Housekeeping (closes #174)

- Remove obsolete directory "legacy"
- Remove obsolete branch "legacy"
- Order index functions consistently alphabetical
  in `setup.py`, `index_functions.py`, and `__init__.py`

CHANGELOG.md

@@ -7,6 +7,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+- Removed obsolete legacy directory
+- Removed obsolete legacy branch
+
+### Fixed
+
+### Security
+
+
 ## [0.12.0] - 2020-02-20
 
 ### Added

climix/index_functions/__init__.py

@@ -4,14 +4,14 @@ from .index_functions import (  # noqa: F401
     CountLevelCrossings,
     CountOccurrences,
     DiurnalTemperatureRange,
-    InterdayDiurnalTemperatureRange,
     ExtremeTemperatureRange,
     FirstOccurrence,
+    InterdayDiurnalTemperatureRange,
     LastOccurrence,
     Percentile,
     SpellLength,
     Statistics,
+    ThresholdedPercentile,
     ThresholdedStatistics,
-    ThresholdedPercentile,    
     TemperatureSum,
 )

climix/index_functions/index_functions.py

@@ -95,29 +95,6 @@ class ExtremeTemperatureRange(IndexFunction):
     lazy_func = call_func
 
 
-class InterdayDiurnalTemperatureRange(IndexFunction):
-    def __init__(self):
-        super().__init__(units=Unit('degree_Celsius'))
-
-    def prepare(self, input_cubes):
-        props = {(cube.dtype, cube.units, cube.standard_name)
-                 for cube in input_cubes.values()}
-        assert len(props) == 1
-        dtype, units, standard_name = props.pop()
-        assert units in [Unit('Kelvin'), Unit('degree_Celsius')]
-        super().prepare(input_cubes)
-
-    def call_func(self, data, axis, **kwargs):
-        res = np.absolute(np.diff(data['high_data'] -
-                                  data['low_data'], axis=axis)).mean(axis=axis)
-        return res.astype('float32')
-
-    def lazy_func(self, data, axis, **kwargs):
-        res = da.absolute(da.diff(data['high_data'] -
-                                  data['low_data'], axis=axis)).mean(axis=axis)
-        return res.astype('float32')
-
-
 class FirstOccurrence(ThresholdMixin, IndexFunction):
     def __init__(self, threshold, condition):
         super().__init__(threshold, condition, units=Unit('days'))
@@ -156,6 +133,29 @@ class FirstOccurrence(ThresholdMixin, IndexFunction):
         return collapsed_cube
 
 
+class InterdayDiurnalTemperatureRange(IndexFunction):
+    def __init__(self):
+        super().__init__(units=Unit('degree_Celsius'))
+
+    def prepare(self, input_cubes):
+        props = {(cube.dtype, cube.units, cube.standard_name)
+                 for cube in input_cubes.values()}
+        assert len(props) == 1
+        dtype, units, standard_name = props.pop()
+        assert units in [Unit('Kelvin'), Unit('degree_Celsius')]
+        super().prepare(input_cubes)
+
+    def call_func(self, data, axis, **kwargs):
+        res = np.absolute(np.diff(data['high_data'] -
+                                  data['low_data'], axis=axis)).mean(axis=axis)
+        return res.astype('float32')
+
+    def lazy_func(self, data, axis, **kwargs):
+        res = da.absolute(da.diff(data['high_data'] -
+                                  data['low_data'], axis=axis)).mean(axis=axis)
+        return res.astype('float32')
+
+
 class LastOccurrence(ThresholdMixin, IndexFunction):
     def __init__(self, threshold, condition):
         super().__init__(threshold, condition, units=Unit('days'))
@@ -196,6 +196,39 @@ class LastOccurrence(ThresholdMixin, IndexFunction):
         return collapsed_cube
 
