def myfunction(d, mx, mn):
from numpy.ma import maximum, minimum, absolute, greater, count
try:
if count(d) == 0: return mx, mn
mx = float(maximum(mx, float(maximum(d))))
mn = float(minimum(mn, float(minimum(d))))
except:
for i in d:
mx, mn = myfunction(i, mx, mn)
return mx, mn
def myfunction(d,mx,mn):
from numpy.ma import maximum,minimum,absolute,greater,count
try:
if count(d)==0 : return mx,mn
mx=float(maximum(mx,float(maximum(d))))
mn=float(minimum(mn,float(minimum(d))))
except:
for i in d:
mx,mn=myfunction(i,mx,mn)
return mx,mn
def myfunction(d, mx, mn):
from numpy.ma import maximum, minimum, masked_where, absolute, greater, count
try:
d = masked_where(greater(absolute(d), 9.9E19), d)
if count(d) == 0: return mx, mn
mx = float(maximum(mx, float(maximum(d))))
mn = float(minimum(mn, float(minimum(d))))
except:
for i in d:
mx, mn = myfunction(i, mx, mn)
return mx, mn
def myfunction(d,mx,mn):
from numpy.ma import maximum,minimum,masked_where,absolute,greater,count
try:
d=masked_where(greater(absolute(d),9.9E19),d)
if count(d)==0 : return mx,mn
mx=float(maximum(mx,float(maximum(d))))
mn=float(minimum(mn,float(minimum(d))))
except:
for i in d:
mx,mn=myfunction(i,mx,mn)
return mx,mn
def flux_limiter(
stage,
f_old,
Uf,
z):
"""Applies the flux (numerical and positivity) limiter to the
ith nominal flux matrix Uf, shape = (z1.N, z2.N)
inputs:
f_old -- (ndarray, dim=2) density from previous time step
CFL -- (instance) Courant numbers dictating phase space advection
Uf -- (ndarray, dim=2) the normalized flux (high order or not) used in the CS update
outputs:
Uf -- (ndarray, dim=2) final normalized flux for MC originating at prepoints[i,j]
after numerical and positivity limiter has been applied
Note: for a 768 x 1536 grid
the masked implementation here takes about 285 ms
the looped implementation over all i,j takes 3.85 s for the whole grid
for a 1536 x 3072 grid
the masked implementation here takes about 1.44 s
the looped implementation over all i,j takes 17.9 s for the whole grid
i.e. the computational savings is at least a factor of 10
"""
# local masked array (ma) copy of CFL.frac used to leave CFL.frac unchanged
Uf_ma = ma.array(z.CFL.frac[stage,:,:])
# mask negative values, keep positives
Uf_ma[z.CFL.numbers[stage,:,:] < 0] = ma.masked
# assign the mask to a zero matrix of same size for pairwise ma.minimum/maximum operations below
zeros = ma.zeros(Uf.shape)
zeros.mask = Uf_ma.mask
# operating only on positive values (negatives masked out)
Uf_pos = ma.minimum(ma.maximum(zeros, Uf), 1.0*f_old)
# mask positives, keep negatives
Uf_ma.mask = np.logical_not(Uf_ma.mask)
zeros.mask = Uf_ma.mask
#operating only on negative values
Uf_neg = ma.minimum(ma.maximum(-1.0*f_old, Uf), zeros)
# combine masked values in a single matrix Uf_final
Uf = np.where(Uf_neg.mask == False, Uf_neg.data, Uf_pos.data)
return Uf
def test_testMinMax2(self):
# Test of minimum, maximum.
assert_(eq(minimum([1, 2, 3], [4, 0, 9]), [1, 0, 3]))
assert_(eq(maximum([1, 2, 3], [4, 0, 9]), [4, 2, 9]))
x = arange(5)
y = arange(5) - 2
x[3] = masked
y[0] = masked
assert_(eq(minimum(x, y), where(less(x, y), x, y)))
assert_(eq(maximum(x, y), where(greater(x, y), x, y)))
assert_(minimum.reduce(x) == 0)
assert_(maximum.reduce(x) == 4)
def test_testMinMax2(self):
# Test of minimum, maximum.
assert_(eq(minimum([1, 2, 3], [4, 0, 9]), [1, 0, 3]))
assert_(eq(maximum([1, 2, 3], [4, 0, 9]), [4, 2, 9]))
x = arange(5)
y = arange(5) - 2
x[3] = masked
y[0] = masked
assert_(eq(minimum(x, y), where(less(x, y), x, y)))
assert_(eq(maximum(x, y), where(greater(x, y), x, y)))
assert_(minimum.reduce(x) == 0)
assert_(maximum.reduce(x) == 4)
def make_solution(case):
N, K = case
increasing = np.array(list(range(N)))
decreasing = np.array(increasing[::-1])
# status variables
free = np.ones(N, dtype=bool)
left = np.zeros(N, dtype=int)
right = np.zeros(N, dtype=int)
# init with initial distances
left[0:N] = increasing
right[0:N] = decreasing
for k in range(K):
# print("customer {}".format(k))
# mask with current occupancy status
left = ma.array(left, mask=~free)
right = ma.array(right, mask=~free)
#print("left",left)
#print("right", right)
mins = ma.minimum(left, right)
maxs = ma.maximum(left, right)
#print("mins", mins)
#print("maxs", maxs)
# candidates are all stalls where mins are maximal
max_mins = mins.max()
candidates = ma.where(mins == max_mins)[0]
#print(max_mins, candidates)
# from those candidates select the one where max is also maximal
selected = ma.argmax(maxs[candidates])
selected = candidates[selected]
#print(selected)
# occupy stall and update left and right
free[selected] = False
if selected > 0:
# left of selected, right distance has to be updated
right[0:selected] = ma.minimum(decreasing[-selected:], right[0:selected])
if selected < N -1:
# right of selected, left distance has to be updated
left[selected+1:] = ma.minimum(increasing[:N-selected -1], left[selected+1:])
if k == K -1:
return maxs[selected], mins[selected]
def __init__(self, MetricTable, opts):
epsilon = 0.0
if opts.cpu:
epsilon = 0.01
# Create empty ratio table
nprobs = MetricTable.nprobs
nsolvs = MetricTable.nsolvs
self.ratios = ma.zeros((nprobs, nsolvs), dtype=numpy.float)
# Compute best relative performance ratios across
# solvers for each problem
for prob in range(nprobs):
metrics = MetricTable.prob_mets(prob) + epsilon
best_met = ma.minimum(metrics)
self.ratios[prob,:] = metrics * (1.0 / best_met)
# Sort each solvers performance ratios
for solv in range(nsolvs):
self.ratios[:,solv] = ma.sort(self.ratios[:,solv])
# Compute largest ratio and use to replace failure entries
self.maxrat = ma.maximum(self.ratios)
self.ratios = ma.filled(self.ratios, 10 * self.maxrat)
def __init__(self, MetricTable):
# Create empty ratio table
nprobs = MetricTable.nprobs
nsolvs = MetricTable.nsolvs
self.ratios = ma.masked_array(1.0 * ma.zeros((nprobs + 1, nsolvs)))
# Compute best relative performance ratios across
# solvers for each problem
for prob in range(nprobs):
metrics = MetricTable.prob_mets(prob)
best_met = ma.minimum(metrics)
if (ma.count(metrics) == nsolvs
and ma.maximum(metrics) <= opts.minlimit):
self.ratios[prob + 1, :] = 1.0
else:
self.ratios[prob + 1, :] = metrics * (1.0 / best_met)
# Sort each solvers performance ratios
for solv in range(nsolvs):
self.ratios[:, solv] = ma.sort(self.ratios[:, solv])
# Compute largest ratio and use to replace failures entries
self.maxrat = ma.maximum(self.ratios)
self.ratios = ma.filled(self.ratios, 1.01 * self.maxrat)
def _breakList(self, inList, index, parameter):
par = float(parameter)
array = N.empty(shape=[len(inList),],dtype=N.float64)
i = 0
for parameters in inList:
array[i] = parameters[index]
i = i + 1
greater = MA.masked_less(array, par)
less = MA.masked_greater(array, par)
upper = MA.minimum(greater)
lower = MA.maximum(less)
upperArray = MA.masked_inside(array, par, upper)
lowerArray = MA.masked_inside(array, lower, par)
upperList = []
lowerList = []
i = 0
for parameters in inList:
if upperArray.mask[i]:
upperList.append(parameters)
if lowerArray.mask[i]:
lowerList.append(parameters)
i = i + 1
return upperList, lowerList
def __init__(self, MetricTable):
# Create empty ratio table
nprobs = MetricTable.nprobs
nsolvs = MetricTable.nsolvs
self.ratios = ma.masked_array(1.0 * ma.zeros((nprobs+1, nsolvs)))
# Compute best relative performance ratios across
# solvers for each problem
for prob in range(nprobs):
metrics = MetricTable.prob_mets(prob)
best_met = ma.minimum(metrics)
if (ma.count(metrics)==nsolvs and
ma.maximum(metrics)<=opts.minlimit):
self.ratios[prob+1,:] = 1.0;
else:
self.ratios[prob+1,:] = metrics * (1.0 / best_met)
# Sort each solvers performance ratios
for solv in range(nsolvs):
self.ratios[:,solv] = ma.sort(self.ratios[:,solv])
# Compute largest ratio and use to replace failures entries
self.maxrat = ma.maximum(self.ratios)
self.ratios = ma.filled(self.ratios, 1.01 * self.maxrat)
def test_testMinMax(self):
# Test minimum and maximum.
(x, y, a10, m1, m2, xm, ym, z, zm, xf, s) = self.d
xr = np.ravel(x) # max doesn't work if shaped
xmr = ravel(xm)
# true because of careful selection of data
self.assertTrue(eq(max(xr), maximum(xmr)))
self.assertTrue(eq(min(xr), minimum(xmr)))
def ln_shifted_auto(v):
"""If 'v' has values <= 0, it is shifted in a way that min(v)=1 before doing log.
Otherwise the log is done on the original 'v'."""
vmin = ma.minimum(v)
if vmin <= 0:
values = v - vmin + 1
else:
values = v
return ma.log(values)
def _train(self, blob_generator):
for blob in blob_generator:
if self.min is None or self.max is None:
self.min = blob.data
self.max = blob.data
else:
self.min = minimum(self.min, blob.data)
self.max = maximum(self.max, blob.data)
yield blob
def test_testMinMax(self):
# Test minimum and maximum.
(x, y, a10, m1, m2, xm, ym, z, zm, xf, s) = self.d
xr = np.ravel(x) # max doesn't work if shaped
xmr = ravel(xm)
# true because of careful selection of data
self.assertTrue(eq(max(xr), maximum(xmr)))
self.assertTrue(eq(min(xr), minimum(xmr)))
def ln_shifted_auto(v):
"""If 'v' has values <= 0, it is shifted in a way that min(v)=1 before doing log.
Otherwise the log is done on the original 'v'."""
vmin = ma.minimum(v)
if vmin <= 0:
values = v - vmin + 1
else:
values = v
return ma.log(values)
def _contour_args(self, *args):
if self.filled: fn = 'contourf'
else: fn = 'contour'
Nargs = len(args)
if Nargs <= 2:
z = ma.asarray(args[0], dtype=np.float64)
x, y = self._initialize_x_y(z)
elif Nargs <=4:
x,y,z = self._check_xyz(args[:3])
else:
raise TypeError("Too many arguments to %s; see help(%s)" % (fn,fn))
z = ma.masked_invalid(z, copy=False)
self.zmax = ma.maximum(z)
self.zmin = ma.minimum(z)
if self.logscale and self.zmin <= 0:
z = ma.masked_where(z <= 0, z)
warnings.warn('Log scale: values of z <=0 have been masked')
self.zmin = z.min()
self._auto = False
if self.levels is None:
if Nargs == 1 or Nargs == 3:
lev = self._autolev(z, 7)
else: # 2 or 4 args
level_arg = args[-1]
try:
if type(level_arg) == int:
lev = self._autolev(z, level_arg)
else:
lev = np.asarray(level_arg).astype(np.float64)
except:
raise TypeError(
"Last %s arg must give levels; see help(%s)" % (fn,fn))
if self.filled and len(lev) < 2:
raise ValueError("Filled contours require at least 2 levels.")
self.levels = lev
self._levels = list(self.levels)
if self.extend in ('both', 'min'):
self._levels.insert(0, min(self.levels[0],self.zmin) - 1)
if self.extend in ('both', 'max'):
self._levels.append(max(self.levels[-1],self.zmax) + 1)
self._levels = np.asarray(self._levels)
self.vmin = np.amin(self.levels) # alternative would be self.layers
self.vmax = np.amax(self.levels)
if self.extend in ('both', 'min'):
self.vmin = 2 * self.levels[0] - self.levels[1]
if self.extend in ('both', 'max'):
self.vmax = 2 * self.levels[-1] - self.levels[-2]
self.layers = self._levels # contour: a line is a thin layer
if self.filled:
self.layers = 0.5 * (self._levels[:-1] + self._levels[1:])
if self.extend in ('both', 'min'):
self.layers[0] = 0.5 * (self.vmin + self._levels[1])
if self.extend in ('both', 'max'):
self.layers[-1] = 0.5 * (self.vmax + self._levels[-2])
return (x, y, z)
def test_testScalarArithmetic(self):
xm = array(0, mask=1)
#TODO FIXME: Find out what the following raises a warning in r8247
with np.errstate(divide='ignore'):
assert_((1 / array(0)).mask)
assert_((1 + xm).mask)
assert_((-xm).mask)
assert_((-xm).mask)
assert_(maximum(xm, xm).mask)
assert_(minimum(xm, xm).mask)
assert_(xm.filled().dtype is xm._data.dtype)
x = array(0, mask=0)
assert_(x.filled() == x._data)
assert_equal(str(xm), str(masked_print_option))
def test_testScalarArithmetic(self):
xm = array(0, mask=1)
#TODO FIXME: Find out what the following raises a warning in r8247
with np.errstate(divide='ignore'):
assert_((1 / array(0)).mask)
assert_((1 + xm).mask)
assert_((-xm).mask)
assert_((-xm).mask)
assert_(maximum(xm, xm).mask)
assert_(minimum(xm, xm).mask)
assert_(xm.filled().dtype is xm._data.dtype)
x = array(0, mask=0)
assert_(x.filled() == x._data)
assert_equal(str(xm), str(masked_print_option))
def _process_args(self, *args, **kwargs):
"""
Process args and kwargs.
"""
if isinstance(args[0], QuadContourSet):
C = args[0].Cntr
if self.levels is None:
self.levels = args[0].levels
self.zmin = args[0].zmin
self.zmax = args[0].zmax
else:
x, y, z = self._contour_args(args, kwargs)
x0 = ma.minimum(x)
x1 = ma.maximum(x)
y0 = ma.minimum(y)
y1 = ma.maximum(y)
self.ax.update_datalim([(x0,y0), (x1,y1)])
self.ax.autoscale_view(tight=True)
_mask = ma.getmask(z)
if _mask is ma.nomask:
_mask = None
C = _cntr.Cntr(x, y, z.filled(), _mask)
self.Cntr = C
def _contour_args(self, args, kwargs):
if self.filled: fn = 'contourf'
else: fn = 'contour'
Nargs = len(args)
if Nargs <= 2:
z = ma.asarray(args[0], dtype=np.float64)
x, y = self._initialize_x_y(z)
args = args[1:]
elif Nargs <=4:
x,y,z = self._check_xyz(args[:3], kwargs)
args = args[3:]
else:
raise TypeError("Too many arguments to %s; see help(%s)" % (fn,fn))
z = ma.masked_invalid(z, copy=False)
self.zmax = ma.maximum(z)
self.zmin = ma.minimum(z)
if self.logscale and self.zmin <= 0:
z = ma.masked_where(z <= 0, z)
warnings.warn('Log scale: values of z <= 0 have been masked')
self.zmin = z.min()
self._contour_level_args(z, args)
return (x, y, z)
def _contour_args(self, *args):
if self.filled: fn = 'contourf'
else: fn = 'contour'
Nargs = len(args)
if Nargs <= 2:
z = ma.asarray(args[0], dtype=np.float64)
x, y = self._initialize_x_y(z)
elif Nargs <= 4:
x, y, z = self._check_xyz(args[:3])
else:
raise TypeError("Too many arguments to %s; see help(%s)" %
(fn, fn))
z = ma.masked_invalid(z, copy=False)
self.zmax = ma.maximum(z)
self.zmin = ma.minimum(z)
if self.logscale and self.zmin <= 0:
z = ma.masked_where(z <= 0, z)
warnings.warn('Log scale: values of z <=0 have been masked')
self.zmin = z.min()
self._auto = False
if self.levels is None:
if Nargs == 1 or Nargs == 3:
lev = self._autolev(z, 7)
else: # 2 or 4 args
level_arg = args[-1]
try:
if type(level_arg) == int:
lev = self._autolev(z, level_arg)
else:
lev = np.asarray(level_arg).astype(np.float64)
except:
raise TypeError(
"Last %s arg must give levels; see help(%s)" %
(fn, fn))
if self.filled and len(lev) < 2:
raise ValueError("Filled contours require at least 2 levels.")
self.levels = lev
return (x, y, z)
def _contour_args(self, *args):
if self.filled: fn = 'contourf'
else: fn = 'contour'
Nargs = len(args)
if Nargs <= 2:
z = ma.asarray(args[0], dtype=np.float64)
x, y = self._initialize_x_y(z)
elif Nargs <=4:
x,y,z = self._check_xyz(args[:3])
else:
raise TypeError("Too many arguments to %s; see help(%s)" % (fn,fn))
z = ma.masked_invalid(z, copy=False)
self.zmax = ma.maximum(z)
self.zmin = ma.minimum(z)
if self.logscale and self.zmin <= 0:
z = ma.masked_where(z <= 0, z)
warnings.warn('Log scale: values of z <=0 have been masked')
self.zmin = z.min()
self._auto = False
if self.levels is None:
if Nargs == 1 or Nargs == 3:
lev = self._autolev(z, 7)
else: # 2 or 4 args
level_arg = args[-1]
try:
if type(level_arg) == int:
lev = self._autolev(z, level_arg)
else:
lev = np.asarray(level_arg).astype(np.float64)
except:
raise TypeError(
"Last %s arg must give levels; see help(%s)" % (fn,fn))
if self.filled and len(lev) < 2:
raise ValueError("Filled contours require at least 2 levels.")
self.levels = lev
return (x, y, z)
def comp_g(
dert__
): # cross-comp of g in 2x2 kernels, between derts in ma.stack dert__
# initialize return variable
new_dert__ = ma.zeros(
(dert__.shape[0], dert__.shape[1] - 1, dert__.shape[2] - 1))
new_dert__.mask = True # initialize mask
ig__, idy__, idx__, gg__, dgy__, dgx__, mg__ = new_dert__ # assign 'views'. Use [:] to update views
# Unpack relevant params
g__, dy__, dx__ = dert__[[3, 4, 5]] # g, dy, dx -> local i, idy, idx
g__.data[np.where(
g__.data == 0
)] = 1 # replace 0 values with 1 to avoid error, not needed in high-g blobs?
