def step(self, mcs):
if mcs > 100 and not mcs % 100:
# get <Plugin Name="LengthConstraint"> section of XML file
lengthConstraintXMLData = self.simulator.getCC3DModuleData(
"Plugin", "LengthConstraint")
# check if we were able to successfully get the section from simulator
if lengthConstraintXMLData:
# get <LengthEnergyParameters CellType="Body1" TargetLength="xxx" LambdaLength="xxx" /> element
lengthEnergyParametersBody1 = lengthConstraintXMLData.getFirstElement(
"LengthEnergyParameters", d2mss({"CellType": "Body1"}))
# check if the attempt was succesful
if lengthEnergyParametersBody1:
# get value of the TargetLength attribute from <LengthEnergyParameters CellType="Body1" TargetLength="xxx" LambdaLength="xxx" /> element
targetLength = lengthEnergyParametersBody1.getAttributeAsDouble(
"TargetLength")
#increase targetLength by 1
targetLength += 0.5
# update <LengthEnergyParameters CellType="Body1" TargetLength="xxx" LambdaLength="xxx" /> element remembering abuot converting targetLength to string
lengthEnergyParametersBody1.updateElementAttributes(
d2mss({"TargetLength": str(targetLength)}))
# finally call simulator.updateCC3DModule(lengthConstraintXMLData) to tell simulator to update model parameters - this is actual steering
self.simulator.updateCC3DModule(lengthConstraintXMLData)
if mcs > 3000:
# here we relax connectivity constraint at MCS>3000
connectivityXMLData = self.simulator.getCC3DModuleData(
"Plugin", "Connectivity")
if connectivityXMLData:
penaltyElement = connectivityXMLData.getFirstElement("Penalty")
if penaltyElement:
penaltyElement.updateElementValue(str(0))
self.simulator.updateCC3DModule(connectivityXMLData)
def step(self,mcs):
if mcs>100 and not mcs%100:
# get <Plugin Name="LengthConstraint"> section of XML file
lengthConstraintXMLData=self.simulator.getCC3DModuleData("Plugin","LengthConstraint")
# check if we were able to successfully get the section from simulator
if lengthConstraintXMLData:
# get <LengthEnergyParameters CellType="Body1" TargetLength="xxx" LambdaLength="xxx" /> element
lengthEnergyParametersBody1=lengthConstraintXMLData.getFirstElement("LengthEnergyParameters",d2mss({"CellType":"Body1"}))
# check if the attempt was succesful
if lengthEnergyParametersBody1:
# get value of the TargetLength attribute from <LengthEnergyParameters CellType="Body1" TargetLength="xxx" LambdaLength="xxx" /> element
targetLength=lengthEnergyParametersBody1.getAttributeAsDouble("TargetLength")
#increase targetLength by 1
targetLength+=0.5
# update <LengthEnergyParameters CellType="Body1" TargetLength="xxx" LambdaLength="xxx" /> element remembering abuot converting targetLength to string
lengthEnergyParametersBody1.updateElementAttributes(d2mss({"TargetLength":str(targetLength)}))
# finally call simulator.updateCC3DModule(lengthConstraintXMLData) to tell simulator to update model parameters - this is actual steering
self.simulator.updateCC3DModule(lengthConstraintXMLData)
if mcs>3000:
# here we relax connectivity constraint at MCS>3000
connectivityXMLData=self.simulator.getCC3DModuleData("Plugin","Connectivity")
if connectivityXMLData:
penaltyElement=connectivityXMLData.getFirstElement("Penalty")
if penaltyElement:
penaltyElement.updateElementValue(str(0))
self.simulator.updateCC3DModule(connectivityXMLData)
def adjustGravity(self):
extPotXMLData=self.simulator.getCC3DModuleData("Plugin","ExternalPotential")
if extPotXMLData:
waterExtPotElem=extPotXMLData.getFirstElement("ExternalPotentialParameters",d2mss({"CellType":"Water"}))
if waterExtPotElem:
y=waterExtPotElem.getAttributeAsDouble("y")
y=20
waterExtPotElem.updateElementAttributes(d2mss({"y":str(y)}))
self.simulator.updateCC3DModule(extPotXMLData)
def adjustGravity(self):
extPotXMLData = self.simulator.getCC3DModuleData("Plugin", "ExternalPotential")
if extPotXMLData:
waterExtPotElem = extPotXMLData.getFirstElement("ExternalPotentialParameters", d2mss({"CellType": "Water"}))
if waterExtPotElem:
y = waterExtPotElem.getAttributeAsDouble("y")
y = 20
waterExtPotElem.updateElementAttributes(d2mss({"y": str(y)}))
self.simulator.updateCC3DModule(extPotXMLData)
def step(self,mcs):
if mcs>100 and not mcs%100:
# get <Plugin Name="Chemotaxis"> section of XML file
chemotaxisXMLData=self.simulator.getCC3DModuleData("Plugin","Chemotaxis")
# check if we were able to successfully get the section from simulator
if chemotaxisXMLData:
# get <ChemicalField Source="DiffusionSolverFE" Name="ATTR" > element
chemicalField=chemotaxisXMLData.getFirstElement("ChemicalField",d2mss({"Source":"DiffusionSolverFE", "Name":"ATTR"}))
# check if the attempt was succesful
if chemicalField:
# get <ChemotaxisByType Type="Macrophage" Lambda="xxx"/> - notice we only specify "Type":"Macrophage" because Lambda is subject to change - i.e. this is steerable parameter
chemotaxisByTypeMacrophageElement=chemicalField.getFirstElement("ChemotaxisByType",d2mss({"Type":"Macrophage"}))
if chemotaxisByTypeMacrophageElement:
# get value of Lambda from <ChemotaxisByType Type="Macrophage" Lambda="xxx"/>
# notice that no conversion fro strin to float is necessary as getAttributeAsDouble returns floating point value
lambdaVal=chemotaxisByTypeMacrophageElement.getAttributeAsDouble("Lambda")
print "lambdaVal=",lambdaVal
# decrease lambda by 0.2
lambdaVal-=3
# update attribute value of Lambda - but remember about float to string conversion
chemotaxisByTypeMacrophageElement.updateElementAttributes(d2mss({"Lambda":str(lambdaVal)}))
self.simulator.updateCC3DModule(chemotaxisXMLData);
def setValue(self, value):
self.__itemValue = value
if self.__elementType=="attribute":
from XMLUtils import dictionaryToMapStrStr as d2mss
self.__domNode.updateElementAttributes(d2mss({self.__itemName:str(self.__itemValue)}))
# # # print MODULENAME,"UPDATING ATTRIBUTE ",self.__itemName," to value ",self.__itemValue
else:
self.__domNode.updateElementValue(str(self.__itemValue))
# # # print MODULENAME,"UPDATING ELEMENT ",self.__itemName," to value ",self.__itemValue," __domNode.getName()=",self.__domNode.getName()
# # # print MODULENAME,"VALUE CHECK ",self.__domNode.getText()
if self.type() is None:
self.setType(value)
def setValue(self, value):
self.__itemValue = value
if self.__elementType == "attribute":
from XMLUtils import dictionaryToMapStrStr as d2mss
self.__domNode.updateElementAttributes(
d2mss({self.__itemName: str(self.__itemValue)}))
# # # print MODULENAME,"UPDATING ATTRIBUTE ",self.__itemName," to value ",self.__itemValue
else:
self.__domNode.updateElementValue(str(self.__itemValue))
# # # print MODULENAME,"UPDATING ELEMENT ",self.__itemName," to value ",self.__itemValue," __domNode.getName()=",self.__domNode.getName()
# # # print MODULENAME,"VALUE CHECK ",self.__domNode.getText()
if self.type() is None:
self.setType(value)
def step(self, mcs):
if mcs > 100:
# get <Steppable Type="FlexibleDiffusionSolverFE"> section of XML file
fiexDiffXMLData = self.simulator.getCC3DModuleData(
"Steppable", "FlexibleDiffusionSolverFE")
# check if we were able to successfully get the section from simulator
if fiexDiffXMLData:
# get a list of <DiffusionField> elements - notice how we use CC3DXMLListPy to construct Python iterable list
diffusionFieldsElementVec = CC3DXMLListPy(
fiexDiffXMLData.getElements("DiffusionField"))
# go over all <DiffusionFields> elements - here we have only one such element but if you have more fields in the solver
# you will need chek all of them to find required element
for diffusionFieldElement in diffusionFieldsElementVec:
# here we assume that <DiffusionData>
# <FieldName>xxx</FieldName> element exists and pick the one whose value is "FGF"
if diffusionFieldElement.getFirstElement(
"DiffusionData").getFirstElement(
"FieldName").getText() == "FGF":
# we get diffusion constant element , again no checking if such element exists - we assume it does
diffConstElement = diffusionFieldElement.getFirstElement(
"DiffusionData").getFirstElement(
"DiffusionConstant")
# convert string value of <DiffusionConstant> element to float
diffConst = float(diffConstElement.getText())
# increase diffusion constant
diffConst += 0.01
# update the value of the <DiffusionConstant> element - convert flot to string
diffConstElement.updateElementValue(str(diffConst))
# getting <SecretionData> section
if mcs > 500:
# get <SecretionData>
# <Secretion Type="Bacterium">2</Secretion>
# notice we skip checking if the attemt was sucessful and assume it was
secretionElement = diffusionFieldElement.getFirstElement(
"SecretionData").getFirstElement(
"Secretion", d2mss({"Type": "Bacterium"}))
secretionConst = float(secretionElement.getText())
#increase secretion of Bacterium by 2
secretionConst += 2
print "secretionConst=", secretionConst
#update value of the <Secretion Type="Bacterium">
secretionElement.updateElementValue(
str(secretionConst))
# finally call simulator.updateCC3DModule(fiexDiffXMLData) to tell simulator to update model parameters - this is actual steering
self.simulator.updateCC3DModule(fiexDiffXMLData)
def modifyContactEnergies(self,
BB_offset,
GG_offset,
steadyStateOffset,
BB_scale=-30.0,
GG_scale=-10.0,
MM_scale=30.0,
MB_scale=-10.0,
MG_scale=0.0,
BG_scale=10.0):
contactXMLData = self.simulator.getCC3DModuleData("Plugin", "Contact")
BB = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Blue",
"Type2": "Blue"
}))
GG = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Green",
"Type2": "Green"
}))
MM = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Medium",
"Type2": "Medium"
}))
MB = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Medium",
"Type2": "Blue"
}))
MG = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Medium",
"Type2": "Green"
}))
BG = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Blue",
"Type2": "Green"
}))
BB.updateElementValue(str(BB_scale + BB_offset - steadyStateOffset))
GG.updateElementValue(str(GG_scale + GG_offset - steadyStateOffset))
MM.updateElementValue(str(MM_scale))
MB.updateElementValue(str(MB_scale))
MG.updateElementValue(str(MG_scale))
BG.updateElementValue(str(BG_scale))
self.simulator.updateCC3DModule(contactXMLData)
def step(self, mcs):
if mcs > 100:
# get <Steppable Type="FlexibleDiffusionSolverFE"> section of XML file
fiexDiffXMLData = self.simulator.getCC3DModuleData("Steppable", "FlexibleDiffusionSolverFE")
# check if we were able to successfully get the section from simulator
if fiexDiffXMLData:
# get a list of <DiffusionField> elements - notice how we use CC3DXMLListPy to construct Python iterable list
diffusionFieldsElementVec = CC3DXMLListPy(fiexDiffXMLData.getElements("DiffusionField"))
# go over all <DiffusionFields> elements - here we have only one such element but if you have more fields in the solver
# you will need chek all of them to find required element
for diffusionFieldElement in diffusionFieldsElementVec:
# here we assume that <DiffusionData>
# <FieldName>xxx</FieldName> element exists and pick the one whose value is "FGF"
if (
diffusionFieldElement.getFirstElement("DiffusionData").getFirstElement("FieldName").getText()
== "FGF"
):
# we get diffusion constant element , again no checking if such element exists - we assume it does
diffConstElement = diffusionFieldElement.getFirstElement("DiffusionData").getFirstElement(
"DiffusionConstant"
)
# convert string value of <DiffusionConstant> element to float
diffConst = float(diffConstElement.getText())
# increase diffusion constant
diffConst += 0.01
# update the value of the <DiffusionConstant> element - convert flot to string
diffConstElement.updateElementValue(str(diffConst))
# getting <SecretionData> section
if mcs > 500:
# get <SecretionData>
# <Secretion Type="Bacterium">2</Secretion>
# notice we skip checking if the attemt was sucessful and assume it was
secretionElement = diffusionFieldElement.getFirstElement("SecretionData").getFirstElement(
"Secretion", d2mss({"Type": "Bacterium"})
)
secretionConst = float(secretionElement.getText())
# increase secretion of Bacterium by 2
secretionConst += 2
print "secretionConst=", secretionConst
# update value of the <Secretion Type="Bacterium">
secretionElement.updateElementValue(str(secretionConst))
# finally call simulator.updateCC3DModule(fiexDiffXMLData) to tell simulator to update model parameters - this is actual steering
self.simulator.updateCC3DModule(fiexDiffXMLData)
def writeContactEnergies( self, mcs, fileName = "contactEnergies.txt", append = "w" ):
contactXMLData = self.simulator.getCC3DModuleData( "Plugin", "Contact" )
BB = contactXMLData.getFirstElement( "Energy", d2mss({"Type1":"Blue", "Type2":"Blue"}) ).getText()
GG = contactXMLData.getFirstElement( "Energy", d2mss({"Type1":"Green", "Type2":"Green"}) ).getText()
MM = contactXMLData.getFirstElement( "Energy", d2mss({"Type1":"Medium", "Type2":"Medium"}) ).getText()
MB = contactXMLData.getFirstElement( "Energy", d2mss({"Type1":"Medium", "Type2":"Blue"}) ).getText()
MG = contactXMLData.getFirstElement( "Energy", d2mss({"Type1":"Medium", "Type2":"Green"}) ).getText()
BG = contactXMLData.getFirstElement( "Energy", d2mss({"Type1":"Blue", "Type2":"Green"}) ).getText()
outputFile = open( fileName, append )
if( append == "w" ):
outputFile.write( "\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( "BB", "GG", "MM", "MB", "MG", "BG" ) )
outputFile.write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( mcs, BB, GG, MM, MB, MG, BG ) )
outputFile.close()
def writeContactEnergies(self,
mcs,
fileName="contactEnergies.txt",
append="w"):
contactXMLData = self.simulator.getCC3DModuleData("Plugin", "Contact")
BB = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Blue",
"Type2": "Blue"
})).getText()
GG = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Green",
"Type2": "Green"
})).getText()
MM = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Medium",
"Type2": "Medium"
})).getText()
MB = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Medium",
"Type2": "Blue"
})).getText()
MG = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Medium",
"Type2": "Green"
})).getText()
BG = contactXMLData.getFirstElement(
"Energy", d2mss({
"Type1": "Blue",
"Type2": "Green"
})).getText()
outputFile = open(fileName, append)
if (append == "w"):
outputFile.write("\t%s\t%s\t%s\t%s\t%s\t%s\n" %
("BB", "GG", "MM", "MB", "MG", "BG"))
outputFile.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\n" %
(mcs, BB, GG, MM, MB, MG, BG))
outputFile.close()
def modifyContactEnergies( self, BB_offset, GG_offset, steadyStateOffset,
BB_scale = -30.0, GG_scale = -10.0,
MM_scale = 30.0, MB_scale = -10.0,
MG_scale = 0.0, BG_scale = 10.0 ):
contactXMLData = self.simulator.getCC3DModuleData( "Plugin", "Contact" )
BB = contactXMLData.getFirstElement( "Energy", d2mss( {"Type1":"Blue", "Type2":"Blue"} ) )
GG = contactXMLData.getFirstElement( "Energy", d2mss( {"Type1":"Green", "Type2":"Green"} ) )
