source: branches/inundation-numpy-branch/pyvolution/util.py @ 7248

"""This module contains various auxiliary function used by pyvolution.

It is also a clearing house for functions that may later earn a module
of their own.
"""


import anuga.utilities.polygon
from warnings import warn



def file_function(filename,
                  domain = None,
                  quantities = None,
                  interpolation_points = None,
                  verbose = False,
                  use_cache = False):
    """Read time history of spatial data from NetCDF file and return
    a callable object.

    Input variables:
    
    filename - Name of sww or tms file
       
       If the file has extension 'sww' then it is assumed to be spatio-temporal
       or temporal and the callable object will have the form f(t,x,y) or f(t)
       depending on whether the file contains spatial data

       If the file has extension 'tms' then it is assumed to be temporal only
       and the callable object will have the form f(t)

       Either form will return interpolated values based on the input file
       using the underlying interpolation_function.

    domain - Associated domain object   
       If domain is specified, model time (domain.starttime)
       will be checked and possibly modified.
    
       All times are assumed to be in UTC
       
       All spatial information is assumed to be in absolute UTM coordinates.

    quantities - the name of the quantity to be interpolated or a
                 list of quantity names. The resulting function will return
                 a tuple of values - one for each quantity  

    interpolation_points - list of absolute UTM coordinates for points at
    which values are sought
    
    use_cache: True means that caching of intermediate result of
               Interpolation_function is attempted

    
    See Interpolation function for further documentation
    """


    if use_cache is True:
        try:
            from caching import cache
        except:
            msg = 'Caching was requested, but caching module'+\
                  'could not be imported'
            raise msg


        f = cache(_file_function,
                  filename,
                  {'domain': domain,
                   'quantities': quantities,
                   'interpolation_points': interpolation_points,
                   'verbose': verbose},
                  dependencies = [filename],
                  compression = False,
                  verbose = verbose)
        #FIXME (Ole): Pass cache arguments, such as compression, in some sort of
        #structure
        
    else:
        f = _file_function(filename,
                           domain,
                           quantities,
                           interpolation_points,
                           verbose)            

    return f



def _file_function(filename,
                   domain = None,
                   quantities = None,
                   interpolation_points = None,
                   verbose = False):
    """Internal function
    
    See file_function for documentatiton
    """
    

    #FIXME (OLE): Should check origin of domain against that of file
    #In fact, this is where origin should be converted to that of domain
    #Also, check that file covers domain fully.
    #If we use the suggested Point_set class for interpolation points
    #here it would be easier

    #Take into account:
    #- domain's georef
    #- sww file's georef
    #- interpolation points as absolute UTM coordinates


    assert type(filename) == type(''),\
               'First argument to File_function must be a string'

    try:
        fid = open(filename)
    except Exception, e:
        msg = 'File "%s" could not be opened: Error="%s"'\
                  %(filename, e)
        raise msg

    line = fid.readline()
    fid.close()

    if quantities is None: 
        if domain is not None:
            quantities = domain.conserved_quantities



    if line[:3] == 'CDF':
        return get_netcdf_file_function(filename, domain, quantities,
                                        interpolation_points,
                                        verbose = verbose)
    else:
        raise 'Must be a NetCDF File'



def get_netcdf_file_function(filename,
                             domain=None,
                             quantity_names=None,
                             interpolation_points=None,
                             verbose = False):
    """Read time history of spatial data from NetCDF sww file and
    return a callable object f(t,x,y)
    which will return interpolated values based on the input file.

    If domain is specified, model time (domain.starttime)
    will be checked and possibly modified
    
    All times are assumed to be in UTC

    See Interpolation function for further documetation
    
    """
    
    
    #FIXME: Check that model origin is the same as file's origin
    #(both in UTM coordinates)
    #If not - modify those from file to match domain
    #Take this code from e.g. dem2pts in data_manager.py
    #FIXME: Use geo_reference to read and write xllcorner...
        