'''
for all operations below: only mask kernels with more than one masked dert
'''
majority_mask = (
g__[:-1, :-1].mask.astype(int) + g__[:-1, 1:].mask.astype(int) +
g__[1:, 1:].mask.astype(int) + g__[1:, :-1].mask.astype(int)) > 1
g__.mask = dy__.mask = dx__.mask = majority_mask
g0__, dy0__, dx0__ = g__[:-1, :
-1].data, dy__[:-1, :
-1].data, dx__[:-1, :
-1].data # top left
g1__, dy1__, dx1__ = g__[:-1,
1:].data, dy__[:-1,
1:].data, dx__[:-1,
1:].data # top right
g2__, dy2__, dx2__ = g__[1:, 1:].data, dy__[1:, 1:].data, dx__[
1:, 1:].data # bottom right
g3__, dy3__, dx3__ = g__[1:, :-1].data, dy__[1:, :-1].data, dx__[
1:, :-1].data # bottom left
sin0__ = dy0__ / g0__
cos0__ = dx0__ / g0__
sin1__ = dy1__ / g1__
cos1__ = dx1__ / g1__
sin2__ = dy2__ / g2__
cos2__ = dx2__ / g2__
sin3__ = dy3__ / g3__
cos3__ = dx3__ / g3__
'''
cosine of difference between diagonally opposite angles, in vector representation
print(cos_da1__.shape, type(cos_da1__))
'''
cos_da0__ = (cos2__ * cos0__) + (sin2__ * sin0__
) # top left to bottom right
cos_da1__ = (cos3__ * cos1__) + (sin3__ * sin1__
) # top right to bottom left
dgy__[:] = ((g3__ + g2__) - (g0__ * cos_da0__ + g1__ * cos_da0__))
# y-decomposed cosine difference between gs
dgx__[:] = ((g1__ + g2__) - (g0__ * cos_da0__ + g3__ * cos_da1__))
# x-decomposed cosine difference between gs
gg__[:] = ma.hypot(dgy__, dgx__) # gradient of gradient
mg0__ = ma.minimum(g0__, g2__) * (cos_da1__ + 1) # +1 to make all positive
mg1__ = ma.minimum(g1__, g3__) * (cos_da1__ + 1)
mg__[:] = mg0__ + mg1__ # match of gradient
ig__[:] = g__[:-1, :
-1] # remove last row and column to align with derived params
idy__[:] = dy__[:-1, :-1]
idx__[:] = dx__[:-1, :-1] # -> idy, idx to compute cos for comp rg
# unnecessary?:
gg__.mask = mg__.mask = dgy__.mask = dgx__.mask = majority_mask
'''
next comp_rg will use g, dy, dx
next comp_gg will use gg, dgy, dgx
'''
return new_dert__ # new_dert__ has been updated along with 'view' arrays: ig__, idy__, idx__, gg__, dgy__, dgx__, mg__
def autoscale_None(self, A):
' autoscale only None-valued vmin or vmax'
if self.vmin is None: self.vmin = ma.minimum(A)
if self.vmax is None: self.vmax = ma.maximum(A)
def __init__(self, ax, *args, **kwargs):
"""
Draw contour lines or filled regions, depending on
whether keyword arg 'filled' is False (default) or True.
The first argument of the initializer must be an axes
object. The remaining arguments and keyword arguments
are described in ContourSet.contour_doc.
"""
self.ax = ax
self.levels = kwargs.get('levels', None)
self.filled = kwargs.get('filled', False)
self.linewidths = kwargs.get('linewidths', None)
self.linestyles = kwargs.get('linestyles', None)
self.alpha = kwargs.get('alpha', 1.0)
self.origin = kwargs.get('origin', None)
self.extent = kwargs.get('extent', None)
cmap = kwargs.get('cmap', None)
self.colors = kwargs.get('colors', None)
norm = kwargs.get('norm', None)
self.extend = kwargs.get('extend', 'neither')
self.antialiased = kwargs.get('antialiased', True)
self.nchunk = kwargs.get('nchunk', 0)
self.locator = kwargs.get('locator', None)
if (isinstance(norm, colors.LogNorm)
or isinstance(self.locator, ticker.LogLocator)):
self.logscale = True
if norm is None:
norm = colors.LogNorm()
if self.extend is not 'neither':
raise ValueError('extend kwarg does not work yet with log scale')
else:
self.logscale = False
if self.origin is not None: assert(self.origin in
['lower', 'upper', 'image'])
if self.extent is not None: assert(len(self.extent) == 4)
if cmap is not None: assert(isinstance(cmap, colors.Colormap))
if self.colors is not None and cmap is not None:
raise ValueError('Either colors or cmap must be None')
if self.origin == 'image': self.origin = mpl.rcParams['image.origin']
if isinstance(args[0], ContourSet):
C = args[0].Cntr
if self.levels is None:
self.levels = args[0].levels
else:
x, y, z = self._contour_args(*args)
x0 = ma.minimum(x)
x1 = ma.maximum(x)
y0 = ma.minimum(y)
y1 = ma.maximum(y)
self.ax.update_datalim([(x0,y0), (x1,y1)])
self.ax.autoscale_view()
_mask = ma.getmask(z)
if _mask is ma.nomask:
_mask = None
C = _cntr.Cntr(x, y, z.filled(), _mask)
self.Cntr = C
self._process_levels()
if self.colors is not None:
cmap = colors.ListedColormap(self.colors, N=len(self.layers))
if self.filled:
self.collections = cbook.silent_list('collections.PathCollection')
else:
self.collections = cbook.silent_list('collections.LineCollection')
self.labelTexts = []
self.labelCValues = []
kw = {'cmap': cmap}
if norm is not None:
kw['norm'] = norm
cm.ScalarMappable.__init__(self, **kw) # sets self.cmap;
self._process_colors()
if self.filled:
if self.linewidths is not None:
warnings.warn('linewidths is ignored by contourf')
lowers = self._levels[:-1]
uppers = self._levels[1:]
for level, level_upper in zip(lowers, uppers):
nlist = C.trace(level, level_upper, nchunk = self.nchunk)
nseg = len(nlist)//2
segs = nlist[:nseg]
kinds = nlist[nseg:]
paths = self._make_paths(segs, kinds)
col = collections.PathCollection(paths,
antialiaseds = (self.antialiased,),
edgecolors= 'none',
alpha=self.alpha)
self.ax.add_collection(col)
self.collections.append(col)
else:
tlinewidths = self._process_linewidths()
self.tlinewidths = tlinewidths
tlinestyles = self._process_linestyles()
for level, width, lstyle in zip(self.levels, tlinewidths, tlinestyles):
nlist = C.trace(level)
nseg = len(nlist)//2
segs = nlist[:nseg]
col = collections.LineCollection(segs,
linewidths = width,
linestyle = lstyle,
alpha=self.alpha)
col.set_label('_nolegend_')
self.ax.add_collection(col, False)
self.collections.append(col)
self.changed() # set the colors
def flux_limiter(
stage,
f_old,
Uf,
z
):
"""Applies the flux (numerical and positivity) limiter to the
ith nominal flux matrix Uf, shape = (z1.N, z2.N)
inputs:
f_old -- (ndarray, dim=2) density from previous time step
CFL -- (instance) Courant numbers dictating phase space advection
Uf -- (ndarray, dim=2) the normalized flux (high order or not) used in the CS update
outputs:
Uf -- (ndarray, dim=2) final normalized flux for MC originating at prepoints[i,j]
after numerical and positivity limiter has been applied
Note: for a 768 x 1536 grid
the masked implementation here takes about 285 ms
the looped implementation over all i,j takes 3.85 s for the whole grid
for a 1536 x 3072 grid
the masked implementation here takes about 1.44 s
the looped implementation over all i,j takes 17.9 s for the whole grid
i.e. the computational savings is at least a factor of 10
"""
# note that before we apply the limiter, there is no guarantee that sign(Uf) == sign(z.CFL.numbers)
# this is one of the functions of the limiter, to make these signs agree if the unlimited value of Uf
# has been unphysically flipped in sign. Recall that since f >= 0 by initial condition, sign(Uf) == sign(U)
# for all points f > 0, and where f = 0 then Uf = 0.0 and its role in remapping is to add zero contribution.
#
# here, U is the high order correction to z.CFL.frac, i.e.
#
# U = z.CFL.frac + high order terms
#
# there isn't a restriction on the size of each high order term or the sign. It is possible for
# the correction to cause sign(U) != sign(z.CFL.frac) which is not physical.
# Put in other words, this is unphysical because "if f[i] -> f[i+k] lies between grid points i+k and i+k+1, then
# the high order correction df keeps (f[i] + Uf[i]) should also between grid points i+k and i+k+1.
# if U suffers a sign reversal from the high order term contributions, this maps the density packet to
# outside the interval we know to zeroeth order it must lie in (z.CFL.frac gives the remap fraction to zereoth order)
# Finally, note that z.CFL.frac and z.CFL.number by construction have the same sign. We often prefer doing
# sign checks on z.CFL.numbers, but this is not of consequence.
# assign the mask to a zero matrix of same size for pairwise ma.minimum/maximum operations below
zeros = ma.zeros(Uf.shape)
zeros[z.CFL.numbers[stage,:,:] < 0] = ma.masked
# operating only on positive values (negatives masked out), assert the limiter criteria
# note: there is some decision making we let python make here (at the cost of slight efficiency, but at the benefit
# of less storage for local copies of the same arrays). Uf and f_old are ndarrays (not a masked arrays)
# however, having one masked object (here, the zeros array) is sufficient so that the ma.minimum and
# ma.maximum operations will act only on the unmasked entries of zeros and hence will pairwise operate on comparing
# minima and maximum for the nested objects that are compared.
Uf_pos = ma.minimum(ma.maximum(zeros, Uf), 1.0*f_old)
# mask positives, keep negatives
zeros.mask = np.logical_not(zeros.mask)
# operating only on negative values; see note just before U_pos calculation regarding how this operation
# plays out given f_old and Uf are unmasked and zeros is masked.
Uf_neg = ma.minimum(ma.maximum(-1.0*f_old, Uf), zeros)
# combine masked data that has been limited by the operations above
# into a final Uf object to return.
# Here, we can interpret the np.where call as "where Uf_neg is unmasked [i.e. is negative]
# insert the negative data at those entries in Uf, wherever there are masked values [i.e.
# corresponded to masked value], insert the positive data that has been limited at those
# [i,j] locations in Uf"
Uf = np.where(Uf_neg.mask == False, Uf_neg.data, Uf_pos.data)
return Uf
def get_development_constrained_capacity(self,
constraints,
dataset_pool,
index = None,
recompute_flag = False,
maximum_commercial_development_capacity = 4000000, ### TODO: Remove this default value and require this parameter.
maximum_industrial_development_capacity = 1200000, ### TODO: Remove this default value and require this parameter.
maximum_residential_development_capacity = 2800, ### TODO: Remove this default value and require this parameter.
):
"""
Truncate the development capacity to the range
min <= development capacity <= max, as defined by the given constraints.
"""
if (self.development_capacity <> None) and (not recompute_flag):
if (index <> None) and (index.size == self.development_capacity["index"].size) and \
alltrue(self.development_capacity["index"] == index):
return self.development_capacity
constraints.load_dataset_if_not_loaded()
attributes = remove_elements_with_matched_prefix_from_list(
constraints.get_attribute_names(), ["min", "max"])
attributes = remove_all(attributes, constraints.get_id_name()[0])
attributes_with_prefix = map(lambda attr: "urbansim.gridcell." +
attr, attributes)
self.compute_variables(attributes_with_prefix, dataset_pool=dataset_pool)
if index == None:
index = arange(self.size())
development_constraints_array = ones((constraints.size(),index.size), dtype=bool8)
for attr in attributes:
values = self.get_attribute_by_index(attr, index)
constr = reshape(constraints.get_attribute(attr), (constraints.size(),1))
constr = repeat(constr, index.size, axis=1)
tmp = logical_or(constr == values, constr < 0)
development_constraints_array = logical_and(development_constraints_array, tmp)
self.development_capacity = {
"commercial":zeros((index.size,2)),
"residential":zeros((index.size,2)),
"industrial":zeros((index.size,2)),
"index": index,
}
#reasonable maxima
self.development_capacity["commercial"][:,1] = maximum_commercial_development_capacity
self.development_capacity["industrial"][:,1] = maximum_industrial_development_capacity
self.development_capacity["residential"][:,1] = maximum_residential_development_capacity
for iconstr in range(constraints.size()):
w = where(development_constraints_array[iconstr,:])[0]
if w.size > 0:
self.development_capacity["commercial"][w,0] = \
maximum(self.development_capacity["commercial"][w,0], \
constraints.get_attribute_by_index("min_commercial_sqft", iconstr))
self.development_capacity["commercial"][w,1] = \
ma.minimum(self.development_capacity["commercial"][w,1], \
constraints.get_attribute_by_index("max_commercial_sqft", iconstr))
self.development_capacity["industrial"][w,0] = \
maximum(self.development_capacity["industrial"][w,0], \
constraints.get_attribute_by_index("min_industrial_sqft", iconstr))
self.development_capacity["industrial"][w,1] = \
ma.minimum(self.development_capacity["industrial"][w,1], \
constraints.get_attribute_by_index("max_industrial_sqft", iconstr))
self.development_capacity["residential"][w,0] = \
maximum(self.development_capacity["residential"][w,0], \
constraints.get_attribute_by_index("min_units", iconstr))
self.development_capacity["residential"][w,1] = \
ma.minimum(self.development_capacity["residential"][w,1], \
constraints.get_attribute_by_index("max_units", iconstr))
return self.development_capacity
def specify(self,slab,axes,specification,confined_by,aux):
''' First part: confine the slab within a Domain wide enough to do the exact in post'''
import string,copy
from numpy.ma import minimum,maximum
# myconfined is for later, we can't confine a dimension twice with an argument plus a keyword or 2 keywords
myconfined=[None]*len(axes)
self.aux=copy.copy(specification)
# First look at the arguments (i.e not keywords) and confine the dimensions
# in the order of the arguments
for i in range(len(self.args)):
if confined_by[i] is None : # Check it hasn't been confined by somebody else
myconfined[i]=1 # dim confined by argument list
confined_by[i]=self # for cdms I want to confine this dimension
self.aux[i]=specs=list(self.args[i]) # How do we want to confine this dim ?
if type(specs)==type(slice(0)):
specification[i]=specs # If it's a slicing nothing to do
else: # But if it's not...
