def _autolev(self, z, N):
'''
Select contour levels to span the data.
We need two more levels for filled contours than for
line contours, because for the latter we need to specify
the lower and upper boundary of each range. For example,
a single contour boundary, say at z = 0, requires only
one contour line, but two filled regions, and therefore
three levels to provide boundaries for both regions.
'''
zmax = self.zmax
zmin = self.zmin
zmargin = (zmax - zmin) * 0.001 # so z < (zmax + zmargin)
zmax = zmax + zmargin
intv = Interval(Value(zmin), Value(zmax))
if self.locator is None:
self.locator = MaxNLocator(N + 1)
self.locator.set_view_interval(intv)
self.locator.set_data_interval(intv)
lev = self.locator()
self._auto = True
if self.filled:
return lev
return lev[1:-1]
def _autolev(self, z, N):
'''
Select contour levels to span the data.
We need two more levels for filled contours than for
line contours, because for the latter we need to specify
the lower and upper boundary of each range. For example,
a single contour boundary, say at z = 0, requires only
one contour line, but two filled regions, and therefore
three levels to provide boundaries for both regions.
'''
zmax = self.zmax
zmin = self.zmin
zmargin = (zmax - zmin) * 0.001 # so z < (zmax + zmargin)
zmax = zmax + zmargin
intv = Interval(Value(zmin), Value(zmax))
if self.locator is None:
self.locator = MaxNLocator(N+1)
self.locator.set_view_interval(intv)
self.locator.set_data_interval(intv)
lev = self.locator()
self._auto = True
if self.filled:
return lev
return lev[1:-1]
class ContourSet(ScalarMappable, ContourLabeler):
"""
Create and store a set of contour lines or filled regions.
User-callable method: clabel
Useful attributes:
ax - the axes object in which the contours are drawn
collections - a silent_list of LineCollections or PolyCollections
levels - contour levels
layers - same as levels for line contours; half-way between
levels for filled contours. See _process_colors method.
"""
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.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.clip_ends = kwargs.get('clip_ends', None) ########
self.extend = kwargs.get('extend', 'neither')
if self.clip_ends is not None:
warnings.warn("'clip_ends' has been replaced by 'extend'")
self.levels = self.levels[1:-1] # discard specified end levels
self.extend = 'both' # regenerate end levels
self.antialiased = kwargs.get('antialiased', True)
self.nchunk = kwargs.get('nchunk', 0)
self.locator = kwargs.get('locator', None)
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, 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 = rcParams['image.origin']
x, y, z = self._contour_args(*args) # also sets self.levels,
# self.layers
if self.colors is not None:
cmap = ListedColormap(self.colors, N=len(self.layers))
if self.filled:
self.collections = silent_list('PolyCollection')
else:
self.collections = silent_list('LineCollection')
# label lists must be initialized here
self.cl = []
self.cl_cvalues = []
kw = {'cmap': cmap}
if norm is not None:
kw['norm'] = norm
ScalarMappable.__init__(self, **kw) # sets self.cmap;
self._process_colors()
if self.filled:
if self.linewidths is None:
self.linewidths = 0.05 # Good default for Postscript.
