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NifTK / NiftyNet

[unmaintained] An open-source convolutional neural networks platform for research in medical image analysis and image-guided therapy
http://niftynet.io
Apache License 2.0
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Problem with Installation of Niftynet (incompatible version of numpy and tensorbord between tensorflow and Niftynet) #447

Closed IsaacLord closed 4 years ago

IsaacLord commented 4 years ago

Im trying to install niftynet with "pip install tensorflow-gpu>=1.13.2" and continuing with "pip install niftynet". the python version=3.6.0

After installation I got the numpy mismatch as follow:

ERROR: tensorflow 1.12.0 has requirement tensorboard<1.13.0,>=1.12.0, but you'll have tensorboard 2.0.0 which is incompatible.

ERROR: tensorflow-gpu 2.0.0 has requirement numpy<2.0,>=1.16.0, but you'll have numpy 1.14.5 which is incompatible. Installing collected packages: numpy Found existing installation: numpy 1.17.2 Uninstalling numpy-1.17.2: Successfully uninstalled numpy-1.17.2 Successfully installed numpy-1.14.5

i can install with version tensorflow-gpu=1.12.0. however it doesn't work with tensor 1.13.! with this version i got the GPU->CPU Memcpy failed error.

Is there any suggestion for installation ?

GPU=2080ti CPU=i7 (9generation) Ram=32 Gb(DDR4)

danieltudosiu commented 4 years ago

Firstly please create a new virtual environment as described here. Then activate the virtual environment by using the "source /path/to/virtual/environment/bin/activate" and use the following command to install the required packages: "pip install -r requirements-gpu.txt". Where requirements_gpu.txt can be find in our git repository.

Edit: wrote the command to activate the environment

IsaacLord commented 4 years ago

Thanks for reply. I tried with different virtual environments (creating by using python, pip and conda (at windows)) however i still get this error! I followed the instrction as https://niftynet.readthedocs.io/en/dev/installation.html.

Would you please kindly advise me?

" ERROR: tensorflow-gpu 2.0.0 has requirement numpy<2.0,>=1.16.0, but you'll have numpy 1.14.5 which is incompatible. "