if specs[0] is None:
tmp=axes[i].getBounds()
if tmp is None:
raise ValueError, 'Region error, axis:'+axes[i].id+' has no bounds'
specs[0]=minimum(minimum(tmp[0],tmp[-1]))
if specs[1] is None:
tmp=axes[i].getBounds()
if tmp is None:
raise ValueError, 'Region error, axis:'+axes[i].id+' has no bounds'
specs[1]=maximum(maximum(tmp[0],tmp[-1]))
if axes[i].isTime(): # Time is as always "Special"
import cdtime
tc=type(cdtime.comptime(0)) # component time type
tr=type(cdtime.reltime(0,'months since 0')) # relative time type
t=type(specs[0]) # my first spec type
if t==type(''): #if my first spec is passed as a string
specs[0]=cdtime.s2r(specs[0],axes[i].units)
elif t==tc or t==tr: #if my first spec is passed as a cdtime object
specs[0]=cdtime.torel(specs[0],axes[i].units)
else: # If not it has to be that the users knows the time values in the axis
pass
t=type(specs[1]) # my second spec type
if t==type(''): #if my second spec is passed as a string
specs[1]=cdtime.s2r(specs[1],axes[i].units)
elif t==tc or t==tr: #if my second spec is passed as a cdtime object
specs[1]=cdtime.torel(specs[1],axes[i].units)
sp=[specs[0],specs[1],'oob'] # Now retrieve the values wide enough for the exact specification[i]=sp # sets the specifications
else:
return 1
for kw in self.kargs.keys():
axis=None
for i in range(len(axes)):
if axes[i].id==kw : axis=i
if axis is None:
if kw=='time' :
for i in range(len(axes)):
if axes[i].isTime() : axis=i
elif kw=='level' :
for i in range(len(axes)):
if axes[i].isLevel() : axis=i
elif kw=='longitude' :
for i in range(len(axes)):
if axes[i].isLongitude() : axis=i
elif kw=='latitude' :
for i in range(len(axes)):
if axes[i].isLatitude() : axis=i
elif not kw in ['exact','atol','rtol']: # keyword not a recognised keyword or dimension name
raise 'Error, keyword: '+kw+' not recognized'
# At this point, if axis is None:
# we are dealing with a keyword for the selector
# so we'll skip it
if not axis is None :
if confined_by[axis] is None:
confined_by[axis]=self
myconfined[axis]=1
self.aux[axis]=specs=list(self.kargs[kw])
if type(specs)!=type(slice(0)):
if specs[0] is None:
tmp=axes[axis].getBounds()
if tmp is None:
raise ValueError, 'Region error, axis:'+axes[axis].id+' has no bounds'
specs[0]=minimum(minimum(tmp[0],tmp[-1]))
if specs[1] is None:
tmp=axes[axis].getBounds()
if tmp is None:
raise ValueError, 'Region error, axis:'+axes[axis].id+' has no bounds'
specs[1]=maximum(maximum(tmp[0],tmp[-1]))
if axes[axis].isTime():
import cdtime
tc=type(cdtime.comptime(0))
tr=type(cdtime.reltime(0,'months since 0'))
t=type(specs[0])
if t==type(''):
specs[0]=cdtime.s2r(specs[0],axes[i].units)
elif t==tc or t==tr:
specs[0]=cdtime.torel(specs[0],axes[i].units)
t=type(specs[1])
if t==type(''):
specs[1]=cdtime.s2r(specs[1],axes[i].units)
elif t==tc or t==tr:
specs[1]=cdtime.torel(specs[1],axes[i].units)
sp=[specs[0],specs[1],'oob']
specification[axis]=sp
else:
specification[axis]=specs
else:
if myconfined[axis]==1:
raise 'Error you are attempting to set the axis: '+str(axes[axis].id)+' more than once'
else:
return 1
return 0
def _contour_args(self, *args):
if self.filled: fn = 'contourf'
else: fn = 'contour'
Nargs = len(args)
if Nargs <= 2:
z = ma.asarray(args[0], dtype=np.float64)
x, y = self._initialize_x_y(z)
elif Nargs <=4:
x,y,z = self._check_xyz(args[:3])
else:
raise TypeError("Too many arguments to {0!s}; see help({1!s})".format(fn, fn))
self.zmax = ma.maximum(z)
self.zmin = ma.minimum(z)
if self.logscale and self.zmin <= 0:
z = ma.masked_where(z <= 0, z)
warnings.warn('Log scale: values of z <=0 have been masked')
self.zmin = z.min()
self._auto = False
if self.levels is None:
if Nargs == 1 or Nargs == 3:
lev = self._autolev(z, 7)
else: # 2 or 4 args
level_arg = args[-1]
try:
if type(level_arg) == int:
lev = self._autolev(z, level_arg)
else:
lev = np.asarray(level_arg).astype(np.float64)
except:
raise TypeError(
"Last {0!s} arg must give levels; see help({1!s})".format(fn, fn))
if self.filled and len(lev) < 2:
raise ValueError("Filled contours require at least 2 levels.")
# Workaround for cntr.c bug wrt masked interior regions:
#if filled:
# z = ma.masked_array(z.filled(-1e38))
# It's not clear this is any better than the original bug.
self.levels = lev
#if self._auto and self.extend in ('both', 'min', 'max'):
# raise TypeError("Auto level selection is inconsistent "
# + "with use of 'extend' kwarg")
self._levels = list(self.levels)
if self.extend in ('both', 'min'):
self._levels.insert(0, min(self.levels[0],self.zmin) - 1)
if self.extend in ('both', 'max'):
self._levels.append(max(self.levels[-1],self.zmax) + 1)
self._levels = np.asarray(self._levels)
self.vmin = np.amin(self.levels) # alternative would be self.layers
self.vmax = np.amax(self.levels)
if self.extend in ('both', 'min'):
self.vmin = 2 * self.levels[0] - self.levels[1]
if self.extend in ('both', 'max'):
self.vmax = 2 * self.levels[-1] - self.levels[-2]
self.layers = self._levels # contour: a line is a thin layer
if self.filled:
self.layers = 0.5 * (self._levels[:-1] + self._levels[1:])
if self.extend in ('both', 'min'):
self.layers[0] = 0.5 * (self.vmin + self._levels[1])
if self.extend in ('both', 'max'):
self.layers[-1] = 0.5 * (self.vmax + self._levels[-2])
return (x, y, z)
def autoscale(self, A):
'''
Set vmin, vmax to min, max of A.
'''
self.vmin = ma.minimum(A)
self.vmax = ma.maximum(A)
def create( self, parent=None, min=None, max=None, save_file=None, thread_it = 1, rate=None, bitrate=None, ffmpegoptions='' ):
from vcs import minmax
from numpy.ma import maximum,minimum
##from tkMessageBox import showerror
# Cannot "Run" or "Create" an animation while already creating an animation
if self.run_flg == 1: return
if self.vcs_self.canvas.creating_animation() == 1: return
if self.vcs_self.animate_info == []:
str = "No data found!"
showerror( "Error Message to User", str )
return
finish_queued_X_server_requests( self.vcs_self )
self.vcs_self.canvas.BLOCK_X_SERVER()
# Stop the (thread) execution of the X main loop (if it is running).
self.vcs_self.canvas.stopxmainloop( )
# Force VCS to update its orientation, needed when the user changes the
# VCS Canvas size.
self.vcs_self.canvas.updateorientation()
# Make sure the animate information is up-to-date for creating images
if ((self.gui_popup == 1) and (self.create_flg == 0)):
self.update_animate_display_list( )
# Save the min and max values for the graphics methods.
# Will need to restore values back when animation is done.
self.save_original_min_max()
# Set up the animation min and max values by changing the graphics method
# Note: cannot set the min and max values if the default graphics method is set.
do_min_max = 'yes'
try:
if (parent is not None) and (parent.iso_spacing == 'Log'):
do_min_max = 'no'
except:
pass
# Draw specified continental outlines if needed.
self.continents_hold_value = self.vcs_self.canvas.getcontinentstype( )
self.vcs_self.canvas.setcontinentstype( self.continents_value )
if ( do_min_max == 'yes' ):
minv = []
maxv=[]
if (min is None) or (max is None):
for i in range(len(self.vcs_self.animate_info)):
minv.append( 1.0e77 )
maxv.append( -1.0e77 )
for i in range(len(self.vcs_self.animate_info)):
dpy, slab = self.vcs_self.animate_info[i]
mins, maxs = minmax(slab)
minv[i] = float(minimum(float(minv[i]), float(mins)))
maxv[i] = float(maximum(float(maxv[i]), float(maxs)))
if isinstance(min,list) or isinstance(max,list):
for i in range(len(self.vcs_self.animate_info)):
try:
minv.append( min[i] )
except:
minv.append( min[-1] )
try:
maxv.append( max[i] )
except:
maxv.append( max[-1] )
else:
for i in range(len(self.vcs_self.animate_info)):
minv.append( min )
maxv.append( max )
# Set the min an max for each plot in the page. If the same graphics method is used
# to display the plots, then the last min and max setting of the data set will be used.
for i in range(len(self.vcs_self.animate_info)):
try:
self.set_animation_min_max( minv[i], maxv[i], i )
except Exception,err:
pass # if it is default, then you cannot set the min and max, so pass.
def create(self, parent=None, min=None, max=None, save_file=None,
thread_it=1, rate=None, bitrate=None, ffmpegoptions=''):
from vcs import minmax
from numpy.ma import maximum, minimum
# Cannot "Run" or "Create" an animation while already creating an
# animation
if self.run_flg == 1:
return
if self.vcs_self.canvas.creating_animation() == 1:
return
if self.vcs_self.animate_info == []:
str = "No data found!"
showerror("Error Message to User", str)
return
# Stop the (thread) execution of the X main loop (if it is running).
self.vcs_self.canvas.stopxmainloop()
# Force VCS to update its orientation, needed when the user changes the
# VCS Canvas size.
self.vcs_self.canvas.updateorientation()
# Make sure the animate information is up-to-date for creating images
if ((self.gui_popup == 1) and (self.create_flg == 0)):
self.update_animate_display_list()
# Save the min and max values for the graphics methods.
# Will need to restore values back when animation is done.
self.save_original_min_max()
# Set up the animation min and max values by changing the graphics method
# Note: cannot set the min and max values if the default graphics
# method is set.
do_min_max = 'yes'
try:
if (parent is not None) and (parent.iso_spacing == 'Log'):
do_min_max = 'no'
except:
pass
# Draw specified continental outlines if needed.
self.continents_hold_value = self.vcs_self.canvas.getcontinentstype()
self.vcs_self.canvas.setcontinentstype(self.continents_value)
if (do_min_max == 'yes'):
minv = []
maxv = []
if (min is None) or (max is None):
for i in range(len(self.vcs_self.animate_info)):
minv.append(1.0e77)
maxv.append(-1.0e77)
for i in range(len(self.vcs_self.animate_info)):
dpy, slab = self.vcs_self.animate_info[i]
mins, maxs = minmax(slab)
minv[i] = float(minimum(float(minv[i]), float(mins)))
maxv[i] = float(maximum(float(maxv[i]), float(maxs)))
if isinstance(min, list) or isinstance(max, list):
for i in range(len(self.vcs_self.animate_info)):
try:
minv.append(min[i])
except:
minv.append(min[-1])
try:
maxv.append(max[i])
except:
maxv.append(max[-1])
else:
for i in range(len(self.vcs_self.animate_info)):
minv.append(min)
maxv.append(max)
# Set the min an max for each plot in the page. If the same graphics method is used
# to display the plots, then the last min and max setting of the
# data set will be used.
for i in range(len(self.vcs_self.animate_info)):
try:
self.set_animation_min_max(minv[i], maxv[i], i)
except:
# if it is default, then you cannot set the min and max, so
# pass.
pass
if save_file is None or save_file.split('.')[-1].lower() == 'ras':
if thread_it:
thread.start_new_thread(
self.vcs_self.canvas.animate_init, (save_file,))
else:
self.vcs_self.canvas.animate_init(save_file)
else: # ffmpeg stuff
save_info = self.vcs_self.animate_info
animation_info = self.animate_info_from_python()
slabs = []
templates = []
dpys = []
for i in range(len(self.vcs_self.animate_info)):
dpy, slab = self.vcs_self.animate_info[i]
slabs.append(slab)
dpys.append(dpy)
templates.append(dpy.template)
sh = slabs[0].shape
if dpy.g_type in ['boxfill', 'isofill', 'isoline', 'meshfill',
'outfill', 'outline', 'taylordiagram', 'vector', ]:
r = len(sh) - 2
else:
r = len(sh) - 1
# now create the list of all previous indices to plot
indices = []
for i in range(r):
this = list(range(sh[i]))
tmp = []
if indices == []:
for k in this:
indices.append([k, ])
else:
for j in range(len(indices)):
for k in this:
tmp2 = copy.copy(indices[j])
tmp2.append(k)
tmp.append(tmp2)
indices = tmp
count = 1
white_square = self.vcs_self.createfillarea()
white_square.color = 240
white_square.x = [0, 1, 1, 0]
white_square.y = [0, 0, 1, 1]
new_vcs = self.vcs_self
if self.vcs_self.orientation() == 'portrait':
new_vcs.portrait()
# self.vcs_self.close()
for index in indices:
new_vcs.clear()
new_vcs.plot(white_square, bg=1)
for i in range(len(save_info)):
slab = slabs[i]
template = templates[i]
gtype = animation_info["gtype"][i].lower()
gname = animation_info["gname"][i]
gm = None # for flake8 to be happy
exec("gm = new_vcs.get%s('%s')" % (gtype, gname))
for j in index:
slab = slab[j]
new_vcs.plot(slab, gm, new_vcs.gettemplate(template), bg=1)
new_vcs.png("tmp_anim_%i" % count)
count += 1
new_vcs.ffmpeg(
save_file,
"tmp_anim_%d.png",
bitrate=bitrate,
rate=rate,
options=ffmpegoptions)
for i in range(count - 1):
os.remove("tmp_anim_%i.png" % (i + 1))
del(new_vcs)
self.create_flg = 1
def get_development_constrained_capacity(self,
constraints,
dataset_pool,
index = None,
recompute_flag = False,
maximum_commercial_development_capacity = 4000000, ### TODO: Remove this default value and require this parameter.
maximum_industrial_development_capacity = 1200000, ### TODO: Remove this default value and require this parameter.
maximum_residential_development_capacity = 2800, ### TODO: Remove this default value and require this parameter.
):
"""
Truncate the development capacity to the range
min <= development capacity <= max, as defined by the given constraints.
"""
if (self.development_capacity <> None) and (not recompute_flag):
if (index <> None) and (index.size == self.development_capacity["index"].size) and \
alltrue(self.development_capacity["index"] == index):
return self.development_capacity
constraints.load_dataset_if_not_loaded()
attributes = remove_elements_with_matched_prefix_from_list(
constraints.get_attribute_names(), ["min", "max"])
attributes = remove_all(attributes, constraints.get_id_name()[0])
attributes_with_prefix = map(lambda attr: "urbansim.gridcell." +
attr, attributes)
self.compute_variables(attributes_with_prefix, dataset_pool=dataset_pool)
if index == None:
index = arange(self.size())
development_constraints_array = ones((constraints.size(),index.size), dtype=bool8)
for attr in attributes:
values = self.get_attribute_by_index(attr, index)
constr = reshape(constraints.get_attribute(attr), (constraints.size(),1))
constr = repeat(constr, index.size, axis=1)
tmp = logical_or(constr == values, constr < 0)
development_constraints_array = logical_and(development_constraints_array, tmp)
self.development_capacity = {
"commercial":zeros((index.size,2)),
"residential":zeros((index.size,2)),
"industrial":zeros((index.size,2)),
"index": index,
}
#reasonable maxima
self.development_capacity["commercial"][:,1] = maximum_commercial_development_capacity
self.development_capacity["industrial"][:,1] = maximum_industrial_development_capacity
self.development_capacity["residential"][:,1] = maximum_residential_development_capacity
for iconstr in range(constraints.size()):
w = where(development_constraints_array[iconstr,:])[0]
if w.size > 0:
self.development_capacity["commercial"][w,0] = \
maximum(self.development_capacity["commercial"][w,0], \
constraints.get_attribute_by_index("min_commercial_sqft", iconstr))
self.development_capacity["commercial"][w,1] = \
ma.minimum(self.development_capacity["commercial"][w,1], \
constraints.get_attribute_by_index("max_commercial_sqft", iconstr))
self.development_capacity["industrial"][w,0] = \
maximum(self.development_capacity["industrial"][w,0], \
constraints.get_attribute_by_index("min_industrial_sqft", iconstr))
self.development_capacity["industrial"][w,1] = \
ma.minimum(self.development_capacity["industrial"][w,1], \
constraints.get_attribute_by_index("max_industrial_sqft", iconstr))
self.development_capacity["residential"][w,0] = \
maximum(self.development_capacity["residential"][w,0], \
constraints.get_attribute_by_index("min_units", iconstr))
self.development_capacity["residential"][w,1] = \
ma.minimum(self.development_capacity["residential"][w,1], \
constraints.get_attribute_by_index("max_units", iconstr))
return self.development_capacity
def create(self,
parent=None,
min=None,
max=None,
save_file=None,
thread_it=1,
rate=None,
bitrate=None,
ffmpegoptions=''):
from vcs import minmax
from numpy.ma import maximum, minimum
##from tkMessageBox import showerror
# Cannot "Run" or "Create" an animation while already creating an animation
if self.run_flg == 1: return
if self.vcs_self.canvas.creating_animation() == 1: return
if self.vcs_self.animate_info == []:
str = "No data found!"
showerror("Error Message to User", str)
return
finish_queued_X_server_requests(self.vcs_self)
self.vcs_self.canvas.BLOCK_X_SERVER()
# Stop the (thread) execution of the X main loop (if it is running).
self.vcs_self.canvas.stopxmainloop()
# Force VCS to update its orientation, needed when the user changes the
# VCS Canvas size.
self.vcs_self.canvas.updateorientation()
# Make sure the animate information is up-to-date for creating images
if ((self.gui_popup == 1) and (self.create_flg == 0)):
self.update_animate_display_list()
# Save the min and max values for the graphics methods.
# Will need to restore values back when animation is done.
self.save_original_min_max()
# Set up the animation min and max values by changing the graphics method
# Note: cannot set the min and max values if the default graphics method is set.
do_min_max = 'yes'
try:
if (parent is not None) and (parent.iso_spacing == 'Log'):
do_min_max = 'no'
except:
pass
# Draw specified continental outlines if needed.
self.continents_hold_value = self.vcs_self.canvas.getcontinentstype()
self.vcs_self.canvas.setcontinentstype(self.continents_value)
if (do_min_max == 'yes'):
minv = []
maxv = []
if (min is None) or (max is None):
for i in range(len(self.vcs_self.animate_info)):
minv.append(1.0e77)
maxv.append(-1.0e77)
for i in range(len(self.vcs_self.animate_info)):
dpy, slab = self.vcs_self.animate_info[i]
mins, maxs = minmax(slab)
minv[i] = float(minimum(float(minv[i]), float(mins)))
maxv[i] = float(maximum(float(maxv[i]), float(maxs)))
if isinstance(min, list) or isinstance(max, list):
for i in range(len(self.vcs_self.animate_info)):
try:
minv.append(min[i])
except:
minv.append(min[-1])
try:
maxv.append(max[i])
except:
maxv.append(max[-1])
else:
for i in range(len(self.vcs_self.animate_info)):
minv.append(min)
maxv.append(max)
# Set the min an max for each plot in the page. If the same graphics method is used
# to display the plots, then the last min and max setting of the data set will be used.
for i in range(len(self.vcs_self.animate_info)):
try:
self.set_animation_min_max(minv[i], maxv[i], i)
except Exception, err:
pass # if it is default, then you cannot set the min and max, so pass.
def autoscale(self, A):
"""
Set *vmin*, *vmax* to min, max of *A*.
