Failing on last step of notebook #158
Description
Hello! I am trying to use this package and I have gotten everything working inside of WSL2. I am running a conda environment and I am able to make it to the last step in the notebook upon where the program fails.
I think I first started with this error:
{
"name": "ModuleNotFoundError",
"message": "No module named 'bioimageio.core.build_spec'",
"stack": "---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
Cell In[32], line 1
----> 1 model.export_TF(name='Noise2Void - 2D RGB Example',
2 description='This is the 2D Noise2Void example trained on RGB data in python.',
3 authors=[\"Max\"],
4 test_img=X_val[0], axes='YXC',
5 patch_shape=patch_shape)
File ~/miniconda3/envs/n2v10/lib/python3.9/site-packages/csbdeep/models/base_model.py:32, in suppress_without_basedir.<locals>._suppress_without_basedir.<locals>.wrapper(*args, **kwargs)
30 warn is False or warnings.warn(\"Suppressing call of '%s' (due to basedir=None).\" % f.__name__)
31 else:
---> 32 return f(*args, **kwargs)
File ~/miniconda3/envs/n2v10/lib/python3.9/site-packages/n2v/models/n2v_standard.py:542, in N2V.export_TF(self, name, description, authors, test_img, axes, patch_shape, license, result_path)
539 files = [str(config_path.absolute()), str(model_path.absolute())]
540 result_archive_path = result_path / (result_path.stem + Extensions.BIOIMAGE_EXT.value)
--> 542 build_modelzoo(
543 result_archive_path,
544 model_path,
545 result_path,
546 input_file,
547 output_file,
548 preprocessing,
549 postprocessing,
550 doc,
551 name,
552 authors,
553 algorithm,
554 tf.__version__,
555 cite,
556 new_axes,
557 files
558 )
560 print(\"\
Model exported in BioImage ModelZoo format:\
%s\" % str(result_archive_path.resolve()))
File ~/miniconda3/envs/n2v10/lib/python3.9/site-packages/n2v/utils/export_utils.py:126, in build_modelzoo(result_path, weights_path, bundle_path, inputs, outputs, preprocessing, postprocessing, doc, name, authors, algorithm, tf_version, cite, axes, files, **kwargs)
108 def build_modelzoo(
109 result_path: Union[str, Path],
110 weights_path: Union[str, Path],
(...)
124 **kwargs,
125 ):
--> 126 from bioimageio.core.build_spec import build_model
128 tags_dim = \"3d\" if len(axes) == 5 else \"2d\"
130 build_model(
131 root=bundle_path,
132 weight_uri=weights_path,
(...)
156 **kwargs,
157 )
ModuleNotFoundError: No module named 'bioimageio.core.build_spec'"
}
Despite having the package:
pip show bioimageio.core
Name: bioimageio.core
Version: 0.7.0
Summary: Python functionality for the bioimage model zoo
Home-page: https://github.com/bioimage-io/core-bioimage-io-python
Author: Bioimage Team
Author-email:
License: UNKNOWN
Location: /home/max/miniconda3/envs/n2v10/lib/python3.9/site-packages
Requires: bioimageio.spec, h5py, imageio, loguru, numpy, pydantic, pydantic-settings, requests, ruyaml, tqdm, typing-extensions, xarray
Required-by: n2v
conda list bioimageio
# packages in environment at /home/max/miniconda3/envs/n2v10:
#
# Name Version Build Channel
bioimageio-core 0.7.0 pypi_0 pypi
bioimageio-spec 0.5.3.5 pypi_0 pypi
Can anyone please verify what I am doing wrong from this point?