davidmstraub / flavio-tutorial Goto Github PK

Hi David,
I think there is a problem in the determination of the errors for the FastFit.
You solve:

err_l = brentq(lambda x: -2*fit.log_likelihood([x]) - 1, a=0.03, b=bf['x'])

err_r = brentq(lambda x: -2*fit.log_likelihood([x]) - 1, a=bf['x'], b=0.05)

but we should actually solve Delta Chi^2 == 0, i.e.:

err_l = brentq(lambda x: -2*(fit.log_likelihood([x])-bf['log_likelihood']) - 1 , a=0.03, b=bf['x'])
err_r = brentq(lambda x: -2*(fit.log_likelihood([x])-bf['log_likelihood']) - 1 , a=bf['x'], ##b=0.05)
Best,
Marta

When I try to run this line:
fpl.error_budget_pie(err_bsmumu);

I get this:

`Error in callback <function install_repl_displayhook..post_execute at 0x11402c268> (for post_execute):

CalledProcessError Traceback (most recent call last)
~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/texmanager.py in make_dvi(self, tex, fontsize)
392 cwd=self.texcache,
--> 393 stderr=subprocess.STDOUT)
394 except subprocess.CalledProcessError as exc:

~/anaconda3/envs/myenv/lib/python3.6/subprocess.py in check_output(timeout, *popenargs, **kwargs)
335 return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
--> 336 **kwargs).stdout
337

~/anaconda3/envs/myenv/lib/python3.6/subprocess.py in run(input, timeout, check, *popenargs, **kwargs)
417 raise CalledProcessError(retcode, process.args,
--> 418 output=stdout, stderr=stderr)
419 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '['latex', '-interaction=nonstopmode', '9a9941363900849bf4a11d578a4291c3.tex']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

RuntimeError Traceback (most recent call last)
~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/pyplot.py in post_execute()
148 def post_execute():
149 if matplotlib.is_interactive():
--> 150 draw_all()
151
152 # IPython >= 2

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/_pylab_helpers.py in draw_all(cls, force)
148 for f_mgr in cls.get_all_fig_managers():
149 if force or f_mgr.canvas.figure.stale:
--> 150 f_mgr.canvas.draw_idle()
151
152 atexit.register(Gcf.destroy_all)

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/backend_bases.py in draw_idle(self, *args, **kwargs)
2059 if not self._is_idle_drawing:
2060 with self._idle_draw_cntx():
-> 2061 self.draw(*args, **kwargs)
2062
2063 def draw_cursor(self, event):

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in draw(self)
428 # if toolbar:
429 # toolbar.set_cursor(cursors.WAIT)
--> 430 self.figure.draw(self.renderer)
431 finally:
432 # if toolbar:

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
53 renderer.start_filter()
54
---> 55 return draw(artist, renderer, *args, **kwargs)
56 finally:
57 if artist.get_agg_filter() is not None:

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/figure.py in draw(self, renderer)
1297
1298 mimage._draw_list_compositing_images(
-> 1299 renderer, self, artists, self.suppressComposite)
1300
1301 renderer.close_group('figure')

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
136 if not_composite or not has_images:
137 for a in artists:
--> 138 a.draw(renderer)
139 else:
140 # Composite any adjacent images together

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
53 renderer.start_filter()
54
---> 55 return draw(artist, renderer, *args, **kwargs)
56 finally:
57 if artist.get_agg_filter() is not None:

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/axes/_base.py in draw(self, renderer, inframe)
2435 renderer.stop_rasterizing()
2436
-> 2437 mimage._draw_list_compositing_images(renderer, self, artists)
2438
2439 renderer.close_group('axes')

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
136 if not_composite or not has_images:
137 for a in artists:
--> 138 a.draw(renderer)
139 else:
140 # Composite any adjacent images together

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
53 renderer.start_filter()
54
---> 55 return draw(artist, renderer, *args, **kwargs)
56 finally:
57 if artist.get_agg_filter() is not None:

