Source code for pwem

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin ( [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * 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
# * 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 ''
# *
# **************************************************************************
This module contains classes related with EM
import logging
logger = logging.getLogger(__name__)
import os
import re
from pkg_resources import parse_version

import pyworkflow as pw
from pyworkflow.protocol import Protocol
from pyworkflow.utils import  getSubclasses
from pyworkflow.viewer import Viewer
from pyworkflow.wizard import Wizard
import pyworkflow.plugin

from .constants import *
from .objects import EMObject
from .tests import defineDatasets
from .utils import *

__version__ = '3.6.0'

_logo = "scipion_icon.png"
_references = ["delaRosaTrevin201693"]

[docs]class Config(pw.Config): _get = pw.Config._get _join = pw.Config._join EM_ROOT = _join(_get(EM_ROOT_VAR, _join(pw.Config.SCIPION_SOFTWARE, 'em'))) # Default XMIPP_HOME: needed here for ShowJ viewers XMIPP_HOME = _join(_get('XMIPP_HOME', os.path.join(EM_ROOT, 'xmipp'))) # Get java home, we might need to provide correct default value. Use SCIPION_JAVA_HOME to force it when there is other JAVA_HOME you don't want/cant to change: e.g. pycharm debugging. JAVA_HOME = _get('SCIPION_JAVA_HOME', _get('JAVA_HOME', '')) JAVA_MAX_MEMORY = _get('JAVA_MAX_MEMORY', '4') # MPI MPI_LIBDIR = _get('MPI_LIBDIR', '/usr/lib64/mpi/gcc/openmpi/lib') MPI_BINDIR = _get('MPI_BINDIR', '/usr/lib64/mpi/gcc/openmpi/bin') # CUDA CUDA_LIB = _get(CUDA_LIB_VAR, '/usr/local/cuda/lib64') CUDA_BIN = _get('CUDA_BIN', '/usr/local/cuda/bin') MAX_PREVIEW_FILE_SIZE = float(_get("MAX_PREVIEW_FILE_SIZE", DEFAULT_MAX_PREVIEW_FILE_SIZE)) # OLD CHIMERA variable CHIMERA_OLD_BINARY_PATH = _get("CHIMERA_OLD_BINARY_PATH",'') # Path to either ImageJ or Fiji binary program IMAGEJ_BINARY_PATH = _get("IMAGEJ_BINARY_PATH",'')
[docs]class Domain(pyworkflow.plugin.Domain): _name = __name__ _objectClass = EMObject _protocolClass = Protocol _viewerClass = Viewer _wizardClass = Wizard _baseClasses = getSubclasses(EMObject, globals())
[docs]class Plugin(pyworkflow.plugin.Plugin): _url = URL @classmethod def _defineEmVar(cls, varName, defaultValue): """ Shortcut method to define variables prepending EM_ROOT if variable is not absolute""" # Get the value, either whatever is in the environment or a join of EM_ROOT + defaultValue value = os.environ.get(varName, os.path.join(Config.EM_ROOT, defaultValue)) # CASE-1 : Users might have used ~ and that has to be expanded value = os.path.expanduser(value) # CASE-2 :Old configs 2.0 will likely have: # EM_ROOT = software/em # CHIMERA_HOME = %(EM_ROOT)s/chimera-13.0.1 # ... # # this end up in the environment resolved like: software/em/chimera-13.0.1 # whereas as default values will come as absolute: # /<scipion_home>/software/em/chimera-13.0.1 # In any case we join it (absolute paths will not join) value = os.path.join(pw.Config.SCIPION_HOME, value) cls._addVar(varName, value)
[docs] @classmethod def getMaxitHome(cls): return cls.getVar(MAXIT_HOME)
[docs] @classmethod def getMaxitBin(cls): return os.path.join(cls.getMaxitHome(), 'bin', MAXIT)
@classmethod def _defineVariables(cls): # Avoid defining variables from children that does not define variables. if cls == Plugin: cls._defineVar(EM_ROOT_VAR, pwem.Config.EM_ROOT) cls._defineEmVar(MAXIT_HOME, 'maxit-10.1') # Take this initialization event to define own datasets defineDatasets() # Register filehandlers too cls._registerFileHandlers()
[docs] @classmethod def defineBinaries(cls, env): cls.defineBinariesMaxit(False, env)
