Jupyter 5、Python 3.6 和 Latex
Jupyter 5, Python 3.6, and Latex
我想使用 Jupyter notebook 来记录我的研究结果。以前，我用过 Python 2.7 和 Jupyter 4 的笔记本，没有任何问题。我最近一直在尝试使用 Anaconda 提供的 Jupyter 5 和 Python 3.6。但是，当我尝试显示热图时，收到错误消息。
用简单的折线图编辑
# -- 编码：utf-8 --
%matplotlib 内联
from future.builtins import *
from future.utils import (viewitems, viewkeys, viewvalues)
import sys
from os import (environ, path)
from collections import OrderedDict
# Numpy and related libraries
import numpy as np
import scipy
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from scipy import (linalg, stats)
from matplotlib import (cm, colors, ticker)
from mpl_toolkits import axes_grid1
from IPython.display import (display, )
# Display full list of DataFrame
pd.set_option("display.max_rows", None)
pd.set_option("display.max_columns", None)
pd.set_option("display.notebook_repr_html",True)
# Update parameters for matplotlib
params = {"text.usetex": True,
"text.latex.unicode": True,
"axes.unicode_minus": True,
}
plt.rcParams.update(params)
pd.set_option("precision", 2)
# This sets reasonable defaults for font size for
# a figure that will go in a paper
sns.set_context("paper")
# Set the font to be serif, rather than sans
sns.set(font='serif')
# Make the background white, and specify the
# specific font family
sns.set_style("white",
{
"font.family": "serif",
"font.serif": ["Times New Roman", "Palatino", "serif"],
"font.sans-serif": ["Arial", "Helvetica"],
"font.monospace": ["Courier New", "Courier"]
})
sns.set_style("ticks")
models = ("calpha", "caside", "ncsc", "polar")
# Simple test case
data = np.random.random(10)
data = pd.Series(data=data, dtype=np.float)
fig, ax = plt.subplots()
data.plot(ax=ax, title="Linear randomness", kind="line", use_index=True)
ax.set_xlabel(r"Time (${\mu}$s)")
ax.set_ylabel("r.m.s.d. (Å)")
ax.xaxis.set_major_locator(ticker.MultipleLocator(0.1))
ax.xaxis.set_major_formatter(ticker.StrMethodFormatter("{x:.0f}"))
ax.yaxis.set_major_formatter(ticker.StrMethodFormatter("{x:.1f}"))
ax.grid()
fig.tight_layout()
但是，我收到以下错误：
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-5-727fbc0d285c> in <module>()
10 ax.yaxis.set_major_formatter(ticker.StrMethodFormatter("{x:.1f}"))
11 ax.grid()
---> 12 fig.tight_layout()
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/figure.py in tight_layout(self, renderer, pad, h_pad, w_pad, rect)
2005 kwargs = get_tight_layout_figure(
2006 self, self.axes, subplotspec_list, renderer,
-> 2007 pad=pad, h_pad=h_pad, w_pad=w_pad, rect=rect)
2008 self.subplots_adjust(**kwargs)
2009
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/tight_layout.py in get_tight_layout_figure(fig, axes_list, subplotspec_list, renderer, pad, h_pad, w_pad, rect)
349 subplot_list=subplot_list,
350 ax_bbox_list=ax_bbox_list,
--> 351 pad=pad, h_pad=h_pad, w_pad=w_pad)
352
353 if rect is not None:
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/tight_layout.py in auto_adjust_subplotpars(fig, renderer, nrows_ncols, num1num2_list, subplot_list, ax_bbox_list, pad, h_pad, w_pad, rect)
127 continue
128
--> 129 tight_bbox_raw = union([ax.get_tightbbox(renderer) for ax in subplots
130 if ax.get_visible()])
131 tight_bbox = TransformedBbox(tight_bbox_raw,
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/tight_layout.py in <listcomp>(.0)
128
129 tight_bbox_raw = union([ax.get_tightbbox(renderer) for ax in subplots
--> 130 if ax.get_visible()])
131 tight_bbox = TransformedBbox(tight_bbox_raw,
132 fig.transFigure.inverted())
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/axes/_base.py in get_tightbbox(self, renderer, call_axes_locator)
3952
3953 if self.title.get_visible():
-> 3954 bb.append(self.title.get_window_extent(renderer))
3955 if self._left_title.get_visible():
3956 bb.append(self._left_title.get_window_extent(renderer))
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/text.py in get_window_extent(self, renderer, dpi)
968 raise RuntimeError('Cannot get window extent w/o renderer')
969
--> 970 bbox, info, descent = self._get_layout(self._renderer)
971 x, y = self.get_unitless_position()
972 x, y = self.get_transform().transform_point((x, y))
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/text.py in _get_layout(self, renderer)
352 tmp, lp_h, lp_bl = renderer.get_text_width_height_descent('lp',
353 self._fontproperties,
--> 354 ismath=False)
355 offsety = (lp_h - lp_bl) * self._linespacing
356
/opt/homebrew/anaconda3/envs/mda-dev/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
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/texmanager.py in get_text_width_height_descent(self, tex, fontsize, renderer)
602 dvifile = self.make_dvi(tex, fontsize)
603 with dviread.Dvi(dvifile, 72 * dpi_fraction) as dvi:
--> 604 page = next(iter(dvi))
605 # A total height (including the descent) needs to be returned.
