def main():
args = get_parser().parse_args()
projName = args.project
# Create a manager and load the project
manager = Manager()
cwd = os.getcwd() # Keep current directory to restore it later
project = manager.loadProject(projName)
# Export protocols as a dict
jsonDict = project.getProtocolsDict()
os.chdir(cwd) # Restore after project load
if args.output:
print("Writing workflow to file: ", args.output)
with open(args.output, 'w') as f:
json.dump(list(jsonDict.values()),
f,
indent=4,
separators=(',', ': '))
else:
print(
json.dumps(list(jsonDict.values()),
indent=4,
separators=(',', ': ')))
def __init__(self):
projName = self.__class__.__name__
manager = Manager()
if manager.hasProject(projName):
self.project = manager.loadProject(projName)
else:
self.project = manager.createProject(projName)
# Use graph view as default
settings = self.project.getSettings()
settings.setRunsView(1) # graph view
settings.write()
self.loadWorkflow()
def main():
if len(sys.argv) != 3:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
searchDir = os.path.abspath(sys.argv[2])
# Create a new project
manager = Manager()
if not manager.hasProject(projName):
usage("Nonexistent project: %s" % pwutils.red(projName))
if not os.path.exists(searchDir):
usage("Nonexistent SEARCH_DIR: %s" % pwutils.red(searchDir))
project = manager.loadProject(projName)
project.fixLinks(searchDir)
def _writeSubset(self, subset):
""" Generated the output of this subset. """
newSubsetName = 'outputParticles_%03d' % self._counter
self.info("Creating new subset: %s" % newSubsetName)
subset.write()
self._defineOutputs(**{newSubsetName: subset})
self._defineTransformRelation(self.inputParticles, subset)
# The following is required to commit the changes to the database
self._store(subset)
subset.close()
manager = Manager()
project = manager.loadProject(self.getProject().getName())
input2D = self.input2dProtocol.get()
copyProt = project.copyProtocol(project.getProtocol(input2D.getObjId()))
copyProt.inputParticles.set(project.getProtocol(self.getObjId()))
copyProt.inputParticles.setExtended(newSubsetName)
project.scheduleProtocol(copyProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(copyProt.getObjId())
Use readOnly=True (or False) to set/unset read only property
Use lifeTime=X for setting X hours or None to unset life time of the project.
""" % error
sys.exit(1)
n = len(sys.argv)
if n < 2 or n > 4:
usage("Incorrect number of input parameters")
# Load the given project
projectsDir = os.path.join(pw.Config.SCIPION_USER_DATA, 'projects')
projName = sys.argv[1]
manager = Manager()
project = manager.loadProject(projName)
if project is None:
usage("Project '%s' does not exist in: \n %s" % (projName, projectsDir))
setReadOnly = False
setLifeTime = False
for arg in sys.argv:
if arg.startswith('readOnly='):
setReadOnly = True
value = arg.split('readOnly=')[1]
b = Boolean(value=value)
readOnlyValue = b.get()
elif arg.startswith('lifeTime='):
setLifeTime = True
def monitorStep(self):
self._runPrerequisites = []
manager = Manager()
project = manager.loadProject(self.getProject().getName())
percentage = [1.14, 2.29, 3.44, 5.74, 9.19, 14.94, 24.13, 39.08]
numGlobalIters = len(percentage) + 2
self.consecutiveBimodal = 2
self.listConsecutiveBimodal = []
targetResolution = self.minimumTargetResolution.get()
#Global iterations
for i in range(numGlobalIters):
self.convertInputStep(percentage, i)
print("Target resolution - group %s: %f " %
(chr(65 + i), float(targetResolution)))
sys.stdout.flush()
if i == 0:
previousProtVol = self
namePreviousVol = 'outputVolumesInit'
else:
previousProtVol = newHighRes
namePreviousVol = 'outputVolume'
newHighRes = project.newProtocol(
XmippProtReconstructHighRes,
objLabel='HighRes - group %s' % chr(65 + i),
symmetryGroup=self.symmetryGroup.get(),
numberOfIterations=1,
particleRadius=self.particleRadius.get(),
maximumTargetResolution=targetResolution,
alignmentMethod=XmippProtReconstructHighRes.GLOBAL_ALIGNMENT,
angularMaxShift=self.maxShift.get(),
angularMinTilt=self.angularMinTilt.get(),
angularMaxTilt=self.angularMaxTilt.get(),
postAdHocMask=self.postAdHocMask.get(),
postSymmetryWithinMask=self.postSymmetryWithinMask.get(),
postSymmetryWithinMaskType=self.postSymmetryWithinMaskType.get(
),
postSymmetryWithinMaskMask=self.postSymmetryWithinMaskMask.get(
),
postSymmetryHelical=self.postSymmetryHelical.get(),
postSymmetryHelicalRadius=self.postSymmetryHelicalRadius.get(),
postSymmetryHelicalDihedral=self.postSymmetryHelicalDihedral.
