# TypeError when I ran the tutorial **URL:** \ **Category:** Support & Discussions\ **Tags:** installation\ **Created:** [September 25, 2023, 8:02pm UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571 "2023-09-25T20:02:29Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![tokoma](https://avatars.discourse-cdn.com/v4/letter/t/c57346/32.png) [@tokoma](https://mne.discourse.group/u/tokoma)\ **Post date:** [September 25, 2023, 8:02pm UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/1 "2023-09-25T20:02:29Z")
In the same code of [Overview of MEG/EEG analysis with MNE-Python — MNE 1.5.1 documentation](https://mne.tools/stable/auto_tutorials/intro/10_overview.html#sphx-glr-auto-tutorials-intro-10-overview-py), when I ran the following lines: ```python evoked_diff = mne.combine_evoked([aud_evoked, vis_evoked], weights=[1, -1]) evoked_diff.pick_types(meg="mag").plot_topo(color="r", legend=False) ``` there was the following warning: ```python NOTE: pick_types() is a legacy function. New code should use inst.pick(...). Removing projector ``` and the following error occurred: ```python TypeError: 'clipbox' must be an instance of matplotlib.transforms.BboxBase or None, not a tuple ``` Should I modify or change the environment of MNE-python ? Version info is as follows: - MNE version: Version: 1.5.1 - operating system: MacOS13.5.2（Ventura） ---
**Author:** ![mscheltienne](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/mscheltienne/32/827_2.png) [@mscheltienne](https://mne.discourse.group/u/mscheltienne)\ **Post date:** [September 26, 2023, 2:03pm UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/2 "2023-09-26T14:03:01Z")
Hello, Can you try to update matplotlib? Mathieu ---
**Author:** ![tokoma](https://avatars.discourse-cdn.com/v4/letter/t/c57346/32.png) [@tokoma](https://mne.discourse.group/u/tokoma)\ **Post date:** [September 26, 2023, 3:22pm UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/3 "2023-09-26T15:22:11Z")
Hello Mathieu, Yes, I’ve already updated matplotlib. ```shell pip show matplotlib Name: matplotlib Version: 3.8.0 Summary: Python plotting package Home-page: https://matplotlib.org Author: John D. Hunter, Michael Droettboom Author-email: matplotlib-users@python.org License: PSF Location: /Users/makoto/opt/anaconda3/envs/myenv/lib/python3.9/site-packages Requires: contourpy, cycler, fonttools, importlib-resources, kiwisolver, numpy, packaging, pillow, pyparsing, python-dateutil Required-by: mglearn, mlxtend, mne, pyvista, qulacsvis, seaborn, vtk ``` ---
**Author:** ![mscheltienne](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/mscheltienne/32/827_2.png) [@mscheltienne](https://mne.discourse.group/u/mscheltienne)\ **Post date:** [September 26, 2023, 8:28pm UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/4 "2023-09-26T20:28:44Z")
Ok, can you share the entire traceback (not just the last line with the `TypeError`) and the output of: ```python import mne mne.sys_info() ``` Mathieu ---
**Author:** ![tokoma](https://avatars.discourse-cdn.com/v4/letter/t/c57346/32.png) [@tokoma](https://mne.discourse.group/u/tokoma)\ **Post date:** [September 27, 2023, 1:57am UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/5 "2023-09-27T01:57:52Z")
Yes, ```python NOTE: pick_types() is a legacy function. New code should use inst.pick(...). Removing projector --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[18], line 2 1 evoked_diff = mne.combine_evoked([aud_evoked, vis_evoked], weights=[1, -1]) ----> 2 evoked_diff.pick_types(meg="mag").plot_topo(color="r", legend=False) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/evoked.py:565, in Evoked.plot_topo(self, layout, layout_scale, color, border, ylim, scalings, title, proj, vline, fig_background, merge_grads, legend, axes, background_color, noise_cov, exclude, show) 539 @copy_function_doc_to_method_doc(plot_evoked_topo) 540 def plot_topo( 541 self, (...) 