Coverage for /usr/local/lib/python3.11/dist-packages/grond/optimisers/plot.py: 12%
282 statements
« prev ^ index » next coverage.py v6.5.0, created at 2023-10-26 16:25 +0000
1import logging
2import numpy as num
3from scipy import signal
5from matplotlib import cm, pyplot as plt
7from pyrocko.guts import Tuple, Float, Int, StringChoice, Bool
8from pyrocko.plot import mpl_margins, mpl_graph_color, mpl_init
10from grond.plot.config import PlotConfig
11from grond.plot.collection import PlotItem
13logger = logging.getLogger('grond.problem.plot')
15guts_prefix = 'grond'
18def fixlim(lo, hi):
19 if lo == hi:
20 return lo - 1.0, hi + 1.0
21 else:
22 return lo, hi
25class SequencePlot(PlotConfig):
26 '''
27 Draws all parameter values evaluated during the optimisation
29 The sequence of all the parameter values is either a function of the
30 optimisation in progress or of the misfit from high to low. This plot can
31 be used to check on convergence or see if model parameters push the given
32 bounds. The color always shows the relative misfit. Relatively high misfits
33 are in cold blue colors and relatively low misfits in red. The last panel
34 gives the corresponding misfit values.
35 '''
37 name = 'sequence'
38 size_cm = Tuple.T(2, Float.T(), default=(14., 6.))
39 misfit_cutoff = Float.T(optional=True)
40 ibootstrap = Int.T(optional=True)
41 sort_by = StringChoice.T(
42 choices=['iteration', 'misfit'],
43 default='iteration')
44 subplot_layout = Tuple.T(2, Int.T(), default=(1, 1))
45 marker_size = Float.T(default=1.5)
46 show_reference = Bool.T(default=True)
48 def make(self, environ):
49 cm = environ.get_plot_collection_manager()
50 history = environ.get_history()
51 optimiser = environ.get_optimiser()
53 mpl_init(fontsize=self.font_size)
54 cm.create_group_mpl(
55 self,
56 self.draw_figures(history, optimiser),
57 title=u'Sequence Plots',
58 section='optimiser',
59 description=u'''
60Sequence plots for all parameters of the optimisation.
62The sequence of all the parameter values is either a function of the
63optimisation in progress or of the misfit from high to low. This plot can be
64used to check on convergence or to see if model parameters push the given
65bounds.
67The color always shows the relative misfit. Relatively high misfits are in
68cold blue colors and relatively low misfits in red. The last panel gives the
69corresponding misfit values.
70''',
71 feather_icon='fast-forward')
73 def draw_figures(self, history, optimiser):
74 misfit_cutoff = self.misfit_cutoff
75 sort_by = self.sort_by
77 problem = history.problem
78 models = history.models
80 npar = problem.nparameters
81 ndep = problem.ndependants
82 fontsize = self.font_size
83 nfx, nfy = self.subplot_layout
85 imodels = num.arange(history.nmodels)
86 bounds = problem.get_combined_bounds()
88 xref = problem.get_reference_model()
90 gms = history.get_primary_chain_misfits()
91 gms_softclip = num.where(gms > 1.0, 0.2 * num.log10(gms) + 1.0, gms)
93 isort = num.argsort(gms)[::-1]
95 if sort_by == 'iteration':
96 imodels = imodels[isort]
97 elif sort_by == 'misfit':
98 imodels = num.arange(imodels.size)
99 else:
100 assert False
102 gms = gms[isort]
103 gms_softclip = gms_softclip[isort]
104 models = models[isort, :]
106 iorder = num.empty_like(isort)
107 iorder = num.arange(iorder.size)
109 if misfit_cutoff is None:
110 ibest = num.ones(gms.size, dtype=bool)
111 else:
112 ibest = gms < misfit_cutoff
114 def config_axes(axes, nfx, nfy, impl, iplot, nplots):
115 if (impl - 1) % nfx != nfx - 1:
116 axes.get_yaxis().tick_left()
