emcore

Basic image processing library for Electron Microscopy

Building the library

git clone [email protected]:3dem/emcore.git
cd emcore
mkdir build
cd build
# Activating most of development options
cmake .. -DBUILD_TIFF=ON -DBUILD_PNG=ON -DBUILD_JPEG=ON \
-DBUILD_TESTS=ON -DBUILD_DOCS=ON -DBUILD_EXAMPLES=ON \
-DCMAKE_BUILD_TYPE=Debug -DBUILD_DOCOPT=ON -DBUILD_PYBIND=ON

Building and installing in a given conda environment

# First activate the conda environment
conda activate myEnv
# Then execute the Python installation script
python conda/install_to_env.py

Building with Google-tests (REVIEW)

In order to enable google test, you need to pull the test git-module and pass the proper option to cmake. From the root emcore directory:

cd libs/googletest/
git submodule update --init

# Then follow the normal building process...so from build directory:

cmake .. -DBUILD_TESTS=ON

Generating documentation

FIXME: Update this section to use Doxygen+Sphinx docs generation

Release protocol:

Releasing to conda:

Step 1: Create a Pull-Request from devel to master

Step 2: Make sure that the version has been properly updated (find and replace old version by new one)

Step 3: Build the recipe and upload binaries to conda.

Make sure that you have conda-build (to build the recipe) and anaconda-client (to upload binaries) installed in the current conda environment. Then build the recipe with conda.

$ conda install conda-build anaconda-client
$ cd emcore
$ conda build conda/recipe

If there are no errors during the building process, we can upload the generated binaries to the emcore user:

$ anaconda upload -u emforge /home/josem/installs/miniconda3/envs/pyem37-docs/conda-bld/linux-64/emcore-0.0.4-py37h6bb024c_0.tar.bz2
$ anaconda upload -u emforge /home/josem/installs/miniconda3/envs/pyem37-docs/conda-bld/linux-64/emcore-0.0.4-py27h6bb024c_0.tar.bz2
$ anaconda upload -u emforge /home/josem/installs/miniconda3/envs/pyem37-docs/conda-bld/linux-64/emcore-0.0.4-py35h6bb024c_0.tar.bz2
$ anaconda upload -u emforge /home/josem/installs/miniconda3/envs/pyem37-docs/conda-bld/linux-64/emcore-0.0.4-py36h6bb024c_0.tar.bz2

Step 4: Merge the PR to master and create a tag with the version

$ git checkout master
$ git tag 0.0.4
$ git push -u origin 0.0.4

Extra

Specify path of Conda environment to CMAKE:

export CMAKE_PREFIX_PATH=/home/josem/installs/devel/miniconda3/envs/py27-emqt/
# Also remote build artifacts:
cd build
rm *
cmake ...

Specifying a different search root (e.g Kino's machine at LMB)

cd build
rm *
cmake3 .. -DBUILD_TESTS=ON -DBUILD_DOCS=ON -DBUILD_EXAMPLES=ON \
-DCMAKE_BUILD_TYPE=Debug -DBUILD_DOCOPT=ON -DBUILD_PYBIND=ON \
-DCMAKE_FIND_ROOT_PATH=./opt/anaconda3/ \
-DCMAKE_C_COMPILER=/public/gcc/7_2_0/bin/gcc \
-DCMAKE_CXX_COMPILER=/public/gcc/7_2_0/bin/g++

Building Relion with emcore (old)

For the moment, we need to pass a variable to cmake where the emcore library is:

cmake ../relion-devel-tcblab/ -DGUI=OFF -DCUDA=OFF -DALTCPU=OFF \
-DEMCORE_ROOT_PATH=/home/dari/Projects/emcore/emcore/