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I tried to run napari-empanada following the tutorial https://empanada.readthedocs.io/en/latest/tutorials/3d_tutorial.html#d-inference-tutorial
I installed it on windows 11 with the GPU support:
conda create -y -n empanada -c conda-forge python=3.9 conda activate empanada conda install pyqt pip install "napari[all]" conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia pip install empanada-napari=1.1.1
I started napari, started the plugin 3D inference, loaded the image Hela Cell FibSEM ( https://www.dropbox.com/s/2gu3go2puzc47ip/hela_cell_em.tif?dl=0 ) and pressed "Run 3D inference" and get the following error logs:
napari
3D inference
napari ImportError: _multiarray_umath failed to import C:\Users\u0094799\.conda\envs\empanada\lib\site-packages\torch\_subclasses\functional_tensor.py:258: UserWarning: Failed to initialize NumPy: CPU dispatcher tracer already initlized (Triggered internally at C:\cb\pytorch_1000000000000\work\torch\csrc\utils\tensor_numpy.cpp:84.)! Running without zarr storage directory, this may use a lot of memory! Predicting xy... 0%| | 0/256 [00:00<?, ?it/s] --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) File ~\.conda\envs\empanada\lib\site-packages\superqt\utils\_qthreading.py:613, in create_worker.<locals>.reraise(e=RuntimeError('Numpy is not available')) 612 def reraise(e): --> 613 raise e e = RuntimeError('Numpy is not available') File ~\.conda\envs\empanada\lib\site-packages\superqt\utils\_qthreading.py:175, in WorkerBase.run(self=<napari._qt.qthreading.FunctionWorker object>) 173 warnings.filterwarnings("always") 174 warnings.showwarning = lambda *w: self.warned.emit(w) --> 175 result = self.work() self = <napari._qt.qthreading.FunctionWorker object at 0x0000021E8C513940> 176 if isinstance(result, Exception): 177 if isinstance(result, RuntimeError): 178 # The Worker object has likely been deleted. 179 # A deleted wrapped C/C++ object may result in a runtime 180 # error that will cause segfault if we try to do much other 181 # than simply notify the user. File ~\.conda\envs\empanada\lib\site-packages\superqt\utils\_qthreading.py:354, in FunctionWorker.work(self=<napari._qt.qthreading.FunctionWorker object>) 353 def work(self) -> _R: --> 354 return self._func(*self._args, **self._kwargs) self._func = <function volume_inference_widget.<locals>.stack_inference at 0x0000021E28751DC0> self = <napari._qt.qthreading.FunctionWorker object at 0x0000021E8C513940> self._args = (<empanada_napari.inference.Engine3d object at 0x0000021E8C516FD0>, <class 'numpy.ndarray'> (256, 256, 256) uint8, 'xy') self._kwargs = {} File ~\.conda\envs\empanada\lib\site-packages\empanada_napari\_volume_inference.py:27, in volume_inference_widget.