118 if (impl - 1) >= (nfx * (nfy - 1)) or iplot >= nplots - nfx:
119 axes.set_xlabel('Iteration')
120 if not (impl - 1) // nfx == 0:
121 axes.get_xaxis().tick_bottom()
122 elif (impl - 1) // nfx == 0:
123 axes.get_xaxis().tick_top()
124 axes.set_xticklabels([])
125 else:
126 axes.get_xaxis().set_visible(False)
128 # nfz = (npar + ndep + 1 - 1) / (nfx*nfy) + 1
129 cmap = cm.YlOrRd
130 cmap = cm.jet
131 msize = self.marker_size
132 axes = None
133 fig = None
134 item_fig = None
135 nfigs = 0
136 alpha = 0.5
137 for ipar in range(npar):
138 impl = ipar % (nfx * nfy) + 1
140 if impl == 1:
141 if item_fig:
142 yield item_fig
143 nfigs += 1
145 fig = plt.figure(figsize=self.size_inch)
146 labelpos = mpl_margins(
147 fig, nw=nfx, nh=nfy,
148 left=7.,
149 right=2.,
150 top=1.,
151 bottom=5.,
152 wspace=7., hspace=2., units=fontsize)
154 item = PlotItem(name='fig_%i' % (nfigs+1))
155 item.attributes['parameters'] = []
156 item_fig = (item, fig)
158 par = problem.parameters[ipar]
160 item_fig[0].attributes['parameters'].append(par.name)
162 axes = fig.add_subplot(nfy, nfx, impl)
163 labelpos(axes, 2.5, 2.0)
165 axes.set_ylabel(par.get_label())
166 axes.get_yaxis().set_major_locator(plt.MaxNLocator(4))
168 config_axes(axes, nfx, nfy, impl, ipar, npar + ndep + 1)
170 axes.set_ylim(*fixlim(*par.scaled(bounds[ipar])))
171 axes.set_xlim(0, history.nmodels)
173 axes.scatter(
174 imodels[ibest], par.scaled(models[ibest, ipar]), s=msize,
175 c=iorder[ibest], edgecolors='none', cmap=cmap, alpha=alpha,
176 rasterized=True)
178 if self.show_reference:
179 axes.axhline(par.scaled(xref[ipar]), color='black', alpha=0.3)
181 for idep in range(ndep):
182 # ifz, ify, ifx = num.unravel_index(ipar, (nfz, nfy, nfx))
183 impl = (npar + idep) % (nfx * nfy) + 1
185 if impl == 1:
186 if item_fig:
187 yield item_fig
188 nfigs += 1
190 fig = plt.figure(figsize=self.size_inch)
191 labelpos = mpl_margins(
192 fig, nw=nfx, nh=nfy,
193 left=7.,
194 right=2.,
195 top=1.,
196 bottom=5.,
197 wspace=7., hspace=2., units=fontsize)
199 item = PlotItem(name='fig_%i' % (nfigs+1))
200 item.attributes['parameters'] = []
202 item_fig = (item, fig)
204 par = problem.dependants[idep]
205 item_fig[0].attributes['parameters'].append(par.name)
207 axes = fig.add_subplot(nfy, nfx, impl)
208 labelpos(axes, 2.5, 2.0)
210 axes.set_ylabel(par.get_label())
211 axes.get_yaxis().set_major_locator(plt.MaxNLocator(4))
213 config_axes(axes, nfx, nfy, impl, npar + idep, npar + ndep + 1)
215 axes.set_ylim(*fixlim(*par.scaled(bounds[npar + idep])))
216 axes.set_xlim(0, history.nmodels)
218 ys = problem.make_dependant(models[ibest, :], par.name)
219 axes.scatter(
220 imodels[ibest], par.scaled(ys), s=msize, c=iorder[ibest],
221 edgecolors='none', cmap=cmap, alpha=alpha, rasterized=True)
223 if self.show_reference:
224 y = problem.make_dependant(xref, par.name)
225 axes.axhline(par.scaled(y), color='black', alpha=0.3)
227 impl = (npar + ndep) % (nfx * nfy) + 1
228 if impl == 1:
229 if item_fig:
230 yield item_fig
231 nfigs += 1
233 fig = plt.figure(figsize=self.size_inch)
234 labelpos = mpl_margins(
235 fig, nw=nfx, nh=nfy,
236 left=7.,
237 right=2.,
238 top=1.,
239 bottom=5.,
240 wspace=7., hspace=2., units=fontsize)
242 item = PlotItem(name='fig_%i' % (nfigs+1))
243 item.attributes['parameters'] = []
245 item_fig = (item, fig)
247 axes = fig.add_subplot(nfy, nfx, impl)
248 labelpos(axes, 2.5, 2.0)
250 config_axes(axes, nfx, nfy, impl, npar + ndep, npar + ndep + 1)
252 axes.set_ylim(0., 1.5)
253 axes.set_yticks([0., 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4])
254 axes.set_yticklabels(
