def plottimeseries(series, outfile, t0=0, zeroline=False, **kwargs):
"""
Plot a REALXTimeSeries.
"""
# construct list of series
if hasattr(series, "__contains__"):
serieslist = series
else:
serieslist = [series]
# get limits
xlim = kwargs.pop("xlim", None)
ylim = kwargs.pop("ylim", None)
if xlim:
start, end = xlim
else:
start = min(float(s.epoch) for s in serieslist)
end = max(
float(s.epoch + s.data.length * s.deltaT) for s in serieslist)
# get axis scales
logx = kwargs.pop("logx", False)
logy = kwargs.pop("logy", False)
# get legend loc
loc = kwargs.pop("loc", 0)
alpha = kwargs.pop("alpha", 0.8)
# get colorbar options
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# get savefig option
bbox_inches = kwargs.pop("bbox_inches", None)
#
# get labels
#
xlabel = kwargs.pop("xlabel", None)
if xlabel:
unit = 1
if not xlabel:
unit, timestr = plotutils.time_axis_unit(end - start)
if not t0:
t0 = start
t0 = lal.LIGOTimeGPS(t0)
if int(t0.gpsNanoSeconds) == 0:
xlabel = datetime.datetime(*lal.GPSToUTC(int(t0))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)" % (timestr, xlabel, int(t0))
else:
xlabel = datetime.datetime(*lal.GPSToUTC(t0.gpsSeconds)[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC",".%.3s UTC" % t0.gpsNanoSeconds),\
t0)
t0 = float(t0)
ylabel = kwargs.pop("ylabel", "Amplitude (counts)")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
#
# set default line params
#
color = kwargs.pop("color", None)
if isinstance(color, str):
color = color.split(',')
if len(color) == 1:
color = [color[0]] * len(serieslist)
kwargs2 = dict()
kwargs2.update(kwargs)
if kwargs.has_key("marker"):
kwargs.setdefault("markersize", 5)
kwargs2.setdefault("markersize", 2)
else:
kwargs.setdefault("linestyle", "-")
kwargs.setdefault("linewidth", "1")
kwargs2.setdefault("linewidth", "0.1")
#
# make plot
#
allnames = [s.name for s in serieslist]
namedseries = [
s for s in serieslist if not re.search("(min|max)\Z", s.name)
]
plot = plotutils.SimplePlot(xlabel, ylabel, title, subtitle)
for i,(series,c) in enumerate(itertools.izip(namedseries,\
plotutils.default_colors())):
if color:
c = color[serieslist.index(series)]
x = numpy.arange(series.data.length) * series.deltaT +\
float(series.epoch) - float(t0)
x = x.astype(float)
x /= unit
d = series.data.data
if logy and ylim:
numpy.putmask(d, d == 0, ylim[0] - abs(ylim[0]) * 0.01)
plot.add_content(x, d, color=c,\
label=plotutils.display_name(series.name), **kwargs)
# find min/max and plot
for i, name in enumerate(allnames):
for ext in ["min", "max"]:
if re.match("%s[- _]%s" % (re.escape(series.name), ext), name):
if color:
c = color[i]
series2 = serieslist[i]
x2 = numpy.arange(series2.data.length) * series2.deltaT\
+ float(series2.epoch) - float(t0)
x2 /= unit
d2 = series2.data.data
if logy and ylim:
numpy.putmask(d2, d2 == 0,
ylim[0] - abs(ylim[0]) * 0.01)
plot.ax.plot(x2, d2, color=c, **kwargs2)
plot.ax.fill_between(x2, d, d2, alpha=0.1,\
color=c)
# finalize
plot.finalize(loc=loc, alpha=alpha)
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
# add zero line
axis_lims = plot.ax.get_ylim()
if zeroline:
plot.ax.plot([0, 0], [axis_lims[0], axis_lims[1]], 'r--', linewidth=2)
plot.ax.set_ylim([axis_lims[0], axis_lims[1]])
# set logscale
if logx:
plot.ax.xaxis.set_scale("log")
if logy:
plot.ax.yaxis.set_scale("log")
plot.ax._update_transScale()
# format axes
if xlim:
xlim = (numpy.asarray(xlim).astype(float) - t0) / unit
plot.ax.set_xlim(xlim)
if ylim:
plot.ax.set_ylim(ylim)
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax, x=False)
# save and close
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plottimeseries(series, outfile, t0=0, zeroline=False, **kwargs):
"""
Plot a REALXTimeSeries.
"""
# construct list of series
if hasattr(series, "__contains__"):
serieslist = series
else:
serieslist = [series]
# get limits
xlim = kwargs.pop("xlim", None)
ylim = kwargs.pop("ylim", None)
if xlim:
start,end = xlim
else:
start = min(float(s.epoch) for s in serieslist)
end = max(float(s.epoch + s.data.length*s.deltaT) for s in serieslist)
# get axis scales
logx = kwargs.pop("logx", False)
logy = kwargs.pop("logy", False)
# get legend loc
loc = kwargs.pop("loc", 0)
alpha = kwargs.pop("alpha", 0.8)
# get colorbar options
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# get savefig option
bbox_inches = kwargs.pop("bbox_inches", None)
#
# get labels
#
xlabel = kwargs.pop("xlabel", None)
if xlabel:
unit = 1
if not xlabel:
unit, timestr = plotutils.time_axis_unit(end-start)
if not t0:
t0 = start
t0 = lal.LIGOTimeGPS(t0)
if int(t0.gpsNanoSeconds) == 0:
xlabel = datetime.datetime(*lal.GPSToUTC(int(t0))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)" % (timestr, xlabel, int(t0))
else:
xlabel = datetime.datetime(*lal.GPSToUTC(t0.gpsSeconds)[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC",".%.3s UTC" % t0.gpsNanoSeconds),\
t0)
t0 = float(t0)
ylabel = kwargs.pop("ylabel", "Amplitude (counts)")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
#
# set default line params
#
color = kwargs.pop("color", None)
if isinstance(color, str):
color = color.split(',')
if len(color) == 1:
color = [color[0]]*len(serieslist)
kwargs2 = dict()
kwargs2.update(kwargs)
if kwargs.has_key("marker"):
kwargs.setdefault("markersize", 5)
kwargs2.setdefault("markersize", 2)
else:
kwargs.setdefault("linestyle", "-")
kwargs.setdefault("linewidth", "1")
kwargs2.setdefault("linewidth", "0.1")
#
# make plot
#
allnames = [s.name for s in serieslist]
namedseries = [s for s in serieslist if not re.search("(min|max)\Z",s.name)]
plot = plotutils.SimplePlot(xlabel, ylabel, title, subtitle)
for i,(series,c) in enumerate(itertools.izip(namedseries,\
plotutils.default_colors())):
if color:
c = color[serieslist.index(series)]
x = numpy.arange(series.data.length) * series.deltaT +\
float(series.epoch) - float(t0)
x = x.astype(float)
x /= unit
d = series.data.data
if logy and ylim:
numpy.putmask(d, d==0, ylim[0]-abs(ylim[0])*0.01)
plot.add_content(x, d, color=c,\
label=plotutils.display_name(series.name), **kwargs)
# find min/max and plot
for i,name in enumerate(allnames):
for ext in ["min", "max"]:
if re.match("%s[- _]%s" % (re.escape(series.name), ext), name):
if color:
c = color[i]
series2 = serieslist[i]
x2 = numpy.arange(series2.data.length) * series2.deltaT\
+ float(series2.epoch) - float(t0)
x2 /= unit
d2 = series2.data.data
if logy and ylim:
numpy.putmask(d2, d2==0, ylim[0]-abs(ylim[0])*0.01)
plot.ax.plot(x2, d2, color=c, **kwargs2)
plot.ax.fill_between(x2, d, d2, alpha=0.1,\
color=c)
# finalize
plot.finalize(loc=loc, alpha=alpha)
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
# add zero line
axis_lims = plot.ax.get_ylim()
if zeroline:
plot.ax.plot([0, 0], [axis_lims[0], axis_lims[1]], 'r--', linewidth=2)
plot.ax.set_ylim([ axis_lims[0], axis_lims[1] ])
# set logscale
if logx:
plot.ax.xaxis.set_scale("log")
if logy:
plot.ax.yaxis.set_scale("log")
plot.ax._update_transScale()
# format axes
if xlim:
xlim = (numpy.asarray(xlim).astype(float)-t0)/unit
plot.ax.set_xlim(xlim)
if ylim:
plot.ax.set_ylim(ylim)
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax, x=False)
# save and close
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plotspectrogram(sequencelist, outfile, epoch=0, deltaT=1, f0=0, deltaF=1,\
t0=0, ydata=None, **kwargs):
"""
Plots a list of REAL?VectorSequences on a time-frequency-amplitude colour
map. The epochand deltaT arguments define the spacing in the x direction
for the given VectorSequence, and similarly f0 and deltaF in the
y-direction. If a list of VectorSequences is given, any of these arguments
can be in list form, one for each sequence.
