# **************************************************************************
# *
# * 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__ = '3.0.15'
_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)