# ValueError: All picks must be \< n\_channels (73), got 73 **URL:** \ **Category:** Support & Discussions\ **Tags:** eeg\ **Created:** [August 15, 2023, 10:16pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375 "2023-08-15T22:16:03Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 15, 2023, 10:16pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/1 "2023-08-15T22:16:03Z")
- MNE Version: 1.5.0 - Operating System: Windows 10 I am using Jupyter Notebook. ```python # imports import numpy as np import os import os.path as op import matplotlib.pyplot as plt import mne import mneflow import sklearn import pandas as pd import torch from tqdm import tqdm # Load data data_path = "C:/Users/Raahul Pathak/Research/Raahul/Thesis-Project/Participant-Information/" p01 = "p1.bdf" p02 = "P02.bdf" p03 = "p3.bdf" p04 = "P04.bdf" p05 = "P5.bdf" p06 = "p6.bdf" p07 = "p7.bdf" p08 = "p8.bdf" p09 = "p9.bdf" p10 = "p10.bdf" p11 = "p11.bdf" p12 = "p12.bdf" # Create raw info structures p01_raw = data_path + p01 for i in tqdm(mne.io.read_raw_bdf(p01_raw)): pass ``` This gives me the following error: ValueError: All picks must be \< n\_channels (73), got 73 Can anyone please help me solve this error? ---
**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:** [August 16, 2023, 8:00am UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/2 "2023-08-16T08:00:27Z")
Can you do: ```python import mne data_path = "C:/Users/Raahul Pathak/Research/Raahul/Thesis-Project/Participant-Information/" p01_raw = data_path + p01 raw = mne.io.read_raw_bdf(p01_raw) print (raw) print (raw.info) ``` and return the 2 prints here. Then: ```python for _ in raw: pass ``` And confirm that this last code snippet raises the `ValueError`. Please also post the **full** traceback of the error. Mathieu ---
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 16, 2023, 12:31pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/3 "2023-08-16T12:31:54Z")
```python import mne p01_raw = data_path + p01 raw = mne.io.read_raw_bdf(p01_raw) print (raw) print (raw.info) ``` The block above you asked me to run yields the following: ```python Extracting EDF parameters from C:\Users\Raahul Pathak\Research\Raahul\Thesis-Project\Participant-Information\p1.bdf... BDF file detected Setting channel info structure... Creating raw.info structure... in ----> 1 for _ in raw: 2 pass c:\users\raahul pathak\appdata\local\programs\python\python39\lib\site-packages\mne\io\base.py in __getitem__ (self, item) 840 841 """ # noqa: E501 --> 842 return self._getitem(item) 843 844 def _getitem(self, item, return_times=True): c:\users\raahul pathak\appdata\local\programs\python\python39\lib\site-packages\mne\io\base.py in _getitem(self, item, return_times) 843 844 def _getitem(self, item, return_times=True): --> 845 sel, start, stop = self._parse_get_set_params(item) 846 if self.preload: 847 data = self._data[sel, start:stop] c:\users\raahul pathak\appdata\local\programs\python\python39\lib\site-packages\mne\io\base.py in _parse_get_set_params(self, item) 776 ) 777 --> 778 sel = _picks_to_idx(self.info, item[0]) 779 780 if isinstance(item[1], slice): c:\users\raahul pathak\appdata\local\programs\python\python39\lib\site-packages\mne\io\pick.py in _picks_to_idx(info, picks, none, exclude, allow_empty, with_ref_meg, return_kind, picks_on) 1302 raise ValueError("All picks must be >= %d, got %r" % (-n_chan, orig_picks)) 1303 if (picks >= n_chan).any(): -> 1304 raise ValueError( 1305 "All picks must be < n_%s (%d), got %r" % (picks_on, n_chan, orig_picks) 1306 ) ValueError: All picks must be < n_channels (73), got 73 ``` ---
**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:** [August 16, 2023, 2:09pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/4 "2023-08-16T14:09:48Z")
I can reproduce on `main` with: ```python import numpy as np from mne import create_info from mne.io import RawArray info = create_info(["EEG1", "EEG2", "STI1"], 1000, ["eeg", "eeg", "stim"]) data = np.random.randn(3, 1000) raw = RawArray(data, info) for _ in raw: pass ``` Will look into it, Mathieu ---
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 16, 2023, 8:59pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/5 "2023-08-16T20:59:15Z")
Thank you. Please let me know if you find anything. It would be greatly appreciated. ---
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 17, 2023, 3:34pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/6 "2023-08-17T15:34:10Z")
@mscheltienne, if it helps, it is not just p01 that is an issue. I believe it is all of them because I just tried to do the same with p02 and the same ValueError showed up with the same number of channels it stopped at. ---
