Exemple #1
0
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}
Exemple #2
0
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}