(NiftyNetVirtualEnv) C:\PIPENVS\NiftyNetVirtualEnv\Scripts>cd C:\PIPENVS\NifNets

(NiftyNetVirtualEnv) C:\PIPENVS\NifNets>pip install -r requirements-gpu.txt Collecting six>=1.10 (from -r requirements-gpu.txt (line 1)) Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl Collecting nibabel>=2.1.0 (from -r requirements-gpu.txt (line 2)) Using cached https://files.pythonhosted.org/packages/01/13/392132019093ddb7bc997f7f9843d406dc3302a27f01827d2fd028e03c50/nibabel-2.5.1-py3-none-any.whl Collecting numpy<=1.14.5,>=1.13.3 (from -r requirements-gpu.txt (line 3)) Using cached https://files.pythonhosted.org/packages/94/80/c49b01d8632f58aef25fbe9a05be56339b7bb94b1eefd4f5d8c087d002b5/numpy-1.14.5-cp37-none-win_amd64.whl Collecting scipy>=0.18 (from -r requirements-gpu.txt (line 4)) Using cached https://files.pythonhosted.org/packages/50/eb/defa40367863304e1ef01c6572584c411446a5f29bdd9dc90f91509e9144/scipy-1.3.1-cp37-cp37m-win_amd64.whl Collecting configparser (from -r requirements-gpu.txt (line 5)) Using cached https://files.pythonhosted.org/packages/7a/2a/95ed0501cf5d8709490b1d3a3f9b5cf340da6c433f896bbe9ce08dbe6785/configparser-4.0.2-py2.py3-none-any.whl Collecting tensorflow-gpu>=1.13.2 (from -r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/63/13/ea9ff554aa0043540a2387c28dd7926575eb25cf89e598caecea836d189d/tensorflow_gpu-2.0.0-cp37-cp37m-win_amd64.whl Collecting pandas (from -r requirements-gpu.txt (line 7)) Using cached https://files.pythonhosted.org/packages/b1/69/fcc29820befae2b96fd0b01225577af653e87cd0914634bb2d372a457bd7/pandas-0.25.1-cp37-cp37m-win_amd64.whl Collecting pillow (from -r requirements-gpu.txt (line 8)) Downloading https://files.pythonhosted.org/packages/14/db/f4c72818297d4d92083c1b3d3404efdb6b2734bea11c0950cfc48b832021/Pillow-6.2.0-cp37-cp37m-win_amd64.whl (2.0MB) |████████████████████████████████| 2.0MB 100kB/s Collecting blinker (from -r requirements-gpu.txt (line 9)) Using cached https://files.pythonhosted.org/packages/1b/51/e2a9f3b757eb802f61dc1f2b09c8c99f6eb01cf06416c0671253536517b6/blinker-1.4.tar.gz Collecting packaging (from -r requirements-gpu.txt (line 10)) Using cached https://files.pythonhosted.org/packages/cf/94/9672c2d4b126e74c4496c6b3c58a8b51d6419267be9e70660ba23374c875/packaging-19.2-py2.py3-none-any.whl Collecting google-pasta>=0.1.6 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/d0/33/376510eb8d6246f3c30545f416b2263eee461e40940c2a4413c711bdf62d/google_pasta-0.1.7-py3-none-any.whl Collecting opt-einsum>=2.3.2 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/b8/83/755bd5324777875e9dff19c2e59daec837d0378c09196634524a3d7269ac/opt_einsum-3.1.0.tar.gz Collecting wrapt>=1.11.1 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/23/84/323c2415280bc4fc880ac5050dddfb3c8062c2552b34c2e512eb4aa68f79/wrapt-1.11.2.tar.gz Collecting grpcio>=1.8.6 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/9a/28/18db422098a56a01bb753611a718b148963393f22efe9089711fb93440a3/grpcio-1.24.0-cp37-cp37m-win_amd64.whl Collecting tensorflow-estimator<2.1.0,>=2.0.0 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/95/00/5e6cdf86190a70d7382d320b2b04e4ff0f8191a37d90a422a2f8ff0705bb/tensorflow_estimator-2.0.0-py2.py3-none-any.whl Collecting keras-applications>=1.0.8 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl Collecting keras-preprocessing>=1.0.5 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/28/6a/8c1f62c37212d9fc441a7e26736df51ce6f0e38455816445471f10da4f0a/Keras_Preprocessing-1.1.0-py2.py3-none-any.whl Collecting gast==0.2.2 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/4e/35/11749bf99b2d4e3cceb4d55ca22590b0d7c2c62b9de38ac4a4a7f4687421/gast-0.2.2.tar.gz Requirement already satisfied: wheel>=0.26 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) (0.33.6) Collecting astor>=0.6.0 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/d1/4f/950dfae467b384fc96bc6469de25d832534f6b4441033c39f914efd13418/astor-0.8.0-py2.py3-none-any.whl Collecting absl-py>=0.7.0 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/3c/0d/7cbf64cac3f93617a2b6b079c0182e4a83a3e7a8964d3b0cc3d9758ba002/absl-py-0.8.0.tar.gz Collecting termcolor>=1.1.0 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/8a/48/a76be51647d0eb9f10e2a4511bf3ffb8cc1e6b14e9e4fab46173aa79f981/termcolor-1.1.0.tar.gz Collecting tensorboard<2.1.0,>=2.0.0 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/9b/a6/e8ffa4e2ddb216449d34cfcb825ebb38206bee5c4553d69e7bc8bc2c5d64/tensorboard-2.0.0-py3-none-any.whl Collecting protobuf>=3.6.1 (from tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/92/4e/a90c0000a8dee84c3717ccf86eaafd892f342b0aa242d3cb34d62b1b19dd/protobuf-3.9.2-cp37-cp37m-win_amd64.whl