Warnings and tensorflow 1.15 #5

Gresliebear · 2021-02-18T03:51:31Z

test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ python main.py
WARNING:tensorflow:
The TensorFlow contrib module will not be included in TensorFlow 2.0.
For more information, please see:

https://github.com/tensorflow/community/blob/master/rfcs/20180907-contrib-sunset.md
https://github.com/tensorflow/addons
https://github.com/tensorflow/io (for I/O related ops)
If you depend on functionality not listed there, please file an issue.

/media/sdb1/liver_open/liverseg-2017-nipsws/results
Running step: seg_liver_test

Started loading files...
Done initializing Dataset
WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:590: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.

WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:594: The name tf.logging.set_verbosity is deprecated. Please use tf.compat.v1.logging.set_verbosity instead.

WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:594: The name tf.logging.INFO is deprecated. Please use tf.compat.v1.logging.INFO instead.

WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:603: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.

WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:75: The name tf.variable_scope is deprecated. Please use tf.compat.v1.variable_scope instead.

WARNING:tensorflow:From /media/sdb1/liver_open/test_env/local/lib/python2.7/site-packages/tensorflow_core/contrib/layers/python/layers/layers.py:1057: apply (from tensorflow.python.keras.engine.base_layer) is deprecated and will be removed in a future version.
Instructions for updating:
Please use layer.__call__ method instead.
WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:50: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Deprecated in favor of operator or tf.math.divide.
WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:612: The name tf.train.Saver is deprecated. Please use tf.compat.v1.train.Saver instead.

WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:612: The name tf.global_variables is deprecated. Please use tf.compat.v1.global_variables instead.

WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:614: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.

2021-02-17 22:47:05.508984: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2021-02-17 22:47:05.529184: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 4099895000 Hz
2021-02-17 22:47:05.529475: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x562f725d0b20 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2021-02-17 22:47:05.529487: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
2021-02-17 22:47:05.530404: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2021-02-17 22:47:05.530414: E tensorflow/stream_executor/cuda/cuda_driver.cc:318] failed call to cuInit: UNKNOWN ERROR (303)
2021-02-17 22:47:05.530422: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (john-desktop): /proc/driver/nvidia/version does not exist
WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:615: The name tf.global_variables_initializer is deprecated. Please use tf.compat.v1.global_variables_initializer instead.

WARNING:tensorflow:From /media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py:168: The name tf.assign is deprecated. Please use tf.compat.v1.assign instead.

INFO:tensorflow:Restoring parameters from /media/sdb1/liver_open/liverseg-2017-nipsws/train_files/seg_liver_ck/networks/seg_liver.ckpt
Traceback (most recent call last):
File "main.py", line 170, in
liver_lesion.test()
File "main.py", line 112, in test
step()
File "main.py", line 53, in seg_liver_test
seg_liver_test(self.config, self.number_slices)
File "/media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver_test.py", line 40, in seg_liver_test
segmentation.test(dataset, checkpoint_path, result_path, number_slices)
File "/media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py", line 629, in test
image = preprocess_img(curr_img, number_slices)
File "/media/sdb1/liver_open/liverseg-2017-nipsws/seg_liver.py", line 185, in preprocess_img
images[j].append(np.array(scipy.io.loadmat(image[0][i])['section'], dtype=np.float32))
File "/media/sdb1/liver_open/test_env/local/lib/python2.7/site-packages/scipy/io/matlab/mio.py", line 207, in loadmat
MR, file_opened = mat_reader_factory(file_name, appendmat, **kwargs)
File "/media/sdb1/liver_open/test_env/local/lib/python2.7/site-packages/scipy/io/matlab/mio.py", line 62, in mat_reader_factory
byte_stream, file_opened = _open_file(file_name, appendmat)
File "/media/sdb1/liver_open/test_env/local/lib/python2.7/site-packages/scipy/io/matlab/mio.py", line 37, in _open_file
return open(file_like, 'rb'), True
IOError: [Errno 2] No such file or directory: '/media/sdb1/liver_open/liverseg-2017-nipsws/LiTS_database/images_volumes/105/1.mat'
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ ls
config.py det_DatasetList det_lesion_test.pyc init.py main.py seg_lesion.pyc seg_liver.py seg_liver_train.pyc
config.pyc detection_results det_lesion_train.py InstallGuide.txt README.md seg_lesion_test.py seg_liver.pyc train_files
daisychain_test.txt det_lesion.py det_lesion_train.pyc LICENSE requirements.txt seg_lesion_test.pyc seg_liver_test.py utils
daisychain_train.txt det_lesion.pyc dev_script.py 'LiTS database' seg_DatasetList seg_lesion_train.py seg_liver_test.pyc
dataset det_lesion_test.py img LiTS_database seg_lesion.py seg_lesion_train.pyc seg_liver_train.py
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ cd LiTS dataset/
-bash: cd: too many arguments
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ ls
config.py det_DatasetList det_lesion_test.pyc init.py main.py seg_lesion.pyc seg_liver.py seg_liver_train.pyc
config.pyc detection_results det_lesion_train.py InstallGuide.txt README.md seg_lesion_test.py seg_liver.pyc train_files
daisychain_test.txt det_lesion.py det_lesion_train.pyc LICENSE requirements.txt seg_lesion_test.pyc seg_liver_test.py utils
daisychain_train.txt det_lesion.pyc dev_script.py 'LiTS database' seg_DatasetList seg_lesion_train.py seg_liver_test.pyc
dataset det_lesion_test.py img LiTS_database seg_lesion.py seg_lesion_train.pyc seg_liver_train.py
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ cd LiTS_database
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws/LiTS_database$ ks
ks: command not found
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws/LiTS_database$ ls
seg_liver_ck
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws/LiTS_database$ cd ..
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ rm -r LiTS_database/
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ Rename 'LiTS database'/ LiTS_database

