def unmasked_index_ranges(mask, compressed=True):
'''
Calculate the good data ranges in a masked 1-D array, based on mask.
Returns Nx2 array with each row the start and stop indices
for slices of the compressed array corresponding to each of N
uninterrupted runs of unmasked values.
If optional argument compressed is False, it returns the
start and stop indices into the original array, not the
compressed array.
In either case, an empty array is returned if there are no
unmasked values.
Example:
y = ma.array(arange(5), mask = [0,0,1,0,0])
#ii = unmasked_index_ranges(y.mask())
ii = unmasked_index_ranges(ma.getmask(y))
# returns [[0,2,] [2,4,]]
y.compressed().filled()[ii[1,0]:ii[1,1]]
# returns array [3,4,]
# (The 'filled()' method converts the masked array to a numerix array.)
#i0, i1 = unmasked_index_ranges(y.mask(), compressed=False)
i0, i1 = unmasked_index_ranges(ma.getmask(y), compressed=False)
# returns [[0,3,] [2,5,]]
y.filled()[ii[1,0]:ii[1,1]]
# returns array [3,4,]
'''
m = concatenate(((1, ), mask, (1, )))
indices = arange(len(mask) + 1)
mdif = m[1:] - m[:-1]
i0 = compress(mdif == -1, indices)
i1 = compress(mdif == 1, indices)
assert len(i0) == len(i1)
if not compressed:
if len(i1):
return concatenate((i0[:, ma.NewAxis], i1[:, ma.NewAxis]), axis=1)
else:
return zeros((0, 0), 'i')
seglengths = i1 - i0
breakpoints = cumsum(seglengths)
try:
ic0 = concatenate(((0, ), breakpoints[:-1]))
ic1 = breakpoints
return concatenate((ic0[:, ma.NewAxis], ic1[:, ma.NewAxis]), axis=1)
except:
return zeros((0, 0), 'i')
def unmasked_index_ranges(mask, compressed = True):
'''
Calculate the good data ranges in a masked 1-D array, based on mask.
Returns Nx2 array with each row the start and stop indices
for slices of the compressed array corresponding to each of N
uninterrupted runs of unmasked values.
If optional argument compressed is False, it returns the
start and stop indices into the original array, not the
compressed array.
In either case, an empty array is returned if there are no
unmasked values.
Example:
y = ma.array(arange(5), mask = [0,0,1,0,0])
#ii = unmasked_index_ranges(y.mask())
ii = unmasked_index_ranges(ma.getmask(y))
# returns [[0,2,] [2,4,]]
y.compressed().filled()[ii[1,0]:ii[1,1]]
# returns array [3,4,]
# (The 'filled()' method converts the masked array to a numerix array.)
#i0, i1 = unmasked_index_ranges(y.mask(), compressed=False)
i0, i1 = unmasked_index_ranges(ma.getmask(y), compressed=False)
# returns [[0,3,] [2,5,]]
y.filled()[ii[1,0]:ii[1,1]]
# returns array [3,4,]
'''
m = concatenate(((1,), mask, (1,)))
indices = arange(len(mask) + 1)
mdif = m[1:] - m[:-1]
i0 = compress(mdif == -1, indices)
i1 = compress(mdif == 1, indices)
assert len(i0) == len(i1)
if not compressed:
if len(i1):
return concatenate((i0[:, ma.NewAxis], i1[:, ma.NewAxis]), axis=1)
else:
return zeros((0,0), 'i')
seglengths = i1 - i0
breakpoints = cumsum(seglengths)
try:
ic0 = concatenate(((0,), breakpoints[:-1]))
ic1 = breakpoints
return concatenate((ic0[:, ma.NewAxis], ic1[:, ma.NewAxis]), axis=1)
except:
return zeros((0,0), 'i')
def hist(y, bins=10, normed=0):
"""
Return the histogram of y with bins equally sized bins. If bins
is an array, use the bins. Return value is
(n,x) where n is the count for each bin in x
If normed is False, return the counts in the first element of the
return tuple. If normed is True, return the probability density