558 show=True, 559 ): 560 """ 561 Notes 562 ----- 563 .. versionadded:: 0.10.0 564 """ --> 565 return plot_evoked_topo( 566 self, 567 layout=layout, 568 layout_scale=layout_scale, 569 color=color, 570 border=border, 571 ylim=ylim, 572 scalings=scalings, 573 title=title, 574 proj=proj, 575 vline=vline, 576 fig_background=fig_background, 577 merge_grads=merge_grads, 578 legend=legend, 579 axes=axes, 580 background_color=background_color, 581 noise_cov=noise_cov, 582 exclude=exclude, 583 show=show, 584 ) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/viz/evoked.py:1288, in plot_evoked_topo(evoked, layout, layout_scale, color, border, ylim, scalings, title, proj, vline, fig_background, merge_grads, legend, axes, background_color, noise_cov, exclude, show) 1285 raise ValueError("color must be of type tuple, list, str, or None.") 1286 color = cycle([color]) -> 1288 return _plot_evoked_topo( 1289 evoked=evoked, 1290 layout=layout, 1291 layout_scale=layout_scale, 1292 color=color, 1293 border=border, 1294 ylim=ylim, 1295 scalings=scalings, 1296 title=title, 1297 proj=proj, 1298 vline=vline, 1299 fig_facecolor=fig_facecolor, 1300 fig_background=fig_background, 1301 axis_facecolor=axis_facecolor, 1302 font_color=font_color, 1303 merge_channels=merge_grads, 1304 legend=legend, 1305 axes=axes, 1306 exclude=exclude, 1307 show=show, 1308 noise_cov=noise_cov, 1309 ) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/viz/topo.py:1079, in _plot_evoked_topo(evoked, layout, layout_scale, color, border, ylim, scalings, title, proj, vline, hline, fig_facecolor, fig_background, axis_facecolor, font_color, merge_channels, legend, axes, exclude, show, noise_cov) 1077 time_min = min([t[0] for t in times]) 1078 time_max = max([t[-1] for t in times]) -> 1079 fig = _plot_topo( 1080 info=info, 1081 times=[time_min, time_max], 1082 show_func=show_func, 1083 click_func=click_func, 1084 layout=layout, 1085 colorbar=False, 1086 ylim=ylim_, 1087 cmap=None, 1088 layout_scale=layout_scale, 1089 border=border, 1090 fig_facecolor=fig_facecolor, 1091 font_color=font_color, 1092 axis_facecolor=axis_facecolor, 1093 title=title, 1094 x_label="Time (s)", 1095 y_label=y_label, 1096 unified=True, 1097 axes=axes, 1098 ) 1100 add_background_image(fig, fig_background) 1102 if legend is not False: File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/viz/topo.py:334, in _plot_topo(info, times, show_func, click_func, layout, vmin, vmax, ylim, colorbar, border, axis_facecolor, fig_facecolor, cmap, layout_scale, title, x_label, y_label, font_color, unified, img, axes) 331 else: 332 ylim_ = ylim --> 334 show_func(ax, ch_idx, tmin=tmin, tmax=tmax, vmin=vmin, vmax=vmax, ylim=ylim_) 336 if title is not None: 337 plt.figtext(0.03, 0.95, title, color=font_color, fontsize=15, va="top") File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/viz/topo.py:669, in _plot_timeseries_unified(bn, ch_idx, tmin, tmax, vmin, vmax, ylim, data, color, times, vline, x_label, y_label, colorbar, hline, hvline_color) 666 # XXX These calls could probably be made faster by using collections 667 for data_, color_, times_ in zip(data, color, times): 668 data_lines.append( --> 669 ax.plot( 670 bn.x_t + bn.x_s * times_, 671 bn.y_t + bn.y_s * data_[ch_idx], 672 linewidth=0.5, 673 color=color_, 674 clip_on=True, 675 clip_box=tuple(pos), 676 )[0] 677 ) 678 if vline: 679 vline = np.array(vline) * bn.x_s + bn.x_t File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/axes/_axes.py:1721, in Axes.plot(self, scalex, scaley, data, *args, **kwargs) 1478 """ 1479 Plot y versus x as lines and/or markers. 