Source code for

import subprocess
import copy
import numpy as np
import os
import tempfile
import shutil

import radvel

print_basis = 'per tc e w k'
units = {'per': 'days',
         'tp': 'JD',
         'tc': 'JD',
         'e': '',
         'w': 'radians',
         'k': 'm s$^{-1}$',
         'logk': '$\\ln{(\\rm m\\ s^{-1})}$',
         'secosw': '',
         'sesinw': '',
         'gamma': 'm s$-1$',
         'jitter': 'm s$-1$',
         'logjit': '$\\ln{(\\rm m\\ s^{-1})}$',
         'jit': '$\\rm m\\ s^{-1}$',
         'dvdt': 'm s$^{-1}$ day$^{-1}$',
         'curv': 'm s$^{-1}$ day$^{-2}$'}

[docs]class RadvelReport(): """Radvel report Class to handle the creation of the radvel summary PDF Args: planet (planet object): planet configuration object loaded in `` using `imp.load_source` post (radvel.posterior): radvel.posterior object containing the best-fit parameters in post.params chains (DataFrame): output DataFrame from a `radvel.mcmc` run """ def __init__(self, planet, post, chains, compstats=None): self.planet = planet = post self.starname = planet.starname self.starname_tex = planet.starname.replace('_', '\_') self.runname = self.starname_tex printpost = copy.deepcopy(post) printpost.params = printpost.params.basis.to_synth(printpost.params) printpost.params = printpost.params.basis.from_synth(printpost.params, print_basis) self.latex_dict = printpost.params.tex_labels() printchains = copy.copy(chains) for p in post.params.keys(): if p not in chains.columns: chains[p] = post.params[p].value self.chains = printpost.params.basis.to_synth(chains, basis_name=planet.fitting_basis) self.chains = printpost.params.basis.from_synth(self.chains, print_basis) self.quantiles = self.chains.quantile([0.159, 0.5, 0.841]) self.compstats = compstats def _preamble(self): return """ \\documentclass{{emulateapj}} \\usepackage{{graphicx,textcomp,fancyhdr,hyperref}} \\begin{{document}} \\pagestyle{{fancy}} \\pagenumbering{{gobble}} \\chead{{Summary of \\texttt{{RadVel}} results for {}}} """.format(self.starname_tex) def _postamble(self): return """ \\lfoot{{\\footnotesize{{report produced by \\texttt{{RadVel}} v{}: \ \\href{{}}{{}}}}}} \\end{{document}}""".format(radvel.__version__)
[docs] def texdoc(self): """TeX for entire document TeX code for the entire output results PDF Returns: string: TeX code for report """ out = self._preamble() + self.tabletex() if os.path.exists(self.runname+"_rv_multipanel.pdf"): out += self.figtex(self.runname+"_rv_multipanel.pdf", caption=self._bestfit_caption()) if os.path.exists(self.runname+"_corner.pdf"): out += self.figtex(self.runname+"_corner.pdf", caption="Posterior distributions for all free parameters.") if os.path.exists(self.runname+"_corner_derived_pars.pdf"): out += self.figtex(self.runname+"_corner_derived_pars.pdf", caption="Posterior distributions for all derived parameters.") out += self._postamble() return out
def tabletex(self, tabtype='all'): return TexTable(self).tex(tabtype=tabtype)
[docs] def figtex(self, infile, caption=""): """Generate TeX for figure Generate TeX to insert a figure into the report Args: infile (string): file name of figure caption (string): (optional) figure caption Returns: string: TeX code """ fstr = """ \\begin{figure*}[!h] \\centering \\includegraphics[height=8.0in,width=6.0in,keepaspectratio]{%s} \\caption{%s} \\end{figure*} """ % (infile, caption) return fstr
def _bestfit_caption(self): cap = """ Best-fit %d-planet Keplerian orbital model for %s. The maximum likelihood model is plotted while the orbital parameters listed in Table \\ref{tab:params} are the median values of the posterior distributions. The thin blue line is the best fit %d-planet model. We add in quadrature the RV jitter term(s) listed in Table \\ref{tab:params} with the measurement uncertainties for all RVs. {\\bf b)} Residuals to the best fit %d-planet model. {\\bf c)} RVs phase-folded to the ephemeris of planet %s. The Keplerian orbital models for all other planets (if any) have been subtracted. The small point colors and symbols are the same as in panel {\\bf a}. Red circles (if present) are the same velocities binned in 0.08 units of orbital phase. The phase-folded model for planet %s is shown as the blue line. """ % (, self.starname_tex,,, chr(int(1)+97), chr(int(1)+97)) for i in range(1, cap += "Panel {\\bf %s)} is the same as panel {\\bf %s)} but for planet %s %s.\n" % (chr(int(i)+99), chr(int(i)+98), self.starname_tex, chr(int(i)+98)) return cap
