def getEnviron():
""" Setup the environment variables needed to launch Bsoft. """
environ = Environ(os.environ)
BSOFT_HOME = os.environ['BSOFT_HOME']
environ.update({
'BSOFT': BSOFT_HOME,
'BPARAM': join(BSOFT_HOME, 'params'),
'PATH': join(BSOFT_HOME, 'bin'),
'LD_LIBRARY_PATH': join(BSOFT_HOME, 'lib')
}, position=Environ.BEGIN)
return environ
def getEnviron():
""" Setup the environment variables needed to launch Bsoft. """
environ = Environ(os.environ)
BSOFT_HOME = os.environ['BSOFT_HOME']
environ.update({
'BSOFT': BSOFT_HOME,
'BPARAM': join(BSOFT_HOME, 'params'),
'PATH': join(BSOFT_HOME, 'bin'),
'LD_LIBRARY_PATH': join(BSOFT_HOME, 'lib')
}, position=Environ.BEGIN)
return environ
def readSetOfCoordinates(outputDir, micSet, coordSet):
""" Read from Bsoft .star files.
Params:
outputDir: the directory where the .star files are.
micSet: the SetOfMicrographs to associate the .star, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
addBsoftLabelAliases()
boxSize = 0
for mic in micSet:
outputFile = join(outputDir, replaceBaseExt(mic.getFileName(), 'star'))
#scipionPosFile = join(outputDir, "scipion_" + replaceBaseExt(mic.getFileName(), 'pos'))
if exists(outputFile):
posMd = xmipp.MetaData(outputFile)
for objId in posMd:
coord = rowToCoordinate(rowFromMd(posMd, objId))
boxSize = 2 * posMd.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE,
objId)
coord.setMicrograph(mic)
coord.setX(coord.getX())
coord.setY(coord.getY())
coordSet.append(coord)
# Add an unique ID that will be propagated to particles
posMd.setValue(xmipp.MDL_ITEM_ID, long(coord.getObjId()),
objId)
# if not posMd.isEmpty():
# posMd.write("particles@%s" % scipionPosFile)
#reading origin.x value and converting to particle size, can change, we take last value
coordSet.setBoxSize(boxSize)
def readSetOfCoordinates(outputDir, micSet, coordSet):
""" Read from Bsoft .star files.
Params:
outputDir: the directory where the .star files are.
micSet: the SetOfMicrographs to associate the .star, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
addBsoftLabelAliases()
boxSize = 0
for mic in micSet:
outputFile = join(outputDir, replaceBaseExt(mic.getFileName(), 'star'))
#scipionPosFile = join(outputDir, "scipion_" + replaceBaseExt(mic.getFileName(), 'pos'))
if exists(outputFile):
posMd = xmipp.MetaData(outputFile)
for objId in posMd:
coord = rowToCoordinate(rowFromMd(posMd, objId))
boxSize = 2 * posMd.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, objId)
coord.setMicrograph(mic)
coord.setX(coord.getX())
coord.setY(coord.getY())
coordSet.append(coord)
# Add an unique ID that will be propagated to particles
posMd.setValue(xmipp.MDL_ITEM_ID, long(coord.getObjId()), objId)
# if not posMd.isEmpty():
# posMd.write("particles@%s" % scipionPosFile)
#reading origin.x value and converting to particle size, can change, we take last value
coordSet.setBoxSize(boxSize)
def check_gauss(self):
# Function to check if gaussian algorithm was used to pick and is so
# ask user if she wants to perform an automatic picking for the remaining micrographs
gaussJsonFile = join("e2boxercache", "gauss_box_DB.json")
# Check if gauss json file exists and load it
if os.path.exists(gaussJsonFile):
jsonGaussDict = loadJson(gaussJsonFile)
gaussParsDict = None
micList = [os.path.relpath(mic.getFileName(), self.workingDir.get()) for mic in self.inputMics]
# Go over the list of input micrographs and see if gaussian was used to pick any of them
for mic in micList:
if mic in jsonGaussDict:
gaussParsDict = jsonGaussDict[mic]
break
if gaussParsDict is not None:
# If found ask user if she wats to perform an automatic gaussian picking for the rest of mics
# if askYesNo(Message.TITLE_PICK_GAUSS, Message.LABEL_PICK_GAUSS, None):
self._params['boxSize'] = gaussParsDict['boxsize']
