def plotBox(self, name, data, data_range=None):
box = Frame(self, border=2, relief=SUNKEN)
box.pack(side=TOP, fill=BOTH, expand=YES)
frame = Frame(box, background='grey')
frame.pack(side=TOP, fill=X, expand=NO)
Label(frame, text=string.capitalize(string.join(
string.split(name , '_'), ' ')),
background='grey').pack(side=LEFT)
if data_range is None:
min = Numeric.minimum.reduce(data[:,1])
max = Numeric.maximum.reduce(data[:,1])
min, max = plotRange(min, max)
else:
min, max = data_range
plot_objects = []
plot_data = data
time = plot_data[:,0]
jumps = Numeric.repeat(Numeric.arange(len(time)-1),
Numeric.less(time[1:], time[:-1]))+1
for i in self.master.restarts:
plot_objects.append(PolyLine([(self.time[i], min),
(self.time[i], max)],
color='black',
stipple='gray25'))
plot_objects.insert(0, PolyLine(plot_data, color = 'red'))
plot = PlotCanvas(box, 400, 100, zoom=1,
select=self.master._selectRange)
plot.pack(side=LEFT, fill=BOTH, expand=YES)
plot.draw(PlotGraphics(plot_objects),
'automatic', (min, max))
plot.bind('<Double-Button-1>', lambda event, d=plot_data:
externalPlot(d))
self.registerPlot(plot)
self.setSelection(plot)
class ModeViewer2D(Toplevel):
def __init__(self, master, mode_projector):
Toplevel.__init__(self, master)
self.title("2D Mode Projection")
self.mode_projector = mode_projector
frame = Frame(self)
frame.pack(side=TOP, fill=BOTH, expand=YES)
self.xnum = IntEntry(frame, "X mode number: ", 6, 6,
mode_projector.numberOfModes()-1)
self.xnum.pack(side=LEFT)
self.xnum.bind('<Return>', self.draw)
self.ynum = IntEntry(frame, " Y mode number: ", 7, 6,
mode_projector.numberOfModes()-1)
self.ynum.pack(side=LEFT)
self.ynum.bind('<Return>', self.draw)
self.plot = PlotCanvas(self, 400, 400)
self.plot.pack(side=TOP, fill=BOTH, expand=YES)
self.draw()
def draw(self, event=None):
xnum = self.xnum.get()
ynum = self.ynum.get()
self.mode_projector.calculateProjections([xnum, ynum])
data = self.mode_projector[ynum]
data[:, 0] = self.mode_projector[xnum][:, 1]
self.plot.clear()
self.plot.draw(PolyLine(data, color = 'red'))
class ModeViewer2D(Toplevel):
def __init__(self, master, mode_projector):
Toplevel.__init__(self, master)
self.title("2D Mode Projection")
self.mode_projector = mode_projector
frame = Frame(self)
frame.pack(side=TOP, fill=BOTH, expand=YES)
self.xnum = IntEntry(frame, "X mode number: ", 6, 6,
mode_projector.numberOfModes() - 1)
self.xnum.pack(side=LEFT)
self.xnum.bind('<Return>', self.draw)
self.ynum = IntEntry(frame, " Y mode number: ", 7, 6,
mode_projector.numberOfModes() - 1)
self.ynum.pack(side=LEFT)
self.ynum.bind('<Return>', self.draw)
self.plot = PlotCanvas(self, 400, 400)
self.plot.pack(side=TOP, fill=BOTH, expand=YES)
self.draw()
def draw(self, event=None):
xnum = self.xnum.get()
ynum = self.ynum.get()
self.mode_projector.calculateProjections([xnum, ynum])
data = self.mode_projector[ynum]
data[:, 0] = self.mode_projector[xnum][:, 1]
self.plot.clear()
self.plot.draw(PolyLine(data, color='red'))
def __init__(self, master, rb_projector):
PlotWindow.__init__(self, master, "Rigid-body motion projections")
plot_range = 0.
