def set_arbitrary_ticks(ax,axis,events,index1,index2,fontsize=10,fontname='sans'):
"""
if an axis is using an unknown scale or we just with to use the data to scale
the axis
"""
buff = 0.02
formatter = ScalarFormatter(useMathText=True)
formatter.set_scientific(True)
formatter.set_powerlimits((-3,3))
## handle data edge buffers
if axis in ['x','both']:
bufferX = buff * (events[:,index1].max() - events[:,index1].min())
ax.set_xlim([events[:,index1].min()-bufferX,events[:,index1].max()+bufferX])
ax.xaxis.set_major_formatter(formatter)
if axis in ['y','both']:
bufferY = buff * (events[:,index2].max() - events[:,index2].min())
ax.set_ylim([events[:,index2].min()-bufferY,events[:,index2].max()+bufferY])
ax.yaxis.set_major_formatter(formatter)
if axis in ['x','both']:
for tick in ax.xaxis.get_major_ticks():
tick.label.set_fontsize(fontsize-2)
tick.label.set_fontname(fontname)
if axis in ['y','both']:
for tick in ax.yaxis.get_major_ticks():
tick.label.set_fontsize(fontsize-2)
tick.label.set_fontname(fontname)
def age_vs_plot(track, infile, ycol='logl', ax=None, annotate=True, xlabels=True,
save_plot=True, ylabels=True):
agb_mix = infile.agb_mix
set_name = infile.set_name
if ycol == 'logl':
ydata= track.get_col('L_star')
majL = MultipleLocator(.2)
minL = MultipleLocator(.1)
ylab = '$\log\ L_{\odot}$'
elif ycol == 'logt':
ydata = track.get_col('T_star')
majL = MultipleLocator(.1)
minL = MultipleLocator(.05)
ylab = '$\log\ Te$'
elif ycol == 'C/O':
ydata = track.get_col('CO')
majL = MaxNLocator(4)
minL = MaxNLocator(2)
ylab = '$C/O$'
else:
print 'logl, logt, C/O only choices for y.'
return
age = track.get_col('ageyr')
addpt = track.addpt
Qs = list(track.Qs)
if ax is None:
fig, ax = plt.subplots()
ax.plot(age, ydata, color='black')
ax.plot(age[Qs], ydata[Qs], 'o', color='green')
if len(addpt) > 0:
ax.plot(age[addpt], ydata[addpt], 'o', color='purple')
ax.yaxis.set_major_locator(majL)
ax.yaxis.set_minor_locator(minL)
majorFormatter = ScalarFormatter()
majorFormatter.set_powerlimits((-3, 4))
ax.xaxis.set_major_formatter(majorFormatter)
if annotate is True:
ax.text(0.06, 0.87, '${\\rm %s}$' % agb_mix.replace('_', '\ '),
transform=ax.transAxes)
ax.text(0.06, 0.77,'${\\rm %s}$' % set_name.replace('_', '\ '),
transform=ax.transAxes)
ax.text(0.06, 0.67, '$M=%.2f$' % track.mass,
transform=ax.transAxes)
if ylabels is True:
ax.set_ylabel('$%s$' % ylab, fontsize=20)
if xlabels is True:
ax.set_xlabel('$\rm{Age (yr)}$', fontsize=20)
if save_plot is True:
plotpath = os.path.join(infile.diagnostic_dir, 'age_v/')
fileIO.ensure_dir(plotpath)
fname = os.path.split(track.name)[1].replace('.dat', '')
fig_name = os.path.join(plotpath, '_'.join(('diag', fname)))
plt.savefig('%s_age_v.png' % fig_name, dpi=300)
plt.close()
return
def quickPlot(filename, path, datalist, xlabel="x", ylabel="y", xrange=["auto", "auto"], yrange=["auto", "auto"], yscale="linear", xscale="linear", col=["r", "b"]):
"""Plots Data to .pdf File in Plots Folder Using matplotlib"""
if "plots" not in os.listdir(path):
os.mkdir(os.path.join(path, "plots"))
coltab = col*10
seaborn.set_context("notebook", rc={"lines.linewidth": 1.0})
formatter = ScalarFormatter(useMathText=True)
formatter.set_scientific(True)
formatter.set_powerlimits((-2, 3))
fig = Figure(figsize=(6, 6))
ax = fig.add_subplot(111)
for i, ydata in enumerate(datalist[1:]):
ax.plot(datalist[0], ydata, c=coltab[i])
ax.set_title(filename)
ax.set_yscale(yscale)
ax.set_xscale(xscale)
ax.set_xlabel(xlabel)
ax.set_ylabel(ylabel)
if xrange[0] != "auto":
ax.set_xlim(xmin=xrange[0])
if xrange[1] != "auto":
ax.set_xlim(xmax=xrange[1])
if yrange[0] != "auto":
ax.set_ylim(ymin=yrange[0])
if yrange[1] != "auto":
ax.set_ylim(ymax=yrange[1])
if yscale == "linear":
ax.yaxis.set_major_formatter(formatter)
ax.xaxis.set_major_formatter(formatter)
canvas = FigureCanvasPdf(fig)
canvas.print_figure(os.path.join(path, "plots", filename+".pdf"))
return
def funcPlotEnd(fig, ax, theme, width, height, x_showTicks=True, x_showTickLabels=True, y_showTicks=True, y_showTickLabels=True, drawAxis=True, showGrid=True): """ set some layout options """ if not x_showTicks: ax.set_xticks([]) if not x_showTickLabels: ax.set_xticklabels([]) else: xfmt = ScalarFormatter(useMathText=True) xfmt.set_powerlimits((-2,3)) ax.xaxis.set_major_formatter(xfmt) if not y_showTicks: ax.set_yticks([]) if not y_showTickLabels: ax.set_yticklabels([]) ax.grid(showGrid, which="both", color=theme.getGridColor(), linestyle="-") ax.patch.set_facecolor(theme.getBackgroundColor()) if drawAxis: axisColor = theme.getGridColor() else: axisColor = theme.getBackgroundColor() ax.spines["bottom"].set_color(axisColor) ax.spines["top"].set_color(axisColor) ax.spines["right"].set_color(axisColor) ax.spines["left"].set_color(axisColor) ax.tick_params(axis="x", colors=theme.getGridColor(), which="both", labelsize=theme.getFontSize()) ax.tick_params(axis="y", colors=theme.getGridColor(), which="both", labelsize=theme.getFontSize()) ax.xaxis.label.set_color(theme.getFontColor()) ax.yaxis.label.set_color(theme.getFontColor()) [x_ticklabel.set_color(theme.getFontColor()) for x_ticklabel in ax.get_xticklabels()] [y_ticklabel.set_color(theme.getFontColor()) for y_ticklabel in ax.get_yticklabels()] fig.set_size_inches(width, height)
def __init__(self, ndec=None, useOffset=True, useMathText=False):
ScalarFormatter.__init__(self, useOffset, useMathText)
if ndec is None or ndec < 0:
self.format = None
elif ndec == 0:
self.format = "%d"
else:
self.format = "%%1.%if" % ndec
class AbsFormatter(object):
def __init__(self, useMathText=True):
self._fmt = ScalarFormatter(useMathText=useMathText, useOffset=False)
self._fmt.create_dummy_axis()
def __call__(self, direction, factor, values):
self._fmt.set_locs(values)
return [self._fmt(abs(v)) for v in values]
def get_colorbar_formatter(varname):
if varname in ["STFL", "STFA"]:
return None
else:
# format the colorbar tick labels
sfmt = ScalarFormatter(useMathText=True)
sfmt.set_powerlimits((-3, 3))
return sfmt
def scale(args):
dataset_name = args.get('dataset')
scale = args.get('scale')
scale = [float(component) for component in scale.split(',')]
variable = args.get('variable')
if variable.endswith('_anom'):
variable = variable[0:-5]
anom = True
else:
anom = False
variable = variable.split(',')
with open_dataset(get_dataset_url(dataset_name)) as dataset:
variable_unit = get_variable_unit(dataset_name,
dataset.variables[variable[0]])
variable_name = get_variable_name(dataset_name,
dataset.variables[variable[0]])
if variable_unit.startswith("Kelvin"):
variable_unit = "Celsius"
if anom:
cmap = colormap.colormaps['anomaly']
variable_name = gettext("%s Anomaly") % variable_name
else:
cmap = colormap.find_colormap(variable_name)
if len(variable) == 2:
if not anom:
cmap = colormap.colormaps.get('speed')
variable_name = re.sub(
r"(?i)( x | y |zonal |meridional |northward |eastward )", " ",
variable_name)
variable_name = re.sub(r" +", " ", variable_name)
fig = plt.figure(figsize=(2, 5), dpi=75)
ax = fig.add_axes([0.05, 0.05, 0.25, 0.9])
norm = matplotlib.colors.Normalize(vmin=scale[0], vmax=scale[1])
formatter = ScalarFormatter()
formatter.set_powerlimits((-3, 4))
bar = ColorbarBase(ax, cmap=cmap, norm=norm, orientation='vertical',
format=formatter)
bar.set_label("%s (%s)" % (variable_name.title(),
utils.mathtext(variable_unit)))
buf = StringIO()
try:
plt.savefig(buf, format='png', dpi='figure', transparent=False,
bbox_inches='tight', pad_inches=0.05)
plt.close(fig)
return buf.getvalue()
finally:
buf.close()
def setAxes(ax):
globalAxesSettings(ax)
ax.yaxis.set_major_locator(MaxNLocator(4))
ax.xaxis.set_minor_locator(AutoMinorLocator(2))
ax.yaxis.set_minor_locator(AutoMinorLocator(2))
f = ScalarFormatter(useMathText=True)
f.set_scientific(True)
f.set_powerlimits((0, 3))
ax.yaxis.set_major_formatter(f)
def plot_comparison_hydrographs(basin_name_to_out_indices_map, rea_config=None, gcm_config=None):
"""
:type basin_name_to_out_indices_map: dict
"""
assert isinstance(rea_config, RunConfig)
assert isinstance(gcm_config, RunConfig)
assert hasattr(rea_config, "data_daily")
assert hasattr(gcm_config, "data_daily")
bname_to_indices = OrderedDict([item for item in sorted(basin_name_to_out_indices_map.items(),
key=lambda item: item[1][1], reverse=True)])
print(bname_to_indices)
plot_utils.apply_plot_params(font_size=12, width_pt=None, width_cm=25, height_cm=12)
fig = plt.figure()
ncols = 3
nrows = len(bname_to_indices) // ncols + int(len(bname_to_indices) % ncols != 0)
gs = GridSpec(nrows, ncols)
ax_last = None
for pl_index, (bname, (i, j)) in enumerate(bname_to_indices.items()):
row = pl_index // ncols
col = pl_index % ncols
ax = fig.add_subplot(gs[row, col])
ax.plot(rea_config.data_daily[0], rea_config.data_daily[1][:, i, j], color="b", lw=2,
label=rea_config.label)
ax.plot(gcm_config.data_daily[0], gcm_config.data_daily[1][:, i, j], color="r", lw=2,
label=gcm_config.label)
ax.xaxis.set_major_locator(MonthLocator())
ax.xaxis.set_minor_locator(MonthLocator(bymonthday=15))
ax.xaxis.set_minor_formatter(FuncFormatter(lambda d, pos: num2date(d).strftime("%b")[0]))
plt.setp(ax.xaxis.get_majorticklabels(), visible=False)
ax.grid()
sfmt = ScalarFormatter(useMathText=True)
sfmt.set_powerlimits([-2, 2])
ax.yaxis.set_major_formatter(sfmt)
bbox_props = dict(boxstyle="round,pad=0.3", fc="cyan", ec="b", lw=1, alpha=0.5)
ax.annotate(bname, (0.9, 0.1), xycoords="axes fraction", bbox=bbox_props, zorder=10,
alpha=0.5, horizontalalignment="right", verticalalignment="bottom")
ax_last = ax
ax_last.legend(loc="upper right", bbox_to_anchor=(1, -0.2), borderaxespad=0, ncol=2)
img_file = img_folder.joinpath("bfe_hydrographs.eps")
with img_file.open("wb") as f:
fig.tight_layout()
fig.savefig(f, bbox_inches="tight", format="eps")
def plotResults(a1, a2, b1, b2, fname, ofname):
#read data from csv file
print('Reading data from csv file...')
a = np.genfromtxt(fname, delimiter=';')
noRows = a.shape[0]
noCols = a.shape[1]
a = a[0:noRows, 0:(noCols-1)]
deltaX = a2-a1
deltaY = b2-b1
stepX = deltaX / (noRows)
stepY = deltaY / (noCols-1)
print('done.')
print('Preparing plot...')
fig = plt.figure(figsize=(5, 3), dpi=500)
ax = fig.gca(projection='3d')
X = np.arange(a1, a2, stepX)
Y = np.arange(b1, b2, stepY)
X, Y = np.meshgrid(X, Y)
Z = a
vMax=Z.max()
vMin=Z.min()
vMax=vMax+0.1*abs(vMax)
vMin=vMin-0.1*abs(vMin)
surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.Greys_r,
linewidth=0, antialiased=True, vmin=vMin, vmax=vMax)
zAxisFormatter = ScalarFormatter()
zAxisFormatter.set_scientific(True)
zAxisFormatter.set_powerlimits((0, 1))
#ax.zaxis.set_major_formatter(zAxisFormatter)
print('Drawing...')
fontSize=8 #set fontsize on plot
ax.set_xlabel('x', fontsize=fontSize)
ax.set_ylabel('y', fontsize=fontSize)
ax.zaxis.set_rotate_label(False)
ax.set_zlabel('u(x,y)', fontsize=fontSize, rotation=90)
ax.view_init(27, 35)
t = ax.zaxis.get_offset_text()
t.set_size(fontSize-2)
#t.set_position((0,0))
t.set_rotation(45)
t.set_verticalalignment('center')
#t.set_z(0)
plt.setp(ax.get_xticklabels(), fontsize=fontSize)
plt.setp(ax.get_yticklabels(), fontsize=fontSize)
plt.setp(ax.get_zticklabels(), fontsize=fontSize)
plt.legend()
cbar=fig.colorbar(surf, shrink=0.75, aspect=15)
cbar.ax.tick_params(labelsize=fontSize)
#plt.show()
plt.savefig(filename=ofname, format='eps')
plt.close()
def tick_formatter(powerlimits=None):
try:
from matplotlib.ticker import ScalarFormatter
except ImportError:
raise (MatplotlibUnavailableError("Matplotlib is required but unavailable on your system."))
except RuntimeError:
raise (MatplotlibDisplayError("Matplotlib unable to open display"))
if powerlimits is None:
powerlimits = (3, 3)
formatter = ScalarFormatter()
formatter.set_powerlimits(powerlimits)
return formatter
def show_slice_overlay(self, x_range, y_range, x, slice_y_data, y, slice_x_data):
"""sum along x and z within the box defined by qX- and qZrange.
sum along qx is plotted to the right of the data,
sum along qz is plotted below the data.
Transparent white rectangle is overlaid on data to show summing region"""
from matplotlib.ticker import FormatStrFormatter, ScalarFormatter
if self.fig == None:
print ("No figure for this dataset is available")
return
fig = self.fig
ax = fig.ax
extent = fig.im.get_extent()
if fig.slice_overlay == None:
fig.slice_overlay = ax.fill(
[x_range[0], x_range[1], x_range[1], x_range[0]],
[y_range[0], y_range[0], y_range[1], y_range[1]],
fc="white",
alpha=0.3,
)
fig.ax.set_ylim(extent[2], extent[3])
else:
fig.slice_overlay[0].xy = [
(x_range[0], y_range[0]),
(x_range[1], y_range[0]),
(x_range[1], y_range[1]),
(x_range[0], y_range[1]),
]
fig.sz.clear()
default_fmt = ScalarFormatter(useMathText=True)
default_fmt.set_powerlimits((-2, 4))
fig.sz.xaxis.set_major_formatter(default_fmt)
fig.sz.yaxis.set_major_formatter(default_fmt)
fig.sz.xaxis.set_major_formatter(FormatStrFormatter("%.2g"))
fig.sz.set_xlim(x[0], x[-1])
fig.sz.plot(x, slice_y_data)
fig.sx.clear()
fig.sx.yaxis.set_major_formatter(default_fmt)
fig.sx.xaxis.set_major_formatter(default_fmt)
fig.sx.yaxis.set_ticks_position("right")
fig.sx.yaxis.set_major_formatter(FormatStrFormatter("%.2g"))
fig.sx.set_ylim(y[0], y[-1])
fig.sx.plot(slice_x_data, y)
fig.im.set_extent(extent)
fig.canvas.draw()
def __init__(self, figure, x_label='', y_label=''):
"""
Initializes a _plot_list, which contains plot_data.
Keyword arguments:
figure -- The matplotlib figure to which the plots are added.
x_label -- The x-axis label to use for all plots (default: '')
y_label -- The y-axis label to use for all plots (default: '')
"""
self.x_label = x_label
self.y_label = y_label
self.figure = figure
self.sub_plots = []
# set default formatter for the time being
frmt = ScalarFormatter(useOffset = True)
frmt.set_powerlimits((-3,3))
frmt.set_scientific(True)
self.default_formatter = (frmt, frmt)
def plot_learn_zips_summary(name,control_zip,learn_zips,vals,skip_rows=0,png=False,num_mins=3):
_,control = read_zip(control_zip,skip_rows=skip_rows)
baseline = 1
scale = baseline/numpy.mean(control)
figsize = (5,2.5)
pylab.figure(figsize=figsize,dpi=300)
means = []
for learn_zip in learn_zips:
_,learn = read_zip(learn_zip,skip_rows=skip_rows)
means.append(numpy.mean(learn)*scale)
sorted_means = list(means)
sorted_means.sort()
min_means_loc = [vals[means.index(sorted_means[i])] for i in range(num_mins)]
ax = pylab.axes((0.18,0.2,0.8,0.7))
fmt = ScalarFormatter()
fmt.set_powerlimits((-3,4))
fmt.set_scientific(True)
ax.xaxis.set_major_formatter(fmt)
ax.xaxis.set_minor_locator(MultipleLocator(float(vals[1])-float(vals[0])))
pylab.plot(vals,means,color='k',linewidth=2)
pylab.plot(min_means_loc,sorted_means[:num_mins],'o',markerfacecolor='None')
pylab.plot(min_means_loc[0],sorted_means[0],'ko')
pylab.axhline(baseline,linestyle='--',linewidth=1,color='k')
pylab.ylabel('Mean relative error\n(learning vs. analytic)\n\n',ha='center')
pylab.xlabel(name)
pylab.axis('tight')
if png:
if not os.path.exists('png'):
os.mkdir('png')
pylab.savefig('png/'+learn_zips[0].split('-')[0]+'-summary.png',figsize=figsize,dpi=600)
else:
pylab.show()
def _plot_soil_hydraulic_conductivity(ax, basemap, x, y, field, title="", cmap=None):
ax.set_title(title)
if cmap is not None:
levels = np.linspace(field.min(), field.max(), cmap.N + 1)
levels = np.round(levels, decimals=6)
bn = BoundaryNorm(levels, cmap.N)
im = basemap.pcolormesh(x, y, field, ax=ax, cmap=cmap, norm = bn)
fmt = ScalarFormatter(useMathText=True)
fmt.set_powerlimits([-2, 3])
cb = basemap.colorbar(im, ticks=levels, format=fmt)
cax = cb.ax
cax.yaxis.get_offset_text().set_position((-3, 5))
else:
im = basemap.pcolormesh(x, y, field, ax=ax)
basemap.colorbar(im, format="%.1f")
def CreatePlot(self): #just sample plot, it will be replaced with real one after you load some data
formatter = ScalarFormatter()
formatter.set_scientific(True)
formatter.set_powerlimits((0,0))
self.figure = Figure()
self.figure.set_facecolor('white')
self.figure.subplots_adjust(bottom=0.3, left=0.25)
self.axes = self.figure.add_subplot(111)
self.axes.xaxis.set_major_formatter(formatter)
self.axes.yaxis.set_major_formatter(formatter)
x = np.arange(0,6,.01)
y = np.sin(x**2)*np.exp(-x)
self.axes.plot(x,y, ls = 'dotted',label = "This is just a sample plot and it will be replaced with\nthe real plot once when you load some data...")