Collecting python-dateutil>=2.6.1 (from pandas->-r requirements-gpu.txt (line 7)) Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl Collecting pytz>=2017.2 (from pandas->-r requirements-gpu.txt (line 7)) Using cached https://files.pythonhosted.org/packages/87/76/46d697698a143e05f77bec5a526bf4e56a0be61d63425b68f4ba553b51f2/pytz-2019.2-py2.py3-none-any.whl Collecting pyparsing>=2.0.2 (from packaging->-r requirements-gpu.txt (line 10)) Using cached https://files.pythonhosted.org/packages/11/fa/0160cd525c62d7abd076a070ff02b2b94de589f1a9789774f17d7c54058e/pyparsing-2.4.2-py2.py3-none-any.whl Collecting h5py (from keras-applications>=1.0.8->tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/a1/6b/7f62017e3f0b32438dd90bdc1ff0b7b1448b6cb04a1ed84f37b6de95cd7b/h5py-2.10.0-cp37-cp37m-win_amd64.whl Collecting markdown>=2.6.8 (from tensorboard<2.1.0,>=2.0.0->tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/c0/4e/fd492e91abdc2d2fcb70ef453064d980688762079397f779758e055f6575/Markdown-3.1.1-py2.py3-none-any.whl Requirement already satisfied: setuptools>=41.0.0 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from tensorboard<2.1.0,>=2.0.0->tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) (41.2.0) Collecting werkzeug>=0.11.15 (from tensorboard<2.1.0,>=2.0.0->tensorflow-gpu>=1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/ce/42/3aeda98f96e85fd26180534d36570e4d18108d62ae36f87694b476b83d6f/Werkzeug-0.16.0-py2.py3-none-any.whl Building wheels for collected packages: blinker, opt-einsum, wrapt, gast, absl-py, termcolor Building wheel for blinker (setup.py) ... done Created wheel for blinker: filename=blinker-1.4-cp37-none-any.whl size=13452 sha256=d90429db2816d14935bd09a93f29c40d1449d604d5917adadafbb531fe0df98f Stored in directory: C:\Users\AI-Machine\AppData\Local\pip\Cache\wheels\92\a0\00\8690a57883956a301d91cf4ec999cc0b258b01e3f548f86e89 Building wheel for opt-einsum (setup.py) ... done Created wheel for opt-einsum: filename=opt_einsum-3.1.0-cp37-none-any.whl size=61701 sha256=cc7added8e60ad7e32146aabf898e96dc373a463224ea155ad748c0cdb72084c Stored in directory: C:\Users\AI-Machine\AppData\Local\pip\Cache\wheels\2c\b1\94\43d03e130b929aae7ba3f8d15cbd7bc0d1cb5bb38a5c721833 Building wheel for wrapt (setup.py) ... done Created wheel for wrapt: filename=wrapt-1.11.2-cp37-none-any.whl size=19597 sha256=c15a64412483ba6b6262b2d66f799ec6fd8cf7ca11f7b61dfe2b2be94388124f Stored in directory: C:\Users\AI-Machine\AppData\Local\pip\Cache\wheels\d7\de\2e\efa132238792efb6459a96e85916ef8597fcb3d2ae51590dfd Building wheel for gast (setup.py) ... done Created wheel for gast: filename=gast-0.2.2-cp37-none-any.whl size=7546 sha256=cc59ccac235c5222a5335d8628059f3548586640c03c0c5b99f20d1d8f4099b3 Stored in directory: C:\Users\AI-Machine\AppData\Local\pip\Cache\wheels\5c\2e\7e\a1d4d4fcebe6c381f378ce7743a3ced3699feb89bcfbdadadd Building wheel for absl-py (setup.py) ... done Created wheel for absl-py: filename=absl_py-0.8.0-cp37-none-any.whl size=120992 sha256=912ce7eecbe90819044339e1db77c5ba90ed44fc46bf7a2c8c0670577dae3576 Stored in directory: C:\Users\AI-Machine\AppData\Local\pip\Cache\wheels\9a\1e\7a\456008eb5e47fd5de792c6139df6d5b3d5f71d51c6a0b94799 Building wheel for termcolor (setup.py) ... done Created wheel for termcolor: filename=termcolor-1.1.0-cp37-none-any.whl size=4835 sha256=cf38a56ce32e0d66522c760357005d3984ca19a44e2c2a9c5c1d6bf9ae564541 Stored in directory: C:\Users\AI-Machine\AppData\Local\pip\Cache\wheels\7c\06\54\bc84598ba1daf8f970247f550b175aaaee85f68b4b0c5ab2c6 Successfully built blinker opt-einsum wrapt gast absl-py termcolor ERROR: tensorflow-gpu 2.0.0 has requirement numpy<2.0,>=1.16.0, but you'll have numpy 1.14.5 which is incompatible. Installing collected packages: six, numpy, nibabel, scipy, configparser, google-pasta, opt-einsum, wrapt, grpcio, tensorflow-estimator, h5py, keras-applications, keras-preprocessing, gast, astor, absl-py, termcolor, markdown, werkzeug, protobuf, tensorboard, tensorflow-gpu, python-dateutil, pytz, pandas, pillow, blinker, pyparsing, packaging Successfully installed absl-py-0.8.0 astor-0.8.0 blinker-1.4 configparser-4.0.2 gast-0.2.2 google-pasta-0.1.7 grpcio-1.24.0 h5py-2.10.0 keras-applications-1.0.8 keras-preprocessing-1.1.0 markdown-3.1.1 nibabel-2.5.1 numpy-1.14.5 opt-einsum-3.1.0 packaging-19.2 pandas-0.25.1 pillow-6.2.0 protobuf-3.9.2 pyparsing-2.4.2 python-dateutil-2.8.0 pytz-2019.2 scipy-1.3.1 six-1.12.0 tensorboard-2.0.0 tensorflow-estimator-2.0.0 tensorflow-gpu-2.0.0 termcolor-1.1.0 werkzeug-0.16.0 wrapt-1.11.2

