Streamlit fails to import package included in requirements.txt

[Karol-G]

Hi,

I want to build an app that uses the package ‘SimpleITK’. This is a normal pip package https://pypi.org/project/SimpleITK/ and normally easy to install / makes no problems.

The package is included in my requirements.txt, which looks like this:

numpy
scikit-image
SimpleITK

However, when I execute my code with streamlit run streamlit.py, I get the following error:

2022-06-07 22:04:16.959 Uncaught app exception
Traceback (most recent call last):
  File "/home/k539i/.local/lib/python3.8/site-packages/streamlit/scriptrunner/script_runner.py", line 554, in _run_script
    exec(code, module.__dict__)
  File "/home/k539i/Documents/projects/pytorch.3D_U-Net_baseline/streamlit.py", line 39, in <module>
    prediction, prediction_name = inference()
  File "/home/k539i/Documents/projects/pytorch.3D_U-Net_baseline/streamlit.py", line 9, in inference
    import SimpleITK as sitk
ModuleNotFoundError: No module named 'SimpleITK'

My streamlit.py:

import streamlit as st
import os
import time
import numpy as np
from skimage import transform as ski_transform
import SimpleITK as sitk


def inference():
    my_bar = st.progress(0)
    for percent_complete in range(100):
        time.sleep(0.1)
        my_bar.progress(percent_complete + 1)
    prediction = np.zeros((100, 100, 100), dtype=np.uint8)
    prediction = sitk.GetImageFromArray(prediction)
    spacing = (0.1, 0.1, 0.1)
    prediction.SetSpacing(spacing)
    # prediction = None
    return prediction, "test"

st.title('Mineral particle segmentation')

# Initialization
if 'key' not in st.session_state:
    st.session_state['key'] = 'Init'

# Upload
uploaded_file = st.file_uploader("Upload a an image", type=['.nii.gz'])
if uploaded_file is not None:
    file_details = {"FileName": uploaded_file.name, "FileType": uploaded_file.type}
    # st.write(file_details)
    with open(os.path.join("streamlit_uploaded", uploaded_file.name), "wb") as f:
        f.write(uploaded_file.getbuffer())
    st.success("Saved image")
    st.session_state['key'] = 'Uploaded'

if st.session_state['key'] == 'Uploaded':
    st.session_state['key'] = 'Inference'
    prediction, prediction_name = inference()

    st.download_button(
         label="Download prediction",
         data=prediction,
         file_name='prediction_name.nii.gz',
         mime='file',
     )

It seems SimpleITK could not be installed even though it is in the requirements.txt. Any ideas?

Best,
Karol

[natecooperjones]

Hi Karol.

Before running the Streamlit app, are you ensuring that all requirements are installed with:

pip install -r requirements.txt

[Karol-G]

Hi,

ah, thanks! Yes, that worked.

Best,
Karol