<locals>.stack_inference(engine=<empanada_napari.inference.Engine3d object>, volume=<class 'numpy.ndarray'> (256, 256, 256) uint8, axis_name='xy') 25 @thread_worker 26 def stack_inference(engine, volume, axis_name): ---> 27 stack, trackers = engine.infer_on_axis(volume, axis_name) volume = <class 'numpy.ndarray'> (256, 256, 256) uint8 axis_name = 'xy' engine = <empanada_napari.inference.Engine3d object at 0x0000021E8C516FD0> 28 trackers_dict = {axis_name: trackers} 29 return stack, axis_name, trackers_dict File ~\.conda\envs\empanada\lib\site-packages\empanada_napari\inference.py:513, in Engine3d.infer_on_axis(self=<empanada_napari.inference.Engine3d object>, volume=<class 'numpy.ndarray'> (256, 256, 256) uint8, axis_name='xy') 510 matcher_proc.start() 512 print(f'Predicting {axis_name}...') --> 513 for batch in tqdm(dataloader, total=len(dataloader)): dataloader = <torch.utils.data.dataloader.DataLoader object at 0x0000021E8C509A90> 514 image = batch['image'] 515 size = batch['size'] File ~\.conda\envs\empanada\lib\site-packages\tqdm\std.py:1181, in tqdm.__iter__(self=<tqdm.std.tqdm object>) 1178 time = self._time 1180 try: -> 1181 for obj in iterable: iterable = <torch.utils.data.dataloader.DataLoader object at 0x0000021E8C509A90> 1182 yield obj 1183 # Update and possibly print the progressbar. 1184 # Note: does not call self.update(1) for speed optimisation. File ~\.conda\envs\empanada\lib\site-packages\torch\utils\data\dataloader.py:630, in _BaseDataLoaderIter.__next__(self=<torch.utils.data.dataloader._SingleProcessDataLoaderIter object>) 627 if self._sampler_iter is None: 628 # TODO(https://github.com/pytorch/pytorch/issues/76750) 629 self._reset() # type: ignore[call-arg] --> 630 data = self._next_data() self = <torch.utils.data.dataloader._SingleProcessDataLoaderIter object at 0x0000021E98B7EFD0> 631 self._num_yielded += 1 632 if self._dataset_kind == _DatasetKind.Iterable and \ 633 self._IterableDataset_len_called is not None and \ 634 self._num_yielded > self._IterableDataset_len_called: File ~\.conda\envs\empanada\lib\site-packages\torch\utils\data\dataloader.py:673, in _SingleProcessDataLoaderIter._next_data(self=<torch.utils.data.dataloader._SingleProcessDataLoaderIter object>) 671 def _next_data(self): 672 index = self._next_index() # may raise StopIteration --> 673 data = self._dataset_fetcher.fetch(index) # may raise StopIteration index = [0] self = <torch.utils.data.dataloader._SingleProcessDataLoaderIter object at 0x0000021E98B7EFD0> self._dataset_fetcher = <torch.utils.data._utils.fetch._MapDatasetFetcher object at 0x0000021E98B7EFA0> 674 if self._pin_memory: 675 data = _utils.pin_memory.pin_memory(data, self._pin_memory_device) File ~\.conda\envs\empanada\lib\site-packages\torch\utils\data\_utils\fetch.py:52, in _MapDatasetFetcher.fetch(self=<torch.utils.data._utils.fetch._MapDatasetFetcher object>, possibly_batched_index=[0]) 50 data = self.dataset.