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/text.py in draw(self, renderer)
713
714 with _wrap_text(self) as textobj:
--> 715 bbox, info, descent = textobj._get_layout(renderer)
716 trans = textobj.get_transform()
717

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/text.py in _get_layout(self, renderer)
306 tmp, lp_h, lp_bl = renderer.get_text_width_height_descent('lp',
307 self._fontproperties,
--> 308 ismath=False)
309 offsety = (lp_h - lp_bl) * self._linespacing
310

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in get_text_width_height_descent(self, s, prop, ismath)
224 fontsize = prop.get_size_in_points()
225 w, h, d = texmanager.get_text_width_height_descent(
--> 226 s, fontsize, renderer=self)
227 return w, h, d
228

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/texmanager.py in get_text_width_height_descent(self, tex, fontsize, renderer)
600 else:
601 # use dviread. It sometimes returns a wrong descent.
--> 602 dvifile = self.make_dvi(tex, fontsize)
603 with dviread.Dvi(dvifile, 72 * dpi_fraction) as dvi:
604 page = next(iter(dvi))

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/texmanager.py in make_dvi(self, tex, fontsize)
398 'Here is the full report generated by LaTeX:\n%s '
399 '\n\n' % (repr(tex.encode('unicode_escape')),
--> 400 exc.output.decode("utf-8"))))
401 mpl.verbose.report(report, 'debug')
402 for fname in glob.glob(basefile + '*'):

RuntimeError: LaTeX was not able to process the following string:
b'lp'

Here is the full report generated by LaTeX:
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=latex)
restricted \write18 enabled.
entering extended mode
(./9a9941363900849bf4a11d578a4291c3.tex
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 22 language(s) loaded.
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/size10.clo))

! LaTeX Error: File `type1cm.sty' not found.

Type X to quit or to proceed,
or enter new name. (Default extension: sty)

Enter file name:
! Emergency stop.
<read *>

l.3 ^^M

No pages of output.
Transcript written on 9a9941363900849bf4a11d578a4291c3.log.

---

CalledProcessError Traceback (most recent call last)
~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/texmanager.py in make_dvi(self, tex, fontsize)
392 cwd=self.texcache,
--> 393 stderr=subprocess.STDOUT)
394 except subprocess.CalledProcessError as exc:

~/anaconda3/envs/myenv/lib/python3.6/subprocess.py in check_output(timeout, *popenargs, **kwargs)
335 return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
--> 336 **kwargs).stdout
337

~/anaconda3/envs/myenv/lib/python3.6/subprocess.py in run(input, timeout, check, *popenargs, **kwargs)
417 raise CalledProcessError(retcode, process.args,
--> 418 output=stdout, stderr=stderr)
419 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '['latex', '-interaction=nonstopmode', '9a9941363900849bf4a11d578a4291c3.tex']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

RuntimeError Traceback (most recent call last)
~/anaconda3/envs/myenv/lib/python3.6/site-packages/IPython/core/formatters.py in call(self, obj)
339 pass
340 else:
--> 341 return printer(obj)
342 # Finally look for special method names
343 method = get_real_method(obj, self.print_method)

~/anaconda3/envs/myenv/lib/python3.6/site-packages/IPython/core/pylabtools.py in (fig)
236
237 if 'png' in formats:
--> 238 png_formatter.for_type(Figure, lambda fig: print_figure(fig, 'png', **kwargs))
239 if 'retina' in formats or 'png2x' in formats:
240 png_formatter.for_type(Figure, lambda fig: retina_figure(fig, **kwargs))

~/anaconda3/envs/myenv/lib/python3.6/site-packages/IPython/core/pylabtools.py in print_figure(fig, fmt, bbox_inches, **kwargs)
120
121 bytes_io = BytesIO()
--> 122 fig.canvas.print_figure(bytes_io, **kw)
123 data = bytes_io.getvalue()
124 if fmt == 'svg':

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/backend_bases.py in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs)
2214 orientation=orientation,
2215 dryrun=True,
-> 2216 **kwargs)
2217 renderer = self.figure._cachedRenderer
2218 bbox_inches = self.figure.get_tightbbox(renderer)