[docs] @classmethod def defineBinariesMaxit(cls, default, env): # If not defined already (several plugins needs this and call this but has to be added once if not env.hasPackage(MAXIT): MAXIT_URL = '' MAXIT_TAR = 'maxit-v10.100-prod-src.tar.gz' maxit_commands = [('make -j 1 binary ', ['bin/maxit'])] env.addPackage(MAXIT, version='10.1', tar=MAXIT_TAR, url=MAXIT_URL, neededProgs=['gcc', 'flex', 'make', 'bison', 'tcsh'], commands=maxit_commands, default=default) # scipion installb maxit # requirements bison, flex, gcc maxit10 = env.getTarget(env._getExtName(MAXIT, "10.1")) maxit10.setDefault(default)
[docs] @classmethod def guessCudaVersion(cls, variable, default="10.1"): """ Guesses the cuda version from a variable :param variable: Name of a variable defined by a plugin :param default: Default value in case cuda is not found :return Version after parsing the variable or default""" return cls.getVersionFromVariable(variable, default=default, pattern="cuda")
[docs] @classmethod def getVersionFromVariable(cls, variable, default=NO_VERSION_FOUND_STR, pattern=None): """ Returns a Version instance from parsing the content of a variable :param variable: Variable name to use and parse :param default: Optional. Default value to return in case version is not found :param pattern: Optional. If passed, the pattern will be used to locate the folder :return Version after parsing the variable""" value = cls.getVar(variable) return cls.getVersionFromPath(value, default= default, pattern=pattern)
[docs] @classmethod def getVersionFromPath(cls, path, separator="-", default=NO_VERSION_FOUND_STR, pattern=None): """ Resolves path to the realpath (links) and returns the last part of the path after the separator as a Version object. If separator is not present returns None :param path: string containing a path with a version as part of its name :param separator: Optional. defaults to "-". :param default: Optional. Default version ("X.Y" string) to return if no version is found :param pattern: Optional. If passed, the pattern will be used to locate the folder :return Version object filled with version found or 0.0 """ path = os.path.realpath(path) if pattern is not None: path = findFolderWithPattern(path, pattern) if path is None: return parse_version(default) parts = path.split(separator) if len(parts)>=2: # Version should be the last bit versionStr = parts[-1] versionStr ="\d+\.\d+", versionStr)[0] # Match only numbers return parse_version(versionStr) else: return parse_version(default)
@classmethod def _registerFileHandlers(cls): # register file handlers to preview info in the Filebrowser.... from pyworkflow.gui.browser import FileTreeProvider, STANDARD_IMAGE_EXTENSIONS from .viewers.filehandlers import MdFileHandler, ParticleFileHandler, VolFileHandler, StackHandler, ChimeraHandler, ImajeJFileHandler register = FileTreeProvider.registerFileHandler register(MdFileHandler(), '.xmd', '.star', '.pos', '.ctfparam', '.doc') register(ParticleFileHandler(), '.xmp', '.tif', '.tiff', '.spi', '.mrc', '.map', '.raw', '.inf', '.dm3', '.em', '.pif', '.psd', '.spe', '.ser', '.img', '.hed', *STANDARD_IMAGE_EXTENSIONS) register(VolFileHandler(), '.vol', '.hdf', '.rec') register(StackHandler(), '.stk', '.mrcs', '.st', '.pif', '.dm4', '.ali') register(ChimeraHandler(), '.bild', '.mrc', '.pdb', '.vol', '.hdf', '.cif', '.mmcif') if Config.IMAGEJ_BINARY_PATH: register(ImajeJFileHandler(), '.mrcs', '.mrc', '.st', '.ali', '.rec', '.tif', '.tiff', *STANDARD_IMAGE_EXTENSIONS)
[docs]def findFolderWithPattern(path, pattern): """ Returns the first folder found from the right that matches the pattern :param path: path to do the search on :param pattern: pattern to look for. No regex for now, just a contains :return the folder matching the pattern or None """ previous, last = os.path.split(path) # If end reached: windows Paths and linux paths seems to end in a different way if previous == "" or last=="": return None elif pattern in last: return last else: return findFolderWithPattern(previous, pattern)