606 return page.width, page.height + page.descent, page.descent
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in __iter__(self)
247 """
248 while True:
--> 249 have_page = self._read()
250 if have_page:
251 yield self._output()
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _read(self)
308 while True:
309 byte = ord(self.file.read(1)[0])
--> 310 self._dtable[byte](self, byte)
311 if byte == 140: # end of page
312 return True
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in wrapper(self, byte)
164 if state is not None and self.state != state:
165 raise ValueError("state precondition failed")
--> 166 return method(self, *[f(self, byte-min) for f in get_args])
167 if max is None:
168 table[min] = wrapper
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _fnt_def(self, k, c, s, d, a, l)
455 @dispatch(min=243, max=246, args=('olen1', 'u4', 'u4', 'u4', 'u1', 'u1'))
456 def _fnt_def(self, k, c, s, d, a, l):
--> 457 self._fnt_def_real(k, c, s, d, a, l)
458
459 def _fnt_def_real(self, k, c, s, d, a, l):
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _fnt_def_real(self, k, c, s, d, a, l)
460 n = self.file.read(a + l)
461 fontname = n[-l:].decode('ascii')
--> 462 tfm = _tfmfile(fontname)
463 if tfm is None:
464 if six.PY2:
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _tfmfile(texname)
1074
1075 def _tfmfile(texname):
-> 1076 return _fontfile(texname, Tfm, '.tfm', _tfmcache)
1077
1078
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _fontfile(texname, class_, suffix, cache)
1063 pass
1064
-> 1065 filename = find_tex_file(texname + suffix)
1066 if filename:
1067 result = class_(filename)
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in find_tex_file(filename, format)
1043 # https://github.com/matplotlib/matplotlib/issues/633
1044 pipe = subprocess.Popen(cmd, stdout=subprocess.PIPE,
-> 1045 stderr=subprocess.PIPE)
1046 result = pipe.communicate()[0].rstrip()
1047 matplotlib.verbose.report('find_tex_file result: %s' % result,
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
707 c2pread, c2pwrite,
708 errread, errwrite,
--> 709 restore_signals, start_new_session)
710 except:
711 # Cleanup if the child failed starting.
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
1342 if errno_num == errno.ENOENT:
1343 err_msg += ': ' + repr(err_filename)
-> 1344 raise child_exception_type(errno_num, err_msg, err_filename)
1345 raise child_exception_type(err_msg)
1346
FileNotFoundError: [Errno 2] No such file or directory: 'kpsewhich': 'kpsewhich'
我知道 Latex 是使用 mathjax 显示的，但是 anaconda（和 pip，就此而言）在 Python 3.6 中不可用。我什至尝试使用 Python 2.7 的不同内核，但没有成功。如上所述，我之前在 Python 2.7.
