def pyray_save(self,S):
        """
            save node positions into ini file, compliant with pyray standard

        Parameters
        ----------
        
        filename : string 
                   name of the pyray file
        S        : Simulation
                   Scipy.Simulation object
        """


        assert len(self.SubNet.keys()) == 1 , NameError('when network.ini_save() \
        is used , only 1 rat must be involved in the Network.\
        Please modify agent.ini')


        height= 1.5
        pos=nx.get_node_attributes(self,'p').items()

        ### create ini files
        if self.idx == 0:
            self.init_save(height=height)
        ### save agent positions
        for i in range(len(pos)):
            if self.node[pos[i][0]]['type'] !='ap':
                config = ConfigParser.ConfigParser()
                config.read(pyu.getlong(str(pos[i][0]) + '.ini',pstruc['DIRNETSAVE']))
                config.set('coordinates',str(self.idx+1),value = str(pos[i][1][0]) + ' ' + str(pos[i][1][1]) + ' '+str(height))
                file=open(pyu.getlong(str(pos[i][0]) + '.ini',pstruc['DIRNETSAVE']),'w')
                config.write(file)
                file.close()

    def load(self):
        """
        Load simulnet_data configuration file
        """
        if not os.path.isfile(pyu.getlong(self.simnetfile,pstruc['DIRNETSAVE'])):
            raise NameError(self.simnetfile +' cannot be reached.\
 Have you launch a simulnet simulation before ? \
 Please use \'>>> Simnet2cir?\' to see help ')
        self.simcfg = ConfigParser.ConfigParser()
        self.simcfg.read(pyu.getlong(self.simnetfile,pstruc['DIRNETSAVE']))
        self.Lfilename = self.simcfg.get('layout','layoutname')
        self.lAG = eval(self.simcfg.get('nodes','ag'))
        self.lAP = eval(self.simcfg.get('nodes','ap'))
        self.uptime = eval(self.simcfg.get('simulation','updatetime'))
        # create a Simul object with the correct layout
        self.S = Simul()
        self.S.layout(self.Lfilename,'matDB.ini','slabDB.ini')
        self.lap = len(self.lAP)
        self.lag = len(self.lAG)

        self.L = self.S.L
        try:
            self.L.dumpr()
            print 'Layout graphs are loaded from ',basename,'/struc'
        except:
        #self.L.sl = sl
        #self.L.loadGr(G1)
            print 'First time your use the Layout.Graphs are curently build, it may take few minutes.'
            self.L.buildGt()
            self.L.dumpw()

    def ini_save(self,S,filename='simulnet_data.ini',height=1.5):
        """
        ----------
        DEPRECATED
        ----------
        Save an .ini file of node position . 
        Only links  which involve mobile nodes (type 'ag') are kept.

        The produced init file is filled as follow:

            [timestamp]
            nodeID1_nodeID2 = x1,y1,z1,x2,y2,z2
            nodeID2_nodeID4 = x2,y2,z2,x4,y4,z4
            ....


        Attributes:
        ----------
        
        S        : Simulation
                   Scipy.Simulation object

        filename  : string
                   name of the saved ini file

        height    : float
                   height of the nodes





        """

        assert len(self.SubNet.keys()) == 1 , NameError('when network.ini_save() \
        is used , only 1 rat must be involved in the Network.\
        Please modify agent.ini')


        if self.idx == 0:
            file=open(pyu.getlong(filename ,'output'),'w')
        else:
            file=open(pyu.getlong(filename ,'output'),'a')

        config = ConfigParser.ConfigParser()
        timestamp = pyu.timestamp(S.now())
        config.add_section(timestamp)
        for e in self.edges():
            if not ((self.node[e[0][0]]['type'] == 'ap') and  (self.node[e[1][0]]['type'] == 'ap')):
                key=str(e[0]) +'_' +str(e[1])
                value1 = str(self.node[e[0][0]]['p'][0])+ ',' +str(self.node[e[0][0]]['p'][1])+','+str(height)
                value2 = str(self.node[e[1][0]]['p'][0])+ ',' +str(self.node[e[1][0]]['p'][1])+','+str(height)
                config.set(timestamp, key, value1 + ' , ' + value2)

        config.write(file)
        file.close()

        self.idx=self.idx+1

    def geomfile(self,iframe=0,verbose=False,topos=False,tag=''):
        """ create a geomview file from a body configuration 