for i in range(6):
series = rb_projector[i][:, 1]
lower = Numeric.minimum.reduce(series)
upper = Numeric.maximum.reduce(series)
lower, upper = plotRange(lower, upper)
plot_range = max(plot_range, upper - lower)
for column, offset, type in [(0, 0, "Translation "),
(1, 3, "Rotation ")]:
for i in range(3):
data = rb_projector[i + offset]
box = Frame(self, border=2, relief=SUNKEN)
box.grid(row=i, column=column, sticky=N + W + E + S)
frame = Frame(box, background='grey')
frame.pack(side=TOP, fill=X, expand=NO)
Label(frame, text=type + ["X", "Y", "Z"][i],
background='grey').pack(side=LEFT)
minv = Numeric.minimum.reduce(data[:, 1])
maxv = Numeric.maximum.reduce(data[:, 1])
minv, maxv = plotRange(minv, maxv)
middle = 0.5 * (maxv + minv)
if maxv - minv < plot_range:
minv = middle - 0.5 * plot_range
maxv = middle + 0.5 * plot_range
plot_objects = [PolyLine(data, color='red')]
plot = PlotCanvas(box,
400,
100,
zoom=1,
select=self.master._selectRange)
plot.pack(side=LEFT, fill=BOTH, expand=YES)
plot.draw(PlotGraphics(plot_objects), 'automatic',
(minv, maxv))
plot.bind('<Double-Button-1>',
lambda event, d=data: externalPlot(d))
self.registerPlot(plot)
self.setSelection(plot)
def __init__(self, master, rb_projector):
PlotWindow.__init__(self, master, "Rigid-body motion projections")
plot_range = 0.
for i in range(6):
series = rb_projector[i][:, 1]
lower = Numeric.minimum.reduce(series)
upper = Numeric.maximum.reduce(series)
lower, upper = plotRange(lower, upper)
plot_range = max(plot_range, upper-lower)
for column, offset, type in [(0, 0, "Translation "),
(1, 3, "Rotation ")]:
for i in range(3):
data = rb_projector[i+offset]
box = Frame(self, border=2, relief=SUNKEN)
box.grid(row=i, column=column, sticky=N+W+E+S)
frame = Frame(box, background='grey')
frame.pack(side=TOP, fill=X, expand=NO)
Label(frame, text=type + ["X", "Y", "Z"][i],
background='grey').pack(side=LEFT)
minv = Numeric.minimum.reduce(data[:,1])
maxv = Numeric.maximum.reduce(data[:,1])
minv, maxv = plotRange(minv, maxv)
middle = 0.5*(maxv+minv)
if maxv-minv < plot_range:
minv = middle-0.5*plot_range
maxv = middle+0.5*plot_range
plot_objects = [PolyLine(data, color = 'red')]
plot = PlotCanvas(box, 400, 100, zoom=1,
select=self.master._selectRange)
plot.pack(side=LEFT, fill=BOTH, expand=YES)
plot.draw(PlotGraphics(plot_objects), 'automatic',
(minv, maxv))
plot.bind('<Double-Button-1>', lambda event, d=data:
externalPlot(d))
self.registerPlot(plot)
self.setSelection(plot)
def plotBox(self, name, data, data_range=None):
box = Frame(self, border=2, relief=SUNKEN)
box.pack(side=TOP, fill=BOTH, expand=YES)
frame = Frame(box, background='grey')
frame.pack(side=TOP, fill=X, expand=NO)
Label(frame,
text=string.capitalize(string.join(string.split(name, '_'),
' ')),
background='grey').pack(side=LEFT)
if data_range is None:
min = Numeric.minimum.reduce(data[:, 1])
max = Numeric.maximum.reduce(data[:, 1])
min, max = plotRange(min, max)
else:
min, max = data_range
plot_objects = []
plot_data = data
time = plot_data[:, 0]
jumps = Numeric.repeat(Numeric.arange(len(time) - 1),
Numeric.less(time[1:], time[:-1])) + 1
for i in self.master.restarts:
plot_objects.append(
PolyLine([(self.time[i], min), (self.time[i], max)],
color='black',
stipple='gray25'))
plot_objects.insert(0, PolyLine(plot_data, color='red'))
plot = PlotCanvas(box,
400,
100,
zoom=1,
select=self.master._selectRange)
plot.pack(side=LEFT, fill=BOTH, expand=YES)
plot.draw(PlotGraphics(plot_objects), 'automatic', (min, max))
plot.bind('<Double-Button-1>',
lambda event, d=plot_data: externalPlot(d))
self.registerPlot(plot)
self.setSelection(plot)
class TkPlotCanvasDemo1:
def __init__(self, parent):
self.master = parent
self.ncurves = 3 # number of curves
self.npoints = 20 # number of points on each curve
