Source code for cryocare

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import pwem
import os
from pyworkflow.utils import Environ
from cryocare.constants import CRYOCARE_ENV_ACTIVATION, DEFAULT_ACTIVATION_CMD, CRYOCARE_ENV_NAME, \
    CRYOCARE_DEFAULT_VERSION, CRYOCARE_HOME, CRYOCARE_CUDA_LIB, CRYOCARE

_logo = "icon.png"
_references = ['buchholz2019cryo', 'buchholz2019content']
__version__ = "3.0.1"


class Plugin(pwem.Plugin):

    _homeVar = CRYOCARE_HOME
    _url = 'https://github.com/scipion-em/scipion-em-cryocare'

    @classmethod
    def _defineVariables(cls):
        # cryoCARE does NOT need EmVar because it uses a conda environment.
        cls._defineVar(CRYOCARE_ENV_ACTIVATION, DEFAULT_ACTIVATION_CMD)

    @classmethod
    def getCryocareEnvActivation(cls):
        return cls.getVar(CRYOCARE_ENV_ACTIVATION)

    @classmethod
    def getEnviron(cls, gpuId='0'):
        """ Setup the environment variables needed to launch cryocare. """
        environ = Environ(os.environ)
        if 'PYTHONPATH' in environ:
            # this is required for python virtual env to work
            del environ['PYTHONPATH']

        environ.update({'CUDA_VISIBLE_DEVICES': gpuId})

        cudaLib = environ.get(CRYOCARE_CUDA_LIB, pwem.Config.CUDA_LIB)
        environ.addLibrary(cudaLib)
        return environ

    @classmethod
    def defineBinaries(cls, env):
        CRYOCARE_INSTALLED = '%s_%s_installed' % (CRYOCARE, CRYOCARE_DEFAULT_VERSION)

        # try to get CONDA activation command
        installationCmd = cls.getCondaActivationCmd()

        # Create the environment
        installationCmd += 'conda create -y -n %s -c conda-forge -c anaconda python=3.8 ' \
                           'cudnn=7.6.5=cuda10.1_0 && ' % CRYOCARE_ENV_NAME

        # Activate new the environment
        installationCmd += 'conda activate %s && ' % CRYOCARE_ENV_NAME

        # Install non-conda required packages
        installationCmd += 'pip install tensorflow-gpu==2.3.3 && '
        installationCmd += 'pip install mrcfile && '
        installationCmd += 'pip install csbdeep '
        # I had the same issue and was able to fix this by setting h5py < 3.0.0.
        # Looks like here was a 3.0 release of h5py recently where they changed how strings are stored/read.
        # https://github.com/keras-team/keras/issues/14265

        # Install cryoCARE
        installationCmd += 'pip install %s==%s &&' % (CRYOCARE, CRYOCARE_DEFAULT_VERSION)

        # Flag installation finished
        installationCmd += 'touch %s' % CRYOCARE_INSTALLED

        cryocare_commands = [(installationCmd, CRYOCARE_INSTALLED)]

        envPath = os.environ.get('PATH', "")  # keep path since conda likely in there
        installEnvVars = {'PATH': envPath} if envPath else None

        env.addPackage(CRYOCARE,
                       version=CRYOCARE_DEFAULT_VERSION,
                       tar='void.tgz',
                       commands=cryocare_commands,
                       neededProgs=cls.getDependencies(),
                       vars=installEnvVars,
                       default=bool(cls.getCondaActivationCmd()))

    @classmethod
    def getDependencies(cls):
        # try to get CONDA activation command
        condaActivationCmd = cls.getCondaActivationCmd()
        neededProgs = []
        if not condaActivationCmd:
            neededProgs.append('conda')

        return neededProgs

    @classmethod
    def runCryocare(cls, protocol, program, args, cwd=None, gpuId='0'):
        """ Run cryoCARE command from a given protocol. """
        fullProgram = '%s %s && %s' % (cls.getCondaActivationCmd(),
                                       cls.getCryocareEnvActivation(),
                                       program)
        protocol.runJob(fullProgram, args, env=cls.getEnviron(gpuId=gpuId), cwd=cwd, numberOfMpi=1)