__getitems__(possibly_batched_index) 51 else: ---> 52 data = [self.dataset[idx] for idx in possibly_batched_index] self = <torch.utils.data._utils.fetch._MapDatasetFetcher object at 0x0000021E98B7EFA0> self.dataset = <empanada.data.volume_dataset.VolumeDataset object at 0x0000021E8C509D30> possibly_batched_index = [0] 53 else: 54 data = self.dataset[possibly_batched_index] File ~\.conda\envs\empanada\lib\site-packages\torch\utils\data\_utils\fetch.py:52, in <listcomp>(.0=<list_iterator object>) 50 data = self.dataset.__getitems__(possibly_batched_index) 51 else: ---> 52 data = [self.dataset[idx] for idx in possibly_batched_index] self = <torch.utils.data._utils.fetch._MapDatasetFetcher object at 0x0000021E98B7EFA0> self.dataset = <empanada.data.volume_dataset.VolumeDataset object at 0x0000021E8C509D30> idx = 0 53 else: 54 data = self.dataset[possibly_batched_index] File ~\.conda\envs\empanada\lib\site-packages\empanada\data\volume_dataset.py:51, in VolumeDataset.__getitem__(self=<empanada.data.volume_dataset.VolumeDataset object>, idx=0) 48 assert (image.shape[0] * self.scale) >= h 49 assert (image.shape[1] * self.scale) >= w ---> 51 image = self.tfs(image=image)['image'] image = <class 'numpy.ndarray'> (256, 256) uint8 self = <empanada.data.volume_dataset.VolumeDataset object at 0x0000021E8C509D30> self.tfs = <empanada_napari.utils.Preprocessor object at 0x0000021E98B65670> 53 return {'index': idx, 'image': image, 'size': (h, w)} File ~\.conda\envs\empanada\lib\site-packages\empanada_napari\utils.py:163, in Preprocessor.__call__(self=<empanada_napari.utils.Preprocessor object>, image=<class 'numpy.ndarray'> (256, 256) float32) 161 max_value = np.iinfo(image.dtype).max 162 image = normalize(image, self.mean, self.std, max_pixel_value=max_value) --> 163 return {'image': to_tensor(image)} image = <class 'numpy.ndarray'> (256, 256) float32 File ~\.conda\envs\empanada\lib\site-packages\empanada_napari\utils.py:148, in to_tensor(img=<class 'numpy.ndarray'> (256, 256) float32) 146 def to_tensor(img): 147 # move channel dim from last to first --> 148 tensor = torch.from_numpy(img[None]) img = <class 'numpy.ndarray'> (256, 256) float32 149 return tensor RuntimeError: Numpy is not available