"""
self.vmin = ma.minimum(A)
self.vmax = ma.maximum(A)
def autoscale(self, A):
'''
Set *vmin*, *vmax* to min, max of *A*.
'''
self.vmin = ma.minimum(A)
self.vmax = ma.maximum(A)
def plot_map(self,
dataset,
attribute_data,
min_value=None,
max_value=None,
file=None,
my_title="",
filter=None,
background=None):
""" Plots a 2D image of attribute given by 'name'. matplotlib required.
The dataset must have a method 'get_2d_attribute' defined that returns
a 2D array that is to be plotted. If min_value/max_value are given, all values
that are smaller/larger than these values are set to min_value/max_value.
Argument background is a value to be used for background. If it is not given,
it is considered as a 1/100 under the minimum value of the array.
Filter is a 2D array. Points where filter is > 0 are masked out (put into background).
"""
import matplotlib
matplotlib.use('Qt4Agg')
from matplotlib.pylab import jet, imshow, colorbar, show, axis, savefig, close, figure, title, normalize
from matplotlib.pylab import rot90
attribute_data = attribute_data[filter]
coord_2d_data = dataset.get_2d_attribute(attribute_data=attribute_data)
data_mask = coord_2d_data.mask
# if filter is not None:
# if isinstance(filter, ndarray):
# if not ma.allclose(filter.shape, coord_2d_data.shape):
# raise StandardError, "Argument filter must have the same shape as the 2d attribute."
# filter_data = filter
# else:
# raise TypeError, "The filter type is invalid. A character string or a 2D numpy array allowed."
# filter_data = where(ma.filled(filter_data,1) > 0, 1,0)
# data_mask = ma.mask_or(data_mask, filter_data)
nonmaskedmin = ma.minimum(coord_2d_data) - .2 * (
ma.maximum(coord_2d_data) - ma.minimum(coord_2d_data))
if max_value == None:
max_value = ma.maximum(coord_2d_data)
if min_value == None:
min_value = nonmaskedmin
coord_2d_data = ma.filled(coord_2d_data, min_value)
if background is None:
value_range = max_value - min_value
background = min_value - value_range / 100
coord_2d_data = ma.filled(
ma.masked_array(coord_2d_data, mask=data_mask), background)
# Our data uses NW as 0,0, while matplotlib uses SW for 0,0.
# Rotate the data so the map is oriented correctly.
coord_2d_data = rot90(coord_2d_data, 1)
jet()
figure()
norm = normalize(min_value, max_value)
im = imshow(
coord_2d_data,
origin='lower',
aspect='equal',
interpolation=None,
norm=norm,
)
tickfmt = '%4d'
if isinstance(min_value, float) or isinstance(max_value, float):
tickfmt = '%1.4f'
colorbar(format=tickfmt)
title(my_title)
axis('off')
if file:
savefig(file)
close()
else:
show()
def _contour_args(self, *args):
if self.filled: fn = 'contourf'
else: fn = 'contour'
Nargs = len(args)
if Nargs <= 2:
z = ma.asarray(args[0], dtype=np.float64)
x, y = self._initialize_x_y(z)
elif Nargs <= 4:
x, y, z = self._check_xyz(args[:3])
else:
raise TypeError("Too many arguments to %s; see help(%s)" %
(fn, fn))
self.zmax = ma.maximum(z)
self.zmin = ma.minimum(z)
if self.logscale and self.zmin <= 0:
z = ma.masked_where(z <= 0, z)
warnings.warn('Log scale: values of z <=0 have been masked')
self.zmin = z.min()
self._auto = False
if self.levels is None:
if Nargs == 1 or Nargs == 3:
lev = self._autolev(z, 7)
else: # 2 or 4 args
level_arg = args[-1]
try:
if type(level_arg) == int:
lev = self._autolev(z, level_arg)
else:
lev = np.asarray(level_arg).astype(np.float64)
except:
raise TypeError(
"Last %s arg must give levels; see help(%s)" %
(fn, fn))
if self.filled and len(lev) < 2:
raise ValueError("Filled contours require at least 2 levels.")
# Workaround for cntr.c bug wrt masked interior regions:
#if filled:
# z = ma.masked_array(z.filled(-1e38))
# It's not clear this is any better than the original bug.
self.levels = lev
#if self._auto and self.extend in ('both', 'min', 'max'):
# raise TypeError("Auto level selection is inconsistent "
# + "with use of 'extend' kwarg")
self._levels = list(self.levels)
if self.extend in ('both', 'min'):
self._levels.insert(0, min(self.levels[0], self.zmin) - 1)
if self.extend in ('both', 'max'):
self._levels.append(max(self.levels[-1], self.zmax) + 1)
self._levels = np.asarray(self._levels)
self.vmin = np.amin(self.levels) # alternative would be self.layers
self.vmax = np.amax(self.levels)
if self.extend in ('both', 'min'):
self.vmin = 2 * self.levels[0] - self.levels[1]
if self.extend in ('both', 'max'):
self.vmax = 2 * self.levels[-1] - self.levels[-2]
self.layers = self._levels # contour: a line is a thin layer
if self.filled:
self.layers = 0.5 * (self._levels[:-1] + self._levels[1:])
if self.extend in ('both', 'min'):
self.layers[0] = 0.5 * (self.vmin + self._levels[1])
if self.extend in ('both', 'max'):
self.layers[-1] = 0.5 * (self.vmax + self._levels[-2])
return (x, y, z)
def make_closea_masks(config=None,domcfg_file=None,mask=None):
#=========================
# 1. Read in domcfg file
#=========================
if config is None:
raise Exception('configuration must be specified')
if domcfg_file is None:
raise Exception('domain_cfg file must be specified')
if mask is None:
mask=False
domcfg = nc.Dataset(domcfg_file,'r+')
lon = domcfg.variables['nav_lon'][:]
lat = domcfg.variables['nav_lat'][:]
top_level = domcfg.variables['top_level'][0][:]
nx = top_level.shape[1]
ny = top_level.shape[0]
# Generate 2D "i" and "j" fields for use in "where" statements.
# These are the Fortran indices, counting from 1, so we have to
# add 1 to np.arange because python counts from 0.
ones_2d = np.ones((ny,nx))
ii1d = np.arange(nx)+1
jj1d = np.arange(ny)+1
ii2d = ii1d * ones_2d
jj2d = np.transpose(jj1d*np.transpose(ones_2d))
#=====================================
# 2. Closea definitions (old style)
#=====================================
# NB. The model i and j indices defined here are Fortran indices,
# ie. counting from 1 as in the NEMO code. Also the indices
# of the arrays (ncsi1 etc) count from 1 in order to match
# the Fortran code.
# This means that you can cut and paste the definitions from
# the NEMO code and change round brackets to square brackets.
# But BEWARE: Fortran array(a:b) == Python array[a:b+1] !!!
#
# If use_runoff_box = True then specify runoff area as all sea points within
# a rectangular area. If use_runoff_box = False then specify a list of points
# as in the old NEMO code. Default to false.
use_runoff_box = False
#================================================================
if config == 'ORCA2':
num_closea = 4
max_runoff_points = 4
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea (spread over globe)
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 11 ; ncsj1[1] = 103
ncsi2[1] = 17 ; ncsj2[1] = 112
# Great Lakes - North America - put at St Laurent mouth
ncsnr[2] = 1 ; ncstt[2] = 2
ncsi1[2] = 97 ; ncsj1[2] = 107
ncsi2[2] = 103 ; ncsj2[2] = 111
ncsir[2,1] = 110 ; ncsjr[2,1] = 111
# Black Sea (crossed by the cyclic boundary condition)
# put in Med Sea (north of Aegean Sea)
ncsnr[3:5] = 4 ; ncstt[3:5] = 2
ncsir[3:5,1] = 171; ncsjr[3:5,1] = 106
ncsir[3:5,2] = 170; ncsjr[3:5,2] = 106
ncsir[3:5,3] = 171; ncsjr[3:5,3] = 105
ncsir[3:5,4] = 170; ncsjr[3:5,4] = 105
# west part of the Black Sea
ncsi1[3] = 174 ; ncsj1[3] = 107
ncsi2[3] = 181 ; ncsj2[3] = 112
# east part of the Black Sea
ncsi1[4] = 2 ; ncsj1[4] = 107
ncsi2[4] = 6 ; ncsj2[4] = 112
#================================================================
elif config == 'eORCA1':
num_closea = 1
max_runoff_points = 1
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea (spread over the globe)
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 332 ; ncsj1[1] = 243
ncsi2[1] = 344 ; ncsj2[1] = 275
#================================================================
elif config == 'eORCA025_UK':
num_closea = 10
max_runoff_points = 1
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 1330 ; ncsj1[1] = 831
ncsi2[1] = 1375 ; ncsj2[1] = 981
# Aral Sea
ncsnr[2] = 1 ; ncstt[2] = 0
ncsi1[2] = 1376 ; ncsj1[2] = 900
ncsi2[2] = 1400 ; ncsj2[2] = 981
# Azov Sea
ncsnr[3] = 1 ; ncstt[3] = 0
ncsi1[3] = 1284 ; ncsj1[3] = 908
ncsi2[3] = 1304 ; ncsj2[3] = 933
# Lake Superior
ncsnr[4] = 1 ; ncstt[4] = 0
ncsi1[4] = 781 ; ncsj1[4] = 905
ncsi2[4] = 815 ; ncsj2[4] = 926
# Lake Michigan
ncsnr[5] = 1 ; ncstt[5] = 0
ncsi1[5] = 795 ; ncsj1[5] = 871
ncsi2[5] = 813 ; ncsj2[5] = 905
# Lake Huron part 1
ncsnr[6] = 1 ; ncstt[6] = 0
ncsi1[6] = 814 ; ncsj1[6] = 882
ncsi2[6] = 825 ; ncsj2[6] = 905
# Lake Huron part 2
ncsnr[7] = 1 ; ncstt[7] = 0
ncsi1[7] = 826 ; ncsj1[7] = 889
ncsi2[7] = 833 ; ncsj2[7] = 905
# Lake Erie
ncsnr[8] = 1 ; ncstt[8] = 0
ncsi1[8] = 816 ; ncsj1[8] = 871
ncsi2[8] = 837 ; ncsj2[8] = 881
# Lake Ontario
ncsnr[9] = 1 ; ncstt[9] = 0
ncsi1[9] = 831 ; ncsj1[9] = 882
ncsi2[9] = 847 ; ncsj2[9] = 889
# Lake Victoria
ncsnr[10] = 1 ; ncstt[10] = 0
ncsi1[10] = 1274 ; ncsj1[10] = 672
ncsi2[10] = 1289 ; ncsj2[10] = 687
#================================================================
elif config == 'eORCA025_UK_rnf':
num_closea = 10
max_runoff_points = 1
use_runoff_box = True
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir1 = np.zeros(num_closea+1,dtype=np.int) ; ncsjr1 = np.zeros(num_closea+1,dtype=np.int)
ncsir2 = np.zeros(num_closea+1,dtype=np.int) ; ncsjr2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 1330 ; ncsj1[1] = 831
ncsi2[1] = 1375 ; ncsj2[1] = 981
# Aral Sea
ncsnr[2] = 1 ; ncstt[2] = 0
ncsi1[2] = 1376 ; ncsj1[2] = 900
ncsi2[2] = 1400 ; ncsj2[2] = 981
# Azov Sea
ncsnr[3] = 1 ; ncstt[3] = 0
ncsi1[3] = 1284 ; ncsj1[3] = 908
ncsi2[3] = 1304 ; ncsj2[3] = 933
# Lake Superior
ncsnr[4] = 1 ; ncstt[4] = 1
ncsi1[4] = 781 ; ncsj1[4] = 905
ncsi2[4] = 815 ; ncsj2[4] = 926
# runff points the St Laurence Seaway for all Great Lakes
ncsir1[4:10] = 873 ; ncsjr1[4:10] = 909
ncsir2[4:10] = 884 ; ncsjr2[4:10] = 920
# Lake Michigan
ncsnr[5] = 1 ; ncstt[5] = 1
ncsi1[5] = 795 ; ncsj1[5] = 871
ncsi2[5] = 813 ; ncsj2[5] = 905
# Lake Huron part 1
ncsnr[6] = 1 ; ncstt[6] = 1
ncsi1[6] = 814 ; ncsj1[6] = 882
ncsi2[6] = 825 ; ncsj2[6] = 905
# Lake Huron part 2
ncsnr[7] = 1 ; ncstt[7] = 1
ncsi1[7] = 826 ; ncsj1[7] = 889
ncsi2[7] = 833 ; ncsj2[7] = 905
# Lake Erie
ncsnr[8] = 1 ; ncstt[8] = 1
ncsi1[8] = 816 ; ncsj1[8] = 871
ncsi2[8] = 837 ; ncsj2[8] = 881
# Lake Ontario
ncsnr[9] = 1 ; ncstt[9] = 1
ncsi1[9] = 831 ; ncsj1[9] = 882
ncsi2[9] = 847 ; ncsj2[9] = 889
# Lake Victoria
ncsnr[10] = 1 ; ncstt[10] = 0
ncsi1[10] = 1274 ; ncsj1[10] = 672
ncsi2[10] = 1289 ; ncsj2[10] = 687
#================================================================
elif config == 'eORCA025_UK_empmr':
num_closea = 10
max_runoff_points = 1
use_runoff_box = True
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir1 = np.zeros(num_closea+1,dtype=np.int) ; ncsjr1 = np.zeros(num_closea+1,dtype=np.int)
ncsir2 = np.zeros(num_closea+1,dtype=np.int) ; ncsjr2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 1330 ; ncsj1[1] = 831
ncsi2[1] = 1375 ; ncsj2[1] = 981
# Aral Sea
ncsnr[2] = 1 ; ncstt[2] = 0
ncsi1[2] = 1376 ; ncsj1[2] = 900
ncsi2[2] = 1400 ; ncsj2[2] = 981
# Azov Sea
ncsnr[3] = 1 ; ncstt[3] = 0
ncsi1[3] = 1284 ; ncsj1[3] = 908
ncsi2[3] = 1304 ; ncsj2[3] = 933
# Lake Superior
ncsnr[4] = 1 ; ncstt[4] = 2
ncsi1[4] = 781 ; ncsj1[4] = 905
ncsi2[4] = 815 ; ncsj2[4] = 926
# runff points the St Laurence Seaway for all Great Lakes
ncsir1[4:10] = 873 ; ncsjr1[4:10] = 909
ncsir2[4:10] = 884 ; ncsjr2[4:10] = 920
# Lake Michigan
ncsnr[5] = 1 ; ncstt[5] = 2
ncsi1[5] = 795 ; ncsj1[5] = 871
ncsi2[5] = 813 ; ncsj2[5] = 905
# Lake Huron part 1
ncsnr[6] = 1 ; ncstt[6] = 2
ncsi1[6] = 814 ; ncsj1[6] = 882
ncsi2[6] = 825 ; ncsj2[6] = 905
# Lake Huron part 2
ncsnr[7] = 1 ; ncstt[7] = 2
ncsi1[7] = 826 ; ncsj1[7] = 889
ncsi2[7] = 833 ; ncsj2[7] = 905
# Lake Erie
ncsnr[8] = 1 ; ncstt[8] = 2
ncsi1[8] = 816 ; ncsj1[8] = 871
ncsi2[8] = 837 ; ncsj2[8] = 881
# Lake Ontario
ncsnr[9] = 1 ; ncstt[9] = 2
ncsi1[9] = 831 ; ncsj1[9] = 882
ncsi2[9] = 847 ; ncsj2[9] = 889
# Lake Victoria
ncsnr[10] = 1 ; ncstt[10] = 0
ncsi1[10] = 1274 ; ncsj1[10] = 672
ncsi2[10] = 1289 ; ncsj2[10] = 687
#=====================================
# 3. Generate mask fields
#=====================================
rnf_count = 0
empmr_count = 0
closea_mask = ma.zeros(top_level.shape,dtype=np.int)
temp_mask_rnf = ma.zeros(top_level.shape,dtype=np.int)
temp_mask_empmr = ma.zeros(top_level.shape,dtype=np.int)
closea_mask_rnf = ma.zeros(top_level.shape,dtype=np.int)
closea_mask_empmr = ma.zeros(top_level.shape,dtype=np.int)
for ics in range(num_closea):
closea_mask = ma.where( ( ii2d[:] >= ncsi1[ics+1] ) & ( ii2d[:] <= ncsi2[ics+1] ) &
( jj2d[:] >= ncsj1[ics+1] ) & ( jj2d[:] <= ncsj2[ics+1] ) &
( top_level == 1 ), ics+1, closea_mask)
if ncstt[ics+1] == 1:
rnf_count = rnf_count + 1
temp_mask_rnf[:] = 0
if use_runoff_box:
temp_mask_rnf = ma.where( ( ii2d[:] >= ncsir1[ics+1] ) & ( ii2d[:] <= ncsir2[ics+1] ) &
( jj2d[:] >= ncsjr1[ics+1] ) & ( jj2d[:] <= ncsjr2[ics+1] ) &
( top_level == 1 ), rnf_count, 0)
else:
for ir in range(ncsnr[ics+1]):
temp_mask_rnf[ncsjr[ics+1],ncsjr[ics+1]] = rnf_count
temp_mask_rnf = ma.where( closea_mask_rnf > 0, ma.minimum(temp_mask_rnf,closea_mask_rnf), temp_mask_rnf)
min_rnf = ma.amin(temp_mask_rnf[ma.where(temp_mask_rnf > 0)])
max_rnf = ma.amax(temp_mask_rnf[ma.where(temp_mask_rnf > 0)])
if min_rnf != max_rnf:
print 'min_rnf, max_rnf : ',min_rnf,max_rnf
raise Exception('Partially overlapping target rnf areas for two closed seas.')
