No module named 'helper' in Use Case notebook

amalia.castro.11 · 15 March 2022 11:56

Dear all, I am in the openEO Platform server and I got the “UC3 - Crop type feature engineering (rule-based).ipynb” and added it to my folder called “sample notebooks”. When I run its first cell, I get the following error:

Thanks for your help!

jeroen.dries · 15 March 2022 12:12

Hi Amalia,
the helper.py file was next to the original notebook, just like the eo_utils.py:

github.com

openEOPlatform/SRR2_notebooks/blob/main/helper.py

"""
Module for calculating a list of vegetation indices from a datacube containing bands without a user having to implement callback functions
"""

from openeo.rest.datacube import DataCube
from openeo.processes import ProcessBuilder, array_modify, power, sqrt, if_, multiply, divide, arccos, add, subtract, linear_scale_range
from shapely.geometry import Point
import numpy as np
import netCDF4 as nc
import glob
import seaborn as sns
from matplotlib.dates import DateFormatter
import geopandas as gpd
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap, BoundaryNorm
import earthpy.plot as ep
import pandas as pd
import rasterio

WL_B04 = 0.6646

This file has been truncated. show original

you’ll want to copy that over as well, or even better, check out the entire repository to avoid that you run into other dependency issues.
Do note that the error in the screenshot is about eo_utils, while there does seem to be an eo_utils.py file, and the error in your post is about ‘helper’. In any case, I believe Python notebooks can import code in files alongside the notebook…

best regards,
Jeroen

amalia.castro.11 · 15 March 2022 13:45

Hi Jeroen, thanks for the quick answer. You are right, I pasted the wrong screenshot. Thanks for your help: I have now cloned the repository SSR_Notebooks and run the UC3 notebook that came inside. However I now get this error:

Thanks again in advance

jeroen.dries · 15 March 2022 16:18

Hi Amalia,
this code has a number of dependencies that are (apparently) not in the Jupyterlab environment by default.
The easy solution is to install the dependency, for instance, running this in a separate cell might already work:

!pip install --user earthpy
Mind the exclamation mark which executes bash commands from inside a notebook, you can also open a ‘terminal’ window and run the same thing without the exclamation mark.

Sometimes, dependencies are not really used after all by a certain notebook, in which case you can comment them out. This is however more tricky as you may get other errors further down the line related to the missing import

Hope that helps!

amalia.castro.11 · 16 March 2022 13:11

That is great to know, I have tried it both from inside the notebook (with the “!”) and from a terminal window (without the “!”) but this error below comes back in both cases:

.

What is the best way to proceed?

benjamin.schumacher · 16 March 2022 13:33

Dear @amalia.castro.11,
as stated by the PyPi documentation earthpy should be installed via conda. The jupyterlab environment itself supports this.
Please use the following command to install earthpy:
conda install -c conda-forge earthpy
Please note that you should always prefer to install packages into a conda environment via conda install and not with pip as this might break the entire environment.

amalia.castro.11 · 16 March 2022 15:01

That solved it, thanks so much !