n/(len(y)*dbin)
If y has rank>1, it will be raveled
Credits: the Numeric 22 documentation
"""
y = asarray(y)
if len(y.shape)>1: y = ravel(y)
if not iterable(bins):
ymin, ymax = min(y), max(y)
if ymin==ymax:
ymin -= 0.5
ymax += 0.5
bins = linspace(ymin, ymax, bins)
n = searchsorted(sort(y), bins)
n = diff(concatenate([n, [len(y)]]))
if normed:
db = bins[1]-bins[0]
return 1/(len(y)*db)*n, bins
else:
return n, bins
def hist(y, bins=10, normed=0):
"""
Return the histogram of y with bins equally sized bins. If bins
is an array, use the bins. Return value is
(n,x) where n is the count for each bin in x
If normed is False, return the counts in the first element of the
return tuple. If normed is True, return the probability density
n/(len(y)*dbin)
If y has rank>1, it will be raveled
Credits: the Numeric 22 documentation
"""
y = asarray(y)
if len(y.shape) > 1: y = ravel(y)
if not iterable(bins):
ymin, ymax = min(y), max(y)
if ymin == ymax:
ymin -= 0.5
ymax += 0.5
bins = linspace(ymin, ymax, bins)
n = searchsorted(sort(y), bins)
n = diff(concatenate([n, [len(y)]]))
if normed:
db = bins[1] - bins[0]
return 1 / (len(y) * db) * n, bins
else:
return n, bins
def plot_surface(self, X, Y, Z, *args, **kwargs):
had_data = self.has_data()
rows, cols = Z.shape
tX,tY,tZ = nx.transpose(X), nx.transpose(Y), nx.transpose(Z)
rstride = cbook.popd(kwargs, 'rstride', 10)
cstride = cbook.popd(kwargs, 'cstride', 10)
#
polys = []
boxes = []
for rs in nx.arange(0,rows,rstride):
for cs in nx.arange(0,cols,cstride):
ps = []
corners = []
for a,ta in [(X,tX),(Y,tY),(Z,tZ)]:
ztop = a[rs][cs:min(cols-1,cs+cstride)]
zleft = ta[min(cols-1,cs+cstride)][rs:min(rows,rs+rstride+1)]
zbase = a[min(rows-1,rs+rstride)][cs:min(cols,cs+cstride+1):]
zbase = zbase[::-1]
zright = ta[cs][rs:min(rows-1,rs+rstride):]
zright = zright[::-1]
corners.append([ztop[0],ztop[-1],zbase[0],zbase[-1]])
z = nx.concatenate((ztop,zleft,zbase,zright))
ps.append(z)
boxes.append(map(nx.array,zip(*corners)))
polys.append(zip(*ps))
#
lines = []
shade = []
for box in boxes:
n = proj3d.cross(box[0]-box[1],
box[0]-box[2])
n = n/proj3d.mod(n)*5
shade.append(nx.dot(n,[-1,-1,0.5]))
lines.append((box[0],n+box[0]))
#
color = nx.array([0,0,1,1])
norm = normalize(min(shade),max(shade))
colors = [color * (0.5+norm(v)*0.5) for v in shade]
for c in colors: c[3] = 1
polyc = art3d.Poly3DCollection(polys, facecolors=colors, *args, **kwargs)
polyc._zsort = 1
self.add_collection(polyc)
#
self.auto_scale_xyz(X,Y,Z, had_data)
return polyc
def levypdf(x, gamma, alpha):
"Returm the levy pdf evaluated at x for params gamma, alpha"
N = len(x)
if N % 2 != 0:
raise ValueError, 'x must be an event length array; try\n' + \
'x = linspace(minx, maxx, N), where N is even'
dx = x[1] - x[0]
f = 1 / (N * dx) * arange(-N / 2, N / 2, Float)
ind = concatenate([arange(N / 2, N, Int), arange(N / 2, Int)])
df = f[1] - f[0]
cfl = exp(-gamma * absolute(2 * pi * f)**alpha)
px = fft(take(cfl, ind) * df).astype(Float)
return take(px, ind)
def labels(self, inline):
levels = self.label_levels
fslist = self.fslist
trans = self.ax.transData
colors = self.label_mappable.to_rgba(self.label_cvalues)
fmt = self.fmt
for icon, lev, color, cvalue, fsize in zip(self.label_indices,
self.label_levels, colors,
self.label_cvalues, fslist):
con = self.collections[icon]
lw = self.get_label_width(lev, fmt, fsize)