# Run sxprocess.py to store parameters
program = eman2.getEmanProgram("sxprocess.py")
argsList = ["'%s'=%s:" %(key, val) for (key, val) in gaussParsDict.iteritems()]
args = 'demoparms --makedb ' + "".join(argsList)
# Remove last ":" to avoid error
args = args[:-1]
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' + args)
self.runJob(program, args)
# Now run e2boxer.py with stored parameters
#arguments = "--gauss_autoboxer=demoparms --write_ptcl --boxsize=%(boxSize)s --norm=normalize.ramp.normvar" + arguments
arguments = "--gauss_autoboxer=demoparms --write_dbbox --boxsize=%(boxSize)s " + "%(inputMics)s"
program = eman2.getEmanProgram("e2boxer.py")
self._log.info('Launching: ' + program + ' ' + arguments % self._params)
self.runJob(program, arguments % self._params)
def _insertAllSteps(self):
self._params = {}
# diameter must be passed in Armstrongs and therefore should be converted
self._params['diam'] = self.diameter.get() * self.getInputMicrographs().getSamplingRate()
# self._params['num-slices'] = self.numberSizes.get()
# self._params['size-range'] = self.sizeRange.get()
self._params['apix'] = self.inputMicrographs.get().getSamplingRate()
self._params['thresh'] = self.threshold.get()
# self._params['max-thresh'] = self.maxThreshold.get()
# self._params['max-area'] = self.maxArea.get()
# self._params['max-peaks'] = self.maxPeaks.get()
args = ""
for par, val in self._params.iteritems():
args += " --%s=%s" % (par, str(val))
if self.invert:
args += " --invert"
args += " " + self.extraParams.get('')
deps = [] # Store all steps ids, final step createOutput depends on all of them
ih = ImageHandler()
for mic in self.inputMicrographs.get():
# Create micrograph folder
micName = mic.getFileName()
micDir = self._getTmpPath(removeBaseExt(micName))
makePath(micDir)
# If needed convert micrograph to mrc format, otherwise link it
if getExt(micName) != ".mrc":
fnMicBase = replaceBaseExt(micName, 'mrc')
inputMic = join(micDir, fnMicBase)
ih.convert(mic.getLocation(), inputMic)
else:
inputMic = join(micDir, basename(micName))
createLink(micName, inputMic)
# Insert step to execute program
stepId = self._insertFunctionStep('executeDogpickerStep', inputMic, args)
deps.append(stepId)
self._insertFinalSteps(deps)
def _insertAllSteps(self):
self._params = {}
# diameter must be passed in Angstrongs and therefore should be converted
self._params['diam'] = self.diameter.get() * self.getInputMicrographs().getSamplingRate()
# self._params['num-slices'] = self.numberSizes.get()
# self._params['size-range'] = self.sizeRange.get()
self._params['apix'] = self.inputMicrographs.get().getSamplingRate()
self._params['thresh'] = self.threshold.get()
# self._params['max-thresh'] = self.maxThreshold.get()
# self._params['max-area'] = self.maxArea.get()
# self._params['max-peaks'] = self.maxPeaks.get()
args = ""
for par, val in self._params.iteritems():
args += " --%s=%s" % (par, str(val))
if self.invert:
args += " --invert"
args += " " + self.extraParams.get('')
deps = [] # Store all steps ids, final step createOutput depends on all of them
ih = ImageHandler()
for mic in self.inputMicrographs.get():
# Create micrograph folder
micName = mic.getFileName()
micDir = self._getTmpPath(removeBaseExt(micName))
makePath(micDir)
# If needed convert micrograph to mrc format, otherwise link it
if getExt(micName) != ".mrc":
fnMicBase = replaceBaseExt(micName, 'mrc')
inputMic = join(micDir, fnMicBase)
ih.convert(mic.getLocation(), inputMic)
else:
inputMic = join(micDir, basename(micName))
createLink(micName, inputMic)
# Insert step to execute program
stepId = self._insertFunctionStep('executeDogpickerStep', inputMic, args)
deps.append(stepId)
self._insertFinalSteps(deps)
def copyTree(self, localFolder, remoteFolder):
"""
Same as shutil.copytree, but allowing
that the dest folder also exists.
dest is a remote folder.
