Source code for gautomatch

# **************************************************************************
# *
# * Authors:     Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk)
# *
# * MRC Laboratory of Molecular Biology (MRC-LMB)
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************

import os

import pwem
import pyworkflow.utils as pwutils
from pwem.emlib.image import ImageHandler

from .constants import *


__version__ = '3.0.14'
_logo = "gautomatch_logo.png"
_references = ['Zhang']


[docs]class Plugin(pwem.Plugin): _homeVar = GAUTOMATCH_HOME _pathVars = [GAUTOMATCH_HOME] _supportedVersions = ['0.53', '0.56'] _url = "https://github.com/scipion-em/scipion-em-gautomatch" @classmethod def _defineVariables(cls): cls._defineEmVar(GAUTOMATCH_HOME, 'gautomatch-0.56') cls._defineVar(GAUTOMATCH, 'Gautomatch_v0.56_sm30-75_cu10.1') cls._defineVar(GAUTOMATCH_CUDA_LIB, pwem.Config.CUDA_LIB)
[docs] @classmethod def defineBinaries(cls, env): env.addPackage('gautomatch', version='0.53', tar='Gautomatch_v0.53.tgz') env.addPackage('gautomatch', version='0.56', tar='gautomatch_v0.56.tgz', default=True)
[docs] @classmethod def getEnviron(cls): """ Return the environ settings to run Gautomatch programs. """ environ = pwutils.Environ(os.environ) # Get Gautomatch CUDA library path if defined cudaLib = cls.getVar(GAUTOMATCH_CUDA_LIB, pwem.Config.CUDA_LIB) environ.addLibrary(cudaLib) return environ
[docs] @classmethod def getProgram(cls): """ Return the program binary that will be used. """ return os.path.join(cls.getHome('bin'), os.path.basename(cls.getVar(GAUTOMATCH)))
[docs] @classmethod def runGautomatch(cls, micNameList, refStack, workDir, extraArgs, env=None, runJob=None): """ Run Gautomatch with the given parameters. If micrographs are not .mrc, they will be converted. If runJob=None, it will use pwutils.runJob. """ args = '' ih = ImageHandler() for micName in micNameList: # We convert the input micrograph on demand if not in .mrc outMic = os.path.join(workDir, pwutils.replaceBaseExt(micName, 'mrc')) if micName.endswith('.mrc'): pwutils.createAbsLink(os.path.abspath(micName), outMic) else: ih.convert(micName, outMic) args += ' %s/*.mrc' % workDir if refStack is not None: args += ' -T %s' % refStack args += ' %s' % extraArgs environ = env if env is not None else cls.getEnviron() if runJob is None: pwutils.runJob(None, cls.getProgram(), args, env=environ) else: runJob(cls.getProgram(), args, env=environ) for micName in micNameList: outMic = os.path.join(workDir, pwutils.replaceBaseExt(micName, 'mrc')) # After picking we can remove the temporary file. pwutils.cleanPath(outMic)