I successfully generated a config.json file and many dependencies were installed. However, after
python run_pipeline.py ./config.json
I find that numpy and frozendict are not in my environment created with requirements.txt as instructed. I installed these manually, but now I get:
Traceback (most recent call last):
File "run_pipeline.py", line 2, in
from pipeline import pipeline
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/pipeline.py", line 9, in
from .segmentation.run_segmentation import *
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/segmentation/run_segmentation.py", line 4, in
from .input_channels import get_input_channels
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/segmentation/input_channels.py", line 3, in
from skimage.external.tifffile import TiffFile
ModuleNotFoundError: No module named 'skimage.external'
Before going any further, please let me know if I likely made a mistake or if there needs to be an update to the requirements list. I am in the same conda environment I used for generating the quality score, Windows Ubuntu 22.04.3 LTS (GNU/Linux 5.15.133.1-microsoft-standard-WSL2 x86_64)
Hello,
I successfully generated a config.json file and many dependencies were installed. However, after
python run_pipeline.py ./config.json
I find that numpy and frozendict are not in my environment created with requirements.txt as instructed. I installed these manually, but now I get:
Traceback (most recent call last): File "run_pipeline.py", line 2, in
from pipeline import pipeline
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/pipeline.py", line 9, in
from .segmentation.run_segmentation import *
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/segmentation/run_segmentation.py", line 4, in
from .input_channels import get_input_channels
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/segmentation/input_channels.py", line 3, in
from skimage.external.tifffile import TiffFile
ModuleNotFoundError: No module named 'skimage.external'
Before going any further, please let me know if I likely made a mistake or if there needs to be an update to the requirements list. I am in the same conda environment I used for generating the quality score, Windows Ubuntu 22.04.3 LTS (GNU/Linux 5.15.133.1-microsoft-standard-WSL2 x86_64)
Here is the result from my conda list
#
Name Version Build Channel
_libgcc_mutex 0.1 main _openmp_mutex 5.1 1_gnu aicsimageio 4.9.4 pypi_0 pypi annotated-types 0.6.0 pypi_0 pypi asciitree 0.3.3 pypi_0 pypi beautifulsoup4 4.12.2 pypi_0 pypi bfio 2.3.3 pypi_0 pypi bioformats-jar 2020.5.27 pypi_0 pypi blas 1.0 mkl ca-certificates 2023.11.17 hbcca054_0 conda-forge certifi 2023.11.17 pypi_0 pypi charset-normalizer 3.3.2 pypi_0 pypi click 8.1.7 pypi_0 pypi cloudpickle 3.0.0 pypi_0 pypi contourpy 1.1.1 pypi_0 pypi cycler 0.12.1 pypi_0 pypi dask 2023.5.0 pypi_0 pypi elementpath 4.1.5 pypi_0 pypi fasteners 0.19 pypi_0 pypi filelock 3.13.1 pypi_0 pypi fonttools 4.46.0 pypi_0 pypi frozendict 2.3.0 pypi_0 pypi fsspec 2023.12.1 pypi_0 pypi gdown 4.7.1 pypi_0 pypi idna 3.6 pypi_0 pypi imagecodecs 2023.3.16 pypi_0 pypi imageio 2.33.0 pypi_0 pypi importlib-metadata 7.0.0 pypi_0 pypi importlib-resources 6.1.1 pypi_0 pypi importlib_metadata 6.0.0 hd3eb1b0_0 intel-openmp 2021.4.0 h06a4308_3561 jgo 1.0.5 pypi_0 pypi joblib 1.3.2 pypi_0 pypi jpype1 1.4.1 pypi_0 pypi kiwisolver 1.4.5 pypi_0 pypi lazy-loader 0.3 pypi_0 pypi libedit 3.1.20221030 h5eee18b_0 libffi 3.2.1 hf484d3e_1007 libgcc-ng 11.2.0 h1234567_1 libgomp 11.2.0 h1234567_1 libllvm11 11.1.0 h9e868ea_6 libstdcxx-ng 11.2.0 h1234567_1 llvmlite 0.39.1 py38he621ea3_0 locket 1.0.0 pypi_0 pypi lxml 4.9.3 pypi_0 pypi matplotlib 3.7.4 pypi_0 pypi mkl 2021.4.0 h06a4308_640 mkl-service 2.4.0 py38h7f8727e_0 mkl_fft 1.3.1 py38hd3c417c_0 mkl_random 1.2.2 py38h51133e4_0 ncurses 6.4 h6a678d5_0 networkx 3.1 pypi_0 pypi numba 0.56.4 py38h417a72b_0 numcodecs 0.12.1 pypi_0 pypi numpy 1.21.6 pypi_0 pypi numpy-base 1.23.5 py38h31eccc5_0 ome-types 0.4.3 pypi_0 pypi opencv-python 4.8.1.78 pypi_0 pypi openssl 1.1.1l h7f98852_0 conda-forge packaging 23.2 pypi_0 pypi pandas 2.0.3 pypi_0 pypi partd 1.4.1 pypi_0 pypi pillow 10.1.0 pypi_0 pypi pint 0.21.1 pypi_0 pypi pip 23.3.1 py38h06a4308_0 psutil 5.9.6 pypi_0 pypi pydantic 2.5.2 pypi_0 pypi pydantic-compat 0.1.2 pypi_0 pypi pydantic-core 2.14.5 pypi_0 pypi pyparsing 3.1.1 pypi_0 pypi pysocks 1.7.1 pypi_0 pypi python 3.8.0 h0371630_2 python-bioformats 4.0.7 pypi_0 pypi python-dateutil 2.8.2 pypi_0 pypi pytz 2023.3.post1 pypi_0 pypi pywavelets 1.4.1 pypi_0 pypi pyyaml 6.0.1 pypi_0 pypi readline 7.0 h7b6447c_5 requests 2.31.0 pypi_0 pypi resource-backed-dask-array 0.1.0 pypi_0 pypi scikit-image 0.21.0 pypi_0 pypi scikit-learn 1.0.2 pypi_0 pypi scipy 1.10.1 pypi_0 pypi scyjava 1.9.1 pypi_0 pypi setuptools 68.0.0 py38h06a4308_0 six 1.16.0 pyhd3eb1b0_1 soupsieve 2.5 pypi_0 pypi sqlite 3.33.0 h62c20be_0 tbb 2021.8.0 hdb19cb5_0 threadpoolctl 3.2.0 pypi_0 pypi tifffile 2023.7.10 pypi_0 pypi tk 8.6.12 h1ccaba5_0 toolz 0.12.0 pypi_0 pypi tqdm 4.66.1 pypi_0 pypi typing-extensions 4.8.0 pypi_0 pypi tzdata 2023.3 pypi_0 pypi urllib3 2.1.0 pypi_0 pypi wheel 0.41.2 py38h06a4308_0 wrapt 1.16.0 pypi_0 pypi xarray 2023.1.0 pypi_0 pypi xmlschema 2.5.0 pypi_0 pypi xmltodict 0.13.0 py38h06a4308_0 xsdata 23.8 pypi_0 pypi xz 5.4.5 h5eee18b_0 zarr 2.16.1 pypi_0 pypi zipp 3.17.0 pypi_0 pypi zlib 1.2.13 h5eee18b_0