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Using AITom in Jupyter Notebook and Google Colab #96

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evaxguo opened this issue Jun 15, 2020 · 6 comments
Open

Using AITom in Jupyter Notebook and Google Colab #96

evaxguo opened this issue Jun 15, 2020 · 6 comments

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@evaxguo
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Contributor

evaxguo commented Jun 15, 2020

It would be great if AITom could be used in Jupyter Notebook and Google Colab.
@xulabs
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Owner

xulabs commented Jun 16, 2020

@evaxguo thanks for the suggestion. You are welcome to discuss with other team members to help to implement this feature.

@geoffwoollard
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Right now my colab is running Python 3.6.9 and Ubuntu 18.04.5 LTS. I see no reason why I couldn't git clone the aitom repo and install it. I am getting an error thorugh.

cd /
git clone https://github.com/xulabs/aitom.git
cd /aitom
sudo apt-get install python python3-dev fftw3-dev libblas3 liblapack3 libarmadillo-dev
pip install -r requirements.txt
sh clean.sh
sh build.sh

Reading package lists...
Building dependency tree...
Reading state information...
liblapack3 is already the newest version (3.7.1-4ubuntu1).
liblapack3 set to manually installed.
python is already the newest version (2.7.15~rc1-1).
python3-dev is already the newest version (3.6.7-1~18.04).
The following additional packages will be installed:
  libarpack2-dev libblas-dev libfftw3-bin libfftw3-long3 libfftw3-quad3
  libfftw3-single3 libsuperlu-dev
Suggested packages:
  libitpp-dev liblapack-doc libfftw3-doc libsuperlu-doc
The following NEW packages will be installed:
  libarmadillo-dev libarpack2-dev libblas-dev libblas3 libfftw3-bin
  libfftw3-dev libfftw3-long3 libfftw3-quad3 libfftw3-single3 libsuperlu-dev
0 upgraded, 10 newly installed, 0 to remove and 6 not upgraded.
Need to get 4,502 kB of archives.
After this operation, 28.0 MB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 libblas3 amd64 3.7.1-4ubuntu1 [140 kB]
Get:2 http://archive.ubuntu.com/ubuntu bionic/main amd64 libblas-dev amd64 3.7.1-4ubuntu1 [143 kB]
Get:3 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libarpack2-dev amd64 3.5.0+real-2 [97.3 kB]
Get:4 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libsuperlu-dev amd64 5.2.1+dfsg1-3 [16.3 kB]
Get:5 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libarmadillo-dev amd64 1:8.400.0+dfsg-2 [340 kB]
Get:6 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfftw3-long3 amd64 3.3.7-1 [308 kB]
Get:7 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfftw3-quad3 amd64 3.3.7-1 [552 kB]
Get:8 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfftw3-single3 amd64 3.3.7-1 [764 kB]
Get:9 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfftw3-bin amd64 3.3.7-1 [32.7 kB]
Get:10 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfftw3-dev amd64 3.3.7-1 [2,108 kB]
Fetched 4,502 kB in 0s (32.0 MB/s)
Selecting previously unselected package libblas3:amd64.
(Reading database ... 144617 files and directories currently installed.)
Preparing to unpack .../0-libblas3_3.7.1-4ubuntu1_amd64.deb ...
Unpacking libblas3:amd64 (3.7.1-4ubuntu1) ...
Selecting previously unselected package libblas-dev:amd64.
Preparing to unpack .../1-libblas-dev_3.7.1-4ubuntu1_amd64.deb ...
Unpacking libblas-dev:amd64 (3.7.1-4ubuntu1) ...
Selecting previously unselected package libarpack2-dev:amd64.
Preparing to unpack .../2-libarpack2-dev_3.5.0+real-2_amd64.deb ...
Unpacking libarpack2-dev:amd64 (3.5.0+real-2) ...
Selecting previously unselected package libsuperlu-dev:amd64.
Preparing to unpack .../3-libsuperlu-dev_5.2.1+dfsg1-3_amd64.deb ...
Unpacking libsuperlu-dev:amd64 (5.2.1+dfsg1-3) ...
Selecting previously unselected package libarmadillo-dev.
Preparing to unpack .../4-libarmadillo-dev_1%3a8.400.0+dfsg-2_amd64.deb ...
Unpacking libarmadillo-dev (1:8.400.0+dfsg-2) ...
Selecting previously unselected package libfftw3-long3:amd64.
Preparing to unpack .../5-libfftw3-long3_3.3.7-1_amd64.deb ...
Unpacking libfftw3-long3:amd64 (3.3.7-1) ...
Selecting previously unselected package libfftw3-quad3:amd64.
Preparing to unpack .../6-libfftw3-quad3_3.3.7-1_amd64.deb ...
Unpacking libfftw3-quad3:amd64 (3.3.7-1) ...
Selecting previously unselected package libfftw3-single3:amd64.
Preparing to unpack .../7-libfftw3-single3_3.3.7-1_amd64.deb ...
Unpacking libfftw3-single3:amd64 (3.3.7-1) ...
Selecting previously unselected package libfftw3-bin.
Preparing to unpack .../8-libfftw3-bin_3.3.7-1_amd64.deb ...
Unpacking libfftw3-bin (3.3.7-1) ...
Selecting previously unselected package libfftw3-dev:amd64.
Preparing to unpack .../9-libfftw3-dev_3.3.7-1_amd64.deb ...
Unpacking libfftw3-dev:amd64 (3.3.7-1) ...
Setting up libfftw3-quad3:amd64 (3.3.7-1) ...
Setting up libblas3:amd64 (3.7.1-4ubuntu1) ...
Setting up libarpack2-dev:amd64 (3.5.0+real-2) ...
Setting up libfftw3-single3:amd64 (3.3.7-1) ...
Setting up libfftw3-long3:amd64 (3.3.7-1) ...
Setting up libfftw3-bin (3.3.7-1) ...
Setting up libblas-dev:amd64 (3.7.1-4ubuntu1) ...
Setting up libsuperlu-dev:amd64 (5.2.1+dfsg1-3) ...
Setting up libfftw3-dev:amd64 (3.3.7-1) ...
Setting up libarmadillo-dev (1:8.400.0+dfsg-2) ...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
Processing triggers for libc-bin (2.27-3ubuntu1.2) ...
/sbin/ldconfig.real: /usr/local/lib/python3.6/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link