# here we store data in plain NumPy arrays
self.vector_x = zeros(self.npoints)
# use a list of y vectors(0:self.ncurves-1)
self.vector_y = [zeros(self.npoints) \
for y in range(self.ncurves)]
self.fill_vectors() # fill the vectors with data for testing
# make graph widget:
self.g = PlotCanvas(self.master,
500,
300,
zoom=True,
relief='sunken',
border=2)
self.g.pack(expand=True, fill='both')
# define a list of colors for the various curves:
colors = ['red', 'yellow', 'blue', 'green', 'black', 'grey']
# plot each curve:
# the x coordinates are in self.vector_x
# the y coordinates are in self.vector_y[i]
self.curves = []
for i in range(self.ncurves):
xy_pairs = array([self.vector_x, self.vector_y[i]]).transpose()
c = PolyLine(xy_pairs, width=1 + i, color=colors[i])
self.curves.append(c)
object = PlotGraphics(self.curves)
self.g.draw(object, xaxis='automatic', yaxis='automatic')
self.buttons = Pmw.ButtonBox(self.master,
labelpos='n',
label_text='Options:')
self.buttons.pack(fill='both', expand=True, padx=10, pady=10)
# add buttons:
self.buttons.add('Move points', command=self.animate)
self.buttons.add('Postscript', command=self.postscript)
self.buttons.add('Symbols', command=self.symbols)
self.buttons.add('Quit', command=self.master.quit)
self.buttons.alignbuttons() # nice loook...
def symbols(self):
"""Turn on symbols (triangles) at all points."""
curves_wsymbol = [PolyMarker(curve.points,
color='blue', marker='triangle') \
for curve in self.curves]
self.g.draw(PlotGraphics(curves_wsymbol)) # plot collection
def fill_vectors(self):
"""Fill NumPy vectors with (random) values."""
# use random numbers for generating plot data:
random.seed(9) # fix the seed for testing
for index in range(self.npoints):
self.vector_x[index] = index # x coordinates
for y in range(self.ncurves):
self.vector_y[y][index] = random.uniform(0, 8)
def animate(self, delay=100):
"""Adjust curves randomly, in an animated fashion."""
self.g.clear() # erase all plot data
for curve in self.curves:
p = curve.points # [[x1,y1],[x,2,y2],...] (NumPy)
for index in range(p.shape[0]):
p[index][1] = random.uniform(0, 8)
self.g.draw(curve, xaxis='automatic',
yaxis=(0, 8)) # plot PolyLine
self.master.after(delay)
self.master.update()
def postscript(self):
"""Generate a hardcopy of the plot in PostScript."""
self.g.canvas.postscript(file='tmp2.ps')
class TkPlotCanvasDemo1:
def __init__(self, parent):
self.master = parent
self.ncurves = 3 # number of curves
self.npoints = 20 # number of points on each curve
# here we store data in plain NumPy arrays
self.vector_x = zeros(self.npoints)
# use a list of y vectors(0:self.ncurves-1)
self.vector_y = [zeros(self.npoints) \
for y in range(self.ncurves)]
self.fill_vectors() # fill the vectors with data for testing
# make graph widget:
self.g = PlotCanvas(self.master, 500, 300, zoom=True,
relief='sunken', border=2)
self.g.pack(expand=True, fill='both')
# define a list of colors for the various curves:
colors = ['red','yellow','blue','green','black','grey']
# plot each curve:
# the x coordinates are in self.vector_x
# the y coordinates are in self.vector_y[i]
self.curves = []
for i in range(self.ncurves):
xy_pairs = array([self.vector_x,self.vector_y[i]]).transpose()
c = PolyLine(xy_pairs,
width=1+i,
color=colors[i])
self.curves.append(c)
object = PlotGraphics(self.curves)
self.g.draw(object, xaxis='automatic', yaxis='automatic')
self.buttons = Pmw.ButtonBox(self.master,
labelpos='n',
label_text='Options:')
self.buttons.pack(fill='both', expand=True, padx=10, pady=10)
# add buttons:
self.buttons.add('Move points',command=self.animate)
self.buttons.add('Postscript', command=self.postscript)
self.buttons.add('Symbols', command=self.symbols)
self.buttons.add('Quit', command=self.master.quit)
self.buttons.alignbuttons() # nice loook...