 
+class Percentile(IndexFunction):
+    def __init__(self, percentiles, interpolation='linear'):
+        super().__init__(units=Unit('days'))
+        points = percentiles.points
+        assert np.all(points > 0)
+        assert np.all(points < 100)
+        self.percentiles = percentiles
+        self.interpolation = interpolation
+        self.units = '%'
+
+    def prepare(self, input_cubes):
+        super().prepare(input_cubes)
+        ref_cube = next(iter(input_cubes.values()))
+        self.standard_name = ref_cube.standard_name
+        self.units = ref_cube.units
+
+    def call_func(self, data, axis, **kwargs):
+        axis = normalize_axis(axis, data.ndim)
+        res = np.percentile(data, q=self.percentiles, axis=axis,
+                            interpolation=self.interpolation)
+        return res.astype('float32')
+
+    def lazy_func(self, data, axis, **kwargs):
+        axis = normalize_axis(axis, data.ndim)
+
+        def percentile(arr):
+            return np.percentile(arr,
+                                 q=self.percentiles.points,
+                                 interpolation=self.interpolation)
+        res = da.apply_along_axis(percentile, axis=axis, arr=data).squeeze()
+        return res.astype('float32')
+
+
 class SpellLength(ThresholdMixin, ReducerMixin, IndexFunction):
     def __init__(self, threshold, condition, reducer):
         super().__init__(threshold, condition, reducer, units=Unit('days'))
@@ -263,38 +296,15 @@ class Statistics(ReducerMixin, IndexFunction):
         return res.astype('float32')
 
 
-class ThresholdedStatistics(ThresholdMixin, ReducerMixin, IndexFunction):
-    def __init__(self, threshold, condition, reducer):
-        super().__init__(threshold, condition, reducer, units=Unit('days'))
-
-    def prepare(self, input_cubes):
-        super().prepare(input_cubes)
-        ref_cube = next(iter(input_cubes.values()))
-        self.standard_name = ref_cube.standard_name
-        self.units = ref_cube.units
-
-    def call_func(self, data, axis, **kwargs):
-        axis = normalize_axis(axis, data.ndim)
-        comb = self.condition(data, self.threshold.points)
-        res = self.reducer(np.ma.masked_where(~comb, data), axis=axis)
-        return res.astype('float32')
-
-    def lazy_func(self, data, axis, **kwargs):
-        axis = normalize_axis(axis, data.ndim)
-        comb = self.lazy_condition(data, self.threshold.points)
-        res = self.lazy_reducer(da.ma.masked_where(~comb, data), axis=axis)
-        return res.astype('float32')
-
-
-class Percentile(IndexFunction):
-    def __init__(self, percentiles, interpolation='linear'):
-        super().__init__(units=Unit('days'))
+class ThresholdedPercentile(ThresholdMixin, IndexFunction):
+    def __init__(self, threshold, condition,
+                 percentiles, interpolation='linear'):
+        super().__init__(threshold, condition)
         points = percentiles.points
         assert np.all(points > 0)
         assert np.all(points < 100)
         self.percentiles = percentiles
         self.interpolation = interpolation
-        self.units = '%'
 
     def prepare(self, input_cubes):
         super().prepare(input_cubes)
@@ -304,30 +314,33 @@ class Percentile(IndexFunction):
 
     def call_func(self, data, axis, **kwargs):
         axis = normalize_axis(axis, data.ndim)
-        res = np.percentile(data, q=self.percentiles, axis=axis,
+        mask = np.ma.getmaskarray(data).any(axis=axis)
+        comb = self.condition(data, self.threshold.points)
+        res = np.percentile(np.ma.masked_where(~comb, data),
+                            q=self.percentiles.points, axis=axis,
                             interpolation=self.interpolation)
+        res = np.ma.masked_array(da.ma.getdata(res), mask)
         return res.astype('float32')
 
     def lazy_func(self, data, axis, **kwargs):
         axis = normalize_axis(axis, data.ndim)
+        mask = da.ma.getmaskarray(data).any(axis=axis)
+        comb = self.condition(data, self.threshold.points)
 
         def percentile(arr):
             return np.percentile(arr,
                                  q=self.percentiles.points,
                                  interpolation=self.interpolation)
-        res = da.apply_along_axis(percentile, axis=axis, arr=data).squeeze()
+        res = da.apply_along_axis(
+            percentile, axis=axis,
+            arr=np.ma.masked_where(~comb, data)).squeeze()
+        res = da.ma.masked_array(da.ma.getdata(res), mask)
         return res.astype('float32')
 