(NiftyNetVirtualEnv) C:\PIPENVS\NifNets>net_regress train -c C:\Wholebody\Niftynet\ThreeD_Training\Extension\Whole_body_AC.ini 'net_regress' is not recognized as an internal or external command, operable program or batch file.

(NiftyNetVirtualEnv) C:\PIPENVS\NifNets>pip install niftynet Collecting niftynet Using cached https://files.pythonhosted.org/packages/ec/7d/f8b8f28e9872f6b00e244007a5c789c7db30cc904bbc0c150a4bfe4d2cfb/NiftyNet-0.5.0-py2.py3-none-any.whl Requirement already satisfied: six>=1.10 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (1.12.0) Requirement already satisfied: pandas in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (0.25.1) Requirement already satisfied: pillow in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (6.2.0) Requirement already satisfied: blinker in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (1.4) Requirement already satisfied: scipy>=0.18 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (1.3.1) Requirement already satisfied: packaging in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (19.2) Requirement already satisfied: nibabel>=2.1.0 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (2.5.1) Requirement already satisfied: configparser in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (4.0.2) Requirement already satisfied: numpy<=1.14.5,>=1.13.3 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from niftynet) (1.14.5) Requirement already satisfied: pytz>=2017.2 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from pandas->niftynet) (2019.2) Requirement already satisfied: python-dateutil>=2.6.1 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from pandas->niftynet) (2.8.0) Requirement already satisfied: pyparsing>=2.0.2 in c:\pipenvs\NiftyNetVirtualEnv\lib\site-packages (from packaging->niftynet) (2.4.2) Installing collected packages: niftynet Successfully installed niftynet-0.5.0

(NiftyNetVirtualEnv) C:\PIPENVS\NifNets>net_regress train -c C:\Wholebody\Niftynet\ThreeD_Training\Extension\E_AC.ini 2019-10-02 09:36:14.893051: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library cudart64_100.dll ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' ImportError: numpy.core.multiarray failed to import

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "", line 980, in _find_and_load SystemError: <class '_frozen_importlib._ModuleLockManager'> returned a result with an error set ImportError: numpy.core._multiarray_umath failed to import ImportError: numpy.core.umath failed to import 2019-10-02 09:36:15.130867: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr

(NiftyNetVirtualEnv) C:\PIPENVS\NifNets>

danieltudosiu commented 4 years ago

1) Is it correct if I assume you are on Windows? 2) Could you please write the sequence of commands that you enter to install the requirements? 3) Please get the requirements-gpu.txt install the requirements based on that file and then install NiftyNet via pip. 4) Just out of curiosity, could you please do "pip install numpy==1.16.0" 5) If 4) does not solve it could you please do "pip install tensorflow-gpu==1.13.2"

IsaacLord commented 4 years ago

I'm using windows 10. Python 3.7.3 I changed the requirement as you said:\ six>=1.10 nibabel>=2.1.0 numpy==1.16.0 scipy>=0.18 configparser tensorflow-gpu==1.13.2 pandas pillow blinker packaging

thena i follow this line : conda create -n NIFTYNETENVS conda activate NIFTYNETENVS the i download the repositry, and extract on C drive .

cd c:/ANIFTYNETS

pip install -r requirements-gpu.txt

then tried following lin: net_regress train -c C:\Wholebody\Niftynet\ThreeD_Training\Extension\Whole_body_AC.ini i got : 'net_regress' is not recognized as an internal or external command, operable program or batch file.

then : pip install niftynet

i got

(NIFTYNETENVS) C:\ANIFTYNETS>pip install niftynet Collecting niftynet Using cached https://files.pythonhosted.org/packages/ec/7d/f8b8f28e9872f6b00e244007a5c789c7db30cc904bbc0c150a4bfe4d2cfb/NiftyNet-0.5.0-py2.py3-none-any.whl Requirement already satisfied: pillow in c:\programdata\anaconda3\lib\site-packages (from niftynet) (6.1.0) Requirement already satisfied: configparser in c:\programdata\anaconda3\lib\site-packages (from niftynet) (4.0.2) Requirement already satisfied: nibabel>=2.1.0 in c:\programdata\anaconda3\lib\site-packages (from niftynet) (2.5.1) Requirement already satisfied: pandas in c:\programdata\anaconda3\lib\site-packages (from niftynet) (0.25.1) Requirement already satisfied: scipy>=0.18 in c:\programdata\anaconda3\lib\site-packages (from niftynet) (1.2.1) Requirement already satisfied: packaging in c:\programdata\anaconda3\lib\site-packages (from niftynet) (19.0) Collecting numpy<=1.14.5,>=1.13.3 (from niftynet) Using cached https://files.pythonhosted.org/packages/94/80/c49b01d8632f58aef25fbe9a05be56339b7bb94b1eefd4f5d8c087d002b5/numpy-1.14.5-cp37-none-win_amd64.whl Requirement already satisfied: blinker in c:\programdata\anaconda3\lib\site-packages (from niftynet) (1.4) Requirement already satisfied: six>=1.10 in c:\programdata\anaconda3\lib\site-packages (from niftynet) (1.12.0) Requirement already satisfied: python-dateutil>=2.6.1 in c:\programdata\anaconda3\lib\site-packages (from pandas->niftynet) (2.8.0) Requirement already satisfied: pytz>=2017.2 in c:\programdata\anaconda3\lib\site-packages (from pandas->niftynet) (2019.1) Requirement already satisfied: pyparsing>=2.0.2 in c:\programdata\anaconda3\lib\site-packages (from packaging->niftynet) (2.4.0) ERROR: tensorflow 1.14.0 requires google-pasta>=0.1.6, which is not installed. ERROR: tensorflow 1.14.0 has requirement tensorboard<1.15.0,>=1.14.0, but you'll have tensorboard 1.13.1 which is incompatible. ERROR: tensorflow 1.14.0 has requirement tensorflow-estimator<1.15.0rc0,>=1.14.0rc0, but you'll have tensorflow-estimator 1.13.0 which is incompatible. ERROR: orange3 3.23.0 has requirement numpy>=1.16.0, but you'll have numpy 1.14.5 which is incompatible. ERROR: opentsne 0.3.11 has requirement numpy>=1.14.6, but you'll have numpy 1.14.5 which is incompatible. Installing collected packages: numpy, niftynet Found existing installation: numpy 1.16.0 Uninstalling numpy-1.16.0: Successfully uninstalled numpy-1.16.0 Successfully installed niftynet-0.5.0 numpy-1.14.5

then :

(NIFTYNETENVS) C:\ANIFTYNETS>net_regress train -c C:\Wholebody\Niftynet\ThreeD_Training\Extension\Whole_body_AC.ini ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' ImportError: numpy.core.multiarray failed to import

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "", line 980, in _find_and_load SystemError: <class '_frozen_importlib._ModuleLockManager'> returned a result with an error set ImportError: numpy.core._multiarray_umath failed to import ImportError: numpy.core.umath failed to import 2019-10-02 11:49:25.001140: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr

(NIFTYNETENVS) C:\ANIFTYNETS>

also during installation igot:

