def manage(argv, verbose, mapkwargs): for k in argv.keys(): if k in ['main', "_keyorder"]: continue # private keys if k not in authorized_keys: raise Exception('option %s is not recognized' % k) rootnames0 = argv['main'] if rootnames0 == []: rootnames0 = glob.glob(default_rootnames) assert len(rootnames0) # exclude rootnames with no run file rootnames = [] runfiles = [] for rootname in rootnames0: runfile = "%s/_HerrMet.run" % rootname if os.path.exists(runfile): rootnames.append(rootname) runfiles.append(runfile) else: pass #print "%s : %s does not exist" % (rootname, runfile) del rootnames0 assert len(rootnames) and len(rootnames) == len(runfiles) # summarize all files for rootname, runfile in zip(rootnames, runfiles): with RunFile(runfile, verbose=False) as rundb: rundb.summary(head=rootname + " : ") showfun = showme if "-inline" in argv.keys(): showfun = plt.show # more options if np.any([ opt in argv.keys() for opt in "-stats", "-delbad", "-delchains", "-plot" ]): for rootname, runfile in zip(rootnames, runfiles): with RunFile(runfile, verbose=verbose) as rundb: # ------------ print chains stats if "-stats" in argv.keys(): rundb.stats(head=rootname + " : ") # ------------ rm if "-delbad" in argv.keys(): rundb.del_bad(llkmin=argv['-delbad'][0]) if "-delchains" in argv.keys(): rundb.del_chain(chainid=argv['-delchains']) # ------------ plot if "-plot" in argv.keys(): vmin = argv['-plot'][0] if len(argv['-plot']) else None s = rundb.select(''' select CHAINID, group_concat(NITER), group_concat(LLK) from MODELS group by CHAINID ''') plt.figure(figsize=(8, 4)) ax0 = gcf().add_subplot(121) ax1 = gcf().add_subplot(122, sharey=ax0) LLKs = [] for CHAINID, NITER, LLK in s: NITER = np.asarray(NITER.split(','), int) LLK = np.asarray(LLK.split(','), float) ax0.plot(NITER, LLK) ax0.text(NITER[-1], LLK[-1], CHAINID) LLKs = np.concatenate((LLKs, LLK)) ax1.plot(np.sort(LLKs)[::-1]) if vmin is not None: ax0.set_ylim(vmin, 0) ax0.set_xlabel('# iteration') ax0.set_ylabel('log likelihood') ax1.set_xlabel('# rank') ax0.grid(True, linestyle=":") ax1.grid(True, linestyle=":") gcf().suptitle(rootname.split('_HerrMet_')[-1]) showfun() gcf().savefig("%s/_HerrMet.stats.png" % rootname) plt.close(gcf())
def _display_function(rootname, argv, verbose, mapkwargs): """private""" targetfile = "%s/_HerrMet.target" % rootname paramfile = "%s/_HerrMet.param" % rootname runfile = '%s/_HerrMet.run' % rootname pngfile = '%s/_HerrMet.png' % rootname #HerrLininitfile = '%s/_HerrLin.init' % rootname # ------ Initiate the displayer using the target data if exists if "-compact" in argv.keys(): # compact mode which_displayer = DepthDispDisplayCompact else: which_displayer = DepthDispDisplay if os.path.exists(targetfile): rd = which_displayer(targetfile=targetfile) d = makedatacoder( targetfile, which=Datacoder_log) # datacoder based on observations dobs, _ = d.target() else: print "no target file found in %s" % rootname rd = which_displayer() # ------ Display run results if exist if os.path.exists(runfile) and ("-plot" in argv.keys() or "-pdf" in argv.keys()): with RunFile(runfile, verbose=verbose) as rundb: s = rundb.select('select MODELID from MODELS limit 1') if s is not None: # --- display best models if "-plot" in argv.keys(): assert argv["-plot"] == [] or len( argv["-plot"]) == 4 # unexpected argument number if argv["-plot"] == []: plot_mode, plot_limit, plot_llkmin, plot_step = \ default_plot_mode, default_plot_limit, \ default_plot_llkmin, default_plot_step elif len(argv['-plot']) == 4: plot_mode, plot_limit, plot_llkmin, plot_step = argv[ '-plot'] else: raise Exception() print "plot : %s, limit %d, llkmin %f, step %d" % ( plot_mode, plot_limit, plot_llkmin, plot_step), if plot_mode == "best": chainids, weights, llks, ms, ds = \ rundb.getzip(limit=plot_limit, llkmin=plot_llkmin, step=plot_step, algo="METROPOLIS") elif plot_mode == "last": chainids, weights, llks, ms, ds = \ rundb.getlastszip(limit=plot_limit, llkmin=plot_llkmin, step=plot_step, algo="METROPOLIS") else: raise Exception('unexpected plot mode %s' % plot_mode) vmin, vmax = llks.min(), llks.max() # colors = values2colors(llks, vmin=vmin, vmax=vmax, cmap=argv['-cmap']) if "-overdisp" in argv.keys(): """note : recomputing dispersion with another frequency array might result in a completely different dispersion curve in case of root search failure """ waves, types, modes, freqs, _ = ds[0] overwaves, overtypes, overmodes, _, _ = zip(*list( groupbywtm(waves, types, modes, freqs, np.arange(len(freqs)), None, True))) overfreqs = [ freqspace(0.6 * min(freqs), 1.4 * max(freqs), 100, "plog") for _ in xrange(len(overwaves)) ] overwaves, overtypes, overmodes, overfreqs = \ igroupbywtm(overwaves, overtypes, overmodes, overfreqs) for llk, (mms, dds) in zip( llks[::-1], overdisp(ms[::-1], overwaves, overtypes, overmodes, overfreqs, verbose=verbose, **mapkwargs)): # rd.plotmodel(color=clr, alpha=1.0, linewidth=3, *mms) rd.addmodel(colorvalue=llk, *mms) try: # rd.plotdisp(color=clr, alpha=1.0, linewidth=3, *dds) rd.adddisp(colorvalue=llk, *dds) except KeyboardInterrupt: raise except Exception as e: print "Error : could not plot dispersion curve (%s)" % str( e) # cb = makecolorbar(vmin=vmin, vmax=vmax, cmap=argv['-cmap']) # pos = rd.axdisp[-1].get_position() # cax = rd.fig.add_axes((pos.x0, 0.12, pos.width, 0.01)) # rd.fig.colorbar(cb, cax=cax, label="log likelyhood", orientation="horizontal") else: "display the dispersion curves as stored in the database" for i in range(len(llks))[::-1]: # rd.plotmodel(color=colors[i], alpha=1.0, linewidth=3, *ms[i]) # rd.plotdisp(color=colors[i], alpha=1.0, linewidth=3, *ds[i]) rd.addmodel(colorvalue=llks[i], *ms[i]) rd.adddisp(colorvalue=llks[i], *ds[i]) # cb = makecolorbar(vmin=vmin, vmax=vmax, cmap=argv['-cmap']) # pos = rd.axdisp[-1].get_position() # cax = rd.fig.add_axes((pos.x0, 0.12, pos.width, 0.01)) # rd.fig.colorbar(cb, cax=cax, label="log likelyhood", orientation="horizontal") # cax.set_xticklabels(cax.get_xticklabels(), rotation=90., horizontalalignment="center") rd.showdispcoll(vmin=vmin, vmax=vmax, cmap=argv['-cmap'], alpha=1.0, linewidth=3) rd.showdepthcoll(vmin=vmin, vmax=vmax, cmap=argv['-cmap'], alpha=1.0, linewidth=3) rd.colorbar(vmin=vmin, vmax=vmax, cmap=argv['-cmap'], label="log likelyhood", orientation="horizontal") print rd.cax.get_position() rd.cax.set_xticklabels(rd.cax.get_xticklabels(), rotation=90., horizontalalignment="center") # ---- display posterior pdf if "-pdf" in argv.keys(): assert argv["-pdf"] == [] or len( argv["-pdf"]) == 4 # unexpected argument number if argv["-pdf"] == []: pdf_mode, pdf_limit, pdf_llkmin, pdf_step = \ default_pdf_mode, default_pdf_limit, default_pdf_llkmin, default_pdf_step elif len(argv['-pdf']) == 4: pdf_mode, pdf_limit, pdf_llkmin, pdf_step = argv[ '-pdf'] else: raise Exception() print "pdf : %s, limit %d, llkmin %f, step %d" % ( pdf_mode, pdf_limit, pdf_llkmin, pdf_step), if pdf_mode == "best": chainids, weights, llks, ms, ds = \ rundb.getzip(limit=pdf_limit, llkmin=pdf_llkmin, step=pdf_step, algo="METROPOLIS") elif