1480 (...) 1718 (``'green'``) or hex strings (``'#008000'``). 1719 """ 1720 kwargs = cbook.normalize_kwargs(kwargs, mlines.Line2D) -> 1721 lines = [*self._get_lines(self, *args, data=data, **kwargs)] 1722 for line in lines: 1723 self.add_line(line) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/axes/_base.py:303, in _process_plot_var_args. __call__ (self, axes, data, *args, **kwargs) 301 this += args[0], 302 args = args[1:] --> 303 yield from self._plot_args( 304 axes, this, kwargs, ambiguous_fmt_datakey=ambiguous_fmt_datakey) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/axes/_base.py:539, in _process_plot_var_args._plot_args(self, axes, tup, kwargs, return_kwargs, ambiguous_fmt_datakey) 537 return list(result) 538 else: --> 539 return [l[0] for l in result] File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/axes/_base.py:539, in (.0) 537 return list(result) 538 else: --> 539 return [l[0] for l in result] File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/axes/_base.py:532, in (.0) 529 else: 530 labels = [label] * n_datasets --> 532 result = (make_artist(axes, x[:, j % ncx], y[:, j % ncy], kw, 533 {**kwargs, 'label': label}) 534 for j, label in enumerate(labels)) 536 if return_kwargs: 537 return list(result) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/axes/_base.py:346, in _process_plot_var_args._makeline(self, axes, x, y, kw, kwargs) 344 default_dict = self._getdefaults(set(), kw) 345 self._setdefaults(default_dict, kw) --> 346 seg = mlines.Line2D(x, y, **kw) 347 return seg, kw File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/lines.py:407, in Line2D. __init__ (self, xdata, ydata, linewidth, linestyle, color, gapcolor, marker, markersize, markeredgewidth, markeredgecolor, markerfacecolor, markerfacecoloralt, fillstyle, antialiased, dash_capstyle, solid_capstyle, dash_joinstyle, solid_joinstyle, pickradius, drawstyle, markevery, **kwargs) 403 self.set_markeredgewidth(markeredgewidth) 405 # update kwargs before updating data to give the caller a 406 # chance to init axes (and hence unit support) --> 407 self._internal_update(kwargs) 408 self.pickradius = pickradius 409 self.ind_offset = 0 File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/artist.py:1219, in Artist._internal_update(self, kwargs) 1212 def _internal_update(self, kwargs): 1213 """ 1214 Update artist properties without prenormalizing them, but generating 1215 errors as if calling `set`. 1216 1217 The lack of prenormalization is to maintain backcompatibility. 1218 """ -> 1219 return self._update_props( 1220 kwargs, "{cls. __name__ }.set() got an unexpected keyword argument " 1221 "{prop_name!r}") File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/artist.py:1195, in Artist._update_props(self, props, errfmt) 1192 if not callable(func): 1193 raise AttributeError( 1194 errfmt.format(cls=type(self), prop_name=k)) -> 1195 ret.append(func(v)) 1196 if ret: 1197 self.pchanged() File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/artist.py:766, in Artist.set_clip_box(self, clipbox) 754 def set_clip_box(self, clipbox): 755 """ 756 Set the artist's clip `.Bbox`. 757 (...) 