else:
# source area:
closea_mask_rnf[ma.where(closea_mask==ics+1)] = min_rnf
# target area:
closea_mask_rnf[ma.where(temp_mask_rnf>0)] = min_rnf
# reset rnf_count:
rnf_count = min_rnf
if ncstt[ics+1] == 2:
empmr_count = empmr_count + 1
temp_mask_empmr[:] = 0
if use_runoff_box:
temp_mask_empmr = ma.where( ( ii2d[:] >= ncsir1[ics+1] ) & ( ii2d[:] <= ncsir2[ics+1] ) &
( jj2d[:] >= ncsjr1[ics+1] ) & ( jj2d[:] <= ncsjr2[ics+1] ) &
( top_level == 1 ), empmr_count, 0)
else:
for ir in range(ncsnr[ics+1]):
temp_mask_empmr[ncsjr[ics+1],ncsjr[ics+1]] = empmr_count
temp_mask_empmr = ma.where( closea_mask_empmr > 0, ma.minimum(temp_mask_empmr,closea_mask_empmr), temp_mask_empmr)
min_empmr = ma.amin(temp_mask_empmr[ma.where(temp_mask_empmr > 0)])
max_empmr = ma.amax(temp_mask_empmr[ma.where(temp_mask_empmr > 0)])
if min_empmr != max_empmr:
raise Exception('Partially overlapping target empmr areas for two closed seas.')
else:
# source area:
closea_mask_empmr[ma.where(closea_mask==ics+1)] = min_empmr
# target area:
closea_mask_empmr[ma.where(temp_mask_empmr>0)] = min_empmr
# reset empmr_count:
empmr_count = min_empmr
if mask:
# apply land-sea mask if required
closea_mask.mask = np.where(top_level==0,True,False)
closea_mask_rnf.mask = np.where(top_level==0,True,False)
closea_mask_empmr.mask = np.where(top_level==0,True,False)
#=====================================
# 4. Append masks to domain_cfg file.
#=====================================
domcfg.createVariable('closea_mask',datatype='i',dimensions=('y','x'),fill_value=closea_mask.fill_value,chunksizes=(1000,1000))
domcfg.variables['closea_mask'][:]=closea_mask
if rnf_count > 0:
domcfg.createVariable('closea_mask_rnf',datatype='i',dimensions=('y','x'),fill_value=closea_mask_rnf.fill_value,chunksizes=(1000,1000))
domcfg.variables['closea_mask_rnf'][:]=closea_mask_rnf
if empmr_count > 0:
domcfg.createVariable('closea_mask_empmr',datatype='i',dimensions=('y','x'),fill_value=closea_mask_empmr.fill_value,chunksizes=(1000,1000))
domcfg.variables['closea_mask_empmr'][:]=closea_mask_empmr
domcfg.close()
def specify(self, slab, axes, specification, confined_by, aux):
''' First part: confine the slab within a Domain wide enough to do the exact in post'''
import string, copy
from numpy.ma import minimum, maximum
# myconfined is for later, we can't confine a dimension twice with an argument plus a keyword or 2 keywords
myconfined = [None] * len(axes)
self.aux = copy.copy(specification)
# First look at the arguments (i.e not keywords) and confine the dimensions
# in the order of the arguments
for i in range(len(self.args)):
if confined_by[
i] is None: # Check it hasn't been confined by somebody else
myconfined[i] = 1 # dim confined by argument list
confined_by[
i] = self # for cdms I want to confine this dimension
self.aux[i] = specs = list(
self.args[i]) # How do we want to confine this dim ?
if type(specs) == type(slice(0)):
specification[i] = specs # If it's a slicing nothing to do
else: # But if it's not...
if specs[0] is None:
tmp = axes[i].getBounds()
if tmp is None:
raise ValueError, 'Region error, axis:' + axes[
i].id + ' has no bounds'
specs[0] = minimum(minimum(tmp[0], tmp[-1]))
if specs[1] is None:
tmp = axes[i].getBounds()
if tmp is None:
raise ValueError, 'Region error, axis:' + axes[
i].id + ' has no bounds'
specs[1] = maximum(maximum(tmp[0], tmp[-1]))
if axes[i].isTime(): # Time is as always "Special"
import cdtime
tc = type(cdtime.comptime(0)) # component time type
tr = type(cdtime.reltime(
0, 'months since 0')) # relative time type
t = type(specs[0]) # my first spec type
if t == type(
''): #if my first spec is passed as a string
specs[0] = cdtime.s2r(specs[0], axes[i].units)
elif t == tc or t == tr: #if my first spec is passed as a cdtime object
specs[0] = cdtime.torel(specs[0], axes[i].units)
else: # If not it has to be that the users knows the time values in the axis
pass
t = type(specs[1]) # my second spec type
if t == type(
''): #if my second spec is passed as a string
specs[1] = cdtime.s2r(specs[1], axes[i].units)
elif t == tc or t == tr: #if my second spec is passed as a cdtime object
specs[1] = cdtime.torel(specs[1], axes[i].units)
sp = [
specs[0], specs[1], 'oob'
] # Now retrieve the values wide enough for the exact specification[i]=sp # sets the specifications
else:
return 1
for kw in self.kargs.keys():
axis = None
for i in range(len(axes)):
if axes[i].id == kw: axis = i
if axis is None:
if kw == 'time':
for i in range(len(axes)):
if axes[i].isTime(): axis = i
elif kw == 'level':
for i in range(len(axes)):
if axes[i].isLevel(): axis = i
elif kw == 'longitude':
for i in range(len(axes)):
if axes[i].isLongitude(): axis = i
elif kw == 'latitude':
for i in range(len(axes)):
if axes[i].isLatitude(): axis = i
elif not kw in [
'exact', 'atol', 'rtol'
]: # keyword not a recognised keyword or dimension name
raise 'Error, keyword: ' + kw + ' not recognized'
# At this point, if axis is None:
# we are dealing with a keyword for the selector
# so we'll skip it
if not axis is None:
if confined_by[axis] is None:
confined_by[axis] = self
myconfined[axis] = 1
self.aux[axis] = specs = list(self.kargs[kw])
if type(specs) != type(slice(0)):
if specs[0] is None:
tmp = axes[axis].getBounds()
if tmp is None:
raise ValueError, 'Region error, axis:' + axes[
axis].id + ' has no bounds'
specs[0] = minimum(minimum(tmp[0], tmp[-1]))
if specs[1] is None:
tmp = axes[axis].getBounds()
if tmp is None:
raise ValueError, 'Region error, axis:' + axes[
axis].id + ' has no bounds'
specs[1] = maximum(maximum(tmp[0], tmp[-1]))
if axes[axis].isTime():
import cdtime
tc = type(cdtime.comptime(0))
tr = type(cdtime.reltime(0, 'months since 0'))
t = type(specs[0])
if t == type(''):
specs[0] = cdtime.s2r(specs[0], axes[i].units)
elif t == tc or t == tr:
specs[0] = cdtime.torel(
specs[0], axes[i].units)
t = type(specs[1])
if t == type(''):
specs[1] = cdtime.s2r(specs[1], axes[i].units)
elif t == tc or t == tr:
specs[1] = cdtime.torel(
specs[1], axes[i].units)
sp = [specs[0], specs[1], 'oob']
specification[axis] = sp
else:
specification[axis] = specs
else:
if myconfined[axis] == 1:
raise 'Error you are attempting to set the axis: ' + str(
axes[axis].id) + ' more than once'
else:
return 1
return 0
def _plot_with_flag(self, scan, showflag=False):
# total number of panles to plot as a whole
nptot = scan.nrow()
# remaining panels to plot
n = nptot - self._ipanel - 1
ganged = False
maxpanel = 25
if n > 1:
ganged = rcParams['plotter.ganged']
if self._rows and self._cols:
n = min(n,self._rows*self._cols)
self._plotter.set_panels(rows=self._rows,cols=self._cols,
nplots=n,margin=self._margins,ganged=ganged)
else:
n = min(n,maxpanel)
self._plotter.set_panels(rows=n,cols=0,nplots=n,margin=self._margins,ganged=ganged)
else:
self._plotter.set_panels(margin=self._margins)
#r = 0
r = self._startrow
# total row number of scantable
nr = scan.nrow()
panelcount = 0
allylim = []
allxlim = []
while r < nr:
# always plot to new panel
self._plotter.subplot(panelcount)
self._plotter.palette(0)
# title and axes labels
xlab = self._abcissa and self._abcissa[panelcount] \
or scan._getabcissalabel()
if self._offset and not self._abcissa:
xlab += " (relative)"
ylab = self._ordinate and self._ordinate[panelcount] \
or scan._get_ordinate_label()
self._plotter.set_axes('xlabel', xlab)
self._plotter.set_axes('ylabel', ylab)
lbl = self._get_label(scan, r, mode='title', userlabel=self._title)
if type(lbl) in (list, tuple):
if 0 <= panelcount < len(lbl):
lbl = lbl[panelcount]
else:
# get default label
lbl = self._get_label(scan, r, 'title')
self._plotter.set_axes('title',lbl)
panelcount += 1
# Now get data to plot
y = scan._getspectrum(r)
# Check for FLAGROW column
mr = scan._getflagrow(r)
from numpy import ma, array
if mr:
ys = ma.masked_array(y,mask=mr)
if showflag:
yf = ma.masked_array(y, mask=(not mr))
else:
m = scan._getmask(r)
from numpy import logical_not, logical_and
if self._maskselection and len(self._usermask) == len(m):
if d[self._stacking](r) in self._maskselection[self._stacking]:
m = logical_and(m, self._usermask)
ys = ma.masked_array(y,mask=logical_not(array(m,copy=False)))
if showflag:
yf = ma.masked_array(y,mask=m)
x = array(scan._getabcissa(r))
if self._offset:
x += self._offset
#llbl = self._get_label(scan, r, mode='legend', userlabel=self._lmap)
#if type(llbl) in (list, tuple):
# llbl = llbl[0]
#self._plotter.set_line(label=llbl)
self._plotter.set_line(label="data")
#plotit = self._plotter.plot
#if self._hist: plotit = self._plotter.hist
self._plotter.plot(x,ys)
if showflag:
self._plotter.set_line(label="flagged")
self._plotter.plot(x,yf)
ylim = self._minmaxy or [min(y),max(y)]
xlim= self._minmaxx or [min(x),max(x)]
elif mr or ys.mask.all():
ylim = self._minmaxy or []
xlim = self._minmaxx or []
else:
ylim = self._minmaxy or [ma.minimum(ys),ma.maximum(ys)]
xlim= self._minmaxx or [min(x),max(x)]
allylim += ylim
allxlim += xlim
if (panelcount == n) or (r == nr-1):
break
r+=1 # next row
# Set x- and y- limts of subplots
if ganged:
xlim = None
ylim = None
if len(allylim) > 0:
allylim.sort()
ylim = allylim[0],allylim[-1]
if len(allxlim) > 0:
allxlim.sort()
xlim = allxlim[0],allxlim[-1]
self._plotter.set_limits(xlim=xlim,ylim=ylim)
# save the current counter for multi-page plotting
self._startrow = r+1
self._ipanel += panelcount
if self.casabar_exists():
if self._ipanel >= nptot-1:
self._plotter.figmgr.casabar.disable_next()
else:
self._plotter.figmgr.casabar.enable_next()
if self._ipanel + 1 - panelcount > 0:
self._plotter.figmgr.casabar.enable_prev()
else:
self._plotter.figmgr.casabar.disable_prev()
def run_model(self):
"""
Run the model
:return:
"""
shape = self._shape
tew = self._tew
taw = self._taw
start_time = datetime.now()
pkcb = zeros(shape)
swe = zeros(shape)
tot_snow = zeros(shape)
tot_mass = zeros(shape)
cum_mass = zeros(shape)
ref_et = zeros(shape)
a_min = ones(shape) * 0.45
a_max = ones(shape) * 0.90
a = a_max
pA = a_min
days = list(rrule.rrule(rrule.DAILY, dtstart=self._start, until=self._end))
nsteps = len(days)
plt_day = zeros(nsteps)
plt_rain = zeros(nsteps)
plt_eta = zeros(nsteps)
plt_snow_fall = zeros(nsteps)
plt_ro = zeros(nsteps)
plt_dr = zeros(nsteps)
plt_de = zeros(nsteps)
plt_drew = zeros(nsteps)
plt_temp = zeros(nsteps)
plt_dp_r = zeros(nsteps)
plt_ks = zeros(nsteps)
plt_pdr = zeros(nsteps)
plt_etrs = zeros(nsteps)
plt_kcb = zeros(nsteps)
plt_ppt = zeros(nsteps)
plt_ke = zeros(nsteps)
plt_kr = zeros(nsteps)
plt_mlt = zeros(nsteps)
plt_swe = zeros(nsteps)
plt_tempm = zeros(nsteps)
plt_fs1 = zeros(nsteps)
plt_mass = zeros(nsteps)
p_mo_et = zeros(shape)
p_mo_precip = zeros(shape)
p_mo_ro = zeros(shape)
p_mo_deps = self._dr + self._de + self._drew
p_mo_infil = zeros(shape)
p_mo_etrs = zeros(shape)
p_yr_et = zeros(shape)
p_yr_precip = zeros(shape)
p_yr_ro = zeros(shape)
p_yr_deps = self._dr + self._de + self._drew
p_yr_infil = zeros(shape)
p_yr_etrs = zeros(shape)
start_month = self._start_month
end_month = self._end_month
for i, dday in enumerate(days):
if i > 0:
pkcb = kcb
doy = dday.timetuple().tm_yday
year = dday.year
month = dday.month
day = dday.day
msg = 'Time : {} day {}_{}'.format(datetime.now() - start_time, doy, year)
logging.debug(msg)
# -------------- kcb -------------------
if year == 2000:
ndvi = self.calculate_ndvi_2000(doy)
elif year == 2001:
ndvi = self.calculate_ndvi_2001(doy)
else:
ndvi = self.calculate_ndvi(year, doy)
kcb = ndvi * 1.25
kcb = maximum(kcb, self._min_val)
kcb = where(isnan(kcb), pkcb, kcb)
# -------------- PRISM -------------------
ppt, ppt_tom, max_temp, min_temp, mid_temp = self.load_prism(dday)
# -------------- PM -------------------
# PM data to etrs
name = os.path.join('PM{}'.format(year),
'PM_NM_{}_{:03n}'.format(year, doy))
etrs = tif_to_array(self._pm_data_root, name)
etrs = maximum(etrs, self._min_val)
name = os.path.join('PM{}'.format(year),
'RLIN_NM_{}_{:03n}'.format(year, doy))
rlin = tif_to_array(self._pm_data_root, name)
rlin = maximum(rlin, zeros(shape))
name = os.path.join('rad{}'.format(year),
'RTOT_{}_{:03n}'.format(year, doy))
rg = tif_to_array(self._pm_data_root, name)
rg = maximum(rg, zeros(shape))
if i == 0:
# Total evaporable water is depth of water in the evaporable
# soil layer, i.e., the water available to both stage 1 and 2 evaporation
rew = minimum((2 + (tew / 3.)), 0.8 * tew)
# del tew1, tew2
# you should have all these from previous model runs
pDr = self._dr
pDe = self._de
pDrew = self._drew
dr = self._dr
de = self._de
drew = self._drew
nom = 2 if start_month <= doy <= end_month else 6
ksat = self._ksat * nom / 24.