self.setScales()
handles, labels = self.axes.get_legend_handles_labels()
self.axes.legend(handles[::-1], labels[::-1], fancybox=True)
frame=self.axes.get_frame()
frame.set_alpha(0.4)
self.canvas = FigCanvas(self.plotPanel, wx.ID_ANY, self.figure) #jako bitna stavka
return 1
def run(self): """ computation """ (name, nameA, nameB, labelA, labelB, stat_1, stat_2, correlation, theme) = self.getParams() plt.ioff() def funcHexBin(ax): gridsize = correlation["Binning"]["Grid Size"] frequencies = correlation["Binning"]["Absolute Frequencies"] max = correlation["Binning"]["Max Frequency"] offsets = correlation["Binning"]["Offsets"] paths = correlation["Binning"]["Paths"] x_min = stat_1["Location"]["Min"] x_max = stat_1["Location"]["Max"] y_min = stat_2["Location"]["Min"] y_max = stat_2["Location"]["Max"] for i in range(len(frequencies)): color = Theme.RGBA2RGB( theme.getPlotColor(), math.log(frequencies[i]+1,10)/math.log(max+1,10), theme.getBackgroundColor() ) path = paths.transformed(mpl.transforms.Affine2D().translate( offsets[i][0], offsets[i][1] )) ax.add_patch(patches.PathPatch( path, facecolor = color, linestyle = "solid", linewidth = 0 )) ax.set_xlim([x_min, x_max]) ax.set_ylim([y_min, y_max]) ax.set_xlabel(labelA) ax.set_ylabel(labelB) ax2 = ax.twinx() ax2.set_ylabel(nameB) ax2.set_yticks([]) ax3 = ax.twiny() ax3.set_xlabel(nameA) ax3.set_xticks([]) fig = plt.figure() ax = fig.gca() funcHexBin(ax) xfmt = ScalarFormatter(useMathText=True) xfmt.set_powerlimits((-1,1)) ax.xaxis.set_major_formatter(xfmt) yfmt = ScalarFormatter(useMathText=True) yfmt.set_powerlimits((-1,1)) ax.yaxis.set_major_formatter(yfmt) fig.set_size_inches(4, 3.75) return self.save( name, fig, "scatter." + nameA + " - " + nameB )
def _polish(self,f): # Handle properties of axes directly #a = plt.gca() # Current set of axes formatter_scalar = ScalarFormatter(useOffset=True,useMathText=False) formatter_scalar.set_powerlimits((-3,3)) formatter_log = LogFormatterMathtext(base=10.0,labelOnlyBase=False) # Neaten axes formatters for ax in f.get_axes(): if not isinstance(ax.xaxis.get_major_formatter(),NullFormatter): if ax.xaxis.get_scale() == "log": ax.xaxis.set_major_locator(LogLocator(base=10.0, subs=[1.0], numdecs=1)) ax.xaxis.set_major_formatter(formatter_log) else: ax.xaxis.set_major_formatter(formatter_scalar) if not isinstance(ax.yaxis.get_major_formatter(),NullFormatter): if ax.yaxis.get_scale() == "log": ax.yaxis.set_major_locator(LogLocator(base=10.0, subs=[1.0], numdecs=1)) ax.yaxis.set_major_formatter(formatter_log) #ax.yaxis.set_minor_locator(LogLocator(base=10.0, subs=[10], numdecs=1)) # why is this necessary? else: ax.yaxis.set_major_formatter(formatter_scalar)
def update_ticks(self, draw_canvas=True):
xMajorFormatter = ScalarFormatter()
yMajorFormatter = ScalarFormatter()
xMajorFormatter.set_powerlimits((-3,4))
yMajorFormatter.set_powerlimits((-3,4))
xaxis=self.axes.get_xaxis()
yaxis=self.axes.get_yaxis()
xaxis.set_major_formatter(xMajorFormatter)
yaxis.set_major_formatter(yMajorFormatter)
if self.plot.x_majorticks_enable:
xMajorLocator = MaxNLocator(self.plot.x_majorticks_maxn)
xaxis.set_major_locator(xMajorLocator)
else:
xaxis.set_major_locator(NullLocator())
if self.plot.y_majorticks_enable:
yMajorLocator = MaxNLocator(self.plot.y_majorticks_maxn)
yaxis.set_major_locator(yMajorLocator)
else:
yaxis.set_major_locator(NullLocator())
if self.plot.x_minorticks_enable:
xMinorLocator = MaxNLocator(self.plot.x_minorticks_maxn)
xaxis.set_minor_locator(xMinorLocator)
else:
xaxis.set_minor_locator(NullLocator())
if self.plot.y_minorticks_enable:
yMinorLocator = MaxNLocator(self.plot.y_minorticks_maxn)
yaxis.set_minor_locator(yMinorLocator)
else:
yaxis.set_minor_locator(NullLocator())
self.update_margins(draw_canvas=False)
if draw_canvas:
self.canvas.draw()
def __init__(self, diagnostics, filename, ntMax=0, nPlot=1):
'''
Constructor
'''
# matplotlib.rc('text', usetex=True)
matplotlib.rc('font', family='sans-serif', size='22')
self.prefix = filename
self.ntMax = diagnostics.nt
if self.ntMax > ntMax and ntMax > 0:
self.ntMax = ntMax
self.nPlot = nPlot
self.diagnostics = diagnostics
self.energy = np.zeros(self.ntMax+1)
self.helicity = np.zeros(self.ntMax+1)
self.magnetic = np.zeros(self.ntMax+1)
self.potential = np.zeros(self.ntMax+1)
print("")
for i in range(0, self.ntMax+1):
print("Reading timestep %5i" % (i))
self.diagnostics.read_from_hdf5(i)
self.diagnostics.update_invariants(i)
if self.diagnostics.plot_energy:
self.energy [i] = self.diagnostics.energy
else:
self.energy [i] = self.diagnostics.E_error
if self.diagnostics.plot_helicity:
self.helicity[i] = self.diagnostics.helicity
else:
self.helicity[i] = self.diagnostics.H_error
if self.diagnostics.plot_magnetic:
self.magnetic[i] = self.diagnostics.magnetic
else:
self.magnetic[i] = self.diagnostics.M_error
if self.diagnostics.inertial_mhd:
if self.diagnostics.plot_L2_X:
self.potential[i] = self.diagnostics.L2_X
else:
self.potential[i] = self.diagnostics.L2_X_error
else:
if self.diagnostics.plot_L2_A:
self.potential[i] = self.diagnostics.L2_A
else:
self.potential[i] = self.diagnostics.L2_A_error
# set up tick formatter
majorFormatter = ScalarFormatter(useOffset=False, useMathText=True)
## -> limit to 1.1f precision
majorFormatter.set_powerlimits((-1,+1))
majorFormatter.set_scientific(True)
# set up figure for energy plot
self.figure1 = plt.figure(num=1, figsize=(16,4))
# set up plot margins
plt.subplots_adjust(hspace=0.25, wspace=0.2)
plt.subplots_adjust(left=0.1, right=0.95, top=0.9, bottom=0.25)
axesE = plt.subplot(1,1,1)
axesE.plot(self.diagnostics.tGrid[0:ntMax+1:self.nPlot], self.energy[0:ntMax+1:self.nPlot])
axesE.set_xlabel('$t$', labelpad=15, fontsize=26)
axesE.set_xlim(self.diagnostics.tGrid[0], self.diagnostics.tGrid[ntMax])
if self.diagnostics.plot_energy:
axesE.set_ylabel('$E (t)$', labelpad=15, fontsize=26)
else:
axesE.set_ylabel('$(E (t) - E (0)) / E (0)$', labelpad=15, fontsize=26)
axesE.yaxis.set_label_coords(-0.075, 0.5)
axesE.yaxis.set_major_formatter(majorFormatter)
for tick in axesE.xaxis.get_major_ticks():
tick.set_pad(12)
for tick in axesE.yaxis.get_major_ticks():
tick.set_pad(8)
plt.draw()
filename = self.prefix + str('_energy_%06d' % self.ntMax) + '.png'
plt.savefig(filename, dpi=300)
filename = self.prefix + str('_energy_%06d' % self.ntMax) + '.pdf'
plt.savefig(filename)
# set up figure for helicity plot
self.figure2 = plt.figure(num=2, figsize=(16,4))
# set up plot margins
plt.subplots_adjust(hspace=0.25, wspace=0.2)
plt.subplots_adjust(left=0.1, right=0.95, top=0.9, bottom=0.25)
axesH = plt.subplot(1,1,1)
axesH.plot(self.diagnostics.tGrid[0:ntMax+1:self.nPlot], self.helicity[0:ntMax+1:self.nPlot])
axesH.set_xlim(self.diagnostics.tGrid[0], self.diagnostics.tGrid[ntMax])
axesH.set_xlabel('$t$', labelpad=15, fontsize=26)
if self.diagnostics.plot_helicity:
axesH.set_ylabel('$C_{\mathrm{CH}} (t)$', labelpad=15, fontsize=24)
axesH.yaxis.set_label_coords(-0.075, 0.5)
else:
axesH.set_ylabel('$(C_{\mathrm{CH}} (t) - C_{\mathrm{CH}} (0)) / C_{\mathrm{CH}} (0)$', labelpad=15, fontsize=24)
axesH.yaxis.set_label_coords(-0.075, 0.38)
axesH.yaxis.set_major_formatter(majorFormatter)
for tick in axesH.xaxis.get_major_ticks():
tick.set_pad(12)
for tick in axesH.yaxis.get_major_ticks():
tick.set_pad(8)
plt.draw()
filename = self.prefix + str('_c_helicity_%06d' % self.ntMax) + '.png'
plt.savefig(filename, dpi=300)
filename = self.prefix + str('_c_helicity_%06d' % self.ntMax) + '.pdf'
plt.savefig(filename)
# set up figure for helicity plot
self.figure3 = plt.figure(num=3, figsize=(16,4))
# set up plot margins
plt.subplots_adjust(hspace=0.25, wspace=0.2)
plt.subplots_adjust(left=0.1, right=0.95, top=0.9, bottom=0.25)
axesM = plt.subplot(1,1,1)
axesM.plot(self.diagnostics.tGrid[0:ntMax+1:self.nPlot], self.magnetic[0:ntMax+1:self.nPlot])
axesM.set_xlabel('$t$', labelpad=15, fontsize=26)
axesM.set_xlim(self.diagnostics.tGrid[0], self.diagnostics.tGrid[ntMax])
if self.diagnostics.plot_magnetic:
axesM.set_ylabel('$C_{\mathrm{MH}} (t)$', labelpad=15, fontsize=24)
axesM.yaxis.set_label_coords(-0.075, 0.5)
else:
axesM.set_ylabel('$(C_{\mathrm{MH}} (t) - C_{\mathrm{MH}} (0)) / C_{\mathrm{MH}} (0)$', labelpad=15, fontsize=24)
axesM.yaxis.set_label_coords(-0.075, 0.38)
axesM.yaxis.set_major_formatter(majorFormatter)
for tick in axesM.xaxis.get_major_ticks():
tick.set_pad(12)
for tick in axesM.yaxis.get_major_ticks():
tick.set_pad(8)
plt.draw()
filename = self.prefix + str('_m_helicity_%06d' % self.ntMax) + '.png'
plt.savefig(filename, dpi=300)
filename = self.prefix + str('_m_helicity_%06d' % self.ntMax) + '.pdf'
plt.savefig(filename)
# set up figure for potential plot
self.figure4 = plt.figure(num=4, figsize=(16,4))
# set up plot margins
plt.subplots_adjust(hspace=0.25, wspace=0.2)
plt.subplots_adjust(left=0.1, right=0.95, top=0.9, bottom=0.25)
axesL = plt.subplot(1,1,1)
axesL.plot(self.diagnostics.tGrid[0:ntMax+1:self.nPlot], self.potential[0:ntMax+1:self.nPlot])
axesL.set_xlabel('$t$', labelpad=15, fontsize=26)
axesL.set_xlim(self.diagnostics.tGrid[0], self.diagnostics.tGrid[ntMax])
if self.diagnostics.inertial_mhd:
if self.diagnostics.plot_L2_X:
axesL.set_ylabel('$C_{L^2} (t)$', labelpad=15, fontsize=24)
axesL.yaxis.set_label_coords(-0.075, 0.5)
else:
axesL.set_ylabel('$(C_{L^2} (t) - C_{L^2} (0)) / C_{L^2} (0)$', labelpad=15, fontsize=24)
axesL.yaxis.set_label_coords(-0.075, 0.4)
else:
if self.diagnostics.plot_L2_A:
axesL.set_ylabel('$C_{L^2} (t)$', labelpad=15, fontsize=24)
axesL.yaxis.set_label_coords(-0.075, 0.5)
else:
axesL.set_ylabel('$(C_{L^2} (t) - C_{L^2} (0)) / C_{L^2} (0)$', labelpad=15, fontsize=24)
axesL.yaxis.set_label_coords(-0.075, 0.4)
axesL.yaxis.set_major_formatter(majorFormatter)
for tick in axesL.xaxis.get_major_ticks():
tick.set_pad(12)
for tick in axesL.yaxis.get_major_ticks():
tick.set_pad(8)
plt.draw()
filename = self.prefix + str('_l2_psi_%06d' % self.ntMax) + '.png'
plt.savefig(filename, dpi=300)
filename = self.prefix + str('_l2_psi_%06d' % self.ntMax) + '.pdf'
plt.savefig(filename)
def create_graph(graphs):
import matplotlib
if graphs[-1].output:
# disables screen requirement for plotting
# must be called before importing matplotlib.pyplot
matplotlib.use('Agg')
else:
# sets backend to qt4
# required for python2
matplotlib.rcParams['backend'] = 'Qt5Agg'
import matplotlib.pyplot as plt
from matplotlib.ticker import PercentFormatter, ScalarFormatter
# set global fontsize if any
if Graph.fontsize[1]:
plt.rcParams.update({'font.size': Graph.fontsize[0]})
# TODO: override individual font settings
if Graph.label_fontsize[1] is False:
Graph.xlabel_fontsize = (None, False)
Graph.ylabel_fontsize = (None, False)
if Graph.tick_fontsize[1] is False:
Graph.xtick_fontsize = (None, False)
Graph.ytick_fontsize = (None, False)
# make Graph.global = (val, flag) just val
Graph.remove_global_flags()
# create figure
fig, ax = plt.subplots(figsize=(Graph.figsize))
# iterate over graphs array
for graph in graphs:
if graph.bar:
x = np.arange(len(graph.xcol))
ax.bar(x + graph.offset, graph.ycol, align='center',
label=graph.legend, color=graph.color, width=graph.width)
plt.xticks(x, graph.xcol)
elif graph.barh:
x = np.arange(len(graph.xcol))
ax.barh(x + graph.offset, graph.ycol, align='center',
label=graph.legend, color=graph.color, height=graph.width)
plt.yticks(x, graph.xcol)
elif graph.hist or graph.hist_perc:
bins = graph.bins
if bins is None and graph.bin_size is None:
# default: one bin for each
bins = int((graph.ycol.max() - graph.ycol.min()))
elif graph.bin_size:
_min, _max, _bin = graph.ycol.min(), graph.ycol.max(), graph.bin_size
bins = np.arange(_min - (_min % _bin),
_max + (_bin - (_max % _bin)), _bin)
weights = np.ones_like(graph.ycol)
if graph.hist_perc:
weights = weights * 100.0 / len(graph.ycol)
ax.yaxis.set_major_formatter(PercentFormatter(xmax=100, decimals=1))
ax.hist(graph.ycol, bins=bins, weights=weights)
else:
l = ax.plot(graph.xcol, graph.ycol, label=graph.legend,
marker=graph.marker, color=graph.color, linestyle=graph.style,
linewidth=graph.width, markersize=graph.markersize)[0]
if not graph.timeseries:
yformat = ScalarFormatter(useOffset=False, useMathText=True)
xformat = ScalarFormatter(useOffset=False, useMathText=True)
yformat.set_powerlimits(Graph.exponent_range)
xformat.set_powerlimits(Graph.exponent_range)
ax.yaxis.set_major_formatter(yformat)
ax.xaxis.set_major_formatter(xformat)
if graph.fill:
ax.fill_between(graph.xcol, graph.ycol, alpha=0.1,
color=l.get_color())
if graph.output:
apply_globals(plt, ax, graphs)
plt.savefig(graph.output)
elif graph == graphs[-1]:
apply_globals(plt, ax, graphs)
plt.show()
data[algorithm] = dict()
if not core in data[algorithm]:
data[algorithm][core] = dict()
if not depth in data[algorithm][core]:
data[algorithm][core][depth] = list()
data[algorithm][core][depth].append(duration)
return (data, depth_set, core_set)
outputfile = sys.argv[1]
data_set, depth_set, core_set = get_dataset(outputfile)
runtime_results = dict()
for depth_val in sorted(depth_set.keys()):
print "Results for " + str(depth_val) + " depth"
ax = plt.gca()
formatter = ScalarFormatter()
formatter.set_scientific(False)
ax.yaxis.set_major_formatter(formatter)
color = iter(cm.rainbow(np.linspace(0, 1, 10)))
marker = iter([
"\\", "/", "\\", "/", "\\", "/", "\\", "/", "\\", "/", "\\", "/", "\\",
"/", "\\", "/", "\\", "/", "\\", "/"
])
m = next(marker)
c = next(color)
core_vals = sorted(core_set.keys())
num_cores = len(core_set.keys())
num_algorithms = len(data_set.keys())
bar_width = 1.0 / float(num_algorithms + 1)
indices = np.arange(num_cores)
runtime_cnt = 0
# Fixing random state for reproducibility
np.random.seed(19680801)
fig, ax = plt.subplots()
years = np.arange(2004, 2009)
box_colors = [(0.8, 0.2, 0.2),
(0.2, 0.8, 0.2),
(0.2, 0.2, 0.8),
(0.7, 0.5, 0.8),
(0.3, 0.8, 0.7),
]
heights = np.random.random(years.shape) * 7000 + 3000
fmt = ScalarFormatter(useOffset=False)
ax.xaxis.set_major_formatter(fmt)
for year, h, bc in zip(years, heights, box_colors):
bbox0 = Bbox.from_extents(year - 0.4, 0., year + 0.4, h)
bbox = TransformedBbox(bbox0, ax.transData)
rb_patch = RibbonBoxImage(bbox, bc, interpolation="bicubic")
ax.add_artist(rb_patch)
ax.annotate(r"%d" % (int(h/100.)*100),
(year, h), va="bottom", ha="center")
patch_gradient = BboxImage(ax.bbox, interpolation="bicubic", zorder=0.1)
gradient = np.zeros((2, 2, 4))
gradient[:, :, :3] = [1, 1, 0.]
def __init__(self, useMathText=True):
self._fmt = ScalarFormatter(useMathText=useMathText, useOffset=False)
self._fmt.create_dummy_axis()
def plot_all(data, graph_title, y_axis_label, graph_filename, is_port_data,
max_y):
"""
Create a graph from the data given. Each element in the data represents
a subplot in the graph. The graph will be titled with the param: graph_title
and label the y axis with the param: y axis label. Finally, it will be saved
as a png file named with the param: graph_filename.
"""
#how many rows and columns to use for the subplots
dimension = generate_subplot_dimension(len(data))
#generate the subplots. The figsize is the width and height of the whole graph in inches
fig, axlist = plt.subplots(dimension[0],
dimension[1],
figsize=(dimension[1] * 4, dimension[0] * 4))
#the original axlist is a list of lists. This coverts it to just a list
axlist = axlist.flatten()
#check that there aren't going to be any empty subplots
difference = (dimension[0] * dimension[1]) - len(data)
#if there are empty subplots, reduce the number of subplots
for _ in range(difference, 0, -1):
fig.delaxes(axlist[0])
#update the ax list in case we deleted some subplots
axlist = fig.axes
#dont use scientific notation
y_formatter = ScalarFormatter(useOffset=False)
y_formatter.set_scientific(False)
i = 0
for d in data:
#get a subplot to draw in
ax = axlist[i]
#set y axis to not use scientific notation
ax.yaxis.set_major_formatter(y_formatter)
ax.set_xlabel("Time (sec)")
#The y label gets split into lines of 40 characters for readability
ax.set_ylabel("\n".join(wrap(y_axis_label, 40)))
ax.set_title("Attempt {:03d}".format(i))
#Get the length of a random list in the data (they should all be
#the same length) and create the x axis tick labels based on this
x_axis = create_x_axis_tick_labels(len(d.itervalues().next()))
#Finally, draw the plot
if is_port_data:
#set y axis bounds and pad the top
ax.set_ylim([0, max_y + (max_y * 0.01)])
ax.stackplot(x_axis, d.values(), labels=d.keys(), colors=COLOURS)
else:
j = 0
for key in d.iterkeys():
x_axis = create_x_axis_tick_labels(len(d.get(key)))
colour = COLOURS[j]
if MASTER_HOSTNAME not in d:
colour = COLOURS[j + 1]
ax.plot(x_axis, d.get(key), label=key, color=colour)
j += 1
i += 1
#The title gets split into lines of 80 characters for readability
title = plt.suptitle("\n".join(wrap(graph_title, 80)))
legend = plt.legend(bbox_to_anchor=(0, -0.4), ncol=4, loc="lower center")
#ensures that none of the subplots are overlapping
plt.tight_layout(rect=[0, 0, 1, 0.95])
fig.savefig(graph_filename,
dpi=300,
bbox_extra_artists=(
title,
legend,
),
bbox_inches='tight')
def hist1d_oneset(label='',
dolog=True,
val='mvir',
lims=[],
binnum=20,
binsize=0,
types=[]):
# new version of mass_spec function
# label is the name of the data set (eg 30dor, pcc, etc.)
# val is the input from the label_physprop_add.txt columns
# global deltav, avgbeam, dist, freq, axes
# deltav = dvkms * u.km / u.s
# avgbeam = beam * u.arcsec
# dist = distpc * u.pc
# freq = fghz * u.GHz
# sanity check on label
if label == '':
label = str(
input('No label [dataset_line] given, enter name to continue: '))
# default types is all of them, can be specified to only put a few
# loop below catches types not consistent with parameters
if len(types) == 0:
types = ['trunks', 'branches', 'leaves', 'clusters']
else:
for t in types:
if t not in ['trunks', 'branches', 'leaves', 'clusters']:
print(
'Type \'{}\' not recognized from default types, exiting...'