conda list >conda list # packages in environment at C:\Users\u0094799\.conda\envs\empanada: # # Name Version Build Channel alabaster 0.7.16 pypi_0 pypi albumentations 1.3.1 pypi_0 pypi alembic 1.13.3 pypi_0 pypi aniso8601 9.0.1 pypi_0 pypi annotated-types 0.7.0 pypi_0 pypi app-model 0.2.8 pypi_0 pypi appdirs 1.4.4 pypi_0 pypi asciitree 0.3.3 pypi_0 pypi asttokens 2.4.1 pypi_0 pypi attrs 24.2.0 pypi_0 pypi babel 2.16.0 pypi_0 pypi blas 1.0 mkl conda-forge blinker 1.8.2 pypi_0 pypi brotli-python 1.1.0 py39ha51f57c_2 conda-forge build 1.2.2 pypi_0 pypi bzip2 1.0.8 h2466b09_7 conda-forge ca-certificates 2024.8.30 h56e8100_0 conda-forge cachetools 5.5.0 pypi_0 pypi cachey 0.2.1 pypi_0 pypi certifi 2024.8.30 pyhd8ed1ab_0 conda-forge cffi 1.17.1 py39ha55e580_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 pypi_0 pypi cloudpickle 3.0.0 pypi_0 pypi colorama 0.4.6 pypi_0 pypi comm 0.2.2 pypi_0 pypi connected-components-3d 3.18.0 pypi_0 pypi contourpy 1.2.1 pypi_0 pypi cuda-cccl 12.6.77 0 nvidia cuda-cccl_win-64 12.6.77 0 nvidia cuda-cudart 11.8.89 0 nvidia cuda-cudart-dev 11.8.89 0 nvidia cuda-cupti 11.8.87 0 nvidia cuda-libraries 11.8.0 0 nvidia cuda-libraries-dev 11.8.0 0 nvidia cuda-nvrtc 11.8.89 0 nvidia cuda-nvrtc-dev 11.8.89 0 nvidia cuda-nvtx 11.8.86 0 nvidia cuda-profiler-api 12.6.77 0 nvidia cuda-runtime 11.8.0 0 nvidia cuda-version 12.6 3 nvidia cycler 0.12.1 pypi_0 pypi cztile 0.1.2 pypi_0 pypi dask 2024.8.0 pypi_0 pypi databricks-sdk 0.33.0 pypi_0 pypi debugpy 1.8.6 pypi_0 pypi decorator 5.1.1 pypi_0 pypi deprecated 1.2.14 pypi_0 pypi docker 7.1.0 pypi_0 pypi docstring-parser 0.16 pypi_0 pypi docutils 0.17.1 pypi_0 pypi empanada-dl 0.1.7 pypi_0 pypi empanada-napari 1.1.1 pypi_0 pypi et-xmlfile 1.1.0 pypi_0 pypi exceptiongroup 1.2.2 pypi_0 pypi executing 2.1.0 pypi_0 pypi fasteners 0.19 pypi_0 pypi filelock 3.16.1 pyhd8ed1ab_0 conda-forge flask 3.0.3 pypi_0 pypi flexcache 0.3 pypi_0 pypi flexparser 0.3.1 pypi_0 pypi fonttools 4.54.1 pypi_0 pypi freetype 2.12.1 hdaf720e_2 conda-forge freetype-py 2.5.1 pypi_0 pypi fsspec 2024.9.0 pypi_0 pypi gitdb 4.0.11 pypi_0 pypi gitpython 3.1.43 pypi_0 pypi glib 2.82.1 h7025463_0 conda-forge glib-tools 2.82.1 h4394cf3_0 conda-forge google-auth 2.35.0 pypi_0 pypi graphene 3.3 pypi_0 pypi graphql-core 3.2.4 pypi_0 pypi graphql-relay 3.2.0 pypi_0 pypi greenlet 3.1.1 pypi_0 pypi gst-plugins-base 1.24.7 hb0a98b8_0 conda-forge gstreamer 1.24.7 h5006eae_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge heapdict 1.0.1 pypi_0 pypi hpack 4.0.0 pyh9f0ad1d_0 conda-forge hsluv 5.0.4 pypi_0 pypi hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 75.1 he0c23c2_0 conda-forge idna 3.10 pyhd8ed1ab_0 conda-forge imagecodecs 2024.9.22 pypi_0 pypi imagehash 4.3.1 pypi_0 pypi imageio 2.35.1 pypi_0 pypi imagesize 1.4.1 pypi_0 pypi importlib-metadata 8.4.0 pypi_0 pypi importlib-resources 6.4.5 pypi_0 pypi in-n-out 0.2.1 pypi_0 pypi intel-openmp 2024.2.1 h57928b3_1083 conda-forge ipykernel 6.29.5 pypi_0 pypi ipython 8.18.1 pypi_0 pypi itsdangerous 2.2.0 pypi_0 pypi jedi 0.19.1 pypi_0 pypi jinja2 3.1.4 