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in print_png(self, filename_or_obj, *args, **kwargs)
505
506 def print_png(self, filename_or_obj, *args, **kwargs):
--> 507 FigureCanvasAgg.draw(self)
508 renderer = self.get_renderer()
509 original_dpi = renderer.dpi

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in draw(self)
428 # if toolbar:
429 # toolbar.set_cursor(cursors.WAIT)
--> 430 self.figure.draw(self.renderer)
431 finally:
432 # if toolbar:

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
53 renderer.start_filter()
54
---> 55 return draw(artist, renderer, *args, **kwargs)
56 finally:
57 if artist.get_agg_filter() is not None:

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/figure.py in draw(self, renderer)
1297
1298 mimage._draw_list_compositing_images(
-> 1299 renderer, self, artists, self.suppressComposite)
1300
1301 renderer.close_group('figure')

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
136 if not_composite or not has_images:
137 for a in artists:
--> 138 a.draw(renderer)
139 else:
140 # Composite any adjacent images together

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
53 renderer.start_filter()
54
---> 55 return draw(artist, renderer, *args, **kwargs)
56 finally:
57 if artist.get_agg_filter() is not None:

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/axes/_base.py in draw(self, renderer, inframe)
2435 renderer.stop_rasterizing()
2436
-> 2437 mimage._draw_list_compositing_images(renderer, self, artists)
2438
2439 renderer.close_group('axes')

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
136 if not_composite or not has_images:
137 for a in artists:
--> 138 a.draw(renderer)
139 else:
140 # Composite any adjacent images together

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
53 renderer.start_filter()
54
---> 55 return draw(artist, renderer, *args, **kwargs)
56 finally:
57 if artist.get_agg_filter() is not None:

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/text.py in draw(self, renderer)
713
714 with _wrap_text(self) as textobj:
--> 715 bbox, info, descent = textobj._get_layout(renderer)
716 trans = textobj.get_transform()
717

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/text.py in _get_layout(self, renderer)
306 tmp, lp_h, lp_bl = renderer.get_text_width_height_descent('lp',
307 self._fontproperties,
--> 308 ismath=False)
309 offsety = (lp_h - lp_bl) * self._linespacing
310

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py in get_text_width_height_descent(self, s, prop, ismath)
224 fontsize = prop.get_size_in_points()
225 w, h, d = texmanager.get_text_width_height_descent(
--> 226 s, fontsize, renderer=self)
227 return w, h, d
228

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/texmanager.py in get_text_width_height_descent(self, tex, fontsize, renderer)
600 else:
601 # use dviread. It sometimes returns a wrong descent.
--> 602 dvifile = self.make_dvi(tex, fontsize)
603 with dviread.Dvi(dvifile, 72 * dpi_fraction) as dvi:
604 page = next(iter(dvi))

~/anaconda3/envs/myenv/lib/python3.6/site-packages/matplotlib/texmanager.py in make_dvi(self, tex, fontsize)
398 'Here is the full report generated by LaTeX:\n%s '
399 '\n\n' % (repr(tex.encode('unicode_escape')),
--> 400 exc.output.decode("utf-8"))))
401 mpl.verbose.report(report, 'debug')
402 for fname in glob.glob(basefile + '*'):

RuntimeError: LaTeX was not able to process the following string:
b'lp'

Here is the full report generated by LaTeX:
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=latex)
restricted \write18 enabled.
entering extended mode
(./9a9941363900849bf4a11d578a4291c3.tex
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 22 language(s) loaded.
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/size10.clo))

! LaTeX Error: File `type1cm.sty' not found.

Type X to quit or to proceed,
or enter new name. (Default extension: sty)

Enter file name:
! Emergency stop.
<read *>

l.3 ^^M

No pages of output.
Transcript written on 9a9941363900849bf4a11d578a4291c3.log.

<matplotlib.figure.Figure at 0x114023da0>`

I have already installed: matplotlib/flavio[plotting]/numpy/scipy