.format(t))
return
else:
continue
# makes directory in which plots will be created if it doesn't already exist
if os.path.isdir('../prophists') == 0:
os.mkdir('../prophists')
# formatting parameters
params = {'text.usetex': False, 'mathtext.fontset': 'stixsans'}
plt.rcParams.update(params)
# read in data
if os.path.isfile('../props/' + label + '_physprop_add.txt'):
pcat = Table.read('../props/' + label + '_physprop_add.txt',
format='ascii.ecsv')
else:
pcat = Table.read('../props/' + label + '_physprop.txt',
format='ascii.ecsv')
# get indicies of types
idc = [0, 0, 0, 0]
for i, typ in enumerate(types):
with open('../props/' + label + '_' + typ + '.txt', 'r') as f:
reader = csv.reader(f, delimiter=' ')
a = zip(*reader)
idc[i] = map(int, a[0])
# data flattening
pltdata = []
for i in range(len(types)):
data = pcat[val][idc[i]]
xdata = np.log10(data[data > 0])
pltdata.append(xdata)
# limit and bin size determination
if len(lims) == 0:
limvals = [item for sublist in pltdata for item in sublist]
limmin = np.around(np.nanmin(limvals), 2)
limmax = np.around(np.nanmax(limvals), 2)
elif len(lims) == 1:
print('Only one limit ({}) specified, exiting...'.format(lims[0]))
return
else:
if len(lims) > 2:
print('Only first two limits will be used')
limmin = lims[0]
limmax = lims[1]
if binsize == 0:
limdif = limmax - limmin
optsize = np.around(limdif / binnum, 3)
# choosing logic, presets are arbitrary but work well for 30dor and pcc
if (optsize < .01):
binsize = .01
elif (.01 <= optsize < .025):
binsize = .02
elif (.025 <= optsize < .06):
binsize = .04
elif (.06 <= optsize < .09):
binsize = .08
elif (.09 <= optsize < .15):
binsize = .1
elif (.15 <= optsize < .25):
binsize = .2
elif (.25 <= optsize < .6):
binsize = .4
elif (.6 <= optsize < .9):
binsize = .8
elif (.9 <= optsize):
binsize = 1
# bin spacing, extra space for clarity
binlist = np.arange((limmin - 2 * binsize), (limmax + 2 * binsize),
binsize)
# plotting section
fig, axes = plt.subplots()
n, bins, patches = axes.hist(pltdata,
binlist,
normed=0,
log=dolog,
histtype='bar',
label=types,
rwidth=.8)
# changes y-axis to linear for small distributions (looks much cleaner)
nummax = max([np.max(o) for o in n])
if (nummax < 14):
plt.cla()
n, bins, patches = axes.hist(pltdata,
binlist,
normed=0,
log=0,
histtype='bar',
label=types,
rwidth=.8)
axes.xaxis.set_minor_locator(FixedLocator(binlist[1::2] + binsize / 2))
axes.xaxis.set_major_locator(FixedLocator(binlist[0::2] + binsize / 2))
axes.tick_params(labelsize=6)
axes.set_xlabel('log ' + val + ' [' + str(pcat[val].unit) + ']')
axes.set_ylabel('Number of objects binned')
axes.yaxis.set_major_formatter(ScalarFormatter())
plt.title('{0}_{1}'.format(label, val))
plt.legend(loc='best', fontsize='medium')
#plt.show()
plt.savefig('../prophists/' + label + '_' + val + '_hist.pdf',
bbox_inches='tight')
plt.close()
print('Plot created successfully for {0}_{1}'.format(label, val))
return
def generate_plot(partial_quota, number_of_instances, f, a0, a1, tmp_y2, tmp_x,
tmp_y, blocks_x, start_point, Xtics, yearly_quota, x_start,
finished, User_t, System_t, y_start2, y_end2, beginning_dt,
nutzergraph, fig, x_end, Data, filter_n, months):
if filter_n:
f.suptitle(str(filter_n), fontweight="bold")
else:
f.suptitle(str(Data[0]['Account'])[2:-1], fontweight="bold")
global daily_eff_days
global daily_eff_eff
fmt = "%Y-%m-%d-%H-%M" # standard format for Dates, year month, day, hour, minute
myFmt = mdates.DateFormatter('%b %y')
nothing = mdates.DateFormatter(' ')
monthly_cputime = []
monthly_used = []
effarray = []
tmp_y2.append(tmp_y[-1])
if partial_quota: #### drawing of the quota####
for i in range(0, number_of_instances
): # not possible for the last area, hence skipping it.
col = colorization(
D_.find_y_from_given_time(
datetime.datetime.fromtimestamp(blocks_x[i * 2 + 1]),
tmp_x, tmp_y) - D_.find_y_from_given_time(
datetime.datetime.fromtimestamp(blocks_x[i * 2]),
tmp_x, tmp_y), partial_quota)
coordinates_x = (datetime.datetime.fromtimestamp(blocks_x[i * 2]),
datetime.datetime.fromtimestamp(blocks_x[i * 2]),
datetime.datetime.fromtimestamp(blocks_x[i * 2 +
1]))
coordinates_y = [
tmp_y2[i * 2], tmp_y2[i * 2 + 1], tmp_y2[i * 2 + 1]
]
a0.fill_between(coordinates_x,
0,
coordinates_y,
color=col,
alpha=0.99)
monthly_cputime.append(tmp_y2[i * 2 + 1] - tmp_y2[i * 2])
value1 = D_.find_y_from_given_time(
datetime.datetime.fromtimestamp(blocks_x[-1]), tmp_x, tmp_y)
value2 = D_.find_y_from_given_time(
datetime.datetime.fromtimestamp(blocks_x[-2]), tmp_x, tmp_y)
col = colorization(value1 - value2, partial_quota)
coordinates_x = (datetime.datetime.fromtimestamp(blocks_x[-2]),
datetime.datetime.fromtimestamp(blocks_x[-2]),
datetime.datetime.fromtimestamp(blocks_x[-1]))
coordinates_y = (value2, value2 + partial_quota,
value2 + partial_quota)
a0.fill_between(coordinates_x, 0, coordinates_y, color=col, alpha=0.99)
# determines the last interval's color and draws it (uses the highest
# recorded value as the end value of the ongoing time span).
axis = plt.gca() # for plotting/saving the plot as it's own image
# Sets the visual borders for the graphs; area of occurring values (main graph) +- 5%.
if start_point: # setting the beginning and end of the graph
beginning = start_point.timestamp()
end = start_point.timestamp() + 365 * 24 * 3600
beginning = beginning - 30 * 24 * 3600
end = end + 30 * 24 * 3600
extrapolation_x = []
extrapolation_y = []
if len(tmp_y2) < 3:
tmp_y2.append(0)
tmp_y2.append(0)
usedmonths = 0
usedmonths += 12 * (int(x_end.strftime("%Y")) -
int(x_start.strftime("%Y")))
usedmonths += int(x_end.strftime("%m")) - int(x_start.strftime("%m"))
monthsleft = int(months - usedmonths)
if yearly_quota and len(tmp_x) >= 1:
extrapolation_point_x = D_.first_of_month(x_end)
extrapolation_point_y = D_.find_y_from_given_time(
tmp_x[-1], tmp_x, tmp_y)
extrapolation_point_y = max(
extrapolation_point_y,
D_.find_y_from_given_time(D_.first_of_month(extrapolation_point_x),
tmp_x, tmp_y) + partial_quota)
extrapolation_x.append(D_.first_of_month(extrapolation_point_x))
extrapolation_x.append(D_.first_of_month(extrapolation_point_x))
extrapolation_x.append(
D_.first_of_month(
datetime.datetime.fromtimestamp(
extrapolation_point_x.timestamp() + 2851200)))
extrapolation_y.append(
D_.find_y_from_given_time(extrapolation_point_x, tmp_x, tmp_y))
extrapolation_y.append(
max(extrapolation_y[0] + partial_quota, tmp_y[-1]))
extrapolation_y.append(extrapolation_y[-1])
expoint_y = extrapolation_y[-1]
extrapolation_y[-2] = tmp_y[-1]
extrapolation_y[-1] = tmp_y[-1]
expoint_y = extrapolation_y[-1]
xtr_pt_x = extrapolation_point_x
xtr_pt_y = extrapolation_point_y
for i in range(1,
monthsleft): # The three points required for each block
extrapolation_x.append(
D_.first_of_month(
datetime.datetime.fromtimestamp(xtr_pt_x.timestamp() +
i * 2851200)))
extrapolation_x.append(
D_.first_of_month(
datetime.datetime.fromtimestamp(xtr_pt_x.timestamp() +
i * 2851200)))
extrapolation_x.append(
D_.first_of_month(
datetime.datetime.fromtimestamp(xtr_pt_x.timestamp() +
(i + 1) * 2851200)))
extrapolation_y.append(expoint_y + (i - 1) * partial_quota)
extrapolation_y.append(expoint_y + i * partial_quota)
extrapolation_y.append(expoint_y + i * partial_quota)
if monthsleft:
a0.plot(extrapolation_x[3:], extrapolation_y[3:], "black")
if monthsleft:
extrapolation_y.append(0)
else:
extrapolation_y = [0]
beg_14_months = beginning + 36817200
fourteen_dt = datetime.datetime.fromtimestamp(beg_14_months)
# Print statements, to give feedback either onscreen or into a dedicated file to be piped into.
print('The accumulated TotalCPU time is',
int((User_t[-1] + System_t[-1]) * 100) / 100, "hours")
print('and the number of accumulated corehours is',
int(tmp_y[-1] * 100) / 100)
efficiency = (User_t[-1] + System_t[-1]) / tmp_y[-1]
# Added rounding to the efficiency percentage feedback.
print('Which results in an efficiency of',
int(efficiency * 10000) / 100 + 0.005, "%")
if efficiency < 0 or efficiency > 1:
print(
"Efficiency is outside of it's boundaries, valid is only between 0 and 1"
)
accum_total_time = np.zeros(len(tmp_x))
for i in range(0, len(accum_total_time)):
accum_total_time[i] = User_t[i] + System_t[i]
delta = [0]
total_time = []
total_time.append(accum_total_time[0])
total_time.append(accum_total_time[0])
difference = [0]
for i in range(1, len(accum_total_time)):
total_time.append(accum_total_time[i] - accum_total_time[i - 1])
delta.append(100 * ((accum_total_time[i] - accum_total_time[i - 1]) /
(tmp_y[i] - tmp_y[i - 1])))
if delta[i] > 100:
a = 0
if yearly_quota: # ensuring that the extrapolated quota is still in frame
a0.set_ylim([
y_start2 - (0.05 * y_end2),
max(tmp_y[-1], max(extrapolation_y), max(coordinates_y)) * 1.2
])
# print("limit",a0.get_ylim()[1])
else: # No quota given, image is focused around occupied and utilized resources.
print("NO YEARLY DETECTED")
a0.set_ylim([y_start2 - (0.05 * y_end2), tmp_y[-1] * 1.05])
##### Creation of patches for Legend #####
red_patch = mpatches.Patch(color='#ff0000', alpha=0.7, label='>=150%')
orange_patch = mpatches.Patch(color='#ffa500',
alpha=0.7,
label='>=110%,<150%')
green_patch = mpatches.Patch(color='#008000',
alpha=0.8,
label='>=70%,<110%')
light_green_patch = mpatches.Patch(color='#81c478',
alpha=0.8,
label='<70%')
grey_patch = mpatches.Patch(color='dimgrey',
alpha=0.75,
label='Allocated corehours')
yellow_patch = mpatches.Patch(color='#d9e72e',
alpha=0.49,
label='Utilized corehours')
black_patch = mpatches.Patch(color='black',
alpha=1,
label='Granted corehours')
a0.plot(tmp_x, accum_total_time, '#d9e72e') # plotting the TotatlCPU Graph
if yearly_quota: # Legends for if there is a quota, or a shorter Legend in case there isn't.
a0.legend(handles=[
red_patch, orange_patch, green_patch, light_green_patch,
grey_patch, yellow_patch, black_patch
])
else:
a0.legend(handles=[grey_patch, yellow_patch])
a0.fill_between(tmp_x, 0, accum_total_time, color='#d9e72e',
alpha=0.70) # plotting the area below TotalCPU graph
a0.plot(tmp_x, tmp_y, 'dimgrey', fillstyle='bottom',
alpha=0.75) # plotting the main graph (cores * hours)
a0.fill_between(tmp_x, 0, tmp_y, color="grey",
alpha=0.45) # plotting the area below the corehours graph
for i in range(len(accum_total_time), number_of_instances * 3 +
4): # ensuring that empty months will be accounted for
accum_total_time = np.append(
accum_total_time,
accum_total_time[-1]) # filling accumulated time with most recent
if yearly_quota:
for i in range(0, int(number_of_instances)
): # not possible for the last area, hence skipping it.
monthly_used.append(accum_total_time[i * 3 + 3] -
accum_total_time[i * 3])
percentages = [0]
for i in range(len(monthly_cputime)):
if monthly_used[i] >= 1:
percentages.append(10 * (monthly_cputime[i] / monthly_used[i]))
for i in range(len(percentages)):
effarray.append(percentages[i])
a0.grid(True)
axis2 = fig.add_subplot(212)
a1legend1 = mpatches.Patch(color='Red', alpha=0.8, label="per day")
a1legend2 = mpatches.Patch(color='purple', alpha=0.8, label='per job')
a1.plot(tmp_x, delta, '.', color="purple", markersize=5,
alpha=0.35) # percentages amplified by the lower bound to
a1.legend(handles=[a1legend1, a1legend2])
plt.ylabel('Efficiency') # be more visible.
daily = []
dates = []
for i in range(int(x_start.timestamp()), int(x_end.timestamp()), 2764800):
r = D_.gather_efficiencies_for_month(
datetime.datetime.fromtimestamp(i), Data)
daily_eff_days = r[-2]
daily_eff_eff = r[-1]
r = r[:-2]
for j in range(len(r[0])):
if r[1][j] > 0:
daily.append(100 * r[1][j] / r[0][j])
dates.append(r[2][j])
formatteddates = []
for i in dates:
if len(str(i)) > 5 and "." not in str(i):
transp = str(i)[2:18]
formatteddates.append(datetime.datetime.strptime(transp, fmt))
eff_days = []
#for i in dates:
# eff_days.append(datetime.datetime.strptime(str(i)[2:18], fmt))
a1.plot(formatteddates, daily, '.', color="Red", markersize=3, alpha=0.85)
eff_distance = 0 - axis.get_ylim()[0]
a1.grid(
True
) # Creates a grid in the image to aid the viewer in visually processing the data.
a1.set_ylim([-5, 105])
if nutzergraph:
a1.set_ylim(
[0,
100]) # Usergraphs don't display anything above 100% or below 0%.
a1.set_yticks(
np.arange(0, 101, 10),
minor=True) # minor tick-lines are much thinner than regular ones
a1.set_yticks(np.arange(0, 101, 25))
a1.yaxis.set_major_formatter(mtick.PercentFormatter())
plt.xlabel('Efficiency')
plt.xlabel(' ')
a0.xaxis.tick_top()
a0.set_xlim((beginning_dt, fourteen_dt))
a1.xlim = (beginning_dt, fourteen_dt)
plt.sca(a0)
a0.yaxis.set_major_formatter(ScalarFormatter(useOffset=True))
plt.xticks(Xtics)
plt.ylabel('CPUhours')
emptylabels = []
for i in a0.get_xticklabels():
emptylabels.append(["", ""])
new_ylabels, unit = get_scaled_ylabels(a0.get_yticks())
plt.ylabel("CPUhours (" + unit + ")")
a0.set_xticklabels = emptylabels
a0.set_yticklabels(new_ylabels)
plt.sca(a1)
# dictates gap in height, left border, right border, gap in width, bottom border, top border
plt.subplots_adjust(hspace=0.03,
left=0.1,
right=0.925,
wspace=0.07,
bottom=0.035,
top=0.95)
plt.xlim(beginning_dt, fourteen_dt)
plt.xticks(Xtics)
a0.xaxis.set_major_formatter(nothing) # removes the x-tic notations
a1.xaxis.set_major_formatter(myFmt)
a1.grid(which='minor', alpha=0.2)
a1.grid(which='major', alpha=0.5)
f.set_size_inches((11, 8.5), forward=False)
## for png compression
#ram = io.BytesIO()
#plt.savefig(ram, format='png')
#ram.seek(0)
#im = Image.open(ram)
#im2 = im.convert('RGB').convert('P', palette=Image.ADAPTIVE)
#return im2
#print(tmp_x)
#print(tmp_y)
return f
def minimize():
#set variables
cur_f = 0 #current objective function value at defined point
iters = 0 #Iteration variable
precision = 0.0000001 #alarm to stop algo
iterations = 100000 #set max number of iterations
previous_step_size = 1
ai = [] #list for observation points
fnval = [] #list for objective function value wit each iteration
Error_Overflow = False # scalar exception error
Plot = True #Variable to differentiate plots without error or with error!
lstep = 0.0002 # set the step for gradient algo
# initialize a point with some random value b/w [-5,5]
a = np.array([np.random.randint(-5, 5), np.random.randint(-5, 5)])
initial_point = a
#when starting point itself is a minimum
if a[0] == 1.00 and a[1] == 1.00:
print("\tStarting point itself is a minima.\n")
Plot = False
#loop to minimize objective function
while previous_step_size > precision and iters < iterations:
prev_f = cur_f
#objective function
f = ((1 - a[0])**2) + (100 * ((a[1] - a[0]**2)**2))
#raise OverflowError() true
if abs(f) == float('inf'):
Error_Overflow = True
f = fnval
break
#append the point and its obj function to ai/fnval lists
ai.append([a, f])
fnval.append(f) #mainly for plot
#reassign objective function value at point a
cur_f = f
#compute its derrivative on point a
fi = np.array(DerivativeRosenbrock(a))
#reassign step value at point a
a = a - lstep * fi
previous_step_size = abs(cur_f - prev_f)
#increase iteration by 1.
iters = iters + 1
# convert ai/fnval into a numpy array and do operations
ai = np.array(ai)
minFnVal = min(np.array(fnval))
minIndex = fnval.index(minFnVal)
#print the findings
#print(f'\n\tThe minimum is: {minFnVal} at point: {ai[minIndex,0]} after iterations: {iters}.')
print(
f'\t\tStarting Point: {[initial_point[0],initial_point[1]]}\n\t\tFinal Point: {ai[minIndex,0]}\
\n\t\tMinimum Value: {round(minFnVal,5)}\n\t\tTotal Iterations: {iters}'
)
# Plot the decline in function value
if (Plot == True):
fig1, ax = plt.subplots()
ax.set_xscale('log')
ax.set_yscale('log')
#Plot with red line if there were an overflow while calculating function value
#Print appropriate message
if Error_Overflow:
ax.plot(range(iters), fnval, color="r")
print(
"overflow encountered. Function is NOT going to minimize with starting point:{} and step-size:0.002"
.format(ai[0, 0]))
else:
ax.plot(range(iters), fnval, color="b")
#loop for formatting x/y axis ticks
for axis in [ax.xaxis, ax.yaxis]:
axis.set_major_formatter(ScalarFormatter())
ax.yaxis.set_major_formatter(
ticker.FuncFormatter(lambda y, pos: ('{{:.{:1d}f}}'.format(
int(np.maximum(-np.log10(y), 0)))).format(y)))
#draw a red line for function decline intersection at function value 0.001 for ease in understanding
plt.axhline(y=minFnVal, color="r", linestyle='--')
#Title and label the graph
plt.title("Objective Function Value vs Iteartions\n",
fontsize=16,
fontweight='bold')
plt.xlabel("Iterations", fontsize=16, fontweight='bold')
plt.ylabel("Objective Function value", fontsize=16, fontweight='bold')
plt.show()
import matplotlib.pylab as plt
import matplotlib.pyplot
from matplotlib.font_manager import FontProperties
from matplotlib.ticker import ScalarFormatter
from matplotlib.ticker import FixedFormatter
import pylab as pl
import numpy as np
import math, os
import glob, pickle
formatter = ScalarFormatter(useMathText=True)
fig_width_pt = 246.0 * 2 # Get this from LaTex using \the\columnwidth
inches_per_pt = 1.0 / 72.27
golden_mean = (np.sqrt(5) - 1.0) / 2.0
fig_width = fig_width_pt * inches_per_pt # width in inches
fig_height = fig_width * golden_mean # height in inches
fig_size = [fig_width, fig_height]
params = {
'axes.labelsize': 10,
'text.fontsize': 6,
'legend.fontsize': 6,
'xtick.labelsize': 11.0,
'ytick.labelsize': 11.0,
'figure.figsize': fig_size,
'font.family': 'serif'
}
pl.rcParams.update(params)
pl.clf()
pl.figure()
def plot_lc(df, y, tag, highlight):
sns.set()
sns.set_style("white")
#sns.set_context("paper")
y_mean = y + '_mean'
y_std = y + '_std'
avg_folds = df.groupby(
['Data', 'Model', 'Alg', 'nQuery', 'TrainAug', 'Samples']).agg({
y: ['mean', pop_std, 'count']
}).reset_index()
avg_folds[y_mean] = avg_folds[y]['mean']
avg_folds[y_std] = avg_folds.apply(
lambda row: row[y]['pop_std'] / sqrt(row[y]['count']), axis=1)
avg_folds = avg_folds.drop([y], axis=1)
print(avg_folds)
setting_col = ['Data', 'Model', 'nQuery', 'TrainAug']
for setting, g_setting in avg_folds.groupby(setting_col):
data, model, nQuery, TrainAug = setting
setting_t = param_to_str_t(OrderedDict(zip(setting_col, setting)))
setting_fn = param_to_str_fn(OrderedDict(zip(setting_col, setting)))
df_rand = g_setting[g_setting['Alg'] == 'rand']
if nQuery != 10000 and highlight:
for samp in sorted(list(df_rand['Samples'])):
acc_vals = g_setting[g_setting['Samples'] ==
samp][y_mean].values
#print(max(acc_vals) / min(acc_vals))
if max(acc_vals) / min(acc_vals) > 1.08:
break
st_samp = samp
stopFrac = 0.99
endSamp = max(df_rand['Samples'])
endAcc = np.mean(
df_rand[df_rand['Samples'] == endSamp][y_mean].values)
for samp in sorted(list(df_rand['Samples'])):
acc = np.mean(
df_rand[df_rand['Samples'] == samp][y_mean].values)
if acc / endAcc > stopFrac:
cut_samp = samp
break
g_setting = g_setting[(g_setting['Samples'] <= cut_samp)
& (g_setting['Samples'] >= st_samp)]
else:
algs = g_setting['Alg'].unique()
cut_samp = 1e+8
st_samp = -1
for a in algs:
df = g_setting[g_setting['Alg'] == a]
mx = max(df['Samples'])
mn = min(df['Samples'])
cut_samp = min(cut_samp, mx)
st_samp = max(st_samp, mn)
plt.figure(figsize=(fig_w, fig_h))
for alg, g_alg in g_setting.groupby(['Alg']):
ns = list(g_alg['Samples'])
accs = list(g_alg[y_mean])
stds = list(g_alg[y_std])
if float(setting[2]) < 10.1:
accs = smooth(accs, 10)[:-10]
ns = ns[:-10]
stds = stds[:-10]
plt.plot(ns,
accs,
label=str(name_dict[alg]),
linewidth=1.0,
color=color_dict[alg],
zorder=10 - order_dict[alg])
acc_up = [avg + ci for avg, ci in zip(accs, stds)]
acc_dn = [avg - ci for avg, ci in zip(accs, stds)]
plt.fill_between(ns,
acc_up,
acc_dn,
alpha=0.2,
color=color_dict[alg],
zorder=10 - order_dict[alg])
plt.gca().yaxis.set_major_formatter(FormatStrFormatter('%.2f'))
plt.gca().yaxis.get_offset_text().set_fontsize(tick_size)
if y == 'Time':
plt.gca().yaxis.set_major_formatter(
ScalarFormatter(useMathText=True))
plt.gca().ticklabel_format(axis='y', style='sci', scilimits=(0, 0))
plt.xticks(fontsize=tick_size)
plt.yticks(fontsize=tick_size)
plt.title(setting_t, fontsize=title_size)
plt.xlabel('#Labels queried', fontsize=label_size)
plt.subplots_adjust(bottom=0.15)
plt.ylabel(y, fontsize=label_size)
plt.gca().set_xlim([st_samp, cut_samp])
#plt.legend(frameon=False)
plt.grid(linestyle='--', linewidth=1)
n_alg = len(g_setting['Alg'].unique())
save_legend(n_alg)
plt.savefig(all_dir + '/' + tag + '_' + y + '_' + setting_fn + '_' +
'.pdf')
def plot_partial_dependence(gbrt,
X,
features,
feature_names=None,
label=None,
n_cols=3,
grid_resolution=100,
percentiles=(0.05, 0.95),
n_jobs=None,
verbose=0,
ax=None,
line_kw=None,
contour_kw=None,
**fig_kw):
"""Partial dependence plots for ``features``.