ydata can be given as to explicitly define the frequencies at which the
sequences are sampled.
"""
# construct list of series
if not hasattr(sequencelist, "__contains__"):
sequencelist = [sequencelist]
numseq = len(sequencelist)
# format variables
if isinstance(epoch, numbers.Number) or isinstance(epoch, lal.LIGOTimeGPS):
epoch = [epoch] * numseq
epoch = map(float, epoch)
if not len(epoch) == numseq:
raise ValueError("Wrong number of epoch arguments given.")
if isinstance(deltaT, numbers.Number):
deltaT = [deltaT] * numseq
deltaT = map(float, deltaT)
if not len(deltaT) == numseq:
raise ValueError("Wrong number of deltaT arguments given.")
if not ydata is None:
if isinstance(f0, numbers.Number):
f0 = [f0] * numseq
f0 = map(float, f0)
if not len(f0) == numseq:
raise ValueError("Wrong number of f0 arguments given.")
if isinstance(deltaF, numbers.Number):
deltaF = [deltaF] * numseq
deltaF = map(float, deltaF)
if not len(deltaF) == numseq:
raise ValueError("Wrong number of deltaF arguments given.")
# get limits
xlim = kwargs.pop("xlim", None)
ylim = kwargs.pop("ylim", None)
colorlim = kwargs.pop("colorlim", None)
if xlim:
start, end = xlim
else:
start = min(epoch)
end = max(e + l.length * dt\
for e,l,dt in zip(epoch, sequencelist, deltaT))
if not ydata is None and not ylim:
ylim = [ydata.min(), ydata.max()]
# get axis scales
logx = kwargs.pop("logx", False)
logy = kwargs.pop("logy", False)
logcolor = kwargs.pop("logcolor", False)
# get legend loc
loc = kwargs.pop("loc", 0)
alpha = kwargs.pop("alpha", 0.8)
# get colorbar options
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# get savefig option
bbox_inches = kwargs.pop("bbox_inches", None)
#
# get labels
#
xlabel = kwargs.pop("xlabel", None)
if xlabel:
unit = 1
if not xlabel:
unit, timestr = plotutils.time_axis_unit(end - start)
if not t0:
t0 = start
t0 = lal.LIGOTimeGPS(t0)
if int(t0.gpsNanoSeconds) == 0:
xlabel = datetime.datetime(*lal.GPSToUTC(int(t0))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)" % (timestr, xlabel, int(t0))
else:
xlabel = datetime.datetime(*lal.GPSToUTC(t0.gpsSeconds)[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC",".%.3s UTC" % t0.gpsNanoSeconds),\
t0)
t0 = float(t0)
ylabel = kwargs.pop("ylabel", "Frequency (Hz)")
colorlabel = kwargs.pop("colorlabel", "Amplitude")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
#
# restrict data to the correct limits for plotting
#
interpolate = logy and ydata is None
for i, sequence in enumerate(sequencelist):
if interpolate:
# interpolate the data onto a log-scale
sequence, ydata = loginterpolate(sequence, f0[i], deltaF[i])
if logy and ylim:
plotted = (ydata > ylim[0]) & (ydata <= ylim[1])
newVectorLength = int(plotted.sum())
newsequence = lal.CreateREAL8VectorSequence(sequence.length,\
newVectorLength)
for j in range(sequence.length):
newsequence.data[j, :] = sequence.data[j, :][plotted]
del sequence
sequencelist[i] = newsequence
if len(sequencelist) and logy and ylim:
ydata = ydata[plotted]
#
# format bins
#
xbins = []
for i in range(numseq):
xmin = epoch[i]
xmax = epoch[i] + sequencelist[i].length * deltaT[i]
xbins.append(rate.LinearBins(float(xmin-t0)/unit, float(xmax-t0)/unit,\
2))
ybins = []
for i in range(numseq):
if ydata is not None:
ydata = numpy.asarray(ydata)
ymin = ydata.min()
ymax = ydata.max()
else:
ymin = f0[i]
ymax = f0[i] + sequencelist[i].vectorLength * deltaF[i]
if logy:
if ymin == 0:
ymin = deltaF[i]
ybins.append(rate.LogarithmicBins(ymin, ymax, 2))
else:
ybins.append(rate.LinearBins(ymin, ymax, 2))
#
# plot
#
kwargs.setdefault("interpolation", "kaiser")
plot = plotutils.ImagePlot(xlabel=xlabel, ylabel=ylabel, title=title,\
subtitle=subtitle, colorlabel=colorlabel)
for sequence, x, y in zip(sequencelist, xbins, ybins):
data = numpy.ma.masked_where(numpy.isnan(sequence.data), sequence.data,\
copy=False)
plot.add_content(data.T, x, y, **kwargs)
# finalize
plot.finalize(colorbar=True, logcolor=logcolor, minorticks=True,\
clim=colorlim)
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
# set logscale
if logx:
plot.ax.xaxis.set_scale("log")
if logy:
plot.ax.yaxis.set_scale("log")
plot.ax._update_transScale()
# format axes
if xlim:
xlim = (numpy.asarray(xlim).astype(float) - t0) / unit
plot.ax.set_xlim(xlim)
if ylim:
plot.ax.set_ylim(ylim)
# set grid and ticks
plot.ax.grid(True, which="both")
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax)
# save and close
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plottable(lsctable, outfile, xcolumn="time", ycolumn="snr",\
colorcolumn=None, rankcolumn=None, t0=None, **kwargs):
"""
Plot any column of a valid LigoLW table against any other, coloured by any
other, or plot all the same if you're that way inclined. Multiple tables
can be given for any non-coloured plot.