additions = []
for segNum, linecontour in enumerate(con._segments):
# for closed contours add one more point to
# avoid division by zero
if all(linecontour[0] == linecontour[-1]):
linecontour = concatenate(
(linecontour, linecontour[1][newaxis, :]))
#linecontour.append(linecontour[1])
# transfer all data points to screen coordinates
slc = trans.seq_xy_tups(linecontour)
if self.print_label(slc, lw):
x, y, rotation, ind = self.locate_label(slc, lw)
# transfer the location of the label back to
# data coordinates
dx, dy = trans.inverse_xy_tup((x, y))
t = Text(dx,
dy,
rotation=rotation,
horizontalalignment='center',
verticalalignment='center')
text = self.get_text(lev, fmt)
self.set_label_props(t, text, color)
self.cl.append(t)
self.cl_cvalues.append(cvalue)
if inline:
new = self.break_linecontour(linecontour, rotation, lw,
ind)
con._segments[segNum] = new[0]
additions.append(new[1])
con._segments.extend(additions)
def labels(self, inline):
levels = self.label_levels
fslist = self.fslist
trans = self.ax.transData
colors = self.label_mappable.to_rgba(self.label_cvalues)
fmt = self.fmt
for icon, lev, color, cvalue, fsize in zip(self.label_indices,
self.label_levels,
colors,
self.label_cvalues, fslist):
con = self.collections[icon]
lw = self.get_label_width(lev, fmt, fsize)
additions = []
for segNum, linecontour in enumerate(con._segments):
# for closed contours add one more point to
# avoid division by zero
if all(linecontour[0] == linecontour[-1]):
linecontour = concatenate((linecontour,
linecontour[1][newaxis,:]))
#linecontour.append(linecontour[1])
# transfer all data points to screen coordinates
slc = trans.seq_xy_tups(linecontour)
if self.print_label(slc,lw):
x,y, rotation, ind = self.locate_label(slc, lw)
# transfer the location of the label back to
# data coordinates
dx,dy = trans.inverse_xy_tup((x,y))
t = Text(dx, dy, rotation = rotation,
horizontalalignment='center',
verticalalignment='center')
text = self.get_text(lev,fmt)
self.set_label_props(t, text, color)
self.cl.append(t)
self.cl_cvalues.append(cvalue)
if inline:
new = self.break_linecontour(linecontour, rotation,
lw, ind)
con._segments[segNum] = new[0]
additions.append(new[1])
con._segments.extend(additions)
def levypdf(x, gamma, alpha):
"Returm the levy pdf evaluated at x for params gamma, alpha"
N = len(x)
if N%2 != 0:
raise ValueError, 'x must be an event length array; try\n' + \
'x = linspace(minx, maxx, N), where N is even'
dx = x[1]-x[0]
f = 1/(N*dx)*arange(-N/2, N/2, Float)
ind = concatenate([arange(N/2, N, Int),
arange(N/2,Int)])
df = f[1]-f[0]
cfl = exp(-gamma*absolute(2*pi*f)**alpha)
px = fft(take(cfl,ind)*df).astype(Float)
return take(px, ind)
def break_linecontour(self, linecontour, rot, labelwidth, ind):
"break a contour in two contours at the location of the label"
lcsize = len(linecontour)
hlw = int(labelwidth / 2)
#length of label in screen coords
ylabel = abs(hlw * sin(rot * pi / 180))
xlabel = abs(hlw * cos(rot * pi / 180))
trans = self.ax.transData
slc = trans.seq_xy_tups(linecontour)
x, y = slc[ind]
xx = asarray(slc)[:, 0].copy()
yy = asarray(slc)[:, 1].copy()
#indices which are under the label
inds = nonzero(((xx < x + xlabel) & (xx > x - xlabel))
& ((yy < y + ylabel) & (yy > y - ylabel)))
if len(inds) > 0:
#if the label happens to be over the beginning of the
#contour, the entire contour is removed, i.e.
