def main(): utils.parser nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml') #mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml") table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41', 'vm') table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0', 'vm') moose.setClock(0, 5e-6) moose.useClock(0, '/##', 'process') moose.useClock(0, '/##', 'init') moose.reinit() utils.run(0.1) graphviz.writeGraphviz(__file__+".dot", ignore='/library')
def main(): utils.parser p = os.path.join(modeldir, "two_cells_nml_1.8/two_cells.nml") nml.loadNeuroML_L123(p) # mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml") table1 = utils.recordTarget("/tableA", "/cells/purkinjeGroup_0/Dend_37_41", "vm") table2 = utils.recordTarget("/tableB", "/cells/granuleGroup_0/Soma_0", "vm") moose.setClock(0, 5e-6) moose.useClock(0, "/##", "process") moose.useClock(0, "/##", "init") moose.reinit() utils.run(0.1, verify=True) graphviz.writeGraphviz("test_mumble.dot", ignore="/library") utils.plotRecords({"Dend 37": table1, "Soma 0": table2}, outfile="%s.png" % sys.argv[0], subplot=True)
def main(): utils.parser nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml') #mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml") table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41', 'vm') table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0', 'vm') moose.setClock(0, 5e-6) moose.useClock(0, '/##', 'process') moose.useClock(0, '/##', 'init') moose.reinit() utils.run(0.1, verify=True) graphviz.writeGraphviz(__file__ + ".dot", ignore='/library') utils.plotTables([table1, table2])
def main(): utils.parser nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml') #mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml") table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41', 'vm') table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0', 'vm') moose.setClock(0, 5e-6) moose.useClock(0, '/##', 'process') moose.useClock(0, '/##', 'init') moose.reinit() utils.run(0.1, verify=True) graphviz.writeGraphviz(__file__+".dot", ignore='/library') utils.plotRecords({ 'Dend 37' : table1, 'Soma 0' : table2 } , outfile = '%s.png' % sys.argv[0] , subplot = True )
def main(): utils.parser p = os.path.join(modeldir, 'two_cells_nml_1.8/two_cells.nml') nml.loadNeuroML_L123(p) #mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml") table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41', 'vm') table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0', 'vm') moose.setClock(0, 5e-6) moose.useClock(0, '/##', 'process') moose.useClock(0, '/##', 'init') moose.reinit() utils.run(0.1, verify=True) graphviz.writeGraphviz('test_mumble.dot', ignore='/library') utils.plotRecords({ 'Dend 37': table1, 'Soma 0': table2 }, outfile='%s.png' % sys.argv[0], subplot=True)
def loadFile(filename, target, merge=True): """Try to load a model from specified `filename` under the element `target`. if `merge` is True, the contents are just loaded at target. If false, everything is deleted from the parent of target unless the parent is root. Returns ------- a dict containing at least these three entries: modeltype: type of the loaded model. subtype: subtype of the loaded model, None if no specific subtype modelroot: root element of the model, None if could not be located - as is the case with Python scripts """ istext = True with open(filename, 'rb') as infile: istext = mtypes.istextfile(infile) if not istext: print 'Cannot handle any binary formats yet' return None parent, child = posixpath.split(target) p = moose.Neutral(parent) if not merge and p.path != '/': for ch in p.children: moose.delete(ch) try: modeltype = mtypes.getType(filename) subtype = mtypes.getSubtype(filename, modeltype) except KeyError: raise FileLoadError('Do not know how to handle this filetype: %s' % (filename)) pwe = moose.getCwe() if modeltype == 'genesis': if subtype == 'kkit' or subtype == 'prototype': model = moose.loadModel(filename, target) else: print 'Only kkit and prototype files can be loaded.' elif modeltype == 'cspace': model = moose.loadModel(filename, target) elif modeltype == 'xml' and subtype == 'neuroml': model = neuroml.loadNeuroML_L123(filename) else: raise FileLoadError('Do not know how to handle this filetype: %s' % (filename)) moose.setCwe(pwe) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour # TODO: check with Aditya how to specify the target for # neuroml reader return {'modeltype': modeltype, 'subtype': subtype, 'model': model}