 
-class ThresholdedPercentile(ThresholdMixin, IndexFunction):
-    def __init__(self, threshold, condition,
-                 percentiles, interpolation='linear'):
-        super().__init__(threshold, condition)
-        points = percentiles.points
-        assert np.all(points > 0)
-        assert np.all(points < 100)
-        self.percentiles = percentiles
-        self.interpolation = interpolation
+class ThresholdedStatistics(ThresholdMixin, ReducerMixin, IndexFunction):
+    def __init__(self, threshold, condition, reducer):
+        super().__init__(threshold, condition, reducer, units=Unit('days'))
 
     def prepare(self, input_cubes):
         super().prepare(input_cubes)
@@ -337,27 +350,14 @@ class ThresholdedPercentile(ThresholdMixin, IndexFunction):
 
     def call_func(self, data, axis, **kwargs):
         axis = normalize_axis(axis, data.ndim)
-        mask = np.ma.getmaskarray(data).any(axis=axis)
         comb = self.condition(data, self.threshold.points)
-        res = np.percentile(np.ma.masked_where(~comb, data),
-                            q=self.percentiles.points, axis=axis,
-                            interpolation=self.interpolation)
-        res = np.ma.masked_array(da.ma.getdata(res), mask)
+        res = self.reducer(np.ma.masked_where(~comb, data), axis=axis)
         return res.astype('float32')
 
     def lazy_func(self, data, axis, **kwargs):
         axis = normalize_axis(axis, data.ndim)
-        mask = da.ma.getmaskarray(data).any(axis=axis)
-        comb = self.condition(data, self.threshold.points)
-
-        def percentile(arr):
-            return np.percentile(arr,
-                                 q=self.percentiles.points,
-                                 interpolation=self.interpolation)
-        res = da.apply_along_axis(
-            percentile, axis=axis,
-            arr=np.ma.masked_where(~comb, data)).squeeze()
-        res = da.ma.masked_array(da.ma.getdata(res), mask)
+        comb = self.lazy_condition(data, self.threshold.points)
+        res = self.lazy_reducer(da.ma.masked_where(~comb, data), axis=axis)
         return res.astype('float32')
 
 