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pypi_0 pypi jsonschema 4.23.0 pypi_0 pypi jsonschema-specifications 2023.12.1 pypi_0 pypi jupyter-client 8.6.3 pypi_0 pypi jupyter-core 5.7.2 pypi_0 pypi kiwisolver 1.4.7 pypi_0 pypi krb5 1.21.3 hdf4eb48_0 conda-forge lazy-loader 0.4 pypi_0 pypi lcms2 2.16 h67d730c_0 conda-forge lerc 4.0.0 h63175ca_0 conda-forge libblas 3.9.0 1_h8933c1f_netlib conda-forge libcblas 3.9.0 5_hd5c7e75_netlib conda-forge libclang13 19.1.0 default_ha5278ca_0 conda-forge libcublas 11.11.3.6 0 nvidia libcublas-dev 11.11.3.6 0 nvidia libcufft 10.9.0.58 0 nvidia libcufft-dev 10.9.0.58 0 nvidia libcurand 10.3.7.77 0 nvidia libcurand-dev 10.3.7.77 0 nvidia libcusolver 11.4.1.48 0 nvidia libcusolver-dev 11.4.1.48 0 nvidia libcusparse 11.7.5.86 0 nvidia libcusparse-dev 11.7.5.86 0 nvidia libdeflate 1.21 h2466b09_0 conda-forge libffi 3.4.2 h8ffe710_5 conda-forge libglib 2.82.1 h7025463_0 conda-forge libhwloc 2.11.1 default_h8125262_1000 conda-forge libiconv 1.17 hcfcfb64_2 conda-forge libintl 0.22.5 h5728263_3 conda-forge libintl-devel 0.22.5 h5728263_3 conda-forge libjpeg-turbo 3.0.0 hcfcfb64_1 conda-forge liblapack 3.9.0 5_hd5c7e75_netlib conda-forge libnpp 11.8.0.86 0 nvidia libnpp-dev 11.8.0.86 0 nvidia libnvjpeg 11.9.0.86 0 nvidia libnvjpeg-dev 11.9.0.86 0 nvidia libogg 1.3.5 h2466b09_0 conda-forge libpng 1.6.44 h3ca93ac_0 conda-forge libsqlite 3.46.1 h2466b09_0 conda-forge libtiff 4.7.0 hb151862_0 conda-forge libuv 1.49.0 h2466b09_0 conda-forge libvorbis 1.3.7 h0e60522_0 conda-forge libwebp-base 1.4.0 hcfcfb64_0 conda-forge libxcb 1.16 h013a479_1 conda-forge libxml2 2.12.7 h0f24e4e_4 conda-forge libzlib 1.3.1 h2466b09_2 conda-forge llvmlite 0.42.0 pypi_0 pypi locket 1.0.0 pypi_0 pypi m2w64-gcc-libgfortran 5.3.0 6 conda-forge m2w64-gcc-libs 5.3.0 7 conda-forge m2w64-gcc-libs-core 5.3.0 7 conda-forge m2w64-gmp 6.1.0 2 conda-forge m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge magicgui 0.9.1 pypi_0 pypi mako 1.3.5 pypi_0 pypi markdown 3.7 pypi_0 pypi markdown-it-py 3.0.0 pypi_0 pypi markupsafe 2.1.5 py39ha55e580_1 conda-forge matplotlib 3.8.4 pypi_0 pypi matplotlib-inline 0.1.7 pypi_0 pypi mdurl 0.1.2 pypi_0 pypi mkl 2023.1.0 h6a75c08_48682 conda-forge mlflow 2.16.2 pypi_0 pypi mlflow-skinny 2.16.2 pypi_0 pypi mpmath 1.3.0 pyhd8ed1ab_0 conda-forge msys2-conda-epoch 20160418 1 conda-forge napari 0.4.18 pypi_0 pypi napari-console 0.1.0 pypi_0 pypi napari-plugin-engine 0.2.0 pypi_0 pypi napari-plugin-manager 0.1.3 pypi_0 pypi napari-svg 0.2.0 pypi_0 pypi nest-asyncio 1.6.0 pypi_0 pypi networkx 3.2.1 pyhd8ed1ab_0 conda-forge npe2 0.7.7 pypi_0 pypi numba 0.59.0 pypi_0 pypi numcodecs 0.12.1 pypi_0 pypi numpy 1.22.0 pypi_0 pypi numpydoc 1.5.0 pypi_0 pypi opencv-python 4.9.0.80 pypi_0 