The ``len(features)`` plots are arranged in a grid with ``n_cols``
columns. Two-way partial dependence plots are plotted as contour
plots.
Read more in the :ref:`User Guide <partial_dependence>`.
Parameters
----------
gbrt : BaseGradientBoosting
A fitted gradient boosting model.
X : array-like, shape=(n_samples, n_features)
The data on which ``gbrt`` was trained.
features : seq of ints, strings, or tuples of ints or strings
If seq[i] is an int or a tuple with one int value, a one-way
PDP is created; if seq[i] is a tuple of two ints, a two-way
PDP is created.
If feature_names is specified and seq[i] is an int, seq[i]
must be < len(feature_names).
If seq[i] is a string, feature_names must be specified, and
seq[i] must be in feature_names.
feature_names : seq of str
Name of each feature; feature_names[i] holds
the name of the feature with index i.
label : object
The class label for which the PDPs should be computed.
Only if gbrt is a multi-class model. Must be in ``gbrt.classes_``.
n_cols : int
The number of columns in the grid plot (default: 3).
grid_resolution : int, default=100
The number of equally spaced points on the axes.
percentiles : (low, high), default=(0.05, 0.95)
The lower and upper percentile used to create the extreme values
for the PDP axes.
n_jobs : int or None, optional (default=None)
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
for more details.
verbose : int
Verbose output during PD computations. Defaults to 0.
ax : Matplotlib axis object, default None
An axis object onto which the plots will be drawn.
line_kw : dict
Dict with keywords passed to the ``matplotlib.pyplot.plot`` call.
For one-way partial dependence plots.
contour_kw : dict
Dict with keywords passed to the ``matplotlib.pyplot.plot`` call.
For two-way partial dependence plots.
**fig_kw : dict
Dict with keywords passed to the figure() call.
Note that all keywords not recognized above will be automatically
included here.
Returns
-------
fig : figure
The Matplotlib Figure object.
axs : seq of Axis objects
A seq of Axis objects, one for each subplot.
Examples
--------
>>> from sklearn.datasets import make_friedman1
>>> from sklearn.ensemble import GradientBoostingRegressor
>>> X, y = make_friedman1()
>>> clf = GradientBoostingRegressor(n_estimators=10).fit(X, y)
>>> fig, axs = plot_partial_dependence(clf, X, [0, (0, 1)]) #doctest: +SKIP
...
"""
import matplotlib.pyplot as plt
from matplotlib import transforms
from matplotlib.ticker import MaxNLocator
from matplotlib.ticker import ScalarFormatter
if not isinstance(gbrt, BaseGradientBoosting):
raise ValueError('gbrt has to be an instance of BaseGradientBoosting')
check_is_fitted(gbrt, 'estimators_')
# set label_idx for multi-class GBRT
if hasattr(gbrt, 'classes_') and np.size(gbrt.classes_) > 2:
if label is None:
raise ValueError('label is not given for multi-class PDP')
label_idx = np.searchsorted(gbrt.classes_, label)
if gbrt.classes_[label_idx] != label:
raise ValueError('label %s not in ``gbrt.classes_``' % str(label))
else:
# regression and binary classification
label_idx = 0
X = check_array(X, dtype=DTYPE, order='C')
if gbrt.n_features_ != X.shape[1]:
raise ValueError('X.shape[1] does not match gbrt.n_features_')
if line_kw is None:
line_kw = {'color': 'green'}
if contour_kw is None:
contour_kw = {}
# convert feature_names to list
if feature_names is None:
# if not feature_names use fx indices as name
feature_names = [str(i) for i in range(gbrt.n_features_)]
elif isinstance(feature_names, np.ndarray):
feature_names = feature_names.tolist()
def convert_feature(fx):
if isinstance(fx, str):
try:
fx = feature_names.index(fx)
except ValueError:
raise ValueError('Feature %s not in feature_names' % fx)
return fx
# convert features into a seq of int tuples
tmp_features = []
for fxs in features:
if isinstance(fxs, (numbers.Integral, str)):
fxs = (fxs, )
try:
fxs = np.array([convert_feature(fx) for fx in fxs], dtype=np.int32)
except TypeError:
raise ValueError('features must be either int, str, or tuple '
'of int/str')
if not (1 <= np.size(fxs) <= 2):
raise ValueError('target features must be either one or two')
tmp_features.append(fxs)
features = tmp_features
names = []
try:
for fxs in features:
l = []
# explicit loop so "i" is bound for exception below
for i in fxs:
l.append(feature_names[i])
names.append(l)
except IndexError:
raise ValueError('All entries of features must be less than '
'len(feature_names) = {0}, got {1}.'.format(
len(feature_names), i))
# compute PD functions
pd_result = Parallel(n_jobs=n_jobs, verbose=verbose)(delayed(
partial_dependence
)(gbrt, fxs, X=X, grid_resolution=grid_resolution, percentiles=percentiles)
for fxs in features)
# get global min and max values of PD grouped by plot type
pdp_lim = {}
for pdp, axes in pd_result:
min_pd, max_pd = pdp[label_idx].min(), pdp[label_idx].max()
n_fx = len(axes)
old_min_pd, old_max_pd = pdp_lim.get(n_fx, (min_pd, max_pd))
min_pd = min(min_pd, old_min_pd)
max_pd = max(max_pd, old_max_pd)
pdp_lim[n_fx] = (min_pd, max_pd)
# create contour levels for two-way plots
if 2 in pdp_lim:
Z_level = np.linspace(*pdp_lim[2], num=8)
if ax is None:
fig = plt.figure(**fig_kw)
else:
fig = ax.get_figure()
fig.clear()
n_cols = min(n_cols, len(features))
n_rows = int(np.ceil(len(features) / float(n_cols)))
axs = []
for i, fx, name, (pdp, axes) in zip(count(), features, names, pd_result):
ax = fig.add_subplot(n_rows, n_cols, i + 1)
if len(axes) == 1:
ax.plot(axes[0], pdp[label_idx].ravel(), **line_kw)
else:
# make contour plot
assert len(axes) == 2
XX, YY = np.meshgrid(axes[0], axes[1])
Z = pdp[label_idx].reshape(list(map(np.size, axes))).T
CS = ax.contour(XX,
YY,
Z,
levels=Z_level,
linewidths=0.5,
colors='k')
ax.contourf(XX,
YY,
Z,
levels=Z_level,
vmax=Z_level[-1],
vmin=Z_level[0],
alpha=0.75,
**contour_kw)
ax.clabel(CS, fmt='%2.2f', colors='k', fontsize=10, inline=True)
# plot data deciles + axes labels
deciles = mquantiles(X[:, fx[0]], prob=np.arange(0.1, 1.0, 0.1))
trans = transforms.blended_transform_factory(ax.transData,
ax.transAxes)
ylim = ax.get_ylim()
ax.vlines(deciles, [0], 0.05, transform=trans, color='k')
ax.set_xlabel(name[0])
ax.set_ylim(ylim)
# prevent x-axis ticks from overlapping
ax.xaxis.set_major_locator(MaxNLocator(nbins=6, prune='lower'))
tick_formatter = ScalarFormatter()
tick_formatter.set_powerlimits((-3, 4))
ax.xaxis.set_major_formatter(tick_formatter)
if len(axes) > 1:
# two-way PDP - y-axis deciles + labels
deciles = mquantiles(X[:, fx[1]], prob=np.arange(0.1, 1.0, 0.1))
trans = transforms.blended_transform_factory(
ax.transAxes, ax.transData)
xlim = ax.get_xlim()
ax.hlines(deciles, [0], 0.05, transform=trans, color='k')
ax.set_ylabel(name[1])
# hline erases xlim
ax.set_xlim(xlim)
else:
ax.set_ylabel('Partial dependence')
if len(axes) == 1:
ax.set_ylim(pdp_lim[1])
axs.append(ax)
fig.subplots_adjust(bottom=0.15,
top=0.7,
left=0.1,
right=0.95,
wspace=0.4,
hspace=0.3)
return fig, axs
def hist1d_multiset(labels=['30dor', 'pcc'],
lines=['12'],
val='mvir',
binnum=20,
binsize=0,
dolog=True,
lims=[],
types=[]):
# function will be able to run from any dataset's pyscript folder given that directory
# structure is identical between datasets (i.e. parallel directories)
# default types is all of them, can be specified to only plot a few
# loop below catches types not consistent with parameters
if len(types) == 0:
types = ['trunks', 'branches', 'leaves', 'clusters']
else:
for t in types:
if t not in ['trunks', 'branches', 'leaves', 'clusters']:
print(
'Type \'{}\' not recognized from default types (trunks, branches, leaves, clusters), exiting...'
.format(t))
return
else:
continue
# default output folder will be in parallel to running directory
if os.path.isdir('../multiprop') == 0:
os.mkdir('../multiprop')
# formatting parameters
params = {'text.usetex': False, 'mathtext.fontset': 'stixsans'}
plt.rcParams.update(params)
# dictionaries initialized for looping
pcats = {} # dictionary of data from respepctive physprop_add files
idcs = {
} # dictionary of indicies of data for different types in physprop_add
pltdatum = {} # dictionary of data to plot
# read in data
for lb in range(len(labels)):
for ln in range(len(lines)):
fname = '../../' + labels[lb] + '/props/' + labels[
lb] + '_' + lines[ln] + '_physprop_add.txt'
lname = labels[lb] + '_' + lines[ln]
if os.path.isfile(fname):
pcats[lname] = Table.read(fname, format='ascii.ecsv')
else:
pcats[lname] = Table.read(fname.replace('prop_add', 'prop'),
format='ascii.ecsv')
# idc indicies are in the order of types list
idc = [0, 0, 0, 0]
for i, typ in enumerate(types):
with open(fname.replace('physprop_add', typ), 'r') as f:
reader = csv.reader(f, delimiter=' ')
a = zip(*reader)
idc[i] = map(int, a[0])
idcs[lname] = idc
# data flattening
pltdata = []
for i in range(len(types)):
data = pcats[lname][val][idcs[lname][i]]
xdata = np.log10(data[data > 0])
pltdata.append(xdata)
pltdatum[lname] = pltdata
# begin limit calculation
# need to create list from all datasets that are being plotted
if len(lims) == 0:
limvals = []
for p in pltdatum:
#print(pltdatum[p])
lim_swp = [item for sublist in pltdatum[p] for item in sublist]
limvals.extend(lim_swp)
limmin = np.around(np.nanmin(limvals), 2)
limmax = np.around(np.nanmax(limvals), 2)
elif len(lims) == 1:
print('Only one limit ({}) specified, exiting...'.format(lims[0]))
return
else:
if len(lims) > 2:
print('Only first two limits will be used')
limmin = lims[0]
limmax = lims[1]
if binsize == 0:
limdif = limmax - limmin
optsize = np.around(limdif / binnum, 3)
# arbitrary choosing logic
if (optsize < .01):
binsize = .01
elif (.01 <= optsize < .025):
binsize = .02
elif (.025 <= optsize < .06):
binsize = .04
elif (.06 <= optsize < .09):
binsize = .08
elif (.09 <= optsize < .15):
binsize = .1
elif (.15 <= optsize < .25):
binsize = .2
elif (.25 <= optsize < .6):
binsize = .4
elif (.6 <= optsize < .9):
binsize = .8
elif (.9 <= optsize):
binsize = 1
# bin spacing
binlist = np.arange((limmin - 2 * binsize), (limmax + 2 * binsize),
binsize)
# plotting
fig, axes = plt.subplots()
for p in pltdatum:
temp_types = [p + ' ' + t for t in types]
axes.hist(pltdatum[p],
binlist,
normed=0,
log=dolog,
histtype='bar',
label=temp_types,
rwidth=.8)
axes.xaxis.set_minor_locator(FixedLocator(binlist[1::2] + binsize / 2))
axes.xaxis.set_major_locator(FixedLocator(binlist[::2] + binsize / 2))
axes.tick_params(labelsize=6)
axes.set_xlabel('log ' + val + ' [' +
str(pcats[labels[0] + '_' + lines[0]][val].unit) + ']')
axes.set_ylabel('Number of objects binned')
axes.set_yscale('log')
axes.yaxis.set_major_formatter(ScalarFormatter())
plt.legend(loc='best', fontsize='medium')
# automated looping for title, output name, output message
title = '{} for '.format(val)
for i in range(len(labels)):
for j in range(len(lines)):
title += '{}, '.format(labels[i] + '_' + lines[j])
title = title[:len(title) - 2]
plt.title(title)
#plt.show()
outname = '../multiprop/'
msg = 'Plot created successfully for {} '.format(val)
for i in range(len(labels)):
outname += '{}_'.format(labels[i])
msg += '{} '.format(labels[i])
for j in range(len(lines)):
outname += '{}CO_'.format(lines[j])
msg += '{}CO '.format(lines[j])
msg = msg[:len(msg) - 1]
outname += '{}.pdf'.format(val)
plt.savefig(outname, bbox_inches='tight')
plt.close()
print(msg)
return
df['beta'], 3.) * nanoToMili / htc2) * df['pionFF']
df['deltaCheck'] = 1. / (3. * df['S'] / np.pi / alf / alf / np.power(
df['beta'], 3.) * nanoToMili / htc2) * df['deltaPionFF']
print(df[['sqrtS', 'S', 'CS', 'check', 'deltaCheck']])
# df.to_csv(out_filename)
fig = plt.figure(figsize=(10, 7))
fig.canvas.manager.set_window_title('Figure name')
ax1 = plt.subplot(111)
ax1.set_title('CMD-2')
ax1.set_xlabel('$\\sqrt{s}$ [GeV]')
ax1.set_ylabel('$\\sigma$ [nb]')
ax1.errorbar(dataX, dataY, yerr=dataEY, marker='o', linestyle='', markersize=6)
# ax1.yaxis.set_major_formatter(FormatStrFormatter('%.1e'))
yfmt = ScalarFormatter(useOffset=False)
yfmt.set_powerlimits((-4, 4))
ax1.yaxis.set_major_formatter(yfmt)
ax1.yaxis.grid()
# fig = plt.figure(figsize=(10, 7))
# ax2 = plt.subplot(111)
# ax2.errorbar(dataX, df['FF'], yerr=df['deltaFF'], marker='o', linestyle='', markersize=6)
fig.tight_layout()
save_file = os.path.join(dev_name, 'plot_CMD-2_CS.png')
fig.savefig(save_file, dpi=150)
plt.show()
def plot_histograms(
path="/home/huziy/skynet3_rech1/hdf_store/quebec_0.1_crcm5-hcd-rl-intfl_spinup_ecoclimap.hdf"
):
fig = plt.figure()
assert isinstance(fig, Figure)
gs = gridspec.GridSpec(3, 3)
lons2d, lats2d, basemap = analysis.get_basemap_from_hdf(file_path=path)
# slope
ch_slope = analysis.get_array_from_file(path=path, var_name="slope")
ch_slope = maskoceans(lons2d, lats2d, ch_slope)
ch_slope = np.ma.masked_where(ch_slope.mask | (ch_slope < 0), ch_slope)
ax = fig.add_subplot(gs[0, 0])
assert isinstance(ax, Axes)
ch_slope_flat = ch_slope[~ch_slope.mask]
the_hist, positions = np.histogram(
ch_slope_flat, bins=25, range=[0, np.percentile(ch_slope_flat, 90)])
the_hist = the_hist.astype(float)
the_hist /= the_hist.sum()
barwidth = (positions[1] - positions[0]) * 0.9
ax.bar(positions[:-1], the_hist, color="0.75", linewidth=0, width=barwidth)
ax.set_title(r"$\alpha$")
ax.grid()
ax.xaxis.set_major_locator(MaxNLocator(nbins=3))
ax.yaxis.set_major_locator(MaxNLocator(nbins=5))
# drainage density
dd = analysis.get_array_from_file(path=path,
var_name="drainage_density_inv_meters")
dd *= 1000 # convert to km^-1
ax = fig.add_subplot(gs[0, 1])
assert isinstance(ax, Axes)
dd_flat = dd[~ch_slope.mask]
the_hist, positions = np.histogram(dd_flat,
bins=25,
range=[0, np.percentile(dd_flat, 90)])
the_hist = the_hist.astype(np.float)
the_hist /= the_hist.sum()
print(the_hist.max(), the_hist.min())
barwidth = (positions[1] - positions[0]) * 0.9
ax.bar(positions[:-1], the_hist, color="0.75", linewidth=0, width=barwidth)
ax.xaxis.set_major_locator(MaxNLocator(nbins=3))
ax.yaxis.set_major_locator(MaxNLocator(nbins=5))
ax.set_title(r"$DD {\rm \left( km^{-1} \right)}$")
ax.grid()
# vertical soil hydraulic conductivity
vshc = analysis.get_array_from_file(
path=path, var_name=infovar.HDF_VERT_SOIL_HYDR_COND_NAME)
if vshc is not None:
# get only on the first layer
vshc = vshc[0, :, :]
ax = fig.add_subplot(gs[1, 0])
assert isinstance(ax, Axes)
vshc_flat = vshc[~ch_slope.mask]
the_hist, positions = np.histogram(
vshc_flat, bins=25, range=[0, np.percentile(vshc_flat, 90)])
the_hist = the_hist.astype(np.float)
the_hist /= the_hist.sum()
print(the_hist.max(), the_hist.min())
barwidth = (positions[1] - positions[0]) * 0.9
ax.bar(positions[:-1],
the_hist,
color="0.75",
linewidth=0,
width=barwidth)
ax.xaxis.set_major_locator(MaxNLocator(nbins=3))
ax.yaxis.set_major_locator(MaxNLocator(nbins=5))
# set a scalar formatter
sfmt = ScalarFormatter(useMathText=True)
sfmt.set_powerlimits([-2, 2])
ax.xaxis.set_major_formatter(sfmt)
ax.set_title(r"$ K_{\rm V} {\rm (m/s)}$")
ax.grid()
# Kv * slope * DD
ax = fig.add_subplot(gs[1, 1])
assert isinstance(ax, Axes)
interflow_h = 0.2 # Soulis et al 2000
# 1e-3 is to convert drainage density to m^-1
the_prod = dd_flat * 1e-3 * vshc_flat * ch_slope_flat * 48 * interflow_h
print("product median: {0}".format(np.median(the_prod)))
print("product maximum: {0}".format(the_prod.max()))
print("product 90-quantile: {0}".format(np.percentile(the_prod, 90)))
the_hist, positions = np.histogram(
the_prod, bins=25, range=[0, np.percentile(the_prod, 90)])
the_hist = the_hist.astype(np.float)
the_hist /= the_hist.sum()
print(the_hist.max(), the_hist.min())
barwidth = (positions[1] - positions[0]) * 0.9
ax.bar(positions[:-1],
the_hist,
color="0.75",
linewidth=0,
width=barwidth)
ax.xaxis.set_major_locator(MaxNLocator(nbins=3))
ax.yaxis.set_major_locator(MaxNLocator(nbins=5))
# set a scalar formatter
sfmt = ScalarFormatter(useMathText=True)
sfmt.set_powerlimits([-2, 2])
ax.xaxis.set_major_formatter(sfmt)
ax.set_title(
r"$ \beta_{\rm max}\cdot K_{\rm v} \cdot \alpha \cdot DD \cdot H {\rm (m/s)}$ "
)
ax.grid()
# read flow directions
flow_directions = analysis.get_array_from_file(
path=path, var_name=infovar.HDF_FLOW_DIRECTIONS_NAME)
# read cell areas
# cell_areas = analysis.get_array_from_file(path=path, var_name=infovar.HDF_CELL_AREA_NAME)
cell_manager = CellManager(flow_directions)
acc_index = cell_manager.get_accumulation_index()
acc_index_flat = acc_index[acc_index > 1]
print(
"acc_index: min={0}; max={1}; median={2}; 90-quantile={3}".format(
acc_index_flat.min(), acc_index_flat.max(),
np.median(acc_index_flat), np.percentile(acc_index_flat, 90)))
# plot the range of the accumulation index
ax = fig.add_subplot(gs[0, 2])
assert isinstance(ax, Axes)
the_hist, positions = np.histogram(
acc_index_flat,
bins=25,
range=[0, np.percentile(acc_index_flat, 90)])
the_hist = the_hist.astype(np.float)
the_hist /= the_hist.sum()
print(the_hist.max(), the_hist.min())
barwidth = (positions[1] - positions[0]) * 0.9
ax.bar(positions[:-1],
the_hist,
color="0.75",
linewidth=0,
width=barwidth)
ax.xaxis.set_major_locator(MaxNLocator(nbins=3))
ax.yaxis.set_major_locator(MaxNLocator(nbins=5))
# set a scalar formatter
sfmt = ScalarFormatter(useMathText=True)
sfmt.set_powerlimits([-2, 2])
ax.xaxis.set_major_formatter(sfmt)
ax.set_title(r"Accum. index")
ax.grid()
# lake fraction
# sand
# clay
fig_path = os.path.join(images_folder, "static_fields_histograms.jpeg")
fig.tight_layout()
fig.savefig(fig_path, dpi=cpp.FIG_SAVE_DPI, bbox_inches="tight")
data[i] / pc.percent,
uncert[i] / pc.percent,
fmt='o',
alpha=0.7,
ms=ms,
mew=0.25,
color='b',
elinewidth=lw,
capthick=lw,
zorder=3,
label='Data')
ax1.tick_params(labelsize=fs - 1, direction='in', which='both')
if ax1.get_xlim()[1] > 3:
ax1.set_xscale('log')
plt.gca().xaxis.set_minor_formatter(NullFormatter())
ax1.get_xaxis().set_major_formatter(ScalarFormatter())
ax1.set_xticks(logxticks)
ax1.set_xlim(1.0, 5.5)
else:
ax1.set_xlim(1.0, 2.0)
ax1.text(0.997,
0.89,
names[i],
fontsize=fs - 1,
ha='right',
transform=ax1.transAxes)
if sticks[i] is not None:
ax1.yaxis.set_major_locator(MultipleLocator(sticks[i]))
plt.ylabel(r'$(R_{\rm p}/R_{\rm s})^2$ (%)', fontsize=fs)
# The posteriors:
axes = [
##>>>and plot on the screen and output figure file using matplotlib-python
import Tkinter as tk
from Tkinter import *
import matplotlib
matplotlib.use('Agg')
from matplotlib.ticker import MaxNLocator
from matplotlib import cm
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
from matplotlib.figure import Figure
from matplotlib.ticker import ScalarFormatter
yformatter = ScalarFormatter()
yformatter.set_powerlimits((-3, 3))
import matplotlib.pyplot as plt
import matplotlib as mpl
import matplotlib.ticker as ticker
from numpy import arange, sin, pi
import numpy as np
import h5py as h5
import math
font = {
'family': 'sans-serif',
'weight': 'bold',
FillContour1.set_norm(norm)
FillContour2.set_norm(norm)
FillContour3.set_norm(norm)
FillContour4.set_norm(norm)
FillContour5.set_norm(norm)
FillContour6.set_norm(norm)
#plt.suptitle("GridSpec")
make_ticklabels_invisible(plt.gcf())
ax3.locator_params(tight=True, nbins=4)
ax5.locator_params(tight=True, nbins=4)
ax6.locator_params(tight=True, nbins=4)
#myformatter = ScalarFormatter(useMathText=True)
myformatter = ScalarFormatter()
myformatter.set_powerlimits((-1,1))
ax3.xaxis.set_major_formatter(myformatter)
ax5.xaxis.set_major_formatter(myformatter)
ax6.yaxis.set_major_formatter(myformatter)
ax6.xaxis.set_major_formatter(myformatter)
cax = f.add_axes([0.2, 0.06, 0.6, 0.02])
f.colorbar(FillContour1, cax, orientation='horizontal')
plt.tight_layout()
plt.savefig('higuchi_proj.eps')
plt.savefig('higuchi_proj.pdf')
plt.show()
def GlobalSignature(self,
ax=None,
fig=1,
freq_ax=False,
time_ax=False,
z_ax=True,
mask=None,
scatter=False,
xaxis='nu',
ymin=None,
ymax=50,
zmax=None,
rotate_xticks=False,
rotate_yticks=False,
force_draw=False,
zlim=80,
temp_unit='mK',
yscale='linear',
take_abs=False,
**kwargs):
"""
Plot differential brightness temperature vs. redshift (nicely).