legacy/Precip_Sums.py

-import numpy as np
-
-import iris
-import iris.coords
-import iris.coord_categorisation
-
-from cf_units import Unit
-
-# from change_pr_units import change_pr_units
-
-# import pprint
-# import check_cubes
-
-var = 'pr'
-indir = '/home/rossby/imports/obs/UERRA/SURFEX-MESCAN/input/mon/'
-inroot = '_EUR-055_UERRA-HARMONIE_RegRean_v1d1-v1d2_SURFEX-MESCAN_v1_mon_*.nc'
-filename = '{}{}{}'.format(indir, var, inroot)
-
-cubelist = iris.load(filename)
-
-creation_date = ''
-tracking_id = ''
-for cube in cubelist:
-    creation_date += cube.attributes.pop('creation_date', None) + ' '
-    tracking_id += cube.attributes.pop('tracking_id', None) + ' '
-
-# pprint.pprint(check_cubes(.....))
-
-datacube = cubelist.concatenate()
-if len(datacube) > 1:
-    raise(TypeError)
-else:
-    datacube = datacube[0]
-
-f = np.diff(datacube.coords('time')[0].bounds) * 24 * 60 * 60
-datacube *= f[:, :, np.newaxis]
-datacube.units = Unit('mm')
-datacube.standard_name = 'lwe_thickness_of_precipitation_amount'
-datacube.attributes['creation_date'] = creation_date
-datacube.attributes['tracking_id'] = tracking_id
-
-iris.coord_categorisation.add_month_number(datacube, 'time', name='month')
-iris.coord_categorisation.add_year(datacube, 'time', name='year')
-
-Precip_sum_ANN = datacube.aggregated_by('year', iris.analysis.SUM)
-Precip_sum_ANN.long_name = u'Annual Total Precipitation'
-Precip_sum_ANN.var_name = u'Precip_sum_ANN'
-Precip_sum_ANN.remove_coord('month')
-
-c = Precip_sum_ANN.extract(iris.Constraint(
-    coord_values={'year': lambda cell: 1960 < cell < 1991}))
-Precip_sum_ANN_6190 = c.collapsed('year', iris.analysis.MEAN)
-
-c = datacube.extract(iris.Constraint(
-    coord_values={u'month': lambda cell: 3 < cell < 11}))
-Precip_sum_AMJJASO = c.aggregated_by('year', iris.analysis.SUM)
-Precip_sum_AMJJASO.long_name = u'April-October Total Precipitation'
-Precip_sum_AMJJASO.var_name = u'Precip_sum_AMJJASO'
-Precip_sum_AMJJASO.remove_coord('month')
-e = Precip_sum_AMJJASO.extract(iris.Constraint(
-    coord_values={'year': lambda cell: 1960 < cell < 1991}))
-Precip_sum_AMJJASO_6190 = e.collapsed('year', iris.analysis.MEAN)
-
-outdir = '/home/sm_lbarr/PROJ/B4EST/'
-outroot = '_EUR-055_UERRA-HARMONIE_RegRean_v1d1-v1d2_SURFEX-MESCAN_v1_ann_1961-2015.nc'
-
-iris.save(Precip_sum_ANN,
-          '{}{}{}'.format(outdir, 'Precip_sum_ANN', outroot))
-iris.save(Precip_sum_AMJJASO,
-          '{}{}{}'.format(outdir, 'Precip_sum_AMJJASO', outroot))
-
-iris.save(Precip_sum_ANN_6190,
-          '{}{}{}'.format(outdir, 'Precip_sum_ANN_6190', outroot))
-iris.save(Precip_sum_AMJJASO_6190,
-          '{}{}{}'.format(outdir, 'Precip_sum_AMJJASO_6190', outroot))