pypi opencv-python-headless 4.9.0.80 pypi_0 pypi openjpeg 2.5.2 h3d672ee_0 conda-forge openpyxl 3.1.5 pypi_0 pypi openssl 3.3.2 h2466b09_0 conda-forge opentelemetry-api 1.27.0 pypi_0 pypi opentelemetry-sdk 1.27.0 pypi_0 pypi opentelemetry-semantic-conventions 0.48b0 pypi_0 pypi packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.0.3 pypi_0 pypi parso 0.8.4 pypi_0 pypi partd 1.4.2 pypi_0 pypi pcre2 10.44 h3d7b363_2 conda-forge pillow 10.4.0 py39hfa8c767_1 conda-forge pint 0.24.3 pypi_0 pypi pip 24.2 pyh8b19718_1 conda-forge platformdirs 4.3.6 pypi_0 pypi ply 3.11 pyhd8ed1ab_2 conda-forge pooch 1.8.2 pypi_0 pypi prompt-toolkit 3.0.48 pypi_0 pypi protobuf 5.28.2 pypi_0 pypi psutil 6.0.0 pypi_0 pypi psygnal 0.11.1 pypi_0 pypi pthread-stubs 0.4 hcd874cb_1001 conda-forge pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge pure-eval 0.2.3 pypi_0 pypi pyarrow 17.0.0 pypi_0 pypi pyasn1 0.6.1 pypi_0 pypi pyasn1-modules 0.4.1 pypi_0 pypi pyconify 0.1.6 pypi_0 pypi pycparser 2.22 pyhd8ed1ab_0 conda-forge pydantic 1.10.18 pypi_0 pypi pydantic-compat 0.1.2 pypi_0 pypi pydantic-core 2.23.4 pypi_0 pypi pygments 2.18.0 pypi_0 pypi pyopengl 3.1.7 pypi_0 pypi pyparsing 3.1.4 pypi_0 pypi pyproject-hooks 1.2.0 pypi_0 pypi pyqt 5.15.9 py39hb77abff_5 conda-forge pyqt5-sip 12.12.2 py39h99910a6_5 conda-forge pysocks 1.7.1 pyh0701188_6 conda-forge python 3.9.20 hfaddaf0_1_cpython conda-forge python-dateutil 2.9.0.post0 pypi_0 pypi python_abi 3.9 5_cp39 conda-forge pytorch 2.4.1 py3.9_cuda11.8_cudnn9_0 pytorch pytorch-cuda 11.8 h24eeafa_5 pytorch pytorch-mutex 1.0 cuda pytorch pytz 2024.2 pypi_0 pypi pywavelets 1.4.1 pypi_0 pypi pywin32 307 pypi_0 pypi pyyaml 6.0.2 py39ha55e580_1 conda-forge pyzmq 26.2.0 pypi_0 pypi qt-main 5.15.8 h264fbc2_26 conda-forge qtconsole 5.6.0 pypi_0 pypi qtpy 2.4.1 pypi_0 pypi qudida 0.0.4 pypi_0 pypi referencing 0.35.1 pypi_0 pypi requests 2.32.3 pyhd8ed1ab_0 conda-forge rich 13.9.2 pypi_0 pypi rpds-py 0.20.0 pypi_0 pypi rsa 4.9 pypi_0 pypi scikit-image 0.22.0 pypi_0 pypi scikit-learn 1.5.2 pypi_0 pypi scipy 1.11.4 pypi_0 pypi setuptools 75.1.0 pyhd8ed1ab_0 conda-forge shellingham 1.5.4 pypi_0 pypi simpleitk 2.4.0 pypi_0 pypi sip 6.7.12 py39h99910a6_0 conda-forge six 1.16.0 pypi_0 pypi smmap 5.0.1 pypi_0 pypi snowballstemmer 2.2.0 pypi_0 pypi sphinx 4.5.0 pypi_0 pypi sphinxcontrib-applehelp 2.0.0 pypi_0 pypi sphinxcontrib-devhelp 2.0.0 pypi_0 pypi sphinxcontrib-htmlhelp 2.1.0 pypi_0 pypi sphinxcontrib-jsmath 1.0.1 pypi_0 pypi sphinxcontrib-qthelp 2.0.0 pypi_0 pypi sphinxcontrib-serializinghtml 2.0.0 pypi_0 pypi sqlalchemy 2.0.35 pypi_0 pypi sqlparse 0.5.1 pypi_0 pypi stack-data 0.6.3 pypi_0 pypi superqt 0.6.7 pypi_0 pypi sympy 1.13.3 pyh04b8f61_3 conda-forge tabulate 0.9.0 pypi_0 pypi