"time" as a column means the output of get_peak for Burst tables, get_end
for Inspiral tables, and get_start for ringdown tables
Arguments:
tables : [ dict | glue.ligolw.table.Table ]
dict of ("name", table) pairs, or single LigoLW tables
outfile : string
string path for output plot
Keyword arguments:
xcolumn : string
valid column of triggers table to plot on x-axis
ycolumn : string
valid column of triggers table to plot on y-axis
zcolumn : string
valid column of triggers table to use for colorbar (optional).
"""
# work out dictionary or table
if isinstance(lsctable, table.Table):
tables = {"_": lsctable}
else:
tables = lsctable
tablenames = tables.keys()
tables = [tables[n] for n in tablenames]
# get axis limits
xlim = kwargs.pop('xlim', None)
ylim = kwargs.pop('ylim', None)
zlim = kwargs.pop('zlim', None)
colorlim = kwargs.pop('colorlim', None)
if zlim and not colorlim:
colorlim = zlim
# set up columns
columns = list(map(str.lower, [xcolumn, ycolumn]))
if colorcolumn:
columns.append(colorcolumn.lower())
if rankcolumn:
columns.append(rankcolumn.lower())
else:
columns.append(colorcolumn.lower())
# set up limits
limits = [xlim, ylim, zlim, None]
# get zero
if "time" in columns and not t0:
if xlim:
t0 = float(xlim[0])
else:
t0 = numpy.infty
for t in tables:
timedata = get_column(t, "time").astype(float)
if len(timedata):
t0 = min(t0, timedata.min())
if numpy.isinf(t0):
t0 = 0
t0 = int(t0)
#
# get data
#
# extract columns
data = list()
for i, name in enumerate(tablenames):
data.append(list())
for c in columns:
c = c.lower()
if ((c not in tables[i].columnnames and c != "time")
and not hasattr(tables[i], "get_%s" % c.lower())):
raise RuntimeError("Column '%s' not found in table '%s'."\
% (c,name))
data[-1].append(get_column(tables[i], c.lower()).astype(float))
if not len(data[-1][-1].shape)\
or data[-1][-1].shape[0] != len(tables[i]):
raise AttributeError("No data loaded for column \"%s\" and "\
"table \"%s\"" % (c, name))
# add our own limits
for i in range(len(columns)):
if not limits[i]:
mins = [data[j][i].min() for j in range(len(tablenames))\
if len(data[j][i].shape) and data[j][i].shape[0] != 0]
if len(mins):
lmin = min(mins)
lmax = max(data[j][i].max() for j in range(len(tablenames))\
if len(data[j][i]))
limits[i] = [lmin, lmax]
# get time unit
if "time" in columns:
idx = columns.index("time")
if limits[idx]:
unit, timestr = plotutils.time_axis_unit(limits[idx][1]\
- limits[idx][0])
else:
unit, timestr = plotutils.time_axis_unit(1)
# format data
for i, name in enumerate(tablenames):
for j, column in enumerate(columns):
if column == "time":
data[i][j] = (data[i][j] - t0) / unit
if i == 0 and limits[j]:
limits[j] = [float(limits[j][0] - t0) / unit,\
float(limits[j][1] - t0) / unit]
# format a condition to reject triggers outside the plot range
plotted = True
for j, column in enumerate(columns):
if limits[j]:
plotted = plotted & (limits[j][0] <= data[i][j])\
& (limits[j][1] >= data[i][j])
# apply the limits
if not isinstance(plotted, bool):
for j, d in enumerate(data[i]):
data[i][j] = d[plotted]
#
# find loudest event
#
loudest = None
if len(columns) == 4 and len(tablenames) == 1 and len(data[0][0]) > 0:
idx = data[0][3].argmax()
loudest = [data[0][j][idx] for j in range(len(columns))]
#
# get or set the labels
#
label = {}
for i,(label,column) in enumerate(zip(["xlabel", "ylabel", "colorlabel"],\
columns)):
# get given label
l = kwargs.pop(label, None)
if l is None:
# format time string
if column == "time" and limits[i]:
zerostr = datetime.datetime(\
*date.XLALGPSToUTC(LIGOTimeGPS(t0))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
l = "Time (%s) since %s (%s)" % (timestr, zerostr, t0)
# format any other column
else:
l = plotutils.display_name(column)
if label == "xlabel":
xlabel = l
elif label == "ylabel":
ylabel = l
else:
colorlabel = l
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", None)
if subtitle is None and loudest:
subtitle = "Loudest event by %s:" % plotutils.display_name(columns[-1])
for j, c in enumerate(columns):
if j != 0 and c == columns[j - 1]: continue
lstr = loudest[j]
if c == "time":
lstr = lstr * unit + t0
subtitle += " %s=%.2f" % (plotutils.display_name(c), lstr)
else:
loudest = None
#
# get parameters
#
# get axis scales
logx = kwargs.pop("logx", False)
logy = kwargs.pop("logy", False)
logcolor = kwargs.pop("logcolor", False)
# get legend loc
loc = kwargs.pop("loc", 0)
# get colorbar options
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# get savefig option
bbox_inches = kwargs.pop("bbox_inches", "tight")
# get detchar plot params
dqstyle = (kwargs.pop("detchar", False)
or kwargs.pop('detchar_style', False))
dqthresh = (kwargs.pop('dcthreshold', False)
or kwargs.pop('detchar_style_threshold', 10))
# get greyscale param
greyscale = kwargs.pop("greyscale", False)
if greyscale and not kwargs.has_key("cmap"):
kwargs["cmap"] =\
pylab.matplotlib.colors.LinearSegmentedColormap("clrs",\
pylab.matplotlib.cm.hot_r._segmentdata)
elif not kwargs.has_key("cmap"):
kwargs["cmap"] = jet
#
# make the plot
#
tablenames = map(plotutils.display_name, tablenames)
if len(columns) == 2:
plot = plotutils.ScatterPlot(xlabel, ylabel, title, subtitle)
for i in range(len(tablenames)):
plot.add_content(data[i][0], data[i][1], label=tablenames[i],\
**kwargs)
plot.finalize(loc=loc)
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
else:
if dqstyle:
plot = plotutils.DQScatterPlot(xlabel, ylabel, colorlabel,\
title, subtitle)
else:
plot = plotutils.ColorbarScatterPlot(xlabel, ylabel, colorlabel,\
title, subtitle)
plot.add_content(data[0][0], data[0][1], data[0][2],\
label=tablenames[0], **kwargs)
kwargs.pop("cmap", None)
if dqstyle:
plot.finalize(logcolor=logcolor, clim=colorlim, loc=loc,\
threshold=dqthresh)
else:
plot.finalize(logcolor=logcolor, clim=colorlim, loc=loc)
# plot loudest
if loudest:
plot.ax.plot([loudest[0]], [loudest[1]], marker="*", color="gold",\
markersize=15)
# set axes
if logx:
plot.ax.set_xscale("log")
if logy:
plot.ax.set_yscale("log")
plot.ax.autoscale_view(tight=True, scalex=True, scaley=True)
if limits[0]:
plot.ax.set_xlim(limits[0])
if limits[1]:
plot.ax.set_ylim(limits[1])
plot.ax.grid(True, which="both")
if xcolumn == "time":
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax)
# save and close
if greyscale:
plot.ax.patch.set_facecolor("#E8E8E8")
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plotspectrogram(sequencelist, outfile, epoch=0, deltaT=1, f0=0, deltaF=1,\
t0=0, ydata=None, **kwargs):
"""
Plots a list of REAL?VectorSequences on a time-frequency-amplitude colour
map. The epochand deltaT arguments define the spacing in the x direction
for the given VectorSequence, and similarly f0 and deltaF in the
y-direction. If a list of VectorSequences is given, any of these arguments
can be in list form, one for each sequence.
ydata can be given as to explicitly define the frequencies at which the
sequences are sampled.