"""
if not self.exists(remoteFolder):
self.makePath(remoteFolder)
for path in os.listdir(localFolder):
localPath = join(localFolder, path)
remotePath = join(remoteFolder, path)
# Create folders
if isdir(localPath):
self.copyTree(localPath, remotePath)
elif isfile(localPath):
self.putFile(localPath, remotePath)
def copyTree(self, localFolder, remoteFolder):
"""
Same as shutil.copytree, but allowing
that the dest folder also exists.
dest is a remote folder.
"""
if not self.exists(remoteFolder):
self.makePath(remoteFolder)
for path in os.listdir(localFolder):
localPath = join(localFolder, path)
remotePath = join(remoteFolder, path)
# Create folders
if isdir(localPath):
self.copyTree(localPath, remotePath)
elif isfile(localPath):
self.putFile(localPath, remotePath)
def getEnviron():
""" Setup the environment variables needed to launch Appion. """
environ = Environ(os.environ)
if 'DOGPICKER_HOME' in environ:
environ.update({
'PATH': os.environ['DOGPICKER_HOME'],
'LD_LIBRARY_PATH': join(os.environ['DOGPICKER_HOME'], 'appionlib') + ":" + os.environ['DOGPICKER_HOME'],
}, position=Environ.BEGIN)
else:
#TODO: Find a generic way to warn of this situation
print "DOGPICKER_HOME variable not set on environment."
return environ
def getMethods(self, output):#output is not used but to overwrite getMethods it is used
msg = ""
configfile = join(self._getExtraPath(), 'config.xmd')
existsConfig = exists(configfile)
if existsConfig:
md = xmipp.MetaData('properties@' + configfile)
configobj = md.firstObject()
particleSize = md.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, configobj)
manualParticlesSize = md.getValue(xmipp.MDL_PICKING_MANUALPARTICLES_SIZE, configobj)
msg = 'User picked %d particles with a particle size of %d.' % (manualParticlesSize, particleSize)
return msg
def getDefaultBoxSize(self):
import xmipp
boxSize = 100
importFrom = self.getImportFrom()
scale = self.scale.get()
if importFrom == ProtImportCoordinates.IMPORT_FROM_XMIPP:
configfile = join(self.filesPath.get(), 'config.xmd')
existsConfig = exists(configfile)
if existsConfig:
md = xmipp.MetaData('properties@' + configfile)
configobj = md.firstObject()
boxSize = md.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, configobj)
if importFrom == ProtImportCoordinates.IMPORT_FROM_EMAN:
# Read the boxSize from the e2boxercache/base.json
jsonFnbase = join(self.filesPath.get(), 'e2boxercache', 'base.json')
from pyworkflow.em.packages.eman2 import loadJson
jsonBoxDict = loadJson(jsonFnbase)
boxSize = int(jsonBoxDict["box_size"])
boxSize = (int)(boxSize * scale)
return boxSize
def readSetOfCoordinates(workDir, micSet, coordSet):
""" Read from Appion .txt files.
It is expected a file named: base.txt under the workDir.
Params:
workDir: where the Appion dogpicker output files are located.
micSet: the SetOfMicrographs to associate the .txt, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
for mic in micSet:
micCoordFn = join(workDir, replaceBaseExt(mic.getFileName(), 'txt'))
readCoordinates(mic, micCoordFn, coordSet)
def readSetOfCoordinates(workDir, micSet, coordSet):
""" Read from Appion .txt files.
It is expected a file named: base.txt under the workDir.
