possibly a silly problem, but I'm stuck and I'd really appreciate someone's help. I'm trying to replicate the examples given in the walkthrough tutorial for trackpy (https://soft-matter.github.io/trackpy/dev/tutorial/walkthrough.html). I've been succesful up until I got to the point where I had to fit the ensemble mean-squared displacement to a power law (In [34]):
plt.figure()
plt.ylabel(r'$\langle \Delta r^2 \rangle$ [$\mu$m$^2$]')
plt.xlabel('lag time $t$');
tp.utils.fit_powerlaw(em) # performs linear best fit in log space, plots]
This is the error message I get. Can someone suggest a solution? Thanks!
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
File ~/opt/anaconda3/lib/python3.9/site-packages/pandas/core/indexes/base.py:3621, in Index.get_loc(self, key, method, tolerance)
3620 try:
-> 3621 return self._engine.get_loc(casted_key)
3622 except KeyError as err:
File ~/opt/anaconda3/lib/python3.9/site-packages/pandas/_libs/index.pyx:136, in pandas._libs.index.IndexEngine.get_loc()
File ~/opt/anaconda3/lib/python3.9/site-packages/pandas/_libs/index.pyx:142, in pandas._libs.index.IndexEngine.get_loc()
TypeError: '(slice(None, None, None), None)' is an invalid key
During handling of the above exception, another exception occurred:
InvalidIndexError Traceback (most recent call last)
Input In [178], in <cell line: 4>()
2 plt.ylabel(r'$\langle \Delta r^2 \rangle$ [$\mu$m$^2$]')
3 plt.xlabel('lag time $t$');
----> 4 tp.utils.fit_powerlaw(em)
File ~/opt/anaconda3/lib/python3.9/site-packages/trackpy/utils.py:50, in fit_powerlaw(data, plot, **kwargs)
48 if plot:
49 from trackpy import plots
---> 50 plots.fit(data, fits, logx=True, logy=True, legend=False, **kwargs)
51 return values
File ~/opt/anaconda3/lib/python3.9/site-packages/trackpy/plots.py:50, in make_axes.<locals>.wrapper(*args, **kwargs)
47 # Delete legend keyword so remaining ones can be passed to plot().
48 legend = kwargs.pop('legend', False)
---> 50 result = func(*args, **kwargs)
52 if legend:
53 handles, labels = kwargs['ax'].get_legend_handles_labels()
File ~/opt/anaconda3/lib/python3.9/site-packages/trackpy/plots.py:652, in fit(data, fits, inverted_model, logx, logy, ax, **kwargs)
650 ax.set_yscale('log')
651 if not inverted_model:
--> 652 fitlines = ax.plot(fits.index, fits, **kwargs)
653 else:
654 fitlines = ax.plot(fits.reindex(data.dropna().index),
655 data.dropna(), **kwargs)
File ~/opt/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_axes.py:1632, in Axes.plot(self, scalex, scaley, data, *args, **kwargs)
1390 """
1391 Plot y versus x as lines and/or markers.
1392
(...)
1629 (``'green'``) or hex strings (``'#008000'``).
1630 """
1631 kwargs = cbook.normalize_kwargs(kwargs, mlines.Line2D)
-> 1632 lines = [*self._get_lines(*args, data=data, **kwargs)]
1633 for line in lines:
1634 self.add_line(line)
File ~/opt/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py:312, in _process_plot_var_args.__call__(self, data, *args, **kwargs)
310 this += args[0],
311 args = args[1:]
--> 312 yield from self._plot_args(this, kwargs)
File ~/opt/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py:488, in _process_plot_var_args._plot_args(self, tup, kwargs, return_kwargs)
486 if len(xy) == 2:
487 x = _check_1d(xy[0])
--> 488 y = _check_1d(xy[1])
489 else:
490 x, y = index_of(xy[-1])
File ~/opt/anaconda3/lib/python3.9/site-packages/matplotlib/cbook/__init__.py:1327, in _check_1d(x)
1321 with warnings.catch_warnings(record=True) as w:
1322 warnings.filterwarnings(
1323 "always",
1324 category=Warning,
1325 message='Support for multi-dimensional indexing')
-> 1327 ndim = x[:, None].ndim
1328 # we have definitely hit a pandas index or series object
1329 # cast to a numpy array.
1330 if len(w) > 0:
File ~/opt/anaconda3/lib/python3.9/site-packages/pandas/core/frame.py:3505, in DataFrame.__getitem__(self, key)
3503 if self.columns.nlevels > 1:
3504 return self._getitem_multilevel(key)
-> 3505 indexer = self.columns.get_loc(key)
3506 if is_integer(indexer):
3507 indexer = [indexer]
File ~/opt/anaconda3/lib/python3.9/site-packages/pandas/core/indexes/base.py:3628, in Index.get_loc(self, key, method, tolerance)
3623 raise KeyError(key) from err
3624 except TypeError:
3625 # If we have a listlike key, _check_indexing_error will raise
3626 # InvalidIndexError. Otherwise we fall through and re-raise
3627 # the TypeError.
-> 3628 self._check_indexing_error(key)
3629 raise
3631 # GH#42269
File ~/opt/anaconda3/lib/python3.9/site-packages/pandas/core/indexes/base.py:5637, in Index._check_indexing_error(self, key)
5633 def _check_indexing_error(self, key):
5634 if not is_scalar(key):
5635 # if key is not a scalar, directly raise an error (the code below
5636 # would convert to numpy arrays and raise later any way) - GH29926
-> 5637 raise InvalidIndexError(key)
InvalidIndexError: (slice(None, None, None), None)