"""
# construct list of series
if not hasattr(sequencelist, "__contains__"):
sequencelist = [sequencelist]
numseq = len(sequencelist)
# format variables
if isinstance(epoch, numbers.Number) or isinstance(epoch, lal.LIGOTimeGPS):
epoch = [epoch]*numseq
epoch = map(float, epoch)
if not len(epoch) == numseq:
raise ValueError("Wrong number of epoch arguments given.")
if isinstance(deltaT, numbers.Number):
deltaT = [deltaT]*numseq
deltaT = map(float, deltaT)
if not len(deltaT) == numseq:
raise ValueError("Wrong number of deltaT arguments given.")
if not ydata is None:
if isinstance(f0, numbers.Number):
f0 = [f0]*numseq
f0 = map(float, f0)
if not len(f0) == numseq:
raise ValueError("Wrong number of f0 arguments given.")
if isinstance(deltaF, numbers.Number):
deltaF = [deltaF]*numseq
deltaF = map(float, deltaF)
if not len(deltaF) == numseq:
raise ValueError("Wrong number of deltaF arguments given.")
# get limits
xlim = kwargs.pop("xlim", None)
ylim = kwargs.pop("ylim", None)
colorlim = kwargs.pop("colorlim", None)
if xlim:
start,end = xlim
else:
start = min(epoch)
end = max(e + l.length * dt\
for e,l,dt in zip(epoch, sequencelist, deltaT))
if not ydata is None and not ylim:
ylim = [ydata.min(), ydata.max()]
# get axis scales
logx = kwargs.pop("logx", False)
logy = kwargs.pop("logy", False)
logcolor = kwargs.pop("logcolor", False)
# get legend loc
loc = kwargs.pop("loc", 0)
alpha = kwargs.pop("alpha", 0.8)
# get colorbar options
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# get savefig option
bbox_inches = kwargs.pop("bbox_inches", None)
#
# get labels
#
xlabel = kwargs.pop("xlabel", None)
if xlabel:
unit = 1
if not xlabel:
unit, timestr = plotutils.time_axis_unit(end-start)
if not t0:
t0 = start
t0 = lal.LIGOTimeGPS(t0)
if int(t0.gpsNanoSeconds) == 0:
xlabel = datetime.datetime(*lal.GPSToUTC(int(t0))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)" % (timestr, xlabel, int(t0))
else:
xlabel = datetime.datetime(*lal.GPSToUTC(t0.gpsSeconds)[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC",".%.3s UTC" % t0.gpsNanoSeconds),\
t0)
t0 = float(t0)
ylabel = kwargs.pop("ylabel", "Frequency (Hz)")
colorlabel = kwargs.pop("colorlabel", "Amplitude")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
#
# restrict data to the correct limits for plotting
#
interpolate = logy and ydata is None
for i,sequence in enumerate(sequencelist):
if interpolate:
# interpolate the data onto a log-scale
sequence,ydata = loginterpolate(sequence, f0[i], deltaF[i])
if logy and ylim:
plotted = (ydata > ylim[0]) & (ydata <= ylim[1])
newVectorLength = int(plotted.sum())
newsequence = lal.CreateREAL8VectorSequence(sequence.length,\
newVectorLength)
for j in range(sequence.length):
newsequence.data[j,:] = sequence.data[j,:][plotted]
del sequence
sequencelist[i] = newsequence
if len(sequencelist) and logy and ylim:
ydata = ydata[plotted]
#
# format bins
#
xbins = []
for i in range(numseq):
xmin = epoch[i]
xmax = epoch[i] + sequencelist[i].length * deltaT[i]
xbins.append(rate.LinearBins(float(xmin-t0)/unit, float(xmax-t0)/unit,\
2))
ybins = []
for i in range(numseq):
if ydata is not None:
ydata = numpy.asarray(ydata)
ymin = ydata.min()
ymax = ydata.max()
else:
ymin = f0[i]
ymax = f0[i] + sequencelist[i].vectorLength * deltaF[i]
if logy:
if ymin == 0:
ymin = deltaF[i]
ybins.append(rate.LogarithmicBins(ymin, ymax, 2))
else:
ybins.append(rate.LinearBins(ymin, ymax, 2))
#
# plot
#
kwargs.setdefault("interpolation", "kaiser")
plot = plotutils.ImagePlot(xlabel=xlabel, ylabel=ylabel, title=title,\
subtitle=subtitle, colorlabel=colorlabel)
for sequence,x,y in zip(sequencelist, xbins, ybins):
data = numpy.ma.masked_where(numpy.isnan(sequence.data), sequence.data,\
copy=False)
plot.add_content(data.T, x, y, **kwargs)
# finalize
plot.finalize(colorbar=True, logcolor=logcolor, minorticks=True,\
clim=colorlim)
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
# set logscale
if logx:
plot.ax.xaxis.set_scale("log")
if logy:
plot.ax.yaxis.set_scale("log")
plot.ax._update_transScale()
# format axes
if xlim:
xlim = (numpy.asarray(xlim).astype(float)-t0)/unit
plot.ax.set_xlim(xlim)
if ylim:
plot.ax.set_ylim(ylim)
# set grid and ticks
plot.ax.grid(True, which="both")
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax)
# save and close
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plotdutycycle(segdict, outfile, binlength=3600, keys=None, t0=None,\
showmean=False, **kwargs):
"""
Plot the percentage duty cycle each flag in the given
glue.segments.segmentlistdict, binned over the given duration.