if iterable(self.linewidths):
self.linewidths = self.linewidths[0]
#C = _contour.Cntr(x, y, z.filled(), z.mask())
C = _contour.Cntr(x, y, z.filled(), ma.getmaskorNone(z))
lowers = self._levels[:-1]
uppers = self._levels[1:]
for level, level_upper, color in zip(lowers, uppers, self.tcolors):
nlist = C.trace(level,
level_upper,
points=0,
nchunk=self.nchunk)
col = PolyCollection(nlist,
linewidths=(self.linewidths, ),
antialiaseds=(self.antialiased, ),
facecolors=color,
edgecolors='None')
self.ax.add_collection(col)
self.collections.append(col)
else:
tlinewidths = self._process_linewidths()
self.tlinewidths = tlinewidths
#C = _contour.Cntr(x, y, z.filled(), z.mask())
C = _contour.Cntr(x, y, z.filled(), ma.getmaskorNone(z))
for level, color, width in zip(self.levels, self.tcolors,
tlinewidths):
nlist = C.trace(level, points=0)
col = LineCollection(nlist, colors=color, linewidths=width)
if level < 0.0 and self.monochrome:
col.set_linestyle(
(0, rcParams['contour.negative_linestyle']))
col.set_label(str(level)) # only for self-documentation
self.ax.add_collection(col)
self.collections.append(col)
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.set_xlim((x0, x1))
self.ax.set_ylim((y0, y1))
def changed(self):
tcolors = [(tuple(rgba), )
for rgba in self.to_rgba(self.cvalues, alpha=self.alpha)]
self.tcolors = tcolors
contourNum = 0
for color, collection in zip(tcolors, self.collections):
collection.set_color(color)
for label, cv in zip(self.cl, self.cl_cvalues):
label.set_color(self.label_mappable.to_rgba(cv))
# add label colors
ScalarMappable.changed(self)
def _autolev(self, z, N):
'''
Select contour levels to span the data.
We need two more levels for filled contours than for
line contours, because for the latter we need to specify
the lower and upper boundary of each range. For example,
a single contour boundary, say at z = 0, requires only
one contour line, but two filled regions, and therefore
three levels to provide boundaries for both regions.
'''
zmax = self.zmax
zmin = self.zmin
zmargin = (zmax - zmin) * 0.001 # so z < (zmax + zmargin)
zmax = zmax + zmargin
intv = Interval(Value(zmin), Value(zmax))
if self.locator is None:
self.locator = MaxNLocator(N + 1)
self.locator.set_view_interval(intv)
self.locator.set_data_interval(intv)
lev = self.locator()
self._auto = True
if self.filled:
return lev
return lev[1:-1]
def _initialize_x_y(self, z):
'''
Return X, Y arrays such that contour(Z) will match imshow(Z)
if origin is not None.
The center of pixel Z[i,j] depends on origin:
if origin is None, x = j, y = i;
if origin is 'lower', x = j + 0.5, y = i + 0.5;
if origin is 'upper', x = j + 0.5, y = Nrows - i - 0.5
If extent is not None, x and y will be scaled to match,
as in imshow.
If origin is None and extent is not None, then extent
will give the minimum and maximum values of x and y.
'''
if len(shape(z)) != 2:
raise TypeError("Input must be a 2D array.")
else:
Ny, Nx = shape(z)
if self.origin is None: # Not for image-matching.
if self.extent is None:
return meshgrid(arange(Nx), arange(Ny))
else:
x0, x1, y0, y1 = self.extent
x = linspace(x0, x1, Nx)
y = linspace(y0, y1, Ny)
return meshgrid(x, y)
# Match image behavior:
if self.extent is None:
x0, x1, y0, y1 = (0, Nx, 0, Ny)
else:
x0, x1, y0, y1 = self.extent
dx = float(x1 - x0) / Nx
dy = float(y1 - y0) / Ny
x = x0 + (arange(Nx) + 0.5) * dx
y = y0 + (arange(Ny) + 0.5) * dy
if self.origin == 'upper':
y = y[::-1]
return meshgrid(x, y)
def _check_xyz(self, args):
'''
For functions like contour, check that the dimensions
of the input arrays match; if x and y are 1D, convert
them to 2D using meshgrid.
Possible change: I think we should make and use an ArgumentError
Exception class (here and elsewhere).
Add checking for everything being the same numerix flavor?
