soft-matter / trackpy

Python particle tracking toolkit
http://soft-matter.github.io/trackpy
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link_df_iter giving TypeError when using pd.concat? #745

Open zimengwu opened 11 months ago

zimengwu commented 11 months ago

Hi everyone!

I've recently started using trackpy and it's been amazing. I started using the link_df function on cropped datasets (centroids from segmented data) to figure out the parameters for linking and it worked a charm. However, when I tried using the same pipeline on my full timelapse data (~7000 labels over 60 frames) I found it took quite a long time. So, I turned to link_df_iter as I read it takes a much shorter amount of time to link and I used the same parameters I used with link_df! However, whenever I try to run this code:

linked_df = pd.concat(tp.link_df_iter(df, t_column='frame', pos_columns=['z', 'y', 'x'], search_range=20, memory=8), ignore_index=True)

I've been getting this TypeError which points to the t_column from my dataframe.


TypeError Traceback (most recent call last) Cell In[9], line 6 3 velocity = np.array((0, 0, -5)) # (v_z, v_y, v_x) 4 return particle.pos + velocity * (t1 - particle.t) ----> 6 linked_df = pd.concat(tp.link_df_iter(df, t_column='frame', pos_columns=['z', 'y', 'x'], search_range=20, memory=8), ignore_index=True)

File ~\anaconda3\envs\tracking\lib\site-packages\pandas\core\reshape\concat.py:380, in concat(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy) 377 elif copy and using_copy_on_write(): 378 copy = False --> 380 op = _Concatenator( 381 objs, 382 axis=axis, 383 ignore_index=ignore_index, 384 join=join, 385 keys=keys, 386 levels=levels, 387 names=names, 388 verify_integrity=verify_integrity, 389 copy=copy, 390 sort=sort, 391 ) 393 return op.get_result()

File ~\anaconda3\envs\tracking\lib\site-packages\pandas\core\reshape\concat.py:443, in _Concatenator.init(self, objs, axis, join, keys, levels, names, ignore_index, verify_integrity, copy, sort) 440 self.verify_integrity = verify_integrity 441 self.copy = copy --> 443 objs, keys = self._clean_keys_and_objs(objs, keys) 445 # figure out what our result ndim is going to be 446 ndims = self._get_ndims(objs)

File ~\anaconda3\envs\tracking\lib\site-packages\pandas\core\reshape\concat.py:502, in _Concatenator._clean_keys_and_objs(self, objs, keys) 500 objs_list = [objs[k] for k in keys] 501 else: --> 502 objs_list = list(objs) 504 if len(objs_list) == 0: 505 raise ValueError("No objects to concatenate")

File ~\anaconda3\envs\tracking\lib\site-packages\trackpy\linking\linking.py:278, in link_df_iter(f_iter, search_range, pos_columns, t_column, kwargs) 274 coords_iter = coords_from_df_iter(f_coords_iter, pos_columns, t_column) 276 ids_iter = (_ids for _i, _ids in 277 link_iter(coords_iter, search_range, kwargs)) --> 278 for df, ids in zip(f_iter, ids_iter): 279 df_linked = df.copy() 280 df_linked['particle'] = ids

File ~\anaconda3\envs\tracking\lib\site-packages\trackpy\linking\linking.py:276, in (.0) 273 f_iter, f_coords_iter = itertools.tee(f_iter) 274 coords_iter = coords_from_df_iter(f_coords_iter, pos_columns, t_column) --> 276 ids_iter = (_ids for _i, _ids in 277 link_iter(coords_iter, search_range, **kwargs)) 278 for df, ids in zip(f_iter, ids_iter): 279 df_linked = df.copy()

File ~\anaconda3\envs\tracking\lib\site-packages\trackpy\linking\linking.py:88, in link_iter(coords_iter, search_range, **kwargs) 85 coords_iter = iter(coords_iter) 87 # interpret the first element of the iterable ---> 88 val = next(coords_iter) 89 if isinstance(val, np.ndarray): 90 # the iterable was not enumerated, so enumerate the remainder 91 coords_iter = enumerate(coords_iter, start=1)

File ~\anaconda3\envs\tracking\lib\site-packages\trackpy\linking\utils.py:70, in coords_from_df_iter(df_iter, pos_columns, t_column) 68 yield None, np.empty((0, ndim)) 69 else: ---> 70 yield df[t_column].iloc[0], df[pos_columns].values

TypeError: string indices must be integers

When I also run just the tp.link_df_iter(df, t_column='frame', pos_columns=['z', 'y', 'x'], search_range=20, memory=8) line no error and an output:

<generator object link_df_iter at 0x0000018D83335A10>

Which makes me think it's not to do with the link_df_iter but how it interacts with pd.concat?

I've checked my original df going into and my 'frame' column are all ints and I have no NaN values either. I was just wondering if anyone else experienced anything like this and would know how I should troubleshoot? Thanks for any help!