"""
# get time limits
xlim = kwargs.pop("xlim", None)
if xlim is None:
try:
extents = [seg.extent() for seg in segdict.values()]
start = min(s[0] for s in extents)
end = max(s[1] for s in extents)
except ValueError:
start = 0
end = 1
xlim = start, end
else:
start, end = xlim
# get unit for plot
unit, timestr = plotutils.time_axis_unit(end - start)
# set xlabel and renomalize time
xlabel = kwargs.pop("xlabel", None)
if not xlabel:
if not t0:
t0 = start
unit, timestr = plotutils.time_axis_unit(end - start)
t0 = LIGOTimeGPS(float(t0))
if t0.nanoseconds == 0:
xlabel = datetime.datetime(*date.XLALGPSToUTC(t0)[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)" % (timestr, xlabel, int(t0))
else:
xlabel = datetime.datetime(*date.XLALGPSToUTC(\
LIGOTimeGPS(t0.seconds))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC", ".%.3s UTC" % t0.nanoseconds),\
t0)
t0 = float(t0)
xlim[0] = (start - t0) / unit
xlim[1] = (end - t0) / unit
ylabel = kwargs.pop("ylabel", "")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
# get other parameters
loc = kwargs.pop("loc", 0)
legalpha = kwargs.pop("alpha", 0.8)
labels_inset = kwargs.pop("labels_inset", False)
bbox_inches = kwargs.pop("bbox_inches", "tight")
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# escape underscores for latex text
if not keys:
keys = segdict.keys()
if pylab.rcParams["text.usetex"]:
newdict = segments.segmentlistdict()
for i, key in enumerate(keys):
newkey = re.sub('(?<!\\\\)_', '\_', key)
keys[i] = newkey
newdict[newkey] = segdict[key]
segdict = newdict
#
# generate duty cycle info
#
# generate bins
binlength = float(binlength)
if int(end - start) % binlength == 0:
numbins = int(end - start) / binlength
else:
numbins = float(end - start) // binlength + 1
bins = numpy.arange(float(start), float(end), binlength) + binlength / 2
duty = dict((key, numpy.zeros(numbins)) for key in keys)
bs = float(start)
for i in range(numbins):
be = float(bs + binlength)
seg = segments.segmentlist([segments.segment(bs, be)])
for key in keys:
duty[key][i] = float(abs(segdict[key] & seg)) / abs(seg) * 100
bs += binlength
if showmean:
mean = dict((key, numpy.zeros(numbins)) for key in keys)
for key in keys:
mean[key] = [duty[key][:i + 1].mean() for i in range(numbins)]
#
# generate plot
#
bins = (bins - t0) / unit
plot = plotutils.BarPlot(xlabel, ylabel, title, subtitle)
for i, key in enumerate(keys):
if showmean:
thislabel = plotutils.display_name(
key) + ' (%.2f\%%)' % (mean[key][-1])
else:
thislabel = plotutils.display_name(key)
plot.add_content(bins, duty[key], label=thislabel,\
alpha=0.8, width=binlength/unit)
plot.finalize(loc=loc, alpha=legalpha)
# add running mean
if showmean:
for i, key in enumerate(keys):
print i, key
plot.ax.plot(bins, mean[key], linestyle='--')
plot.ax.get_legend().get_frame().set_alpha(0.5)
# add colorbar
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
# set limits
plot.ax.autoscale_view(tight=True, scalex=True)
if xlim:
plot.ax.set_xlim(map(float, xlim))
plot.ax.set_ylim(0, 100)
# set grid
plot.ax.grid(True, which="both")
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax, x=False)
# save figure
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
def plotrate(lsctable, outfile, stride=60, column="peak_frequency", bins=[],\
t0=None, **kwargs):
"""
Plot rate versus time for the given ligolw table triggers, binned by the
given bincolumn using the bins list.
Arguments:
lsctable : glue.ligolw.table.Table
LIGOLW table containing a list of triggers
outfile : string
string path for output plot
"""
# get column data
timedata = get_column(lsctable, "time")
ratedata = get_column(lsctable, column)
# sort in time
if timedata.size:
timedata, ratedata = map(numpy.asarray,\
zip(*sorted(zip(timedata,ratedata),\
key=lambda (t,r): t)))
# get x-axis limits
xlim = kwargs.pop("xlim", None)
if xlim:
start, end = xlim
elif timedata.size:
start = timedata.min()
end = timedata.max()
xlim = start, end
else:
start = 0
end = 1
# get other params
logx = kwargs.pop("logx", False)
logy = kwargs.pop("logy", False)
ylim = kwargs.pop("ylim", False)
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
bbox_inches = kwargs.pop("bbox_inches", "tight")
loc = kwargs.pop("loc", 0)
# get bins
xbins = numpy.arange(float(start), float(end), stride)
if not bins:
bins = [[0, float("inf")]]
ybins = [map(float, bin_) for bin_ in bins]
# remove all triggers not in any bins
xextent = (xbins[0], xbins[-1] + stride)
yextent = (ybins[0][0], ybins[-1][-1])
inanybin = (timedata > xextent[0]) & (timedata <= xextent[1])\
& (ratedata > yextent[0]) & (ratedata <= yextent[1])
timedata = timedata[inanybin]
ratedata = ratedata[inanybin]
ydata = numpy.zeros((len(xbins), len(ybins)))
for i, xbin in enumerate(xbins):
# work out index of first trigger outside x bin
try:
idx = (timedata >= xbin + stride).nonzero()[0][0]
# get triggers in this time bin
ratebin = numpy.asarray(sorted(ratedata[:idx]))
break_ = False
# get triggers in this time bin
ratebin = numpy.asarray(sorted(ratedata[:idx]))
except IndexError:
idx = None
ratebin = numpy.asarray(sorted(ratedata))
break_ = True
# loop over ybins
for j, ybin in enumerate(ybins):
# work out index of first trigger outside this y bin
try:
yidx = (ratebin >= ybin[1]).nonzero()[0][0]
except IndexError:
ydata[i][j] = len(ratebin) / stride
break
ydata[i][j] = len(ratebin[:yidx]) / stride
ratebin = ratebin[yidx:]
if break_: break
timedata = timedata[idx:]
xdata = xbins + stride / 2
# set xlabel and renomalize time
if t0:
xdata -= t0
start -= t0
end -= t0
xlabel = kwargs.pop("xlabel", None)
if not xlabel:
if not t0:
t0 = start
start -= t0
end -= t0
xdata -= t0
unit, timestr = plotutils.time_axis_unit(end - start)
start /= unit
end /= unit
xdata = xdata / unit
t0 = LIGOTimeGPS(t0)
if t0.nanoseconds == 0:
xlabel = datetime.datetime(*date.XLALGPSToUTC(LIGOTimeGPS(t0))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
else:
xlabel = datetime.datetime(*date.XLALGPSToUTC(\
LIGOTimeGPS(t0.seconds))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC", ".%.3s UTC" % t0.nanoseconds),\
t0)
ylabel = kwargs.pop("ylabel", "Rate (Hz)")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
#
# plot object
#
plot = plotutils.ScatterPlot(xlabel, ylabel, title, subtitle)
# mask zeros for log plot
if logy:
ydata = numpy.ma.masked_where(ydata == 0, ydata, copy=False)
for i, ybin in enumerate(ybins):
if list(ybin) == [0, numpy.inf]:
label = "_"
else:
label = "%s-%s" % (ybin[0], ybin[1])
plot.add_content(xdata, ydata[:, i], label=label, **kwargs)
plot.finalize(loc=loc)
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
if logx:
plot.ax.set_xscale("log")
if logy:
plot.ax.set_yscale("log")
plot.ax.autoscale_view(tight=True, scalex=True, scaley=True)
plot.ax.set_xlim(start, end)
if ylim:
plot.ax.set_ylim(ylim)
# set grid and ticks
plot.ax.grid(True, which="both")
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax)
# save
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plotsegmentlistdict(segdict, outfile, keys=None, t0=None,\
highlight_segments=None, insetlabels=None,\
**kwargs):
"""
Plots a glue.segments.segmentlistdict using the PlotSegmentsPlot class from
pylal.plotutils.
Arguments:
segdict : glue.segments.segmentlistdict
dictionary of (name, segmentlist) pairs to plot.
outfile : str
filepath to write to
Keyword arguments:
keys : list
ordered list of keys to use in this order on the plot
t0 : float
GPS time around which to zero plot
highlight_segments : glue.segments.segmentlistdict
list of segments to highlight with vertical red dashed lines
insetlabels : [ True | False ]
write labels inside the plot axis
Unnamed keyword arguments:
xlabel : string
label for x-axis
ylabel : string
label for y-axis
title : string
title for plot
subtitle : string
subtitle for plot
bbox_inches : str
use "tight" to get a bounding box tight to the axis.