Requirement already satisfied: cython in /usr/local/lib/python3.6/dist-packages (from -r requirements.txt (line 1)) (0.29.21)
Requirement already satisfied: numpy in /usr/local/lib/python3.6/dist-packages (from -r requirements.txt (line 2)) (1.18.5)
Requirement already satisfied: scipy in /usr/local/lib/python3.6/dist-packages (from -r requirements.txt (line 3)) (1.4.1)
Requirement already satisfied: sklearn in /usr/local/lib/python3.6/dist-packages (from -r requirements.txt (line 4)) (0.0)
Collecting mrcfile
  Downloading https://files.pythonhosted.org/packages/79/aa/52aa135830f66259783207021849a8234551fc5e3db15f685201cb3d1bfa/mrcfile-1.1.2-py2.py3-none-any.whl (41kB)
Requirement already satisfied: matplotlib in /usr/local/lib/python3.6/dist-packages (from -r requirements.txt (line 6)) (3.2.2)
Collecting pypng
  Downloading https://files.pythonhosted.org/packages/bc/fb/f719f1ac965e2101aa6ea6f54ef8b40f8fbb033f6ad07c017663467f5147/pypng-0.0.20.tar.gz (649kB)
Requirement already satisfied: tensorflow in /usr/local/lib/python3.6/dist-packages (from -r requirements.txt (line 8)) (2.3.0)
Collecting keras==2.1.0
  Downloading https://files.pythonhosted.org/packages/bf/c2/b0c2ece713e754d1692aa432ad682751cd1ad6abf7500a534558b1fbfbe7/Keras-2.1.0-py2.py3-none-any.whl (302kB)
Collecting lsm-db
  Downloading https://files.pythonhosted.org/packages/17/f2/dc68ecdece424eb206c42b8db924c5a7f6dd97d26df42a1c9fb41a6fe555/lsm-db-0.6.4.tar.gz (316kB)
Requirement already satisfied: scikit-learn in /usr/local/lib/python3.6/dist-packages (from sklearn->-r requirements.txt (line 4)) (0.22.2.post1)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib->-r requirements.txt (line 6)) (1.2.0)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib->-r requirements.txt (line 6)) (2.8.1)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.6/dist-packages (from matplotlib->-r requirements.txt (line 6)) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib->-r requirements.txt (line 6)) (2.4.7)
Requirement already satisfied: tensorboard<3,>=2.3.0 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (2.3.0)
Requirement already satisfied: termcolor>=1.1.0 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (1.1.0)
Requirement already satisfied: tensorflow-estimator<2.4.0,>=2.3.0 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (2.3.0)
Requirement already satisfied: wrapt>=1.11.1 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (1.12.1)
Requirement already satisfied: h5py<2.11.0,>=2.10.0 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (2.10.0)
Requirement already satisfied: gast==0.3.3 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (0.3.3)
Requirement already satisfied: wheel>=0.26 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (0.35.1)
Requirement already satisfied: six>=1.12.0 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (1.15.0)
Requirement already satisfied: grpcio>=1.8.6 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (1.32.0)
Requirement already satisfied: keras-preprocessing<1.2,>=1.1.1 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (1.1.2)
Requirement already satisfied: astunparse==1.6.3 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (1.6.3)
Requirement already satisfied: protobuf>=3.9.2 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (3.12.4)
Requirement already satisfied: opt-einsum>=2.3.2 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (3.3.0)
Requirement already satisfied: absl-py>=0.7.0 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (0.10.0)
Requirement already satisfied: google-pasta>=0.1.8 in /usr/local/lib/python3.6/dist-packages (from tensorflow->-r requirements.txt (line 8)) (0.2.0)
Requirement already satisfied: pyyaml in /usr/local/lib/python3.6/dist-packages (from keras==2.1.0->-r requirements.txt (line 9)) (3.13)
Requirement already satisfied: joblib>=0.11 in /usr/local/lib/python3.6/dist-packages (from scikit-learn->sklearn->-r requirements.txt (line 4)) (0.16.0)
Requirement already satisfied: setuptools>=41.0.0 in /usr/local/lib/python3.6/dist-packages (from tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (50.3.0)
Requirement already satisfied: requests<3,>=2.21.0 in /usr/local/lib/python3.6/dist-packages (from tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (2.23.0)
Requirement already satisfied: werkzeug>=0.11.15 in /usr/local/lib/python3.6/dist-packages (from tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (1.0.1)
Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in /usr/local/lib/python3.6/dist-packages (from tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (0.4.1)
Requirement already satisfied: markdown>=2.6.8 in /usr/local/lib/python3.6/dist-packages (from tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (3.2.2)
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Requirement already satisfied: google-auth<2,>=1.6.3 in /usr/local/lib/python3.6/dist-packages (from tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (1.17.2)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.6/dist-packages (from requests<3,>=2.21.0->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (1.24.3)
Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.6/dist-packages (from requests<3,>=2.21.0->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (3.0.4)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.6/dist-packages (from requests<3,>=2.21.0->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (2020.6.20)
Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.6/dist-packages (from requests<3,>=2.21.0->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (2.10)
Requirement already satisfied: requests-oauthlib>=0.7.0 in /usr/local/lib/python3.6/dist-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (1.3.0)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /usr/local/lib/python3.6/dist-packages (from markdown>=2.6.8->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (2.0.0)
Requirement already satisfied: rsa<5,>=3.1.4; python_version >= "3" in /usr/local/lib/python3.6/dist-packages (from google-auth<2,>=1.6.3->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (4.6)
Requirement already satisfied: pyasn1-modules>=0.2.1 in /usr/local/lib/python3.6/dist-packages (from google-auth<2,>=1.6.3->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (0.2.8)
Requirement already satisfied: cachetools<5.0,>=2.0.0 in /usr/local/lib/python3.6/dist-packages (from google-auth<2,>=1.6.3->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (4.1.1)
Requirement already satisfied: oauthlib>=3.0.0 in /usr/local/lib/python3.6/dist-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (3.1.0)
Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.6/dist-packages (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (3.2.0)
Requirement already satisfied: pyasn1>=0.1.3 in /usr/local/lib/python3.6/dist-packages (from rsa<5,>=3.1.4; python_version >= "3"->google-auth<2,>=1.6.3->tensorboard<3,>=2.3.0->tensorflow->-r requirements.txt (line 8)) (0.4.8)
Building wheels for collected packages: pypng, lsm-db
  Building wheel for pypng (setup.py): started
  Building wheel for pypng (setup.py): finished with status 'done'
  Created wheel for pypng: filename=pypng-0.0.20-cp36-none-any.whl size=67162 sha256=c4f09a8c98fa4e8e51ffe63b58fdf2b5e6b6557e3607c1f1597f7473439ff79c
  Stored in directory: /root/.cache/pip/wheels/41/6b/ef/0493b536b6d4722c2ae9486691b1d49b922b9877922beeabb3
  Building wheel for lsm-db (setup.py): started
  Building wheel for lsm-db (setup.py): finished with status 'done'
  Created wheel for lsm-db: filename=lsm_db-0.6.4-cp36-cp36m-linux_x86_64.whl size=664712 sha256=9dff42c17e3c01c842ce47b6c0234f755f87871906b1b11201afcf0e67d3d907
  Stored in directory: /root/.cache/pip/wheels/ed/32/8a/b0f3aa15b68f1e6b8f2dcc6285de4796b6b58af71c5f280f48
Successfully built pypng lsm-db
Installing collected packages: mrcfile, pypng, keras, lsm-db
  Found existing installation: Keras 2.4.3
    Uninstalling Keras-2.4.3:
      Successfully uninstalled Keras-2.4.3
Successfully installed keras-2.1.0 lsm-db-0.6.4 mrcfile-1.1.2 pypng-0.0.20
Compiling aitom/tomominer/core/cython/core.pyx because it changed.
[1/1] Cythonizing aitom/tomominer/core/cython/core.pyx
running build_ext
building 'aitom.tomominer.core.core' extension
creating build
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/aitom
creating build/temp.linux-x86_64-3.6/aitom/tomominer
creating build/temp.linux-x86_64-3.6/aitom/tomominer/core
creating build/temp.linux-x86_64-3.6/aitom/tomominer/core/cython
creating build/temp.linux-x86_64-3.6/aitom/tomominer/core/src
creating build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/segmentation
creating build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/segmentation/watershed
