simongraham / hovernet_inference

HoVer-Net inference code for simultaneous nuclear segmentation and classification

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Filoudataset opened this issue · comments

Hi,

Thank you for your very impressive work.
However, I can't run an inference, I probably make a mistake but can't find where.
Below an exemple of my command line and the result I get:
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python run.py --gpu='0' --mode= tile --model=C:/Users/rocha/HVN_infer/models/pannuke.npz --input_dir= C:/Users/rocha/HVN_depart --output_dir=C:/Users/rocha/HVN_arrivee
2021-05-17 21:12:24.939438: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library cudart64_100.dll
WARNING:root:Limited tf.compat.v2.summary API due to missing TensorBoard installation.
WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\tfutils\common.py:151: The name tf.VERSION is deprecated. Please use tf.version.VERSION instead.

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\tfutils\common.py:151: The name tf.VERSION is deprecated. Please use tf.version.VERSION instead.

WARNING:tensorflow:
The TensorFlow contrib module will not be included in TensorFlow 2.0.
For more information, please see:

WARNING:tensorflow:
The TensorFlow contrib module will not be included in TensorFlow 2.0.
For more information, please see:

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\callbacks\graph.py:81: The name tf.GraphKeys is deprecated. Please use tf.compat.v1.GraphKeys instead.

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\callbacks\graph.py:81: The name tf.GraphKeys is deprecated. Please use tf.compat.v1.GraphKeys instead.

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\callbacks\hooks.py:13: The name tf.train.SessionRunHook is deprecated. Please use tf.estimator.SessionRunHook instead.

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\callbacks\hooks.py:13: The name tf.train.SessionRunHook is deprecated. Please use tf.estimator.SessionRunHook instead.

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\tfutils\optimizer.py:16: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\tfutils\optimizer.py:16: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\tfutils\sesscreate.py:20: The name tf.train.SessionCreator is deprecated. Please use tf.compat.v1.train.SessionCreator instead.

WARNING:tensorflow:From C:\Users\rocha\Anaconda3\envs\HVN_infer\lib\site-packages\tensorpack\tfutils\sesscreate.py:20: The name tf.train.SessionCreator is deprecated. Please use tf.compat.v1.train.SessionCreator instead.

Usage:
run.py [--gpu=] [--mode=] [--model=] [--input_dir=] [--output_dir=] [--cache_dir=] [--batch_size=] [--inf_tile_shape=] [--proc_tile_shape=] [--postproc_workers=] [--return_probs]
run.py (-h | --help)
run.py --version
"
Is it an install problem or a command line error.
Thks for your help

Phil