Dear IBL Team,
I am trying to create another pipeline and I have incorperated the IBL pipeline into another environemetn for another sofatware pakcage I am planning on using. I just mention this in case there are conflicts I am not aware of. As far as I can tell everything has installed fine in the same conda env, if you are curious this is the tool I wan to use…Edeno-replay-classifier.
As the title says I am having trouble with some of the libraries that are called, I already posted about this topic but it as reoccurred. In the last post I used pip install ibl-neuropixels and it seemed to solve everything but this time it’s not. Curious if I’ve missed something, also I want to make my environments shareable so I need to be able to post instructions for others to follow of make a script that can set the environments up if it requires a bit more work than just pip installing one environment.
Anything from brainbox is not working. So I can’t for instance get this tutorial working which relies on SpikeSortLoader from brainbox.io.one
Here are the imports I’m running. I can attach or send my requirements.txt for the environment if that would help in anyway.
# libraries
#IBL SWR detector
import os
import subprocess
import numpy as np
import pandas as pd
from scipy import io, signal, stats
from scipy.signal import lfilter
#from fitter import Fitter, get_common_distributions, get_distributions
import scipy.ndimage
from scipy.ndimage import gaussian_filter
from scipy.ndimage import gaussian_filter1d
from scipy import interpolate
import matplotlib.pyplot as plt
# for ripple detection
import ripple_detection
from ripple_detection import filter_ripple_band
import ripple_detection.simulate as ripsim # for making our time vectors
from tqdm import tqdm
from iblatlas.atlas import AllenAtlas
from iblatlas.regions import BrainRegions
from one.api import ONE
import spikeglx
import brainbox.io.one
from brainbox.io.one import load_channel_locations
from brainbox.io.spikeglx import Streamer
from brainbox.io.one import SpikeSortingLoader
from neurodsp.voltage import destripe_lfp
#THIS CODE WORKS THIS CODE LOOPS THROUGH THE SESSIONS AND DOWNLOADS THE DATA, WE NEED TO ADD THE RIPPLE DETECTION CODE TO REMOVE THE DATA AFTER
from neurodsp.voltage import destripe_lfp
from ibllib.plots import Density
import time # for debugging
import traceback
import logging
import logging.handlers
import sys
from multiprocessing import Pool, Process, Queue, Manager, set_start_method
Hello,
I canno’t reproduce the issue on virtualenv nor conda for Python 3.10 on Linux.
There are several possiblities here:
-
your python version is too old, and not compatible with newer ibllib
-
there is a package named brainbox in your current Path
Could you please send your environment info python --version, pip list, which python and your OS
And in a Python console, try:
import brainbox
print(brainbox.__file__)
import os
print(os.getcwd())
Ok so we are using “CentOS Linux”, I do not think its the python version as my env has python 3.12 but I may have installed an outdated brainbox version which I got here. Running from brainbox.io still gives the ModuleNotFoundError: No module named 'brainbox' So I recreated the environment, here is the full list of what I did to do that…
conda create --name replay_trajectory_classification python=3.12
conda activate replay_trajectory_classification
conda install -c edeno replay_trajectory_classification
conda install ipykernel
python -m ipykernel install --user --name replay_trajectory_classification --display-name "Python (replay_trajectory_classification)"
pip install ONE-api
pip install ibl-neuropixel
pip install iblatlas
Python versions and which python are here…
(replay_trajectory_classification) [acampbell@itchy ~]$ python --version
Python 3.12.3
(replay_trajectory_classification) [acampbell@itchy ~]$ which python
~/miniconda3/envs/replay_trajectory_classification/bin/python
then in python…
(replay_trajectory_classification) [acampbell@itchy ~]$ python
Python 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import brainbox
__file__)Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'brainbox'
>>> import brainbox
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'brainbox'
>>> print(brainbox.__file__)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
NameError: name 'brainbox' is not defined
>>> import os
>>> print(os.getcwd())
/home/acampbell
pip list…
(replay_trajectory_classification) [acampbell@itchy ~]$ pip list
Package Version
-------------------------------- ---------
asttokens 2.4.1
bokeh 3.4.1
boto3 1.34.102
botocore 1.34.102
Brotli 1.1.0
certifi 2024.2.2
charset-normalizer 3.3.2
click 8.1.7
cloudpickle 3.0.0
colorama 0.4.6
colorlog 6.8.2
comm 0.2.2
contourpy 1.2.1
cycler 0.12.1
cytoolz 0.12.3
dask 2024.5.0
dask-expr 1.1.0
debugpy 1.8.1
decorator 5.1.1
distributed 2024.5.0
exceptiongroup 1.2.0
executing 2.0.1
flake8 7.0.0
fonttools 4.51.0
fsspec 2024.3.1
ibl-neuropixel 1.0.0
iblatlas 0.5.1
iblutil 1.8.0
idna 3.7
imagecodecs 2024.1.1
imageio 2.34.1
importlib_metadata 7.1.0
ipykernel 6.29.3
ipython 8.24.0
jedi 0.19.1
Jinja2 3.1.4
jmespath 1.0.1
joblib 1.4.2
jupyter_client 8.6.1
jupyter_core 5.7.2
kiwisolver 1.4.5
lazy_loader 0.4
llvmlite 0.42.0
locket 1.0.0
lz4 4.3.3
MarkupSafe 2.1.5
matplotlib 3.8.4
matplotlib-inline 0.1.7
mccabe 0.7.0
msgpack 1.0.7
mtscomp 1.0.2
nest_asyncio 1.6.0
networkx 3.3
nptyping 2.5.0
numba 0.59.1
numpy 1.26.4
ONE-api 2.7.0
packaging 24.0
pandas 2.2.2
parso 0.8.4
partd 1.4.2
patsy 0.5.6
pexpect 4.9.0
pickleshare 0.7.5
pillow 10.3.0
pip 24.0
platformdirs 4.2.1
ply 3.11
prompt-toolkit 3.0.42
psutil 5.9.8
ptyprocess 0.7.0
pure-eval 0.2.2
pyarrow 16.0.0
pyarrow-hotfix 0.6
pycodestyle 2.11.1
pyflakes 3.2.0
Pygments 2.18.0
pynrrd 1.0.0
pyparsing 3.1.2
PyQt5 5.15.9
PyQt5-sip 12.12.2
PySocks 1.7.1
python-dateutil 2.9.0
pytz 2024.1
PyWavelets 1.4.1
PyYAML 6.0.1
pyzmq 26.0.3
regularized-glm 1.0.2
replay-trajectory-classification 1.3.15
requests 2.31.0
s3transfer 0.10.1
scikit-image 0.22.0
scikit-learn 1.4.2
scipy 1.13.0
seaborn 0.13.2
setuptools 69.5.1
sip 6.7.12
six 1.16.0
sortedcontainers 2.4.0
stack-data 0.6.2
statsmodels 0.14.1
tblib 3.0.0
threadpoolctl 3.5.0
tifffile 2024.5.10
toml 0.10.2
tomli 2.0.1
toolz 0.12.1
tornado 6.4
tqdm 4.66.4
track-linearization 2.1.0
traitlets 5.14.3
typing_extensions 4.11.0
tzdata 2024.1
urllib3 2.2.1
wcwidth 0.2.13
wheel 0.43.0
xarray 2024.3.0
xyzservices 2024.4.0
zict 3.0.0
zipp 3.17.0
Oh this brainbox is not from us. We need to change the name so that there is no confusion with this third-party package.
So make sure it is uninstalled:
pip uninstall brainbox
And then install ibllib
pip install ibllib
You do not need ONE-api / ibl-neuropixel nor iblatlas are they are all dependencies of ibllib. Brainbox is a package within ibllib.
Let me know if you still have issues!
You sir are a legend thank you, it works now.