def _plotMTCombined(conf, data, subject='__'):
mt, time, idS, id, p = data['all']
time2 = numpy.linspace(time.min(),time.max(),30000)
figname = os.path.join(grPath,subject+'_'+conf[0]+'-'+conf[1]+'_'+conf[2]+'_'+'_MTGraph_All'+grExt)
figtitle = subject+' '+conf[0]+'-'+conf[1]+' '+conf[2]+'Combined replications'
fig = pylab.figure()
host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
par1 = ParasiteAxes(host, sharex=host)
host.parasites.append(par1)
host.set_ylabel("MT (ms)")
host.set_xlabel("Time (ms)")
host.axis["right"].set_visible(False)
par1.axis["right"].set_visible(True)
par1.set_ylabel("ID")
par1.axis["right"].major_ticklabels.set_visible(True)
par1.axis["right"].label.set_visible(True)
fig.add_axes(host)
sigmoidArr = sigmoid(p,time2)
t2 = time2[numpy.where(abs(sigmoidArr - (sigmoidArr.min() + sigmoidArr.max())/2) < eps2)[0]]
#t50 = abs(t2-time2.max())
t50 = t2
if isinstance(t50, numpy.ndarray):
t50 = t50.mean()
#host.set_ylim(mt.min(),mt.max())
if conf[0] == '4':
host.set_ylim(200,900)
host.set_xlim(0, 70000)
else:
host.set_ylim(200,1600)
host.set_xlim(0, 90000)
host.scatter(time,mt,s=0.1,marker='x',linewidth=0.1,label="MT")
host.plot(time2,sigmoid(p,time2),'-r',linewidth=1.5,label="Fitted MT")
par1.scatter(time, id, s=1, c='r',label="ID", linewidth=0.5)
msg = "MT50 = %f" % t50
host.text( 0.3 , 0.95, msg, fontsize = 8,\
horizontalalignment='left', verticalalignment='center',\
transform = host.transAxes)
host.vlines(t50,mt.min(),mt.max())
#host.set_ylim(mt.min(),mt.max())
if conf[0] == '4':
host.set_ylim(200,900)
host.set_xlim(0, 70000)
else:
host.set_ylim(200,1600)
host.set_xlim(0, 90000)
par1.set_ylim(min(int(conf[0]),int(conf[1])),max(int(conf[0]),int(conf[1])))
#host.legend()
host.set_title(figtitle)
fig.savefig(figname)
pylab.close()
from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes
import matplotlib.pyplot as plt
if __name__ == "__main__":
fig = plt.figure(1)
host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
par1 = ParasiteAxes(host, sharex=host)
par2 = ParasiteAxes(host, sharex=host)
host.parasites.append(par1)
host.parasites.append(par2)
host.set_ylabel("Density")
host.set_xlabel("Distance")
host.axis["right"].set_visible(False)
par1.axis["right"].set_visible(True)
par1.set_ylabel("Temperature")
par1.axis["right"].major_ticklabels.set_visible(True)
par1.axis["right"].label.set_visible(True)
par2.set_ylabel("Velocity")
offset = (60, 0)
new_axisline = par2._grid_helper.new_fixed_axis
par2.axis["right2"] = new_axisline(loc="right", axes=par2, offset=offset)
fig.add_axes(host)
host.set_xlim(0, 2)
host.set_ylim(0, 2)
from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes
import matplotlib.pyplot as plt
if __name__ == "__main__":
fig = plt.figure(1)
host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
par1 = ParasiteAxes(host, sharex=host)
par2 = ParasiteAxes(host, sharex=host)
host.parasites.append(par1)
host.parasites.append(par2)
host.set_ylabel("Density")
host.set_xlabel("Distance")
host.axis["right"].set_visible(False)
par1.axis["right"].set_visible(True)
par1.set_ylabel("Temperature")
par1.axis["right"].major_ticklabels.set_visible(True)
par1.axis["right"].label.set_visible(True)
par2.set_ylabel("Velocity")
offset = (60, 0)
new_axisline = par2._grid_helper.new_fixed_axis
par2.axis["right2"] = new_axisline(loc="right",
axes=par2,
offset=offset)
fig.add_axes(host)
def new_axis(fig, hostax, off=50, loc='bottom', ticks=None, wsadd=0.1,
label='', sharex=False, sharey=False):
"""Make a new axis line using mpl_toolkits.axes_grid's SubplotHost and
ParasiteAxes. The new axis line will be an instance of ParasiteAxes
attached to `hostax`. You can do twinx()/twiny() type axis (off=0) or
completely free-standing axis lines (off > 0).
Parameters
----------
fig : mpl Figure
hostax : Instance of matplotlib.axes.HostAxesSubplot. This is the subplot
of the figure `fig` w.r.t which all new axis lines are placed. See
make_axes_grid_fig().
off : offset in points, used with parax.get_grid_helper().new_fixed_axis
loc : one of 'left', 'right', 'top', 'bottom', where to place the new axis
line
ticks : sequence of ticks (numbers)
wsadd : Whitespace to add at the location `loc` to make space for the new
axis line (only useful if off > 0). The number is a relative unit
and is used to change the bounding box: hostax.get_position().
label : str, xlabel (ylabel) for 'top','bottom' ('left', 'right')
sharex, sharey : bool, share xaxis (yaxis) with `hostax`
Returns
-------
(fig, hostax, parax)
fig : the Figure
hostax : the hostax
parax : the new ParasiteAxes instance
Notes
-----
* The sharex/sharey thing may not work correctly.