get(),
postSymmetryHelicalMinRot=self.postSymmetryHelicalMinRot.get(),
postSymmetryHelicalMaxRot=self.postSymmetryHelicalMaxRot.get(),
postSymmetryHelicalMinZ=self.postSymmetryHelicalMinZ.get(),
postSymmetryHelicalMaxZ=self.postSymmetryHelicalMaxZ.get(),
postScript=self.postScript.get(),
postSignificantDenoise=self.postSignificantDenoise.get(),
postFilterBank=self.postFilterBank.get(),
postLaplacian=self.postLaplacian.get(),
postDeconvolve=self.postDeconvolve.get(),
postSoftNeg=self.postSoftNeg.get(),
postSoftNegK=self.postSoftNegK.get(),
postDifference=self.postDifference.get(),
numberOfMpi=self.numberOfMpi.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get())
previousProtPart = self
namePreviousParticles = 'outputParticles%s' % chr(65 + i)
newHighRes.inputParticles.set(previousProtPart)
newHighRes.inputParticles.setExtended(namePreviousParticles)
newHighRes.inputVolumes.set(previousProtVol)
newHighRes.inputVolumes.setExtended(namePreviousVol)
project.scheduleProtocol(newHighRes)
# Next schedule will be after this one
self._runPrerequisites.append(newHighRes.getObjId())
self.childs.append(newHighRes)
finishedIter = False
while finishedIter == False:
time.sleep(15)
newHighRes = self._updateProtocol(newHighRes)
if newHighRes.isFailed() or newHighRes.isAborted():
raise Exception('XmippProtReconstructHighRes has failed')
if newHighRes.isFinished():
finishedIter = True
fnDir = newHighRes._getExtraPath("Iter%03d" % 1)
fnFSCs = open(self._getExtraPath('fnFSCs.txt'), 'a')
fnFSCs.write(join(fnDir, "fsc.xmd") + " \n")
fnFSCs.close()
targetResolution = self.checkOutputsStep(newHighRes, i, False)
targetResolution = max(targetResolution,
self.maximumTargetResolution.get())
if i >= 7: #We are in the last three iterations
#Check the output particles and remove all the disabled ones
fnOutParticles = newHighRes._getPath('angles.xmd')
params = '-i %s --query select "enabled==1"' % (fnOutParticles)
self.runJob("xmipp_metadata_utilities", params, numberOfMpi=1)
fnFinal = self._getExtraPath('inputLocalHighRes1.xmd')
if i == 7:
copy(fnOutParticles, fnFinal)
else:
params = ' -i %s --set union %s -o %s' % (
fnFinal, fnOutParticles, fnFinal)
self.runJob("xmipp_metadata_utilities",
params,
numberOfMpi=1)
if i == 9:
outputinputSetOfParticles = self._createSetOfParticles(
)
outputinputSetOfParticles.copyInfo(
self.inputParticles.get())
readSetOfParticles(fnFinal, outputinputSetOfParticles)
self._defineOutputs(
outputParticlesLocal1=outputinputSetOfParticles)
self._store(outputinputSetOfParticles)
#Local iterations
numLocalIters = 5
for i in range(numLocalIters):
if i > 2:
minPrevRes = prevTargetResolution
if targetResolution > minPrevRes:
print("Target resolution is stuck")
sys.stdout.flush()
break
prevTargetResolution = targetResolution
print("Target resolution - INPUT local %d: %f " %
((i + 1), float(targetResolution)))
sys.stdout.flush()
previousProtVol = newHighRes
namePreviousVol = 'outputVolume'
#calling highres local with the new input set
newHighRes = project.newProtocol(
XmippProtReconstructHighRes,
objLabel='HighRes - local %d' % (i + 1),
symmetryGroup=self.symmetryGroup.get(),
numberOfIterations=1,
particleRadius=self.particleRadius.get(),
maximumTargetResolution=targetResolution,
alignmentMethod=XmippProtReconstructHighRes.LOCAL_ALIGNMENT,
angularMaxShift=self.maxShift.get(),
angularMinTilt=self.angularMinTilt.get(),
angularMaxTilt=self.angularMaxTilt.get(),
postAdHocMask=self.postAdHocMask.get(),
postSymmetryWithinMask=self.postSymmetryWithinMask.get(),
postSymmetryWithinMaskType=self.postSymmetryWithinMaskType.get(
),
postSymmetryWithinMaskMask=self.postSymmetryWithinMaskMask.get(
),
postSymmetryHelical=self.postSymmetryHelical.get(),
postSymmetryHelicalRadius=self.postSymmetryHelicalRadius.get(),
postSymmetryHelicalDihedral=self.postSymmetryHelicalDihedral.