tbb 2021.13.0 hc790b64_0 conda-forge threadpoolctl 3.5.0 pypi_0 pypi tifffile 2024.8.30 pypi_0 pypi tk 8.6.13 h5226925_1 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.2 pyhd8ed1ab_0 conda-forge tomli-w 1.0.0 pypi_0 pypi toolz 1.0.0 pypi_0 pypi torchaudio 2.4.1 pypi_0 pypi torchvision 0.19.1 pypi_0 pypi tornado 6.4.1 pypi_0 pypi tqdm 4.66.5 pypi_0 pypi traitlets 5.14.3 pypi_0 pypi triangle 20230923 pypi_0 pypi typer 0.12.5 pypi_0 pypi typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024.2 pypi_0 pypi ucrt 10.0.22621.0 h57928b3_0 conda-forge urllib3 2.2.3 pyhd8ed1ab_0 conda-forge vc 14.3 h8a93ad2_21 conda-forge vc14_runtime 14.40.33810 ha82c5b3_21 conda-forge vispy 0.12.2 pypi_0 pypi vs2015_runtime 14.40.33810 h3bf8584_21 conda-forge waitress 3.0.0 pypi_0 pypi wcwidth 0.2.13 pypi_0 pypi werkzeug 3.0.4 pypi_0 pypi wheel 0.44.0 pyhd8ed1ab_0 conda-forge win_inet_pton 1.1.0 pyh7428d3b_7 conda-forge wrapt 1.16.0 pypi_0 pypi xorg-libxau 1.0.11 hcd874cb_0 conda-forge xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge xz 5.2.6 h8d14728_0 conda-forge yaml 0.2.5 h8ffe710_2 conda-forge zarr 2.17.1 pypi_0 pypi zipp 3.20.2 pypi_0 pypi zstandard 0.23.0 py39h9bf74da_1 conda-forge zstd 1.5.6 h0ea2cb4_0 conda-forge
pip list pip list Package Version ---------------------------------- ----------- alabaster 0.7.16 albumentations 1.3.1 alembic 1.13.3 aniso8601 9.0.1 annotated-types 0.7.0 app-model 0.2.8 appdirs 1.4.4 asciitree 0.3.3 asttokens 2.4.1 attrs 24.2.0 babel 2.16.0 blinker 1.8.2 Brotli 1.1.0 build 1.2.2 cachetools 5.5.0 cachey 0.2.1 certifi 2024.8.30 cffi 1.17.1 charset-normalizer 3.3.2 click 8.1.7 cloudpickle 3.0.0 colorama 0.4.6 comm 0.2.2 connected-components-3d 3.18.0 contourpy 1.2.1 cycler 0.12.1 cztile 0.1.2 dask 2024.8.0 databricks-sdk 0.33.0 debugpy 1.8.6 decorator 5.1.1 Deprecated 1.2.14 docker 7.1.0 docstring_parser 0.16 docutils 0.17.1 empanada-dl 0.1.7 empanada-napari 1.1.1 et-xmlfile 1.1.0 exceptiongroup 1.2.2 executing 2.1.0 fasteners 0.19 filelock 3.16.1 Flask 3.0.3 flexcache 0.3 flexparser 0.3.1 fonttools 4.54.1 freetype-py 2.5.1 fsspec 2024.9.0 gitdb 4.0.11 GitPython 3.1.43 google-auth 2.35.0 graphene 3.3 graphql-core 3.2.4 graphql-relay 3.2.0 greenlet 3.1.1 h2 4.1.0 HeapDict 1.0.1 hpack 4.0.0 hsluv 5.0.4 hyperframe 6.0.1 idna 3.10 imagecodecs 2024.9.22 ImageHash 4.3.1 imageio 2.35.1 imagesize 1.4.1 importlib_metadata 8.4.0 importlib_resources 6.4.5 in-n-out 0.2.1 ipykernel 6.29.5 ipython 8.18.1 itsdangerous 2.2.0 jedi 0.19.1 Jinja2 3.1.4 joblib 1.4.2 jsonschema 4.23.0 jsonschema-specifications 2023.12.1 jupyter_client 8.6.3 jupyter_core 5.7.2 kiwisolver 1.4.7 lazy_loader 0.4 llvmlite 0.42.0 locket 1.0.0 magicgui 0.9.1 Mako 1.3.5 Markdown 3.7 markdown-it-py 3.0.0 MarkupSafe 