Parameters
----------
ax : matplotlib.axes.AxesSubplot instance
Axis on which to plot signal.
fig : int
Figure number.
freq_ax : bool
Add top axis denoting corresponding (observed) 21-cm frequency?
time_ax : bool
Add top axis denoting corresponding time since Big Bang?
z_ax : bool
Add top axis denoting corresponding redshift? Only applicable
if xaxis='nu' (see below).
scatter : bool
Plot signal as scatter-plot?
mask : int
If scatter==True, this defines the sampling "rate" of the data,
i.e., only every mask'th element is included in the plot.
xaxis : str
Determines whether x-axis is redshift or frequency.
Options: 'z' or 'nu'
Returns
-------
matplotlib.axes.AxesSubplot instance.
"""
if xaxis == 'nu' and freq_ax:
freq_ax = False
if xaxis == 'z' and z_ax:
z_ax = False
if ax is None:
gotax = False
fig = pl.figure(fig)
ax = fig.add_subplot(111)
else:
gotax = True
conv = 1.
if temp_unit.lower() in ['k', 'kelvin']:
conv = 1e-3
if mask is not None:
nu_plot, dTb_plot = \
self.history[xaxis][mask], self.history['dTb'][mask] * conv
else:
nu_plot, dTb_plot = \
self.history[xaxis], self.history['dTb'] * conv
if take_abs:
dTb_plot = np.abs(dTb_plot)
##
# Plot the stupid thing
##
if scatter is False:
ax.plot(nu_plot, dTb_plot, **kwargs)
else:
ax.scatter(self.history[xaxis][-1::-mask],
self.history['dTb'][-1::-mask] * conv, **kwargs)
if zmax is None:
zmax = self.pf["initial_redshift"]
zmin = self.pf["final_redshift"] if self.pf["final_redshift"] >= 10 \
else 5
# x-ticks
if xaxis == 'z' and hasattr(self, 'pf'):
xticks = list(np.arange(zmin, zmax, zmin))
xticks_minor = list(np.arange(zmin, zmax, 1))
else:
xticks = np.arange(0, 250, 50)
xticks_minor = np.arange(10, 200, 10)
# Some elements deemed objects when run through pipelines...
dTb = np.array(self.history['dTb'], dtype=float)
if ymin is None and yscale == 'linear':
ymin = max(min(min(dTb[np.isfinite(dTb)]), ax.get_ylim()[0]), -500)
# Set lower y-limit by increments of 50 mK
for val in [
-50, -100, -150, -200, -250, -300, -350, -400, -450, -500,
-550, -600
]:
if val <= ymin:
ymin = int(val)
break
if ymax is None:
ymax = max(max(dTb[np.isfinite(dTb)]), ax.get_ylim()[1])
if yscale == 'linear':
if (not gotax) or force_draw:
yticks = np.arange(int(ymin / 50) * 50, 100, 50) * conv
ax.set_yticks(yticks)
else:
# Minor y-ticks - 10 mK increments
yticks = np.linspace(ymin, 50,
int((50 - ymin) / 10. + 1)) * conv
yticks = list(yticks)
# Remove major ticks from minor tick list
if ymin >= -200:
for y in np.linspace(ymin, 50,
int((50 - ymin) / 50. + 1)) * conv:
if y in yticks:
yticks.remove(y)
ax.set_ylim(ymin * conv, ymax * conv)
ax.set_yticks(yticks, minor=True)
if xaxis == 'z' and hasattr(self, 'pf'):
ax.set_xlim(5, self.pf["initial_redshift"])
else:
ax.set_xlim(0, 210)
if (not gotax) or force_draw:
ax.set_xticks(xticks, minor=False)
ax.set_xticks(xticks_minor, minor=True)
xt = []
for x in ax.get_xticklabels():
xt.append(x.get_text())
ax.set_xticklabels(xt, rotation=45. if rotate_xticks else 0)
yt = []
for y in ax.get_yticklabels():
if not y.get_text().strip():
break
yt.append(y.get_text())
if yt == []:
yt = yticks
ax.set_yticklabels(yt, rotation=45. if rotate_yticks else 0)
if ax.get_xlabel() == '':
if xaxis == 'z':
ax.set_xlabel(labels['z'], fontsize='x-large')
else:
ax.set_xlabel(labels['nu'])
if ax.get_ylabel() == '':
if temp_unit.lower() == 'mk':
ax.set_ylabel(labels['dTb'], fontsize='x-large')
else:
ax.set_ylabel(r'$\delta T_b \ (\mathrm{K})$',
fontsize='x-large')
# Twin axes along the top
if freq_ax:
twinax = self.add_frequency_axis(ax)
elif time_ax:
twinax = add_time_axis(ax, self.cosm)
elif z_ax:
twinax = add_redshift_axis(ax, zlim=zmax)
else:
twinax = None
self.twinax = twinax
if gotax and (ax.get_xlabel().strip()) and (not force_draw):
pl.draw()
return ax, twinax
try:
ax.ticklabel_format(style='plain', axis='both')
except AttributeError:
ax.xaxis.set_major_formatter(ScalarFormatter())
ax.yaxis.set_major_formatter(ScalarFormatter())
#twinax.xaxis.set_major_formatter(ScalarFormatter())
ax.ticklabel_format(style='plain', axis='both')
pl.draw()
return ax, twinax
def __call__(self, x, pos):
if pos==0: return ''
else: return ScalarFormatter.__call__(self, x, pos)
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
import numpy as np
import os
from pylab import *
from matplotlib import ticker
from matplotlib.ticker import ScalarFormatter
sformatter = ScalarFormatter(useOffset=True, useMathText=True)
sformatter.set_scientific(True)
sformatter.set_powerlimits((-2, 3))
#plt.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
font = {'family': 'serif', 'weight': 'normal', 'size': 14}
plt.rc('font', **font)
plt.rc('text', usetex=False)
plt.figure(figsize=(6, 5))
fig = plt.figure(1)
ax = fig.add_axes([0.14, 0.125, 0.82, 0.85])
mydata = np.loadtxt('moments_bw_Omega50.dat', skiprows=1, unpack=True)
Omega = mydata[0]
rhoB = mydata[3]
Pbar = mydata[5]
sigma2P = mydata[6]
SsigmaP = mydata[7]
Ksigma2P = mydata[8]
Qbar = mydata[9]
sigma2Q = mydata[10]
SsigmaQ = mydata[11]
Ksigma2Q = mydata[10]
def __decorate_axis(axis, ax_type):
'''Configure axis tickers, locators, and labels'''
if ax_type == 'tonnetz':
axis.set_major_formatter(TonnetzFormatter())
axis.set_major_locator(FixedLocator(0.5 + np.arange(6)))
axis.set_label_text('Tonnetz')
elif ax_type == 'chroma':
axis.set_major_formatter(ChromaFormatter())
axis.set_major_locator(FixedLocator(0.5 +
np.add.outer(12 * np.arange(10),
[0, 2, 4, 5, 7, 9, 11]).ravel()))
axis.set_label_text('Pitch class')
elif ax_type in ['tempo', 'fourier_tempo']:
axis.set_major_formatter(ScalarFormatter())
axis.set_major_locator(LogLocator(base=2.0))
axis.set_label_text('BPM')
elif ax_type == 'time':
axis.set_major_formatter(TimeFormatter(unit=None, lag=False))
axis.set_major_locator(MaxNLocator(prune=None,
steps=[1, 1.5, 5, 6, 10]))
axis.set_label_text('Time')
elif ax_type == 's':
axis.set_major_formatter(TimeFormatter(unit='s', lag=False))
axis.set_major_locator(MaxNLocator(prune=None,
steps=[1, 1.5, 5, 6, 10]))
axis.set_label_text('Time (s)')
elif ax_type == 'ms':
axis.set_major_formatter(TimeFormatter(unit='ms', lag=False))
axis.set_major_locator(MaxNLocator(prune=None,
steps=[1, 1.5, 5, 6, 10]))
axis.set_label_text('Time (ms)')
elif ax_type == 'lag':
axis.set_major_formatter(TimeFormatter(unit=None, lag=True))
axis.set_major_locator(MaxNLocator(prune=None,
steps=[1, 1.5, 5, 6, 10]))
axis.set_label_text('Lag')
elif ax_type == 'lag_s':
axis.set_major_formatter(TimeFormatter(unit='s', lag=True))
axis.set_major_locator(MaxNLocator(prune=None,
steps=[1, 1.5, 5, 6, 10]))
axis.set_label_text('Lag (s)')
elif ax_type == 'lag_ms':
axis.set_major_formatter(TimeFormatter(unit='ms', lag=True))
axis.set_major_locator(MaxNLocator(prune=None,
steps=[1, 1.5, 5, 6, 10]))
axis.set_label_text('Lag (ms)')
elif ax_type == 'cqt_note':
axis.set_major_formatter(NoteFormatter())
axis.set_major_locator(LogLocator(base=2.0))
axis.set_minor_formatter(NoteFormatter(major=False))
axis.set_minor_locator(LogLocator(base=2.0,
subs=2.0**(np.arange(1, 12)/12.0)))
axis.set_label_text('Note')
elif ax_type in ['cqt_hz']:
axis.set_major_formatter(LogHzFormatter())
axis.set_major_locator(LogLocator(base=2.0))
axis.set_minor_formatter(LogHzFormatter(major=False))
axis.set_minor_locator(LogLocator(base=2.0,
subs=2.0**(np.arange(1, 12)/12.0)))
axis.set_label_text('Hz')
elif ax_type in ['mel', 'log']:
axis.set_major_formatter(ScalarFormatter())
axis.set_major_locator(SymmetricalLogLocator(axis.get_transform()))
axis.set_label_text('Hz')
elif ax_type in ['linear', 'hz']:
axis.set_major_formatter(ScalarFormatter())
axis.set_label_text('Hz')
elif ax_type in ['frames']:
axis.set_label_text('Frames')
elif ax_type in ['off', 'none', None]:
axis.set_label_text('')
axis.set_ticks([])
def render_GET(self, request):
q = urlparse.urlparse(request.uri)
args = urlparse.parse_qs(q.query)
if q.path == self.base + '/status':
return serve_json(request,
fast_connected=self.fast.factory.isConnected(),
fast=self.fast.fast_status)
elif q.path == self.base + '/command':
self.fast.factory.message(args['string'][0])
return serve_json(request)
elif q.path == self.base + '/image.jpg':
if self.fast.image:
request.responseHeaders.setRawHeaders("Content-Type",
['image/jpeg'])
request.responseHeaders.setRawHeaders(
"Content-Length", [str(len(self.fast.image))])
return self.fast.image
else:
request.setResponseCode(400)
return "No images"
elif q.path == self.base + '/total_image.jpg':
if self.fast.total_image:
request.responseHeaders.setRawHeaders("Content-Type",
['image/jpeg'])
request.responseHeaders.setRawHeaders(
"Content-Length", [str(len(self.fast.total_image))])
return self.fast.total_image
else:
request.setResponseCode(400)
return "No images"
elif q.path == self.base + '/total_flux.jpg':
width = 800
fig = Figure(facecolor='white',
figsize=(width / 72, width * 0.5 / 72),
tight_layout=True)
ax = fig.add_subplot(111)
ax.yaxis.set_major_formatter(ScalarFormatter(useOffset=False))
x = np.array(self.fast.time)
x = x - x[0]
ax.plot(x, self.fast.mean, '-')
ax.set_xlabel('Time, seconds')
ax.set_ylabel('Flux, counts')
canvas = FigureCanvas(fig)
s = StringIO()
canvas.print_jpeg(s, bbox_inches='tight')
request.responseHeaders.setRawHeaders("Content-Type",
['image/jpeg'])
request.responseHeaders.setRawHeaders("Content-Length",
[str(s.len)])
request.responseHeaders.setRawHeaders(
"Cache-Control",
['no-store, no-cache, must-revalidate, max-age=0'])
return s.getvalue()
elif q.path == self.base + '/current_flux.jpg':
width = 800
fig = Figure(facecolor='white',
figsize=(width / 72, width * 0.5 / 72),
tight_layout=True)
ax = fig.add_subplot(111)
ax.yaxis.set_major_formatter(ScalarFormatter(useOffset=False))
x = np.array(self.fast.time)
if len(x):
x = x - x[0]
y = np.array(self.fast.mean)
ax.plot(x[-1000:], y[-1000:], '-')
ax.set_xlabel('Time, seconds')
ax.set_ylabel('Flux, counts')
canvas = FigureCanvas(fig)
s = StringIO()
canvas.print_jpeg(s, bbox_inches='tight')
request.responseHeaders.setRawHeaders("Content-Type",
['image/jpeg'])
request.responseHeaders.setRawHeaders("Content-Length",
[str(s.len)])
request.responseHeaders.setRawHeaders(
"Cache-Control",
['no-store, no-cache, must-revalidate, max-age=0'])
return s.getvalue()
else:
return q.path
def __init__(self,
artists,
tolerance=5,
formatter=None,
point_labels=None,
display='one-per-axes',
draggable=False,
hover=False,
props_override=None,
keybindings=True,
date_format='%x %X',
display_button=1,
hide_button=3,
keep_inside=True,
magnetic=False,
**kwargs):
"""Create the data cursor and connect it to the relevant figure.
Parameters
-----------
artists : a matplotlib artist or sequence of artists.
The artists to make selectable and display information for.
tolerance : number, optional
The radius (in points) that the mouse click must be within to
select the artist.
formatter : function, optional
A function that accepts arbitrary kwargs and returns a string that
will be displayed with annotate. The `x`, `y`, `event`, `ind`, and
`label` kwargs will always be present. See the
``mpldatacursor.datacursor`` function docstring for more
information.
point_labels : sequence or dict, optional
Labels for "subitems" of an artist, passed to the formatter
function as the `point_label` kwarg. May be either a single
sequence (used for all artists) or a dict of artist:sequence pairs.
display : {'one-per-axes', 'single', 'multiple'}, optional
Controls whether more than one annotation box will be shown.
draggable : boolean, optional
Controls whether or not the annotation box will be interactively
draggable to a new location after being displayed. Default: False.
hover : boolean, optional
If True, the datacursor will "pop up" when the mouse hovers over an
artist. Defaults to False. Enabling hover also sets
`display="single"` and `draggable=False`.
props_override : function, optional
If specified, this function customizes the parameters passed into
the formatter function and the x, y location that the datacursor
"pop up" "points" to. This is often useful to make the annotation
"point" to a specific side or corner of an artist, regardless of
the position clicked. The function is passed the same kwargs as the
`formatter` function and is expected to return a dict with at least
the keys "x" and "y" (and probably several others).
Expected call signature: `props_dict = props_override(**kwargs)`
keybindings : boolean or dict, optional
By default, the keys "d" and "t" will be bound to hiding/showing
all annotation boxes and toggling interactivity for datacursors,
respectively. "<shift> + <right>" and "<shift> + <left>" will be
bound to moving the datacursor to the next and previous item in the
sequence for artists that support it. If keybindings is False, the
ability to hide/toggle datacursors interactively will be disabled.
Alternatively, a dict mapping "hide", "toggle", "next", and
"previous" to matplotlib key specifications may specified to
customize the keyboard shortcuts. Note that hitting the "hide" key
once will hide datacursors, and hitting it again will show all of
the hidden datacursors.
date_format : string, optional
The strftime-style formatting string for dates. Used only if the x
or y axes have been set to display dates. Defaults to "%x %X".
display_button: int, optional
The mouse button that will triggers displaying an annotation box.
Defaults to 1, for left-clicking. (Common options are
1:left-click, 2:middle-click, 3:right-click)
hide_button: int or None, optional
The mouse button that triggers hiding the selected annotation box.
Defaults to 3, for right-clicking. (Common options are
1:left-click, 2:middle-click, 3:right-click, None:hiding disabled)
keep_inside : boolean, optional
Whether or not to adjust the x,y offset to keep the text box inside
the figure. This option has no effect on draggable datacursors.
Defaults to True. Note: Currently disabled on OSX and
NbAgg/notebook backends.
magnetic: boolean, optional
Magnetic will attach the cursor only to the data points.
Default is cursor can be added to interpolated lines.
If exact data point is not clicked, nearby data point will be selected.
Works with artists that have x, y attributes. Other plots will ignore Magnetic.
**kwargs : additional keyword arguments, optional
Additional keyword arguments are passed on to annotate.
"""
def filter_artists(artists):
"""Replace ContourSets, etc with their constituent artists."""
