def init_modules(sim, _cc3dXML2ObjConverter):
"""
:param sim:
:param _cc3dXML2ObjConverter:
:return:
"""
plugin_data_list = XMLUtils.CC3DXMLListPy(_cc3dXML2ObjConverter.root.getElements("Plugin"))
for pluginData in plugin_data_list:
sim.ps.addPluginDataCC3D(pluginData)
steppable_data_list = XMLUtils.CC3DXMLListPy(_cc3dXML2ObjConverter.root.getElements("Steppable"))
for steppableData in steppable_data_list:
sim.ps.addSteppableDataCC3D(steppableData)
potts_data_list = XMLUtils.CC3DXMLListPy(_cc3dXML2ObjConverter.root.getElements("Potts"))
assert potts_data_list.getBaseClass().size() <= 1, 'You have more than 1 definition of the Potts section'
if potts_data_list.getBaseClass().size() == 1:
for pottsData in potts_data_list:
sim.ps.addPottsDataCC3D(pottsData)
metadata_data_list = XMLUtils.CC3DXMLListPy(_cc3dXML2ObjConverter.root.getElements("Metadata"))
assert metadata_data_list.getBaseClass().size() <= 1, 'You have more than 1 definition of the Metadata section'
if metadata_data_list.getBaseClass().size() == 1:
for metadataData in metadata_data_list:
sim.ps.addMetadataDataCC3D(metadataData)
def extract_fields_used_from_file_name(_lds_file: str) -> dict:
lds_xml = _LatticeDataXMLReader(_lds_file)
fields_used = dict()
if lds_xml.fields_element:
field_list = XMLUtils.CC3DXMLListPy(lds_xml.fields_element.getElements("Field"))
fields_used.update({el.getAttribute("Name"): el.getAttribute("Type") for el in field_list})
return fields_used
def extract_custom_vis_scripts_from_file_name(_lds_file: str) -> dict:
lds_xml = _LatticeDataXMLReader(_lds_file)
o = dict()
# ToDo: if a "CustomVis" Type was provided,
# require that a "Script" was also provided; else warn user
if lds_xml.fields_element:
fl = XMLUtils.CC3DXMLListPy(lds_xml.fields_element.getElements("Field"))
o.update({el.getAttribute("Name"): el.getAttribute("Script") for el in fl if el.findAttribute("Script")})
return o
def parseXML( xml_fname):
"""
:param xml_fname:
:return:
"""
cc3dXML2ObjConverter = XMLUtils.Xml2Obj()
root_element = cc3dXML2ObjConverter.Parse(xml_fname)
return cc3dXML2ObjConverter
def __init__(self, lds_file: str):
self.lds_file = os.path.abspath(lds_file)
assert os.path.isfile(self.lds_file)
self.xml2_obj_converter = XMLUtils.Xml2Obj()
self.root_element = self.xml2_obj_converter.Parse(lds_file)
self.dim_element = self.root_element.getFirstElement("Dimensions")
self.output_element = self.root_element.getFirstElement("Output")
self.lattice_element = self.root_element.getFirstElement("Lattice")
self.cell_types_elements = self.root_element.getElements("CellType")
self.fields_element = self.root_element.getFirstElement("Fields")
def extractCurrentModule(
self, _editor, _moduleType, _moduleName
): # editor,_moduleType='Plugin',_moduleName=['Name','Contact']
moduleName = []
try:
if _moduleName[0] == '' and _moduleName[1] == '':
moduleName = []
else:
moduleName = _moduleName
except:
moduleName = _moduleName
# print 'ecm _moduleType,moduleName=',(_moduleType,moduleName)
moduleBegin, moduleEnd = self.cc3dmlHelper.findModuleLine(
_editor=_editor, _moduleType=_moduleType, _moduleName=moduleName)
# moduleBegin,moduleEnd=self.cc3dmlHelper.findModuleLine(_editor=_editor,_moduleType=_moduleType,_moduleName=_moduleName)
# print 'ecm moduleBegin,moduleEnd=',(moduleBegin,moduleEnd)
snippet = self.extractSnippet(_editor, moduleBegin, moduleEnd)
# print 'EXTRACT moduleBegin,moduleEnd=',(moduleBegin,moduleEnd)
if moduleBegin < 0 and moduleEnd < 0:
return None, moduleBegin, moduleEnd
cc3dXML2ObjConverter = XMLUtils.Xml2Obj()
try:
root_element = cc3dXML2ObjConverter.ParseString(snippet)
except xml.parsers.expat.ExpatError as e:
QMessageBox.critical(self.__ui, "Error Parsing CC3DML String ",