255 ['0.0', '0.2', '0.4', '0.6', '0.8', '1', '10', '100'])
257 axes.scatter(
258 imodels[ibest], gms_softclip[ibest], c=iorder[ibest],
259 s=msize, edgecolors='none', cmap=cmap, alpha=alpha)
261 axes.axhspan(1.0, 1.5, color=(0.8, 0.8, 0.8), alpha=0.2)
262 axes.axhline(1.0, color=(0.5, 0.5, 0.5), zorder=2)
264 axes.set_xlim(0, history.nmodels)
265 axes.set_xlabel('Iteration')
267 axes.set_ylabel('Misfit')
269 yield item_fig
270 nfigs += 1
273class ContributionsPlot(PlotConfig):
274 ''' Relative contribution of single targets to the global misfit
275 '''
277 name = 'contributions'
278 size_cm = Tuple.T(2, Float.T(), default=(21., 14.9))
280 def make(self, environ):
281 cm = environ.get_plot_collection_manager()
282 history = environ.get_history()
283 optimiser = environ.get_optimiser()
284 dataset = environ.get_dataset()
286 environ.setup_modelling()
288 mpl_init(fontsize=self.font_size)
289 cm.create_group_mpl(
290 self,
291 self.draw_figures(dataset, history, optimiser),
292 title=u'Target Contributions',
293 section='solution',
294 feather_icon='thermometer',
295 description=u'''
296Contributions of the targets to the total misfit.
298The relative contribution that each single target has in the global misfit
299result is plotted relative and unscales as a function of global misfit
300(descending).
302The target contribution is shown in color-filled curves with the bottom curve
303on the bottom and the best-fit target on top. This plot can be used to analyse
304the balance of targets in the optimisations. For ideal configurations, the
305target contributions are of similar size. If the contribution of a single
306target is much larger than those of all others, the weighting should be
307modified.
308''')
310 def draw_figures(self, dataset, history, optimiser):
312 fontsize = self.font_size
314 fig = plt.figure(figsize=self.size_inch)
315 labelpos = mpl_margins(fig, nw=2, nh=2, w=7., h=5., wspace=2.,
316 hspace=5., units=fontsize)
318 problem = history.problem
319 if not problem:
320 logger.warning('Problem not set.')
321 return []
323 models = history.models
325 if models.size == 0:
326 logger.warning('Empty models vector.')
327 return []
329 for target in problem.targets:
330 target.set_dataset(dataset)
332 imodels = num.arange(history.nmodels)
334 gms = history.get_sorted_primary_misfits()[::-1]
335 isort = history.get_sorted_misfits_idx(chain=0)[::-1]
337 gms **= problem.norm_exponent
338 gms_softclip = num.where(gms > 1.0, 0.1 * num.log10(gms) + 1.0, gms)
340 gcms = problem.combine_misfits(
341 history.misfits,
342 extra_correlated_weights=optimiser.get_correlated_weights(problem),
343 get_contributions=True)
345 gcms = gcms[isort, :]
346 nmisfits = gcms.shape[1] # noqa
348 ncontributions = sum([1 if t.plot_misfits_cumulative else t.nmisfits
349 for t in problem.targets])
350 cum_gcms = num.zeros((history.nmodels, ncontributions))
352 # Squash matrix and sum large targets.nmisifts, eg SatelliteTarget
353 plot_target_labels = []
354 idx = 0
355 idx_cum = 0
356 for itarget, target in enumerate(problem.targets):
357 target_gcms = gcms[:, idx:idx+target.nmisfits]
358 if target.plot_misfits_cumulative:
359 cum_gcms[:, idx_cum] = target_gcms.sum(axis=1)
360 plot_target_labels.append(target.string_id())
361 idx_cum += 1
362 else:
363 cum_gcms[:, idx_cum:idx_cum+target.nmisfits] = target_gcms
364 plot_target_labels.extend(target.misfits_string_ids())
365 idx_cum += target.nmisfits
366 idx += target.nmisfits
368 jsort = num.argsort(cum_gcms[-1, :])[::-1]
370 # ncols = 4
371 # nrows = ((problem.ntargets + 1) - 1) / ncols + 1