764 765 """ --> 766 _api.check_isinstance((BboxBase, None), clipbox=clipbox) 767 if clipbox != self.clipbox: 768 self.clipbox = clipbox File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/matplotlib/_api/ __init__.py:91, in check_isinstance(types, **kwargs) 89 names.remove("None") 90 names.append("None") ---> 91 raise TypeError( 92 "{!r} must be an instance of {}, not a {}".format( 93 k, 94 ", ".join(names[:-1]) + " or " + names[-1] 95 if len(names) > 1 else names[0], 96 type_name(type(v)))) TypeError: 'clipbox' must be an instance of matplotlib.transforms.BboxBase or None, not a tuple ``` Here, mne.info(): ```python Platform macOS-13.5.2-arm64-arm-64bit Python 3.9.16 | packaged by conda-forge | (main, Feb 1 2023, 21:38:11) [Clang 14.0.6] Executable /Users/makoto/opt/anaconda3/envs/myenv/bin/python CPU arm (8 cores) Memory 16.0 GB Core ├☑ mne 1.5.1 ├☑ numpy 1.23.5 (OpenBLAS 0.3.20 with 8 threads) ├☑ scipy 1.10.0 ├☑ matplotlib 3.8.0 (backend=module://matplotlib_inline.backend_inline) ├☑ pooch 1.7.0 └☑ jinja2 3.1.2 Numerical (optional) ├☑ sklearn 1.3.0 ├☑ numba 0.57.1 ├☑ nibabel 5.1.0 ├☑ dipy 1.7.0 ├☑ pandas 2.0.3 └☐ unavailable nilearn, openmeeg, cupy Visualization (optional) ├☑ pyvista 0.42.1 (OpenGL 4.1 Metal - 83.1 via Apple M1) ├☑ pyvistaqt 0.11.0 ├☑ vtk 9.2.6 ├☑ ipywidgets 8.1.1 └☐ unavailable qtpy, ipympl, pyqtgraph, mne-qt-browser, trame_client, trame_server, trame_vtk, trame_vuetify Ecosystem (optional) └☐ unavailable mne-bids, mne-nirs, mne-features, mne-connectivity, mne-icalabel, mne-bids-pipeline ``` ---
**Author:** ![mscheltienne](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/mscheltienne/32/827_2.png) [@mscheltienne](https://mne.discourse.group/u/mscheltienne)\ **Post date:** [September 27, 2023, 7:50am UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/6 "2023-09-27T07:50:27Z")
That was fixed in [BUG: Fix bug with clip box setting by larsoner · Pull Request #11999 · mne-tools/mne-python · GitHub](https://github.com/mne-tools/mne-python/pull/11999) which is not yet released in the stable version. It will be fixed in v1.5.2. If you need it now, you can install the maintenance branch that will be used to release v1.5.2: ```python pip install git+https://github.com/mne-tools/mne-python.git@maint/1.5 ``` Mathieu ---
**Author:** ![tokoma](https://avatars.discourse-cdn.com/v4/letter/t/c57346/32.png) [@tokoma](https://mne.discourse.group/u/tokoma)\ **Post date:** [September 28, 2023, 4:39am UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/7 "2023-09-28T04:39:49Z")
Hello The situarion is the same with installing the version: ```python % pip install git+https://github.com/mne-tools/mne-python.git@maint/1.5 Collecting git+https://github.com/mne-tools/mne-python.git@maint/1.5 Cloning https://github.com/mne-tools/mne-python.git (to revision maint/1.5) to /private/var/folders/q9/hjtxkzvd5yd3ql4lqbq_14cw0000gn/T/pip-req-build-2ro169ru Running command git clone --filter=blob:none --quiet https://github.com/mne-tools/mne-python.git /private/var/folders/q9/hjtxkzvd5yd3ql4lqbq_14cw0000gn/T/pip-req-build-2ro169ru Running command git checkout -b maint/1.5 --track origin/maint/1.5 Switched to a new branch 'maint/1.5' branch 'maint/1.5' set up to track 'origin/maint/1.5'. Resolved https://github.com/mne-tools/mne-python.git to commit 77328c09b8f709bee2c702d66cc8935fcf8c83d5 Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: numpy>=1.15.4 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.5.1) (1.23.5) Requirement already satisfied: scipy>=1.6.3 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.5.1) (1.10.0) Requirement already satisfied: matplotlib>=3.4.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.5.1) (3.8.0) Requirement already satisfied: tqdm in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.5.1) (4.65.0) Requirement already satisfied: pooch>=1.5 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.5.1) (1.7.0) Requirement already satisfied: decorator in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.5.1) (5.1.1) Requirement already satisfied: packaging in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.5.1) (23.1) Requirement already satisfied: jinja2 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.5.1) (3.1.2) Requirement already satisfied: contourpy>=1.0.