"""
# get time limits
xlim = kwargs.pop("xlim", None)
if xlim is None:
try:
extents = [seg.extent() for seg in segdict.values()]
start = min(s[0] for s in extents)
end = max(s[1] for s in extents)
except ValueError:
start = 0
end = 1
xlim = start, end
else:
start, end = xlim
# get unit for plot
unit, timestr = plotutils.time_axis_unit(end - start)
# set xlabel and renomalize time
xlabel = kwargs.pop("xlabel", None)
if not xlabel:
if not t0:
t0 = start
unit, timestr = plotutils.time_axis_unit(end - start)
t0 = LIGOTimeGPS(float(t0))
if t0.nanoseconds == 0:
xlabel = datetime.datetime(*date.XLALGPSToUTC(t0)[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)" % (timestr, xlabel, int(t0))
else:
xlabel = datetime.datetime(*date.XLALGPSToUTC(\
LIGOTimeGPS(t0.seconds))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC", ".%.3s UTC" % t0.nanoseconds),\
t0)
t0 = float(t0)
ylabel = kwargs.pop("ylabel", "")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
# get other parameters
labels_inset = kwargs.pop("labels_inset", False)
bbox_inches = kwargs.pop("bbox_inches", "tight")
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# escape underscores for latex text
if not keys:
keys = segdict.keys()
if pylab.rcParams["text.usetex"]:
newdict = segments.segmentlistdict()
for i, key in enumerate(keys):
newkey = re.sub('(?<!\\\\)_', '\_', key)
keys[i] = newkey
newdict[newkey] = segdict[key]
segdict = newdict
# generate plot
plot = plotutils.PlotSegmentsPlot(xlabel, ylabel, title, subtitle,\
t0=t0, dt=unit)
plot.add_content(segdict, keys, **kwargs)
plot.finalize(labels_inset=insetlabels)
# highlight segments
if highlight_segments:
for seg in highlight_segments:
plot.highlight_segment(seg)
# add colorbar
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
# set axis limits
xlim = [float(start - t0) / unit, float(end - t0) / unit]
plot.ax.set_xlim(*xlim)
# set grid
plot.ax.grid(True, which="both")
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax, x=False)
# save
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plotdutycycle(segdict, outfile, binlength=3600, keys=None, t0=None,\
showmean=False, **kwargs):
"""
Plot the percentage duty cycle each flag in the given
glue.segments.segmentlistdict, binned over the given duration.
"""
# get time limits
xlim = kwargs.pop("xlim", None)
if xlim is None:
try:
extents = [seg.extent() for seg in segdict.values()]
start = min(s[0] for s in extents)
end = max(s[1] for s in extents)
except ValueError:
start = 0
end = 1
xlim = start,end
else:
start,end = xlim
# get unit for plot
unit, timestr = plotutils.time_axis_unit(end-start)
# set xlabel and renomalize time
xlabel = kwargs.pop("xlabel", None)
if not xlabel:
if not t0:
t0 = start
unit, timestr = plotutils.time_axis_unit(end-start)
t0 = LIGOTimeGPS(float(t0))
if t0.nanoseconds==0:
xlabel = datetime.datetime(*date.XLALGPSToUTC(t0)[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)" % (timestr, xlabel, int(t0))
else:
xlabel = datetime.datetime(*date.XLALGPSToUTC(\
LIGOTimeGPS(t0.seconds))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC", ".%.3s UTC" % t0.nanoseconds),\
t0)
t0 = float(t0)
xlim[0] = (start - t0)/unit
xlim[1] = (end - t0)/unit
ylabel = kwargs.pop("ylabel", "")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
# get other parameters
loc = kwargs.pop("loc", 0)
legalpha = kwargs.pop("alpha", 0.8)
labels_inset = kwargs.pop("labels_inset", False)
bbox_inches = kwargs.pop("bbox_inches", "tight")
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# escape underscores for latex text
if not keys:
keys = segdict.keys()
if pylab.rcParams["text.usetex"]:
newdict = segments.segmentlistdict()
for i,key in enumerate(keys):
newkey = re.sub('(?<!\\\\)_', '\_', key)
keys[i] = newkey
newdict[newkey] = segdict[key]
segdict = newdict
#
# generate duty cycle info
#
# generate bins
binlength = float(binlength)
if int(end-start) % binlength == 0:
numbins = int(end-start)/binlength
else:
numbins = float(end-start)//binlength+1
bins = numpy.arange(float(start), float(end), binlength) + binlength/2
duty = dict((key, numpy.zeros(numbins)) for key in keys)
bs = float(start)
for i in range(numbins):
be = float(bs + binlength)
seg = segments.segmentlist([segments.segment(bs, be)])
for key in keys:
duty[key][i] = float(abs(segdict[key] & seg))/abs(seg) * 100
bs += binlength
if showmean:
mean = dict((key, numpy.zeros(numbins)) for key in keys)
for key in keys:
mean[key] = [duty[key][:i+1].mean() for i in range(numbins)]
#
# generate plot
#
bins = (bins-t0)/unit
plot = plotutils.BarPlot(xlabel, ylabel, title, subtitle)
for i,key in enumerate(keys):
if showmean:
thislabel = plotutils.display_name(key) + ' (%.2f\%%)' % (mean[key][-1])
else:
thislabel = plotutils.display_name(key)
plot.add_content(bins, duty[key], label=thislabel,\
alpha=0.8, width=binlength/unit)
plot.finalize(loc=loc, alpha=legalpha)
# add running mean
if showmean:
for i,key in enumerate(keys):
print i, key
plot.ax.plot(bins, mean[key], linestyle = '--')
plot.ax.get_legend().get_frame().set_alpha(0.5)
# add colorbar
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
# set limits
plot.ax.autoscale_view(tight=True, scalex=True)
if xlim:
plot.ax.set_xlim(map(float, xlim))
plot.ax.set_ylim(0, 100)
# set grid
plot.ax.grid(True, which="both")
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax, x=False)
# save figure
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
def plotsegmentlistdict(segdict, outfile, keys=None, t0=None,\
highlight_segments=None, insetlabels=None,\
**kwargs):
"""
Plots a glue.segments.segmentlistdict using the PlotSegmentsPlot class from
pylal.plotutils.
Arguments:
segdict : glue.segments.segmentlistdict
dictionary of (name, segmentlist) pairs to plot.
outfile : str
filepath to write to
Keyword arguments:
keys : list
ordered list of keys to use in this order on the plot
t0 : float
GPS time around which to zero plot
highlight_segments : glue.segments.segmentlistdict
list of segments to highlight with vertical red dashed lines
insetlabels : [ True | False ]
write labels inside the plot axis
Unnamed keyword arguments:
xlabel : string
label for x-axis
ylabel : string
label for y-axis
title : string
title for plot
subtitle : string
subtitle for plot
bbox_inches : str
use "tight" to get a bounding box tight to the axis.