def loadFile(filename, target, solver="gsl", merge=True): """Try to load a model from specified `filename` under the element `target`. if `merge` is True, the contents are just loaded at target. If false, everything is deleted from the parent of target unless the parent is root. Returns ------- a dict containing at least these three entries: modeltype: type of the loaded model. subtype: subtype of the loaded model, None if no specific subtype modelroot: root element of the model, None if could not be located - as is the case with Python scripts """ num = 1 newTarget = target while moose.exists(newTarget): newTarget = target + "-" + str(num) num = num + 1 target = newTarget istext = True with open(filename, 'rb') as infile: istext = mtypes.istextfile(infile) if not istext: print 'Cannot handle any binary formats yet' return None parent, child = posixpath.split(target) p = moose.Neutral(parent) if not merge and p.path != '/': for ch in p.children: moose.delete(ch) try: modeltype = mtypes.getType(filename) subtype = mtypes.getSubtype(filename, modeltype) except KeyError: raise FileLoadError('Do not know how to handle this filetype: %s' % (filename)) pwe = moose.getCwe() #self.statusBar.showMessage('Loading model, please wait') # app = QtGui.qApp # app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) #shows a hourglass - or a busy/working arrow if modeltype == 'genesis': if subtype == 'kkit' or subtype == 'prototype': model, modelpath = loadGenCsp(target, filename, solver) if moose.exists(moose.element(modelpath).path): moose.Annotator(moose.element(modelpath).path + '/info').modeltype = "kkit" else: print " path doesn't exists" moose.le(modelpath) else: print 'Only kkit and prototype files can be loaded.' elif modeltype == 'cspace': model, modelpath = loadGenCsp(target, filename) if moose.exists(modelpath): moose.Annotator( (moose.element(modelpath).path + '/info')).modeltype = "cspace" addSolver(modelpath, 'gsl') elif modeltype == 'xml': if subtype == 'neuroml': popdict, projdict = neuroml.loadNeuroML_L123(filename) # Circus to get the container of populations from loaded neuroml for popinfo in popdict.values(): for cell in popinfo[1].values(): solver = moose.HSolve(cell.path + "/hsolve") solver.target = cell.path # model = cell.parent # break # break # Moving model to a new location under the model name # model name is the filename without extension model = moose.Neutral("/" + splitext(basename(filename))[0]) element = moose.Neutral(model.path + "/model") if (moose.exists("/cells")): moose.move("/cells", element.path) if (moose.exists("/elec")): moose.move("/elec", model.path) if (moose.exists("/library")): moose.move("/library", model.path) # moose.move("cells/", cell.path) elif subtype == 'sbml': if target != '/': if moose.exists(target): moose.delete(target) model = mooseReadSBML(filename, target) if moose.exists(moose.element(model).path): moose.Annotator(moose.element(model).path + '/info').modeltype = "sbml" addSolver(target, 'gsl') else: raise FileLoadError('Do not know how to handle this filetype: %s' % (filename)) moose.setCwe( pwe ) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour # TODO: check with Aditya how to specify the target for # neuroml reader # app.restoreOverrideCursor() return {'modeltype': modeltype, 'subtype': subtype, 'model': model}