        Parameters
        ----------

        iframe : int 
        verbose : boolean
        topos : boolean 
        tag : string 

        """
        cyl = geu.Geomoff('cylinder')
        pt = cyl.loadpt()
        if not topos:
            _filebody = str(iframe).zfill(4)+'body.list'
        else:    
            _filebody = tag+'-body.list'
        filebody = pyu.getlong(_filebody,"geom")
        filestruc = pyu.getlong('DLR.off',"geom")
        fo = open(filebody,"w")
        fo.write("LIST\n")
        fo.write('{<'+filestruc+'}\n')
        if verbose:
            print ("LIST\n")
        for k,e in enumerate(self.g.edges()):
            e0 = e[0]
            e1 = e[1]
            if not topos:
                pA = self.d[:,e0,iframe].reshape(3,1)
                pB = self.d[:,e1,iframe].reshape(3,1)
            else:    
                pA = self.topos[:,e0].reshape(3,1)
                pB = self.topos[:,e1].reshape(3,1)
            pM = (pA+pB)/2.
            T = geu.onbfromaxe(pA,pB)
            R = self.g[e0][e1]['radius']
            Y = np.hstack((pM,pA,pB,pM+R*T[0,:,0].reshape(3,1),pM+R*T[0,:,1].reshape(3,1),pB+R*T[0,:,0].reshape(3,1)))
            A,B = geu.cylmap(Y)
            ptn = np.dot(A,pt.T)+B
            if not topos:
                _filename = 'edge'+str(k)+'-'+str(iframe)+'.off'
            else:
                _filename = tag+'-edge'+str(k)+'.off'
            filename = pyu.getlong(_filename,"geom")
            cyl.savept(ptn.T,_filename)
            fo.write('{<'+filename+'}\n')
            if verbose:
                print('{<'+filename+'}\n')
        fo.close()

    def put(self, typ):
        """ recover last deleted coeff

        Parameters
        ----------
        typ : int
                2 : shape 2  (Nf , N*M   )
                3 : shape 3  (Nf , K )  T ( K x 2 )
        """

        if typ == 2:

            file_ind = pyu.getlong("outfile_i2.txt", pstruc["DIRANT"])
            aux = load(file_ind)
            ind = aux[0]
            ind2 = np.array([aux[1], aux[2]])

            file_s2 = pyu.getlong("outfile_s2.txt", pstruc["DIRANT"])
            s2 = load(file_s2)

            self.s2p = s2

            a = insert(self.ind2, ind, ind2, axis=0)
            b = insert(self.s2, ind, s2, axis=1)

            self.ind2 = a
            self.s2 = b

        if typ == 3:

            file_ind = pyu.getlong("outfile_i3.txt", pstruc["DIRANT"])
            aux = load(file_ind)
            ind = aux[0]
            ind3 = np.array([aux[1], aux[2]])
            k2 = aux[3]

            file_s3 = pyu.getlong("outfile_s3.txt", pstruc["DIRANT"])
            s3 = load(file_s3)

            a = insert(self.ind3, ind, ind3, axis=0)
            b = insert(self.k2, ind, k2)
            c = insert(self.s3, ind, s3[0], axis=1)

            self.ind3 = a
            self.k2 = b
            self.s3 = c

            os.remove(file_ind)
            os.remove(file_s3)

    def __init__(self, **args):

        defaults = {'L': None,
                    'net': None,
                    'sim': None}