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/cython/core.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/cython/core.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/cython/wrap_core.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/cython/wrap_core.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/affine_transform.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/affine_transform.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/align.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/align.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/arma_extend.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/arma_extend.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/dilate.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/dilate.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/fft.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/fft.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/geometry.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/geometry.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/interpolation.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/interpolation.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/io.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/io.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/legendre.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/legendre.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/rotate.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/rotate.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/sht.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/sht.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/wigner.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/wigner.o -std=c++11
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iaitom/tomominer/core/cython -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include -I/usr/local/include -Iaitom/tomominer/core/src/ -I/aitom/ext/include -I/usr/include/python3.6m -c aitom/tomominer/core/src/segmentation/watershed/watershed_segmentation.cpp -o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/segmentation/watershed/watershed_segmentation.o -std=c++11
x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.6/aitom/tomominer/core/cython/core.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/cython/wrap_core.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/affine_transform.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/align.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/arma_extend.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/dilate.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/fft.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/geometry.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/interpolation.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/io.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/legendre.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/rotate.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/sht.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/wigner.o build/temp.linux-x86_64-3.6/aitom/tomominer/core/src/segmentation/watershed/watershed_segmentation.o -L/aitom/ext/lib -lm -lfftw3 -larmadillo -lblas -llapack -o /aitom/aitom/tomominer/core/core.cpython-36m-x86_64-linux-gnu.so
Cloning into 'aitom'...
debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76, <> line 10.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (This frontend requires a controlling tty.)
debconf: falling back to frontend: Teletype
dpkg-preconfigure: unable to re-open stdin: 
ERROR: textgenrnn 1.4.1 has requirement keras>=2.1.5, but you'll have keras 2.1.0 which is incompatible.
In file included from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
                 from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from aitom/tomominer/core/cython/core.cpp:677:
/usr/local/lib/python3.6/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
aitom/tomominer/core/cython/core.cpp: In function ‘PyObject* __pyx_pf_5aitom_9tomominer_4core_4core_4combined_search(PyObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, unsigned int)’:
aitom/tomominer/core/cython/core.cpp:3597:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (__pyx_t_20 = 0; __pyx_t_20 < __pyx_t_19; __pyx_t_20+=1) {
                        ~~~~~~~~~~~^~~~~~~~~~~~
aitom/tomominer/core/cython/core.cpp: In function ‘PyObject* __pyx_pf_5aitom_9tomominer_4core_4core_8local_max_angles(PyObject*, PyArrayObject*, unsigned int)’:
