Source code for xmipptomo

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import xmipp3
import subprocess, os
import pyworkflow.utils as pwutils

_logo = "xmipp_logo.png"
_references = ['delaRosaTrevin2013']
__version__ = "3.0.6"

[docs]class Plugin(xmipp3.Plugin):
[docs] @classmethod def getTensorFlowEnviron(cls): """ Create the needed environment for XmippTomo programs. """ environ = pwutils.Environ(os.environ) environ.update({ "TF_FORCE_GPU_ALLOW_GROWTH": "'true'" }, position=pwutils.Environ.BEGIN) return environ
[docs] @classmethod def defineBinaries(cls, env): preMsgs = [] cudaMsgs = [] nvidiaDriverVer = None if os.environ.get('CUDA', 'True') == 'True': try: nvidiaDriverVer = subprocess.Popen(["nvidia-smi", "--query-gpu=driver_version", "--format=csv,noheader"], env=xmipp3.Plugin.getEnviron(), stdout=subprocess.PIPE ).stdout.read().decode('utf-8').split(".")[0] if int(nvidiaDriverVer) < 390: preMsgs.append("Incompatible driver %s" % nvidiaDriverVer) cudaMsgs.append("Your NVIDIA drivers are too old (<390). " "Tensorflow was installed without GPU support. " "Just CPU computations enabled (slow computations).") nvidiaDriverVer = None except Exception as e: preMsgs.append(str(e)) if nvidiaDriverVer is not None: preMsgs.append("CUDA support find. Driver version: %s" % nvidiaDriverVer) msg = "Tensorflow installed with CUDA SUPPORT." cudaMsgs.append(msg) useGpu = True else: preMsgs.append("CUDA will NOT be USED. (not found or incompatible)") msg = ("Tensorflow installed without GPU. Just CPU computations " "enabled (slow computations). To enable CUDA (drivers>390 needed), " "set CUDA=True in 'scipion.conf' file") cudaMsgs.append(msg) useGpu = False # commands = [(command, target), (cmd, tgt), ...] cmdsInstall = [(cmd, envName + ".yml") for cmd, envName in xmipp3.CondaEnvManager.yieldInstallAllCmds(useGpu=useGpu)] now = xmipp3.datetime.now() installDLvars = {'modelsUrl': "http://scipion.cnb.csic.es/downloads/scipion/software/em", 'syncBin': cls.getHome('bin/xmipp_sync_data'), 'modelsDir': cls.getHome('models'), 'modelsPrefix': "models_UPDATED_on", 'xmippLibToken': 'xmippLibToken', 'libXmipp': cls.getHome('lib/libXmipp.so'), 'preMsgsStr': ' ; '.join(preMsgs), 'afterMsgs': "\n > ".join(cudaMsgs)} installDLvars.update({'modelsTarget': "%s_%s_%s_%s" % (installDLvars['modelsPrefix'], now.day, now.month, now.year)}) modelsDownloadCmd = ("rm %(modelsPrefix)s_* %(xmippLibToken)s 2>/dev/null ; " "echo 'Downloading pre-trained models...' ; " "%(syncBin)s update %(modelsDir)s %(modelsUrl)s DLmodels && " "touch %(modelsTarget)s && echo ' > %(afterMsgs)s'" % installDLvars, # End of command installDLvars['modelsTarget']) # Target xmippInstallCheck = ("if ls %(libXmipp)s > /dev/null ; " "then touch %(xmippLibToken)s; echo ' > %(preMsgsStr)s' ; " "else echo ; echo ' > Xmipp installation not found, " "please install it first (xmippSrc or xmippBin*).';echo;" " fi" % installDLvars, # End of command installDLvars['xmippLibToken']) # Target env.addPackage(xmipp3.constants.XMIPP_DLTK_NAME, version='0.2', urlSuffix='external', commands=[xmippInstallCheck] + cmdsInstall + [modelsDownloadCmd], deps=[], tar=xmipp3.constants.XMIPP_DLTK_NAME + '.tgz', default=True)