##       initialize attributes
        for key, value in defaults.items():
            if key in args:
                setattr(self, key, args[key])
            else:
                setattr(self, key, value)
                args[key] = value
        self.args = args

        Process.__init__(self, name='save', sim=self.args['sim'])


        self.C = ConfigParser.ConfigParser()
        self.C.read(pyu.getlong('save.ini','ini'))
        self.opt = dict(self.C.items('config'))
        self.pos = dict(self.C.items('position'))
        self.ldp = dict(self.C.items('ldp'))
        self.rat = dict(self.C.items('rat'))
        self.lpos = eval(self.pos['position'])
        self.lldp = eval(self.ldp['ldp'])
        self.lrat = eval(self.rat['rat'])


        self.sim = args['sim']
        self.net = args['net']

    def load(self):
        """
        Load simulnet_data configuration file
        """
        self.simcfg = ConfigParser.ConfigParser()
        self.simcfg.read(pyu.getlong(self.simnetfile,pstruc['DIRNETSAVE']))
        pdb.set_trace()
        self.Lfilename = self.simcfg.get('layout','layoutname')
        self.lAG = eval(self.simcfg.get('nodes','ag'))
        self.lAP = eval(self.simcfg.get('nodes','ap'))
        self.uptime = eval(self.simcfg.get('simulation','updatetime'))
        # create a Simul object with the correct layout
        self.S = Simul()
        self.S.layout(self.Lfilename,'matDB.ini','slabDB.ini')
        self.lap = len(self.lAP)
        self.lag = len(self.lAG)

        self.L = self.S.L
        try:
            self.L.dumpr()
            print('Layout graphs are loaded from ',basename,'/struc')
        except:
        #self.L.sl = sl
        #self.L.loadGr(G1)            
            print('First time your use the Layout.Graphs are curently build, it may take few minutes.')
            self.L.buildGt()
            self.L.dumpw()

    def load(self,name,_fileini='defAP.json'):
        """ loading an access point from file

        Parameters
        ----------

        _fileini : string
            access point description ini file

        """

        self._fileini = _fileini
        fileini = pyu.getlong(_fileini,pstruc['DIRSIMUL'])
        fp = open(fileini,"r")
        ap = json.load(fp)

        self['name'] = name
        dap = ap[name]
        self['p'] = eval(dap['pos'])
        wstd = dap['wstd']
        self['PtdBm'] = dap['ptdbm']
        self['channels'] = eval(dap['chan'])
        self['sensdBm'] = dap['snsdbm']
        self['nant'] = dap['nant']

        standard = Wstandard(wstd)
        self.s = standard
        fp.close()

    def loadaster(self,fileaster=[]):
        """ load Aster files

        """


        # construct filename from prefix
        _fileaster = 'ASTGTM2_'+self.prefix+'_dem.tif'

        if fileaster==[]:
            fileaster = pyu.getlong(_fileaster,os.path.join('gis','aster'))
        else:
            _fieleaster = pyu.getshort(fileaster)

        # zip extraction
        ext = _fileaster.split('.')
        if ext[1]=='zip':
            with zipfile.Zipfile(fileaster) as zf:
                for member in zf.infolist():
                    words = member.filename.split('/')
                    path = dest_dir
                    for word in words[:-1]:
                        drive, word = os.path.splitdrive(word)
                        head, word = os.path.split(word)
                        if word in (os.curdir, os.pardir, ''):
                            continue
                        path = os.path.join(path, word)
                    zf.extract(member, path)

        f = gdal.Open(fileaster)
        self.hgta = f.ReadAsArray()

 def __init__(self,_filename):
     """
     """
     if '.h5' not in _filename:
         _filename = _filename+'.h5'
     self._filename = _filename 
     self.filename = pyu.getlong(self._filename,pstruc['DIRMES'])

    def __init__(self,**args):
        defaults={'net':Network(),
                  'L':[],
                  'net_updt_time':0.001,
                  'sim':None,
                  'show_sg':False,
                  'disp_inf':False,
                  'save':[]}