373 axes = fig.add_subplot(2, 2, 1)
374 labelpos(axes, 2.5, 2.0)
376 axes.set_ylabel('Relative contribution (smoothed)')
377 axes.set_ylim(0.0, 1.0)
379 axes2 = fig.add_subplot(2, 2, 3, sharex=axes)
380 labelpos(axes2, 2.5, 2.0)
382 axes2.set_xlabel(
383 'Tested model, sorted descending by global misfit value')
385 axes2.set_ylabel('Square of misfit')
387 axes2.set_ylim(0., 1.5)
388 axes2.axhspan(1.0, 1.5, color=(0.8, 0.8, 0.8))
389 axes2.set_yticks(
390 [0., 0.2, 0.4, 0.6, 0.8, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5])
391 axes2.set_yticklabels(
392 ['0.0', '0.2', '0.4', '0.6', '0.8', '1', '10', '100', '1000',
393 '10000', '100000'])
395 axes2.set_xlim(imodels[0], imodels[-1])
397 rel_ms_sum = num.zeros(history.nmodels)
398 rel_ms_smooth_sum = num.zeros(history.nmodels)
399 ms_smooth_sum = num.zeros(history.nmodels)
400 b = num.hanning(min(100, history.nmodels//5))
401 b /= num.sum(b)
402 a = [1]
403 ii = 0
405 for idx in jsort:
406 target_label = plot_target_labels[idx]
407 ms = cum_gcms[:, idx]
409 ms = num.where(num.isfinite(ms), ms, 0.0)
410 if num.all(ms == 0.0):
411 continue
413 rel_ms = ms / gms
415 if b.shape[0] > 5:
416 rel_ms_smooth = signal.filtfilt(b, a, rel_ms)
417 else:
418 rel_ms_smooth = rel_ms
420 ms_smooth = rel_ms_smooth * gms_softclip
422 rel_poly_y = num.concatenate(
423 [rel_ms_smooth_sum[::-1], rel_ms_smooth_sum + rel_ms_smooth])
424 poly_x = num.concatenate([imodels[::-1], imodels])
426 add_args = {}
427 if ii < 20:
428 add_args['label'] = '%s (%.2g)' % (
429 target_label, num.mean(rel_ms[-1]))
431 axes.fill(
432 poly_x, rel_poly_y,
433 alpha=0.5,
434 color=mpl_graph_color(ii),
435 **add_args)
437 poly_y = num.concatenate(
438 [ms_smooth_sum[::-1], ms_smooth_sum + ms_smooth])
440 axes2.fill(poly_x, poly_y, alpha=0.5, color=mpl_graph_color(ii))
442 rel_ms_sum += rel_ms
444 # axes.plot(
445 # imodels, rel_ms_sum, color='black', alpha=0.1, zorder=-1)
447 ms_smooth_sum += ms_smooth
448 rel_ms_smooth_sum += rel_ms_smooth
449 ii += 1
451 axes.legend(
452 title='Contributions (top twenty)',
453 bbox_to_anchor=(1.05, 0.0, 1.0, 1.0),
454 loc='upper left',
455 ncol=1, borderaxespad=0., prop={'size': 9})
457 axes2.plot(imodels, gms_softclip, color='black')
458 axes2.axhline(1.0, color=(0.5, 0.5, 0.5))
460 return [[PlotItem(name='main'), fig]]
463class BootstrapPlot(PlotConfig):
464 '''
465 Sorted misfit (descending) of single bootstrap chains
467 For each bootstrap configuration, all models are sorted according to their
468 misfit value (red lines) and their global misfit value (black line). (They
469 are sorted individually for each line). The best model of every bootstrap
470 configuration (right end model of red lines) is marked as a cross in the
471 global misfit configuration. The horizontal black lines indicate mean and
472 +- standard deviation of the y-axis values of these crosses. If the
473 bootstrap configurations converge to the same region in model-space, all
474 crosses should be close to the right end of the plot. If this is not the
475 case, some bootstrap configurations have converged to very different places
476 in model-space. This would be an indicator that there might be
477 inconsistencies in the observations (maybe due to faulty or noisy or
478 misoriented data). Also the shape of the curve in general can give
479 information. A well-behaved optimisation run has approximately linear
480 functions in this plot. Only at the end they should have a higher downward
481 gradient. This would be the place where the objective functions of the
482 bootstrap start to disagree.