中成功使用了旧版本的 Jupyter
任何帮助将不胜感激。
因此，经过大量搜索和修改，问题出在以下几行：
# Update parameters for matplotlib
params = {"text.usetex": True,
"text.latex.unicode": True,
"axes.unicode_minus": True,
}
plt.rcParams.update(params)
显然，在最新版本的Jupyter中不再需要上述参数。删除这些行后，我的图形正确显示并带有适当的 Latex 名称。
我想使用 Jupyter notebook 来记录我的研究结果。以前，我用过 Python 2.7 和 Jupyter 4 的笔记本，没有任何问题。我最近一直在尝试使用 Anaconda 提供的 Jupyter 5 和 Python 3.6。但是，当我尝试显示热图时，收到错误消息。
用简单的折线图编辑 # -- 编码：utf-8 -- %matplotlib 内联
from future.builtins import *
from future.utils import (viewitems, viewkeys, viewvalues)
import sys
from os import (environ, path)
from collections import OrderedDict
# Numpy and related libraries
import numpy as np
import scipy
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from scipy import (linalg, stats)
from matplotlib import (cm, colors, ticker)
from mpl_toolkits import axes_grid1
from IPython.display import (display, )
# Display full list of DataFrame
pd.set_option("display.max_rows", None)
pd.set_option("display.max_columns", None)
pd.set_option("display.notebook_repr_html",True)
# Update parameters for matplotlib
params = {"text.usetex": True,
"text.latex.unicode": True,
"axes.unicode_minus": True,
}
plt.rcParams.update(params)
pd.set_option("precision", 2)
# This sets reasonable defaults for font size for
# a figure that will go in a paper
sns.set_context("paper")
# Set the font to be serif, rather than sans
sns.set(font='serif')
# Make the background white, and specify the
# specific font family
sns.set_style("white",
{
"font.family": "serif",
"font.serif": ["Times New Roman", "Palatino", "serif"],
"font.sans-serif": ["Arial", "Helvetica"],
"font.monospace": ["Courier New", "Courier"]
})
sns.set_style("ticks")
models = ("calpha", "caside", "ncsc", "polar")
# Simple test case
data = np.random.random(10)
data = pd.Series(data=data, dtype=np.float)
fig, ax = plt.subplots()
data.plot(ax=ax, title="Linear randomness", kind="line", use_index=True)
ax.set_xlabel(r"Time (${\mu}$s)")
ax.set_ylabel("r.m.s.d. (Å)")
ax.xaxis.set_major_locator(ticker.MultipleLocator(0.1))
ax.xaxis.set_major_formatter(ticker.StrMethodFormatter("{x:.0f}"))
ax.yaxis.set_major_formatter(ticker.StrMethodFormatter("{x:.1f}"))
ax.grid()
fig.tight_layout()
但是，我收到以下错误：
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-5-727fbc0d285c> in <module>()
10 ax.yaxis.set_major_formatter(ticker.StrMethodFormatter("{x:.1f}"))
11 ax.grid()
---> 12 fig.tight_layout()
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/figure.py in tight_layout(self, renderer, pad, h_pad, w_pad, rect)
2005 kwargs = get_tight_layout_figure(
2006 self, self.axes, subplotspec_list, renderer,
-> 2007 pad=pad, h_pad=h_pad, w_pad=w_pad, rect=rect)
2008 self.subplots_adjust(**kwargs)
2009
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/tight_layout.py in get_tight_layout_figure(fig, axes_list, subplotspec_list, renderer, pad, h_pad, w_pad, rect)
349 subplot_list=subplot_list,
350 ax_bbox_list=ax_bbox_list,
--> 351 pad=pad, h_pad=h_pad, w_pad=w_pad)
352
353 if rect is not None:
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/tight_layout.py in auto_adjust_subplotpars(fig, renderer, nrows_ncols, num1num2_list, subplot_list, ax_bbox_list, pad, h_pad, w_pad, rect)
127 continue
128
--> 129 tight_bbox_raw = union([ax.get_tightbbox(renderer) for ax in subplots
130 if ax.get_visible()])
131 tight_bbox = TransformedBbox(tight_bbox_raw,
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/tight_layout.py in <listcomp>(.0)
128
129 tight_bbox_raw = union([ax.get_tightbbox(renderer) for ax in subplots
--> 130 if ax.get_visible()])
131 tight_bbox = TransformedBbox(tight_bbox_raw,
132 fig.transFigure.inverted())
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/axes/_base.py in get_tightbbox(self, renderer, call_axes_locator)
3952
3953 if self.title.get_visible():
-> 3954 bb.append(self.title.get_window_extent(renderer))
3955 if self._left_title.get_visible():
3956 bb.append(self._left_title.get_window_extent(renderer))
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/text.py in get_window_extent(self, renderer, dpi)
968 raise RuntimeError('Cannot get window extent w/o renderer')
969
--> 970 bbox, info, descent = self._get_layout(self._renderer)
971 x, y = self.get_unitless_position()
972 x, y = self.get_transform().transform_point((x, y))
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/text.py in _get_layout(self, renderer)
352 tmp, lp_h, lp_bl = renderer.get_text_width_height_descent('lp',
353 self._fontproperties,
--> 354 ismath=False)
355 offsety = (lp_h - lp_bl) * self._linespacing
356
/opt/homebrew/anaconda3/envs/mda-dev/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
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/texmanager.py in get_text_width_height_descent(self, tex, fontsize, renderer)
602 dvifile = self.make_dvi(tex, fontsize)
603 with dviread.Dvi(dvifile, 72 * dpi_fraction) as dvi:
--> 604 page = next(iter(dvi))
605 # A total height (including the descent) needs to be returned.
