def create_nc_project(self):
"""Creates a neuroConstruct project from the NeuroML2 file(s)."""
from java.io import File
from ucl.physiol.neuroconstruct.project import Project
from ucl.physiol.neuroconstruct.cell.converters import MorphMLConverter
project = Project.createNewProject('/Users/rgerkin/', self.model_name,
None)
morphDir = File(
"%s/osb/showcase/neuroConstructShowcase/Ex3_Morphology/importedMorphologies/"
% NC_HOME)
morphmlFile = File(morphDir, "SimplePurkinjeCell.morph.xml")
converter = MorphMLConverter()
cell = converter.loadFromMorphologyFile(morphmlFile, "NewCell")
project.cellManager.addCellType(cell) # Actually add it to the project
project.cellGroupsInfo.setCellType(
"DefaultCellGroup", cell.getInstanceName(
)) # Set the type of an existing cell group to this
project.saveProject()
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath(
) + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
morphDir = File(
"../osb/showcase/neuroConstructShowcase/Ex3_Morphology/importedMorphologies/"
)
morphmlFile = File(morphDir, "SimplePurkinjeCell.morph.xml")
print "Going to load morphology from: " + morphmlFile.getCanonicalPath()
converter = MorphMLConverter()
cell = converter.loadFromMorphologyFile(morphmlFile, "NewCell")
print "Loaded cell: " + cell.getInstanceName() + " with " + str(
cell.getAllSegments().size()) + " segments"
myProject.cellManager.addCellType(cell) # Actually add it to the project
myProject.cellGroupsInfo.setCellType(
"SampleCellGroup",
cell.getInstanceName()) # Set the type of an existing cell group to this
# Now the project can be generated as in Ex5_MultiSimGenerate.py
# * OR *
# Save project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
morphDir = File("../nCexamples/Ex3_Morphology/importedMorphologies/")
morphmlFile = File(morphDir, "SimplePurkinjeCell.morph.xml")
print "Going to load morphology from: " + morphmlFile.getCanonicalPath()
converter = MorphMLConverter()
cell = converter.loadFromMorphologyFile(morphmlFile, "NewCell")
print "Loaded cell: " + cell.getInstanceName() + " with " + str(cell.getAllSegments().size()) +" segments"
myProject.cellManager.addCellType(cell) # Actually add it to the project
myProject.cellGroupsInfo.setCellType("SampleCellGroup", cell.getInstanceName()) # Set the type of an existing cell group to this
# Now the project can be generated as in Ex5_MultiSimGenerate.py
# * OR *
# Save project
projFile = File(sys.argv[1])
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
saveDir = File(sys.argv[2])
print "Going to save NeuroML files to: " + saveDir.getAbsolutePath()
level = NeuroMLLevel.NEUROML_LEVEL_3
version = NeuroMLVersion.NEUROML_VERSION_1
MorphMLConverter.saveAllCellsInNeuroML(myProject,
OriginalCompartmentalisation(),
level,
version,
None,
saveDir)
# Note: look also in Java class ucl.physiol.neuroconstruct.neuroml.NeuroMLPythonFileManager
# for the method generateNeuroMLFiles() which can be used to export all cells, channels and
# generated network structure to individual NeuroML files or as one large Level 3 file.
print "Done!"
print "Usage: \n ../nC.sh -python Ex7_ExtractNeuroML.py neuroConstruct_project_file folder_for_NeuroML"
print "Example: \n ../nC.sh -python Ex7_ExtractNeuroML.py TestPython/TestPython.neuro.xml /tmp"
print "or: \n ..\\nC.bat -python Ex7_ExtractNeuroML.py TestPython\\TestPython.neuro.xml c:\\temp"
sys.exit(1)
# Load neuroConstruct project
projFile = File(sys.argv[1])
print "Loading project from file: " + projFile.getAbsolutePath(
) + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
saveDir = File(sys.argv[2])
print "Going to save NeuroML files to: " + saveDir.getAbsolutePath()
level = NeuroMLLevel.NEUROML_LEVEL_3
version = NeuroMLVersion.NEUROML_VERSION_1
MorphMLConverter.saveAllCellsInNeuroML(myProject,
OriginalCompartmentalisation(), level,
version, None, saveDir)
# Note: look also in Java class ucl.physiol.neuroconstruct.neuroml.NeuroMLPythonFileManager
# for the method generateNeuroMLFiles() which can be used to export all cells, channels and
# generated network structure to individual NeuroML files or as one large Level 3 file.
print "Done!"