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.0->mne==1.5.1) (1.1.0) Requirement already satisfied: cycler>=0.10 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.0->mne==1.5.1) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.0->mne==1.5.1) (4.40.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.0->mne==1.5.1) (1.4.4) Requirement already satisfied: pillow>=6.2.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.0->mne==1.5.1) (9.5.0) Requirement already satisfied: pyparsing>=2.3.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.0->mne==1.5.1) (3.0.9) Requirement already satisfied: python-dateutil>=2.7 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.0->mne==1.5.1) (2.8.2) Requirement already satisfied: importlib-resources>=3.2.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.0->mne==1.5.1) (6.0.0) Requirement already satisfied: platformdirs>=2.5.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from pooch>=1.5->mne==1.5.1) (3.8.1) Requirement already satisfied: requests>=2.19.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from pooch>=1.5->mne==1.5.1) (2.31.0) Requirement already satisfied: MarkupSafe>=2.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from jinja2->mne==1.5.1) (2.1.3) Requirement already satisfied: zipp>=3.1.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib>=3.4.0->mne==1.5.1) (3.16.0) Requirement already satisfied: six>=1.5 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=3.4.0->mne==1.5.1) (1.16.0) Requirement already satisfied: charset-normalizer<4,>=2 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from requests>=2.19.0->pooch>=1.5->mne==1.5.1) (3.2.0) Requirement already satisfied: idna<4,>=2.5 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from requests>=2.19.0->pooch>=1.5->mne==1.5.1) (3.4) Requirement already satisfied: urllib3<3,>=1.21.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from requests>=2.19.0->pooch>=1.5->mne==1.5.1) (1.26.16) Requirement already satisfied: certifi>=2017.4.17 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from requests>=2.19.0->pooch>=1.5->mne==1.5.1) (2023.7.22) Building wheels for collected packages: mne Building wheel for mne (pyproject.toml) ... done Created wheel for mne: filename=mne-1.5.1-py3-none-any.whl size=7672477 sha256=6ec600a04e83a0684af871f08d0b92afd601c7ee7b4f159badb707c7ecdde61b Stored in directory: /private/var/folders/q9/hjtxkzvd5yd3ql4lqbq_14cw0000gn/T/pip-ephem-wheel-cache-voog9266/wheels/76/53/0d/789084ed88615ca700b564cc0eb3208a73c9d76e94e0164f59 Successfully built mne Installing collected packages: mne Attempting uninstall: mne Found existing installation: mne 1.6.0.dev91+g079c86824 Uninstalling mne-1.6.0.dev91+g079c86824: Successfully uninstalled mne-1.6.0.dev91+g079c86824 Successfully installed mne-1.5.1 (myenv) makoto@MakotonoMacBook-Air ~ % python Python 3.9.16 | packaged by conda-forge | (main, Feb 1 2023, 21:38:11) [Clang 14.0.6] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import mne >>> mne.sys_info() Platform macOS-13.5.2-arm64-arm-64bit Python 3.9.16 | packaged by conda-forge | (main, Feb 1 2023, 21:38:11) [Clang 14.0.6] Executable /Users/makoto/opt/anaconda3/envs/myenv/bin/python CPU arm (8 cores) Memory 16.0 GB Core ├☑ mne 1.5.1 ├☑ numpy 1.23.5 (OpenBLAS 0.3.20 with 8 threads) ├☑ scipy 1.10.0 ├☑ matplotlib 3.8.0 (backend=MacOSX) ├☑ pooch 1.7.0 └☑ jinja2 3.1.2 Numerical (optional) ├☑ sklearn 1.3.0 ├☑ numba 0.57.1 ├☑ nibabel 5.1.0 ├☑ dipy 1.7.0 ├☑ pandas 2.0.3 └☐ unavailable nilearn, openmeeg, cupy Visualization (optional) ├☑ pyvista 0.42.1 (OpenGL 4.1 Metal - 83.1 via Apple M1) ├☑ pyvistaqt 0.11.0 ├☑ vtk 9.2.6 ├☑ ipympl 0.9.3 ├☑ ipywidgets 8.1.1 └☐ unavailable qtpy, pyqtgraph, mne-qt-browser, trame_client, trame_server, trame_vtk, trame_vuetify Ecosystem (optional) └☐ unavailable mne-bids, mne-nirs, mne-features, mne-connectivity, mne-icalabel, mne-bids-pipeline >>> ``` It worked with the latest version: ```python % pip install git+https://github.com/mne-tools/mne-python.git@main Collecting git+https://github.com/mne-tools/mne-python.git@main Cloning https://github.com/mne-tools/mne-python.git (to revision main) to /private/var/folders/q9/hjtxkzvd5yd3ql4lqbq_14cw0000gn/T/pip-req-build-_q8yb2vm Running command git clone --filter=blob:none --quiet https://github.com/mne-tools/mne-python.git /private/var/folders/q9/hjtxkzvd5yd3ql4lqbq_14cw0000gn/T/pip-req-build-_q8yb2vm Resolved https://github.com/mne-tools/mne-python.git to commit 079c868240a898204bf82b2f1bf0e04cdee75da1 Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: numpy>=1.21.2 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (1.23.5) Requirement already satisfied: scipy>=1.7.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (1.10.0) Requirement already satisfied: matplotlib>=3.4.3 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (3.8.0) Requirement already satisfied: tqdm in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (4.65.0) Requirement already satisfied: pooch>=1.5 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (1.7.0) Requirement already satisfied: decorator in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (5.1.1) Requirement already satisfied: packaging in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (23.1) Requirement already satisfied: jinja2 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (3.1.2) Requirement already satisfied: lazy-loader>=0.3 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (0.3) Requirement already satisfied: defusedxml in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from mne==1.6.0.dev91+g079c86824) (0.7.1) Requirement already satisfied: contourpy>=1.0.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (1.1.0) Requirement already satisfied: cycler>=0.10 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (4.40.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (1.4.4) Requirement already satisfied: pillow>=6.2.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (9.5.0) Requirement already satisfied: pyparsing>=2.3.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (3.0.9) Requirement already satisfied: python-dateutil>=2.7 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (2.8.2) Requirement already satisfied: importlib-resources>=3.2.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (6.0.0) Requirement already satisfied: platformdirs>=2.5.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from pooch>=1.5->mne==1.6.0.dev91+g079c86824) (3.8.1) Requirement already satisfied: requests>=2.19.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from pooch>=1.5->mne==1.6.0.dev91+g079c86824) (2.31.0) Requirement already satisfied: MarkupSafe>=2.