    #FIXME: Maybe move caching out to this level rather than at the
    #Interpolation_function level (below)

    import time, calendar, types
    from config import time_format
    from Scientific.IO.NetCDF import NetCDFFile
    from Numeric import array, zeros, Float, alltrue, concatenate, reshape
    from anuga.utilities.numerical_tools import ensure_numeric    

    #Open NetCDF file
    if verbose: print 'Reading', filename
    fid = NetCDFFile(filename, 'r')

    if type(quantity_names) == types.StringType:
        quantity_names = [quantity_names]        
    
    if quantity_names is None or len(quantity_names) < 1:
        #If no quantities are specified get quantities from file
        #x, y, time are assumed as the independent variables so
        #they are excluded as potentiol quantities
        quantity_names = []
        for name in fid.variables.keys():
            if name not in ['x', 'y', 'time']:
                quantity_names.append(name)

    if len(quantity_names) < 1:                
        msg = 'ERROR: At least one independent value must be specified'
        raise msg


    if interpolation_points is not None:
        interpolation_points = ensure_numeric(interpolation_points, Float)



    #Now assert that requested quantitites (and the independent ones)
    #are present in file 
    missing = []
    for quantity in ['time'] + quantity_names:
        if not fid.variables.has_key(quantity):
            missing.append(quantity)

    if len(missing) > 0:
        msg = 'Quantities %s could not be found in file %s'\
              %(str(missing), filename)
        fid.close()
        raise msg

    #Decide whether this data has a spatial dimension
    spatial = True
    for quantity in ['x', 'y']:
        if not fid.variables.has_key(quantity):
            spatial = False

    if filename[-3:] == 'tms' and spatial is True:
        msg = 'Files of type tms must not contain spatial information'
        raise msg

    if filename[-3:] == 'sww' and spatial is False:
        msg = 'Files of type sww must contain spatial information'        
        raise msg        

    #Get first timestep
    try:
        starttime = fid.starttime[0]
    except ValueError:
        msg = 'Could not read starttime from file %s' %filename
        raise msg

    #Get variables
    if verbose: print 'Get variables'    
    time = fid.variables['time'][:]    

    if spatial:
        #Get origin
        xllcorner = fid.xllcorner[0]
        yllcorner = fid.yllcorner[0]
        zone = fid.zone[0]        

        x = fid.variables['x'][:]
        y = fid.variables['y'][:]
        triangles = fid.variables['volumes'][:]

        x = reshape(x, (len(x),1))
        y = reshape(y, (len(y),1))
        vertex_coordinates = concatenate((x,y), axis=1) #m x 2 array

        if interpolation_points is not None:
            #Adjust for georef
            interpolation_points[:,0] -= xllcorner
            interpolation_points[:,1] -= yllcorner        
        



    if domain is not None:
        #Update domain.startime if it is *earlier* than starttime
        if starttime > domain.starttime:
            msg = 'WARNING: Start time as specified in domain (%f)'\
                  %domain.starttime
            msg += ' is earlier than the starttime of file %s (%f).'\
                     %(filename, starttime)
            msg += ' Modifying domain starttime accordingly.'
            
            if verbose: print msg
            domain.starttime = starttime #Modifying model time
            if verbose: print 'Domain starttime is now set to %f'\
               %domain.starttime


        #If domain.startime is *later* than starttime,
        #move time back - relative to domain's time
        if domain.starttime > starttime:
            time = time - domain.starttime + starttime

        #FIXME Use method in geo to reconcile
        #if spatial:
        #assert domain.geo_reference.xllcorner == xllcorner
        #assert domain.geo_reference.yllcorner == yllcorner
        #assert domain.geo_reference.zone == zone        
        
    if verbose:
        print 'File_function data obtained from: %s' %filename
        print '  References:'
        #print '    Datum ....' #FIXME
        if spatial:
            print '    Lower left corner: [%f, %f]'\
                  %(xllcorner, yllcorner)
        print '    Start time:   %f' %starttime                
        
    
    #Produce values for desired data points at
    #each timestep

    quantities = {}
    for i, name in enumerate(quantity_names):
        quantities[name] = fid.variables[name][:]
    fid.close()
    

    from least_squares import Interpolation_function

    if not spatial:
        vertex_coordinates = triangles = interpolation_points = None         


    return Interpolation_function(time,
                                  quantities,
                                  quantity_names,
                                  vertex_coordinates,
                                  triangles,
                                  interpolation_points,
                                  verbose = verbose)





def multiple_replace(text, dictionary):
    """Multiple replace of words in text

    text:       String to be modified
    dictionary: Mapping of words that are to be substituted

    Python Cookbook 3.14 page 88 and page 90
    """

    import re
    
    #Create a regular expression from all of the dictionary keys
    #matching only entire words
    regex = re.compile(r'\b'+ \
                       r'\b|\b'.join(map(re.escape, dictionary.keys()))+ \
                       r'\b' )

    #For each match, lookup the corresponding value in the dictionary
    return regex.sub(lambda match: dictionary[match.group(0)], text)




def apply_expression_to_dictionary(expression, dictionary):#dictionary):
    """Apply arbitrary expression to values of dictionary

    Given an expression in terms of the keys, replace key by the
    corresponding values and evaluate.
   

    expression: Arbitrary, e.g. arithmetric, expression relating keys
                from dictionary. 

    dictionary: Mapping between symbols in expression and objects that
                will be evaluated by expression.
                Values in dictionary must support operators given in
                expression e.g. by overloading

    due to a limitation with Numeric, this can not evaluate 0/0
    In general, the user can fix by adding 1e-30 to the numerator.
    SciPy core can handle this situation.
    """

    import types
    import re

    assert isinstance(expression, basestring)
    assert type(dictionary) == types.DictType

    #Convert dictionary values to textual representations suitable for eval
    D = {}
    for key in dictionary:
        D[key] = 'dictionary["%s"]' %key

    #Perform substitution of variables    
    expression = multiple_replace(expression, D)

    #Evaluate and return
    try:
        return eval(expression)
    except NameError, e:
        msg = 'Expression "%s" could not be evaluated: %s' %(expression, e)
        raise NameError, msg
    except ValueError, e:
        msg = 'Expression "%s" could not be evaluated: %s' %(expression, e)
        raise ValueError, msg
    



####################################
####OBSOLETE STUFF


def angle(v):
    """Temporary Interface to new location"""

    import anuga.utilities.numerical_tools as NT        
    
    msg = 'angle has moved from util.py.  '
    msg += 'Please use "from anuga.utilities.numerical_tools import angle"'
    warn(msg, DeprecationWarning) 

    return NT.angle(v)
    
def anglediff(v0, v1):
    """Temporary Interface to new location"""

    import anuga.utilities.numerical_tools as NT
    
    msg = 'anglediff has moved from util.py.  '
    msg += 'Please use "from anuga.utilities.numerical_tools import anglediff"'
    warn(msg, DeprecationWarning) 

    return NT.anglediff(v0, v1)    

    
def mean(x):
    """Temporary Interface to new location"""

    import anuga.utilities.numerical_tools as NT    
    
    msg = 'mean has moved from util.py.  '
    msg += 'Please use "from anuga.utilities.numerical_tools import mean"'
    warn(msg, DeprecationWarning) 

    return NT.mean(x)    

def point_on_line(*args, **kwargs):
    """Temporary Interface to new location"""

    msg = 'point_on_line has moved from util.py.  '
    msg += 'Please use "from anuga.utilities.polygon import point_on_line"'
    warn(msg, DeprecationWarning) 

    return utilities.polygon.point_on_line(*args, **kwargs)     
    
def inside_polygon(*args, **kwargs):
    """Temporary Interface to new location"""

    print 'inside_polygon has moved from util.py.  ',
    print 'Please use "from anuga.utilities.polygon import inside_polygon"'

    return utilities.polygon.inside_polygon(*args, **kwargs)    
    
def outside_polygon(*args, **kwargs):
    """Temporary Interface to new location"""

    print 'outside_polygon has moved from util.py.  ',
    print 'Please use "from anuga.utilities.polygon import outside_polygon"'

    return utilities.polygon.outside_polygon(*args, **kwargs)    


def separate_points_by_polygon(*args, **kwargs):
    """Temporary Interface to new location"""

    print 'separate_points_by_polygon has moved from util.py.  ',
    print 'Please use "from anuga.utilities.polygon import separate_points_by_polygon"'

    return utilities.polygon.separate_points_by_polygon(*args, **kwargs)    



def read_polygon(*args, **kwargs):
    """Temporary Interface to new location"""

    print 'read_polygon has moved from util.py.  ',
    print 'Please use "from anuga.utilities.polygon import read_polygon"'

    return utilities.polygon.read_polygon(*args, **kwargs)    


def populate_polygon(*args, **kwargs):
    """Temporary Interface to new location"""

    print 'populate_polygon has moved from util.py.  ',
    print 'Please use "from anuga.utilities.polygon import populate_polygon"'

    return utilities.polygon.populate_polygon(*args, **kwargs)    

def read_xya(filename):
    """Read simple xya file, possibly with a header in the first line, just
    x y [attributes]
    separated by whitespace

    Format can be either ASCII or NetCDF

    Return list of points, list of attributes and
    attribute names if present otherwise None
    """
    print "read_xya is obsolete.  Use import_points_file from load_mesh.loadASCII"
    #FIXME: Probably obsoleted by similar function in load_ASCII
    #FIXME: Name read_data_points (or see 'load' in pylab)

    
    from load_mesh.loadASCII import import_points_file

    points_dict = import_points_file(filename)
    return points_dict['pointlist'], points_dict['attributelist']