def symbols(self):
"""Turn on symbols (triangles) at all points."""
curves_wsymbol = [PolyMarker(curve.points,
color='blue', marker='triangle') \
for curve in self.curves]
self.g.draw(PlotGraphics(curves_wsymbol)) # plot collection
def fill_vectors(self):
"""Fill NumPy vectors with (random) values."""
# use random numbers for generating plot data:
random.seed(9) # fix the seed for testing
for index in range(self.npoints):
self.vector_x[index] = index # x coordinates
for y in range(self.ncurves):
self.vector_y[y][index] = random.uniform(0,8)
def animate(self,delay=100):
"""Adjust curves randomly, in an animated fashion."""
self.g.clear() # erase all plot data
for curve in self.curves:
p = curve.points # [[x1,y1],[x,2,y2],...] (NumPy)
for index in range(p.shape[0]):
p[index][1] = random.uniform(0,8)
self.g.draw(curve,xaxis='automatic',yaxis=(0,8)) # plot PolyLine
self.master.after(delay)
self.master.update()
def postscript(self):
"""Generate a hardcopy of the plot in PostScript."""
self.g.canvas.postscript(file='tmp2.ps')
def __init__(self, master, mode_projector, indices):
from Scientific.Statistics import mean, standardDeviation
title = "Normal mode projections (Temperature: %5.1f K)" \
% mode_projector.temperature
PlotWindow.__init__(self, master, title)
self.mode_projector = mode_projector
plot_range = 0.
for i in indices:
series = mode_projector[i][:, 1]
average = mean(series)
deviation = standardDeviation(series)
lower = Numeric.minimum.reduce(series)
lower = min(lower, average-deviation)
upper = Numeric.maximum.reduce(series)
upper = max(upper, average+deviation)
lower, upper = plotRange(lower, upper)
plot_range = max(plot_range, upper-lower)
nmodes = mode_projector.numberOfModes()
for i in range(len(indices)):
if indices[i] < 0:
indices[i] = nmodes+indices[i]
next_indices = []
step = indices[1] - indices[0]
i = indices[-1]
while len(next_indices) < 4:
i = i + step
if i >= nmodes:
break
next_indices.append(i)
previous_indices = []
i = indices[0]
while len(previous_indices) < 4:
i = i - step
if i < 6:
break
previous_indices.insert(0, i)
if next_indices or previous_indices:
frame = Frame(self)
frame.pack(side=BOTTOM, fill=X, expand=YES)
if previous_indices:
Button(frame, text="Previous",
command=lambda s=self, pi=previous_indices:
s.modeProjection(pi)).pack(side=LEFT)
if next_indices:
Button(frame, text="Next",
command=lambda s=self, ni=next_indices:
s.modeProjection(ni)).pack(side=RIGHT)
for i in range(len(indices)):
number = indices[i]
data = mode_projector[number]
fluctuation = self.mode_projector.amplitude(number)
average = mean(data[:, 1])
deviation = standardDeviation(data[:, 1])
box = Frame(self, border=2, relief=SUNKEN)
box.pack(side=TOP, fill=BOTH, expand=YES)
frame = Frame(box, background='grey')
frame.pack(side=TOP, fill=X, expand=NO)
Label(frame, text="Mode %d" % number,
background='grey').pack(side=LEFT)
Button(frame, text="Animation", background='grey',
command=lambda s=self, n=number:
s.animateMode(n, 1.)).pack(side=RIGHT)
Button(frame, text="View", background='grey',
command=lambda s=self, n=number:
s.viewMode(n)).pack(side=RIGHT)
minv = Numeric.minimum.reduce(data[:,1])
maxv = Numeric.maximum.reduce(data[:,1])
minv, maxv = plotRange(minv, maxv)
middle = 0.5*(maxv+minv)
if maxv-minv < plot_range:
minv = middle-0.5*plot_range
maxv = middle+0.5*plot_range
plot_objects = [PolyLine([(data[1, 0], average-fluctuation),
(data[1, 0], average+fluctuation)],
color='blue', width=3),
PolyLine([(data[-1, 0], average-deviation),
(data[-1, 0], average+deviation)],
color='green', width=3)]
plot_objects.insert(0, PolyLine(data, color = 'red'))
plot = PlotCanvas(box, 400, 100, zoom=1,
select=self.master._selectRange)
plot.pack(side=LEFT, fill=BOTH, expand=YES)
plot.draw(PlotGraphics(plot_objects), 'automatic', (minv, maxv))
plot.bind('<Double-Button-1>', lambda event, d=data:
externalPlot(d))
self.registerPlot(plot)
self.setSelection(plot)
def __init__(self, master, mode_projector, indices):
from Scientific.Statistics import mean, standardDeviation
title = "Normal mode projections (Temperature: %5.1f K)" \
% mode_projector.temperature
PlotWindow.__init__(self, master, title)
self.mode_projector = mode_projector
plot_range = 0.