kc_max_1 = kcb + 0.0001
min_val = ones(shape) * 0.0001
kc_max = maximum(min_val, kc_max_1)
self._nlcd_plt_hgt = self._nlcd_plt_hgt * 0.5 + 1
numr = maximum(kcb - self._kc_min, min_val * 10)
denom = maximum((kc_max - self._kc_min), min_val * 10)
fcov_ref = (numr / denom) ** self._nlcd_plt_hgt
fcov_min = minimum(fcov_ref, ones(shape))
fcov = maximum(fcov_min, min_val * 10)
few = maximum(1 - fcov, 0.01) # exposed ground
pKr = kr
kr = minimum(((tew - de) / (tew - rew)), ones(shape))
kr = where(isnan(kr), pKr, kr)
pKs = ks
ks_ref = where(((taw - pDr) / (0.6 * taw)) < zeros(shape), ones(shape) * 0.001,
((taw - pDr) / (0.6 * taw)))
ks_ref = where(isnan(ks), pKs, ks_ref)
ks = minimum(ks_ref, ones(shape))
# Ke evaporation reduction coefficient; stage 1 evaporation
fsa = where(isnan((rew - drew) / (KE_MAX * etrs)), zeros(shape),
(rew - drew) / (KE_MAX * etrs))
fsb = minimum(fsa, ones(shape))
fs1 = maximum(fsb, zeros(shape))
ke = where(drew < rew, minimum((fs1 + (1 - fs1) * kr) * (kc_max - ks * kcb), few * kc_max),
zeros(shape))
transp = (ks * kcb) * etrs
et_init = (ks * kcb + ke) * etrs
eta = maximum(et_init, zeros(shape))
evap_init = ke * etrs
evap_min = maximum(evap_init, zeros(shape))
evap = minimum(evap_min, kc_max)
# Load temp, find swe, melt, and precipitation, load Ksat
# Use SNOTEL data for precip and temps:
# df_snow : (stel_date, stel_snow, stel_precip, stel_tobs, stel_tmax, stel_tmin, stel_tavg, stel_snwd)
snow_fall = where(mid_temp <= 0.0, ppt, zeros(shape))
rain = where(mid_temp >= 0.0, ppt, zeros(shape))
pA = a
a = where(snow_fall > 3.0, ones(shape) * a_max, a)
a = where(snow_fall <= 3.0, a_min + (pA - a_min) * exp(-0.12), a)
a = where(snow_fall == 0.0, a_min + (pA - a_min) * exp(-0.05), a)
a = where(a < a_min, a_min, a)
swe += snow_fall
mlt_init = maximum(((1 - a) * rg * 0.2) + (mid_temp - 1.8) * 11.0,
zeros(shape)) # use calibrate coefficients
mlt = minimum(swe, mlt_init)
swe -= mlt
# Find depletions
pDr = dr
pDe = de
pDrew = drew
watr = rain + mlt
deps = dr + de + drew
ro = zeros(shape)
ro = where(watr > ksat + deps, watr - ksat - deps, ro)
ro = maximum(ro, zeros(shape))
dp_r = zeros(shape)
id1 = where(watr > deps, ones(shape), zeros(shape))
id2 = where(ksat > watr - deps, ones(shape), zeros(shape))
dp_r = where(id1 + id2 > 1.99, maximum(watr - deps, zeros(shape)), dp_r)
dp_r = where(watr > ksat + deps, ksat, dp_r)
dp_r = maximum(dp_r, zeros(shape))
drew_1 = minimum((pDrew + ro + (evap - (rain + mlt))), rew)
drew = maximum(drew_1, zeros(shape))
diff = maximum(pDrew - drew, zeros(shape))
de_1 = minimum((pDe + (evap - (rain + mlt - diff))), tew)
de = maximum(de_1, zeros(shape))
diff = maximum(((pDrew - drew) + (pDe - de)), zeros(shape))
dr_1 = minimum((pDr + ((transp + dp_r) - (rain + mlt - diff))), taw)
dr = maximum(dr_1, zeros(shape))
# Create cumulative rasters to show net over entire run
infil += dp_r
infil = maximum(infil, zeros(shape))
prev_et = et
ref_et += etrs
et = et + evap + transp
et_ind = et / ref_et
et = where(isnan(et) == True, prev_et, et)
et = where(et > ref_et, ref_et / 2., et)
et = maximum(et, ones(shape) * 0.001)
precip = precip + rain + snow_fall
precip = maximum(precip, zeros(shape))
runoff += ro
runoff = maximum(runoff, zeros(shape))
snow_ras = swe + snow_fall - mlt
snow_ras = maximum(snow_ras, zeros(shape))
tot_snow += snow_fall
mo_date = calendar.monthrange(year, month)
if day == mo_date[1]:
infil_mo = infil - p_mo_infil
infil_mo = maximum(infil_mo, zeros(shape))
ref_et_mo = etrs - p_mo_etrs
et_mo = et - p_mo_et
et_mo = where(isnan(et_mo) == True, p_mo_et, et_mo)
et_mo = where(et_mo > ref_et, ref_et / 2., et_mo)
et_mo = maximum(et_mo, ones(shape) * 0.001)
precip_mo = precip - p_mo_precip
precip_mo = maximum(precip_mo, zeros(shape))
runoff_mo = ro - p_mo_ro
runoff_mo = maximum(runoff_mo, zeros(shape))
snow_ras_mo = swe
snow_ras_mo = maximum(snow_ras_mo, zeros(shape))
deps_mo = drew + de + dr
delta_s_mo = p_mo_deps - deps_mo
outputs = (('infil', infil_mo), ('et', et_mo), ('precip', precip_mo), ('runoff', runoff_mo),
('snow_ras', snow_ras_mo), ('delta_s_mo', delta_s_mo), ('deps_mo', deps_mo))
self.save_month_step(outputs, month, year)
p_mo_et = et
p_mo_precip = precip
p_mo_ro = ro
p_mo_deps = deps_mo
p_mo_infil = infil
p_mo_etrs = etrs
if day == 31 and month == 12:
infil_yr = infil - p_yr_infil
infil_yr = maximum(infil_yr, zeros(shape))
ref_et_yr = etrs - p_yr_etrs
et_yr = et - p_yr_et
et_yr = where(isnan(et_yr) == True, p_yr_et, et_yr)
et_yr = where(et_yr > ref_et, ref_et / 2., et_yr)
et_yr = maximum(et_yr, ones(shape) * 0.001)
precip_yr = precip - p_yr_precip
precip_yr = maximum(precip_yr, zeros(shape))
runoff_yr = ro - p_yr_ro
runoff_yr = maximum(runoff_yr, zeros(shape))
snow_ras_yr = swe
snow_ras_yr = maximum(snow_ras_yr, zeros(shape))
deps_yr = drew + de + dr
delta_s_yr = p_yr_deps - deps_yr
outputs = (('infil', infil_yr), ('et', et_yr), ('precip', precip_yr), ('runoff', runoff_yr),
('snow_ras', snow_ras_yr), ('delta_s_yr', delta_s_yr), ('deps_yr', deps_yr))
p_yr_et = et
p_yr_precip = precip
p_yr_ro = ro
p_yr_deps = deps_yr # this was originally p_mo_deps = deps_yr im assuming this is a typo
p_yr_infil = infil
p_yr_etrs = etrs
self.save_year_step(outputs, month, year)
# Check MASS BALANCE for the love of WATER!!!
mass = rain + mlt - (ro + transp + evap + dp_r + ((pDr - dr) + (pDe - de) + (pDrew - drew)))
tot_mass += abs(mass)
cum_mass += mass
plt_day[i] = dday
plt_rain[i] = rain[S, E]
plt_eta[i] = eta[S, E]
plt_snow_fall[i] = snow_fall[S, E]
plt_ro[i] = ro[S, E]
plt_dr[i] = dr[S, E]
plt_de[i] = de[S, E]
plt_drew[i] = drew[S, E]
plt_temp[i] = mid_temp[S, E]
plt_dp_r[i] = dp_r[S, E]
plt_ks[i] = ks[S, E]
plt_pdr[i] = pDr[S, E]
plt_etrs[i] = etrs[S, E]
plt_kcb[i] = kcb[S, E]
plt_ppt[i] = ppt[S, E]
plt_ke[i] = ke[S, E]
plt_kr[i] = kr[S, E]
plt_mlt[i] = mlt[S, E]
plt_swe[i] = swe[S, E]
plt_tempm[i] = max_temp[S, E]
plt_fs1[i] = fs1[S, E]
plt_mass[i] = mass[S, E]
def __init__(self, ax, *args, **kwargs):
"""
Draw contour lines or filled regions, depending on
whether keyword arg 'filled' is False (default) or True.
The first argument of the initializer must be an axes
object. The remaining arguments and keyword arguments
are described in ContourSet.contour_doc.
"""
self.ax = ax
self.levels = kwargs.get("levels", None)
self.filled = kwargs.get("filled", False)
self.linewidths = kwargs.get("linewidths", None)
self.linestyles = kwargs.get("linestyles", None)
self.alpha = kwargs.get("alpha", 1.0)
self.origin = kwargs.get("origin", None)
self.extent = kwargs.get("extent", None)
cmap = kwargs.get("cmap", None)
self.colors = kwargs.get("colors", None)
norm = kwargs.get("norm", None)
self.extend = kwargs.get("extend", "neither")
self.antialiased = kwargs.get("antialiased", True)
self.nchunk = kwargs.get("nchunk", 0)
self.locator = kwargs.get("locator", None)
if isinstance(norm, colors.LogNorm) or isinstance(self.locator, ticker.LogLocator):
self.logscale = True
if norm is None:
norm = colors.LogNorm()
if self.extend is not "neither":
raise ValueError("extend kwarg does not work yet with log scale")
else:
self.logscale = False
if self.origin is not None:
assert self.origin in ["lower", "upper", "image"]
if self.extent is not None:
assert len(self.extent) == 4
if cmap is not None:
assert isinstance(cmap, colors.Colormap)
if self.colors is not None and cmap is not None:
raise ValueError("Either colors or cmap must be None")
if self.origin == "image":
self.origin = mpl.rcParams["image.origin"]
x, y, z = self._contour_args(*args) # also sets self.levels,
# self.layers
if self.colors is not None:
cmap = colors.ListedColormap(self.colors, N=len(self.layers))
if self.filled:
self.collections = cbook.silent_list("collections.PolyCollection")
else:
self.collections = cbook.silent_list("collections.LineCollection")
# label lists must be initialized here
self.labelTexts = []
self.labelCValues = []
kw = {"cmap": cmap}
if norm is not None:
kw["norm"] = norm
cm.ScalarMappable.__init__(self, **kw) # sets self.cmap;
self._process_colors()
_mask = ma.getmask(z)
if _mask is ma.nomask:
_mask = None
if self.filled:
if self.linewidths is not None:
warnings.warn("linewidths is ignored by contourf")
C = _cntr.Cntr(x, y, z.filled(), _mask)
lowers = self._levels[:-1]
uppers = self._levels[1:]
for level, level_upper in zip(lowers, uppers):
nlist = C.trace(level, level_upper, points=0, nchunk=self.nchunk)
col = collections.PolyCollection(
nlist, antialiaseds=(self.antialiased,), edgecolors="none", alpha=self.alpha
)
self.ax.add_collection(col)
self.collections.append(col)
else:
tlinewidths = self._process_linewidths()
self.tlinewidths = tlinewidths
tlinestyles = self._process_linestyles()
C = _cntr.Cntr(x, y, z.filled(), _mask)
for level, width, lstyle in zip(self.levels, tlinewidths, tlinestyles):
nlist = C.trace(level, points=0)
col = collections.LineCollection(nlist, linewidths=width, linestyle=lstyle, alpha=self.alpha)
col.set_label("_nolegend_")
self.ax.add_collection(col, False)
self.collections.append(col)
self.changed() # set the colors
x0 = ma.minimum(x)
x1 = ma.maximum(x)
y0 = ma.minimum(y)
y1 = ma.maximum(y)
self.ax.update_datalim([(x0, y0), (x1, y1)])
self.ax.autoscale_view()
def comp_r(dert__, fig, root_fcr):
'''
Cross-comparison of input param (dert[0]) over rng passed from intra_blob.
This fork is selective for blobs with below-average gradient,
where input intensity didn't vary much in shorter-range cross-comparison.
Such input is predictable enough for selective sampling: skipping current
rim derts as kernel-central derts in following comparison kernels.
Skipping forms increasingly sparse output dert__ for greater-range cross-comp, hence
rng (distance between centers of compared derts) increases as 2^n, starting at 0:
rng = 1: 3x3 kernel,
rng = 2: 5x5 kernel,
rng = 4: 9x9 kernel,
...
Due to skipping, configuration of input derts in next-rng kernel will always be 3x3, see:
https://github.com/boris-kz/CogAlg/blob/master/frame_2D_alg/Illustrations/intra_comp_diagrams.png
'''
# initialize new dert structure
new_dert__ = ma.zeros((dert__.shape[0], (dert__.shape[1] - 1) // 2,
(dert__.shape[2] - 1) // 2),
dtype=dert__.dtype)
new_dert__.mask = True
# extract new_dert__ 'views', use [:] to 'update' views and new_dert__ at the same time
i__center, idy__, idx__, g__, dy__, dx__, m__ = new_dert__
i__ = dert__[0] # i is ig if fig else pixel
'''
sparse aligned i__center and i__rim arrays:
'''
i__center[:] = i__[1:-1:2, 1:-1:2] # also assignment to new_dert__[0]
i__topleft = i__[:-2:2, :-2:2]
i__top = i__[:-2:2, 1:-1:2]
i__topright = i__[:-2:2, 2::2]
i__right = i__[1:-1:2, 2::2]
i__bottomright = i__[2::2, 2::2]
i__bottom = i__[2::2, 1:-1:2]
i__bottomleft = i__[2::2, :-2:2]
i__left = i__[1:-1:2, :-2:2]
'''
unmask all derts in kernels with only one masked dert (can be set to any number of masked derts),
to avoid extreme blob shrinking and loss of info in other derts of partially masked kernels
unmasked derts were computed due to extend_dert() in intra_blob
'''
majority_mask = (i__[:, 1:-1:2, 1:-1:2].mask.astype(int) +
i__[:, :-2:2, :-2:2].mask.astype(int) +
i__[:, :-2:2, 1:-1:2].mask.astype(int) +
i__[:, :-2:2, 2::2].mask.astype(int) +
i__[:, 1:-1:2, 2::2].mask.astype(int) +
i__[:, 2::2, 2::2].mask.astype(int) +
i__[:, 2::2, 1:-1:2].mask.astype(int) +
i__[:, 2::2, :-2:2].mask.astype(int) +
i__[:, 1:-1:2, :-2:2].mask.astype(int)) > 1
i__center.mask = i__topleft.mask = i__top.mask = i__topright.mask = i__right.mask = i__bottomright.mask = \
i__bottom.mask = i__bottomleft.mask = i__left.mask = majority_mask # not only i__center
idy__[:], idx__[:] = dert__[[1, 2], 1:-1:2, 1:-1:2]
if root_fcr: # root fork is comp_r, accumulate derivatives:
dy__[:] = dert__[4, 1:-1:2, 1:-1:2] # sparse to align with i__center
dx__[:] = dert__[5, 1:-1:2, 1:-1:2]
m__[:] = dert__[6, 1:-1:2, 1:-1:2]
dy__.mask = dx__.mask = m__.mask = majority_mask
if not fig: # compare four diametrically opposed pairs of rim pixels:
d_tl_br = i__topleft.data - i__bottomright.data
d_t_b = i__top.data - i__bottom.data
d_tr_bl = i__topright.data - i__bottomleft.data
d_r_l = i__right.data - i__left.data
dy__ += (d_tl_br * YCOEFs[0] + d_t_b * YCOEFs[1] +
d_tr_bl * YCOEFs[2] + d_r_l * YCOEFs[3])
dx__ += (d_tl_br * XCOEFs[0] + d_t_b * XCOEFs[1] +
d_tr_bl * XCOEFs[2] + d_r_l * XCOEFs[3])
g__[:] = ma.hypot(dy__, dx__) # gradient
'''
inverse match = SAD, direction-invariant and more precise measure of variation than g
(all diagonal derivatives can be imported from prior 2x2 comp)
'''
m__ += (abs(i__center.data - i__topleft.data) +
abs(i__center.data - i__top.data) +
abs(i__center.data - i__topright.data) +
abs(i__center.data - i__right.data) +
abs(i__center.data - i__bottomright.data) +
abs(i__center.data - i__bottom.data) +
abs(i__center.data - i__bottomleft.data) +
abs(i__center.data - i__left.data))
else: # fig is TRUE, compare angle and then magnitude of 8 center-rim pairs
i__[ma.where(i__ == 0)] = 1 # to avoid / 0
a__ = dert__[[1, 2]] / i__ # sin = idy / i, cos = idx / i, i = ig
'''
sparse aligned a__center and a__rim arrays:
'''
a__center = a__[:, 1:-1:2, 1:-1:2]
a__topleft = a__[:, :-2:2, :-2:2]
a__top = a__[:, :-2:2, 1:-1:2]
a__topright = a__[:, :-2:2, 2::2]
a__right = a__[:, 1:-1:2, 2::2]
a__bottomright = a__[:, 2::2, 2::2]
a__bottom = a__[:, 2::2, 1:-1:2]
a__bottomleft = a__[:, 2::2, :-2:2]
a__left = a__[:, 1:-1:2, :-2:2]
'''
only mask kernels with more than one masked dert, for all operations below:
'''
majority_mask_a = (a__[:, 1:-1:2, 1:-1:2].mask.astype(int) +
a__[:, :-2:2, :-2:2].mask.astype(int) +
a__[:, :-2:2, 1:-1:2].mask.astype(int) +
a__[:, :-2:2, 2::2].mask.astype(int) +
a__[:, 1:-1:2, 2::2].mask.astype(int) +
a__[:, 2::2, 2::2].mask.astype(int) +
a__[:, 2::2, 1:-1:2].mask.astype(int) +
a__[:, 2::2, :-2:2].mask.astype(int) +
a__[:, 1:-1:2, :-2:2].mask.astype(int)) > 1
a__center.mask = a__topleft.mask = a__top.mask = a__topright.mask = a__right.mask = a__bottomright.mask = \
a__bottom.mask = a__bottomleft.mask = a__left.mask = majority_mask_a
assert (majority_mask_a[0] == majority_mask_a[1]).all()