[docs] def compile(self, pdfname, latex_compiler='pdflatex', depfiles=[]): """Compile radvel report Compile the radvel report from a string containing TeX code and save the resulting PDF to a file. Args: pdfname (string): name of the output PDF file latex_compiler (string): path to latex depfiles (list): list of file names of dependencies needed for LaTex compilation (e.g. figure files) """ texname = os.path.basename(pdfname).split('.')[0] + '.tex' current = os.getcwd() temp = tempfile.mkdtemp() for fname in depfiles: shutil.copy2(os.path.join(current,fname), os.path.join(temp,fname)) os.chdir(temp) f = open(texname, 'w') f.write(self.texdoc()) f.close() try: for i in range(3): # LaTex likes to be compiled a few times # to get the table widths correct proc = subprocess.Popen( [latex_compiler, texname], stdout=subprocess.PIPE, ) proc.communicate() # Let the subprocess complete except OSError: msg = """ WARNING: REPORT: could not run %s. Ensure that %s is in your PATH or pass in the path as an argument """ % (latex_compiler, latex_compiler) print(msg) return shutil.copy(pdfname, current) shutil.copy(texname, current) shutil.rmtree(temp) os.chdir(current)
[docs]class TexTable(RadvelReport): """LaTeX table Class to handle generation of the LaTeX tables within the summary PDF. Args: report ( radvel report object """ def __init__(self, report): = report = self.quantiles = report.quantiles self.fitting_basis = def _header(self): fstr = """ \\begin{deluxetable}{lrrr} \\tablecaption{MCMC Posteriors} \\tablehead{\\colhead{Parameter} & \\colhead{Credible Interval} & \\colhead{Maximum Likelihood} & \\colhead{Units}} \\startdata """ return fstr def _footer(self): fstr = """ \\enddata \\tablenotetext{}{%d links saved} \\tablenotetext{}{Reference epoch for $\\gamma$,$\\dot{\\gamma}$,$\\ddot{\\gamma}$: %15.1f} \\label{tab:params} \\end{deluxetable} """ % (len(, return fstr def _row(self, param, unit): if unit == 'radians': med, low, high = radvel.utils.geterr([param], angular=True) else: med = self.quantiles[param][0.5] low = self.quantiles[param][0.5] - self.quantiles[param][0.159] high = self.quantiles[param][0.841] - self.quantiles[param][0.5] maxlike =[param] tex =[param] low = radvel.utils.round_sig(low) high = radvel.utils.round_sig(high) maxlike, errlow, errhigh = radvel.utils.sigfig(maxlike, low, high) med, errlow, errhigh = radvel.utils.sigfig(med, low, high) if errlow <= 1e-12 or errhigh <= 1e-12: med = maxlike = "$\\equiv$ %s" % round(self.quantiles[param][0.5],4) errfmt = '' else: if errhigh == errlow: errfmt = '$\pm %s$' % (errhigh) else: errfmt = '$^{+%s}_{-%s}$' % (errhigh,errlow) row = "%s & %s %s & %s & %s\\\\\n" % (tex,med,errfmt,maxlike,unit) return row def _data(self, basis, sidehead=None, hline=False): tabledat = "" if hline: tabledat += "\\hline\n" if sidehead is not None: tabledat += "\\sidehead{%s}\n" % sidehead suffixes = ['_'+j for j in] for n in range(1, for p in basis.split(): unit = units.get(p, '') if unit == '': for s in suffixes: if s in p: unit = units.get(p.replace(s, ''), '') break par = p+str(int(n)) try: tabledat += self._row(par, unit) except KeyError: tabledat += self._row(p, unit) return tabledat
[docs] def prior_summary(self): """Summary of priors Summarize the priors in separate table within the report PDF. Returns: string: String containing TeX code for the prior summary table """ out = """ \\begin{deluxetable}{lrr} \\tablecaption{Summary of Priors} \\tablehead{} \\startdata """ texdict = prior_list = for prior in prior_list: out += prior.__str__() + "\\\\\\\\\n" out += """ \\enddata \\end{deluxetable} """ return out
[docs] def tex(self, tabtype='all', compstats=None): """TeX code for table Returns: string: TeX code for the results table in the radvel report. """ # Sort extra params ep = [] order = ['gamma', 'dvdt', 'curv', 'jit'] for o in order: op = [] for p in if o in p: op.append(p) if len(op) == 0: op = [o] [ep.append(i) for i in sorted(op)[::-1]] ep = ' '.join(ep) outstr_params = self._header() + \ self._data(self.fitting_basis, sidehead='\\bf{Modified MCMC Step Parameters}')+\ self._data(print_basis, sidehead='\\bf{Orbital Parameters}', hline=True)+\ self._data(ep, sidehead='\\bf{Other Parameters}', hline=True)+\ self._footer() if tabtype == 'all': outstr = self.tex(tabtype='nplanets', compstats=compstats)+ \ outstr_params + \ self.prior_summary() if tabtype == 'params': outstr = outstr_params if tabtype == 'priors': outstr = self.prior_summary() if tabtype == 'nplanets': outstr = self.comp_table( # Remove duplicate lines from the # step parameters section of the table lines = outstr.split('\n') trimstr = "" for i,line in enumerate(lines): if line not in lines[i+1:] or line.startswith('\\') or line == "": trimstr += line + "\n" return trimstr
[docs] def comp_table(self, statsdict): """Model comparisons Compare models with increasing number of planets Returns: string: String containing TeX code for the model comparison table """ if statsdict is None: return "" n_test = range(len(statsdict)) coldefs = 'r'*len(statsdict) tstr = """ \\begin{deluxetable*}{l%s} \\tablecaption{Model Comparison} \\tablehead{\\colhead{Statistic}""" % coldefs for n in n_test: if n == max(n_test): tstr = tstr + " & \\colhead{{\\bf %d planets (adopted)}}" % n else: tstr = tstr + " & \\colhead{%d planets}" % n tstr += "}\n" tstr += "\\startdata\n\n" statkeys = statsdict[0].keys() for s in statkeys: row = "%s (%s) " % (s, statsdict[0][s][1]) for n in n_test: row += " & %s" % statsdict[n][s][0] row += "\\\\\n" tstr += row tstr += """ \\enddata \\label{tab:comp} \\end{deluxetable*} """ return tstr