for i in indices:
series = mode_projector[i][:, 1]
average = mean(series)
deviation = standardDeviation(series)
lower = Numeric.minimum.reduce(series)
lower = min(lower, average - deviation)
upper = Numeric.maximum.reduce(series)
upper = max(upper, average + deviation)
lower, upper = plotRange(lower, upper)
plot_range = max(plot_range, upper - lower)
nmodes = mode_projector.numberOfModes()
for i in range(len(indices)):
if indices[i] < 0:
indices[i] = nmodes + indices[i]
next_indices = []
step = indices[1] - indices[0]
i = indices[-1]
while len(next_indices) < 4:
i = i + step
if i >= nmodes:
break
next_indices.append(i)
previous_indices = []
i = indices[0]
while len(previous_indices) < 4:
i = i - step
if i < 6:
break
previous_indices.insert(0, i)
if next_indices or previous_indices:
frame = Frame(self)
frame.pack(side=BOTTOM, fill=X, expand=YES)
if previous_indices:
Button(frame,
text="Previous",
command=lambda s=self, pi=previous_indices: s.
modeProjection(pi)).pack(side=LEFT)
if next_indices:
Button(frame,
text="Next",
command=lambda s=self, ni=next_indices: s.
modeProjection(ni)).pack(side=RIGHT)
for i in range(len(indices)):
number = indices[i]
data = mode_projector[number]
fluctuation = self.mode_projector.amplitude(number)
average = mean(data[:, 1])
deviation = standardDeviation(data[:, 1])
box = Frame(self, border=2, relief=SUNKEN)
box.pack(side=TOP, fill=BOTH, expand=YES)
frame = Frame(box, background='grey')
frame.pack(side=TOP, fill=X, expand=NO)
Label(frame, text="Mode %d" % number,
background='grey').pack(side=LEFT)
Button(frame,
text="Animation",
background='grey',
command=lambda s=self, n=number: s.animateMode(n, 1.)).pack(
side=RIGHT)
Button(frame,
text="View",
background='grey',
command=lambda s=self, n=number: s.viewMode(n)).pack(
side=RIGHT)
minv = Numeric.minimum.reduce(data[:, 1])
maxv = Numeric.maximum.reduce(data[:, 1])
minv, maxv = plotRange(minv, maxv)
middle = 0.5 * (maxv + minv)
if maxv - minv < plot_range:
minv = middle - 0.5 * plot_range
maxv = middle + 0.5 * plot_range
plot_objects = [
PolyLine([(data[1, 0], average - fluctuation),
(data[1, 0], average + fluctuation)],
color='blue',
width=3),
PolyLine([(data[-1, 0], average - deviation),
(data[-1, 0], average + deviation)],
color='green',
width=3)
]
plot_objects.insert(0, PolyLine(data, color='red'))
plot = PlotCanvas(box,
400,
100,
zoom=1,
select=self.master._selectRange)
plot.pack(side=LEFT, fill=BOTH, expand=YES)
plot.draw(PlotGraphics(plot_objects), 'automatic', (minv, maxv))
plot.bind('<Double-Button-1>',
lambda event, d=data: externalPlot(d))
self.registerPlot(plot)
self.setSelection(plot)
class ScatteringFunctionPlot(Frame):
def __init__(self, master, filename):
Frame.__init__(self, master)
file = NetCDFFile(filename)
self.q = file.variables['q'][1:]
self.t = file.variables['time'][:]
self.fn = file.variables['sf'][1:, :]
Label(self, text='S(t) for various q').pack(side=TOP, fill=X)
self.plot1 = PlotCanvas(self, 600, 250, zoom=1)