'''
x, y, z = args
if len(shape(z)) != 2:
raise TypeError("Input z must be a 2D array.")
else:
Ny, Nx = shape(z)
if shape(x) == shape(z) and shape(y) == shape(z):
return x, y, z
if len(shape(x)) != 1 or len(shape(y)) != 1:
raise TypeError("Inputs x and y must be 1D or 2D.")
nx, = shape(x)
ny, = shape(y)
if nx != Nx or ny != Ny:
raise TypeError("Length of x must be number of columns in z,\n" +
"and length of y must be number of rows.")
x, y = meshgrid(x, y)
return x, y, z
def _contour_args(self, *args):
if self.filled: fn = 'contourf'
else: fn = 'contour'
Nargs = len(args)
if Nargs <= 2:
z = args[0]
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.asarray(
z) # Convert to native masked array format if necessary.
self.zmax = ma.maximum(z)
self.zmin = ma.minimum(z)
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]
if type(level_arg) == int:
lev = self._autolev(z, level_arg)
elif iterable(level_arg) and len(shape(level_arg)) == 1:
lev = array([float(fl) for fl in level_arg])
else:
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, self.zmin - 1)
if self.extend in ('both', 'max'):
self._levels.append(self.zmax + 1)
self._levels = asarray(self._levels)
self.vmin = amin(self.levels) # alternative would be self.layers
self.vmax = amax(self.levels)
if self.extend in ('both', 'min') or self.clip_ends:
self.vmin = 2 * self.levels[0] - self.levels[1]
if self.extend in ('both', 'max') or self.clip_ends:
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') or self.clip_ends:
self.layers[0] = 0.5 * (self.vmin + self._levels[1])
if self.extend in ('both', 'max') or self.clip_ends:
self.layers[-1] = 0.5 * (self.vmax + self._levels[-2])
return (x, y, z)
def _process_colors(self):
"""
Color argument processing for contouring.
Note that we base the color mapping on the contour levels,
not on the actual range of the Z values. This means we
don't have to worry about bad values in Z, and we always have
the full dynamic range available for the selected levels.
The color is based on the midpoint of the layer, except for
an extended end layers.
"""
self.monochrome = self.cmap.monochrome
if self.colors is not None:
i0, i1 = 0, len(self.layers)
if self.extend in ('both', 'min'):
i0 = -1
if self.extend in ('both', 'max'):
i1 = i1 + 1
self.cvalues = range(i0, i1)
self.set_norm(no_norm())
else:
self.cvalues = self.layers
if not self.norm.scaled():
self.set_clim(self.vmin, self.vmax)
if self.extend in ('both', 'max', 'min'):
self.norm.clip = False
self.set_array(self.layers)
# self.tcolors will be set by the "changed" method
def _process_linewidths(self):
linewidths = self.linewidths
Nlev = len(self.levels)
if linewidths is None:
tlinewidths = [(rcParams['lines.linewidth'], )] * Nlev
else:
if iterable(linewidths) and len(linewidths) < Nlev:
linewidths = list(linewidths) * int(
ceil(Nlev / len(linewidths)))
elif not iterable(linewidths) and type(linewidths) in [int, float]:
linewidths = [linewidths] * Nlev
tlinewidths = [(w, ) for w in linewidths]
return tlinewidths
contour_doc = """
class ContourSet(ScalarMappable, ContourLabeler):
"""
Create and store a set of contour lines or filled regions.
User-callable method: clabel
Useful attributes:
ax - the axes object in which the contours are drawn
collections - a silent_list of LineCollections or PolyCollections
levels - contour levels
layers - same as levels for line contours; half-way between
levels for filled contours. See _process_colors method.