pdf_mode == "last": chainids, weights, llks, ms, ds = \ rundb.getlastszip(limit=pdf_limit, llkmin=pdf_llkmin, step=pdf_step, algo="METROPOLIS") else: raise Exception('unexpected pdf mode %s' % pdf_mode) dms = [ depthmodel_from_arrays(ztop, vp, vs, rh) for ztop, vp, vs, rh in ms ] # display percentiles of model and data pdfs clr = "b" if "-plot" not in argv.keys() else "k" alp = 1.0 if "-plot" not in argv.keys() else 0.5 for p, (vppc, vspc, rhpc, prpc) in \ dmstats1(dms, percentiles=[0.01, 0.16, 0.5, 0.84, 0.99], Ndepth=100, Nvalue=100, weights=weights, **mapkwargs): try: l = 3 if p == 0.5 else 1 for what, where in zip([vppc, vspc, rhpc, prpc], [ rd.axdepth['VP'], rd.axdepth['VS'], rd.axdepth['RH'], rd.axdepth['PR'] ]): if where is not None: what.show(where, color=clr, linewidth=l, alpha=alp) except KeyboardInterrupt: raise except Exception as e: print "Error", str(e) # display the disp pdf for p, (wpc, tpc, mpc, fpc, vpc) in \ dispstats(ds, percentiles=[0.01, 0.16, 0.5, 0.84, 0.99], Ndisp=100, weights=weights, **mapkwargs): try: l = 3 if p == 0.5 else 1 rd.plotdisp(wpc, tpc, mpc, fpc, vpc, dvalues=None, color=clr, alpha=alp, linewidth=l) except KeyboardInterrupt: raise except Exception as e: print "Error", str(e) # ------ if os.path.exists(paramfile): p, _ = load_paramfile(paramfile) showvp, showvs, showrh, showpr = True, True, True, True if isinstance(p, Parameterizer_mZVSVPRH): showpr = False elif isinstance(p, Parameterizer_mZVSPRRH): showvp = False elif isinstance(p, Parameterizer_mZVSPRzRHvp): showvp = showpr = showrh = False elif isinstance(p, Parameterizer_mZVSPRzRHz): showvp = showpr = showrh = False else: raise Exception('') # vplow, vphgh, vslow, vshgh, rhlow, rhhgh, prlow, prhgh = p.boundaries() for what, where in zip(\ [vplow, vphgh, vslow, vshgh, rhlow, rhhgh, prlow, prhgh], [rd.axdepth['VP'], rd.axdepth['VP'], rd.axdepth['VS'], rd.axdepth['VS'], rd.axdepth['RH'], rd.axdepth['RH'], rd.axdepth['PR'], rd.axdepth['PR']]): if where is not None: what.show(where, alpha=1.0, color="k", marker="o--", linewidth=1, markersize=3) zmax = 1.1 * p.inv(p.MINF)[0][-1] if isinstance(p, Parameterizer_mZVSPRzRHvp): rd.axdepth['PR'].plot(p.PRz(np.linspace(0., zmax, 100)), np.linspace(0., zmax, 100), "r--", linewidth=3) legendtext(rd.axdepth['PR'], p.PRzName, loc=4) legendtext(rd.axdepth['RH'], p.RHvpName, loc=4) elif isinstance(p, Parameterizer_mZVSPRzRHz): rd.axdepth['PR'].plot(p.PRz(np.linspace(0., zmax, 100)), np.linspace(0., zmax, 100), "r--", linewidth=3) rd.axdepth['RH'].plot(p.RHz(np.linspace(0., zmax, 100)), np.linspace(0., zmax, 100), "r--", linewidth=3) legendtext(rd.axdepth['PR'], p.PRzName, loc=4) legendtext(rd.axdepth['RH'], p.RHzName, loc=4) rd.set_zlim(np.array([0, zmax])) else: print "call option --param to see prior depth boundaries" # -------------------- if "-m96" in argv.keys(): # plot user data on top for m96 in argv['-m96']: try: dm = depthmodel_from_mod96(m96) dm.vp.show(rd.axdepth['VP'], "m", linewidth=3, label=m96) dm.vs.show(rd.axdepth['VS'], "m", linewidth=3) dm.rh.show(rd.axdepth['RH'], "m", linewidth=3) dm.pr().show(rd.axdepth['PR'], "m", linewidth=3) except KeyboardInterrupt: raise except: #Exception as e: print 'could not read or display %s (reason : %s)' % (m96, str(e)) rd.axdepth['VP'].legend(loc=3) if "-ritt" in argv.keys(): a = AsciiFile('/mnt/labex2/home/max/data/boreholes/GRT1/GRT1.logsonic') for what, where in zip( [a.data['VS'], a.data['VP'], a.data['VP'] / a.data['VS']], [rd.axdepth['VS'], rd.axdepth['VP'], rd.axdepth['PR']]): if