e.__str__())
raise UserWarning(e.__str__())
# return root_element,moduleBegin,moduleEnd
return cc3dXML2ObjConverter, moduleBegin, moduleEnd # have to return cc3dXML2ObjConverter instead of root_element because if we return root_element then cc3dXML2ObjConverter
def get_results_reader_no_ui(lds_file):
"""
Generate CML Results Reader instance for a results lattice description file
:param lds_file: Path to lattice description file
:return: CMLResultsReader instance
"""
xml2_obj_converter = XMLUtils.Xml2Obj()
root_element = xml2_obj_converter.Parse(lds_file)
dim_element = root_element.getFirstElement("Dimensions")
field_dim = Dim3D()
field_dim.x = int(dim_element.getAttribute("x"))
field_dim.y = int(dim_element.getAttribute("y"))
field_dim.z = int(dim_element.getAttribute("z"))
ui_dummy = CC3DUIDummy(field_dim)
return CMLResultReader(ui_dummy), ui_dummy
def extract_lattice_description_info(self, file_name: str) -> None:
"""
Reads the xml that summarizes serialized simulation files
:param file_name:{str} xml metadata file name
:return: None
"""
# lattice data simulation file
lds_file = os.path.abspath(file_name)
self.ldsDir = os.path.dirname(lds_file)
xml2_obj_converter = XMLUtils.Xml2Obj()
root_element = xml2_obj_converter.Parse(lds_file)
dim_element = root_element.getFirstElement("Dimensions")
self.fieldDim = CompuCell.Dim3D()
self.fieldDim.x = int(dim_element.getAttribute("x"))
self.fieldDim.y = int(dim_element.getAttribute("y"))
self.fieldDim.z = int(dim_element.getAttribute("z"))
output_element = root_element.getFirstElement("Output")
self.ldsCoreFileName = output_element.getAttribute("CoreFileName")
self.frequency = int(output_element.getAttribute("Frequency"))
self.numberOfSteps = int(output_element.getAttribute("NumberOfSteps"))
# obtaining list of files in the ldsDir
lattice_element = root_element.getFirstElement("Lattice")
self.latticeType = lattice_element.getAttribute("Type")
# getting information about cell type names and cell ids.
# It is necessary during generation of the PIF files from VTK output
cell_types_elements = root_element.getElements("CellType")
list_cell_type_elements = CC3DXMLListPy(cell_types_elements)
for cell_type_element in list_cell_type_elements:
type_name = cell_type_element.getAttribute("TypeName")
type_id = cell_type_element.getAttributeAsInt("TypeId")
self.typeIdTypeNameDict[type_id] = type_name
# now will convert python dictionary into C++ map<int, string>
self.typeIdTypeNameCppMap = CC3DXML.MapIntStr()
for type_id in list(self.typeIdTypeNameDict.keys()):
self.typeIdTypeNameCppMap[int(
type_id)] = self.typeIdTypeNameDict[type_id]
lds_file_list = os.listdir(self.ldsDir)
for fName in lds_file_list:
if re.match(".*\.vtk$", fName):
self.ldsFileList.append(fName)
self.ldsFileList.sort()
# extracting information about fields in the lds file
fields_element = root_element.getFirstElement("Fields")
if fields_element:
field_list = XMLUtils.CC3DXMLListPy(
fields_element.getElements("Field"))
for field_elem in field_list:
field_name = field_elem.getAttribute("Name")
self.fieldsUsed[field_elem.getAttribute(
"Name")] = field_elem.getAttribute("Type")
if field_elem.findAttribute(
"Script"): # True or False if present
# ToDo: if a "CustomVis" Type was provided,
# require that a "Script" was also provided; else warn user
custom_vis_script = field_elem.getAttribute("Script")
self.customVis = CompuCellSetup.createCustomVisPy(
field_name)
self.customVis.registerVisCallbackFunction(
CompuCellSetup.vtkScriptCallback)
self.customVis.addActor(field_name, "vtkActor")
# we'll piggyback off the actorsDict
self.customVis.addActor("customVTKScript",
custom_vis_script)
def treeNode(itemNode, _superParent=None):