"""
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.filled = kwargs.get('filled', False)
self.linewidths = kwargs.get('linewidths', 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.clip_ends = kwargs.get('clip_ends', True)
self.antialiased = kwargs.get('antialiased', True)
self.nchunk = kwargs.get('nchunk', 0)
self.locator = kwargs.get('locator', None)
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, 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 = rcParams['image.origin']
x, y, z = self._contour_args(*args) # also sets self.levels,
# self.layers
if self.colors is not None:
cmap = ListedColormap(self.colors, N=len(self.layers))
if self.filled:
self.collections = silent_list('PolyCollection')
else:
self.collections = silent_list('LineCollection')
# label lists must be initialized here
self.cl = []
self.cl_cvalues = []
kw = {'cmap': cmap}
if norm is not None:
kw['norm'] = norm
ScalarMappable.__init__(self, **kw) # sets self.cmap;
self._process_colors()
if self.filled:
if self.linewidths is None:
self.linewidths = 0.05 # Good default for Postscript.
if iterable(self.linewidths):
self.linewidths = self.linewidths[0]
#C = _contour.Cntr(x, y, z.filled(), z.mask())
C = _contour.Cntr(x, y, z.filled(), ma.getmaskorNone(z))
lowers = self.levels[:-1]
uppers = self.levels[1:]
for level, level_upper, color in zip(lowers, uppers, self.tcolors):
nlist = C.trace(level, level_upper, points = 1,
nchunk = self.nchunk)
col = PolyCollection(nlist,
linewidths = (self.linewidths,),
antialiaseds = (self.antialiased,))
col.set_color(color) # sets both facecolor and edgecolor
self.ax.add_collection(col)
self.collections.append(col)
else:
tlinewidths = self._process_linewidths()
#C = _contour.Cntr(x, y, z.filled(), z.mask())
C = _contour.Cntr(x, y, z.filled(), ma.getmaskorNone(z))
for level, color, width in zip(self.levels, self.tcolors, tlinewidths):
nlist = C.trace(level, points = 1)
col = LineCollection(nlist)
col.set_color(color)
col.set_linewidth(width)
if level < 0.0 and self.monochrome:
col.set_linestyle((0, (6.,6.)),)
col.set_label(str(level)) # only for self-documentation
self.ax.add_collection(col)
self.collections.append(col)
## check: seems like set_xlim should also be inside
if not self.ax.ishold():
self.ax.cla()
self.ax.set_xlim((ma.minimum(x), ma.maximum(x)))
self.ax.set_ylim((ma.minimum(y), ma.maximum(y)))
def changed(self):
tcolors = [ (tuple(rgba),) for rgba in
self.to_rgba(self.cvalues, alpha=self.alpha)]
self.tcolors = tcolors
contourNum = 0
for color, collection in zip(tcolors, self.collections):
collection.set_color(color)
for label, cv in zip(self.cl, self.cl_cvalues):
label.set_color(self.label_mappable.to_rgba(cv))
# add label colors
ScalarMappable.changed(self)
def _autolev(self, z, N):
'''
Select contour levels to span the data.
We need two more levels for filled contours than for
line contours, because for the latter we need to specify
the lower and upper boundary of each range. For example,
a single contour boundary, say at z = 0, requires only
one contour line, but two filled regions, and therefore
three levels to provide boundaries for both regions.
'''
zmax = ma.maximum(z)
zmin = ma.minimum(z)
zmargin = (zmax - zmin) * 0.001 # so z < (zmax + zmargin)
zmax += zmargin
intv = Interval(Value(zmin), Value(zmax))
if self.locator is None:
self.locator = MaxNLocator(N+1)
self.locator.set_view_interval(intv)
self.locator.set_data_interval(intv)
lev = self.locator()
if self.filled:
return lev
return lev[1:-1]
def _initialize_x_y(self, z):
'''
Return X, Y arrays such that contour(Z) will match imshow(Z)
if origin is not None.
The center of pixel Z[i,j] depends on origin:
if origin is None, x = j, y = i;
if origin is 'lower', x = j + 0.5, y = i + 0.5;
if origin is 'upper', x = j + 0.5, y = Nrows - i - 0.5
If extent is not None, x and y will be scaled to match,
as in imshow.
If origin is None and extent is not None, then extent
will give the minimum and maximum values of x and y.