"""
# get time limits
xlim = kwargs.pop("xlim", None)
if xlim is None:
try:
extents = [seg.extent() for seg in segdict.values()]
start = min(s[0] for s in extents)
end = max(s[1] for s in extents)
except ValueError:
start = 0
end = 1
xlim = start,end
else:
start,end = xlim
# get unit for plot
unit, timestr = plotutils.time_axis_unit(end-start)
# set xlabel and renomalize time
xlabel = kwargs.pop("xlabel", None)
if not xlabel:
if not t0:
t0 = start
unit, timestr = plotutils.time_axis_unit(end-start)
t0 = LIGOTimeGPS(float(t0))
if t0.nanoseconds==0:
xlabel = datetime.datetime(*date.XLALGPSToUTC(t0)[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)" % (timestr, xlabel, int(t0))
else:
xlabel = datetime.datetime(*date.XLALGPSToUTC(\
LIGOTimeGPS(t0.seconds))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC", ".%.3s UTC" % t0.nanoseconds),\
t0)
t0 = float(t0)
ylabel = kwargs.pop("ylabel", "")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
# get other parameters
labels_inset = kwargs.pop("labels_inset", False)
bbox_inches = kwargs.pop("bbox_inches", "tight")
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# escape underscores for latex text
if not keys:
keys = segdict.keys()
if pylab.rcParams["text.usetex"]:
newdict = segments.segmentlistdict()
for i,key in enumerate(keys):
newkey = re.sub('(?<!\\\\)_', '\_', key)
keys[i] = newkey
newdict[newkey] = segdict[key]
segdict = newdict
# generate plot
plot = plotutils.PlotSegmentsPlot(xlabel, ylabel, title, subtitle,\
t0=t0, dt=unit)
plot.add_content(segdict, keys, **kwargs)
plot.finalize(labels_inset=insetlabels)
# highlight segments
if highlight_segments:
for seg in highlight_segments:
plot.highlight_segment(seg)
# add colorbar
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
# set axis limits
xlim = [float(start-t0)/unit, float(end-t0)/unit]
plot.ax.set_xlim(*xlim)
# set grid
plot.ax.grid(True, which="both")
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax, x=False)
# save
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plottable(lsctable, outfile, xcolumn="time", ycolumn="snr",\
colorcolumn=None, rankcolumn=None, t0=None, **kwargs):
"""
Plot any column of a valid LigoLW table against any other, coloured by any
other, or plot all the same if you're that way inclined. Multiple tables
can be given for any non-coloured plot.
"time" as a column means the output of get_peak for Burst tables, get_end
for Inspiral tables, and get_start for ringdown tables
Arguments:
tables : [ dict | glue.ligolw.table.Table ]
dict of ("name", table) pairs, or single LigoLW tables
outfile : string
string path for output plot
Keyword arguments:
xcolumn : string
valid column of triggers table to plot on x-axis
ycolumn : string
valid column of triggers table to plot on y-axis
zcolumn : string
valid column of triggers table to use for colorbar (optional).
"""
# work out dictionary or table
if isinstance(lsctable, table.Table):
tables = {"_":lsctable}
else:
tables = lsctable
tablenames = tables.keys()
tables = [tables[n] for n in tablenames]
# get axis limits
xlim = kwargs.pop('xlim', None)
ylim = kwargs.pop('ylim', None)
zlim = kwargs.pop('zlim', None)
colorlim = kwargs.pop('colorlim', None)
if zlim and not colorlim:
colorlim = zlim
# set up columns
columns = list(map(str.lower, [xcolumn, ycolumn]))
if colorcolumn:
columns.append(colorcolumn.lower())
if rankcolumn:
columns.append(rankcolumn.lower())
else:
columns.append(colorcolumn.lower())
# set up limits
limits = [xlim, ylim, zlim, None]
# get zero
if "time" in columns and not t0:
if xlim:
t0 = float(xlim[0])
else:
t0 = numpy.infty
for t in tables:
timedata = get_column(t, "time").astype(float)
if len(timedata):
t0 = min(t0, timedata.min())
if numpy.isinf(t0):
t0 = 0
t0 = int(t0)
#
# get data
#
# extract columns
data = list()
for i,name in enumerate(tablenames):
data.append(list())
for c in columns:
c = c.lower()
if ((c not in tables[i].columnnames and c != "time") and not
hasattr(tables[i], "get_%s" % c.lower())):
raise RuntimeError("Column '%s' not found in table '%s'."\
% (c,name))
data[-1].append(get_column(tables[i], c.lower()).astype(float))
if not len(data[-1][-1].shape)\
or data[-1][-1].shape[0] != len(tables[i]):
raise AttributeError("No data loaded for column \"%s\" and "\
"table \"%s\"" % (c, name))
# add our own limits
for i in range(len(columns)):
if not limits[i]:
mins = [data[j][i].min() for j in range(len(tablenames))\
if len(data[j][i].shape) and data[j][i].shape[0] != 0]
if len(mins):
lmin = min(mins)
lmax = max(data[j][i].max() for j in range(len(tablenames))\
if len(data[j][i]))
limits[i] = [lmin, lmax]
# get time unit
if "time" in columns:
idx = columns.index("time")
if limits[idx]:
unit, timestr = plotutils.time_axis_unit(limits[idx][1]\
- limits[idx][0])
else:
unit, timestr = plotutils.time_axis_unit(1)
# format data
for i,name in enumerate(tablenames):
for j,column in enumerate(columns):
if column == "time":
data[i][j] = (data[i][j] - t0) / unit
if i==0 and limits[j]:
limits[j] = [float(limits[j][0] - t0) / unit,\
float(limits[j][1] - t0) / unit]
# format a condition to reject triggers outside the plot range
plotted = True
for j,column in enumerate(columns):
if limits[j]:
plotted = plotted & (limits[j][0] <= data[i][j])\
& (limits[j][1] >= data[i][j])
# apply the limits
if not isinstance(plotted, bool):
for j,d in enumerate(data[i]):
data[i][j] = d[plotted]
#
# find loudest event
#
loudest = None
if len(columns) == 4 and len(tablenames) == 1 and len(data[0][0]) > 0:
idx = data[0][3].argmax()
loudest = [data[0][j][idx] for j in range(len(columns))]
#
# get or set the labels
#
label = {}
for i,(label,column) in enumerate(zip(["xlabel", "ylabel", "colorlabel"],\
columns)):
# get given label
l = kwargs.pop(label, None)
if l is None:
# format time string
if column == "time" and limits[i]:
zerostr = datetime.datetime(\
*date.XLALGPSToUTC(LIGOTimeGPS(t0))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
l = "Time (%s) since %s (%s)" % (timestr, zerostr, t0)
# format any other column
else:
l = plotutils.display_name(column)
if label == "xlabel":
xlabel = l
elif label == "ylabel":
ylabel = l
else:
colorlabel = l
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", None)
if subtitle is None and loudest:
subtitle = "Loudest event by %s:" % plotutils.display_name(columns[-1])