ERROR: tensorflow 1.14.0 requires google-pasta>=0.1.6, which is not installed. ERROR: tensorflow 1.14.0 has requirement tensorboard<1.15.0,>=1.14.0, but you'll have tensorboard 1.13.1 which is incompatible. ERROR: tensorflow 1.14.0 has requirement tensorflow-estimator<1.15.0rc0,>=1.14.0rc0, but you'll have tensorflow-estimator 1.13.0 which is incompatible.

as follow:

(NIFTYNETENVS) C:\ANIFTYNETS>pip install -r requirements-gpu.txt Requirement already satisfied: six>=1.10 in c:\programdata\anaconda3\lib\site-packages (from -r requirements-gpu.txt (line 1)) (1.12.0) Requirement already satisfied: nibabel>=2.1.0 in c:\programdata\anaconda3\lib\site-packages (from -r requirements-gpu.txt (line 2)) (2.5.1) Collecting numpy==1.16.0 (from -r requirements-gpu.txt (line 3)) Using cached https://files.pythonhosted.org/packages/dd/3e/0d7a914ee6cceef588dd83b18e257dc474ac67028a8d340dfec644878128/numpy-1.16.0-cp37-cp37m-win_amd64.whl Requirement already satisfied: scipy>=0.18 in c:\programdata\anaconda3\lib\site-packages (from -r requirements-gpu.txt (line 4)) (1.2.1) Collecting configparser (from -r requirements-gpu.txt (line 5)) Using cached https://files.pythonhosted.org/packages/7a/2a/95ed0501cf5d8709490b1d3a3f9b5cf340da6c433f896bbe9ce08dbe6785/configparser-4.0.2-py2.py3-none-any.whl Collecting tensorflow-gpu==1.13.2 (from -r requirements-gpu.txt (line 6)) Downloading https://files.pythonhosted.org/packages/c3/b7/fb82f6cd82ffa6f68db2a64fbc32254544d152b1d464f24a01dcdebc3017/tensorflow_gpu-1.13.2-cp37-cp37m-win_amd64.whl (259.7MB) |████████████████████████████████| 259.7MB 177kB/s Requirement already satisfied: pandas in c:\programdata\anaconda3\lib\site-packages (from -r requirements-gpu.txt (line 7)) (0.25.1) Requirement already satisfied: pillow in c:\programdata\anaconda3\lib\site-packages (from -r requirements-gpu.txt (line 8)) (6.1.0) Collecting blinker (from -r requirements-gpu.txt (line 9)) Requirement already satisfied: packaging in c:\programdata\anaconda3\lib\site-packages (from -r requirements-gpu.txt (line 10)) (19.0) Requirement already satisfied: gast>=0.2.0 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (0.2.2) Requirement already satisfied: protobuf>=3.6.1 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (3.8.0) Requirement already satisfied: keras-applications>=1.0.6 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (1.0.8) Collecting tensorflow-estimator<1.14.0rc0,>=1.13.0 (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/bb/48/13f49fc3fa0fdf916aa1419013bb8f2ad09674c275b4046d5ee669a46873/tensorflow_estimator-1.13.0-py2.py3-none-any.whl Collecting tensorboard<1.14.0,>=1.13.0 (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) Using cached https://files.pythonhosted.org/packages/0f/39/bdd75b08a6fba41f098b6cb091b9e8c7a80e1b4d679a581a0ccd17b10373/tensorboard-1.13.1-py3-none-any.whl Requirement already satisfied: absl-py>=0.1.6 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (0.7.1) Requirement already satisfied: grpcio>=1.8.6 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (1.16.1) Requirement already satisfied: keras-preprocessing>=1.0.5 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (1.1.0) Requirement already satisfied: termcolor>=1.1.0 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (1.1.0) Requirement already satisfied: astor>=0.6.0 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (0.8.0) Requirement already satisfied: wheel>=0.26 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (0.33.4) Requirement already satisfied: python-dateutil>=2.6.1 in c:\programdata\anaconda3\lib\site-packages (from pandas->-r requirements-gpu.txt (line 7)) (2.8.0) Requirement already satisfied: pytz>=2017.2 in c:\programdata\anaconda3\lib\site-packages (from pandas->-r requirements-gpu.txt (line 7)) (2019.1) Requirement already satisfied: pyparsing>=2.0.2 in c:\programdata\anaconda3\lib\site-packages (from packaging->-r requirements-gpu.txt (line 10)) (2.4.0) Requirement already satisfied: setuptools in c:\programdata\anaconda3\lib\site-packages (from protobuf>=3.6.1->tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (41.2.0) Requirement already satisfied: h5py in c:\programdata\anaconda3\lib\site-packages (from keras-applications>=1.0.6->tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (2.8.0) Requirement already satisfied: mock>=2.0.0 in c:\programdata\anaconda3\lib\site-packages (from tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (3.0.5) Requirement already satisfied: werkzeug>=0.11.15 in c:\programdata\anaconda3\lib\site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (0.15.4) Requirement already satisfied: markdown>=2.6.8 in c:\programdata\anaconda3\lib\site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow-gpu==1.13.2->-r requirements-gpu.txt (line 6)) (3.1.1) ERROR: tensorflow 1.14.0 requires google-pasta>=0.1.6, which is not installed. ERROR: tensorflow 1.14.0 has requirement tensorboard<1.15.0,>=1.14.0, but you'll have tensorboard 1.13.1 which is incompatible. ERROR: tensorflow 1.14.0 has requirement tensorflow-estimator<1.15.0rc0,>=1.14.0rc0, but you'll have tensorflow-estimator 1.13.0 which is incompatible. Installing collected packages: numpy, configparser, tensorflow-estimator, tensorboard, tensorflow-gpu, blinker Found existing installation: numpy 1.16.4 Uninstalling numpy-1.16.4: Successfully uninstalled numpy-1.16.4 Found existing installation: tensorflow-estimator 1.14.0 Uninstalling tensorflow-estimator-1.14.0: Successfully uninstalled tensorflow-estimator-1.14.0 Found existing installation: tensorboard 1.14.0 Uninstalling tensorboard-1.14.0: Successfully uninstalled tensorboard-1.14.0 Successfully installed blinker-1.4 configparser-4.0.2 numpy-1.16.0 tensorboard-1.13.1 tensorflow-estimator-1.13.0 tensorflow-gpu-1.13.2