##       initialize attributes
        for key, value in defaults.items():
            if args.has_key(key):
                setattr(self, key, args[key])
            else:
                setattr(self, key, value)
                args[key]=value  
        self.args=args

        Process.__init__(self,name='PNetwork',sim=self.sim)
        self.cpt=self.sim.now()
        self.filename='pos'

        if 'mysql' in self.save:
           config = ConfigParser.ConfigParser()
           config.read(pyu.getlong('simulnet.ini','ini'))
           sql_opt = dict(config.items('Mysql'))
           self.net.db = Database(sql_opt['host'],sql_opt['user'],sql_opt['passwd'],sql_opt['dbname'])

    def fill_dexist(self,key,grpname):
        """Check if the key's data with a given groupname
            already exists in the h5py file

        Parameters
        ----------

        key: string
            key of the h5py group
        grpname : string
            groupe name of the h5py file

        Notes
        -----

        update the key grpname of self.dexist[key] dictionnary

        """
        try :
            lfilename=pyu.getlong(self.filename,pstruc['DIRLNK'])
            f=h5py.File(lfilename,'r')
            if grpname.decode('utf8') in f[key].keys():
                self.dexist[key]['exist']=True
            else :
                self.dexist[key]['exist']=False
            f.close()
        except:
            f.close()
            raise NameError('Link exist: issue during stacking')

def vrml2geom(tg, rac):
    """ convert vrml object into geomview files

    Parameters
    ----------
    tg   : list of objects
    rac  : filename prefix
    """
    for l in tg:
        # prepare geomview file
        fi1 = rac+l['name']
        _fi1 = fi1+'.list'
        fina = pyu.getlong(_fi1, 'geom')
        fd = open(fina, 'w')
        fd.write('LIST')
        for k in l.keys():
            if k != 'name':
                filename = fi1+'-'+str(k)
                fd.write('{<'+filename+'.off}\n')
                G = geo.Geomoff(filename)
                c = l[k]['coord']
                i = l[k]['index']
                tt = []
                ltt = []
                for u in i:
                    if u == -1:
                        ltt.append(tt)
                        tt = []
                    else:
                        tt.append(u)
                # build a geomview list of polygons
                G.polygons(c, ltt)
        fd.close()

def devicels():
    """ list available devices in project directory
    """
    fp = open(pyu.getlong('devices.json', pstruc['DIRSIMUL']))
    dev = json.load(fp)
    fp.close()
    print dev.keys()

    def stack(self,key,array):
        """ stack new array in h5py file
            for a given key (dataframe/group)

        Parameters
        ----------

        key : string

        array : np.ndarray

        Returns
        -------

        idx : int
            indice of last element of the array of key

        """
        try :
            lfilename=pyu.getlong(self.filename,pstruc['DIRLNK'])
            f=h5py.File(lfilename,'a')
            if key != 'T_map':
                sc = f[key].shape
                f[key].resize((sc[0]+1,sc[1]))
                f[key][-1,:]=array
            else:
                sc = f[key].shape
                f[key].resize((sc[0]+1,sc[1],sc[2]))
                f[key][-1,:,:]=array
            f.close()
            return np.array([sc[0]])
        except:
            f.close()
            raise NameError('Link stack: issue during stacking')

def importsn(_filename='pos.csv'):
    """ import simulnet csv file


    ****DEPRECATED

    Parameters
    ----------

    filename : string
        default 'pos.csv'

    Returns
    -------

    lt : list of trajectory

    """
    filename = pyu.getlong(_filename, pstruc['DIRNETSAVE'])
    dt = pd.read_csv(filename)
    dtk = dt.keys()
    N = len(dtk)
    Ntraj = (N-1)/3
    lt = []
    for it in range(Ntraj):
        x = dt[dtk[3*it+1]].values
        y = dt[dtk[3*it+2]].values
        z = np.zeros(len(x))
        pt = np.vstack((x, y, z))
        T=Trajectory()
        lt.append(T.generate(t=dt['time'].values, pt=pt.T, unit='s'))

    return(lt)

    def saveini(self,ical=1,_fileini='vna_config.ini'):
        """ save calibration parameters in .ini file

