https://www.mediawiki.org/wiki/Special:Code/MediaWiki/113494
Revision: 113494
Author: giovanni
Date: 2012-03-09 18:29:56 +0000 (Fri, 09 Mar 2012)
Log Message:
-----------
added signal-to-noise ratio filtering to fitting
Modified Paths:
--------------
trunk/tools/wsor/editor_lifecycle/scripts/fitting
Modified: trunk/tools/wsor/editor_lifecycle/scripts/fitting
===================================================================
--- trunk/tools/wsor/editor_lifecycle/scripts/fitting 2012-03-09 18:29:50 UTC
(rev 113493)
+++ trunk/tools/wsor/editor_lifecycle/scripts/fitting 2012-03-09 18:29:56 UTC
(rev 113494)
@@ -53,6 +53,8 @@
parent.add_argument('-minsize', type=int)
parent.add_argument('-c', '--chop-tail', type=int, default=0, metavar='NUM',
help='remove %(metavar)s tail observations')
+parent.add_argument('-xmax', type=int, help='show only (0,xmax) interval')
+parent.add_argument('-snr', type=float, help='minimum signal-to-noise ratio')
parser = ArgumentParser(description=__doc__)
subparsers = parser.add_subparsers(help='Parametric models supported')
@@ -80,13 +82,16 @@
yy = model(xx)
kwargs['ecolor'] = 'none'
kwargs['ls'] = 'none'
- pp.errorbar(x, y, ye / 2, label=label, **kwargs)
+ kwargs['mfc'] = kwargs.get('color', 'k')
+ kwargs['ms'] = 4
+ pp.errorbar(x, y, ye, label=label, **kwargs)
+# pp.plot(x, y, label=label, **kwargs)
model_label = model.name.split()
if len(model_label) > 1:
model_label[1] = model_label[1][:3] + '.'
model_label = ' '.join(model_label[:2]).capitalize()
c = kwargs.get('color', 'r')
- pp.plot(xx, yy, '--', color=c, label='{} fit'.format(model_label), lw=2.5)
+ pp.plot(xx, yy, '--', color=c, lw=2)
if ns.loglog:
pp.xscale('log')
pp.yscale('log')
@@ -105,6 +110,8 @@
# r /= np.abs(rm)
pp.axhline(y=0, c='k')
kwargs['ls'] = ':'
+ kwargs['lw'] = 2
+ kwargs['ms'] = 4
pp.plot(x, r, label=label, **kwargs)
pp.title('Fit residuals')
pp.xlabel('Days since registration')
@@ -143,13 +150,17 @@
* both : A = y[0] and C = y[-1]
'''
x, y, ye, n = np.loadtxt(data_file, unpack=True)
- x = x[:-ns.chop_tail]
- y = y[:-ns.chop_tail]
- ye = ye[:-ns.chop_tail]
- n = n[:-ns.chop_tail]
- idx = ye > 0
- if minsize:
- idx = idx * (n > minsize)
+ # XXX using the S/N ratio to filter out noisy estimates of the ratio
+ s = ye / np.sqrt(n)
+ snr = y / s
+ idx = snr >= ns.snr
+# x = x[:-ns.chop_tail]
+# y = y[:-ns.chop_tail]
+# ye = ye[:-ns.chop_tail]
+# n = n[:-ns.chop_tail]
+ idx = idx * (ye > 0)
+# if minsize:
+# idx = idx * (n > minsize)
if not np.any(idx):
raise EmptyDataError()
if np.sum(idx) < len(modelclass.__params__):
@@ -157,6 +168,11 @@
x = x[idx]
y = y[idx]
ye = ye[idx]
+ n = n[idx]
+ # XXX <Sat Oct 29 17:30:38 CEST 2011> getting the standard error of the
+ # mean. This should be really computed in in lifecycle.rates and new data
+ # files be produced using mkrates.
+ ye = ye / np.sqrt(n)
model = modelclass()
if constrain in ['head', 'both']:
model.A = y[np.argmin(np.abs(x))]
@@ -177,11 +193,14 @@
def main(ns):
# import matploblib
- from matplotlib.lines import lineMarkers as markers
- markers = dict(filter(
- lambda k : isinstance(k[0],str) and k[1] is not '_draw_nothing',
- markers.items())).keys()
- colors = 'bgcmykw'
+# from matplotlib.lines import lineMarkers as markers
+# markers = dict(filter(
+# lambda k : isinstance(k[0],str) and k[1] is not '_draw_nothing',
+# markers.items())).keys()
+# markers.remove('.')
+# markers.remove(',')
+ markers = 'oD^vs*hHpdv<>'
+ colors = 'brgkcmyw'
data = []
models = []
@@ -199,7 +218,8 @@
continue
data.append((x,y,ye))
models.append(model)
- labels.append(os.path.splitext(f)[0])
+ lab = os.path.splitext(os.path.basename(f))[0]
+ labels.append(lab.replace('_','\\_'))
# plot fits
pp.figure()
@@ -208,6 +228,8 @@
m = markers[i % len(markers)]
c = colors[i % len(colors)]
plotfit(model, x, y, ye, label, marker=m, color=c)
+ if ns.xmax is not None:
+ pp.xlim(0, ns.xmax)
# plot residuals
pp.figure()
@@ -216,6 +238,8 @@
m = markers[i % len(markers)]
c = colors[i % len(colors)]
plotresid(model, x, y, label, marker=m, color=c)
+ if ns.xmax is not None:
+ pp.xlim(0, ns.xmax)
# save figures
if ns.output_file is not None:
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