aitom/tomominer/core/cython/core.cpp:4823:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) {
                        ~~~~~~~~~~~^~~~~~~~~~~~
In file included from aitom/tomominer/core/cython/wrap_core.cpp:9:0:
aitom/tomominer/core/src/segmentation/active_contour/zy_binary_boundary_detection.hpp: In function ‘void zy_BinaryBoundaryDetection(char*, int, int, int, int, char*)’:
aitom/tomominer/core/src/segmentation/active_contour/zy_binary_boundary_detection.hpp:15:26: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
  int i, j, k, idx, idx0, count;
                          ^~~~~
aitom/tomominer/core/src/segmentation/active_contour/zy_binary_boundary_detection.hpp:16:6: warning: unused variable ‘on_boundary’ [-Wunused-variable]
  int on_boundary = 0;
      ^~~~~~~~~~~
In file included from aitom/tomominer/core/cython/wrap_core.cpp:10:0:
aitom/tomominer/core/src/segmentation/active_contour/ac_div_AOS_3D_dll.hpp: In instantiation of ‘void div_AOS_3D(C3DImage<double>&, T&, double, C3DImage<double>&) [with T = C3DImage<double>]’:
aitom/tomominer/core/cython/wrap_core.cpp:214:38:   required from here
aitom/tomominer/core/src/segmentation/active_contour/ac_div_AOS_3D_dll.hpp:195:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(j = 0; j < g.m_dims[0]; j++)
                ~~^~~~~~~~~~~
aitom/tomominer/core/src/segmentation/active_contour/ac_div_AOS_3D_dll.hpp:197:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(k = 0; k < g.m_dims[1]; k++)
                    ~~^~~~~~~~~~~
aitom/tomominer/core/src/segmentation/active_contour/ac_div_AOS_3D_dll.hpp:213:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(j = 0; j < g.m_dims[0]; j++)
                ~~^~~~~~~~~~~
aitom/tomominer/core/src/segmentation/active_contour/ac_div_AOS_3D_dll.hpp:215:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(k = 0; k < g.m_dims[2]; k++)
                    ~~^~~~~~~~~~~
aitom/tomominer/core/src/segmentation/active_contour/ac_div_AOS_3D_dll.hpp:228:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(j = 0; j < g.m_dims[1]; j++)
                ~~^~~~~~~~~~~
aitom/tomominer/core/src/segmentation/active_contour/ac_div_AOS_3D_dll.hpp:230:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(k = 0; k < g.m_dims[2]; k++)
                    ~~^~~~~~~~~~~
aitom/tomominer/core/src/dilate.cpp: In function ‘arma::cube dilate_small_se(const cube&, int)’:
aitom/tomominer/core/src/dilate.cpp:47:35: warning: ‘static eT arma::Math<eT>::inf() [with eT = double]’ is deprecated [-Wdeprecated-declarations]
     arma::cube out = -arma::math::inf() * arma::ones<arma::cube>(vol.n_rows, vol.n_cols, vol.n_slices);
                                   ^~~
In file included from /usr/include/armadillo:119:0,
                 from aitom/tomominer/core/src/dilate.cpp:2:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
aitom/tomominer/core/src/dilate.cpp:47:39: warning: ‘static eT arma::Math<eT>::inf() [with eT = double]’ is deprecated [-Wdeprecated-declarations]
     arma::cube out = -arma::math::inf() * arma::ones<arma::cube>(vol.n_rows, vol.n_cols, vol.n_slices);
                                       ^
In file included from /usr/include/armadillo:119:0,
                 from aitom/tomominer/core/src/dilate.cpp:2:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
aitom/tomominer/core/src/interpolation.cpp: In constructor ‘interpolater::interpolater(const cube&)’:
aitom/tomominer/core/src/interpolation.cpp:14:78: warning: ‘static eT arma::Math<eT>::nan() [with eT = double]’ is deprecated [-Wdeprecated-declarations]
 interpolater::interpolater(const arma::cube &f_) : data(f_), ext(arma::math::nan()) {}
                                                                              ^~~
In file included from /usr/include/armadillo:119:0,
                 from aitom/tomominer/core/src/interpolation.cpp:2:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
aitom/tomominer/core/src/interpolation.cpp:14:82: warning: ‘static eT arma::Math<eT>::nan() [with eT = double]’ is deprecated [-Wdeprecated-declarations]
 interpolater::interpolater(const arma::cube &f_) : data(f_), ext(arma::math::nan()) {}
                                                                                  ^
In file included from /usr/include/armadillo:119:0,
                 from aitom/tomominer/core/src/interpolation.cpp:2:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
aitom/tomominer/core/src/rotate.cpp:13:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for private(x,y)
 