output = []
for item in artists:
if isinstance(item, ContourSet):
output += item.collections
elif isinstance(item, Container):
children = item.get_children()
for child in children:
child._mpldatacursor_label = item.get_label()
child._mpldatacursor_parent = item
output += children
else:
output.append(item)
return output
if not np.iterable(artists):
artists = [artists]
#-- Deal with contour sets... -------------------------------------
# These are particularly difficult, as the original z-value array
# is never associated with the ContourSet, and they're not "normal"
# artists (they're not actually added to the axes). Not only that, but
# the PatchCollections created by filled contours don't even fire a
# pick event for points inside them, only on their edges. At any rate,
# this is a somewhat hackish way of handling contours, but it works.
self.artists = filter_artists(artists)
self.contour_levels = {}
for cs in [x for x in artists if isinstance(x, ContourSet)]:
for z, artist in zip(cs.levels, cs.collections):
self.contour_levels[artist] = z
valid_display_options = ['single', 'one-per-axes', 'multiple']
if display in valid_display_options:
self.display = display
else:
raise ValueError('"display" must be one of the following: '\
', '.join(valid_display_options))
self.hover = hover
if self.hover:
self.display = 'single'
self.draggable = False
self.magnetic = magnetic
self.keep_inside = keep_inside
self.tolerance = tolerance
self.point_labels = point_labels
self.draggable = draggable
self.date_format = date_format
self.props_override = props_override
self.display_button = display_button
self.hide_button = hide_button
self.axes = tuple(set(art.axes for art in self.artists))
self.figures = tuple(set(ax.figure for ax in self.axes))
self._mplformatter = ScalarFormatter(useOffset=False, useMathText=True)
self._hidden = False
self._last_event = None
self._last_annotation = None
if self.draggable:
# If we're dealing with draggable cursors, don't try to override
# the x,y position. Otherwise, dragging the cursor outside the
# figure will have unexpected consequences.
self.keep_inside = False
if formatter is None:
self.formatter = self._formatter
else:
self.formatter = formatter
self._annotation_kwargs = kwargs
self.annotations = {}
if self.display is not 'multiple':
for ax in self.axes:
self.annotations[ax] = self.annotate(ax, **kwargs)
# Hide the annotation box until clicked...
self.annotations[ax].set_visible(False)
if keybindings:
if keybindings is True:
self.keybindings = self.default_keybindings
else:
self.keybindings = self.default_keybindings.copy()
self.keybindings.update(keybindings)
for fig in self.figures:
fig.canvas.mpl_connect('key_press_event', self._on_keypress)
self.enable()
# We need to make sure the DataCursor isn't garbage collected until the
# figure is. Matplotlib's weak references won't keep this DataCursor
# instance alive in all cases.
for fig in self.figures:
try:
fig._mpldatacursors.append(self)
except AttributeError:
fig._mpldatacursors = [self]
def __init__(self, format='%.0f', division=1e0):
ScalarFormatter.__init__(self, useOffset=None, useMathText=None)
self.format = format
self.division = division
def xnor_plot_error(mean_error):
"""Plot Generalization Errors"""
algorithms = [
"Hoeffding Tree ",
"Mondrian Forest",
"Stream Decision Tree",
"Stream Decision Forest",
"Synergistic Forest",
]
fontsize = 30
labelsize = 28
ls = ["-", "--"]
colors = sns.color_palette("bright")
fig = plt.figure(figsize=(21, 14))
gs = fig.add_gridspec(14, 21)
ax1 = fig.add_subplot(gs[7:, :6])
# Hoeffding Tree XOR
ax1.plot(
(100 * np.arange(0.25, 22.75, step=0.25)).astype(int),
mean_error[0],
label=algorithms[0],
c=colors[4],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
# Mondrian Forest XOR
ax1.plot(
(100 * np.arange(0.25, 22.75, step=0.25)).astype(int),
mean_error[2],
label=algorithms[1],
c=colors[5],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
# Stream Decision Tree XOR
ax1.plot(
(100 * np.arange(0.25, 22.75, step=0.25)).astype(int),
mean_error[4],
label=algorithms[2],
c=colors[2],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
# Stream Decision Forest XOR
ax1.plot(
(100 * np.arange(0.25, 22.75, step=0.25)).astype(int),
mean_error[6],
label=algorithms[3],
c=colors[3],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
# Synergistic Forest XOR
ax1.plot(
(100 * np.arange(0.25, 22.75, step=0.25)).astype(int),
mean_error[8],
label=algorithms[4],
c=colors[9],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
ax1.set_ylabel("Generalization Error (XOR)", fontsize=fontsize)
ax1.set_xlabel("Total Sample Size", fontsize=fontsize)
ax1.tick_params(labelsize=labelsize)
ax1.set_yscale("log")
ax1.yaxis.set_major_formatter(ScalarFormatter())
ax1.set_yticks([0.1, 0.3, 0.5, 0.9])
ax1.set_xticks([0, 750, 1500, 2250])
ax1.axvline(x=750, c="gray", linewidth=1.5, linestyle="dashed")
ax1.axvline(x=1500, c="gray", linewidth=1.5, linestyle="dashed")
right_side = ax1.spines["right"]
right_side.set_visible(False)
top_side = ax1.spines["top"]
top_side.set_visible(False)
ax1.text(200, np.mean(ax1.get_ylim()) + 0.5, "XOR", fontsize=26)
ax1.text(850, np.mean(ax1.get_ylim()) + 0.5, "XNOR", fontsize=26)
ax1.text(1700, np.mean(ax1.get_ylim()) + 0.5, "XOR", fontsize=26)
######## XNOR
ax1 = fig.add_subplot(gs[7:, 8:14])
xnor_range = (100 * np.arange(0.25, 22.75, step=0.25)).astype(int)[30:]
# Hoeffding Tree XNOR
ax1.plot(
xnor_range,
mean_error[1, 30:],
label=algorithms[0],
c=colors[4],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
# Mondrian Forest XNOR
ax1.plot(
xnor_range,
mean_error[3, 30:],
label=algorithms[1],
c=colors[5],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
# Stream Decision Tree XNOR
ax1.plot(
xnor_range,
mean_error[5, 30:],
label=algorithms[2],
c=colors[2],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
# Stream Decision Forest XNOR
ax1.plot(
xnor_range,
mean_error[7, 30:],
label=algorithms[3],
c=colors[3],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
# Synergistic Forest XNOR
ax1.plot(
xnor_range,
mean_error[9, 30:],
label=algorithms[4],
c=colors[9],
ls=ls[np.sum(1 > 1).astype(int)],
lw=3,
)
ax1.set_ylabel("Generalization Error (%s)" % "XNOR", fontsize=fontsize)
ax1.legend(bbox_to_anchor=(1.05, 1.0),
loc="upper left",
fontsize=20,
frameon=False)
ax1.set_xlabel("Total Sample Size", fontsize=fontsize)
ax1.tick_params(labelsize=labelsize)
ax1.set_yscale("log")
ax1.yaxis.set_major_formatter(ScalarFormatter())
ax1.set_yticks([0.1, 0.3, 0.5, 0.9])
ax1.set_xticks([0, 750, 1500, 2250])
ax1.axvline(x=750, c="gray", linewidth=1.5, linestyle="dashed")
ax1.axvline(x=1500, c="gray", linewidth=1.5, linestyle="dashed")
right_side = ax1.spines["right"]
right_side.set_visible(False)
top_side = ax1.spines["top"]
top_side.set_visible(False)
ax1.text(200, np.mean(ax1.get_ylim()) + 0.5, "XOR", fontsize=26)
ax1.text(850, np.mean(ax1.get_ylim()) + 0.5, "XNOR", fontsize=26)
ax1.text(1700, np.mean(ax1.get_ylim()) + 0.5, "XOR", fontsize=26)
def main():
start_year = 1980
end_year = 2010
start_date = datetime(start_year, 1, 1)
end_date = datetime(end_year, 12, 31)
ids_with_lakes_upstream = [
"104001", "093806", "093801", "081002", "081007", "080718"
]
selected_station_ids = ["092715", "074903", "080104", "081007", "061905",
"093806", "090613", "081002", "093801", "080718", "104001"]
selected_station_ids = ids_with_lakes_upstream
# Get the list of stations to do the comparison with
stations = cehq_station.read_station_data(
start_date=start_date,
end_date=end_date,
selected_ids=selected_station_ids
)
# add hydat stations
# province = "QC"
# min_drainage_area_km2 = 10000.0
# stations_hd = cehq_station.load_from_hydat_db(start_date=start_date, end_date=end_date,
# province=province, min_drainage_area_km2=min_drainage_area_km2)
# if not len(stations_hd):
# print "No hydat stations satisying the conditions: period {0}-{1}, province {2}".format(
# str(start_date), str(end_date), province
# )
# stations.extend(stations_hd)
# brewer2mpl.get_map args: set name set type number of colors
bmap = brewer2mpl.get_map("Set1", "qualitative", 9)
path1 = "/skynet3_rech1/huziy/hdf_store/quebec_0.1_crcm5-hcd-r.hdf5"
label1 = "CRCM5-L1"
path2 = "/skynet3_rech1/huziy/hdf_store/quebec_0.1_crcm5-hcd-rl.hdf5"
label2 = "CRCM5-L2"
color2, color1 = bmap.mpl_colors[:2]
fldirs = analysis.get_array_from_file(path=path1, var_name=infovar.HDF_FLOW_DIRECTIONS_NAME)
lons2d, lats2d, basemap = analysis.get_basemap_from_hdf(path1)
lake_fractions = analysis.get_array_from_file(path=path1, var_name=infovar.HDF_LAKE_FRACTION_NAME)
# cell_areas = analysis.get_array_from_file(path=path1, var_name=infovar.HDF_CELL_AREA_NAME)
acc_area = analysis.get_array_from_file(path=path1, var_name=infovar.HDF_ACCUMULATION_AREA_NAME)
cell_manager = CellManager(fldirs, lons2d=lons2d, lats2d=lats2d, accumulation_area_km2=acc_area)
station_to_mp = cell_manager.get_model_points_for_stations(station_list=stations,
lake_fraction=lake_fractions,
drainaige_area_reldiff_limit=0.3)
fig, axes = plt.subplots(1, 2, gridspec_kw=dict(top=0.80, wspace=0.4))
q90_obs_list = []
q90_mod1_list = []
q90_mod2_list = []
q10_obs_list = []
q10_mod1_list = []
q10_mod2_list = []
for the_station, the_mp in station_to_mp.items():
assert isinstance(the_station, Station)
compl_years = the_station.get_list_of_complete_years()
if len(compl_years) < 3:
continue
t, stfl1 = analysis.get_daily_climatology_for_a_point(path=path1, years_of_interest=compl_years,
i_index=the_mp.ix, j_index=the_mp.jy, var_name="STFA")
_, stfl2 = analysis.get_daily_climatology_for_a_point(path=path2, years_of_interest=compl_years,
i_index=the_mp.ix, j_index=the_mp.jy, var_name="STFA")
_, stfl_obs = the_station.get_daily_climatology_for_complete_years(stamp_dates=t, years=compl_years)
# Q90
q90_obs = np.percentile(stfl_obs, 90)
q90_mod1 = np.percentile(stfl1, 90)
q90_mod2 = np.percentile(stfl2, 90)
# Q10
q10_obs = np.percentile(stfl_obs, 10)
q10_mod1 = np.percentile(stfl1, 10)
q10_mod2 = np.percentile(stfl2, 10)
# save quantiles to lists for correlation calculation
q90_obs_list.append(q90_obs)
q90_mod1_list.append(q90_mod1)
q90_mod2_list.append(q90_mod2)
q10_mod1_list.append(q10_mod1)
q10_mod2_list.append(q10_mod2)
q10_obs_list.append(q10_obs)
# axes[0].annotate(the_station.id, (q90_obs, np.percentile(stfl1, 90)))
# axes[1].annotate(the_station.id, (q10_obs, np.percentile(stfl1, 10)))
# Plot scatter plot of Q90
the_ax = axes[0]
# the_ax.annotate(the_station.id, (q90_obs, np.percentile(stfl1, 90)))
the_ax.scatter(q90_obs_list, q90_mod1_list, label=label1, c=color1)
the_ax.scatter(q90_obs_list, q90_mod2_list, label=label2, c=color2)
# plot scatter plot of Q10
the_ax = axes[1]
# the_ax.annotate(the_station.id, (q10_obs, np.percentile(stfl1, 10)))
h1 = the_ax.scatter(q10_obs_list, q10_mod1_list, label=label1, c=color1)
h2 = the_ax.scatter(q10_obs_list, q10_mod2_list, label=label2, c=color2)
# Add correlation coefficients to the axes
fp = FontProperties(size=14, weight="bold")
axes[0].annotate(r"$R^2 = {0:.2f}$".format(np.corrcoef(q90_mod1_list, q90_obs_list)[0, 1] ** 2),
(0.1, 0.85), color=color1, xycoords="axes fraction", font_properties=fp)
axes[0].annotate(r"$R^2 = {0:.2f}$".format(np.corrcoef(q90_mod2_list, q90_obs_list)[0, 1] ** 2),
(0.1, 0.70), color=color2, xycoords="axes fraction", font_properties=fp)
axes[1].annotate(r"$R^2 = {0:.2f}$".format(np.corrcoef(q10_mod1_list, q10_obs_list)[0, 1] ** 2),
(0.1, 0.85), color=color1, xycoords="axes fraction", font_properties=fp)
axes[1].annotate(r"$R^2 = {0:.2f}$".format(np.corrcoef(q10_mod2_list, q10_obs_list)[0, 1] ** 2),
(0.1, 0.70), color=color2, xycoords="axes fraction", font_properties=fp)
sf = ScalarFormatter(useMathText=True)
sf.set_powerlimits((-2, 3))
for ind, the_ax in enumerate(axes):
plot_one_to_one_line(the_ax)
if ind == 0:
the_ax.set_xlabel(r"Observed $\left({\rm m^3/s} \right)$")
the_ax.set_ylabel(r"Modelled $\left({\rm m^3/s} \right)$")
the_ax.annotate(r"$Q_{90}$" if ind == 0 else r"$Q_{10}$",
(0.95, 0.95), xycoords="axes fraction",
bbox=dict(facecolor="white"),
va="top", ha="right")
the_ax.xaxis.set_major_formatter(sf)
the_ax.yaxis.set_major_formatter(sf)
locator = MaxNLocator(nbins=5)
the_ax.xaxis.set_major_locator(locator)
the_ax.yaxis.set_major_locator(locator)
x1, x2 = the_ax.get_xlim()
# Since streamflow percentiles can only be positive
the_ax.set_xlim(0, x2)
the_ax.set_ylim(0, x2)
fig.legend([h1, h2], [label1, label2], loc="upper center", ncol=2)
figpath = os.path.join(images_folder, "percentiles_comparison.png")
# plt.tight_layout()
fig.savefig(figpath, dpi=cpp.FIG_SAVE_DPI, bbox_inches="tight")
def plot_partial_dependence(gbrt, X, features, feature_names=None,
label=None, n_cols=3, grid_resolution=100,
percentiles=(0.05, 0.95), n_jobs=None,
verbose=0, ax=None, line_kw=None,
contour_kw=None, **fig_kw):
"""Partial dependence plots for ``features``.
The ``len(features)`` plots are arranged in a grid with ``n_cols``
columns. Two-way partial dependence plots are plotted as contour
plots.
Read more in the :ref:`User Guide <partial_dependence>`.
Parameters
----------
gbrt : BaseGradientBoosting
A fitted gradient boosting model.
X : array-like, shape=(n_samples, n_features)
The data on which ``gbrt`` was trained.
features : seq of ints, strings, or tuples of ints or strings
If seq[i] is an int or a tuple with one int value, a one-way
PDP is created; if seq[i] is a tuple of two ints, a two-way
PDP is created.
If feature_names is specified and seq[i] is an int, seq[i]
must be < len(feature_names).
If seq[i] is a string, feature_names must be specified, and
seq[i] must be in feature_names.
feature_names : seq of str
Name of each feature; feature_names[i] holds
the name of the feature with index i.
label : object
The class label for which the PDPs should be computed.
Only if gbrt is a multi-class model. Must be in ``gbrt.classes_``.
n_cols : int
The number of columns in the grid plot (default: 3).
grid_resolution : int, default=100
The number of equally spaced points on the axes.
percentiles : (low, high), default=(0.05, 0.95)
The lower and upper percentile used to create the extreme values
for the PDP axes.
n_jobs : int or None, optional (default=None)
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
for more details.
verbose : int
Verbose output during PD computations. Defaults to 0.
ax : Matplotlib axis object, default None
An axis object onto which the plots will be drawn.
line_kw : dict
Dict with keywords passed to the ``matplotlib.pyplot.plot`` call.
For one-way partial dependence plots.
contour_kw : dict
Dict with keywords passed to the ``matplotlib.pyplot.plot`` call.
For two-way partial dependence plots.
**fig_kw : dict
Dict with keywords passed to the figure() call.
Note that all keywords not recognized above will be automatically
included here.
Returns
-------
fig : figure
The Matplotlib Figure object.
axs : seq of Axis objects
A seq of Axis objects, one for each subplot.
Examples
--------
>>> from sklearn.datasets import make_friedman1
>>> from sklearn.ensemble import GradientBoostingRegressor
>>> X, y = make_friedman1()
>>> clf = GradientBoostingRegressor(n_estimators=10).fit(X, y)
>>> fig, axs = plot_partial_dependence(clf, X, [0, (0, 1)]) #doctest: +SKIP
...
"""
import matplotlib.pyplot as plt
from matplotlib import transforms
from matplotlib.ticker import MaxNLocator
from matplotlib.ticker import ScalarFormatter
if not isinstance(gbrt, BaseGradientBoosting):
raise ValueError('gbrt has to be an instance of BaseGradientBoosting')
check_is_fitted(gbrt, 'estimators_')
# set label_idx for multi-class GBRT
if hasattr(gbrt, 'classes_') and np.size(gbrt.classes_) > 2:
if label is None:
raise ValueError('label is not given for multi-class PDP')
label_idx = np.searchsorted(gbrt.classes_, label)
if gbrt.classes_[label_idx] != label:
raise ValueError('label %s not in ``gbrt.classes_``' % str(label))
else:
# regression and binary classification
label_idx = 0
X = check_array(X, dtype=DTYPE, order='C')
if gbrt.n_features_ != X.shape[1]:
raise ValueError('X.shape[1] does not match gbrt.n_features_')
if line_kw is None:
line_kw = {'color': 'green'}
if contour_kw is None:
contour_kw = {}
# convert feature_names to list
if feature_names is None:
# if not feature_names use fx indices as name
feature_names = [str(i) for i in range(gbrt.n_features_)]
elif isinstance(feature_names, np.ndarray):
feature_names = feature_names.tolist()
def convert_feature(fx):
if isinstance(fx, str):
try:
fx = feature_names.index(fx)
except ValueError:
raise ValueError('Feature %s not in feature_names' % fx)
return fx
# convert features into a seq of int tuples
tmp_features = []
for fxs in features:
if isinstance(fxs, (numbers.Integral, str)):
fxs = (fxs,)
try:
fxs = np.array([convert_feature(fx) for fx in fxs], dtype=np.int32)
except TypeError:
raise ValueError('features must be either int, str, or tuple '
'of int/str')
if not (1 <= np.size(fxs) <= 2):
raise ValueError('target features must be either one or two')
tmp_features.append(fxs)
features = tmp_features
names = []
try:
for fxs in features:
l = []
# explicit loop so "i" is bound for exception below
for i in fxs:
l.append(feature_names[i])
names.append(l)
except IndexError:
raise ValueError('All entries of features must be less than '
'len(feature_names) = {0}, got {1}.'
.format(len(feature_names), i))
# compute PD functions
pd_result = Parallel(n_jobs=n_jobs, verbose=verbose)(
delayed(partial_dependence)(gbrt, fxs, X=X,
grid_resolution=grid_resolution,
percentiles=percentiles)
for fxs in features)
# get global min and max values of PD grouped by plot type
pdp_lim = {}
for pdp, axes in pd_result:
min_pd, max_pd = pdp[label_idx].min(), pdp[label_idx].max()
n_fx = len(axes)
old_min_pd, old_max_pd = pdp_lim.get(n_fx, (min_pd, max_pd))
min_pd = min(min_pd, old_min_pd)
max_pd = max(max_pd, old_max_pd)
pdp_lim[n_fx] = (min_pd, max_pd)
# create contour levels for two-way plots
if 2 in pdp_lim:
Z_level = np.linspace(*pdp_lim[2], num=8)
if ax is None:
fig = plt.figure(**fig_kw)
else:
fig = ax.get_figure()
fig.clear()
n_cols = min(n_cols, len(features))
n_rows = int(np.ceil(len(features) / float(n_cols)))
axs = []
for i, fx, name, (pdp, axes) in zip(count(), features, names,
pd_result):
ax = fig.add_subplot(n_rows, n_cols, i + 1)
if len(axes) == 1:
ax.plot(axes[0], pdp[label_idx].ravel(), **line_kw)
else:
# make contour plot
assert len(axes) == 2
XX, YY = np.meshgrid(axes[0], axes[1])
Z = pdp[label_idx].reshape(list(map(np.size, axes))).T
CS = ax.contour(XX, YY, Z, levels=Z_level, linewidths=0.5,
colors='k')
ax.contourf(XX, YY, Z, levels=Z_level, vmax=Z_level[-1],
vmin=Z_level[0], alpha=0.75, **contour_kw)
ax.clabel(CS, fmt='%2.2f', colors='k', fontsize=10, inline=True)
# plot data deciles + axes labels
deciles = mquantiles(X[:, fx[0]], prob=np.arange(0.1, 1.0, 0.1))
trans = transforms.blended_transform_factory(ax.transData,
ax.transAxes)
ylim = ax.get_ylim()
ax.vlines(deciles, [0], 0.05, transform=trans, color='k')
ax.set_xlabel(name[0])
ax.set_ylim(ylim)
# prevent x-axis ticks from overlapping
ax.xaxis.set_major_locator(MaxNLocator(nbins=6, prune='lower'))
tick_formatter = ScalarFormatter()
tick_formatter.set_powerlimits((-3, 4))
ax.xaxis.set_major_formatter(tick_formatter)
if len(axes) > 1:
# two-way PDP - y-axis deciles + labels
deciles = mquantiles(X[:, fx[1]], prob=np.arange(0.1, 1.0, 0.1))
trans = transforms.blended_transform_factory(ax.transAxes,
ax.transData)
xlim = ax.get_xlim()
ax.hlines(deciles, [0], 0.05, transform=trans, color='k')
ax.set_ylabel(name[1])
# hline erases xlim
ax.set_xlim(xlim)
else:
ax.set_ylabel('Partial dependence')
if len(axes) == 1:
ax.set_ylim(pdp_lim[1])
axs.append(ax)
fig.subplots_adjust(bottom=0.15, top=0.7, left=0.1, right=0.95, wspace=0.4,
hspace=0.3)
return fig, axs
def plot_partial_dependence(estimator, X, features, feature_names=None,
target=None, response_method='auto', n_cols=3,
grid_resolution=100, percentiles=(0.05, 0.95),
method='auto', n_jobs=None, verbose=0, fig=None,
line_kw=None, contour_kw=None):
"""Partial dependence plots.
The ``len(features)`` plots are arranged in a grid with ``n_cols``
columns. Two-way partial dependence plots are plotted as contour plots.
Read more in the :ref:`User Guide <partial_dependence>`.
Parameters
----------
estimator : BaseEstimator
A fitted estimator object implementing `predict`, `predict_proba`,
or `decision_function`. Multioutput-multiclass classifiers are not
supported.
X : array-like, shape (n_samples, n_features)
The data to use to build the grid of values on which the dependence
will be evaluated. This is usually the training data.
features : list of {int, str, pair of int, pair of str}
The target features for which to create the PDPs.
If features[i] is an int or a string, a one-way PDP is created; if
features[i] is a tuple, a two-way PDP is created. Each tuple must be
of size 2.
if any entry is a string, then it must be in ``feature_names``.
feature_names : seq of str, shape (n_features,), optional
Name of each feature; feature_names[i] holds the name of the feature
with index i. By default, the name of the feature corresponds to
their numerical index.
target : int, optional (default=None)
- In a multiclass setting, specifies the class for which the PDPs
should be computed. Note that for binary classification, the
positive class (index 1) is always used.
- In a multioutput setting, specifies the task for which the PDPs
should be computed
Ignored in binary classification or classical regression settings.
response_method : 'auto', 'predict_proba' or 'decision_function', \
optional (default='auto') :
Specifies whether to use :term:`predict_proba` or
:term:`decision_function` as the target response. For regressors
this parameter is ignored and the response is always the output of
:term:`predict`. By default, :term:`predict_proba` is tried first
and we revert to :term:`decision_function` if it doesn't exist. If
``method`` is 'recursion', the response is always the output of
:term:`decision_function`.
n_cols : int, optional (default=3)
The maximum number of columns in the grid plot.
grid_resolution : int, optional (default=100)
The number of equally spaced points on the axes of the plots, for each
target feature.
percentiles : tuple of float, optional (default=(0.05, 0.95))
The lower and upper percentile used to create the extreme values
for the PDP axes. Must be in [0, 1].
method : str, optional (default='auto')
The method to use to calculate the partial dependence predictions:
- 'recursion' is only supported for objects inheriting from
`BaseGradientBoosting`, but is more efficient in terms of speed.