IsaacLord commented 4 years ago

Also, after that i tried with pip install numpy==1.16.0 then
pip install tensorflow-gpu==1.13.2

Now its seems ok! However , when i'm trying use it : net_regress train -c C:\Wholebody\Niftynet\ThreeD_Training\Extension\Whole_body_AC.ini i got:

(NIFTYNETENVS) C:\ANIFTYNETS>net_regress train -c C:\Wholebody\Niftynet\ThreeD_Training\Extension\Whole_body_AC.ini c:\programdata\anaconda3\lib\site-packages\h5py__init.py:72: UserWarning: h5py is running against HDF5 1.10.2 when it was built against 1.10.3, this may cause problems '{0}.{1}.{2}'.format(*version.hdf5_built_version_tuple) Traceback (most recent call last): File "c:\programdata\anaconda3\lib\runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "c:\programdata\anaconda3\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\ProgramData\Anaconda3\Scripts\net_regress.exe\main.py", line 5, in File "c:\programdata\anaconda3\lib\site-packages\niftynet\init__.py", line 48, in set_logger() File "c:\programdata\anaconda3\lib\site-packages\niftynet\io\misc_io.py", line 756, in set_logger from tensorflow.python.platform.tf_logging import _get_logger ImportError: cannot import name '_get_logger' from 'tensorflow.python.platform.tf_logging' (c:\programdata\anaconda3\lib\site-packages\tensorflow\python\platform\tf_logging.py)

(NIFTYNETENVS) C:\ANIFTYNETS>

IsaacLord commented 4 years ago

I found this this issue here: https://stackoverflow.com/questions/54271943/importerror-cannot-import-name-get-logger-niftynet

however when im using tensor 1.12.0, i cant run on gpu as i mentioned in :
GPU->CPU Memcpy failed https://github.com/NifTK/NiftyNet/issues/created_by/DeepMedi

I'm looking forward to hear your kind advice. thanks.