# itemNode can only be Element!
# itemNode is of type CC3DXMLElement
if not itemNode:
return None
try:
itemNode.name
node = itemNode
except AttributeError:
node = itemNode.root
# node = itemNode
t_node = TreeItem(node.name, node.cdata)
# Setting item values for Potts, Metadata, Plugins and Steppables.
# Those settings are for display purposes only and do not affect CC3DXML element that
# Compucell3d uses to configure the data
# all we do is to label Potts tree element as Posst and Plugin and Steppables are named
# using their names extracted from xml file.
# we are using _itemValue to label label those elements and do not change cdata of the CC3DXMLelement
if node.name == "Potts":
t_node.setItemValueOnly("Potts")
if node.name == "Metadata":
t_node.setItemValueOnly("Metadata")
# handling opening elements for Plugin and Steppables
if node.name == "Plugin":
t_node.setItemValueOnly(node.getAttribute("Name"))
if node.name == "Steppable":
t_node.setItemValueOnly(node.getAttribute("Type"))
t_node.setCC3DXMLElement(
node) # domNode holds reference to current CC3DXMLElement
# setting superParents -they are either Potts, Plugin or Steppable. SuperParents are used in steering.
# Essentially when we change any TreeItem in the TreeView
# we can quickly extract name of the superParent and tell CC3D to reinitialize module that superParent describes.
# Otherwise if we dont keep track of super parents we would either have to do:
# 1. time consuming and messy tracking back of which module needs to be changed in response
# to change in one of the parameter
# or
# 2. reinitialize all modules each time a single parameter is changed
superParent = _superParent
if not _superParent:
if node.name in ("Plugin", "Steppable", "Potts", "Metadata"):
superParent = t_node
t_node.setSuperParent(superParent)
# FOR AN UNKNOWN REASON "regular" map iteration does not work so i had to implement by hand iterators
# in C++ and Python to walk through all the elements in the map<string,string> in python
if node.attributes.size():
for attr_combo in node.attributes.items():
attribute_name = attr_combo[0]
attribute_value = attr_combo[1]
if node.name == "Plugin" and attribute_name == "Name":
continue
if node.name == "Steppable" and attribute_name == "Type":
continue
tree_child = TreeItem(
attribute_name,
attribute_value) # attribute name, attribute value pair
tree_child.setCC3DXMLElement(node)
tree_child.setSuperParent(superParent)
tree_child.setElementType("attribute")
t_node.addChild(tree_child)
children = XMLUtils.CC3DXMLListPy(node.children)
for child in children:
t_child = treeNode(child, superParent)
t_node.addChild(t_child)
return t_node
def __insertSnippet(self, _snippetName):
# print "GOT REQUEST FOR SNIPPET ",_snippetName
snippetNameStr = str(_snippetName)
self.handlerDict = self.snippetUtils.getHandlersDict()
text = self.snippetDictionary[str(_snippetName)]
editor = self.__ui.getCurrentEditor()
curFileName = str(self.__ui.getCurrentDocumentName())
basename, ext = os.path.splitext(curFileName)
if ext != ".xml" and ext != ".cc3dml":
QMessageBox.warning(self.__ui, "CC3DML files only", "CC3DML code snippets work only for xml/cc3dml files")
return
# here we parse cell type plugin if found
cc3dXML2ObjConverter = XMLUtils.Xml2Obj()
# root_element=cc3dXML2ObjConverter.ParseString(str(editor.text()))
# print 'root_element=',root_element
cellTypeData = self.getCellTypeData()
gpd = self.getPottsData()
print('cellTypeData=', cellTypeData)
