def draw_image(img, label=None, dpi=72, facecolor='white', cmap=cm.gray, output_filename=None, **extra): #@UndefinedVariable
'''
'''
img = img.copy()
pylab.clf()
fig = pylab.figure(0, dpi=dpi, facecolor=facecolor, figsize=(img.shape[0]/dpi, img.shape[1]/dpi))#, tight_layout=True
fig.frameon=False
#pylab.subplots_adjust(wspace=0, hspace=0, left=0, right=1, bottom=0, top=1)
if img.min() != img.max():
img -= img.min()
img /= img.max()
#fig.set_size_inches(10, 10)
#ax = pylab.Axes(fig, [0., 0., 10., 10.])
#ax.set_axis_off()
#fig.add_axes(ax)
ax = fig.add_axes((0,0,1,1), frameon=False)
#ax = pylab.axes(frameon=False)
ax.set_axis_off()
ax.imshow(img, cmap=cmap)#, aspect = 'normal')
if label is not None:
ax.text(10, 20, label, color='black', backgroundcolor='white', fontsize=8)
if output_filename is not None:
fig.savefig(format_utility.new_filename(output_filename, ext='png'), dpi=dpi)
return fig, ax
def plot_scatter(output, x, x_label, y, y_label, color=None, dpi=72):
''' Plot a scatter plot
'''
if pylab is None: return
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
if color is not None:
sc = ax.scatter(x, y, cmap=cm.cool, c=color) #@UndefinedVariable
v1 = min(numpy.min(x), numpy.min(y))
v2 = max(numpy.max(x), numpy.max(y))
ax.plot(numpy.asarray([v1, v2]), numpy.asarray([v1, v2]))
pylab.colorbar(sc)
else:
ax.scatter(x, y)
pylab.xlabel(x_label)
pylab.ylabel(y_label)
fig.savefig(format_utility.new_filename(
output,
x_label.lower().replace(' ', '_') + "_" +
y_label.lower().replace(' ', '_') + "_summary_",
ext="png"),
dpi=dpi)
def plot_lines(output,
lines,
labels,
ylabel=None,
xlabel=None,
dpi=72,
prefix=None):
'''
'''
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
cmap = cm.jet #@UndefinedVariable
markers = ['s', 'o', '^', '>', 'v', 'd', 'p', 'h', '8', '+', 'x']
for i in xrange(len(lines)):
ax.plot(lines[i],
markers[i],
c=cmap(float(i + 1) / len(lines)),
label=labels[i])
if ylabel is not None: pylab.ylabel(ylabel)
if xlabel is not None: pylab.xlabel(xlabel)
lgd = ax.legend(bbox_to_anchor=(1.05, 1),
loc=2,
borderaxespad=0.,
prop={'size': 8})
fig.savefig(format_utility.new_filename(output, ext="png", prefix=prefix),
dpi=dpi,
bbox_extra_artists=(lgd, ),
bbox_inches='tight')
def plot_line(output, x, y, x_label=None, y_label=None, color=None, marker_idx=None, dpi=72):
''' Plot a scatter plot
'''
if pylab is None: return
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
if x is None:
x = numpy.arange(len(y))
x = numpy.asarray(x)
y = numpy.asarray(y)
ax.plot(x, y)
if marker_idx is not None:
ax.plot(x[marker_idx], y[marker_idx], linestyle='None', marker='+', color='r')
ax.invert_xaxis()
if x_label is not None: pylab.xlabel(x_label)
if y_label is not None: pylab.ylabel(y_label)
prefix = ""
if x_label is not None: prefix += x_label.lower().replace(' ', '_')+"_"
if y_label is not None: prefix += y_label.lower().replace(' ', '_')+"_"
fig.savefig(format_utility.new_filename(output, prefix+"summary_", ext="png"), dpi=dpi)
def plot_histogram_cum(output, vals, x_label, y_label, th=None, dpi=72):
''' Plot a histogram of the distribution
'''
if pylab is None: return
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
vals = ax.hist(-vals, bins=numpy.sqrt(len(vals)), cumulative=True)
if th is not None:
h = pylab.gca().get_ylim()[1]
pylab.plot((th, th), (0, h))
pylab.xlabel(x_label)
pylab.ylabel('Cumulative '+y_label)
fig.savefig(format_utility.new_filename(output, x_label.lower().replace(' ', '_')+"_"+y_label.lower().replace(' ', '_')+"_summary_", ext="png"), dpi=dpi)
def plot_lines(output, lines, labels, ylabel=None, xlabel=None, dpi=72, prefix=None):
'''
'''
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
cmap = cm.jet#@UndefinedVariable
markers = ['s', 'o', '^', '>', 'v', 'd', 'p', 'h', '8', '+', 'x']
for i in xrange(len(lines)):
ax.plot(lines[i], markers[i], c=cmap(float(i+1)/len(lines)), label=labels[i])
if ylabel is not None: pylab.ylabel(ylabel)
if xlabel is not None: pylab.xlabel(xlabel)
lgd=ax.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0., prop={'size':8})
fig.savefig(format_utility.new_filename(output, ext="png", prefix=prefix), dpi=dpi, bbox_extra_artists=(lgd,), bbox_inches='tight')
def plot_embedding(x, y, selected=None, group=None, dpi=80, **extra):
''' Plot an embedding
:Parameters:
x : array
X coordindates
y : array
Y coordindates
selected : array, optional
Plot selected points
dpi : int
Figure resolution
extra : dict
Unused key word arguments
:Returns:
fig : Figure
Matplotlib figure
ax : Axes
Matplotlib axes
'''
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
if group is not None:
refs = numpy.unique(group)
beg, inc = 0.0, 1.0 / len(refs)
for r in refs:
sel = r == group
color = cm.spectral(beg) #@UndefinedVariable
ax.plot(x[sel],
y[sel],
'o',
ls='.',
markersize=3,
c=color,
**extra)
beg += inc
else:
ax.plot(x, y, 'ro', ls='.', markersize=3, **extra)
if selected is not None:
ax.plot(x[selected], y[selected], 'k+', ls='.', markersize=2, **extra)
return fig, ax
def draw_image(img,
label=None,
dpi=72,
facecolor='white',
cmap=cm.gray,
output_filename=None,
**extra): #@UndefinedVariable
'''
'''
img = img.copy()
pylab.clf()
fig = pylab.figure(0,
dpi=dpi,
facecolor=facecolor,
figsize=(img.shape[0] / dpi,
img.shape[1] / dpi)) #, tight_layout=True
fig.frameon = False
#pylab.subplots_adjust(wspace=0, hspace=0, left=0, right=1, bottom=0, top=1)
if img.min() != img.max():
img -= img.min()
img /= img.max()
#fig.set_size_inches(10, 10)
#ax = pylab.Axes(fig, [0., 0., 10., 10.])
#ax.set_axis_off()
#fig.add_axes(ax)
ax = fig.add_axes((0, 0, 1, 1), frameon=False)
#ax = pylab.axes(frameon=False)
ax.set_axis_off()
ax.imshow(img, cmap=cmap) #, aspect = 'normal')
if label is not None:
ax.text(10,
20,
label,
color='black',
backgroundcolor='white',
fontsize=8)
if output_filename is not None:
fig.savefig(format_utility.new_filename(output_filename, ext='png'),
dpi=dpi)
return fig, ax
def plot_scatter(output, x, x_label, y, y_label, color=None, dpi=72):
''' Plot a scatter plot
'''
if pylab is None: return
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
if color is not None:
sc = ax.scatter(x, y, cmap=cm.cool, c=color)#@UndefinedVariable
v1 = min(numpy.min(x),numpy.min(y))
v2 = max(numpy.max(x),numpy.max(y))
ax.plot(numpy.asarray([v1, v2]), numpy.asarray([v1, v2]))
pylab.colorbar(sc)
else:
ax.scatter(x, y)
pylab.xlabel(x_label)
pylab.ylabel(y_label)
fig.savefig(format_utility.new_filename(output, x_label.lower().replace(' ', '_')+"_"+y_label.lower().replace(' ', '_')+"_summary_", ext="png"), dpi=dpi)
def plot_histogram_cum(output, vals, x_label, y_label, th=None, dpi=72):
''' Plot a histogram of the distribution
'''
if pylab is None: return
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
vals = ax.hist(-vals, bins=numpy.sqrt(len(vals)), cumulative=True)
if th is not None:
h = pylab.gca().get_ylim()[1]
pylab.plot((th, th), (0, h))
pylab.xlabel(x_label)
pylab.ylabel('Cumulative ' + y_label)
fig.savefig(format_utility.new_filename(
output,
x_label.lower().replace(' ', '_') + "_" +
y_label.lower().replace(' ', '_') + "_summary_",
ext="png"),
dpi=dpi)
def plot_line(output,
x,
y,
x_label=None,
y_label=None,
color=None,
marker_idx=None,
dpi=72):
''' Plot a scatter plot
'''
if pylab is None: return
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
if x is None:
x = numpy.arange(len(y))
x = numpy.asarray(x)
y = numpy.asarray(y)
ax.plot(x, y)
if marker_idx is not None:
ax.plot(x[marker_idx],
y[marker_idx],
linestyle='None',
marker='+',
color='r')
ax.invert_xaxis()
if x_label is not None: pylab.xlabel(x_label)
if y_label is not None: pylab.ylabel(y_label)
prefix = ""
if x_label is not None: prefix += x_label.lower().replace(' ', '_') + "_"
if y_label is not None: prefix += y_label.lower().replace(' ', '_') + "_"
fig.savefig(format_utility.new_filename(output,
prefix + "summary_",
ext="png"),
dpi=dpi)
def plot_embedding(x, y, selected=None, group=None, dpi=80, **extra):
''' Plot an embedding
:Parameters:
x : array
X coordindates
y : array
Y coordindates
selected : array, optional
Plot selected points
dpi : int
Figure resolution
extra : dict
Unused key word arguments
:Returns:
fig : Figure
Matplotlib figure
ax : Axes
Matplotlib axes
'''
fig = pylab.figure(dpi=dpi)
ax = fig.add_subplot(111)
if group is not None:
refs = numpy.unique(group)
beg, inc = 0.0, 1.0/len(refs)
for r in refs:
sel = r == group
color = cm.spectral(beg)#@UndefinedVariable
ax.plot(x[sel], y[sel], 'o', ls='.', markersize=3, c=color, **extra)
beg += inc
else:
ax.plot(x, y, 'ro', ls='.', markersize=3, **extra)
if selected is not None:
ax.plot(x[selected], y[selected], 'k+', ls='.', markersize=2, **extra)
return fig, ax