# what does that do?
dy__.mask = dx__.mask = m__.mask = majority_mask_a[0]
'''
8-tuple of differences between central dert angle and rim dert angle:
'''
cos_da = [((a__topleft[1].data * a__center[1].data) +
(a__center[0].data * a__topleft[0].data)),
((a__top[1].data * a__center[1].data) +
(a__center[0].data * a__top[0].data)),
((a__topright[1].data * a__center[1].data) +
(a__center[0].data * a__topright[0].data)),
((a__right[1].data * a__center[1].data) +
(a__center[0].data * a__right[0].data)),
((a__bottomright[1].data * a__center[1].data) +
(a__center[0].data * a__bottomright[0].data)),
((a__bottom[1].data * a__center[1].data) +
(a__center[0].data * a__bottom[0].data)),
((a__bottomleft[1].data * a__center[1].data) +
(a__center[0].data * a__bottomleft[0].data)),
((a__left[1].data * a__center[1].data) +
(a__center[0].data * a__left[0].data))]
'''
8-tuple of cosine matches per direction:
'''
m__ += (ma.minimum(i__center.data, i__topleft.data) * cos_da[0] +
ma.minimum(i__center.data, i__top.data) * cos_da[1] +
ma.minimum(i__center.data, i__topright.data) * cos_da[2] +
ma.minimum(i__center.data, i__right.data) * cos_da[3] +
ma.minimum(i__center.data, i__bottomright.data) * cos_da[4] +
ma.minimum(i__center.data, i__bottom.data) * cos_da[5] +
ma.minimum(i__center.data, i__bottomleft.data) * cos_da[6] +
ma.minimum(i__center.data, i__left.data) * cos_da[7])
'''
8-tuple of cosine differences per direction:
'''
dt__ = [(i__center.data - i__topleft.data * cos_da[0]),
(i__center.data - i__top.data * cos_da[1]),
(i__center.data - i__topright.data * cos_da[2]),
(i__center.data - i__right.data * cos_da[3]),
(i__center.data - i__bottomright.data * cos_da[4]),
(i__center.data - i__bottom.data * cos_da[5]),
(i__center.data - i__bottomleft.data * cos_da[6]),
(i__center.data - i__left.data * cos_da[7])]
for d__, YCOEF, XCOEF in zip(dt__, YCOEFs, XCOEFs):
dy__ += d__ * YCOEF # decompose differences into dy and dx,
dx__ += d__ * XCOEF # accumulate with prior-rng dy, dx
'''
accumulate in prior-range dy, dx: 3x3 -> 5x5 -> 9x9
'''
g__[:] = ma.hypot(dy__, dx__)
'''
next comp_r will use full dert
next comp_g will use g__, dy__, dx__
'''
return new_dert__ # new_dert__ has been updated along with 'view' arrays: i__center, idy__, idx__, g__, dy__, dx__, m__
def run_model(self):
"""
Run the model
:return:
"""
shape = self._shape
tew = self._tew
taw = self._taw
start_time = datetime.now()
pkcb = zeros(shape)
swe = zeros(shape)
tot_snow = zeros(shape)
tot_mass = zeros(shape)
cum_mass = zeros(shape)
ref_et = zeros(shape)
a_min = ones(shape) * 0.45
a_max = ones(shape) * 0.90
a = a_max
pA = a_min
days = list(
rrule.rrule(rrule.DAILY, dtstart=self._start, until=self._end))
nsteps = len(days)
plt_day = zeros(nsteps)
plt_rain = zeros(nsteps)
plt_eta = zeros(nsteps)
plt_snow_fall = zeros(nsteps)
plt_ro = zeros(nsteps)
plt_dr = zeros(nsteps)
plt_de = zeros(nsteps)
plt_drew = zeros(nsteps)
plt_temp = zeros(nsteps)
plt_dp_r = zeros(nsteps)
plt_ks = zeros(nsteps)
plt_pdr = zeros(nsteps)
plt_etrs = zeros(nsteps)
plt_kcb = zeros(nsteps)
plt_ppt = zeros(nsteps)
plt_ke = zeros(nsteps)
plt_kr = zeros(nsteps)
plt_mlt = zeros(nsteps)
plt_swe = zeros(nsteps)
plt_tempm = zeros(nsteps)
plt_fs1 = zeros(nsteps)
plt_mass = zeros(nsteps)
p_mo_et = zeros(shape)
p_mo_precip = zeros(shape)
p_mo_ro = zeros(shape)
p_mo_deps = self._dr + self._de + self._drew
p_mo_infil = zeros(shape)
p_mo_etrs = zeros(shape)
p_yr_et = zeros(shape)
p_yr_precip = zeros(shape)
p_yr_ro = zeros(shape)
p_yr_deps = self._dr + self._de + self._drew
p_yr_infil = zeros(shape)
p_yr_etrs = zeros(shape)
start_month = self._start_month
end_month = self._end_month
for i, dday in enumerate(days):
if i > 0:
pkcb = kcb
doy = dday.timetuple().tm_yday
year = dday.year
month = dday.month
day = dday.day
msg = 'Time : {} day {}_{}'.format(datetime.now() - start_time,
doy, year)
logging.debug(msg)
# -------------- kcb -------------------
if year == 2000:
ndvi = self.calculate_ndvi_2000(doy)
elif year == 2001:
ndvi = self.calculate_ndvi_2001(doy)
else:
ndvi = self.calculate_ndvi(year, doy)
kcb = ndvi * 1.25
kcb = maximum(kcb, self._min_val)
kcb = where(isnan(kcb), pkcb, kcb)
# -------------- PRISM -------------------
ppt, ppt_tom, max_temp, min_temp, mid_temp = self.load_prism(dday)
# -------------- PM -------------------
# PM data to etrs
name = os.path.join('PM{}'.format(year),
'PM_NM_{}_{:03n}'.format(year, doy))
etrs = tif_to_array(self._pm_data_root, name)
etrs = maximum(etrs, self._min_val)
name = os.path.join('PM{}'.format(year),
'RLIN_NM_{}_{:03n}'.format(year, doy))
rlin = tif_to_array(self._pm_data_root, name)
rlin = maximum(rlin, zeros(shape))
name = os.path.join('rad{}'.format(year),
'RTOT_{}_{:03n}'.format(year, doy))
rg = tif_to_array(self._pm_data_root, name)
rg = maximum(rg, zeros(shape))
if i == 0:
# Total evaporable water is depth of water in the evaporable
# soil layer, i.e., the water available to both stage 1 and 2 evaporation
rew = minimum((2 + (tew / 3.)), 0.8 * tew)
# del tew1, tew2
# you should have all these from previous model runs
pDr = self._dr
pDe = self._de
pDrew = self._drew
dr = self._dr
de = self._de
drew = self._drew
nom = 2 if start_month <= doy <= end_month else 6
ksat = self._ksat * nom / 24.
kc_max_1 = kcb + 0.0001
min_val = ones(shape) * 0.0001
kc_max = maximum(min_val, kc_max_1)
self._nlcd_plt_hgt = self._nlcd_plt_hgt * 0.5 + 1
numr = maximum(kcb - self._kc_min, min_val * 10)
denom = maximum((kc_max - self._kc_min), min_val * 10)
fcov_ref = (numr / denom)**self._nlcd_plt_hgt
fcov_min = minimum(fcov_ref, ones(shape))
fcov = maximum(fcov_min, min_val * 10)
few = maximum(1 - fcov, 0.01) # exposed ground
pKr = kr
kr = minimum(((tew - de) / (tew - rew)), ones(shape))
kr = where(isnan(kr), pKr, kr)
pKs = ks
ks_ref = where(((taw - pDr) / (0.6 * taw)) < zeros(shape),
ones(shape) * 0.001, ((taw - pDr) / (0.6 * taw)))
ks_ref = where(isnan(ks), pKs, ks_ref)
ks = minimum(ks_ref, ones(shape))
# Ke evaporation reduction coefficient; stage 1 evaporation
fsa = where(isnan((rew - drew) / (KE_MAX * etrs)), zeros(shape),
(rew - drew) / (KE_MAX * etrs))
fsb = minimum(fsa, ones(shape))
fs1 = maximum(fsb, zeros(shape))
ke = where(
drew < rew,
minimum((fs1 + (1 - fs1) * kr) * (kc_max - ks * kcb),
few * kc_max), zeros(shape))
transp = (ks * kcb) * etrs
et_init = (ks * kcb + ke) * etrs
eta = maximum(et_init, zeros(shape))
evap_init = ke * etrs
evap_min = maximum(evap_init, zeros(shape))
evap = minimum(evap_min, kc_max)
# Load temp, find swe, melt, and precipitation, load Ksat
# Use SNOTEL data for precip and temps:
# df_snow : (stel_date, stel_snow, stel_precip, stel_tobs, stel_tmax, stel_tmin, stel_tavg, stel_snwd)
snow_fall = where(mid_temp <= 0.0, ppt, zeros(shape))
rain = where(mid_temp >= 0.0, ppt, zeros(shape))
pA = a
a = where(snow_fall > 3.0, ones(shape) * a_max, a)
a = where(snow_fall <= 3.0, a_min + (pA - a_min) * exp(-0.12), a)
a = where(snow_fall == 0.0, a_min + (pA - a_min) * exp(-0.05), a)
a = where(a < a_min, a_min, a)
swe += snow_fall
mlt_init = maximum(((1 - a) * rg * 0.2) + (mid_temp - 1.8) * 11.0,
zeros(shape)) # use calibrate coefficients
mlt = minimum(swe, mlt_init)
swe -= mlt
# Find depletions
pDr = dr
pDe = de
pDrew = drew
watr = rain + mlt
deps = dr + de + drew
ro = zeros(shape)
ro = where(watr > ksat + deps, watr - ksat - deps, ro)
ro = maximum(ro, zeros(shape))
dp_r = zeros(shape)
id1 = where(watr > deps, ones(shape), zeros(shape))
id2 = where(ksat > watr - deps, ones(shape), zeros(shape))
dp_r = where(id1 + id2 > 1.99, maximum(watr - deps, zeros(shape)),
dp_r)
dp_r = where(watr > ksat + deps, ksat, dp_r)
dp_r = maximum(dp_r, zeros(shape))
drew_1 = minimum((pDrew + ro + (evap - (rain + mlt))), rew)
drew = maximum(drew_1, zeros(shape))
diff = maximum(pDrew - drew, zeros(shape))
de_1 = minimum((pDe + (evap - (rain + mlt - diff))), tew)
de = maximum(de_1, zeros(shape))
diff = maximum(((pDrew - drew) + (pDe - de)), zeros(shape))
dr_1 = minimum((pDr + ((transp + dp_r) - (rain + mlt - diff))),
taw)
dr = maximum(dr_1, zeros(shape))
# Create cumulative rasters to show net over entire run
infil += dp_r
infil = maximum(infil, zeros(shape))
prev_et = et
ref_et += etrs
et = et + evap + transp
et_ind = et / ref_et
et = where(isnan(et) == True, prev_et, et)
et = where(et > ref_et, ref_et / 2., et)
et = maximum(et, ones(shape) * 0.001)
precip = precip + rain + snow_fall
precip = maximum(precip, zeros(shape))
runoff += ro
runoff = maximum(runoff, zeros(shape))
snow_ras = swe + snow_fall - mlt
snow_ras = maximum(snow_ras, zeros(shape))
tot_snow += snow_fall
mo_date = calendar.monthrange(year, month)
if day == mo_date[1]:
infil_mo = infil - p_mo_infil
infil_mo = maximum(infil_mo, zeros(shape))
ref_et_mo = etrs - p_mo_etrs
et_mo = et - p_mo_et
et_mo = where(isnan(et_mo) == True, p_mo_et, et_mo)
et_mo = where(et_mo > ref_et, ref_et / 2., et_mo)
et_mo = maximum(et_mo, ones(shape) * 0.001)
precip_mo = precip - p_mo_precip
precip_mo = maximum(precip_mo, zeros(shape))
runoff_mo = ro - p_mo_ro
runoff_mo = maximum(runoff_mo, zeros(shape))
snow_ras_mo = swe
snow_ras_mo = maximum(snow_ras_mo, zeros(shape))
deps_mo = drew + de + dr
delta_s_mo = p_mo_deps - deps_mo
outputs = (('infil', infil_mo), ('et', et_mo), ('precip',
precip_mo),
('runoff', runoff_mo), ('snow_ras', snow_ras_mo),
('delta_s_mo', delta_s_mo), ('deps_mo', deps_mo))
self.save_month_step(outputs, month, year)
p_mo_et = et
p_mo_precip = precip
p_mo_ro = ro
p_mo_deps = deps_mo
p_mo_infil = infil
p_mo_etrs = etrs
if day == 31 and month == 12:
infil_yr = infil - p_yr_infil
infil_yr = maximum(infil_yr, zeros(shape))
ref_et_yr = etrs - p_yr_etrs
et_yr = et - p_yr_et
et_yr = where(isnan(et_yr) == True, p_yr_et, et_yr)
et_yr = where(et_yr > ref_et, ref_et / 2., et_yr)
et_yr = maximum(et_yr, ones(shape) * 0.001)
precip_yr = precip - p_yr_precip
precip_yr = maximum(precip_yr, zeros(shape))
runoff_yr = ro - p_yr_ro
runoff_yr = maximum(runoff_yr, zeros(shape))
snow_ras_yr = swe
snow_ras_yr = maximum(snow_ras_yr, zeros(shape))
deps_yr = drew + de + dr
delta_s_yr = p_yr_deps - deps_yr
outputs = (('infil', infil_yr), ('et', et_yr), ('precip',
precip_yr),
('runoff', runoff_yr), ('snow_ras', snow_ras_yr),
('delta_s_yr', delta_s_yr), ('deps_yr', deps_yr))
p_yr_et = et
p_yr_precip = precip
p_yr_ro = ro
p_yr_deps = deps_yr # this was originally p_mo_deps = deps_yr im assuming this is a typo
p_yr_infil = infil
p_yr_etrs = etrs
self.save_year_step(outputs, month, year)
# Check MASS BALANCE for the love of WATER!!!
mass = rain + mlt - (ro + transp + evap + dp_r +
((pDr - dr) + (pDe - de) + (pDrew - drew)))
tot_mass += abs(mass)
cum_mass += mass
plt_day[i] = dday
plt_rain[i] = rain[S, E]
plt_eta[i] = eta[S, E]
plt_snow_fall[i] = snow_fall[S, E]
plt_ro[i] = ro[S, E]
plt_dr[i] = dr[S, E]
plt_de[i] = de[S, E]
plt_drew[i] = drew[S, E]
plt_temp[i] = mid_temp[S, E]
plt_dp_r[i] = dp_r[S, E]
plt_ks[i] = ks[S, E]
plt_pdr[i] = pDr[S, E]
plt_etrs[i] = etrs[S, E]
plt_kcb[i] = kcb[S, E]
plt_ppt[i] = ppt[S, E]
plt_ke[i] = ke[S, E]
plt_kr[i] = kr[S, E]
plt_mlt[i] = mlt[S, E]
plt_swe[i] = swe[S, E]
plt_tempm[i] = max_temp[S, E]
plt_fs1[i] = fs1[S, E]
plt_mass[i] = mass[S, E]
def specify(self, slab, axes, specification, confined_by, aux):
''' First part: confine the slab within a Domain wide enough to do the exact in post'''
import string, copy
from numpy.ma import minimum, maximum
# myconfined is for later, we can't confine a dimension twice with an argument plus a keyword or 2 keywords
myconfined = [None] * len(axes)
self.aux = copy.copy(specification)
# First look at the arguments (i.e not keywords) and confine the dimensions
# in the order of the arguments
for i in range(len(self.args)):
if confined_by[
i] is None: # Check it hasn't been confined by somebody else
myconfined[i] = 1 # dim confined by argument list
confined_by[
i] = self # for cdms I want to confine this dimension
self.aux[i] = specs = list(
self.args[i]) # How do we want to confine this dim ?
if not (isinstance(specs, list) or isinstance(specs, tuple)):
raise Exception, "Error in Selector, you must specify a list or a tuple, you passed:" + str(
specs)
elif type(specs[0]) == type(
cdtime.comptime(1999)) or type(specs[0]) == type(
cdtime.reltime(0, 'days since 1999')) or type(
specs[0]) == type(''):
list2 = []
for l in specs:
if type(l) != type(''):
list2.append(l.torel('days since 1900').value)
else:
list2.append(
cdtime.s2r(l, 'days since 1900').value)
min = minimum(list2)
max = maximum(list2)
specification[i] = cdtime.reltime(
min, 'days since 1900'), cdtime.reltime(
max, 'days since 1900')
else: # But if it's not...
specification[i] = minimum(specs), maximum(
specs) # sets the specifications
else:
return 1
for kw in self.kargs.keys():
axis = None
for i in range(len(axes)):
if axes[i].id == kw: axis = i
if axis is None:
if kw == 'time':
for i in range(len(axes)):
if axes[i].isTime(): axis = i
elif kw == 'level':
for i in range(len(axes)):
if axes[i].isLevel(): axis = i
elif kw == 'longitude':
for i in range(len(axes)):
if axes[i].isLongitude(): axis = i
elif kw == 'latitude':
for i in range(len(axes)):
if axes[i].isLatitude(): axis = i
elif not kw in [
'match'
]: # keyword not a recognised keyword or dimension name
raise Exception, 'Error, keyword: ' + kw + ' not recognized'
# At this point, if axis is None:
# we are dealing with a keyword for the selector
# so we'll skip it
if not axis is None:
if confined_by[axis] is None:
confined_by[axis] = self
myconfined[axis] = 1
self.aux[axis] = specs = list(self.kargs[kw])
if type(specs[0]) == type(cdtime.comptime(1999)) or type(
specs[0]) == type(
cdtime.reltime(0, 'days since 1999')) or type(
specs[0]) == type(''):
list2 = []
for l in specs:
if type(l) != type(''):
list2.append(l.torel('days since 1900').value)
else:
list2.append(
cdtime.s2r(l, 'days since 1900').value)
min = minimum(list2)
max = maximum(list2)
specification[axis] = cdtime.reltime(
min, 'days since 1900'), cdtime.reltime(
max, 'days since 1900')
else: # But if it's not...
specification[axis] = minimum(specs), maximum(specs)
else:
if myconfined[axis] == 1:
raise 'Error you are attempting to set the axis: ' + str(
axes[axis].id) + ' more than once'
else:
return 1
return 0
def autoscale(self, A):
'''
Set *vmin*, *vmax* to min, max of *A*.