legacy/Tmean_Means.py

-# import pprint
-
-import iris
-import iris.coords
-import iris.coord_categorisation
-
-from cf_units import Unit
-
-# import check_cubes
-
-var = 'tas'
-indir = '/home/rossby/imports/obs/UERRA/SURFEX-MESCAN/input/mon/'
-inroot = '_EUR-055_UERRA-HARMONIE_RegRean_v1d1-v1d2_SURFEX-MESCAN_v1_mon_*.nc'
-filename = '{}{}{}'.format(indir, var, inroot)
-
-cubelist = iris.load(filename)
-
-creation_date = ''
-tracking_id = ''
-for cube in cubelist:
-    creation_date += cube.attributes.pop('creation_date', None) + ' '
-    tracking_id += cube.attributes.pop('tracking_id', None) + ' '
-
-# pprint.pprint(check_cubes(.....))
-
-datacube = cubelist.concatenate()
-if len(datacube) > 1:
-    raise(TypeError)
-else:
-    datacube = datacube[0]
-
-datacube.convert_units(Unit('degree_Celsius'))
-datacube.attributes['creation_date'] = creation_date
-datacube.attributes['tracking_id'] = tracking_id
-
-iris.coord_categorisation.add_month(datacube, 'time', name='month')
-iris.coord_categorisation.add_year(datacube, 'time', name='year')
-
-Tmean_ANN = datacube.aggregated_by('year', iris.analysis.MEAN)
-Tmean_ANN.long_name = u'Annual Mean Near-Surface Air Temperature'
-Tmean_ANN.var_name = u'Tmean_ANN'
-Tmean_ANN.remove_coord('month')
-c = Tmean_ANN.extract(iris.Constraint(
-    coord_values={'year': lambda cell: 1960 < cell < 1991}))
-Tmean_ANN_6190 = c.collapsed('year', iris.analysis.MEAN)
-
-Tmean_JAN = datacube.extract(iris.Constraint(coord_values={u'month': 'Jan'}))
-Tmean_JAN.long_name = u'January Mean Near-Surface Air Temperature'
-Tmean_JAN.var_name = u'Tmean_JAN'
-Tmean_JAN.remove_coord('month')
-c = Tmean_JAN.extract(iris.Constraint(
-    coord_values={'year': lambda cell: 1960 < cell < 1991}))
-Tmean_JAN_6190 = c.collapsed('year', iris.analysis.MEAN)
-
-Tmean_FEB = datacube.extract(iris.Constraint(coord_values={u'month': 'Feb'}))
-Tmean_FEB.long_name = u'February Mean Near-Surface Air Temperature'
-Tmean_FEB.var_name = u'Tmean_FEB'
-Tmean_FEB.remove_coord('month')
-c = Tmean_FEB.extract(iris.Constraint(
-    coord_values={'year': lambda cell: 1960 < cell < 1991}))
-Tmean_FEB_6190 = c.collapsed('year', iris.analysis.MEAN)
-
-Tmean_JUL = datacube.extract(iris.Constraint(coord_values={u'month': 'Jul'}))
-Tmean_JUL.long_name = u'July Mean Near-Surface Air Temperature'
-Tmean_JUL.var_name = u'Tmean_JUL'
-Tmean_JUL.remove_coord('month')
-c = Tmean_JUL.extract(iris.Constraint(
-    coord_values={'year': lambda cell: 1960 < cell < 1991}))
-Tmean_JUL_6190 = c.collapsed('year', iris.analysis.MEAN)
-
-Tmean_max = datacube.aggregated_by('year', iris.analysis.MAX)
-Tmean_min = datacube.aggregated_by('year', iris.analysis.MIN)
-Tmean_RANGE = Tmean_max - Tmean_min
-Tmean_RANGE.attributes = Tmean_ANN.attributes
-Tmean_RANGE.standard_name = u'air_temperature'
-Tmean_RANGE.long_name = u'Near-Surface Air Temperature Annual Range'
-Tmean_RANGE.var_name = u'Tmean_RANGE'
-Tmean_RANGE.units = Unit('degree_Celsius')
-Tmean_RANGE.remove_coord('month')
-Tmean_RANGE.cell_methods = (iris.coords.CellMethod(method='mean',
-                                                   coords='time',
-                                                   intervals='within month'),
-                            iris.coords.CellMethod(method='range',
-                                                   coords='time',
-                                                   intervals='within year'))
-c = Tmean_RANGE.extract(iris.Constraint(
-    coord_values={'year': lambda cell: 1960 < cell < 1991}))
-Tmean_RANGE_6190 = c.collapsed('year', iris.analysis.MEAN)
-
-outdir = '/home/sm_lbarr/PROJ/B4EST/'
-outroot = '_EUR-055_UERRA-HARMONIE_RegRean_v1d1-v1d2_SURFEX-MESCAN_v1_ann_1961-2015.nc'
-
-iris.save(Tmean_ANN, '{}{}{}'.format(outdir, 'Tmean_ANN', outroot))
-iris.save(Tmean_JAN, '{}{}{}'.format(outdir, 'Tmean_JAN', outroot))
-iris.save(Tmean_FEB, '{}{}{}'.format(outdir, 'Tmean_FEB', outroot))
-iris.save(Tmean_JUL, '{}{}{}'.format(outdir, 'Tmean_JUL', outroot))
-iris.save(Tmean_RANGE, '{}{}{}'.format(outdir, 'Tmean_RANGE', outroot))
-
-iris.save(Tmean_ANN_6190, '{}{}{}'.format(outdir, 'Tmean_ANN_6190', outroot))
-iris.save(Tmean_JAN_6190, '{}{}{}'.format(outdir, 'Tmean_JAN_6190', outroot))
-iris.save(Tmean_FEB_6190, '{}{}{}'.format(outdir, 'Tmean_FEB_6190', outroot))
-iris.save(Tmean_JUL_6190, '{}{}{}'.format(outdir, 'Tmean_JUL_6190', outroot))
-iris.save(Tmean_RANGE_6190, '{}{}{}'.format(outdir, 'Tmean_RANGE_6190', outroot))