where is not None: where.plot(what, a.data['TVD'] / 1000., "m", alpha=0.5) # -------------------- if os.path.exists(targetfile): # plot data on top rd.plotdisp(d.waves, d.types, d.modes, d.freqs, d.inv(dobs), dvalues=d.dvalues, alpha=.5, color="r", linewidth=2) if "-overdisp" in argv.keys(): rd.set_vlim((0.5 * d.values.min(), 1.5 * d.values.max())) rd.set_plim((0.8 / overfreqs.max(), 1.2 / overfreqs.min())) else: rd.set_vlim((0.8 * d.values.min(), 1.2 * d.values.max())) rd.set_plim((0.8 / d.freqs.max(), 1.2 / d.freqs.min())) rd.tick() rd.grid() rd.fig.suptitle(rootname.split('_HerrMet_')[-1]) if "-ftsz" in argv.keys(): chftsz(rd.fig, argv["-ftsz"][0]) else: chftsz(rd.fig, default_fontsize) if "-png" in argv.keys(): dpi = argv['-png'][0] if len(argv['-png']) else default_dpi if verbose: print "writing %s" % pngfile rd.fig.savefig(pngfile, dpi=dpi) elif "-inline" in argv.keys(): plt.show() else: showme() plt.close(rd.fig)
def manage(argv, verbose, mapkwargs): if '-h' in argv.keys() or "-help" in argv.keys(): print(long_help) return for k in argv.keys(): if k in ['main', "_keyorder"]: continue # private keys if k not in authorized_keys: raise Exception('option {} is not recognized'.format(k)) rootnames0 = argv['main'] if rootnames0 == []: rootnames0 = glob.glob(default_rootnames) assert len(rootnames0) # exclude rootnames with no run file rootnames = [] runfiles = [] for rootname in rootnames0: runfile = HERRMETRUNFILE.format(rootname=rootname) if os.path.exists(runfile): rootnames.append(rootname) runfiles.append(runfile) else: pass # print "%s : %s does not exist" % (rootname, runfile) del rootnames0 assert len(rootnames) and len(rootnames) == len(runfiles) # summarize all files for rootname, runfile in zip(rootnames, runfiles): with RunFile(runfile, verbose=False) as rundb: rundb.summary(head=rootname + " : ") showfun = showme if "-inline" in argv.keys(): showfun = plt.show # more options if np.any([opt in argv.keys() for opt in ["-stats", "-delbad", "-delchains", "-plot"]]): fig = None if "-plot" in argv.keys(): fig = plt.figure(figsize=(8, 4)) for rootname, runfile in zip(rootnames, runfiles): with RunFile(runfile, verbose=verbose) as rundb: # ------------ print chains stats if "-stats" in argv.keys(): rundb.stats(head=rootname + " : ") # ------------ rm if "-delbad" in argv.keys(): rundb.del_bad(llkmin=argv['-delbad'][0]) if "-delchains" in argv.keys(): rundb.del_chain(chainid=argv['-delchains']) # ------------ plot if "-plot" in argv.keys(): vmin = argv['-plot'][0] if len(argv['-plot']) else None s = rundb.select(''' select CHAINID, group_concat(NITER), group_concat(LLK) from MODELS group by CHAINID ''') if s is None: warnings.warn('no chains found, if the inversion is running, ' 'please wait for the next commit') continue fig.clf() ax0 = fig.add_subplot(121) ax1 = fig.add_subplot(122, sharey=ax0) LLKs = [] for CHAINID, NITER, LLK in s: NITER = np.asarray(NITER.split(','), int) LLK = np.asarray(LLK.split(','), float) ax0.plot(NITER, LLK) ax0.text(NITER[-1], LLK[-1], CHAINID).set_clip_on(True) LLKs = np.concatenate((LLKs, LLK)) ax1.plot(np.sort(LLKs)[::-1]) if vmin is not None: ax0.set_ylim(vmin, 0) ax0.set_xlabel('# iteration') ax0.set_ylabel('log likelihood') ax1.set_xlabel('# rank') ax0.grid(True, linestyle=":") ax1.grid(True, linestyle=":") fig.suptitle(rootname_to_nodename(rootname)) showfun() statsfile = HERRMETSTATSFILE.format(rootname=rootname) if verbose: print('saving ' + statsfile) fig.savefig(statsfile) if "-plot" in argv.keys(): plt.close(fig)