        Parameters
        ----------

        _fileini  : string
            calibration ini file
        ical : int
            calibration number
        """

        dcal = self.dcal[str(ical)]
        config = ConfigParser.ConfigParser()

        # stimulus section
        config.add_section("stimulus")
        config.set("stimulus",'fminghz',dcal['fminghz'])
        config.set("stimulus",'fmaxghz',dcal['fmaxghz'])
        config.set("stimulus",'nf',dcal['nf'])
        config.set("stimulus",'power',dcal['power'])

        # response section
        config.add_section("response")
        config.set("response",'param',dcal['param'])
        config.set("response",'average','on')
        config.set("response",'navrg',dcal['navrg'])
        config.set("response",'ifbhz',dcal['ifbhz'])
        config.set("response",'win',1)

        fileini = pyu.getlong(_fileini,pstruc['DIRMES'])
        fd = open(fileini,"w")
        config.write(fd)
        fd.close()

    def save(self, force=False):

        if self.filename == "" or force:
            filename = QFileDialog.getSaveFileName(
                self, "Save Layout", pyu.getlong("", pstruc["DIRINI"]), "(*.ini);;(*.osm)"
            )
            try:
                _filename = pyu.getshort(str(filename))
            except:
                pass
        else:
            _filename = self.L.filename
        try:
            oldCursor = QCursor()
            QApplication.setOverrideCursor(QCursor(Qt.BusyCursor))
            self.L.saveini(_filename)
            self.L.saveosm(_filename.split(".")[0] + ".osm")
            self.L = Layout(_filename)
            self.filename = self.L.filename
            self.setWindowTitle(self.L.filename + "- Pylayers : Stand Alone Editor (Beta)")
            QApplication.setOverrideCursor(oldCursor)

            print "saved"
        except:
            pass

def importsn(_filename='pos.csv'):
    """ import simulnet csv file
    
    Parameters
    ----------

    filename : string 
        default 'pos.csv'

    Returns
    -------

    lt : list of trajectory

    """
    filename = pyu.getlong(_filename,'save_data')
    dt = pd.read_csv(filename)
    dtk = dt.keys()
    N = len(dtk)
    Ntraj = (N-1)/3
    lt = []
    for it in range(Ntraj):
        pt = np.vstack((dt[dtk[3*it+1]].values,dt[dtk[3*it+2]].values))
        lt.append(Trajectory(dt['time'].values,pt=pt.T,unit='s'))
    return(lt)    

    def mat_save(self,S):
        """
            save node positions into a matlab structure file


        Attributes:
        ----------
        
        filename : string 
                   name of the mat file
        S        : Simulation
                   Scipy.Simulation object
        """

        pos=nx.get_node_attributes(self,'p').items()
        for i in range(len(pos)):
            if not 'BS' in pos[i][0]:
                try:
                    self.mat[pos[i][0]]['pos']=np.vstack((self.mat[pos[i][0]]['pos'],pos[i][1]))
                    self.mat[pos[i][0]]['time']=np.vstack((self.mat[pos[i][0]]['time'],S.now()))
                except:
                    self.mat[pos[i][0]]={}
                    self.mat[pos[i][0]]['pos']=pos[i][1]
                    self.mat[pos[i][0]]['time']=np.array(S.now())
            else :
                try:
                    self.mat[pos[i][0]]['pos']=pos[i][1]
                except:
                    self.mat[pos[i][0]]={}
                    self.mat[pos[i][0]]['pos']=pos[i][1]

                   
        sp.io.savemat(pyu.getlong('mat.mat','save_data'),self.mat)