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from jinja2->mne==1.6.0.dev91+g079c86824) (2.1.3) Requirement already satisfied: zipp>=3.1.0 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (3.16.0) Requirement already satisfied: six>=1.5 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=3.4.3->mne==1.6.0.dev91+g079c86824) (1.16.0) Requirement already satisfied: charset-normalizer<4,>=2 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from requests>=2.19.0->pooch>=1.5->mne==1.6.0.dev91+g079c86824) (3.2.0) Requirement already satisfied: idna<4,>=2.5 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from requests>=2.19.0->pooch>=1.5->mne==1.6.0.dev91+g079c86824) (3.4) Requirement already satisfied: urllib3<3,>=1.21.1 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from requests>=2.19.0->pooch>=1.5->mne==1.6.0.dev91+g079c86824) (1.26.16) Requirement already satisfied: certifi>=2017.4.17 in ./opt/anaconda3/envs/myenv/lib/python3.9/site-packages (from requests>=2.19.0->pooch>=1.5->mne==1.6.0.dev91+g079c86824) (2023.7.22) Building wheels for collected packages: mne Building wheel for mne (pyproject.toml) ... done Created wheel for mne: filename=mne-1.6.0.dev91+g079c86824-py3-none-any.whl size=7700694 sha256=8d856b0989a445533ecce2fd3bf138c43c0014f2147bf8bcfbd868790fced0f0 Stored in directory: /private/var/folders/q9/hjtxkzvd5yd3ql4lqbq_14cw0000gn/T/pip-ephem-wheel-cache-geqbvloe/wheels/1e/ea/29/e55eee9c5b26218259e60fd0ff2afdaf13b34d12c1c128f23c Successfully built mne Installing collected packages: mne Attempting uninstall: mne Found existing installation: mne 1.5.1 Uninstalling mne-1.5.1: Successfully uninstalled mne-1.5.1 Successfully installed mne-1.6.0.dev91+g079c86824 ``` ![スクリーンショット 2023-09-28 13.42.36](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/4/440b1f0d9aa40ec6db7d014903e994fa42cde1e0.jpeg) ---
**Author:** ![tokoma](https://avatars.discourse-cdn.com/v4/letter/t/c57346/32.png) [@tokoma](https://mne.discourse.group/u/tokoma)\ **Post date:** [September 28, 2023, 4:57am UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/8 "2023-09-28T04:57:52Z")
Using ether 1.5.1 or the latest fails at the following code: ```python # path to subjects' MRI files subjects_dir = sample_data_folder / "subjects" # plot the STC stc.plot( initial_time=0.1, hemi="split", views=["lat", "med"], subjects_dir=subjects_dir ) ``` The error is as follows: ```python /Users/makoto/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/pyvista/jupyter/notebook.py:33: UserWarning: Failed to use notebook backend: No module named 'trame' Falling back to a static output. warnings.warn( --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[20], line 4 2 subjects_dir = sample_data_folder / "subjects" 3 # plot the STC ----> 4 stc.plot( 5 initial_time=0.1, hemi="split", views=["lat", "med"], subjects_dir=subjects_dir 6 ) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/source_estimate.py:740, in _BaseSourceEstimate.plot(self, subject, surface, hemi, colormap, time_label, smoothing_steps, transparent, alpha, time_viewer, subjects_dir, figure, views, colorbar, clim, cortex, size, background, foreground, initial_time, time_unit, backend, spacing, title, show_traces, src, volume_options, view_layout, add_data_kwargs, brain_kwargs, verbose) 706 @copy_function_doc_to_method_doc(plot_source_estimates) 707 def plot( 708 self, (...) 738 verbose=None, 739 ): --> 740 brain = plot_source_estimates( 741 self, 742 subject, 743 surface=surface, 744 hemi=hemi, 745 colormap=colormap, 746 time_label=time_label, 747 smoothing_steps=smoothing_steps, 748 transparent=transparent, 749 alpha=alpha, 750 time_viewer=time_viewer, 751 subjects_dir=subjects_dir, 752 figure=figure, 753 views=views, 754 colorbar=colorbar, 755 clim=clim, 756 cortex=cortex, 757 size=size, 758 background=background, 759 foreground=foreground, 760 initial_time=initial_time, 761 time_unit=time_unit, 762 backend=backend, 763 spacing=spacing, 764 title=title, 765 show_traces=show_traces, 766 src=src, 767 volume_options=volume_options, 768 view_layout=view_layout, 769 add_data_kwargs=add_data_kwargs, 