'''
if len(shape(z)) != 2:
raise TypeError("Input must be a 2D array.")
else:
Ny, Nx = shape(z)
if self.origin is None: # Not for image-matching.
if self.extent is None:
return meshgrid(arange(Nx), arange(Ny))
else:
x0,x1,y0,y1 = self.extent
x = linspace(x0, x1, Nx)
y = linspace(y0, y1, Ny)
return meshgrid(x, y)
# Match image behavior:
if self.extent is None:
x0,x1,y0,y1 = (0, Nx, 0, Ny)
else:
x0,x1,y0,y1 = self.extent
dx = float(x1 - x0)/Nx
dy = float(y1 - y0)/Ny
x = x0 + (arange(Nx) + 0.5) * dx
y = y0 + (arange(Ny) + 0.5) * dy
if self.origin == 'upper':
y = y[::-1]
return meshgrid(x,y)
def _check_xyz(self, args):
'''
For functions like contour, check that the dimensions
of the input arrays match; if x and y are 1D, convert
them to 2D using meshgrid.
Possible change: I think we should make and use an ArgumentError
Exception class (here and elsewhere).
Add checking for everything being the same numerix flavor?
'''
x,y,z = args
if len(shape(z)) != 2:
raise TypeError("Input z must be a 2D array.")
else: Ny, Nx = shape(z)
if shape(x) == shape(z) and shape(y) == shape(z):
return x,y,z
if len(shape(x)) != 1 or len(shape(y)) != 1:
raise TypeError("Inputs x and y must be 1D or 2D.")
nx, = shape(x)
ny, = shape(y)
if nx != Nx or ny != Ny:
raise TypeError("Length of x must be number of columns in z,\n" +
"and length of y must be number of rows.")
x,y = meshgrid(x,y)
return x,y,z
def _contour_args(self, *args):
if self.filled: fn = 'contourf'
else: fn = 'contour'
Nargs = len(args)
if Nargs <= 2:
z = args[0]
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.asarray(z) # Convert to native masked array format if necessary.
if Nargs == 1 or Nargs == 3:
lev = self._autolev(z, 7)
else: # 2 or 4 args
level_arg = args[-1]
if type(level_arg) == int:
lev = self._autolev(z, level_arg)
elif iterable(level_arg) and len(shape(level_arg)) == 1:
lev = array([float(fl) for fl in level_arg])
else:
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
self.layers = self.levels # contour: a line is a thin layer
if self.filled:
self.layers = 0.5 * (self.levels[:-1] + self.levels[1:])
return (x, y, z)
def _process_colors(self):
"""
Color argument processing for contouring.
Note that we base the color mapping on the contour levels,
not on the actual range of the Z values. This means we
don't have to worry about bad values in Z, and we always have
the full dynamic range available for the selected levels.
The color is based on the midpoint of the layer, except for
the end layers when clip_ends is True.
"""
self.monochrome = self.cmap.monochrome
if self.colors is not None:
self.cvalues = range(len(self.layers))
self.set_norm(no_norm())
else:
self.cvalues = self.layers
if self.filled and len(self.layers) > 2 and self.clip_ends:
vmin = 2 * self.levels[1] - self.levels[2]
vmax = 2 * self.levels[-2] - self.levels[-3]
else:
vmin = amin(self.levels) # alternative would be self.layers
vmax = amax(self.levels)
self.set_clim(vmin, vmax)
self.set_array(self.layers)
self.tcolors = [ (tuple(rgba),) for rgba in self.to_rgba(self.cvalues)]
def _process_linewidths(self):
linewidths = self.linewidths
Nlev = len(self.levels)
if linewidths is None:
tlinewidths = [rcParams['lines.linewidth']] *Nlev
else:
if iterable(linewidths) and len(linewidths) < Nlev:
linewidths = list(linewidths) * int(ceil(Nlev/len(linewidths)))
elif not iterable(linewidths) and type(linewidths) in [int, float]:
linewidths = [linewidths] * Nlev
tlinewidths = [(w,) for w in linewidths]
return tlinewidths
contour_doc = """