get(),
postSymmetryHelicalMinRot=self.postSymmetryHelicalMinRot.get(),
postSymmetryHelicalMaxRot=self.postSymmetryHelicalMaxRot.get(),
postSymmetryHelicalMinZ=self.postSymmetryHelicalMinZ.get(),
postSymmetryHelicalMaxZ=self.postSymmetryHelicalMaxZ.get(),
postScript=self.postScript.get(),
postSignificantDenoise=self.postSignificantDenoise.get(),
postFilterBank=self.postFilterBank.get(),
postLaplacian=self.postLaplacian.get(),
postDeconvolve=self.postDeconvolve.get(),
postSoftNeg=self.postSoftNeg.get(),
postSoftNegK=self.postSoftNegK.get(),
postDifference=self.postDifference.get(),
numberOfMpi=self.numberOfMpi.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get())
newHighRes.inputParticles.set(self)
namePreviousParticles = 'outputParticlesLocal%d' % (i + 1)
newHighRes.inputParticles.setExtended(namePreviousParticles)
newHighRes.inputVolumes.set(previousProtVol)
newHighRes.inputVolumes.setExtended(namePreviousVol)
project.scheduleProtocol(newHighRes, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newHighRes.getObjId())
self.childs.append(newHighRes)
finishedIter = False
while finishedIter == False:
time.sleep(15)
newHighRes = self._updateProtocol(newHighRes)
if newHighRes.isFailed() or newHighRes.isAborted():
raise Exception('XmippProtReconstructHighRes has failed')
if newHighRes.isFinished():
finishedIter = True
fnDir = newHighRes._getExtraPath("Iter%03d" % 1)
fnFSCs = open(self._getExtraPath('fnFSCs.txt'), 'a')
fnFSCs.write(join(fnDir, "fsc.xmd") + " \n")
fnFSCs.close()
targetResolution = self.checkOutputsStep(newHighRes,
numGlobalIters + i, True)
targetResolution = max(targetResolution,
self.maximumTargetResolution.get())
#Check the output particles and remove all the disabled ones
fnOutParticles = newHighRes._getPath('angles.xmd')
params = '-i %s --query select "enabled==1"' % (fnOutParticles)
self.runJob("xmipp_metadata_utilities", params, numberOfMpi=1)
fnFinal = self._getExtraPath('inputLocalHighRes%d.xmd' % (i + 2))
copy(fnOutParticles, fnFinal)
if i > 1:
#including the number of particles as stoppping criteria
mdFinal = emlib.MetaData(fnFinal)
Nfinal = mdFinal.size()
Ninit = self.inputParticles.get().getSize()
if Nfinal < Ninit * 0.3:
print("Image set size too small", Nfinal, Ninit)
sys.stdout.flush()
break
outputinputSetOfParticles = self._createSetOfParticles()
outputinputSetOfParticles.copyInfo(self.inputParticles.get())
readSetOfParticles(fnFinal, outputinputSetOfParticles)
result = {
'outputParticlesLocal%d' % (i + 2): outputinputSetOfParticles
}
self._defineOutputs(**result)
self._store(outputinputSetOfParticles)
#self = self._updateProtocol(self)
self.createOutputStep(project)
class ProjectsView(tk.Frame):
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
text=Message.LABEL_IMPORT_PROJECT,
font=self.projNameFont,
command=self._onImportProject)
btn.grid(row=0, column=1, sticky='nw', padx=10, pady=10)
btnFrame.grid(row=0, column=0, sticky='nw')
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, columnspan=2, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def createProjectList(self, text):
"""Load the list of projects"""
r = 0
text.setReadOnly(False)
text.clear()
parent = tk.Frame(text, bg='white')
parent.columnconfigure(0, weight=1)
colors = ['white', '#EAEBFF']
for i, p in enumerate(self.manager.listProjects()):
try:
project = self.manager.loadProject(p.getName(),
chdir=False,
loadAllConfig=False)
# Add creation time to project info
p.cTime = project.getCreationTime()
# Add if it's a link
p.isLink = project.isLink()
# If it's a link, get the linked folder
if p.isLink:
