How to use the pysal.open function in pysal

def _test():
    import doctest
    start_suppress = np.get_printoptions()['suppress']
    np.set_printoptions(suppress=True)
    doctest.testmod()
    np.set_printoptions(suppress=start_suppress)


if __name__ == '__main__':
    _test()

    import numpy as np
    import pysal
    db = pysal.open(pysal.examples.get_path("columbus.dbf"), 'r')
    y_var = 'CRIME'
    y = np.array([db.by_col(y_var)]).reshape(49, 1)
    x_var = ['INC']
    x = np.array([db.by_col(name) for name in x_var]).T
    yd_var = ['HOVAL']
    yd = np.array([db.by_col(name) for name in yd_var]).T
    q_var = ['DISCBD']
    q = np.array([db.by_col(name) for name in q_var]).T
    w = pysal.rook_from_shapefile(pysal.examples.get_path("columbus.shp"))
    w.transform = 'r'
    model = GM_Lag(
        y, x, yd, q, w=w, spat_diag=True, name_y=y_var, name_x=x_var,
        name_yend=yd_var, name_q=q_var, name_ds='columbus', name_w='columbus.gal')
    print model.summary

def _test():
    import doctest
    doctest.testmod()

                     
if __name__ == '__main__':
    _test()    
    import numpy as np
    import pysal
    db=pysal.open("examples/columbus.dbf","r")
    y = np.array(db.by_col("CRIME"))
    y = np.reshape(y, (49,1))
    X = []
    X.append(db.by_col("INC"))
    X = np.array(X).T
    yd = []
    yd.append(db.by_col("HOVAL"))
    yd = np.array(yd).T
    # instrument for HOVAL with DISCBD
    q = []
    q.append(db.by_col("DISCBD"))
    q = np.array(q).T
    reg = BaseTSLS(y, X, yd, q=q, robust='white')
    print reg.betas
    print reg.vm

#x_var = ['smsa']
    x_var = ['smsa','UN']
    x = np.array([db.by_col(name) for name in x_var]).T
    #yend_var = ['UN']
    #yend = np.array([db.by_col(name) for name in yend_var]).T
    #q_var = ['UN']
    #q = np.array([db.by_col(name) for name in q_var]).T
    eq_var = 'time'
    equationID = db.by_col(eq_var)
    w = pysal.open(pysal.examples.get_path("swohio.gal"),'r').read()
    w.transform = 'r'
    #sur1 = ThreeSLS(y, x, equationID, yend, q, name_x=x_var, name_yend=yend_var, name_q=q_var)
    sur1 = ThreeSLS(y, x, equationID, name_x=x_var, name_equationID=eq_var)
    print sur1.summary
    """
    db = pysal.open(pysal.examples.get_path("NAT.dbf"),'r')
    y_var = ['HR80','HR90']
    y = np.vstack((np.array([db.by_col(r)]).T for r in y_var))
    y_name = 'HR'
    x_var = ['PS80','UE80','PS90','UE90']
    x = np.array([db.by_col(name) for name in x_var]).T
    x = np.vstack((x[:,0:2],x[:,2:4]))
    x_name = ['PS','UE']
    yd_var = ['RD80','RD90']
    yd = np.vstack((np.array([db.by_col(r)]).T for r in yd_var))
    yd_name = ['RD']
    q_var = ['FP79','FP89']
    q = np.vstack((np.array([db.by_col(r)]).T for r in q_var))
    q_name = ['FP']
    eq_name = 'Year'
    eq_ID = [1980]*3085 + [1990]*3085
    w = pysal.rook_from_shapefile(pysal.examples.get_path("NAT.shp"))

def OnSaveQueryToDBF(self, event):
        """
        """
        dlg = wx.FileDialog(
            self, message="Save query as a dbf file...", defaultDir=os.getcwd(), 
            defaultFile='%s.dbf' % (self.points_data.name + '_query'), 
            wildcard="dbf file (*.dbf)|*.dbf|All files (*.*)|*.*", 
            style=wx.SAVE
            )
        if dlg.ShowModal() != wx.ID_OK:
            return
        path = dlg.GetPath()
        
        dbf = self.points_data.dbf
        
        newDBF= pysal.open(path,'w')
        newDBF.header = dbf.header
        newDBF.field_spec = dbf.field_spec
        newDBF.header.append('ISQUERYITEM')
        newDBF.field_spec.append(('N',4,0))
       
        for i,row in enumerate(dbf):
            if i in self.current_selected:
                row.append(1)
            newDBF.write(row)
        newDBF.close()
        
        self.ShowMsgBox("Query results have been saved in column 'ISQUERYITEM' of dbf file.",
                        mtype='Information',
                        micon=wx.ICON_INFORMATION)