With this method, ``X`` is optional and is only used to build the
grid and the partial dependences are computed using the training
data. This method does not account for the ``init`` predicor of
the boosting process, which may lead to incorrect values (see
warning below. With this method, the target response of a
classifier is always the decision function, not the predicted
probabilities.
- 'brute' is supported for any estimator, but is more
computationally intensive.
- If 'auto', then 'recursion' will be used for
``BaseGradientBoosting`` estimators with ``init=None``, and
'brute' for all other.
Unlike the 'brute' method, 'recursion' does not account for the
``init`` predictor of the boosting process. In practice this still
produces the same plots, up to a constant offset in the target
response.
n_jobs : int, optional (default=None)
The number of CPUs to use to compute the partial dependences.
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
for more details.
verbose : int, optional (default=0)
Verbose output during PD computations.
fig : Matplotlib figure object, optional (default=None)
A figure object onto which the plots will be drawn, after the figure
has been cleared. By default, a new one is created.
line_kw : dict, optional
Dict with keywords passed to the ``matplotlib.pyplot.plot`` call.
For one-way partial dependence plots.
contour_kw : dict, optional
Dict with keywords passed to the ``matplotlib.pyplot.plot`` call.
For two-way partial dependence plots.
Examples
--------
>>> from sklearn.datasets import make_friedman1
>>> from sklearn.ensemble import GradientBoostingRegressor
>>> X, y = make_friedman1()
>>> clf = GradientBoostingRegressor(n_estimators=10).fit(X, y)
>>> plot_partial_dependence(clf, X, [0, (0, 1)]) #doctest: +SKIP
See also
--------
sklearn.inspection.partial_dependence: Return raw partial
dependence values
Warnings
--------
The 'recursion' method only works for gradient boosting estimators, and
unlike the 'brute' method, it does not account for the ``init``
predictor of the boosting process. In practice this will produce the
same values as 'brute' up to a constant offset in the target response,
provided that ``init`` is a consant estimator (which is the default).
However, as soon as ``init`` is not a constant estimator, the partial
dependence values are incorrect for 'recursion'.
"""
check_matplotlib_support('plot_partial_dependence') # noqa
import matplotlib.pyplot as plt # noqa
from matplotlib import transforms # noqa
from matplotlib.ticker import MaxNLocator # noqa
from matplotlib.ticker import ScalarFormatter # noqa
# set target_idx for multi-class estimators
if hasattr(estimator, 'classes_') and np.size(estimator.classes_) > 2:
if target is None:
raise ValueError('target must be specified for multi-class')
target_idx = np.searchsorted(estimator.classes_, target)
if (not (0 <= target_idx < len(estimator.classes_)) or
estimator.classes_[target_idx] != target):
raise ValueError('target not in est.classes_, got {}'.format(
target))
else:
# regression and binary classification
target_idx = 0
X = check_array(X)
n_features = X.shape[1]
# convert feature_names to list
if feature_names is None:
# if feature_names is None, use feature indices as name
feature_names = [str(i) for i in range(n_features)]
elif isinstance(feature_names, np.ndarray):
feature_names = feature_names.tolist()
if len(set(feature_names)) != len(feature_names):
raise ValueError('feature_names should not contain duplicates.')
def convert_feature(fx):
if isinstance(fx, str):
try:
fx = feature_names.index(fx)
except ValueError:
raise ValueError('Feature %s not in feature_names' % fx)
return int(fx)
# convert features into a seq of int tuples
tmp_features = []
for fxs in features:
if isinstance(fxs, (numbers.Integral, str)):
fxs = (fxs,)
try:
fxs = [convert_feature(fx) for fx in fxs]
except TypeError:
raise ValueError('Each entry in features must be either an int, '
'a string, or an iterable of size at most 2.')
if not (1 <= np.size(fxs) <= 2):
raise ValueError('Each entry in features must be either an int, '
'a string, or an iterable of size at most 2.')
tmp_features.append(fxs)
features = tmp_features
names = []
try:
for fxs in features:
names_ = []
# explicit loop so "i" is bound for exception below
for i in fxs:
names_.append(feature_names[i])
names.append(names_)
except IndexError:
raise ValueError('All entries of features must be less than '
'len(feature_names) = {0}, got {1}.'
.format(len(feature_names), i))
# compute averaged predictions
pd_result = Parallel(n_jobs=n_jobs, verbose=verbose)(
delayed(partial_dependence)(estimator, X, fxs,
response_method=response_method,
method=method,
grid_resolution=grid_resolution,
percentiles=percentiles)
for fxs in features)
# For multioutput regression, we can only check the validity of target
# now that we have the predictions.
# Also note: as multiclass-multioutput classifiers are not supported,
# multiclass and multioutput scenario are mutually exclusive. So there is
# no risk of overwriting target_idx here.
avg_preds, _ = pd_result[0] # checking the first result is enough
if is_regressor(estimator) and avg_preds.shape[0] > 1:
if target is None:
raise ValueError(
'target must be specified for multi-output regressors')
if not 0 <= target <= avg_preds.shape[0]:
raise ValueError(
'target must be in [0, n_tasks], got {}.'.format(target))
target_idx = target
else:
target_idx = 0
# get global min and max values of PD grouped by plot type
pdp_lim = {}
for avg_preds, values in pd_result:
min_pd = avg_preds[target_idx].min()
max_pd = avg_preds[target_idx].max()
n_fx = len(values)
old_min_pd, old_max_pd = pdp_lim.get(n_fx, (min_pd, max_pd))
min_pd = min(min_pd, old_min_pd)
max_pd = max(max_pd, old_max_pd)
pdp_lim[n_fx] = (min_pd, max_pd)
# create contour levels for two-way plots
if 2 in pdp_lim:
Z_level = np.linspace(*pdp_lim[2], num=8)
if fig is None:
fig = plt.figure()
else:
fig.clear()
if line_kw is None:
line_kw = {'color': 'green'}
if contour_kw is None:
contour_kw = {}
n_cols = min(n_cols, len(features))
n_rows = int(np.ceil(len(features) / float(n_cols)))
axs = []
for i, fx, name, (avg_preds, values) in zip(
count(), features, names, pd_result):
ax = fig.add_subplot(n_rows, n_cols, i + 1)
if len(values) == 1:
ax.plot(values[0], avg_preds[target_idx].ravel(), **line_kw)
else:
# make contour plot
assert len(values) == 2
XX, YY = np.meshgrid(values[0], values[1])
Z = avg_preds[target_idx].T
CS = ax.contour(XX, YY, Z, levels=Z_level, linewidths=0.5,
colors='k')
ax.contourf(XX, YY, Z, levels=Z_level, vmax=Z_level[-1],
vmin=Z_level[0], alpha=0.75, **contour_kw)
ax.clabel(CS, fmt='%2.2f', colors='k', fontsize=10, inline=True)
# plot data deciles + axes labels
deciles = mquantiles(X[:, fx[0]], prob=np.arange(0.1, 1.0, 0.1))
trans = transforms.blended_transform_factory(ax.transData,
ax.transAxes)
ylim = ax.get_ylim()
ax.vlines(deciles, [0], 0.05, transform=trans, color='k')
ax.set_xlabel(name[0])
ax.set_ylim(ylim)
# prevent x-axis ticks from overlapping
ax.xaxis.set_major_locator(MaxNLocator(nbins=6, prune='lower'))
tick_formatter = ScalarFormatter()
tick_formatter.set_powerlimits((-3, 4))
ax.xaxis.set_major_formatter(tick_formatter)
if len(values) > 1:
# two-way PDP - y-axis deciles + labels
deciles = mquantiles(X[:, fx[1]], prob=np.arange(0.1, 1.0, 0.1))
trans = transforms.blended_transform_factory(ax.transAxes,
ax.transData)
xlim = ax.get_xlim()
ax.hlines(deciles, [0], 0.05, transform=trans, color='k')
ax.set_ylabel(name[1])
# hline erases xlim
ax.set_xlim(xlim)
else:
ax.set_ylabel('Partial dependence')
if len(values) == 1:
ax.set_ylim(pdp_lim[1])
axs.append(ax)
fig.subplots_adjust(bottom=0.15, top=0.7, left=0.1, right=0.95, wspace=0.4,
hspace=0.3)
def __init__(self, diagnostics, nTime=0, ntMax=0, nPlot=1, write=False):
'''
Constructor
'''
self.write = write
self.prefix = 'viRMHD2D_'
self.nrows = 2
self.ncols = 4
if ntMax == 0:
ntMax = diagnostics.nt
if nTime > 0 and nTime < ntMax:
self.nTime = nTime
else:
self.nTime = ntMax
self.iTime = 0
self.nPlot = nPlot
self.diagnostics = diagnostics
self.E_velocity = np.zeros(ntMax + 1)
self.E_magnetic = np.zeros(ntMax + 1)
self.energy = np.zeros(ntMax + 1)
self.helicity = np.zeros(ntMax + 1)
self.x = np.zeros(diagnostics.nx + 1)
self.y = np.zeros(diagnostics.ny + 1)
self.x[0:-1] = self.diagnostics.xGrid
self.x[-1] = self.x[-2] + self.diagnostics.hx
self.y[0:-1] = self.diagnostics.yGrid
self.y[-1] = self.y[-2] + self.diagnostics.hy
self.Bx = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.By = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.Vx = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.Vy = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.P = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.A = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.J = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.PB = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.B = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
self.V = np.zeros((diagnostics.nx + 1, diagnostics.ny + 1))
# set up figure/window size
self.figure = plt.figure(num=None, figsize=(16, 9))
# set up plot margins
plt.subplots_adjust(hspace=0.25, wspace=0.2)
plt.subplots_adjust(left=0.05, right=0.95, top=0.93, bottom=0.05)
# set up plot title
self.title = self.figure.text(0.5,
0.97,
't = 0.0' %
(diagnostics.tGrid[self.iTime]),
horizontalalignment='center')
# set up tick formatter
majorFormatter = ScalarFormatter(useOffset=True)
## -> limit to 1.1f precision
majorFormatter.set_powerlimits((-1, +1))
majorFormatter.set_scientific(True)
# add data for zero timepoint
self.add_timepoint()
# set up plots
self.axes = {}
self.conts = {}
self.cbars = {}
self.lines = {}
self.vecs = {}
self.update_boundaries()
# create subplots
gs = gridspec.GridSpec(4, 3)
self.gs = gs
self.axes["Bx"] = plt.subplot(gs[0, 0])
self.axes["By"] = plt.subplot(gs[0, 1])
self.axes["Vx"] = plt.subplot(gs[1, 0])
self.axes["Vy"] = plt.subplot(gs[1, 1])
self.axes["J"] = plt.subplot(gs[2:4, 0:2])
self.axes["Emag"] = plt.subplot(gs[0, 2])
self.axes["Evel"] = plt.subplot(gs[1, 2])
self.axes["E"] = plt.subplot(gs[2, 2])
self.axes["H"] = plt.subplot(gs[3, 2])
self.axes["Bx"].set_title('$B_{x} (x,y)$')
self.axes["By"].set_title('$B_{y} (x,y)$')
self.axes["Vx"].set_title('$V_{x} (x,y)$')
self.axes["Vy"].set_title('$V_{y} (x,y)$')
self.axes["J"].set_title('$J (x,y)$')
self.conts["Bx"] = self.axes["Bx"].contourf(self.x,
self.y,
self.Bx.T,
self.BxTicks,
cmap=cm.jet,
extend='both')
self.cbars["Bx"] = self.figure.colorbar(self.conts["Bx"],
ax=self.axes["Bx"],
orientation='vertical',
ticks=self.BxTicks)
self.conts["By"] = self.axes["By"].contourf(self.x,
self.y,
self.By.T,
self.ByTicks,
cmap=cm.jet,
extend='both')
self.cbars["By"] = self.figure.colorbar(self.conts["By"],
ax=self.axes["By"],
orientation='vertical',
ticks=self.ByTicks)
self.conts["Vx"] = self.axes["Vx"].contourf(self.x,
self.y,
self.Vx.T,
self.VxTicks,
cmap=cm.jet,
extend='both')
self.cbars["Vx"] = self.figure.colorbar(self.conts["Vx"],
ax=self.axes["Vx"],
orientation='vertical',
ticks=self.VxTicks)
self.conts["Vy"] = self.axes["Vy"].contourf(self.x,
self.y,
self.Vy.T,
self.VyTicks,
cmap=cm.jet,
extend='both')
self.cbars["Vy"] = self.figure.colorbar(self.conts["Vy"],
ax=self.axes["Vy"],
orientation='vertical',
ticks=self.VyTicks)
tStart, tEnd, xStart, xEnd = self.get_timerange()
self.lines["Emag"], = self.axes["Emag"].plot(
self.diagnostics.tGrid[tStart:tEnd], self.E_magnetic[tStart:tEnd])
self.lines["Evel"], = self.axes["Evel"].plot(
self.diagnostics.tGrid[tStart:tEnd], self.E_velocity[tStart:tEnd])
self.lines["E"], = self.axes["E"].plot(
self.diagnostics.tGrid[tStart:tEnd], self.energy[tStart:tEnd])
self.lines["H"], = self.axes["H"].plot(
self.diagnostics.tGrid[tStart:tEnd], self.helicity[tStart:tEnd])
self.axes["Emag"].set_title('$E_{B} (t)$')
self.axes["Evel"].set_title('$E_{V} (t)$')
# if self.diagnostics.plot_energy:
# self.axes["E"].set_title('$E (t)$')
# else:
self.axes["E"].set_title('$(E-E_0) / E_0 (t)$')
# if self.diagnostics.plot_helicity:
# self.axes["H"].set_title('$H (t)$')
# else:
self.axes["H"].set_title('$(H-H_0) / H_0 (t)$')
self.axes["Emag"].set_xlim((xStart, xEnd))
self.axes["Evel"].set_xlim((xStart, xEnd))
self.axes["E"].set_xlim((xStart, xEnd))
self.axes["H"].set_xlim((xStart, xEnd))
self.axes["Emag"].yaxis.set_major_formatter(majorFormatter)
self.axes["Evel"].yaxis.set_major_formatter(majorFormatter)
self.axes["E"].yaxis.set_major_formatter(majorFormatter)
self.axes["H"].yaxis.set_major_formatter(majorFormatter)
# switch off some ticks
plt.setp(self.axes["Bx"].get_xticklabels(), visible=False)
plt.setp(self.axes["By"].get_xticklabels(), visible=False)
# plt.setp(self.axes["Vx" ].get_xticklabels(), visible=False)
plt.setp(self.axes["Emag"].get_xticklabels(), visible=False)
plt.setp(self.axes["Evel"].get_xticklabels(), visible=False)
plt.setp(self.axes["E"].get_xticklabels(), visible=False)
self.update()
def __init__(self, order_of_mag=0, useOffset=True, useMathText=False):
self._order_of_mag = order_of_mag
ScalarFormatter.__init__(self,
useOffset=useOffset,
useMathText=useMathText)
ax.set_xticklabels([]) # remove x axis
#plot C1
plt.subplot(gs[4])
plt.plot(zoomedTime,
zoomedC2_y,
linewidth=2,
color="tab:green",
label=C2_label)
plt.legend(loc="upper right")
plt.grid(True)
plt.xlim(startTime, stopTime)
plt.ylabel('Napětí [V]')
plt.xlabel('Čas [s]')
fig.subplots_adjust(wspace=0, hspace=0.1)
x_formatter = ScalarFormatter(useOffset=False)
plt.yticks(np.arange(0, 6, 2.5))
ax = plt.gca()
ax.xaxis.set_major_formatter(x_formatter)
#plot C2
plt.subplot(gs[0])
plt.plot(zoomedTime, zoomedC3_y, linewidth=2, color="tab:blue", label=C3_label)
plt.legend(loc="upper right")
plt.grid(True)
plt.yticks(np.arange(0, 13, 2.0))
plt.ylabel('Napětí [V]')
plt.xlim(startTime, stopTime)
ax = plt.gca()
ax.set_xticklabels([]) # remove x axis
def __init__(self,useOffset=True, useMathText=False, precision=None):
ScalarFormatter.__init__(self,useOffset=useOffset,useMathText=useMathText )
self.precision = precision
def __init__(self, format='%f', division=1e0):
ScalarFormatter.__init__(self, useOffset=False, useMathText=True)
self.format = format
self.division = division
def compare_plots_one_param_line_hist(list_of_pos_by_name,param,cl,color_by_name,cl_lines_flag=True,legend='right',analyticPDF=None):
"""
Plots a gaussian kernel density estimate for a set
of Posteriors onto the same axis.
@param list_of_pos: a list of Posterior class instances.
@param plot1DParams: a dict; {paramName:Nbins}
"""
from scipy import seterr as sp_seterr
#Create common figure
myfig=plt.figure(figsize=(6,4.5),dpi=150)
#myfig.add_axes([0.1,0.1,0.65,0.85])
#myfig.add_axes([0.15,0.15,0.6,0.76])
axes=plt.Axes(myfig,[0.15,0.15,0.6,0.76])
myfig.add_axes(axes)
majorFormatterX=ScalarFormatter(useMathText=True)
majorFormatterX.format_data=lambda data:'%.6g'%(data)
majorFormatterY=ScalarFormatter(useMathText=True)
majorFormatterY.format_data=lambda data:'%.6g'%(data)
majorFormatterX.set_scientific(True)
majorFormatterY.set_scientific(True)
list_of_pos=list_of_pos_by_name.values()
list_of_pos_names=list_of_pos_by_name.keys()
allmins=map(lambda a: np.min(a[param].samples), list_of_pos)
allmaxes=map(lambda a: np.max(a[param].samples), list_of_pos)
min_pos=np.min(allmins)
max_pos=np.max(allmaxes)
injvals=[]
patch_list=[]
max_y=0
posbins=np.linspace(min_pos,max_pos,50)
for name,posterior in list_of_pos_by_name.items():
colour=color_by_name[name]
#myfig.gca(autoscale_on=True)
if posterior[param].injval:
injvals.append(posterior[param].injval)
try:
n,bins=np.histogram(posterior[param].samples,bins=posbins,normed=True,new=True)
except:
n,bins=np.histogram(posterior[param].samples,bins=posbins,normed=True)
if min(bins)==max(bins):
print 'Skipping '+param
continue
locmaxy=max(n)
if locmaxy>max_y: max_y=locmaxy
#(n, bins, patches)=plt.hist(posterior[param].samples,bins=bins,facecolor='white',label=name,normed=True,hold=True,color=color_by_name[name])#range=(min_pos,max_pos)
(n, bins, patches)=plt.hist(posterior[param].samples,bins=bins,histtype='step',label=name,normed=True,hold=True,color=color_by_name[name])
patch_list.append(patches[0])
Nchars=max(map(lambda d:len(majorFormatterX.format_data(d)),axes.get_xticks()))
if Nchars>8:
Nticks=3
elif Nchars>5:
Nticks=4
elif Nchars>4:
Nticks=6
else:
Nticks=6
locatorX=mpl.ticker.MaxNLocator(nbins=Nticks)
locatorX.view_limits(bins[0],bins[-1])
axes.xaxis.set_major_locator(locatorX)
plt.xlim(min_pos,max_pos)
top_cl_intervals_list={}
pos_names=list_of_pos_by_name.keys()
for name,posterior in list_of_pos_by_name.items():
#toppoints,injectionconfidence,reses,injection_area,cl_intervals=bppu.greedy_bin_one_param(posterior,{param:greedyBinSizes[param]},[cl])
cl_intervals=posterior[param].prob_interval([cl])
colour=color_by_name[name]
if cl_intervals[0] is not None and cl_lines_flag:
try:
plt.plot([cl_intervals[0][0],cl_intervals[0][0]],[0,max_y],color=colour,linestyle='--')
plt.plot([cl_intervals[0][1],cl_intervals[0][1]],[0,max_y],color=colour,linestyle='--')
except:
print "MAX_Y",max_y,[cl_intervals[0][0],cl_intervals[0][0]],[cl_intervals[0][1],cl_intervals[0][1]]
top_cl_intervals_list[name]=(cl_intervals[0][0],cl_intervals[0][1])
if cl_lines_flag:
pos_names.append(str(int(cl*100))+'%')
patch_list.append(mpl.lines.Line2D(np.array([0.,1.]),np.array([0.,1.]),linestyle='--',color='black'))
plt.grid()
plt.xlim(min_pos,max_pos)
if legend is not None:
oned_legend=plt.figlegend(patch_list,pos_names,'right')
for text in oned_legend.get_texts():
text.set_fontsize('small')
plt.xlabel(bppu.plot_label(param))
plt.ylabel('Probability density')
plt.draw()
#plt.tight_layout()
if injvals:
print "Injection parameter is %f"%(float(injvals[0]))
injpar=injvals[0]
#if min(pos_samps)<injpar and max(pos_samps)>injpar:
plt.plot([injpar,injpar],[0,max_y],'r-.',scalex=False,scaley=False,linewidth=4,label='Injection')
#
if analyticPDF is not None:
plt.plot(posbins,map(analyticPDF,posbins),'r')
return myfig,top_cl_intervals_list#,rkde
def plot_everything(*args):
n_rows = 2
n_cols = n_bins / n_rows
print("n_rows: {}, n_cols: {}".format(n_rows, n_cols))
for idx in range(n_bins):
row = idx / n_cols
col = idx % n_cols
print("plotting bin {}, row {} col {}".format(idx, row, col))
plt.figure(1)
#{ Figure 1
ax3 = plt.subplot2grid((n_rows, n_bins / n_rows), (row, col))
m = createMap('cyl')
x_m_meshgrid, y_m_meshgrid = m(y_meshgrid, x_meshgrid)
# m.pcolor(x_m_meshgrid, y_m_meshgrid, bins_rbf_log[idx], cmap=my_cm)
m.pcolor(x_m_meshgrid,
y_m_meshgrid,
bins_rbf_log[idx],
cmap=my_cm,
edgecolor=(1.0, 1.0, 1.0, 0.3),
linewidth=0.005,
vmin=pcolor_min,
vmax=pcolor_max)
formatter = ScalarFormatter()
formatter.set_scientific(False)
cb = m.colorbar(
location="bottom",
label="Z",
format=ticker.FuncFormatter(fake_log_fmt)) # draw colorbar
low_limit = idx * bin_size
high_limit = (idx + 1.0) * bin_size
if idx == (n_bins - 1):
high_limit = 150
plt.title('X-ray/gamma {}-{} keV'.format(low_limit, high_limit),
fontsize=13)
x_m, y_m = m(lons_orig, lats_orig) # project points
cb.set_label('log10(' + x_label + ') ' + x_units)
for image in images:
latitude, longitude, tle_date = getLatLong(image.time)
x, y = m(longitude, latitude)
m.scatter(x, y, 0.2, marker='o', color='grey', zorder=10)
plt.subplots_adjust(left=0.025,
bottom=0.05,
right=0.975,
top=0.95,
wspace=0.2,
hspace=0.3)
#} end of Figure 1
plt.show()
plot_m.set_ylabel("mass [Earths]")
plot_m.grid(True)
plot_I = fig.add_subplot(2, 2, 4, sharex=plot_a)
if isLog:
plot = plot_I.semilogx
else:
plot = plot_I.plot
for planet in range(nb_planete):
plot(t[planet][id_min:id_max+1], I[planet][id_min:id_max+1], color=colors[planet], label='PLANETE'+str(planet))
plot_I.set_xlabel("time [years]")
plot_I.set_ylabel("Inclination [degrees]")
plot_I.grid(True)
myyfmt = ScalarFormatter(useOffset=False)
myyfmt.set_scientific(True)
myyfmt.set_powerlimits((-2, 3))
myxfmt = ScalarFormatter(useOffset=True)
myxfmt._set_offset(1e5)
myxfmt.set_scientific(True)
myxfmt.set_powerlimits((-3, 3))
plot_a.xaxis.set_major_formatter(myxfmt)
plot_I.yaxis.set_major_formatter(myyfmt)
nom_fichier_plot = "evolution_planete"
fig.savefig('%s.%s' % (nom_fichier_plot, OUTPUT_EXTENSION), format=OUTPUT_EXTENSION)
pl.show()
def corner(xs,
bins=20,
range=None,
weights=None,
color="k",
smooth=None,
smooth1d=None,
labels=None,
label_kwargs=None,
show_titles=False,
title_fmt=".2f",
title_kwargs=None,
truths=None,
truth_color="#4682b4",
scale_hist=False,
quantiles=None,
verbose=False,
fig=None,
max_n_ticks=5,
top_ticks=False,
use_math_text=False,
reverse=False,
hist_kwargs=None,
priors=None,
prior_kwargs=None,
**hist2d_kwargs):
"""
Make a *sick* corner plot showing the projections of a data set in a
multi-dimensional space. kwargs are passed to hist2d() or used for
`matplotlib` styling.