IsaacLord commented 4 years ago

Also, I tried in another Environment with default requirement and then changed as you said:

six>=1.10 nibabel>=2.1.0 numpy>=1.13.3, <= 1.14.5 scipy>=0.18 configparser tensorflow-gpu>=1.13.2 pandas pillow blinker packaging

then change : Just out of curiosity, could you please do "pip install numpy==1.16.0" If 4) does not solve it could you please do "pip install tensorflow-gpu==1.13.2"

then i got following error:

(ISACNet) C:\windows\system32>pip install numpy==1.16.0 Collecting numpy==1.16.0 Using cached https://files.pythonhosted.org/packages/31/7e/8905636f7e4f9b9d7078aa0e701500634f832f145855a11beb098d3b0fb1/numpy-1.16.0-cp36-cp36m-win_amd64.whl ERROR: tensorflow 1.12.3 has requirement tensorboard<1.13.0,>=1.12.0, but you'll have tensorboard 1.13.1 which is incompatible. ERROR: niftynet 0.5.0 has requirement numpy<=1.14.5,>=1.13.3, but you'll have numpy 1.16.0 which is incompatible. Installing collected packages: numpy Found existing installation: numpy 1.14.4 Uninstalling numpy-1.14.4: Successfully uninstalled numpy-1.14.4 Successfully installed numpy-1.16.0

(ISACNet) C:\windows\system32>pip install numpy==1.16.0 Requirement already satisfied: numpy==1.16.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (1.16.0)

(ISACNet) C:\windows\system32>pip install tensorflow-gpu==1.13.2 Requirement already satisfied: tensorflow-gpu==1.13.2 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (1.13.2) Requirement already satisfied: gast>=0.2.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (0.2.2) Requirement already satisfied: tensorflow-estimator<1.14.0rc0,>=1.13.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (1.13.0) Requirement already satisfied: numpy<2.0,>=1.16.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (1.16.0) Requirement already satisfied: astor>=0.6.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (0.8.0) Requirement already satisfied: protobuf>=3.6.1 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (3.9.2) Requirement already satisfied: grpcio>=1.8.6 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (1.16.1) Requirement already satisfied: keras-applications>=1.0.6 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (1.0.8) Requirement already satisfied: keras-preprocessing>=1.0.5 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (1.1.0) Requirement already satisfied: tensorboard<1.14.0,>=1.13.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (1.13.1) Requirement already satisfied: six>=1.10.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (1.12.0) Requirement already satisfied: wheel>=0.26 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (0.33.6) Requirement already satisfied: termcolor>=1.1.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (1.1.0) Requirement already satisfied: absl-py>=0.1.6 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-gpu==1.13.2) (0.8.0) Requirement already satisfied: mock>=2.0.0 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow-gpu==1.13.2) (3.0.5) Requirement already satisfied: setuptools in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from protobuf>=3.6.1->tensorflow-gpu==1.13.2) (41.2.0) Requirement already satisfied: h5py in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from keras-applications>=1.0.6->tensorflow-gpu==1.13.2) (2.9.0) Requirement already satisfied: werkzeug>=0.11.15 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow-gpu==1.13.2) (0.16.0) Requirement already satisfied: markdown>=2.6.8 in c:\programdata\anaconda3\envs\isacnet\lib\site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow-gpu==1.13.2) (3.1.1)

(ISACNet) C:\windows\system32>net_regress train -c C:\Wholebody\Niftynet\ThreeD_Training\Extension\Whole_body_AC.ini CRITICAL:tensorflow:Optional Python module cv2 not found, please install cv2 and retry if the application fails. CRITICAL:tensorflow:Optional Python module skimage.io not found, please install skimage.io and retry if the application fails. CRITICAL:tensorflow:Optional Python module SimpleITK not found, please install SimpleITK and retry if the application fails. Traceback (most recent call last): File "c:\programdata\anaconda3\envs\isacnet\lib\runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "c:\programdata\anaconda3\envs\isacnet\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\ProgramData\Anaconda3\envs\ISACNet\Scripts\net_regress.exe__main.py", line 5, in File "c:\programdata\anaconda3\envs\isacnet\lib\site-packages\niftynet\init__.py", line 48, in set_logger() File "c:\programdata\anaconda3\envs\isacnet\lib\site-packages\niftynet\io\misc_io.py", line 756, in set_logger from tensorflow.python.platform.tf_logging import _get_logger ImportError: cannot import name '_get_logger'

(ISACNet) C:\windows\system32>

IsaacLord commented 4 years ago

Find the solution. Just change the : _get_logger -> get_logger in files

It dose work know!