483 '''
485 name = 'bootstrap'
486 size_cm = Tuple.T(2, Float.T(), default=(21., 14.9))
487 show_ticks = Bool.T(default=False)
489 def make(self, environ):
490 cm = environ.get_plot_collection_manager()
491 history = environ.get_history()
492 optimiser = environ.get_optimiser()
493 mpl_init(fontsize=self.font_size)
494 cm.create_group_mpl(
495 self,
496 self.draw_figures(history, optimiser),
497 title=u'Bootstrap Misfit',
498 section='optimiser',
499 feather_icon='trending-down',
500 description=u'''
501Sorted misfit (descending) of single bootstrap chains.
503For each bootstrap configuration, all models are sorted according to their
504misfit value (red lines) and their global misfit value (black line). (They are
505sorted individually for each line). The best model of every bootstrap
506configuration (right end model of red lines) is marked as a cross in the global
507misfit configuration. The horizontal black lines indicate mean and +- standard
508deviation of the y-axis values of these crosses.
510If the bootstrap configurations converge to the same region in model-space, all
511crosses should be close to the right end of the plot. If this is not the case,
512some bootstrap configurations have converged to very different places in
513model-space. This would indicate that there might be inconsistencies in the
514observations (maybe due to faulty or noisy or misoriented data). Also the shape
515of the curve in general can give information. A well-behaved optimisation run
516has approximately linear functions in this plot. Only at the end they should
517have a higher downward gradient. This would be the place where the objective
518functions of the bootstrap start to disagree.
519''')
521 def draw_figures(self, history, optimiser):
523 fig = plt.figure()
525 imodels = num.arange(history.nmodels)
526 gms = history.bootstrap_misfits[:, 0]
528 gms_softclip = num.where(gms > 1.0,
529 0.1 * num.log10(gms) + 1.0,
530 gms)
531 axes = fig.add_subplot(1, 1, 1)
533 ibests = []
534 for ibootstrap in range(history.nchains):
535 # if ibootstrap ==0:
536 # global, no-bootstrapping misfits, chain
537 # gms = history.bootstrap_misfits[:, ibootstrap]
538 # gms_softclip = num.where(gms > 1.0,
539 # 0.1 * num.log10(gms) + 1.0,
540 # gms)
542 bms = history.bootstrap_misfits[:, ibootstrap]
543 isort_bms = num.argsort(bms)[::-1]
544 ibests.append(isort_bms[-1])
546 bms_softclip = num.where(
547 bms > 1.0, 0.1 * num.log10(bms) + 1.0, bms)
548 axes.plot(imodels, bms_softclip[isort_bms], color='red', alpha=0.2)
550 isort = num.argsort(gms)[::-1]
551 iorder = num.empty(isort.size)
552 iorder[isort] = imodels
554 axes.plot(iorder[ibests], gms_softclip[ibests], 'x', color='black')
556 m = num.median(gms_softclip[ibests])
557 s = num.std(gms_softclip[ibests])
558 axes.axhline(m + s, color='black', alpha=0.5)
559 axes.axhline(m, color='black')
560 axes.axhline(m - s, color='black', alpha=0.5)
562 axes.plot(imodels, gms_softclip[isort], color='black')
564 axes.set_xlim(imodels[0], imodels[-1])
565 axes.set_xlabel(
566 'Tested model, sorted descending by global misfit value')
568 return [(PlotItem(name='main'), fig)]
571def get_plot_classes():
572 return [SequencePlot, ContributionsPlot, BootstrapPlot]