'''
self.vmin = ma.minimum(A)
self.vmax = ma.maximum(A)
def __init__(self, ax, *args, **kwargs):
"""
Draw contour lines or filled regions, depending on
whether keyword arg 'filled' is False (default) or True.
The first argument of the initializer must be an axes
object. The remaining arguments and keyword arguments
are described in ContourSet.contour_doc.
"""
self.ax = ax
self.levels = kwargs.get('levels', None)
self.filled = kwargs.get('filled', False)
self.linewidths = kwargs.get('linewidths', None)
self.linestyles = kwargs.get('linestyles', None)
self.alpha = kwargs.get('alpha', 1.0)
self.origin = kwargs.get('origin', None)
self.extent = kwargs.get('extent', None)
cmap = kwargs.get('cmap', None)
self.colors = kwargs.get('colors', None)
norm = kwargs.get('norm', None)
self.extend = kwargs.get('extend', 'neither')
self.antialiased = kwargs.get('antialiased', True)
self.nchunk = kwargs.get('nchunk', 0)
self.locator = kwargs.get('locator', None)
if (isinstance(norm, colors.LogNorm)
or isinstance(self.locator, ticker.LogLocator)):
self.logscale = True
if norm is None:
norm = colors.LogNorm()
if self.extend is not 'neither':
raise ValueError(
'extend kwarg does not work yet with log scale')
else:
self.logscale = False
if self.origin is not None:
assert (self.origin in ['lower', 'upper', 'image'])
if self.extent is not None: assert (len(self.extent) == 4)
if cmap is not None: assert (isinstance(cmap, colors.Colormap))
if self.colors is not None and cmap is not None:
raise ValueError('Either colors or cmap must be None')
if self.origin == 'image': self.origin = mpl.rcParams['image.origin']
if isinstance(args[0], ContourSet):
C = args[0].Cntr
if self.levels is None:
self.levels = args[0].levels
else:
x, y, z = self._contour_args(*args)
x0 = ma.minimum(x)
x1 = ma.maximum(x)
y0 = ma.minimum(y)
y1 = ma.maximum(y)
self.ax.update_datalim([(x0, y0), (x1, y1)])
self.ax.autoscale_view()
_mask = ma.getmask(z)
if _mask is ma.nomask:
_mask = None
C = _cntr.Cntr(x, y, z.filled(), _mask)
self.Cntr = C
self._process_levels()
if self.colors is not None:
cmap = colors.ListedColormap(self.colors, N=len(self.layers))
if self.filled:
self.collections = cbook.silent_list('collections.PathCollection')
else:
self.collections = cbook.silent_list('collections.LineCollection')
# label lists must be initialized here
self.labelTexts = []
self.labelCValues = []
kw = {'cmap': cmap}
if norm is not None:
kw['norm'] = norm
cm.ScalarMappable.__init__(self, **kw) # sets self.cmap;
self._process_colors()
if self.filled:
if self.linewidths is not None:
warnings.warn('linewidths is ignored by contourf')
lowers = self._levels[:-1]
uppers = self._levels[1:]
for level, level_upper in zip(lowers, uppers):
nlist = C.trace(level, level_upper, nchunk=self.nchunk)
nseg = len(nlist) // 2
segs = nlist[:nseg]
kinds = nlist[nseg:]
paths = self._make_paths(segs, kinds)
col = collections.PathCollection(
paths,
antialiaseds=(self.antialiased, ),
edgecolors='none',
alpha=self.alpha)
self.ax.add_collection(col)
self.collections.append(col)
else:
tlinewidths = self._process_linewidths()
self.tlinewidths = tlinewidths
tlinestyles = self._process_linestyles()
for level, width, lstyle in zip(self.levels, tlinewidths,
tlinestyles):
nlist = C.trace(level)
nseg = len(nlist) // 2
segs = nlist[:nseg]
#kinds = nlist[nseg:]
col = collections.LineCollection(segs,
linewidths=width,
linestyle=lstyle,
alpha=self.alpha)
col.set_label('_nolegend_')
self.ax.add_collection(col, False)
self.collections.append(col)
self.changed() # set the colors
def plot_map(self, dataset, attribute_data, min_value=None, max_value=None, file=None,
my_title="", filter=None, background=None):
""" Plots a 2D image of attribute given by 'name'. matplotlib required.
The dataset must have a method 'get_2d_attribute' defined that returns
a 2D array that is to be plotted. If min_value/max_value are given, all values
that are smaller/larger than these values are set to min_value/max_value.
Argument background is a value to be used for background. If it is not given,
it is considered as a 1/100 under the minimum value of the array.
Filter is a 2D array. Points where filter is > 0 are masked out (put into background).
"""
import matplotlib
matplotlib.use('Qt4Agg')
from matplotlib.pylab import jet,imshow,colorbar,show,axis,savefig,close,figure,title,normalize
from matplotlib.pylab import rot90
attribute_data = attribute_data[filter]
coord_2d_data = dataset.get_2d_attribute(attribute_data = attribute_data)
data_mask = coord_2d_data.mask
# if filter is not None:
# if isinstance(filter, ndarray):
# if not ma.allclose(filter.shape, coord_2d_data.shape):
# raise StandardError, "Argument filter must have the same shape as the 2d attribute."
# filter_data = filter
# else:
# raise TypeError, "The filter type is invalid. A character string or a 2D numpy array allowed."
# filter_data = where(ma.filled(filter_data,1) > 0, 1,0)
# data_mask = ma.mask_or(data_mask, filter_data)
nonmaskedmin = ma.minimum(coord_2d_data) - .2 * (ma.maximum(coord_2d_data) - ma.minimum(coord_2d_data))
if max_value == None:
max_value = ma.maximum(coord_2d_data)
if min_value == None:
min_value = nonmaskedmin
coord_2d_data = ma.filled(coord_2d_data,min_value)
if background is None:
value_range = max_value-min_value
background = min_value-value_range/100
coord_2d_data = ma.filled(ma.masked_array(coord_2d_data, mask=data_mask), background)
# Our data uses NW as 0,0, while matplotlib uses SW for 0,0.
# Rotate the data so the map is oriented correctly.
coord_2d_data = rot90(coord_2d_data, 1)
jet()
figure()
norm = normalize(min_value, max_value)
im = imshow(coord_2d_data,
origin='lower',
aspect='equal',
interpolation=None,
norm=norm,
)
tickfmt = '%4d'
if isinstance(min_value, float) or isinstance(max_value, float):
tickfmt='%1.4f'
colorbar(format=tickfmt)
title(my_title)
axis('off')
if file:
savefig(file)
close()
else:
show()
def specify(self, slab, axes, specification, confined_by, aux):
""" First part: confine the slab within a Domain wide enough to do the exact in post"""
import string, copy
from numpy.ma import minimum, maximum
# myconfined is for later, we can't confine a dimension twice with an argument plus a keyword or 2 keywords
myconfined = [None] * len(axes)
self.aux = copy.copy(specification)
# First look at the arguments (i.e not keywords) and confine the dimensions
# in the order of the arguments
for i in range(len(self.args)):
if confined_by[i] is None: # Check it hasn't been confined by somebody else
myconfined[i] = 1 # dim confined by argument list
confined_by[i] = self # for cdms I want to confine this dimension
self.aux[i] = specs = list(self.args[i]) # How do we want to confine this dim ?
if not (isinstance(specs, list) or isinstance(specs, tuple)):
raise Exception, "Error in Selector, you must specify a list or a tuple, you passed:" + str(specs)
elif (
type(specs[0]) == type(cdtime.comptime(1999))
or type(specs[0]) == type(cdtime.reltime(0, "days since 1999"))
or type(specs[0]) == type("")
):
list2 = []
for l in specs:
if type(l) != type(""):
list2.append(l.torel("days since 1900").value)
else:
list2.append(cdtime.s2r(l, "days since 1900").value)
min = minimum(list2)
max = maximum(list2)
specification[i] = cdtime.reltime(min, "days since 1900"), cdtime.reltime(max, "days since 1900")
else: # But if it's not...
specification[i] = minimum(specs), maximum(specs) # sets the specifications
else:
return 1
for kw in self.kargs.keys():
axis = None
for i in range(len(axes)):
if axes[i].id == kw:
axis = i
if axis is None:
if kw == "time":
for i in range(len(axes)):
if axes[i].isTime():
axis = i
elif kw == "level":
for i in range(len(axes)):
if axes[i].isLevel():
axis = i
elif kw == "longitude":
for i in range(len(axes)):
if axes[i].isLongitude():
axis = i
elif kw == "latitude":
for i in range(len(axes)):
if axes[i].isLatitude():
axis = i
elif not kw in ["match"]: # keyword not a recognised keyword or dimension name
raise Exception, "Error, keyword: " + kw + " not recognized"
# At this point, if axis is None:
# we are dealing with a keyword for the selector
# so we'll skip it
if not axis is None:
if confined_by[axis] is None:
confined_by[axis] = self
myconfined[axis] = 1
self.aux[axis] = specs = list(self.kargs[kw])
if (
type(specs[0]) == type(cdtime.comptime(1999))
or type(specs[0]) == type(cdtime.reltime(0, "days since 1999"))
or type(specs[0]) == type("")
):
list2 = []
for l in specs:
if type(l) != type(""):
list2.append(l.torel("days since 1900").value)
else:
list2.append(cdtime.s2r(l, "days since 1900").value)
min = minimum(list2)
max = maximum(list2)
specification[axis] = (
cdtime.reltime(min, "days since 1900"),
cdtime.reltime(max, "days since 1900"),
)
else: # But if it's not...
specification[axis] = minimum(specs), maximum(specs)
else:
if myconfined[axis] == 1:
raise "Error you are attempting to set the axis: " + str(axes[axis].id) + " more than once"
else:
return 1
return 0
def autoscale_None(self, A):
' autoscale only None-valued vmin or vmax'
if self.vmin is None: self.vmin = ma.minimum(A)
if self.vmax is None: self.vmax = ma.maximum(A)
def create(self,
parent=None,
min=None,
max=None,
save_file=None,
thread_it=1,
rate=None,
bitrate=None,
ffmpegoptions=''):
from vcs import minmax
from numpy.ma import maximum, minimum
# Cannot "Run" or "Create" an animation while already creating an
# animation
if self.run_flg == 1:
return
if self.vcs_self.canvas.creating_animation() == 1:
return
if self.vcs_self.animate_info == []:
str = "No data found!"
showerror("Error Message to User", str)
return
# Stop the (thread) execution of the X main loop (if it is running).
self.vcs_self.canvas.stopxmainloop()
# Force VCS to update its orientation, needed when the user changes the
# VCS Canvas size.
self.vcs_self.canvas.updateorientation()
# Make sure the animate information is up-to-date for creating images
if ((self.gui_popup == 1) and (self.create_flg == 0)):
self.update_animate_display_list()
# Save the min and max values for the graphics methods.
# Will need to restore values back when animation is done.
self.save_original_min_max()
# Set up the animation min and max values by changing the graphics method
# Note: cannot set the min and max values if the default graphics
# method is set.
do_min_max = 'yes'
try:
if (parent is not None) and (parent.iso_spacing == 'Log'):
do_min_max = 'no'
except:
pass
# Draw specified continental outlines if needed.
self.continents_hold_value = self.vcs_self.canvas.getcontinentstype()
self.vcs_self.canvas.setcontinentstype(self.continents_value)
if (do_min_max == 'yes'):
minv = []
maxv = []
if (min is None) or (max is None):
for i in range(len(self.vcs_self.animate_info)):
minv.append(1.0e77)
maxv.append(-1.0e77)
for i in range(len(self.vcs_self.animate_info)):
dpy, slab = self.vcs_self.animate_info[i]
mins, maxs = minmax(slab)
minv[i] = float(minimum(float(minv[i]), float(mins)))
maxv[i] = float(maximum(float(maxv[i]), float(maxs)))
if isinstance(min, list) or isinstance(max, list):
for i in range(len(self.vcs_self.animate_info)):
try:
minv.append(min[i])
except:
minv.append(min[-1])
try:
maxv.append(max[i])
except:
maxv.append(max[-1])
else:
for i in range(len(self.vcs_self.animate_info)):
minv.append(min)
maxv.append(max)
# Set the min an max for each plot in the page. If the same graphics method is used
# to display the plots, then the last min and max setting of the
# data set will be used.
for i in range(len(self.vcs_self.animate_info)):
try:
self.set_animation_min_max(minv[i], maxv[i], i)
except:
# if it is default, then you cannot set the min and max, so
# pass.
pass
if save_file is None or save_file.split('.')[-1].lower() == 'ras':
if thread_it:
thread.start_new_thread(self.vcs_self.canvas.animate_init,
(save_file, ))
else:
self.vcs_self.canvas.animate_init(save_file)
else: # ffmpeg stuff
save_info = self.vcs_self.animate_info
animation_info = self.animate_info_from_python()
slabs = []
templates = []
dpys = []
for i in range(len(self.vcs_self.animate_info)):
dpy, slab = self.vcs_self.animate_info[i]
slabs.append(slab)
dpys.append(dpy)
templates.append(dpy.template)
sh = slabs[0].shape
if dpy.g_type in [
'boxfill',
'isofill',
'isoline',
'meshfill',
'outfill',
'outline',
'taylordiagram',
'vector',
]:
r = len(sh) - 2
else:
r = len(sh) - 1
# now create the list of all previous indices to plot
indices = []
for i in range(r):
this = list(range(sh[i]))
tmp = []
if indices == []:
for k in this:
indices.append([
k,
])
else:
for j in range(len(indices)):
for k in this:
tmp2 = copy.copy(indices[j])
tmp2.append(k)
tmp.append(tmp2)
indices = tmp
count = 1
white_square = self.vcs_self.createfillarea()
white_square.color = 240
white_square.x = [0, 1, 1, 0]
white_square.y = [0, 0, 1, 1]
new_vcs = self.vcs_self
if self.vcs_self.orientation() == 'portrait':
new_vcs.portrait()
# self.vcs_self.close()
for index in indices:
new_vcs.clear()
new_vcs.plot(white_square, bg=1)
for i in range(len(save_info)):
slab = slabs[i]
template = templates[i]
gtype = animation_info["gtype"][i].lower()
gname = animation_info["gname"][i]
gm = None # for flake8 to be happy
exec("gm = new_vcs.get%s('%s')" % (gtype, gname))
for j in index:
slab = slab[j]
new_vcs.plot(slab, gm, new_vcs.gettemplate(template), bg=1)
new_vcs.png("tmp_anim_%i" % count)
count += 1
new_vcs.ffmpeg(save_file,
"tmp_anim_%d.png",
bitrate=bitrate,
rate=rate,
options=ffmpegoptions)
for i in range(count - 1):
os.remove("tmp_anim_%i.png" % (i + 1))
del (new_vcs)
self.create_flg = 1