Params:
workDir: where the Appion dogpicker output files are located.
micSet: the SetOfMicrographs to associate the .txt, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
for mic in micSet:
micCoordFn = join(workDir, replaceBaseExt(mic.getFileName(), 'txt'))
readCoordinates(mic, micCoordFn, coordSet)
def getSummary(self, coordsSet):
summary = []
configfile = join(self._getExtraPath(), 'config.xmd')
if exists(configfile):
md = xmipp.MetaData('properties@' + configfile)
configobj = md.firstObject()
activemic = md.getValue(xmipp.MDL_MICROGRAPH, configobj)
manualParticlesSize = md.getValue(xmipp.MDL_PICKING_MANUALPARTICLES_SIZE, configobj)
particleSize = md.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, configobj)
summary.append("Particles picked: %d"%manualParticlesSize)
summary.append("Particle size: %d"%particleSize)
summary.append("Last micrograph: " + activemic)
return "\n".join(summary)
def cleanPath(self, *remotePaths):
"""
Same as pyworkflow.utils.path.cleanPath but for remote folders or files.
"""
for path in remotePaths:
if self.exists(path):
# Create folders
if self.isdir(path):
files = [join(path, f) for f in self.sftp.listdir(path)]
self.cleanPath(*files)
log.info('RemotePath.cleanPath, rmdir path: %s' % path)
self.sftp.rmdir(path)
else:# isfile(path):
log.info('RemotePath.cleanPath, remove path: %s' % path)
self.sftp.remove(path)
def cleanPath(self, *remotePaths):
"""
Same as pyworkflow.utils.path.cleanPath but for remote folders or files.
"""
for path in remotePaths:
if self.exists(path):
# Create folders
if self.isdir(path):
files = [join(path, f) for f in self.sftp.listdir(path)]
self.cleanPath(*files)
log.info('RemotePath.cleanPath, rmdir path: %s' % path)
self.sftp.rmdir(path)
else: # isfile(path):
log.info('RemotePath.cleanPath, remove path: %s' % path)
self.sftp.remove(path)
def check_gauss(self):
if self._useNewBoxer():
# gauss picker is not implemented for Eman v.2.21 yet
pass
else:
# Function to check if gaussian algorithm was used to pick
# and if so ask user if she wants to perform an automatic
# picking for the remaining micrographs
gaussJsonFile = join("e2boxercache", "gauss_box_DB.json")
# Check if gauss json file exists and load it
if os.path.exists(gaussJsonFile):
jsonGaussDict = loadJson(gaussJsonFile)
gaussParsDict = None
micList = [
os.path.relpath(mic.getFileName(), self.workingDir.get())
for mic in self.inputMics
]
# Go over the list of input micrographs and see if
# gaussian was used to pick any of them
for mic in micList:
if mic in jsonGaussDict:
gaussParsDict = jsonGaussDict[mic]
break
if gaussParsDict is not None:
# If found ask user if she wats to perform an automatic gaussian
# picking for the rest of mics
self._params['boxSize'] = gaussParsDict['boxsize']
# Run sxprocess.py to store parameters
program = eman2.Plugin.getProgram("sxprocess.py")
argsList = [
"'%s'=%s:" % (key, val)
for (key, val) in gaussParsDict.iteritems()
]
args = 'demoparms --makedb ' + "".join(argsList)
# Remove last ":" to avoid error
args = args[:-1]
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' + args)
self.runJob(program, args)
# Now run e2boxer.py with stored parameters
arguments = "--gauss_autoboxer=demoparms --write_dbbox "
arguments += " --boxsize=%(boxSize)s " + "%(inputMics)s"
boxer = eman2.Plugin.getBoxerCommand(boxerVersion='old')
program = eman2.Plugin.getProgram(boxer)
self._log.info('Launching: ' + program + ' ' +
arguments % self._params)
self.runJob(program, arguments % self._params)
def getEnviron():
""" Setup the environment variables needed to launch Appion. """
environ = Environ(os.environ)
if 'DOGPICKER_HOME' in environ:
environ.update(
{
'PATH':
os.environ['DOGPICKER_HOME'],
'LD_LIBRARY_PATH':
join(os.environ['DOGPICKER_HOME'], 'appionlib') + ":" +
os.environ['DOGPICKER_HOME'],
},
position=Environ.BEGIN)
else:
#TODO: Find a generic way to warn of this situation
print "DOGPICKER_HOME variable not set on environment."
return environ
