rsanchezgarc
commented
1 month ago Hi, Can you tell me how you installed deepEMhancer?
The error is complaining about your pandas package installation. If I remember correctly, pandas is not a dependency of DeepEMhancer, so it may be conflicting with some already installed versions. Can you check its version and where it is located?
conda activate deepEMhancer_env
python -c "import pandas as pd; print(pd.__version__);print(pd.__file__)"In my installation says
ModuleNotFoundError: No module named 'pandas'Whereas, in yours, if I am correct, it should show some version and location. If so, you need to remove pandas from the PYTHONPATH. Packages installed in the global environment (with pip install -u) can often interfere with local environments. Feel free to let me know if you need any more help.
papaig
Hi,
I just installed DeepEMhancer and when I try to run with the command: deepemhancer -i halfmapA.mrc -i2 halfmapB.mrc -o sharpened.map I got the bellow error. I would greatly appreciate your help. Gabor Error message: updating environment to select gpu: [1] loading model ~/.local/share/deepEMhancerModels/production_checkpoints/deepEMhancer_tightTarget.hd5 ... DONE! Automatic radial noise detected beyond 86.60254037844386 % of volume side DONE!. Shape at 1.00 A/voxel after padding-> (240, 240, 240) Neural net inference 0%| | 0/144 [00:00<?, ?it/s] Traceback (most recent call last): File "~/miniconda3/envs/deepEMhancer_env/bin/deepemhancer", line 8, in
sys.exit(commanLineFun())
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/deepEMhancer/exeDeepEMhancer.py", line 80, in commanLineFun
main( * parseArgs() )
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/deepEMhancer/exeDeepEMhancer.py", line 72, in main
predVol= predictor.predict(inputVolOrFname, outputMap, binary_mask=binaryMask, noise_stats=noiseStats,
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/deepEMhancer/applyProcessVol/processVol.py", line 194, in predict
batch_y_pred= self.model.predict_on_batch(np.expand_dims(batch_x, axis=-1))
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/keras/engine/training.py", line 2599, in predict_on_batch
iterator = data_adapter.single_batch_iterator(
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/keras/engine/data_adapter.py", line 1824, in single_batch_iterator
x, y, sample_weight = _process_tensorlike((x, y, sample_weight))
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/keras/engine/data_adapter.py", line 1140, in _process_tensorlike
inputs = tf.nest.map_structure(_convert_single_tensor, inputs)
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/tensorflow/python/util/nest.py", line 917, in map_structure
structure[0], [func(x) for x in entries],
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/tensorflow/python/util/nest.py", line 917, in
structure[0], [func(*x) for x in entries],
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/keras/engine/data_adapter.py", line 1128, in _convert_single_tensor
if _is_pandas_series(x):
File "~/miniconda3/envs/deepEMhancer_env/lib/python3.9/site-packages/keras/engine/data_adapter.py", line 1875, in _is_pandas_series
return isinstance(x, pd.Series)
AttributeError: module 'pandas' has no attribute 'Series'