MM = contactXMLData.getFirstElement( "Energy", d2mss( {"Type1":"Medium", "Type2":"Medium"} ) )
MB = contactXMLData.getFirstElement( "Energy", d2mss( {"Type1":"Medium", "Type2":"Blue"} ) )
MG = contactXMLData.getFirstElement( "Energy", d2mss( {"Type1":"Medium", "Type2":"Green"} ) )
BG = contactXMLData.getFirstElement( "Energy", d2mss( {"Type1":"Blue", "Type2":"Green"} ) )
BB.updateElementValue( str( BB_scale + BB_offset - steadyStateOffset ) )
GG.updateElementValue( str( GG_scale + GG_offset - steadyStateOffset ) )
MM.updateElementValue( str( MM_scale ) )
MB.updateElementValue( str( MB_scale ) )
MG.updateElementValue( str( MG_scale ) )
BG.updateElementValue( str( BG_scale ) )
self.simulator.updateCC3DModule(contactXMLData)
editor = self.__ui.getCurrentEditor()
cc3dXML2ObjConverter = XMLUtils.Xml2Obj()
try:
root_element = cc3dXML2ObjConverter.ParseString(str(editor.text()))
except xml.parsers.expat.ExpatError, e:
QMessageBox.critical(self.__ui, "Error Parsing CC3DML file",
e.__str__())
print 'GOT PARSING ERROR:', e
return
root_element.getFirstElement('Plugin')
print 'root_element=', root_element
cellTypeElement = root_element.getFirstElement(
"Plugin", d2mss({"Name": "CellType"}))
cellTypeDict = {}
if not cellTypeElement or cellTypeElement is None:
return cellTypeDict
from XMLUtils import CC3DXMLListPy
cellTypeElementVec = cellTypeElement.getElements("CellType")
cellTypeElementVec = CC3DXMLListPy(
cellTypeElement.getElements("CellType"))
for element in cellTypeElementVec:
typeName = ''
typeId = -1
import xml
from XMLUtils import dictionaryToMapStrStr as d2mss
editor = self.__ui.getCurrentEditor()
cc3dXML2ObjConverter = XMLUtils.Xml2Obj()
try:
root_element = cc3dXML2ObjConverter.ParseString(str(editor.text()))
except xml.parsers.expat.ExpatError, e:
QMessageBox.critical(self.__ui, "Error Parsing CC3DML file", e.__str__())
print 'GOT PARSING ERROR:', e
return
root_element.getFirstElement('Plugin')
print 'root_element=', root_element
cellTypeElement = root_element.getFirstElement("Plugin", d2mss({"Name": "CellType"}))
cellTypeDict = {}
if not cellTypeElement or cellTypeElement is None:
return cellTypeDict
from XMLUtils import CC3DXMLListPy
cellTypeElementVec = cellTypeElement.getElements("CellType")
cellTypeElementVec = CC3DXMLListPy(cellTypeElement.getElements("CellType"))
for element in cellTypeElementVec:
typeName = ''
typeId = -1
typeFreeze = False
if element.findAttribute('TypeName'):
pottsXMLData=self.simulator.getCC3DModuleData("Potts")
temperatureElement=pottsXMLData.getFirstElement("Temperature")
currentT=float(temperatureElement.getText())
temperatureElement.updateElementValue(str(newT))
self.simulator.updateCC3DModule(pottsXMLData)
#
Contact Energy Manipulation:
from XMLUtils import dictionaryToMapStrStr as d2mss
contactXMLData=self.simulator.getCC3DModuleData("Plugin","Contact")
Type1name=self.typeIdTypeNameDict[cell.type]
cellNeighborList=self.getCellNeighbors(cell) # generates list of neighbors of cell 'cell'
for neighbor in cellNeighborList:
if neighbor.neighborAddress:
Type2name=self.typeIdTypeNameDict[neighbor.neighborAddress.type]
contactEnergy=contactXMLData.getFirstElement("Energy",d2mss({"Type1":Type1name,"Type2":Type2name}))
if not contactEnergy:
contactEnergy=contactXMLData.getFirstElement("Energy",d2mss({"Type1":Type2name,"Type2":Type1name}))
EnergyValue=float(contactEnergy.getText())
contactEnergy.updateElementValue(str(NEW_VALUE))
#
Mitosis:
from PySteppablesExamples import MitosisSteppableBase
cells2div=[]
for cell in self.cellList:
if cell.volume>50:
cells2div.append(cell)
for cell in cells2div:
self.divideCellRandomOrientation(cell)
self.divideCellOrientationVectorBased(cell,1,0,0)
