Coverage for ion/core/object/cdm_methods/variables : 94.03%

#!/usr/bin/env python 

""" 

@file ion/core/object/cdm_methods/variables.py 

@brief Wrapper methods for the cdm variable object 

@author David Stuebe 

@author Tim LaRocque 

TODO: Implement get_intersecting... 

""" 

# Get the object decorator used on wrapper methods! 

from ion.core.object.object_utils import _gpb_source 

from ion.core.object.object_utils import OOIObjectError 

import ion.util.ionlog 

log = ion.util.ionlog.getLogger(__name__) 

from ion.core.object.cdm_methods import group 

from math import ceil 

#--------------------------------------# 

# Wrapper_Variable Specialized Methods # 

#--------------------------------------# 

@_gpb_source 

def _get_var_units(self): 

    """ 

    Specialized method for CDM Objects to retrieve the value of a variable object's 'units' attribute 

    """ 

    result = None 

    units = group._find_attribute_by_name(self, 'units') 

    if units is not None and len(units.array.value) > 0: 

        result = units.array.value[0] 

    # @attention: Sometimes (string) attribute values come back as unicode values..  we can provide 

    #             a trap here to convert them, but this may not be necessary.  Lets discuss [TPL] 

    return result 

@_gpb_source 

def _get_var_std_name(self): 

    """ 

    Specialized method for CDM Objects to retrieve the value of a variable object's 'standard_name' attribute 

    """ 

    result = None 

    name = group._find_attribute_by_name(self, 'standard_name') 

    if name is not None and len(name.array.value) > 0: 

        result = name.array.value[0] 

    # @attention: Sometimes (string) attribute values come back as unicode values..  we can provide 

    #             a trap here to convert them, but this may not be necessary.  Lets discuss [TPL] 

    return result 

@_gpb_source 

def _get_var_num_dims(self): 

    """ 

    Specialized method for CDM variables to retrieve its dimensionality 

    """ 

    return len(self.shape) 

@_gpb_source 

def _get_var_num_ba(self): 

    """ 

    Specialized method for CDM variables to retrieve the number of bounded arrays used in 

    defining this variables content 

    """ 

    return len(self.content.bounded_arrays) 

@_gpb_source 

def GetValue(self, *args): 

    """ 

    @Brief Get a value from an array structure by its indices 

    @param self - a cdm variable object 

    @param args - a list of integer indices for the value to extract 

    usage for a 3Dimensional variable: 

    as.getValue(1,3,9) 

    """ 

    # @todo: Need tests for multidim arrays 

    # @todo: Check the rank outside the for loop 

    # @todo: Check to make sure args are integers! 

    value = None 

    for ba in self.content.bounded_arrays: 

        for index, bounds in zip(args, ba.bounds): 

            if bounds.origin > index or index >= bounds.origin + bounds.size : 

                break 

        else: 

            # We now have the the ndarray of interest..  extract the value! 

            # Create a list of this bounded_array's sizes and use origin to determine 

            # the given indices position in the ndarray 

            indices = [] 

            shape = [] 

            for index, bounds in zip(args, ba.bounds): 

                  indices.append(index - bounds.origin) 

                  shape.append(bounds.size) 

            # Find the flattened index (make sure to apply the origin values as an offset!) 

            flattened_index = _flatten_index(indices, shape) 

            # Grab the value from the ndarray 

            value = ba.ndarray.value[flattened_index] 

            break 

    return value 

@_gpb_source 

def GetIntersectingBoundedArrays(self, bounded_array): 

    """ 

    @brief get the SHA1 id of the bounded arrays which intersect the give coverage. 

    @param self - a cdm variable object 

    @param bounded_array - a bounded array which specifies an index space coverage of interest 

    usage for a 3Dimensional variable: 

    as.getValue(1,3,9) 

    """ 

    # Get the MyId attribute of the bounded arrays that intersect - that will be the sha1 name for that BA... 

    sha1_list = [] 

    return sha1_list 

def _flatten_index(indices, shape): 

    """ 

    Uses the given indices representing a position in a multidimensional context to determine the 

    equivalent position in a flattened 1D array representation of that same nD context.  The 

    cardinality (also size) of each dimension in multidimensional space is given by "shape". 

    Note: This means that both "indices" and "shape" must be lists with the same rank (aka length.) 

    """ 

    assert(isinstance(indices, list)) 

    assert(isinstance(shape, list)) 

    assert(len(indices) == len(shape)) 

    result = 0 

    for i in range(len(indices)): 

        offset = 1 

        for j in range(i+1, len(shape)): 

            offset *= shape[j] 

        result += indices[i] * offset 

    return result 

def _unflatten_index(index, shape): 

    """ 

    Uses the given storage-flattened index to produce its equivalent multidimentional position (indices) 

    given the shape of the multidimensional space from which it was flattened. 

    """ 

    assert(isinstance(index, int)) 

    assert(isinstance(shape, list)) 

    assert(len(shape) > 0) 

    indices = [] 

    for x in range(len(shape)): 

        # Determine the significance of this dimension 

        sig = 1 

        for i in range(x+1, len(shape)): 

            sig *= shape[i] 

        # Determine this dimension's index for the flattened array index: 

        unflat = ceil(index / sig) 

        if unflat >= shape[x]: 

            unflat %= shape[x] 

        indices.append(unflat) 

    return indices 

""" 

#--------------------------- 

# Test a 1D dataset 

#--------------------------- 

from ion.services.coi.datastore_bootstrap.ion_preload_config import SAMPLE_DLY_DISCHARGE_DATASET_ID 

from ion.services.coi.resource_registry.resource_client import ResourceClient 

rc = ResourceClient() 

ds_d = rc.get_instance(SAMPLE_DLY_DISCHARGE_DATASET_ID) 

ds = ds_d.result.ResourceObject 

root = ds.root_group 

flow = root.FindVariableByName('streamflow') 

-------------------------------------------------------------------- 

from ion.core.object.cdm_methods.variables import GetValue 

for i in range(flow.content.bounded_arrays[0].bounds[0].size): 

    print GetValue(flow, i) 

#--------------------------- 

# Test a 3D/4D dataset 

#--------------------------- 

from ion.services.coi.datastore_bootstrap.ion_preload_config import SAMPLE_HYCOM_DATASET_ID 

from ion.services.coi.resource_registry.resource_client import ResourceClient 

rc = ResourceClient() 

ds_headers_d = rc.get_instance(SAMPLE_HYCOM_DATASET_ID) 

ds_slim = ds_headers_d.result.ResourceObject 

ds_d = ds_slim.Repository.checkout('master', excluded_types=[]) 

ds = ds_d.result.resource_object 

root = ds.root_group 

ssh = root.FindVariableByName('ssh') 

for dim in ssh.shape: 

    print str(dim.name) 

#-------------------------------------------------------------------- 

from ion.core.object.cdm_methods.variables import GetValue 

count = 1 

for bounds in ssh.content.bounded_arrays[0].bounds: 

    count *= bounds.size  

# All values iterated by bounds 

for i in range(ssh.content.bounded_arrays[0].bounds[0].size): 

    for j in range(ssh.content.bounded_arrays[0].bounds[1].size): 

        for k in range(ssh.content.bounded_arrays[0].bounds[2].size): 

            print '(%03i,%03i,%03i) = %s' % (i, j, k, str(ssh.GetValue(i, j, k))) 

# List a specific range of Sea Surface Height Values 

i = 0 

k = 174 

for j in range(ssh.content.bounded_arrays[0].bounds[1].size): 

    print '(%03i,%03i,%03i) = %s' % (i, j, k, str(ssh.GetValue(i, j, k))) 

# List a vertical column of values for temperature 

temp = root.FindVariableByName('layer_temperature') 

depth = root.FindDimensionByName('Layer') 

i = 0 

k = 100 

l = 200 

for j in range(depth.length): 

    print '(%03i,%03i,%03i,%03i) = %s' % (i, j, k, l, str(temp.GetValue(i, j, k, l))) 

"""