# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [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
# * 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'
# *
# **************************************************************************
"""
This module contains classes related with EM
"""
import logging
from pyworkflow import VarTypes
logger = logging.getLogger(__name__)
import os
from packaging import version
import re
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__ = '3.8.0'
NO_VERSION_FOUND_STR = "0.0"
CUDA_LIB_VAR = 'CUDA_LIB'
_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', _join(EM_ROOT, 'xmipp'),
description="Path where XMIPP is installed.",
var_type=VarTypes.FOLDER,
source="pwem"))
# 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', ''),
description="Path where JAVA is located.", var_type=VarTypes.FOLDER, source="pwem")
JAVA_MAX_MEMORY = _get('JAVA_MAX_MEMORY', '4', description="Memory (in GB) to use in java processes. For movies it will be increased. Used in Xmipp viewer.", var_type=VarTypes.INTEGER, source="pwem")
# 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,
description="Maximum size (MB) of files to visualize in the file browser preview."))
# OLD CHIMERA variable
CHIMERA_OLD_BINARY_PATH = _get("CHIMERA_OLD_BINARY_PATH",'',
description="Path to the Chimera OLD binary program (not the folder). Will only "
"be used a viewer. None of the chimera scripts will work.",
var_type=VarTypes.PATH, source="pwem")
# Path to either ImageJ or Fiji binary program
IMAGEJ_BINARY_PATH = _get("IMAGEJ_BINARY_PATH",'',description="Path to the IMAGEJ or FIJI program.",
var_type=VarTypes.PATH, source="pwem")
SCIPION_EM_NEW_FILE_CHECK_SEC = int(_get('SCIPION_EM_NEW_FILE_CHECK_SEC', 10,
description='Number of seconds to wait before checking if new files are '
'available or finished in streamified import protocols.',
var_type=VarTypes.INTEGER, source='pwem'))
[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, description="Missing", var_type:VarTypes=None):
""" 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
defaultValueWithEM= os.path.join(Config.EM_ROOT,defaultValue)
value = os.environ.get(varName, defaultValueWithEM)
def expand(value):
# 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)
return value
value=expand(value)
if varName in os.environ:
defaultValue= expand(defaultValueWithEM)
else:
defaultValue=value
cls._addVar(varName, value, defaultValue, description=description, var_type=var_type)
[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', description="Path where maxit is installed.", var_type=VarTypes.FOLDER)
# 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 = 'https://sw-tools.rcsb.org/apps/MAXIT/maxit-v10.100-prod-src.tar.gz'
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 version.Version(default)
parts = path.split(separator)
if len(parts)>=2:
# Version should be the last bit
versionStr = parts[-1]
return version.Version(versionStr)
else:
return version.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)
with pwutils.weakImport("MetadataFileHandler"):
from .viewers.filehandlers import MetadataFileHandler
register(MetadataFileHandler(), *MetadataFileHandler._compatibleExtensions)
[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)