def writeMeta(self, metaData, out_file):
        shp = pysal.open(out_file, 'w')
        dbf = pysal.open(out_file[:-3] + 'dbf', 'w')
        dbf.header = ['LENGTH', 'NO_PNTS', 'INITIAL_CENTER']
        dbf.field_spec = [('N',9,0)]*2 + [('L',1,0)]
        for link in metaData:
            vertices = list(link)
            vertices = [pysal.cg.Point(v) for v in vertices]
            shp.write(pysal.cg.Chain(vertices))
            dbf.write(metaData[link])
        shp.close()
        dbf.close()

newvertices = s.vertices[:-1]
		for v in newvertices:
			vertices[v].add(i)

	w = collections.defaultdict(set)
	for neighbors in vertices.values():
		for neighbor in neighbors:
			w[neighbor] = w[neighbor] | neighbors
	return w
#####################################################

# obtain a list for the states for each congressional district
cdistricts_dbf = "/Users/avelez/Documents/MGGG_UROP/state-adjacency-graphs/adjacency_graphs_all/MA_case/cb_2013_us_cd113_500k/cb_2013_us_cd113_500k.dbf"
cd_dbf = ps.open(cdistricts_dbf)
STATE_LIST = cd_dbf.by_col_array('STATEFP')
DISTRICT_LIST = [x for x in ps.open(cdistricts_file)]
GEOID_LIST = cd_dbf.by_col_array('GEOID')
# print(dbf.by_col_array('STATEFP'))

# create a dictionaries 
# for each state, map to a list of its districts (as PySAL Polygon objects)
# for each district, map to its GEOID
STATE_TO_DISTRICTS = {}
DISTRICT_TO_GEOID = {}
for i in range(len(DISTRICT_LIST)):
	state = STATE_LIST[i][0]
	district_polygon = DISTRICT_LIST[i]
	if state not in STATE_TO_DISTRICTS:
		STATE_TO_DISTRICTS[state]=[]
	STATE_TO_DISTRICTS[state].append(district_polygon)
	DISTRICT_TO_GEOID[district_polygon] = GEOID_LIST[i][0]

def __init__(self, *args, **kwargs):
        self._varName = 'Unknown'
        args = args[:2]
        FileIO.FileIO.__init__(self, *args, **kwargs)
        self.file = pysal.open(self.dataPath, self.mode)

def ShowModal(self, dbf_path):
        """
        Display the Dialog and add the id var.
        """
        self.db = None
        self.dbf_path = dbf_path
        if os.path.exists(dbf_path):
            self.db = pysal.open(dbf_path, 'r')
            self.existingVarsListBox.Clear()
            self.existingVarsListBox.InsertItems(self.db.header, 0)
            self.idVarName.SetValue('POLY_ID')
            return xrcAddIDVar.ShowModal(self)
        else:
            raise ValueError("Invalid DBF File")

# new approach using dtypes.name to avoid numpy name issue in type
        type2spec = {'int': ('N', 20, 0),
                     'int8': ('N', 20, 0),
                     'int16': ('N', 20, 0),
                     'int32': ('N', 20, 0),
                     'int64': ('N', 20, 0),
                     'float': ('N', 36, 15),
                     'float32': ('N', 36, 15),
                     'float64': ('N', 36, 15),
                     'str': ('C', 14, 0),
                     'object': ('C', 14, 0),
                     'category': ('C', 14, 0)
                     }
        types = [df[i].dtypes.name for i in df.columns]
        specs = [type2spec[t] for t in types]
    db = ps.open(dbf_path, 'w')
    db.header = list(df.columns)
    db.field_spec = specs
    for i, row in df.T.iteritems():
        db.write(row)
    db.close()
    return dbf_path

if hasattr(_basegeom, method):
        locals()[method].__doc__ = getattr(_basegeom,method).__doc__

if __name__=='__main__':
    #step 0, create 2 points
    pt1 = pysal.cg.shapes.Point((0,0))
    pt2 = pysal.cg.shapes.Point((10,10))
    o = pysal.open('step0.shp','w')
    o.write(pt1)
    o.write(pt2)
    o.close()

    #step 1, buffer 2 points
    b1 = buffer(pt1,10)
    b2 = buffer(pt2,10)
    o = pysal.open('step1.shp','w')
    o.write(b1)
    o.write(b2)
    o.close()

    #step 2, intersect 2 buffers
    i = intersection(b1,b2)
    o = pysal.open('step2.shp','w')
    o.write(i)
    o.close()
    
    #step 3, union 2 buffers
    u = union(b1, b2)
    o = pysal.open('step3.shp','w')
    o.write(u)
    o.close()