#indices to be removed are
#inds= [0,1,2,3,305,306,307]
#should rewrite this in a better way
linds = nonzero(inds[1:] - inds[:-1] != 1)
if inds[0] == 0 and len(linds) != 0:
ii = inds[linds[0]]
lc1 = linecontour[ii + 1:inds[ii + 1]]
lc2 = []
else:
lc1 = linecontour[:inds[0]]
lc2 = linecontour[inds[-1] + 1:]
else:
lc1 = linecontour[:ind]
lc2 = linecontour[ind + 1:]
if rot < 0:
new_x1, new_y1 = x - xlabel, y + ylabel
new_x2, new_y2 = x + xlabel, y - ylabel
else:
new_x1, new_y1 = x - xlabel, y - ylabel
new_x2, new_y2 = x + xlabel, y + ylabel
new_x1d, new_y1d = trans.inverse_xy_tup((new_x1, new_y1))
new_x2d, new_y2d = trans.inverse_xy_tup((new_x2, new_y2))
new_xy1 = array(((new_x1d, new_y1d), ))
new_xy2 = array(((new_x2d, new_y2d), ))
if rot > 0:
if (len(lc1) > 0 and (lc1[-1][0] <= new_x1d)
and (lc1[-1][1] <= new_y1d)):
lc1 = concatenate((lc1, new_xy1))
#lc1.append((new_x1d, new_y1d))
if (len(lc2) > 0 and (lc2[0][0] >= new_x2d)
and (lc2[0][1] >= new_y2d)):
lc2 = concatenate((new_xy2, lc2))
#lc2.insert(0, (new_x2d, new_y2d))
else:
if (len(lc1) > 0
and ((lc1[-1][0] <= new_x1d) and (lc1[-1][1] >= new_y1d))):
lc1 = concatenate((lc1, new_xy1))
#lc1.append((new_x1d, new_y1d))
if (len(lc2) > 0
and ((lc2[0][0] >= new_x2d) and (lc2[0][1] <= new_y2d))):
lc2 = concatenate((new_xy2, lc2))
#lc2.insert(0, (new_x2d, new_y2d))
return [lc1, lc2]
def __init__(self, x, y, dx, dy, width=0.001, length_includes_head=False, \
head_width=None, head_length=None, shape='full', overhang=0, \
head_starts_at_zero=False,**kwargs):
"""Returns a new Arrow.
length_includes_head: True if head is counted in calculating the length.
shape: ['full', 'left', 'right']
overhang: distance that the arrow is swept back (0 overhang means
triangular shape).
head_starts_at_zero: if True, the head starts being drawn at coordinate
0 instead of ending at coordinate 0.
"""
if head_width is None:
head_width = 3 * width
if head_length is None:
head_length = 1.5 * head_width
distance = sqrt(dx**2 + dy**2)
if length_includes_head:
length = distance
else:
length = distance + head_length
if not length:
verts = [] #display nothing if empty
else:
#start by drawing horizontal arrow, point at (0,0)
hw, hl, hs, lw = head_width, head_length, overhang, width
left_half_arrow = array([
[0.0, 0.0], #tip
[-hl, -hw / 2.0], #leftmost
[-hl * (1 - hs), -lw / 2.0], #meets stem
[-length, -lw / 2.0], #bottom left
[-length, 0],
])
#if we're not including the head, shift up by head length
if not length_includes_head:
left_half_arrow += [head_length, 0]
#if the head starts at 0, shift up by another head length
if head_starts_at_zero:
left_half_arrow += [head_length / 2.0, 0]
#figure out the shape, and complete accordingly
if shape == 'left':
coords = left_half_arrow
else:
right_half_arrow = left_half_arrow * [1, -1]
if shape == 'right':
coords = right_half_arrow
elif shape == 'full':
coords = concatenate(
[left_half_arrow, right_half_arrow[::-1]])
else:
raise ValueError, "Got unknown shape: %s" % shape
cx = float(dx) / distance
sx = float(dy) / distance
M = array([[cx, sx], [-sx, cx]])
verts = matrixmultiply(coords, M) + (x + dx, y + dy)
Polygon.__init__(self, map(tuple, verts), **kwargs)
def break_linecontour(self, linecontour, rot, labelwidth, ind):
"break a contour in two contours at the location of the label"
lcsize = len(linecontour)
hlw = int(labelwidth/2)
#length of label in screen coords
ylabel = abs(hlw * sin(rot*pi/180))
xlabel = abs(hlw * cos(rot*pi/180))
trans = self.ax.transData
slc = trans.seq_xy_tups(linecontour)
x,y = slc[ind]
xx= asarray(slc)[:,0].copy()
yy=asarray(slc)[:,1].copy()
#indices which are under the label
inds=nonzero(((xx < x+xlabel) & (xx > x-xlabel)) &
((yy < y+ylabel) & (yy > y-ylabel)))
if len(inds) >0:
#if the label happens to be over the beginning of the
#contour, the entire contour is removed, i.e.