**Author:** ![cbrnr](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/cbrnr/32/1409_2.png) [@cbrnr](https://mne.discourse.group/u/cbrnr)\ **Post date:** [August 17, 2023, 4:05pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/7 "2023-08-17T16:05:41Z")
> [@mscheltienne](#): > > ```python > for _ in raw: > pass > > ``` What is this supposed to do? `Raw` does not implement the iterator protocol. It’s not clear what the OP is trying to do, but it looks like the loop should be over the different _paths_ and not over raw objects. ---
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 17, 2023, 4:26pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/8 "2023-08-17T16:26:01Z")
Do you mean what is the overall function of the network/algorithm I am trying to write? Or why I am trying to read in the files? ---
**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:** [August 17, 2023, 5:29pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/9 "2023-08-17T17:29:07Z")
So a for loop on a `raw` object is definitely weird and should likely be prevented. I haven’t look at the code yet, if there is a usecase I am missing which iterates on the `raw`. But if that’s correct, then it should fail with a better error/message anyway. @Raahul You are indeed not interating on the path but on the loaded `p01_raw` object. Try: ```python participants = [p01, p02, ...] for participant in tqdm(participants): raw = mne.io.read_raw_bdf(participant ) ``` ---
**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\ **Post date:** [August 17, 2023, 5:38pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/10 "2023-08-17T17:38:22Z")
> [@cbrnr](#): > > `Raw` does not implement the iterator protocol. agreed, and I’m not sure it should. The only reasonable thing I can think of would be iterating over channels but that seems like a big can of worms and is already possible without too much convoluted code (`for ch in raw.info['ch_names']` followed by `ch_data = raw.get_data(picks=ch)`, or directly with `for ch_data in raw.get_data()`). ---
**Author:** ![cbrnr](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/cbrnr/32/1409_2.png) [@cbrnr](https://mne.discourse.group/u/cbrnr)\ **Post date:** [August 17, 2023, 5:41pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/11 "2023-08-17T17:41:53Z")
> [@mscheltienne](#): > > then it should fail with a better error/message anyway Definitely, it should raise a `TypeError: 'Raw' object is not iterable`. ---
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 17, 2023, 7:31pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/13 "2023-08-17T19:31:43Z")
When you say p01, p02, … in the participants array, do you mean the number of picks in a single bdf file, or the number of bdf files? I have twelve bdf files total and each one has tens of thousands to hundreds of thousands of picks. “p01\_raw” is just a naming scheme I gave to the raw bdf file I was trying to import/read in from my local machine. I am trying to read in a raw bdf file so I can use mne to pre-process, segment it, etc on it. This is all the code I have run recently to do try to read in the bdf file. I want to give you guys an updated version of my code without any comments. This is before I try the participants thing because I am unsure of what exactly you mean by p01, p02, … ```python import numpy as np import pandas as pd import seaborn as sns import matplotlib.pyplot as plt import mne as mne import os.path as op from tqdm import tqdm p01 = "C:/Users/Raahul Pathak/Research/Raahul/Thesis-Project/Participant-Information/p1.bdf" for i in tqdm(mne.io.read_raw_bdf(p01)): pass ``` ---
**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\ **Post date:** [August 17, 2023, 7:55pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/14 "2023-08-17T19:55:28Z")
in your latest code snippet, `p01` is a string variable pointing to a filename. then you load the file using `mne.io.read_raw_bdf(p01)`, and then you pass the result of that (which will be a `Raw` object) to `tqdm()`. I can only guess that what you want to do is show a progress bar for the loading progress? That will not work. What happens now is that all of the file loading happens _before_ `tqdm()` even looks at what you’ve passed to it. Now, `tqdm()` expects an _iterable_ object, and `Raw` objects are not iterable. The code _ought_ to fail in the way @cbrnr indicated above. The fact that it does not fail doesn’t mean that what you’re trying to do is possible. It means that either there’s a subtle bug in MNE (`Raw` has a vacuous ` __iter__ ` method when it shouldn’t) or there’s a bug in TQDM (it should raise an error when passed a non-iterable, but it doesn’t). instead of your `for`-loop, please just do ```python raw = mne.io.read_raw_bdf(p01) # subsequent preprocessing steps go here ``` ---
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 17, 2023, 8:02pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/15 "2023-08-17T20:02:02Z")
Yes. That is right. I want to view a a progress bar as to how much of the bdf file has been loaded/read in. I’ve already tried strictly doing the last code snippit you propose. But, I’ll try it again and let it run for longer this time. I’ll let it run for half-an-hour to an hour and I will touch base with you. ---
**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\ **Post date:** [August 17, 2023, 8:05pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/16 "2023-08-17T20:05:49Z")
how big is the file?? You can pass `preload=False` to the `read_raw_bdf` function to skip loading the data into memory, that should almost always be fast. ---
**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:** [August 17, 2023, 8:20pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/17 "2023-08-17T20:20:09Z")
> The only reasonable thing I can think of would be iterating over channels but that seems like a big can of worms and is already possible without too much convoluted code (`for ch in raw.info['ch_names']` followed by `ch_data = raw.get_data(picks=ch)`, or directly with `for ch_data in raw.get_data()`). That was my thought, some iteration over channels. Raw objects can be indexed, `raw[1, :]` will return the data array of the first channel and associated times (shape (1, n\_samples), shape (n\_samples,)). Thus, a for loop should maybe iterate on the first dimension similar to a numpy array? But I agree that this use case should probably not be supported and simply raise a TypeError. ---
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 17, 2023, 8:23pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/18 "2023-08-17T20:23:57Z")
Between the twelve files I am trying load in, they range between 79,000 kilobytes to 130,000 kilobytes. Where do I put the `preload=False` statement in the read\_raw\_bdf statement? Plus, I thought it defaulted to False, thus didn’t need to be manually set to False. ---
**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\ **Post date:** [August 17, 2023, 8:35pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/19 "2023-08-17T20:35:34Z")
ah yes, you are right that `preload=False` is the default. Can you share a link to download one of the problematic files? Also just to rule out anything unexpected, please post the results of `mne.sys_info()` so we know what all your software versions are. ---
**Author:** ![RPathak](https://avatars.discourse-cdn.com/v4/letter/r/e9bcb4/32.png) [@RPathak](https://mne.discourse.group/u/RPathak)\ **Post date:** [August 17, 2023, 8:59pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/20 "2023-08-17T20:59:12Z")
mne.sys\_info() yields the below: ```python Platform Windows-10-10.0.19045-SP0 Python 3.9.5 (tags/v3.9.5:0a7dcbd, May 3 2021, 17:27:52) [MSC v.1928 64 bit (AMD64)] Executable c:\users\raahul pathak\appdata\local\programs\python\python39\python.exe CPU AMD64 Family 23 Model 113 Stepping 0, AuthenticAMD (24 cores) Memory 15.9 GB ``` > **[p1.bdf](https://drive.google.com/file/d/1b59-O5AHmCkW52inbDkafcf2iQEDcGkj/view?usp=sharing)** > > Google Drive file. ---
**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\ **Post date:** [August 17, 2023, 9:27pm UTC](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375/21 "2023-08-17T21:27:52Z")
I don’t know what’s going on. The below works for me in an IPython interpreter: ```python In [1]: import mne In [2]: %timeit raw = mne.io.read_raw_bdf("p1.bdf", verbose=False) 3.26 ms ± 434 µs per loop (mean ± std. dev. of 7 runs, 1 loop each) ``` and if I actually load the data: ```python In [1]: import mne In [2]: %timeit raw = mne.io.read_raw_bdf("p1.bdf", verbose=False, preload=True) 484 ms ± 2.99 ms per loop (mean ± std. dev. of 7 runs, 1 loop each) ``` note that I’m setting `verbose=False` just to suppress extra output other than the timings. Can you run `mne.sys_info()` again? It should show a lot more than what you’ve provided; it doesn’t even show the version of MNE you’re running (much less other dependencies like numpy, scipy, etc) [Next page](https://mne.discourse.group/t/valueerror-all-picks-must-be-n-channels-73-got-73/7375.md?page=2)