aitom/tomominer/core/src/rotate.cpp: In function ‘arma::cube rotate_vol(const cube&, const rot_matrix&, const vec3&)’:
aitom/tomominer/core/src/rotate.cpp:48:49: warning: ‘static eT arma::Math<eT>::nan() [with eT = double]’ is deprecated [-Wdeprecated-declarations]
     cubic_interpolater cub_int(vol, arma::math::nan());
                                                 ^~~
In file included from /usr/include/armadillo:119:0,
                 from aitom/tomominer/core/src/rotate.hpp:4,
                 from aitom/tomominer/core/src/rotate.cpp:1:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
aitom/tomominer/core/src/rotate.cpp:48:53: warning: ‘static eT arma::Math<eT>::nan() [with eT = double]’ is deprecated [-Wdeprecated-declarations]
     cubic_interpolater cub_int(vol, arma::math::nan());
                                                     ^
In file included from /usr/include/armadillo:119:0,
                 from aitom/tomominer/core/src/rotate.hpp:4,
                 from aitom/tomominer/core/src/rotate.cpp:1:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
aitom/tomominer/core/src/wigner.cpp: In function ‘std::vector<arma::Mat<double> > wigner_d(double, int)’:
aitom/tomominer/core/src/wigner.cpp:35:33: warning: ‘static eT arma::Math<eT>::nan() [with eT = double]’ is deprecated [-Wdeprecated-declarations]
         D.push_back(arma::math::nan() * arma::ones<arma::mat>(2*l+1,2*l+1));
                                 ^~~
In file included from /usr/include/armadillo:119:0,
                 from aitom/tomominer/core/src/wigner.cpp:3:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
aitom/tomominer/core/src/wigner.cpp:35:37: warning: ‘static eT arma::Math<eT>::nan() [with eT = double]’ is deprecated [-Wdeprecated-declarations]
         D.push_back(arma::math::nan() * arma::ones<arma::mat>(2*l+1,2*l+1));
                                     ^
In file included from /usr/include/armadillo:119:0,
                 from aitom/tomominer/core/src/wigner.cpp:3:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /aitom/aitom/tomominer/core/cython/core.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)

@geoffwoollard
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The error seems to be with the version of keras. The requirements.txt file has keras==2.1.0. I took out the specific version and just put in keras, but that didn't solve the issue.

@xulabs
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xulabs commented Oct 6, 2020

@geoffwoollard generally only the fast subtomogram alignment part involves c++ code. If you don't use the subtomogram alignment, then you can just clone the library without compiling it.

The c++ code depends on an older version of armadillo. You are very welcome to help us to update the c++ code so that it is compatible with the current version of armadillo.

@Shadowalker1995
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Shadowalker1995 commented Oct 7, 2020 •
edited
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@geoffwoollard I see that your machine use x86_64-linux-gnu-gcc as the default GCC compiler. I have also encountered some compile errors with this compiler. So, I recommend you add the following two lines in the setup.py file:

os.environ["CC"] = "gcc"
os.environ["CXX"] = "gcc"

It works fine for me.

@genio0815
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Hi all,

so, removing the version specification of keras will work (2.1.0 seems to be due to #20, won't run py > 3.6 and more recent versions of tf)?

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@geoffwoollard @Shadowalker1995 @xulabs @genio0815 @evaxguo