Command 'Rename' not found, did you mean:

command 'rename' from deb rename

Try: sudo apt install

(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ rename 'LiTS database'/ LiTS_database

Command 'rename' not found, but can be installed with:

sudo apt install rename

(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ sudo apt install rename
[sudo] password for leslie:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following NEW packages will be installed:
rename
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 12.3 kB of archives.
After this operation, 37.9 kB of additional disk space will be used.
Get:1 http://us.archive.ubuntu.com/ubuntu bionic/universe amd64 rename all 0.20-7 [12.3 kB]
Fetched 12.3 kB in 0s (95.7 kB/s)
Selecting previously unselected package rename.
(Reading database ... 288571 files and directories currently installed.)
Preparing to unpack .../archives/rename_0.20-7_all.deb ...
Unpacking rename (0.20-7) ...
Setting up rename (0.20-7) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ rename 'LiTS database'/ LiTS_database
Search pattern not terminated at (user-supplied code).
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ sudo rename 'LiTS database'/ LiTS_database
Search pattern not terminated at (user-supplied code).
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ ls
config.py det_DatasetList det_lesion_test.pyc init.py README.md seg_lesion_test.py seg_liver.pyc train_files
config.pyc detection_results det_lesion_train.py InstallGuide.txt requirements.txt seg_lesion_test.pyc seg_liver_test.py utils
daisychain_test.txt det_lesion.py det_lesion_train.pyc LICENSE seg_DatasetList seg_lesion_train.py seg_liver_test.pyc
daisychain_train.txt det_lesion.pyc dev_script.py 'LiTS database' seg_lesion.py seg_lesion_train.pyc seg_liver_train.py
dataset det_lesion_test.py img main.py seg_lesion.pyc seg_liver.py seg_liver_train.pyc
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ mv 'LiTS database'/ LiTS_database
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ ls
config.py det_DatasetList det_lesion_test.pyc init.py README.md seg_lesion_test.py seg_liver.pyc train_files
config.pyc detection_results det_lesion_train.py InstallGuide.txt requirements.txt seg_lesion_test.pyc seg_liver_test.py utils
daisychain_test.txt det_lesion.py det_lesion_train.pyc LICENSE seg_DatasetList seg_lesion_train.py seg_liver_test.pyc
daisychain_train.txt det_lesion.pyc dev_script.py LiTS_database seg_lesion.py seg_lesion_train.pyc seg_liver_train.py
dataset det_lesion_test.py img main.py seg_lesion.pyc seg_liver.py seg_liver_train.pyc
(test_env) leslie@john-desktop:/media/sdb1/liver_open/liverseg-2017-nipsws$ python main.py
WARNING:tensorflow:
The TensorFlow contrib module will not be included in TensorFlow 2.0.
For more information, please see:

https://github.com/tensorflow/community/blob/master/rfcs/20180907-contrib-sunset.md
https://github.com/tensorflow/addons
https://github.com/tensorflow/io (for I/O related ops)
If you depend on functionality not listed there, please file an issue.