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Hi all,
Due to my stuff not working anymore complaining about some pytorch internal issue and core-dumps, I re-installed my conda environment but still my previously working code won't work due to some import error (code and error below).
Is this a me-problem or might something be broken on the bioimage-io side?
This is what I have installed:
bioimageio.core 0.5.11 pyhd8ed1ab_0 conda-forge
bioimageio.spec 0.5.1 pyhd8ed1ab_0 conda-forge
Code:
def run_cebra_net(
input_data
):
# Set up the model
try:
rdf_path = os.path.join(
get_repo_path(), 'models', 'cebranet-cellular-membranes-in-volume-sem_torchscript.zip'
)
print(f'rdf_path = {rdf_path}')
model_resource = bioimageio.core.load_resource_description(rdf_path)
except TypeError:
rdf_doi = "10.5281/zenodo.7274275"
model_resource = bioimageio.core.load_resource_description(rdf_doi)
# Prepare the data
input_array = xr.DataArray(input_data[None, None, :], dims=tuple(model_resource.inputs[0].axes))
# Set up the prediction pipeline
devices = None
weight_format = None
prediction_pipeline = bioimageio.core.create_prediction_pipeline(
model_resource, devices=devices, weight_format=weight_format
)
# Make sure the input and output shapes match
prediction_pipeline.input_specs[0].shape = prediction_pipeline.output_specs[0].shape
tiling = True
# Predict with tiling
result = bioimageio.core.predict_with_tiling(prediction_pipeline, input_array, tiling=tiling, verbose=True)[0]
return (result[0, 0, :] * 255).astype('uint8')
Error:
/home/julian/miniconda3/envs/cebra-em-all-env/lib/python3.9/site-packages/networkx/utils/backends.py:135: RuntimeWarning: networkx backend defined more than once: nx-loopback
backends.update(_get_backends("networkx.backends"))
Traceback (most recent call last):
File "/media/julian/Data/tmp/test_cebra_em/proj/.snakemake/scripts/tmpehogir6d.run_task.py", line 17, in <module>
from cebra_em_core.bioimageio.cebra_net import run_cebra_net
File "/media/julian/Data/src/github/jhennies/CebraEM/cebra-em-core/cebra_em_core/bioimageio/cebra_net.py", line 2, in <module>
import bioimageio.core
File "/home/julian/miniconda3/envs/cebra-em-all-env/lib/python3.9/site-packages/bioimageio/core/__init__.py", line 6, in <module>
from .resource_io import (
File "/home/julian/miniconda3/envs/cebra-em-all-env/lib/python3.9/site-packages/bioimageio/core/resource_io/__init__.py", line 2, in <module>
from .io_ import (
File "/home/julian/miniconda3/envs/cebra-em-all-env/lib/python3.9/site-packages/bioimageio/core/resource_io/io_.py", line 11, in <module>
from bioimageio.core.resource_io.nodes import ResourceDescription
File "/home/julian/miniconda3/envs/cebra-em-all-env/lib/python3.9/site-packages/bioimageio/core/resource_io/nodes.py", line 9, in <module>
from bioimageio.spec.model import raw_nodes as model_raw_nodes
ImportError: cannot import name 'raw_nodes' from 'bioimageio.spec.model' (/home/julian/miniconda3/envs/cebra-em-all-env/lib/python3.9/site-packages/bioimageio/spec/model/__init__.py)
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