legacy/Tmean_Veg.py

-import glob
-import numpy as np
-
-import iris
-import iris.coords
-import iris.coord_categorisation
-from iris.analysis import Aggregator
-from iris.util import rolling_window
-from cf_units import Unit
-
-MISSVAL = 1.0e20
-
-
-def veg_bounds(indata, axis, condition, start_end):
-    """
-    Args:
-    * indata (array):
-        thresholded (indicator) data.
-    * axis (int):
-        number of the array dimension mapping the time sequences.
-        (Can also be negative, e.g. '-1' means last dimension)
-    * condition (int):
-        minimum number of consecutive days to start the vegetation period.
-    * start_end (string):
-        "start" | "end" indicating which bound
-    """
-
-    se = start_end.lower()
-    if se.startswith('s'):
-        data = indata
-        s = True
-    elif se.startswith('e'):
-        data = np.flip(indata, axis=axis)
-        s = False
-    else:
-        raise RuntimeError("Argument start_end not understood <{}>."
-                           "".format(start_end))
-    if axis < 0:
-        # just cope with negative axis numbers
-        axis += indata.ndim
-
-    year_length = indata.shape[-1]
-    # Make an array with data values "windowed" along the time axis.
-    hit_windows = rolling_window(data, window=condition, axis=axis)
-    # Find the windows "full of True-s" (along the added 'window axis').
-    full_windows = np.all(hit_windows, axis=axis+1)
-    # Find first occurence fulfilling the condition (along the time axis).
-    doy = np.argmax(full_windows, axis=axis)
-    # mask gridcells where doy == 0 as a result of the condition not being met
-    ind = map(np.squeeze,
-              np.split(np.mgrid[:doy.shape[0], :doy.shape[1]], 2, 0)) + [doy]
-    mask = (~full_windows[ind]) | (doy > np.ceil(year_length / 2))
-    masked_doy = np.ma.masked_array(np.float32(doy), mask)
-    # convert to day of year in the interval 1..year_length
-    # for end calculations count from end of year
-    if s:
-        masked_doy = masked_doy + 1
-    else:
-        masked_doy = year_length - masked_doy
-    return masked_doy
-
-
-def veg_gdd(data, start, end):
-    doy = np.arange(data.shape[0]) + 1
-    dayix = doy[:, None, None]
-    L = (dayix < start[None, :, :]) | (dayix > end[None, :, :])
-    data.data[L] = 0.0
-    data.data = np.maximum(data.data - 5, 0.0)
-    gdd = data.collapsed('time', iris.analysis.SUM)
-    return gdd, data
-
-
-def main():
-    # Make an aggregator from the user function.
-    VEG_BOUNDS = Aggregator('veg_bounds',
-                            veg_bounds,
-                            units_func=lambda units: 1)
-
-    # Define the parameters of the index.
-    threshold_temperature = 5.0
-    consecutive_days = 4
-
-    var = 'tas'
-    indir = '/home/rossby/imports/obs/UERRA/SURFEX-MESCAN/input/day/'
-    inroot = '_EUR-055_UERRA-HARMONIE_RegRean_v1d1-v1d2_SURFEX-MESCAN_v1_day_*.nc'  # noqa
-    filepattern = '{}{}{}'.format(indir, var, inroot)