self.plot1.pack(side=TOP, fill=BOTH, expand=YES)
Label(self, text='S(q) for various t').pack(side=TOP, fill=X)
self.plot2 = PlotCanvas(self, 600, 250, zoom=1)
self.plot2.pack(side=TOP, fill=BOTH, expand=YES)
frame = Frame(self)
frame.pack(side=TOP, fill=X)
self.first_q = IntEntry(frame, "q range: from ", 0, 0, len(self.q))
self.first_q.grid(row=0, column=0)
self.first_q.bind('<Return>', self.draw)
self.last_q = IntEntry(frame, " to ", len(self.q), 0, len(self.q))
self.last_q.grid(row=0, column=1)
self.skip_q = IntEntry(frame, " skip ", (len(self.q) + 10) / 10, 1,
len(self.q))
self.skip_q.grid(row=0, column=2)
self.first_t = IntEntry(frame, "t range: from ", 0, 0, len(self.t))
self.first_t.grid(row=1, column=0)
self.last_t = IntEntry(frame, " to ", len(self.t), 0, len(self.t))
self.last_t.grid(row=1, column=1)
self.skip_t = IntEntry(frame, " skip ", (len(self.t) + 10) / 10, 1,
len(self.t))
self.skip_t.grid(row=1, column=2)
self.first_q.bind('<Return>', self.draw)
self.last_q.bind('<Return>', self.draw)
self.skip_q.bind('<Return>', self.draw)
self.first_t.bind('<Return>', self.draw)
self.last_t.bind('<Return>', self.draw)
self.skip_t.bind('<Return>', self.draw)
self.draw()
def draw(self, event=None):
try:
first_q = self.first_q.get()
last_q = self.last_q.get()
skip_q = self.skip_q.get()
first_t = self.first_t.get()
last_t = self.last_t.get()
skip_t = self.skip_t.get()
except ValueError:
return
graphics1, graphics2 = self.plot_objects(first_q, last_q, skip_q,
first_t, last_t, skip_t)
self.plot1.clear()
self.plot1.draw(PlotGraphics(graphics1), 'automatic', 'automatic')
self.plot2.clear()
self.plot2.draw(PlotGraphics(graphics2), 'automatic', 'automatic')
def plot_objects(self, first_q, last_q, skip_q, first_t, last_t, skip_t):
plot_objects1 = []
markers1 = []
color_index = 0
dt = (last_t - first_t + 150) / 150
for i in range(first_q, last_q, skip_q):
data = self.fn[i, first_t:last_t:dt]
data_t = self.t[first_t:last_t:dt]
points = N.transpose(N.array([data_t, data]))
plot_objects1.append(
PolyLine(points, color=self.colors[color_index]))
markers1.append(self.q[i], color_index)
color_index = (color_index + 1) % len(self.colors)
plot_objects2 = []
markers2 = []
color_index = 0
dq = (last_q - first_q + 150) / 150
for i in range(first_t, last_t, skip_t):
data = self.fn[first_q:last_q:dq, i]
data_q = self.q[first_q:last_q:dq]
points = N.transpose(N.array([data_q, data]))
plot_objects2.append(
PolyLine(points, color=self.colors[color_index]))
markers2.append(self.t[i], color_index)
color_index = (color_index + 1) % len(self.colors)
for q, color_index in markers1:
plot_objects2.append(
VerticalLine(q,
color=self.colors[color_index],
stipple='gray50'))
for t, color_index in markers2:
plot_objects1.append(
VerticalLine(t,
color=self.colors[color_index],
stipple='gray50'))
return plot_objects1, plot_objects2
colors = [
'red', 'green', 'blue', 'orange', 'brown', 'yellow', 'violet', 'pink',
'cyan', 'grey'
]