770 brain_kwargs=brain_kwargs, 771 verbose=verbose, 772 ) 773 return brain File :12, in plot_source_estimates(stc, subject, surface, hemi, colormap, time_label, smoothing_steps, transparent, alpha, time_viewer, subjects_dir, figure, views, colorbar, clim, cortex, size, background, foreground, initial_time, time_unit, backend, spacing, title, show_traces, src, volume_options, view_layout, add_data_kwargs, brain_kwargs, verbose) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/viz/_3d.py:2467, in plot_source_estimates(stc, subject, surface, hemi, colormap, time_label, smoothing_steps, transparent, alpha, time_viewer, subjects_dir, figure, views, colorbar, clim, cortex, size, background, foreground, initial_time, time_unit, backend, spacing, title, show_traces, src, volume_options, view_layout, add_data_kwargs, brain_kwargs, verbose) 2465 else: 2466 with use_3d_backend(backend): -> 2467 return _plot_stc( 2468 stc, 2469 overlay_alpha=alpha, 2470 brain_alpha=alpha, 2471 vector_alpha=alpha, 2472 cortex=cortex, 2473 foreground=foreground, 2474 size=size, 2475 scale_factor=None, 2476 show_traces=show_traces, 2477 src=src, 2478 volume_options=volume_options, 2479 view_layout=view_layout, 2480 add_data_kwargs=add_data_kwargs, 2481 brain_kwargs=brain_kwargs, 2482 **kwargs, 2483 ) File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/viz/_3d.py:2637, in _plot_stc(stc, subject, surface, hemi, colormap, time_label, smoothing_steps, subjects_dir, views, clim, figure, initial_time, time_unit, background, time_viewer, colorbar, transparent, brain_alpha, overlay_alpha, vector_alpha, cortex, foreground, size, scale_factor, show_traces, src, volume_options, view_layout, add_data_kwargs, brain_kwargs) 2634 del kwargs 2636 if time_viewer: -> 2637 brain.setup_time_viewer(time_viewer=time_viewer, show_traces=show_traces) 2638 else: 2639 brain.show() File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/viz/_brain/_brain.py:604, in Brain.setup_time_viewer( ***failed resolving arguments*** ) 602 # show everything at the end 603 self.toggle_interface() --> 604 self._renderer.show() 606 # sizes could change, update views 607 for hemi in ("lh", "rh"): File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/mne/viz/backends/_notebook.py:1597, in _Renderer.show(self) 1585 viewer = self.plotter.show(jupyter_backend=_JUPYTER_BACKEND, return_viewer=True) 1586 if _JUPYTER_BACKEND == "trame": 1587 # Remove scrollbars, see https://github.com/pyvista/pyvista/pull/4847 1588 # which adds this to the iframe PyVista creates. Once that's merged, this (...) 1591 # live with the ugly 90's-style borders. We can probably remove once we 1592 # require PyVista 0.43 (assuming the above PR is merged). 1593 viewer.value = re.sub( 1594 r" style=[\"'](.+)[\"']>", 1595 # value taken from matplotlib's widget 1596 r" style='\1; border: 1px solid rgb(221,221,221);' scrolling='no'>", # noqa: E501 -> 1597 viewer.value, 1598 ) 1599 rendering_row = list() 1600 if self._docks is not None and "left" in self._docks: File ~/opt/anaconda3/envs/myenv/lib/python3.9/site-packages/PIL/Image.py:528, in Image. __getattr__ (self, name) 526 deprecate("Image categories", 10, "is_animated", plural=True) 527 return self._category --> 528 raise AttributeError(name) AttributeError: value ``` ---
**Author:** ![wmvanvliet](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/wmvanvliet/32/100_2.png) [@wmvanvliet](https://mne.discourse.group/u/wmvanvliet)\ **Post date:** [October 17, 2023, 1:13pm UTC](https://mne.discourse.group/t/typeerror-when-i-ran-the-tutorial/7571/9 "2023-10-17T13:13:53Z")
Try installing the `trane` python module. This is now a dependancy of MNE-Python.