def loadFile(filename, target, solver="gsl", merge=True): """Try to load a model from specified `filename` under the element `target`. if `merge` is True, the contents are just loaded at target. If false, everything is deleted from the parent of target unless the parent is root. Returns ------- a dict containing at least these three entries: modeltype: type of the loaded model. subtype: subtype of the loaded model, None if no specific subtype modelroot: root element of the model, None if could not be located - as is the case with Python scripts """ num = 1 newTarget = target while moose.exists(newTarget): newTarget = target + "-" + str(num) num = num + 1 target = newTarget istext = True with open(filename, "rb") as infile: istext = mtypes.istextfile(infile) if not istext: print("Cannot handle any binary formats yet") return None parent, child = posixpath.split(target) p = moose.Neutral(parent) if not merge and p.path != "/": for ch in p.children: moose.delete(ch) try: modeltype = mtypes.getType(filename) subtype = mtypes.getSubtype(filename, modeltype) except KeyError: raise FileLoadError("Do not know how to handle this filetype: %s" % (filename)) pwe = moose.getCwe() # self.statusBar.showMessage('Loading model, please wait') # app = QtGui.qApp # app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) #shows a hourglass - or a busy/working arrow if modeltype == "genesis": if subtype == "kkit" or subtype == "prototype": model, modelpath = loadGenCsp(target, filename, solver) if moose.exists(moose.element(modelpath).path): moose.Annotator(moose.element(modelpath).path + "/info").modeltype = "kkit" else: print(" path doesn't exists") moose.le(modelpath) else: print("Only kkit and prototype files can be loaded.") elif modeltype == "cspace": model, modelpath = loadGenCsp(target, filename) if moose.exists(modelpath): moose.Annotator((moose.element(modelpath).path + "/info")).modeltype = "cspace" addSolver(modelpath, "gsl") elif modeltype == "xml": if subtype == "neuroml": popdict, projdict = neuroml.loadNeuroML_L123(filename) # Circus to get the container of populations from loaded neuroml for popinfo in list(popdict.values()): for cell in list(popinfo[1].values()): solver = moose.HSolve(cell.path + "/hsolve") solver.target = cell.path # model = cell.parent # break # break # Moving model to a new location under the model name # model name is the filename without extension model = moose.Neutral("/" + splitext(basename(filename))[0]) element = moose.Neutral(model.path + "/model") if moose.exists("/cells"): moose.move("/cells", element.path) if moose.exists("/elec"): moose.move("/elec", model.path) if moose.exists("/library"): moose.move("/library", model.path) # moose.move("cells/", cell.path) elif subtype == "sbml": if target != "/": if moose.exists(target): moose.delete(target) model = mooseReadSBML(filename, target) if moose.exists(moose.element(model).path): moose.Annotator(moose.element(model).path + "/info").modeltype = "sbml" addSolver(target, "gsl") else: raise FileLoadError("Do not know how to handle this filetype: %s" % (filename)) moose.setCwe( pwe ) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour # TODO: check with Aditya how to specify the target for # neuroml reader # app.restoreOverrideCursor() return {"modeltype": modeltype, "subtype": subtype, "model": model}
def loadFile(filename, target, solver="gsl", merge=True): """Try to load a model from specified `filename` under the element `target`. if `merge` is True, the contents are just loaded at target. If false, everything is deleted from the parent of target unless the parent is root. Returns ------- a dict containing at least these three entries: modeltype: type of the loaded model. subtype: subtype of the loaded model, None if no specific subtype modelroot: root element of the model, None if could not be located - as is the case with Python scripts """ loaderror = "" num = 1 libsfound = True model = '/' newTarget = target while moose.exists(newTarget): newTarget = target + "-" + str(num) num = num + 1 target = newTarget istext = True with open(filename, 'rb') as infile: istext = mtypes.istextfile(infile) if not istext: print('Cannot handle any binary formats yet') return None # parent, child = posixpath.split(target) # p = moose.Neutral(parent) # if not merge and p.path != '/': # for ch in p.children: # moose.delete(ch) try: modeltype = mtypes.getType(filename) subtype = mtypes.getSubtype(filename, modeltype) except KeyError: raise FileLoadError('Do not know how to handle this filetype: %s' % (filename)) pwe = moose.getCwe() #self.statusBar.showMessage('Loading model, please wait') # app = QtGui.qApp # app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) #shows a hourglass - or a busy/working arrow if modeltype == 'genesis': if subtype == 'kkit' or subtype == 'prototype': model, modelpath = loadGenCsp(target, filename, solver) xcord, ycord = [], [] if moose.exists(moose.element(modelpath).path): process = True compt = len(moose.wildcardFind(modelpath + '/##[ISA=CubeMesh]')) if not compt: loaderror = "Model has no compartment, atleast one compartment should exist to display the widget" process = False else: p = len(moose.wildcardFind(modelpath + '/##[ISA=PoolBase]')) if p < 2: loaderror = "Model has no pool, atleast two pool should exist to display the widget" process = False if process: if moose.exists(moose.element(modelpath).path): mObj = moose.wildcardFind( moose.element(modelpath).path + '/##[ISA=PoolBase]' + ',' + moose.element(modelpath).path + '/##[ISA=ReacBase]' + ',' + moose.element(modelpath).path + '/##[ISA=EnzBase]' + ',' + moose.element(modelpath).path + '/##[ISA=StimulusTable]') for p in mObj: if not isinstance(moose.element(p.parent), moose.CplxEnzBase): xcord.append(moose.element(p.path + '/info').x) ycord.append(moose.element(p.path + '/info').y) recalculatecoordinatesforKkit(mObj, xcord, ycord) for ememb in moose.wildcardFind( moose.element(modelpath).path + '/##[ISA=EnzBase]'): objInfo = ememb.path + '/info' #Enzyme's textcolor (from kkit) will be bgcolor (in moose) if moose.exists(objInfo): bgcolor = moose.element(objInfo).color moose.element(objInfo).color = moose.element( objInfo).textColor moose.element(objInfo).textColor = bgcolor moose.Annotator(moose.element(modelpath).path + '/info').modeltype = "kkit" else: print(" path doesn't exists") moose.le(modelpath) else: print('Only kkit and prototype files can be loaded.') elif modeltype == 'cspace': model, modelpath = loadGenCsp(target, filename) if moose.exists(modelpath): moose.Annotator( (moose.element(modelpath).path + '/info')).modeltype = "cspace" addSolver(modelpath, 'gsl') elif modeltype == 'xml': if subtype == 'neuroml': popdict, projdict = neuroml.loadNeuroML_L123(filename) # Circus to get the container of populations from loaded neuroml for popinfo in popdict.values(): for cell in popinfo[1].values(): solver = moose.HSolve(cell.path + "/hsolve") solver.target = cell.path # model = cell.parent # break # break # Moving model to a new location under the model name # model name is the filename without extension model = moose.Neutral("/" + splitext(basename(filename))[0]) element = moose.Neutral(model.path + "/model") if (moose.exists("/cells")): moose.move("/cells", element.path) if (moose.exists("/elec")): moose.move("/elec", model.path) if (moose.exists("/library")): moose.move("/library", model.path) # moose.move("cells/", cell.path) elif subtype == 'sbml': foundLibSBML_ = False try: import libsbml foundLibSBML_ = True except ImportError: pass if foundLibSBML_: if target != '/': if moose.exists(target): moose.delete(target) model, loaderror = mooseReadSBML(filename, target) if moose.exists(moose.element(model).path): moose.Annotator(moose.element(model).path + '/info').modeltype = "sbml" addSolver(target, 'gsl') libsfound = foundLibSBML_ else: raise FileLoadError('Do not know how to handle this filetype: %s' % (filename)) moose.setCwe( pwe ) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour # TODO: check with Aditya how to specify the target for # neuroml reader # app.restoreOverrideCursor() return { 'modeltype': modeltype, 'subtype': subtype, 'model': model, 'foundlib': libsfound, 'loaderror': loaderror }
def loadFile(filename, target, merge=True): """Try to load a model from specified `filename` under the element `target`. if `merge` is True, the contents are just loaded at target. If false, everything is deleted from the parent of target unless the parent is root. Returns ------- a dict containing at least these three entries: modeltype: type of the loaded model. subtype: subtype of the loaded model, None if no specific subtype modelroot: root element of the model, None if could not be located - as is the case with Python scripts """ istext = True with open(filename, 'rb') as infile: istext = mtypes.istextfile(infile) if not istext: print 'Cannot handle any binary formats yet' return None parent, child = posixpath.split(target) p = moose.Neutral(parent) if not merge and p.path != '/': for ch in p.children: moose.delete(ch) try: modeltype = mtypes.getType(filename) subtype = mtypes.getSubtype(filename, modeltype) except KeyError: raise FileLoadError('Do not know how to handle this filetype: %s' % (filename)) pwe = moose.getCwe() #self.statusBar.showMessage('Loading model, please wait') # app = QtGui.qApp # app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) #shows a hourglass - or a busy/working arrow if modeltype == 'genesis': if subtype == 'kkit' or subtype == 'prototype': model = moose.loadModel(filename, target,'gsl') #Harsha: Moving the model under /modelname/model and graphs under /model/graphs lmodel = moose.Neutral('%s/%s' %(model.path,"model")) for compt in moose.wildcardFind(model.path+'/##[ISA=ChemCompt]'): moose.move(compt.path,lmodel) if not moose.exists(model.path+'/data'): graphspath = moose.Neutral('%s/%s' %(model.path,"data")) dataPath = moose.element(model.path+'/data') i =0 nGraphs = moose.wildcardFind(model.path+'/graphs/##[TYPE=Table2]') for graphs in nGraphs: if not moose.exists(dataPath.path+'/graph_'+str(i)): graphspath = moose.Neutral('%s/%s' %(dataPath.path,"graph_"+str(i))) else: graphspath = moose.element(dataPath.path+'/graph_'+str(i)) moose.move(graphs.path,graphspath) if len(nGraphs) > 0: i = i+1 #print " i ", i,moose.wildcardFind(model.path+'/moregraphs/##[TYPE=Table2]') for moregraphs in moose.wildcardFind(model.path+'/moregraphs/##[TYPE=Table2]'): if not moose.exists(dataPath.path+'/graph_'+str(i)): graphspath = moose.Neutral('%s/%s' %(dataPath.path,"graph_"+str(i))) else: graphspath = moose.element(dataPath.path+'/graph_'+str(i)) moose.move(moregraphs.path,graphspath) moose.delete(model.path+'/graphs') moose.delete(model.path+'/moregraphs') else: print 'Only kkit and prototype files can be loaded.' elif modeltype == 'cspace': model = moose.loadModel(filename, target,'gsl') #Harsha: Moving the model under /modelname/model and graphs under /model/graphs lmodel = moose.Neutral('%s/%s' %(model.path,"model")) for compt in moose.wildcardFind(model.path+'/##[ISA=ChemCompt]'): moose.move(compt.path,lmodel) if not moose.exists(model.path+'/data'): graphspath = moose.Neutral('%s/%s' %(model.path,"data")) dataPath = moose.element(model.path+'/data') i =0 nGraphs = moose.wildcardFind(model.path+'/graphs/##[TYPE=Table2]') for graphs in nGraphs: if not moose.exists(dataPath.path+'/graph_'+str(i)): graphspath = moose.Neutral('%s/%s' %(dataPath.path,"graph_"+str(i))) else: graphspath = moose.element(dataPath.path+'/graph_'+str(i)) moose.move(graphs.path,graphspath) if len(nGraphs) > 0: i = i+1 #print " i ", i,moose.wildcardFind(model.path+'/moregraphs/##[TYPE=Table2]') for moregraphs in moose.wildcardFind(model.path+'/moregraphs/##[TYPE=Table2]'): if not moose.exists(dataPath.path+'/graph_'+str(i)): graphspath = moose.Neutral('%s/%s' %(dataPath.path,"graph_"+str(i))) else: graphspath = moose.element(dataPath.path+'/graph_'+str(i)) moose.move(moregraphs.path,graphspath) moose.delete(model.path+'/graphs') moose.delete(model.path+'/moregraphs') addSolver(target,'gsl') elif modeltype == 'xml': if subtype == 'neuroml': popdict, projdict = neuroml.loadNeuroML_L123(filename) # Circus to get the container of populations from loaded neuroml for popinfo in popdict.values(): for cell in popinfo[1].values(): solver = moose.HSolve(cell.path + "/hsolve") solver.target = cell.path # model = cell.parent # break # break # Moving model to a new location under the model name # model name is the filename without extension model = moose.Neutral("/" + splitext(basename(filename))[0]) element = moose.Neutral(model.path + "/model") if(moose.exists("/cells")) : moose.move("/cells" , element.path) if(moose.exists("/elec")) : moose.move("/elec" , model.path) if(moose.exists("/library")): moose.move("/library", model.path) # moose.move("cells/", cell.path) elif subtype == 'sbml': model = moose.readSBML(filename,target,'gsl') addSolver(target,'gsl') else: raise FileLoadError('Do not know how to handle this filetype: %s' % (filename)) moose.setCwe(pwe) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour # TODO: check with Aditya how to specify the target for # neuroml reader # app.restoreOverrideCursor() return {'modeltype': modeltype, 'subtype': subtype, 'model': model}