Parameters
----------
xs : array_like[nsamples, ndim]
The samples. This should be a 1- or 2-dimensional array. For a 1-D
array this results in a simple histogram. For a 2-D array, the zeroth
axis is the list of samples and the next axis are the dimensions of
the space.
bins : int or array_like[ndim,]
The number of bins to use in histograms, either as a fixed value for
all dimensions, or as a list of integers for each dimension.
weights : array_like[nsamples,]
The weight of each sample. If `None` (default), samples are given
equal weight.
color : str
A ``matplotlib`` style color for all histograms.
smooth, smooth1d : float
The standard deviation for Gaussian kernel passed to
`scipy.ndimage.gaussian_filter` to smooth the 2-D and 1-D histograms
respectively. If `None` (default), no smoothing is applied.
labels : iterable (ndim,)
A list of names for the dimensions. If a ``xs`` is a
``pandas.DataFrame``, labels will default to column names.
label_kwargs : dict
Any extra keyword arguments to send to the `set_xlabel` and
`set_ylabel` methods.
show_titles : bool
Displays a title above each 1-D histogram showing the 0.5 quantile
with the upper and lower errors supplied by the quantiles argument.
title_fmt : string
The format string for the quantiles given in titles. If you explicitly
set ``show_titles=True`` and ``title_fmt=None``, the labels will be
shown as the titles. (default: ``.2f``)
title_kwargs : dict
Any extra keyword arguments to send to the `set_title` command.
range : iterable (ndim,)
A list where each element is either a length 2 tuple containing
lower and upper bounds or a float in range (0., 1.)
giving the fraction of samples to include in bounds, e.g.,
[(0.,10.), (1.,5), 0.999, etc.].
If a fraction, the bounds are chosen to be equal-tailed.
truths : iterable (ndim,)
A list of reference values to indicate on the plots. Individual
values can be omitted by using ``None``.
truth_color : str
A ``matplotlib`` style color for the ``truths`` makers.
scale_hist : bool
Should the 1-D histograms be scaled in such a way that the zero line
is visible?
quantiles : iterable
A list of fractional quantiles to show on the 1-D histograms as
vertical dashed lines.
verbose : bool
If true, print the values of the computed quantiles.
plot_contours : bool
Draw contours for dense regions of the plot.
use_math_text : bool
If true, then axis tick labels for very large or small exponents will
be displayed as powers of 10 rather than using `e`.
reverse : bool
If true, plot the corner plot starting in the upper-right corner instead
of the usual bottom-left corner
max_n_ticks: int
Maximum number of ticks to try to use
top_ticks : bool
If true, label the top ticks of each axis
fig : matplotlib.Figure
Overplot onto the provided figure object.
hist_kwargs : dict
Any extra keyword arguments to send to the 1-D histogram plots.
priors : iterable (ndim,)
A list of functions used to plot another probability distribution on
top of the 1-D histograms. Individual priors can be omitted by using
``None``. Priors are only calculated over the range of the posteriors.
E.g., to plot flat priors, ``def flat(p): return np.ones_like(p)`` and
pass ``priors=[flat, flat, flat]``.
prior_kwargs : dict
Any extra keyword arguments to send to the prior histogram plots, e.g.,
``prior_kwargs={"color": "blue"}``. The default style is a thin, gray,
dotted line.
**hist2d_kwargs
Any remaining keyword arguments are sent to `corner.hist2d` to generate
the 2-D histogram plots.
"""
if quantiles is None:
quantiles = []
if title_kwargs is None:
title_kwargs = dict()
if label_kwargs is None:
label_kwargs = dict()
# Try filling in labels from pandas.DataFrame columns.
if labels is None:
try:
labels = xs.columns
except AttributeError:
pass
# Deal with 1D sample lists.
xs = np.atleast_1d(xs)
if len(xs.shape) == 1:
xs = np.atleast_2d(xs)
else:
assert len(xs.shape) == 2, "The input sample array must be 1- or 2-D."
xs = xs.T
assert xs.shape[0] <= xs.shape[1], "I don't believe that you want more " \
"dimensions than samples!"
# Parse the weight array.
if weights is not None:
weights = np.asarray(weights)
if weights.ndim != 1:
raise ValueError("Weights must be 1-D")
if xs.shape[1] != weights.shape[0]:
raise ValueError("Lengths of weights must match number of samples")
# Parse the parameter ranges.
if range is None:
if "extents" in hist2d_kwargs:
logging.warn("Deprecated keyword argument 'extents'. "
"Use 'range' instead.")
range = hist2d_kwargs.pop("extents")
else:
range = [[x.min(), x.max()] for x in xs]
# Check for parameters that never change.
m = np.array([e[0] == e[1] for e in range], dtype=bool)
if np.any(m):
raise ValueError(
("It looks like the parameter(s) in "
"column(s) {0} have no dynamic range. "
"Please provide a `range` argument.").format(", ".join(
map("{0}".format,
np.arange(len(m))[m]))))
else:
# If any of the extents are percentiles, convert them to ranges.
# Also make sure it's a normal list.
range = list(range)
for i, _ in enumerate(range):
try:
emin, emax = range[i]
except TypeError:
q = [0.5 - 0.5 * range[i], 0.5 + 0.5 * range[i]]
range[i] = quantile(xs[i], q, weights=weights)
if len(range) != xs.shape[0]:
raise ValueError("Dimension mismatch between samples and range")
# Parse the bin specifications.
try:
bins = [int(bins) for _ in range]
except TypeError:
if len(bins) != len(range):
raise ValueError("Dimension mismatch between bins and range")
# Some magic numbers for pretty axis layout.
K = len(xs)
factor = 2.0 # size of one side of one panel
if reverse:
lbdim = 0.2 * factor # size of left/bottom margin
trdim = 0.5 * factor # size of top/right margin
else:
lbdim = 0.5 * factor # size of left/bottom margin
trdim = 0.2 * factor # size of top/right margin
whspace = 0.05 # w/hspace size
plotdim = factor * K + factor * (K - 1.) * whspace
dim = lbdim + plotdim + trdim
# Create a new figure if one wasn't provided.
if fig is None:
fig, axes = pl.subplots(K, K, figsize=(dim, dim))
else:
try:
axes = np.array(fig.axes).reshape((K, K))
except:
raise ValueError("Provided figure has {0} axes, but data has "
"dimensions K={1}".format(len(fig.axes), K))
# Format the figure.
lb = lbdim / dim
tr = (lbdim + plotdim) / dim
fig.subplots_adjust(left=lb,
bottom=lb,
right=tr,
top=tr,
wspace=whspace,
hspace=whspace)
# Set up the default histogram keywords.
if hist_kwargs is None:
hist_kwargs = dict()
hist_kwargs["color"] = hist_kwargs.get("color", color)
if smooth1d is None:
hist_kwargs["histtype"] = hist_kwargs.get("histtype", "step")
# Set up the defaults for plotting priors
if priors is None:
priors = [None] * xs.shape[0]
if prior_kwargs is None:
prior_kwargs = dict()
prior_kwargs["linestyle"] = prior_kwargs.get("linestyle", ":")
prior_kwargs["linewidth"] = prior_kwargs.get("linewidth", 1)
prior_kwargs["color"] = prior_kwargs.get("color", "gray")
for i, x in enumerate(xs):
# Deal with masked arrays.
if hasattr(x, "compressed"):
x = x.compressed()
if np.shape(xs)[0] == 1:
ax = axes
else:
if reverse:
ax = axes[K - i - 1, K - i - 1]
else:
ax = axes[i, i]
# Plot the histograms.
if smooth1d is None:
n, bin_edges, _ = ax.hist(x,
bins=bins[i],
weights=weights,
range=np.sort(range[i]),
**hist_kwargs)
else:
if gaussian_filter is None:
raise ImportError("Please install scipy for smoothing")
n, bin_edges = np.histogram(x,
bins=bins[i],
weights=weights,
range=np.sort(range[i]))
n = gaussian_filter(n, smooth1d)
x0 = np.array(list(zip(bin_edges[:-1], bin_edges[1:]))).flatten()
y0 = np.array(list(zip(n, n))).flatten()
ax.plot(x0, y0, **hist_kwargs)
if priors[i] is not None:
prior = priors[i](bin_edges)
prior *= np.sum(n) / np.sum(prior)
ax.plot(bin_edges, prior, zorder=1, **prior_kwargs)
if truths is not None and truths[i] is not None:
ax.axvline(truths[i], color=truth_color)
# Plot quantiles if wanted.
if len(quantiles) > 0:
qvalues = quantile(x, quantiles, weights=weights)
for q in qvalues:
ax.axvline(q, ls="dashed", color=color)
if verbose:
print("Quantiles:")
print([item for item in zip(quantiles, qvalues)])
if show_titles:
title = None
if title_fmt is not None:
# Compute the quantiles for the title. This might redo
# unneeded computation but who cares.
q_16, q_50, q_84 = quantile(x, [0.16, 0.5, 0.84],
weights=weights)
q_m, q_p = q_50 - q_16, q_84 - q_50
# Format the quantile display.
fmt = "{{0:{0}}}".format(title_fmt).format
title = r"${{{0}}}_{{-{1}}}^{{+{2}}}$"
title = title.format(fmt(q_50), fmt(q_m), fmt(q_p))
# Add in the column name if it's given.
if labels is not None:
title = "{0} = {1}".format(labels[i], title)
elif labels is not None:
title = "{0}".format(labels[i])
if title is not None:
if reverse:
ax.set_xlabel(title, **title_kwargs)
else:
ax.set_title(title, **title_kwargs)
# Set up the axes.
ax.set_xlim(range[i])
if scale_hist:
maxn = np.max(n)
ax.set_ylim(-0.1 * maxn, 1.1 * maxn)
else:
ax.set_ylim(0, 1.1 * np.max(n))
ax.set_yticklabels([])
if max_n_ticks == 0:
ax.xaxis.set_major_locator(NullLocator())
ax.yaxis.set_major_locator(NullLocator())
else:
ax.xaxis.set_major_locator(MaxNLocator(max_n_ticks, prune="lower"))
ax.yaxis.set_major_locator(NullLocator())
if i < K - 1:
if top_ticks:
ax.xaxis.set_ticks_position("top")
[l.set_rotation(45) for l in ax.get_xticklabels()]
else:
ax.set_xticklabels([])
else:
if reverse:
ax.xaxis.tick_top()
[l.set_rotation(45) for l in ax.get_xticklabels()]
if labels is not None:
if reverse:
ax.set_title(labels[i], y=1.25, **label_kwargs)
else:
ax.set_xlabel(labels[i], **label_kwargs)
# use MathText for axes ticks
ax.xaxis.set_major_formatter(
ScalarFormatter(useMathText=use_math_text))
for j, y in enumerate(xs):
if np.shape(xs)[0] == 1:
ax = axes
else:
if reverse:
ax = axes[K - i - 1, K - j - 1]
else:
ax = axes[i, j]
if j > i:
ax.set_frame_on(False)
ax.set_xticks([])
ax.set_yticks([])
continue
elif j == i:
continue
# Deal with masked arrays.
if hasattr(y, "compressed"):
y = y.compressed()
hist2d(y,
x,
ax=ax,
range=[range[j], range[i]],
weights=weights,
color=color,
smooth=smooth,
bins=[bins[j], bins[i]],
**hist2d_kwargs)
if truths is not None:
if truths[i] is not None and truths[j] is not None:
ax.plot(truths[j], truths[i], "s", color=truth_color)
if truths[j] is not None:
ax.axvline(truths[j], color=truth_color)
if truths[i] is not None:
ax.axhline(truths[i], color=truth_color)
if max_n_ticks == 0:
ax.xaxis.set_major_locator(NullLocator())
ax.yaxis.set_major_locator(NullLocator())
else:
ax.xaxis.set_major_locator(
MaxNLocator(max_n_ticks, prune="lower"))
ax.yaxis.set_major_locator(
MaxNLocator(max_n_ticks, prune="lower"))
if i < K - 1:
ax.set_xticklabels([])
else:
if reverse:
ax.xaxis.tick_top()
[l.set_rotation(45) for l in ax.get_xticklabels()]
if labels is not None:
ax.set_xlabel(labels[j], **label_kwargs)
if reverse:
ax.xaxis.set_label_coords(0.5, 1.4)
else:
ax.xaxis.set_label_coords(0.5, -0.3)
# use MathText for axes ticks
ax.xaxis.set_major_formatter(
ScalarFormatter(useMathText=use_math_text))
if j > 0:
ax.set_yticklabels([])
else:
if reverse:
ax.yaxis.tick_right()
[l.set_rotation(45) for l in ax.get_yticklabels()]
if labels is not None:
if reverse:
ax.set_ylabel(labels[i], rotation=-90, **label_kwargs)
ax.yaxis.set_label_coords(1.3, 0.5)
else:
ax.set_ylabel(labels[i], **label_kwargs)
ax.yaxis.set_label_coords(-0.3, 0.5)
# use MathText for axes ticks
ax.yaxis.set_major_formatter(
ScalarFormatter(useMathText=use_math_text))
return fig
def plot(self, profile, statsResults):
if len(statsResults.activeData) <= 0:
self.emptyAxis()
return
features = statsResults.getColumn('Features')
if len(features) > 200:
QtGui.QApplication.instance().setOverrideCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
reply = QtGui.QMessageBox.question(self, 'Continue?', 'Profile contains ' + str(len(features)) + ' features. ' +
'It may take several seconds to generate this plot. We recommend filtering your profile first. ' +
'Do you wish to continue?', QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
QtGui.QApplication.instance().restoreOverrideCursor()
if reply == QtGui.QMessageBox.No:
self.emptyAxis()
return
# *** Colour of plot elements
axesColour = str(self.preferences['Axes colour'].name())
profile1Colour = str(self.preferences['Sample 1 colour'].name())
profile2Colour = str(self.preferences['Sample 2 colour'].name())
# *** Set sample names
bLogScale = False
xLabel = self.fieldToPlot
# *** Create lists for each quantity of interest
if self.fieldToPlot == 'Number of sequences':
if self.bSortFeatures:
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['Seq1']], True)
field1 = statsResults.getColumn('Seq1')
field2 = statsResults.getColumn('Seq2')
elif self.fieldToPlot == 'Number of parental sequences':
if self.bSortFeatures:
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['ParentalSeq1']], True)
field1 = statsResults.getColumn('ParentalSeq1')
field2 = statsResults.getColumn('ParentalSeq2')
elif self.fieldToPlot == 'Proportion of sequences (%)':
if self.bSortFeatures:
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['RelFreq1']], True)
field1 = statsResults.getColumn('RelFreq1')
field2 = statsResults.getColumn('RelFreq2')
elif self.fieldToPlot == 'p-values':
if self.bSortFeatures:
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['pValues']], False)
field1 = statsResults.getColumn('pValues')
field2 = None
elif self.fieldToPlot == 'p-values (corrected)':
if self.bSortFeatures:
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['pValuesCorrected']], False)
field1 = statsResults.getColumn('pValuesCorrected')
field2 = None
elif self.fieldToPlot == 'Effect size':
if self.bSortFeatures:
statsResults.activeData = TableHelper.SortTable(statsResults.activeData,\
[statsResults.dataHeadings['EffectSize']], True, True,
statsResults.confIntervMethod.bRatio)
field1 = statsResults.getColumn('EffectSize')
field2 = None
bLogScale = statsResults.confIntervMethod.bRatio
xLabel = statsResults.confIntervMethod.plotLabel
features = statsResults.getColumn('Features') # get sorted feature labels
# *** Truncate feature labels
highlightedFeatures = list(self.preferences['Highlighted sample features'])
if self.preferences['Truncate feature names']:
length = self.preferences['Length of truncated feature names']
for i in xrange(0, len(features)):
if len(features[i]) > length+3:
features[i] = features[i][0:length] + '...'
for i in xrange(0, len(highlightedFeatures)):
if len(highlightedFeatures[i]) > length+3:
highlightedFeatures[i] = highlightedFeatures[i][0:length] + '...'
# *** Check that there is at least one significant feature
if len(features) <= 0:
self.emptyAxis('No significant features')
return
# *** Set figure size
padding = 0.2 #inches
heightBottomLabels = 0.4 # inches
imageHeight = len(features)*self.figHeightPerRow + padding + heightBottomLabels
self.fig.set_size_inches(self.figWidth, imageHeight)
yPlotOffsetFigSpace = heightBottomLabels / imageHeight
heightPlotFigSpace = 1.0 - yPlotOffsetFigSpace - padding / imageHeight
yLabelBounds = self.yLabelExtents(features, 8)
xPlotOffsetFigSpace = yLabelBounds.width + 0.1 / self.figWidth
widthPlotFigSpace = 1.0 - xPlotOffsetFigSpace - padding / self.figWidth
axesBar = self.fig.add_axes([xPlotOffsetFigSpace,yPlotOffsetFigSpace,widthPlotFigSpace,heightPlotFigSpace])
# *** Plot data
barHeight = 0.35
if bLogScale:
field1 = np.log10(field1)
xLabel = 'log(' + xLabel + ')'
if field2 != None:
field2 = np.log10(field2)
if field2 == None:
rects1 = axesBar.barh(np.arange(len(features)), field1, height=barHeight)
axesBar.set_yticks(np.arange(len(features)) + 0.5*barHeight)
axesBar.set_ylim([0, len(features)-1.0 + barHeight + 0.1])
elif field2 != None:
rects2 = axesBar.barh(np.arange(len(features)), field2, height=barHeight, color=profile2Colour)
rects1 = axesBar.barh(np.arange(len(features))+barHeight, field1, height=barHeight, color=profile1Colour)
axesBar.set_yticks(np.arange(len(features)) + barHeight)
axesBar.set_ylim([0, len(features)-1.0 + 2*barHeight + 0.1])
axesBar.set_yticklabels(features)
axesBar.set_xlabel(xLabel)
scalarFormatter = ScalarFormatter(useMathText=False)
scalarFormatter.set_scientific(True)
scalarFormatter.set_powerlimits((-3,4))
axesBar.xaxis.set_major_formatter(scalarFormatter)
# *** Prettify plot
if self.legendPos != -1 and field2 != None:
legend = axesBar.legend([rects1[0], rects2[0]], (profile.sampleNames[0], profile.sampleNames[1]), loc=self.legendPos)
legend.get_frame().set_linewidth(0)
for label in axesBar.get_yticklabels():
if label.get_text() in highlightedFeatures:
label.set_color('red')
for a in axesBar.yaxis.majorTicks:
a.tick1On=False
a.tick2On=False
for a in axesBar.xaxis.majorTicks:
a.tick1On=True
a.tick2On=False
for line in axesBar.yaxis.get_ticklines():
line.set_color(axesColour)
for line in axesBar.xaxis.get_ticklines():
line.set_color(axesColour)
for loc, spine in axesBar.spines.iteritems():
if loc in ['right','top']:
spine.set_color('none')
else:
spine.set_color(axesColour)
self.updateGeometry()
self.draw()
#dummy x data for plotting
x = np.arange(min(meanls_list_fyi), max(meanls_list_fyi), 1)
x = np.arange(min(ls_list_fyi), max(ls_list_fyi), 1)
ax.loglog(x,
a * x**k,
linewidth=2,
label=r'$D=%.2f*10^{-6} L^{%.2f}$ (FYI)' % (a * 10e6, k),
c='darkorange')
ax.plot(cix,
ciy_low,
'--',
c='r',
linewidth=1,
label=r'$99\%\,confidence\,band$')
ax.plot(cix, ciy_upp, '--', c='r', linewidth=1)
ax.grid(True)
from matplotlib.ticker import ScalarFormatter, FormatStrFormatter
ax.xaxis.set_major_formatter(ScalarFormatter())
ax.legend(loc='lower left',
prop={'size': 16},
fancybox=True,
framealpha=0.5,
numpoints=1)
fig1.tight_layout()
fig1.savefig(outpath + 'power_law_24h_it_7km_seed_f_masked_n9' + title)
#fig1.savefig(outpath+'power_law_24h_it_7km_'+title)