# self.findModuleLine(editor,_moduleType='Plugin',_moduleName=['Name','CellType'])
# self.findModuleLine(editor,_moduleType='Steppable',_moduleName=['Type','PIFInitializer'])
# self.findModuleLine(editor,_moduleType='Potts',_moduleName=[])
# self.findModuleLine(editor,_moduleType='Plugin',_moduleName=['Name','CenterOfMass'])
if cellTypeData is None: # could not obtain data by parsing xml file - most likely due to parsing error
return
hiding_comments = self.configuration.setting("SkipCommentsInXMLSnippets")
if not len(cellTypeData):
print('self.handlerDict=', self.handlerDict)
print('self.handlerDict[str(_snippetName)]=', self.handlerDict["Plugins CellType"])
pottsBegin, pottsEnd = self.findModuleLine(editor, _moduleType='Potts', _moduleName=[])
if pottsEnd < 0:
editor.setCursorPosition(0, 0)
else:
editor.setCursorPosition(pottsEnd + 1, 0)
self.handlerDict["Plugins CellType"](data=cellTypeData, editor=editor, generalPropertiesData=gpd,
hiding_comments=hiding_comments)
QMessageBox.warning(self.__ui, "Fresh Cell Type Plugin",
"Please check newly inserted code and call %s again" % snippetNameStr)
return
# read freshly inseerted cell type plugin
else:
self.handlerDict[snippetNameStr](data=cellTypeData, editor=editor, generalPropertiesData=gpd,
hiding_comments=hiding_comments)
return
def getCellTypeData(self):
editor = self.__ui.getCurrentEditor()
cc3dXML2ObjConverter = XMLUtils.Xml2Obj()
try:
root_element = cc3dXML2ObjConverter.ParseString(str(editor.text()))
except xml.parsers.expat.ExpatError as 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
cellTypeElementVec = cellTypeElement.getElements("CellType")
cellTypeElementVec = CC3DXMLListPy(cellTypeElement.getElements("CellType"))
for element in cellTypeElementVec:
typeName = ''
typeId = -1
typeFreeze = False
if element.findAttribute('TypeName'):
typeName = element.getAttribute('TypeName')
else:
continue
if element.findAttribute('TypeId'):
typeId = element.getAttributeAsInt('TypeId')
else:
continue
if element.findAttribute('Freeze'):
typeFreeze = True
cellTypeDict[typeId] = [typeName, typeFreeze]
return cellTypeDict
print('cellTypeElementVec=', cellTypeElementVec)
print('cellTypeElement=', dir(cellTypeElement))
def getPottsData(self):
editor = self.__ui.getCurrentEditor()
gpd = {}
# default values
gpd['Dim'] = [0, 0, 0]
gpd['Temperature'] = 0
gpd['NeighborOrder'] = 3
gpd['MCS'] = 10000
gpd['SimulationName'] = 'PLEASE_PUT_SIMULATION_FILE_NAME_HERE'
gpd['LatticeType'] = 'Square'
cc3dXML2ObjConverter = XMLUtils.Xml2Obj()
try:
root_element = cc3dXML2ObjConverter.ParseString(str(editor.text()))
except xml.parsers.expat.ExpatError as e:
QMessageBox.critical(self.__ui, "Error Parsing CC3DML file", e.__str__())
print('GOT PARSING ERROR:', e)
return gpd
root_element.getFirstElement('Plugin')
# print('root_element=', root_element)
pottsElement = root_element.getFirstElement('Potts')
if not pottsElement or pottsElement is None:
return gpd
# extract dimension
dimElement = pottsElement.getFirstElement('Dimensions')
if dimElement:
if dimElement.findAttribute('x'):
gpd['Dim'][0] = dimElement.getAttributeAsUInt('x')
if dimElement.findAttribute('y'):
gpd['Dim'][1] = dimElement.getAttributeAsUInt('y')
if dimElement.findAttribute('z'):
gpd['Dim'][2] = dimElement.getAttributeAsUInt('z')
tempElement = pottsElement.getFirstElement('Temperature')
if tempElement:
gpd['MembraneFluctuations'] = float(tempElement.getText())
nElement = pottsElement.getFirstElement('NeighborOrder')
if nElement:
gpd['NeighborOrder'] = float(nElement.getText())
sElement = pottsElement.getFirstElement('Steps')
if sElement:
gpd['MCS'] = float(sElement.getText())
return gpd
from cc3d.twedit5.twedit.utils.global_imports import *
# Start-Of-Header