for j,c in enumerate(columns):
if j!= 0 and c == columns[j-1]: continue
lstr = loudest[j]
if c == "time":
lstr = lstr * unit + t0
subtitle += " %s=%.2f" % (plotutils.display_name(c), lstr)
else:
loudest = None
#
# get parameters
#
# get axis scales
logx = kwargs.pop("logx", False)
logy = kwargs.pop("logy", False)
logcolor = kwargs.pop("logcolor", False)
# get legend loc
loc = kwargs.pop("loc", 0)
# get colorbar options
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
# get savefig option
bbox_inches = kwargs.pop("bbox_inches", "tight")
# get detchar plot params
dqstyle = (kwargs.pop("detchar", False) or
kwargs.pop('detchar_style', False))
dqthresh = (kwargs.pop('dcthreshold', False) or
kwargs.pop('detchar_style_threshold', 10))
# get greyscale param
greyscale = kwargs.pop("greyscale", False)
if greyscale and not kwargs.has_key("cmap"):
kwargs["cmap"] =\
pylab.matplotlib.colors.LinearSegmentedColormap("clrs",\
pylab.matplotlib.cm.hot_r._segmentdata)
elif not kwargs.has_key("cmap"):
kwargs["cmap"] = jet
#
# make the plot
#
tablenames = map(plotutils.display_name, tablenames)
if len(columns) == 2:
plot = plotutils.ScatterPlot(xlabel, ylabel,title, subtitle)
for i in range(len(tablenames)):
plot.add_content(data[i][0], data[i][1], label=tablenames[i],\
**kwargs)
plot.finalize(loc=loc)
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
else:
if dqstyle:
plot = plotutils.DQScatterPlot(xlabel, ylabel, colorlabel,\
title, subtitle)
else:
plot = plotutils.ColorbarScatterPlot(xlabel, ylabel, colorlabel,\
title, subtitle)
plot.add_content(data[0][0], data[0][1], data[0][2],\
label=tablenames[0], **kwargs)
kwargs.pop("cmap", None)
if dqstyle:
plot.finalize(logcolor=logcolor, clim=colorlim, loc=loc,\
threshold=dqthresh)
else:
plot.finalize(logcolor=logcolor, clim=colorlim, loc=loc)
# plot loudest
if loudest:
plot.ax.plot([loudest[0]], [loudest[1]], marker="*", color="gold",\
markersize=15)
# set axes
if logx:
plot.ax.set_xscale("log")
if logy:
plot.ax.set_yscale("log")
plot.ax.autoscale_view(tight=True, scalex=True, scaley=True)
if limits[0]:
plot.ax.set_xlim(limits[0])
if limits[1]:
plot.ax.set_ylim(limits[1])
plot.ax.grid(True, which="both")
if xcolumn == "time":
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax)
# save and close
if greyscale:
plot.ax.patch.set_facecolor("#E8E8E8")
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
def plotrate(lsctable, outfile, stride=60, column="peak_frequency", bins=[],\
t0=None, **kwargs):
"""
Plot rate versus time for the given ligolw table triggers, binned by the
given bincolumn using the bins list.
Arguments:
lsctable : glue.ligolw.table.Table
LIGOLW table containing a list of triggers
outfile : string
string path for output plot
"""
# get column data
timedata = get_column(lsctable, "time")
ratedata = get_column(lsctable, column)
# sort in time
if timedata.size:
timedata, ratedata = map(numpy.asarray,\
zip(*sorted(zip(timedata,ratedata),\
key=lambda (t,r): t)))
# get x-axis limits
xlim = kwargs.pop("xlim", None)
if xlim:
start,end = xlim
elif timedata.size:
start = timedata.min()
end = timedata.max()
xlim = start, end
else:
start = 0
end = 1
# get other params
logx = kwargs.pop("logx", False)
logy = kwargs.pop("logy", False)
ylim = kwargs.pop("ylim", False)
hidden_colorbar = kwargs.pop("hidden_colorbar", False)
bbox_inches = kwargs.pop("bbox_inches", "tight")
loc = kwargs.pop("loc", 0)
# get bins
xbins = numpy.arange(float(start), float(end), stride)
if not bins:
bins = [[0, float("inf")]]
ybins = [map(float, bin_) for bin_ in bins]
# remove all triggers not in any bins
xextent = (xbins[0], xbins[-1]+stride)
yextent = (ybins[0][0], ybins[-1][-1])
inanybin = (timedata > xextent[0]) & (timedata <= xextent[1])\
& (ratedata > yextent[0]) & (ratedata <= yextent[1])
timedata = timedata[inanybin]
ratedata = ratedata[inanybin]
ydata = numpy.zeros((len(xbins), len(ybins)))
for i,xbin in enumerate(xbins):
# work out index of first trigger outside x bin
try:
idx = (timedata >= xbin+stride).nonzero()[0][0]
# get triggers in this time bin
ratebin = numpy.asarray(sorted(ratedata[:idx]))
break_ = False
# get triggers in this time bin
ratebin = numpy.asarray(sorted(ratedata[:idx]))
except IndexError:
idx = None
ratebin = numpy.asarray(sorted(ratedata))
break_ = True
# loop over ybins
for j,ybin in enumerate(ybins):
# work out index of first trigger outside this y bin
try:
yidx = (ratebin >= ybin[1]).nonzero()[0][0]
except IndexError:
ydata[i][j] = len(ratebin)/stride
break
ydata[i][j] = len(ratebin[:yidx])/stride
ratebin = ratebin[yidx:]
if break_: break
timedata = timedata[idx:]
xdata = xbins + stride/2
# set xlabel and renomalize time
if t0:
xdata -= t0
start -= t0
end -= t0
xlabel = kwargs.pop("xlabel", None)
if not xlabel:
if not t0:
t0 = start
start -= t0
end -= t0
xdata -= t0
unit, timestr = plotutils.time_axis_unit(end-start)
start /= unit
end /= unit
xdata = xdata/unit
t0 = LIGOTimeGPS(t0)
if t0.nanoseconds==0:
xlabel = datetime.datetime(*date.XLALGPSToUTC(LIGOTimeGPS(t0))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
else:
xlabel = datetime.datetime(*date.XLALGPSToUTC(\
LIGOTimeGPS(t0.seconds))[:6])\
.strftime("%B %d %Y, %H:%M:%S %ZUTC")
xlabel = "Time (%s) since %s (%s)"\
% (timestr,
xlabel.replace(" UTC", ".%.3s UTC" % t0.nanoseconds),\
t0)
ylabel = kwargs.pop("ylabel", "Rate (Hz)")
title = kwargs.pop("title", "")
subtitle = kwargs.pop("subtitle", "")
#
# plot object
#
plot = plotutils.ScatterPlot(xlabel, ylabel, title, subtitle)
# mask zeros for log plot
if logy:
ydata = numpy.ma.masked_where(ydata==0, ydata, copy=False)
for i,ybin in enumerate(ybins):
if list(ybin) == [0, numpy.inf]:
label = "_"
else:
label = "%s-%s" % (ybin[0], ybin[1])
plot.add_content(xdata, ydata[:,i], label=label, **kwargs)
plot.finalize(loc=loc)
if hidden_colorbar:
plotutils.add_colorbar(plot.ax, visible=False)
if logx:
plot.ax.set_xscale("log")
if logy:
plot.ax.set_yscale("log")
plot.ax.autoscale_view(tight=True, scalex=True, scaley=True)
plot.ax.set_xlim(start, end)
if ylim:
plot.ax.set_ylim(ylim)
# set grid and ticks
plot.ax.grid(True, which="both")
plotutils.set_time_ticks(plot.ax)
plotutils.set_minor_ticks(plot.ax)
# save
plot.savefig(outfile, bbox_inches=bbox_inches,\
bbox_extra_artists=plot.ax.texts)
plot.close()