606 return page.width, page.height + page.descent, page.descent
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in __iter__(self)
247 """
248 while True:
--> 249 have_page = self._read()
250 if have_page:
251 yield self._output()
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _read(self)
308 while True:
309 byte = ord(self.file.read(1)[0])
--> 310 self._dtable[byte](self, byte)
311 if byte == 140: # end of page
312 return True
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in wrapper(self, byte)
164 if state is not None and self.state != state:
165 raise ValueError("state precondition failed")
--> 166 return method(self, *[f(self, byte-min) for f in get_args])
167 if max is None:
168 table[min] = wrapper
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _fnt_def(self, k, c, s, d, a, l)
455 @dispatch(min=243, max=246, args=('olen1', 'u4', 'u4', 'u4', 'u1', 'u1'))
456 def _fnt_def(self, k, c, s, d, a, l):
--> 457 self._fnt_def_real(k, c, s, d, a, l)
458
459 def _fnt_def_real(self, k, c, s, d, a, l):
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _fnt_def_real(self, k, c, s, d, a, l)
460 n = self.file.read(a + l)
461 fontname = n[-l:].decode('ascii')
--> 462 tfm = _tfmfile(fontname)
463 if tfm is None:
464 if six.PY2:
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _tfmfile(texname)
1074
1075 def _tfmfile(texname):
-> 1076 return _fontfile(texname, Tfm, '.tfm', _tfmcache)
1077
1078
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in _fontfile(texname, class_, suffix, cache)
1063 pass
1064
-> 1065 filename = find_tex_file(texname + suffix)
1066 if filename:
1067 result = class_(filename)
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/site-packages/matplotlib/dviread.py in find_tex_file(filename, format)
1043 # https://github.com/matplotlib/matplotlib/issues/633
1044 pipe = subprocess.Popen(cmd, stdout=subprocess.PIPE,
-> 1045 stderr=subprocess.PIPE)
1046 result = pipe.communicate()[0].rstrip()
1047 matplotlib.verbose.report('find_tex_file result: %s' % result,
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
707 c2pread, c2pwrite,
708 errread, errwrite,
--> 709 restore_signals, start_new_session)
710 except:
711 # Cleanup if the child failed starting.
/opt/homebrew/anaconda3/envs/mda-dev/lib/python3.6/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
1342 if errno_num == errno.ENOENT:
1343 err_msg += ': ' + repr(err_filename)
-> 1344 raise child_exception_type(errno_num, err_msg, err_filename)
1345 raise child_exception_type(err_msg)
1346
FileNotFoundError: [Errno 2] No such file or directory: 'kpsewhich': 'kpsewhich'
我知道 Latex 是使用 mathjax 显示的，但是 anaconda（和 pip，就此而言）在 Python 3.6 中不可用。我什至尝试使用 Python 2.7 的不同内核，但没有成功。如上所述，我之前在 Python 2.7.
中成功使用了旧版本的 Jupyter任何帮助将不胜感激。
因此，经过大量搜索和修改，问题出在以下几行：
# Update parameters for matplotlib
params = {"text.usetex": True,
"text.latex.unicode": True,
"axes.unicode_minus": True,
}
plt.rcParams.update(params)
显然，在最新版本的Jupyter中不再需要上述参数。删除这些行后，我的图形正确显示并带有适当的 Latex 名称。