p.linkedFolder = os.path.realpath(project.path)
frame = self.createProjectLabel(parent, p, color=colors[i % 2])
frame.grid(row=r, column=0, padx=10, pady=5, sticky='new')
r += 1
except Exception, ex:
print "ERROR loading project: %s" % p.getName()
print ex
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def monitorStep(self):
self._runPrerequisites = []
manager = Manager()
project = manager.loadProject(self.getProject().getName())
self.numIter = self.maxNumClasses.get()
for iter in range(1, self.numIter):
if iter == 1:
self.convertInputStep()
newSplitProt = project.newProtocol(
XmippProtSplitVolumeHierarchical,
objLabel='split volume hierarchical - iter %d' % iter,
symmetryGroup=self.symmetryGroup.get(),
angularSampling=self.angularSampling.get(),
angularDistance=self.angularDistance.get(),
maxShift=self.maxShift.get(),
directionalClasses=self.directionalClasses.get(),
homogeneize=self.homogeneize.get(),
targetResolution=self.targetResolution.get(),
class2dIterations=self.class2dIterations.get(),
splitVolume=self.splitVolume.get(),
Niter=self.Niter.get(),
Nrec=self.Nrec.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get())
previousSplitProt = self
newSubsetNameSplitVol = 'outputVolumesInit'
newSplitProt.inputVolume.set(previousSplitProt)
newSplitProt.inputVolume.setExtended(newSubsetNameSplitVol)
newSubsetNameSplitParts = 'outputParticlesInit'
newSplitProt.inputParticles.set(previousSplitProt)
newSplitProt.inputParticles.setExtended(
newSubsetNameSplitParts)
project.scheduleProtocol(newSplitProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newSplitProt.getObjId())
self.childs.append(newSplitProt)
newSignificantProt = project.newProtocol(
XmippProtReconstructHeterogeneous,
objLabel='significant heterogeneity - iter %d' % iter,
symmetryGroup=self.symmetryGroup.get(),
particleRadius=self.particleRadius.get(),
targetResolution=self.targetResolution.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get(),
numberOfIterations=self.numberOfIterations.get(),
nxtMask=self.nextMask.get(),
angularMinTilt=self.angularMinTilt.get(),
angularMaxTilt=self.angularMaxTilt.get(),
numberOfReplicates=self.numberOfReplicates.get(),
angularMaxShift=self.angularMaxShift.get(),
numberVotes=self.numberVotes.get(),
stochastic=self.stochastic.get(),
stochasticAlpha=self.stochasticAlpha.get(),
stochasticN=self.stochasticN.get())
previousSignifProt = newSplitProt
newSubsetNameSignifParts = 'outputParticlesInit'
newSignificantProt.inputParticles.set(previousSplitProt)
newSignificantProt.inputParticles.setExtended(
newSubsetNameSignifParts)
newSubsetNameSignifVol = 'outputVolumes'
newSignificantProt.inputVolumes.set(previousSignifProt)
newSignificantProt.inputVolumes.setExtended(
newSubsetNameSignifVol)
project.scheduleProtocol(newSignificantProt,
self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newSignificantProt.getObjId())
self.childs.append(newSignificantProt)
elif iter > 1 and not self.finished:
newSplitProt = project.newProtocol(
XmippProtSplitVolumeHierarchical,
objLabel='split volume hierarchical - iter %d' % iter,
symmetryGroup=self.symmetryGroup.get(),
angularSampling=self.angularSampling.get(),
angularDistance=self.angularDistance.get(),
maxShift=self.maxShift.get(),
directionalClasses=self.directionalClasses.get(),
homogeneize=self.homogeneize.get(),
targetResolution=self.targetResolution.get(),
class2dIterations=self.class2dIterations.get(),
splitVolume=self.splitVolume.get(),
Niter=self.Niter.get(),
Nrec=self.Nrec.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get())