#indices to be removed are
#inds= [0,1,2,3,305,306,307]
#should rewrite this in a better way
linds = nonzero(inds[1:]- inds[:-1] != 1)
if inds[0] == 0 and len(linds) != 0:
ii = inds[linds[0]]
lc1 =linecontour[ii+1:inds[ii+1]]
lc2 = []
else:
lc1=linecontour[:inds[0]]
lc2= linecontour[inds[-1]+1:]
else:
lc1=linecontour[:ind]
lc2 = linecontour[ind+1:]
if rot <0:
new_x1, new_y1 = x-xlabel, y+ylabel
new_x2, new_y2 = x+xlabel, y-ylabel
else:
new_x1, new_y1 = x-xlabel, y-ylabel
new_x2, new_y2 = x+xlabel, y+ylabel
new_x1d, new_y1d = trans.inverse_xy_tup((new_x1, new_y1))
new_x2d, new_y2d = trans.inverse_xy_tup((new_x2, new_y2))
new_xy1 = array(((new_x1d, new_y1d),))
new_xy2 = array(((new_x2d, new_y2d),))
if rot > 0:
if (len(lc1) > 0 and (lc1[-1][0] <= new_x1d)
and (lc1[-1][1] <= new_y1d)):
lc1 = concatenate((lc1, new_xy1))
#lc1.append((new_x1d, new_y1d))
if (len(lc2) > 0 and (lc2[0][0] >= new_x2d)
and (lc2[0][1] >= new_y2d)):
lc2 = concatenate((new_xy2, lc2))
#lc2.insert(0, (new_x2d, new_y2d))
else:
if (len(lc1) > 0 and ((lc1[-1][0] <= new_x1d)
and (lc1[-1][1] >= new_y1d))):
lc1 = concatenate((lc1, new_xy1))
#lc1.append((new_x1d, new_y1d))
if (len(lc2) > 0 and ((lc2[0][0] >= new_x2d)
and (lc2[0][1] <= new_y2d))):
lc2 = concatenate((new_xy2, lc2))
#lc2.insert(0, (new_x2d, new_y2d))
return [lc1,lc2]
def __init__(
self,
x,
y,
dx,
dy,
width=0.001,
length_includes_head=False,
head_width=None,
head_length=None,
shape="full",
overhang=0,
head_starts_at_zero=False,
**kwargs
):
"""Returns a new Arrow.
length_includes_head: True if head is counted in calculating the length.
shape: ['full', 'left', 'right']
overhang: distance that the arrow is swept back (0 overhang means
triangular shape).
head_starts_at_zero: if True, the head starts being drawn at coordinate
0 instead of ending at coordinate 0.
"""
if head_width is None:
head_width = 3 * width
if head_length is None:
head_length = 1.5 * head_width
distance = sqrt(dx ** 2 + dy ** 2)
if length_includes_head:
length = distance
else:
length = distance + head_length
if not length:
verts = [] # display nothing if empty
else:
# start by drawing horizontal arrow, point at (0,0)
hw, hl, hs, lw = head_width, head_length, overhang, width
left_half_arrow = array(
[
[0.0, 0.0], # tip
[-hl, -hw / 2.0], # leftmost
[-hl * (1 - hs), -lw / 2.0], # meets stem
[-length, -lw / 2.0], # bottom left
[-length, 0],
]
)
# if we're not including the head, shift up by head length
if not length_includes_head:
left_half_arrow += [head_length, 0]
# if the head starts at 0, shift up by another head length
if head_starts_at_zero:
left_half_arrow += [head_length / 2.0, 0]
# figure out the shape, and complete accordingly
if shape == "left":
coords = left_half_arrow
else:
right_half_arrow = left_half_arrow * [1, -1]
if shape == "right":
coords = right_half_arrow
elif shape == "full":
coords = concatenate([left_half_arrow, right_half_arrow[::-1]])
else:
raise ValueError, "Got unknown shape: %s" % shape
cx = float(dx) / distance
sx = float(dy) / distance
M = array([[cx, sx], [-sx, cx]])
verts = matrixmultiply(coords, M) + (x + dx, y + dy)
Polygon.__init__(self, map(tuple, verts), **kwargs)