')[:-1])
-
-        obj = get(node,objPath[1:])
-        currentNode = get(node,nodePath[1:])
-
-        if obj.getClassName() == 'HyperReducedRestShapeSpringsForceField':
-            container = obj
-        else:
-            container = getContainer(currentNode)
-
-        if obj.getClassName() in forceFieldImplemented and container:
-            valueType = forceFieldImplemented[obj.getClassName()]
-
-            if valueType:
-                animate(save, {"node" : currentNode ,'container' : container, 'valueType' : valueType, 'startTime' : 0}, 0)
-
 def createDebug(rootNode,pathToNode,stateFile="stateFile.state"):
     '''
     **Will, from our original scene, remove all unnecessary component and add a ReadState component
@@ -435,4 +394,4 @@ def createDebug(rootNode,pathToNode,stateFile="stateFile.state"):
             node.removeChild(child)
 
     node.addObject('ReadState', filename=stateFile)
-    rootNode.addChild(node)
+    rootNode.addChild(node)

python/mor/utility/utility.py

@@ -27,6 +27,10 @@
 import shutil
 import errno
 
+from subprocess import Popen, PIPE, call
+import tempfile
+import time
+
 
 def update_progress(progress):
     barLength = 50 # Modify this to change the length of the progress bar
@@ -105,4 +109,36 @@ def customLauncher(filesandtemplates,param,resultDir):
         t = Template(content, searchList=param)
         theFile.write(str(t))
         theFile.close()
-        i+=1
+        i+=1
+
+def executeSofaScene(sofaScene,param=["-g", "batch", "-l", "SofaPython3", "-n", "5"],verbose=False):
+
+    if os.path.isfile(sofaScene):
+
+        arg = ["runSofa"]+param+[sofaScene]
+
+        # print(arg)
+        # print(os.path.dirname(sofaScene))
+        begin = time.time()
+        try:
+            a = Popen(arg, stdout=PIPE, stderr=PIPE,universal_newlines=True)
+        except:
+            print("Unable to find runSofa, please add the runSofa location to your PATH and restart sofa-launcher.")
+            sys.exit(-1)
+
+        astdout, astderr = a.communicate()
+        a.stdout.close()
+        a.stderr.close()
+        end = time.time()
+        logfile = open(os.path.dirname(sofaScene)+"/reduction-log", "w+")
+        logfile.write("========= STDOUT-LOG============\n")
+        logfile.write(astdout)
+        logfile.write("========= STDERR-LOG============\n")
+        logfile.write(astderr)
+        logfile.close()
+        if '[ERROR]' in astderr:
+            return False
+        return True
+
+    else:
+        print("ERROR    the file you try to launch doesn't exist, you have to execute the phase first")