newSubsetNameSplitVol = 'outputAuxVolumes'
newSplitProt.inputVolume.set(previousSplitProt)
newSplitProt.inputVolume.setExtended(newSubsetNameSplitVol)
newSubsetNameSplitParts = 'outputAuxParticles'
newSplitProt.inputParticles.set(previousSplitProt)
newSplitProt.inputParticles.setExtended(
newSubsetNameSplitParts)
project.scheduleProtocol(newSplitProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newSplitProt.getObjId())
self.childs.append(newSplitProt)
newSignificantProt = project.newProtocol(
XmippProtReconstructHeterogeneous,
objLabel='significant heterogeneity - iter %d' % iter,
symmetryGroup=self.symmetryGroup.get(),
particleRadius=self.particleRadius.get(),
targetResolution=self.targetResolution.get(),
useGpu=self.useGpu.get(),
gpuList=self.gpuList.get(),
numberOfIterations=self.numberOfIterations.get(),
nxtMask=self.nextMask.get(),
angularMinTilt=self.angularMinTilt.get(),
angularMaxTilt=self.angularMaxTilt.get(),
numberOfReplicates=self.numberOfReplicates.get(),
angularMaxShift=self.angularMaxShift.get(),
numberVotes=self.numberVotes.get(),
stochastic=self.stochastic.get(),
stochasticAlpha=self.stochasticAlpha.get(),
stochasticN=self.stochasticN.get())
previousSignifProt = newSplitProt
newSubsetNameSignifParts = 'outputAuxParticles'
newSignificantProt.inputParticles.set(previousSplitProt)
newSignificantProt.inputParticles.setExtended(
newSubsetNameSignifParts)
newSubsetNameSignifVol = 'outputVolumes'
newSignificantProt.inputVolumes.set(previousSignifProt)
newSignificantProt.inputVolumes.setExtended(
newSubsetNameSignifVol)
project.scheduleProtocol(newSignificantProt,
self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(newSignificantProt.getObjId())
self.childs.append(newSignificantProt)
if not self.finished:
finishedIter = False
while finishedIter == False:
time.sleep(15)
newSplitProt = self._updateProtocol(newSplitProt)
newSignificantProt = self._updateProtocol(
newSignificantProt)
if newSplitProt.isFailed() or newSplitProt.isAborted():
raise Exception(
'XmippProtSplitVolumeHierarchical has failed')
if newSignificantProt.isFailed(
) or newSignificantProt.isAborted():
raise Exception(
'XmippProtReconstructHeterogeneous has failed')
if newSignificantProt.isFinished():
finishedIter = True
for classItem in newSignificantProt.outputClasses:
self.classListSizes.append(classItem.getSize())
self.classListIds.append(classItem.getObjId())
self.classListProtocols.append(newSignificantProt)
finishedSubset = False
finishedLast = False
if iter != self.numIter - 1:
subsetProt = self.checkOutputsStep(project, iter)
while finishedSubset == False and not self.finished:
time.sleep(5)
subsetProt = self._updateProtocol(subsetProt)
if subsetProt.isFailed() or subsetProt.isAborted():
raise Exception(
'XmippMetaProtCreateSubset has failed')
if subsetProt.isFinished():
finishedSubset = True
previousSplitProt = subsetProt
elif iter == self.numIter - 1:
outputMetaProt = self.createOutputStep(project)
while finishedLast == False:
time.sleep(5)
outputMetaProt = self._updateProtocol(outputMetaProt)
if outputMetaProt.isFailed():
raise Exception(
'XmippMetaProtCreateOutput has failed')
if outputMetaProt.isFinished():
finishedLast = True
if self.finished and iter == self.numIter - 1:
finishedLast = False
outputMetaProt = self.createOutputStep(project)
while finishedLast == False:
time.sleep(5)
outputMetaProt = self._updateProtocol(outputMetaProt)
if outputMetaProt.isFailed():
raise Exception('XmippMetaProtCreateOutput has failed')
if outputMetaProt.isFinished():
finishedLast = True
if self.finished and iter < self.numIter - 1:
continue