"""
# Create ParasiteAxes, an ax which overlays hostax.
if sharex and sharey:
parax = ParasiteAxes(hostax, sharex=hostax, sharey=hostax)
elif sharex:
parax = ParasiteAxes(hostax, sharex=hostax)
elif sharey:
parax = ParasiteAxes(hostax, sharey=hostax)
else:
parax = ParasiteAxes(hostax)
hostax.parasites.append(parax)
# If off != 0, the new axis line will be detached from hostax, i.e.
# completely "free standing" below (above, left or right of) the main ax
# (hostax), so we don't need anything visilbe from it b/c we create a
# new_fixed_axis from this one with an offset anyway. We only need to
# activate the label.
for _loc in ['left', 'right', 'top', 'bottom']:
parax.axis[_loc].set_visible(False)
parax.axis[_loc].label.set_visible(True)
# Create axis line. Free-standing if off != 0, else overlaying one of hostax's
# axis lines. In fact, with off=0, one simulates twinx/y().
new_axisline = parax.get_grid_helper().new_fixed_axis
if loc == 'top':
offset = (0, off)
parax.set_xlabel(label)
elif loc == 'bottom':
offset = (0, -off)
parax.set_xlabel(label)
elif loc == 'left':
offset = (-off, 0)
parax.set_ylabel(label)
elif loc == 'right':
offset = (off, 0)
parax.set_ylabel(label)
newax = new_axisline(loc=loc, offset=offset, axes=parax)
# name axis lines: bottom2, bottom3, ...
n=2
while parax.axis.has_key(loc + str(n)):
n += 1
parax.axis[loc + str(n)] = newax
# set ticks
if ticks is not None:
newax.axis.set_ticks(ticks)
# Read out whitespace at the location (loc = 'top', 'bottom', 'left',
# 'right') and adjust whitespace.
#
# indices of the values in the array returned by ax.get_position()
bbox_idx = dict(left=[0,0], bottom=[0,1], right=[1,0], top=[1,1])
old_pos = np.array(hostax.get_position())[bbox_idx[loc][0], bbox_idx[loc][1]]
if loc in ['top', 'right']:
new_ws = old_pos - wsadd
else:
new_ws = old_pos + wsadd
# hack ...
cmd = "fig.subplots_adjust(%s=%f)" %(loc, new_ws)
eval(cmd)
return fig, hostax, parax
def runner (parser, options, args):
options = Options (options)
run_method = getattr(parser, 'run_method', 'subcommand')
if os.name=='posix' and run_method == 'subprocess':
print 'This script cannot be run using subprocess method. Choose subcommand to continue.'
return
if args:
if len (args)==1:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (options.input_path, args[0])
options.input_path = args[0]
if options.input_path is None:
parser.error('Expected --input-path but got nothing')
data, titles = RowFile (options.input_path).read(with_titles = True)
if options.print_keys:
print 'rowfile keys:' + ', '.join(data.keys())
print 'length:', len(data[data.keys()[0]] or [])
return
if not options.x_keys and not options.y_keys:
options.x_keys = titles[0]
options.y_keys = ','.join(titles[1:])
parser.save_options(options, [])
if not options.x_keys or not options.y_keys:
print 'No x or y keys specified for the plot.'
return
x_keys = [str (k).strip() for k in options.x_keys.split (',')]
y_keys = [str (k).strip() for k in options.y_keys.split (',')]
from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes
import matplotlib.pyplot as plt
fig = plt.figure(1, figsize=(12,6))
host = HostAxes(fig, [0.1, 0.1, 0.55, 0.8])
host.axis["right"].set_visible(False)
fig.add_axes(host)
host.set_title(options.input_path)
legend_list = []
axes_ylim = []
plot_axes = []
for x_key in x_keys:
x_data = data.get(x_key)
if x_data is None:
print 'Rowfile does not contain a column named %r' % (x_key)
continue
offset = 20
host.set_xlabel(x_key)
for y_key in y_keys:
plot_str = 'plot'
if y_key.startswith('log:'):
y_key = y_key[4:]
plot_str = 'semilogy'
y_data = data.get(y_key)
if y_data is None:
print 'Rowfile does not contain a column named %r' % (y_key)
continue
if axes_ylim:
ax = ParasiteAxes(host, sharex=host)
host.parasites.append(ax)
#ax.axis["right"].set_visible(True)
#ax.axis["right"].major_ticklabels.set_visible(True)
#ax.axis["right"].label.set_visible(True)
new_axisline = ax._grid_helper.new_fixed_axis
ax_line = ax.axis["right2"] = new_axisline(loc="right",
axes=ax,
offset=(offset,0))
if plot_str=='semilogy':
offset += 60
else:
offset += 40
else:
ax = host
ax_line = ax.axis['left']
ax.set_ylabel(y_key)
p, = getattr(ax, plot_str)(x_data, y_data, label = y_key)
axes_ylim.append((ax, min (y_data), max (y_data)))
plot_axes.append((p, ax_line))
[ax.set_ylim(mn,mx) for ax,mn,mx in axes_ylim]
#[ax_line.label.set_color (p.get_color()) for p, ax in plot_axes]
host.legend()
def on_keypressed(event):
key = event.key
if key=='q':
sys.exit(0)
fig.canvas.mpl_connect('key_press_event', on_keypressed)
plt.draw()
output_path = options.get (output_path='')
if output_path:
plt.savefig (output_path)
print 'wrote',output_path
sys.exit(0)
plt.show()