2.1.5 matplotlib 3.8.4 matplotlib-inline 0.1.7 mdurl 0.1.2 mlflow 2.16.2 mlflow-skinny 2.16.2 mpmath 1.3.0 napari 0.4.18 napari-console 0.1.0 napari-plugin-engine 0.2.0 napari-plugin-manager 0.1.3 napari-svg 0.2.0 nest-asyncio 1.6.0 networkx 3.2.1 npe2 0.7.7 numba 0.59.0 numcodecs 0.12.1 numpy 1.22.0 numpydoc 1.5.0 opencv-python 4.9.0.80 opencv-python-headless 4.9.0.80 openpyxl 3.1.5 opentelemetry-api 1.27.0 opentelemetry-sdk 1.27.0 opentelemetry-semantic-conventions 0.48b0 packaging 24.1 pandas 2.0.3 parso 0.8.4 partd 1.4.2 pillow 10.4.0 Pint 0.24.3 pip 24.2 platformdirs 4.3.6 ply 3.11 pooch 1.8.2 prompt_toolkit 3.0.48 protobuf 5.28.2 psutil 6.0.0 psygnal 0.11.1 pure_eval 0.2.3 pyarrow 17.0.0 pyasn1 0.6.1 pyasn1_modules 0.4.1 pyconify 0.1.6 pycparser 2.22 pydantic 1.10.18 pydantic-compat 0.1.2 pydantic_core 2.23.4 Pygments 2.18.0 PyOpenGL 3.1.7 pyparsing 3.1.4 pyproject_hooks 1.2.0 PyQt5 5.15.9 PyQt5-sip 12.12.2 PySocks 1.7.1 python-dateutil 2.9.0.post0 pytz 2024.2 PyWavelets 1.4.1 pywin32 307 PyYAML 6.0.2 pyzmq 26.2.0 qtconsole 5.6.0 QtPy 2.4.1 qudida 0.0.4 referencing 0.35.1 requests 2.32.3 rich 13.9.2 rpds-py 0.20.0 rsa 4.9 scikit-image 0.22.0 scikit-learn 1.5.2 scipy 1.11.4 setuptools 75.1.0 shellingham 1.5.4 SimpleITK 2.4.0 sip 6.7.12 six 1.16.0 smmap 5.0.1 snowballstemmer 2.2.0 Sphinx 4.5.0 sphinxcontrib-applehelp 2.0.0 sphinxcontrib-devhelp 2.0.0 sphinxcontrib-htmlhelp 2.1.0 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 2.0.0 sphinxcontrib-serializinghtml 2.0.0 SQLAlchemy 2.0.35 sqlparse 0.5.1 stack-data 0.6.3 superqt 0.6.7 sympy 1.13.3 tabulate 0.9.0 threadpoolctl 3.5.0 tifffile 2024.8.30 toml 0.10.2 tomli 2.0.2 tomli_w 1.0.0 toolz 1.0.0 torch 2.4.1 torchaudio 2.4.1 torchvision 0.19.1 tornado 6.4.1 tqdm 4.66.5 traitlets 5.14.3 triangle 20230923 typer 0.12.5 typing_extensions 4.12.2 tzdata 2024.2 urllib3 2.2.3 vispy 0.12.2 waitress 3.0.0 wcwidth 0.2.13 Werkzeug 3.0.4 wheel 0.44.0 win_inet_pton 1.1.0 wrapt 1.16.0 zarr 2.17.1 zipp 3.20.2 zstandard 0.23.0
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I tried to run napari-empanada following the tutorial https://empanada.readthedocs.io/en/latest/tutorials/3d_tutorial.html#d-inference-tutorial
I installed it on windows 11 with the GPU support:
conda create -y -n empanada -c conda-forge python=3.9 conda activate empanada conda install pyqt pip install "napari[all]" conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia pip install empanada-napari=1.1.1I started
napari, started the plugin3D inference, loaded the image Hela Cell FibSEM ( https://www.dropbox.com/s/2gu3go2puzc47ip/hela_cell_em.tif?dl=0 ) and pressed "Run 3D inference" and get the following error logs:The text was updated successfully, but these errors were encountered: