Commit 7d299458 authored by Javier Vegas-Regidor's avatar Javier Vegas-Regidor
Browse files

Merge branch 'master' into 'production'


See merge request !51
parents 1598c138 4e617aee
......@@ -11,7 +11,7 @@ from earthdiagnostics.datafile import StorageStatus
from earthdiagnostics.diagnostic import Diagnostic
from earthdiagnostics.cmorizer import Cmorizer
from earthdiagnostics.datamanager import DataManager
from earthdiagnostics.frequency import Frequencies, Frequency
from earthdiagnostics.frequency import Frequencies
from earthdiagnostics.modelingrealm import ModelingRealms
from earthdiagnostics.utils import TempFile, Utils
from earthdiagnostics.variable import VariableType
# coding=utf-8
"""Compute the sea ice extent , area and volume in both hemispheres or a specified region"""
import os
import six
import numpy as np
import iris
import iris.analysis
......@@ -133,7 +133,7 @@ class Siasiesiv(Diagnostic):
handler.variables[self.sic_varname].coordinates = coordinates
sic = iris.load_cube(self.sic.local_file)
if sic.units.origin == '%' and < 2:
if sic.units.origin == '%' and < 2:
sic.units = '1.0'
sic *=
......@@ -181,17 +181,46 @@ class Siasiesiv(Diagnostic):
if not results:
self._save_file(results.merge_cube(), self.generated[var])
self._save_file(results.merge_cube(), var)
def _save_file(self, data, generated_file):
def _save_file(self, data, var):
generated_file = self.generated[var]
temp = TempFile.get()
region = data.coord('region').points
data.remove_coord('region'), temp, zlib=True)
Utils.rename_variable(temp, 'dim0', 'region', False)
handler = Utils.open_cdf(temp)
var = handler.createVariable('region2', str, ('region',))
var[...] = region
Utils.rename_variable(temp, 'region2', 'region', True)
if len(region) > 1:
Utils.rename_variable(temp, 'dim0', 'region', False)
handler = Utils.open_cdf(temp)
var = handler.createVariable('region2', str, ('region',))
var[...] = region
Utils.rename_variable(temp, 'region2', 'region', True)
handler = Utils.open_cdf(temp)
if 'region' not in handler.dimensions:
new_file = TempFile.get()
new_handler = Utils.open_cdf(new_file, 'w')
new_handler.createDimension('region', 1)
for dimension in handler.dimensions:
Utils.copy_dimension(handler, new_handler, dimension)
for variable in handler.variables.keys():
if variable in (var, 'region'):
Utils.copy_variable(handler, new_handler, variable)
old_var = handler.variables[var]
new_var = new_handler.createVariable(var, old_var.dtype, ('region',) + old_var.dimensions,
zlib=True, fill_value=1.0e20)
Utils.copy_attributes(new_var, old_var)
new_var[0, :] = old_var[:]
new_var = new_handler.createVariable('region', str, ('region',))
new_var[0] = region[0]
temp = new_file
......@@ -109,7 +109,7 @@ class Utils(object):
def rename_variable(filepath, old_name, new_name, must_exist=True):
def rename_variable(filepath, old_name, new_name, must_exist=True, rename_dimension=True):
Rename variable from a NetCDF file
......@@ -127,10 +127,10 @@ class Utils(object):
Utils.rename_variables(filepath, {old_name: new_name}, must_exist)
Utils.rename_variables(filepath, {old_name: new_name}, must_exist, rename_dimension)
def rename_variables(filepath, dic_names, must_exist=True):
def rename_variables(filepath, dic_names, must_exist=True, rename_dimension=True):
Rename multiple variables from a NetCDF file
......@@ -166,9 +166,11 @@ class Utils(object):
original = getattr(original_handler, attribute)
setattr(new_handler, attribute, Utils.convert_to_ascii_if_possible(original))
for dimension in original_handler.dimensions.keys():
Utils.copy_dimension(original_handler, new_handler, dimension, new_names=dic_names)
Utils.copy_dimension(original_handler, new_handler, dimension,
new_names=dic_names, rename_dimension=rename_dimension)
for variable in original_handler.variables.keys():
Utils.copy_variable(original_handler, new_handler, variable, new_names=dic_names)
Utils.copy_variable(original_handler, new_handler, variable,
new_names=dic_names, rename_dimension=rename_dimension)
......@@ -577,7 +579,8 @@ class Utils(object):
return netCDF4.num2date(nctime, units=units, calendar=cal_temps)
def copy_variable(source, destiny, variable, must_exist=True, add_dimensions=False, new_names=None):
def copy_variable(source, destiny, variable, must_exist=True, add_dimensions=False, new_names=None,
Copy the given variable from source to destiny
......@@ -608,14 +611,16 @@ class Utils(object):
if new_name in destiny.variables.keys():
translated_dimensions = Utils._translate(source.variables[variable].dimensions, new_names)
if rename_dimension:
translated_dimensions = Utils._translate(source.variables[variable].dimensions, new_names)
translated_dimensions = list(source.variables[variable].dimensions)
if not set(translated_dimensions).issubset(destiny.dimensions):
if not add_dimensions:
raise Exception('Variable {0} can not be added because dimensions does not match: '
'{1} {2}'.format(variable, translated_dimensions, destiny.dimensions))
for dimension in source.variables[variable].dimensions:
Utils.copy_dimension(source, destiny, dimension, must_exist, new_names)
Utils.copy_dimension(source, destiny, dimension, must_exist, new_names, rename_dimension)
if new_name in destiny.variables.keys():
# Just in case the variable we are copying match a dimension name
......@@ -646,7 +651,7 @@ class Utils(object):
for k in original_var.ncattrs() if k not in omitted_attributtes})
def copy_dimension(source, destiny, dimension, must_exist=True, new_names=None):
def copy_dimension(source, destiny, dimension, must_exist=True, new_names=None, rename_dimension=False):
Copy the given dimension from source to destiny, including dimension variables if present
......@@ -660,7 +665,7 @@ class Utils(object):
if not must_exist and dimension not in source.dimensions.keys():
if not new_names:
if not new_names or not rename_dimension:
new_names = dict()
if dimension in new_names:
new_name = new_names[dimension]
......@@ -672,7 +677,8 @@ class Utils(object):
new_name = dimension
destiny.createDimension(new_name, source.dimensions[dimension].size)
if dimension in source.variables:
Utils.copy_variable(source, destiny, dimension, new_names=new_names)
Utils.copy_variable(source, destiny, dimension,
new_names=new_names, rename_dimension=rename_dimension)
def concat_variables(source, destiny, remove_source=False):
......@@ -5,7 +5,6 @@ import datetime
import operator
import sys
import threading
import time
import traceback
# noinspection PyCompatibility
from concurrent.futures import ThreadPoolExecutor
......@@ -55,5 +55,7 @@ class TestUtils(TestCase):
with mock.patch('earthdiagnostics.utils.Utils.rename_variables') as rename_mock:
Utils.rename_variable('file', 'old', 'new')
Utils.rename_variable('file', 'old', 'new', False)
rename_mock.assert_has_calls(('file', {'old': 'new'}, True),'file', {'old': 'new'}, False)))
Utils.rename_variable('file', 'old', 'new', False, False)
rename_mock.assert_has_calls(('file', {'old': 'new'}, True, True),'file', {'old': 'new'}, False, True),'file', {'old': 'new'}, False, False)))
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