-    filelist = sorted(glob.glob(filepattern))
-
-    creation_date = ''
-    tracking_id = ''
-    vegStart = iris.cube.CubeList([])
-    vegEnd = iris.cube.CubeList([])
-    vegLen = iris.cube.CubeList([])
-    vegGDD = iris.cube.CubeList([])
-
-    for f in filelist:  # one file / year at the time ...
-        datacube = iris.load_cube(f)
-        creation_date += datacube.attributes.pop('creation_date', None) + ' '
-        tracking_id += datacube.attributes.pop('tracking_id', None) + ' '
-        datacube.convert_units(Unit('degC'))
-        iris.coord_categorisation.add_day_of_year(datacube, 'time', name='doy')
-        iris.coord_categorisation.add_year(datacube, 'time', name='year')
-        gtThreshold = datacube.copy()
-        gtThreshold.data = gtThreshold.data > threshold_temperature
-
-        Vstart = gtThreshold.collapsed('time', VEG_BOUNDS,
-                                       condition=consecutive_days,
-                                       start_end='start')
-
-        mask = np.ma.getmaskarray(Vstart.data)
-        # iris.util.mask_cube(Vstart, mask)
-        Vend = gtThreshold.collapsed('time', VEG_BOUNDS,
-                                     condition=consecutive_days,
-                                     start_end='end')
-        mask = mask | np.ma.getmaskarray(Vend.data)
-        Vend.data = np.ma.masked_array(Vend.data, mask)
-        # iris.util.mask_cube(Vend, mask)
-        Vlen = Vend - Vstart + 1
-        Vlen.data[mask] = 0
-        (Vgdd, testgdd) = veg_gdd(datacube.copy(), Vstart.data, Vend.data)
-        Vgdd.data[mask] = 0
-        Vstart.remove_coord('doy')
-        Vend.remove_coord('doy')
-        Vlen.remove_coord('doy')
-        Vgdd.remove_coord('doy')
-        Vstart.remove_coord('year')
-        Vend.remove_coord('year')
-        Vlen.remove_coord('year')
-        Vgdd.remove_coord('year')
-        vegStart.append(Vstart.copy())
-        vegEnd.append(Vend.copy())
-        vegLen.append(Vlen.copy())
-        vegGDD.append(Vgdd.copy())
-
-    dayVegStart5_ANN = vegStart.merge_cube()
-    dayVegStart5_ANN.units = Unit('days')
-    dayVegStart5_ANN._FillValue = MISSVAL
-    dayVegStart5_ANN.valid_min = 1.
-    dayVegStart5_ANN.valid_max = 183.
-    dayVegStart5_ANN.standard_name = None
-    dayVegStart5_ANN.long_name = u'Start of Vegetation Period (first 4 days above 5 degC)'  # noqa
-    dayVegStart5_ANN.var_name = u'dayVegStart5_ANN'
-    dayVegStart5_ANN.attributes = datacube.attributes
-    dayVegStart5_ANN.attributes['creation_date'] = creation_date
-    dayVegStart5_ANN.attributes['tracking_id'] = tracking_id
-
-    dayVegEnd5_ANN = vegEnd.merge_cube()
-    dayVegEnd5_ANN.units = Unit('days')
-    dayVegEnd5_ANN._FillValue = MISSVAL
-    dayVegEnd5_ANN.valid_min = 183.
-    dayVegEnd5_ANN.valid_max = 366.
-    dayVegEnd5_ANN.standard_name = None
-    dayVegEnd5_ANN.long_name = u'End of Vegetation Period (last 4 days above 5 degC)'  # noqa