Source code for pyseg

# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors:     Scipion Team
# *
# * National Center of Biotechnology, CSIC, Spain
# *
# * 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 2 of the License, or
# * (at your option) any later version.
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# * 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.
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# * 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
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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# **************************************************************************

from os.path import join, basename
import pwem
import os

import pyworkflow
from pyworkflow.utils import Environ
from pyseg.constants import PYSEG_HOME, PYSEG, PYSEG_SOURCE_URL, PYSEG_ENV_ACTIVATION, DEFAULT_ACTIVATION_CMD, \
    PYSEG_ENV_NAME, CFITSIO, DISPERSE, DEFAULT_VERSION

_logo = "icon.png"
_references = ['MartinezSanchez2020']
__version__ = '3.0.1'


[docs]class Plugin(pwem.Plugin): _homeVar = PYSEG_HOME @classmethod def _defineVariables(cls): cls._defineVar(PYSEG_ENV_ACTIVATION, DEFAULT_ACTIVATION_CMD) cls._defineEmVar(PYSEG_HOME, PYSEG + '-' + DEFAULT_VERSION)
[docs] @classmethod def getPysegEnvActivation(cls): activation = cls.getVar(PYSEG_ENV_ACTIVATION) scipionHome = pyworkflow.Config.SCIPION_HOME + os.path.sep return activation.replace(scipionHome, "", 1)
[docs] @classmethod def getEnviron(cls): """ Setup the environment variables needed to launch pyseg. """ environ = Environ(os.environ) pySegDir = cls.getHome() # Add required disperse path to PATH and pyto path to PYTHONPATH environ.update({'PATH': join(pySegDir, '%s_build' % DISPERSE, 'bin'), 'PYTHONPATH': join(pySegDir, 'pyseg_system-%s' % DEFAULT_VERSION, 'code') }) return environ
[docs] @classmethod def defineBinaries(cls, env): # At this point of the installation execution cls.getHome() is None, so the em path should be provided pysegHome = join(pwem.Config.EM_ROOT, PYSEG + '-' + DEFAULT_VERSION) PYSEG_INSTALLED = '%s_installed' % PYSEG thirdPartyPath = join(pysegHome, 'pyseg_system-%s' % DEFAULT_VERSION, 'sys', 'install', DISPERSE, '0.9.24_pyseg_gcc7', 'sources') # PySeg Conda environment genPySegCondaEnvCmd = cls._genCmdToDefineSegCondaEnv() # PySeg source code getPySegCmd = cls._genCmdToGetPySegSrcCode(pysegHome) # Third party software - CFitsIO installCFitsIOCmd, CFITSIO_BUILD_PATH = cls._genCmdToInstallCFitsIO(thirdPartyPath, pysegHome) # Third party software - disperse installDisperseCmd = cls._genCmdToInstallDisperse(thirdPartyPath, CFITSIO_BUILD_PATH, pysegHome) installationCmd = ' && '.join([genPySegCondaEnvCmd, getPySegCmd, installCFitsIOCmd, installDisperseCmd]) installationCmd += ' && touch %s' % PYSEG_INSTALLED # Flag installation finished env.addPackage(PYSEG, version=DEFAULT_VERSION, tar='void.tgz', commands=[(installationCmd, PYSEG_INSTALLED)], neededProgs=["wget", "make", "cmake", "tar", "libgsl-dev"], default=True)
@classmethod def _genCmdToGetPySegSrcCode(cls, pySegDir): installationCmd = 'wget ' + PYSEG_SOURCE_URL installationCmd += ' && unzip %s' % join(pySegDir, basename(PYSEG_SOURCE_URL)) installationCmd += ' && rm -rf %s' % join(pySegDir, DEFAULT_VERSION + '.zip') # rm downloaded file (>600 MB) return installationCmd @classmethod def _genCmdToInstallCFitsIO(cls, thirdPartyPath, pySegDir): CFITSIO_BUILD_PATH = join(pySegDir, '%s_build' % CFITSIO) installationCmd = 'tar zxf %s -C %s && ' % (join(thirdPartyPath, 'cfitsio_3.380.tar.gz'), pySegDir) installationCmd += 'cd %s && ' % join(pySegDir, CFITSIO) installationCmd += 'mkdir %s && ' % CFITSIO_BUILD_PATH installationCmd += './configure --prefix=%s && ' % CFITSIO_BUILD_PATH installationCmd += 'make && make install' return installationCmd, CFITSIO_BUILD_PATH @classmethod def _genCmdToInstallDisperse(cls, thirdPartyPath, CFITSIO_BUILD_PATH, pySegDir): DISPERSE_BUILD_PATH = join(pySegDir, '%s_build' % DISPERSE) installationCmd = 'tar zxf %s -C %s && ' % \ (join(thirdPartyPath, 'disperse_v0.9.24_pyseg_gcc7.tar.gz'), pySegDir) installationCmd += 'cd %s && ' % join(pySegDir, DISPERSE) installationCmd += 'mkdir %s && ' % DISPERSE_BUILD_PATH installationCmd += 'cmake . -DCMAKE_INSTALL_PREFIX=%s -DCFITSIO_DIR=%s && ' \ % (DISPERSE_BUILD_PATH, CFITSIO_BUILD_PATH) installationCmd += 'make && make install && ' installationCmd += 'cd ..' return installationCmd @classmethod def _genCmdToDefineSegCondaEnv(cls): installationCmd = cls.getCondaActivationCmd() # Create the environment installationCmd += 'conda create -y -n %s -c conda-forge -c anaconda python=3.6 ' \ 'opencv=4.2.0 ' \ 'graph-tool=2.29 && ' % PYSEG_ENV_NAME # Activate new the environment installationCmd += 'conda activate %s && ' % PYSEG_ENV_NAME # Install non-conda required packages installationCmd += 'pip install beautifulsoup4==4.9.3 && ' installationCmd += 'pip install lxml==4.6.3 && ' installationCmd += 'pip install pillow==6.2.2 &&' installationCmd += 'pip install pyfits==3.5 && ' installationCmd += 'pip install scikit-image==0.14.5 && ' installationCmd += 'pip install scikit-learn==0.20.4 && ' installationCmd += 'pip install scikit-fmm==2021.2.2 && ' installationCmd += 'pip install scipy==1.2.1 && ' installationCmd += 'pip install vtk==8.1.2 ' installationCmd += 'pip install astropy==4.1 ' installationCmd += 'pip install imageio==2.9.0 ' installationCmd += 'pip install future' return installationCmd
[docs] @classmethod def runPySeg(cls, protocol, program, args, cwd=None): """ Run pySeg command from a given protocol. """ fullProgram = '%s %s && %s' % (cls.getCondaActivationCmd(), cls.getPysegEnvActivation(), program) protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd)