def __init__(self,
InSelFile,
InDocFile,
MissingDocFile,
WorkingDir,
DoDeleteWorkingDir,
ProjectDir,
LogDir,
OutputRootName,
NumberOfIterations,
DoKeepAngles,
RestartIter,
Symmetry,
Dimension,
MaximumResolution,
ExtraParamsMLtomo,
DoAlign,
AngularSampling,
AngularSearchRange,
DoPerturb,
NumberOfReferences,
SeedsSelfile,
InitialRegularization,
NumberRegularizationSteps,
MaskName,
NumberOfThreads,
DoParallel,
NumberOfMpi,
SystemFlavour):
import os,sys,shutil
scriptdir=os.path.split(os.path.dirname(os.popen('which xmipp_protocols','r').read()))[0]+'/protocols'
sys.path.append(scriptdir) # add default search path
import log,selfile
self.InSelFile=InSelFile
self.InDocFile=InDocFile
self.MissingDocFile=MissingDocFile
self.WorkingDir=WorkingDir
self.DoDeleteWorkingDir=DoDeleteWorkingDir
self.ProjectDir=ProjectDir
self.LogDir=LogDir
self.OutputRootName=OutputRootName
self.NumberOfIterations=NumberOfIterations
self.DoKeepAngles=DoKeepAngles
self.RestartIter=RestartIter
self.Symmetry=Symmetry
self.Dimension=Dimension
self.MaximumResolution=MaximumResolution
self.ExtraParamsMLtomo=ExtraParamsMLtomo
self.DoAlign=DoAlign
self.AngularSampling=AngularSampling
self.AngularSearchRange=AngularSearchRange
self.DoPerturb=DoPerturb
self.NumberOfReferences=NumberOfReferences
self.SeedsSelfile=SeedsSelfile
self.InitialRegularization=InitialRegularization
self.NumberRegularizationSteps=NumberRegularizationSteps
self.MaskName=MaskName
self.NumberOfThreads=NumberOfThreads
self.DoParallel=DoParallel
self.NumberOfMpi=NumberOfMpi
self.SystemFlavour=SystemFlavour
# Setup logging
self.log=log.init_log_system(self.ProjectDir,
self.LogDir,
sys.argv[0],
self.WorkingDir)
# This is not a restart
if (self.RestartIter < 1):
# Delete working directory if it exists, make a new one
if (DoDeleteWorkingDir):
if (self.WorkingDir==""):
raise RuntimeError,"No working directory given"
if os.path.exists(self.WorkingDir):
shutil.rmtree(self.WorkingDir)
if not os.path.exists(self.WorkingDir):
os.makedirs(self.WorkingDir)
# Backup script
log.make_backup_of_script_file(sys.argv[0],
os.path.abspath(self.WorkingDir))
# This protocol is executed from the ProjectDir
self.execute_MLtomo()
def __init__(self,
InSelFile,
WorkingDir,
ProjectDir,
LogDir,
ReferenceImage,
NumberOfIterations,
DoFilter,
Highpass,
Lowpass,
NumberOfMpi,
SystemFlavour):
scriptdir=os.path.split(os.path.dirname(os.popen('which xmipp_protocols','r').read()))[0]+'/protocols'
sys.path.append(scriptdir) # add default search path
import log
self.WorkingDir=WorkingDir
self.ProjectDir=ProjectDir
self.InSelFile=InSelFile
self.ReferenceImage=ReferenceImage
self.NumberOfIterations=NumberOfIterations
self.DoFilter=DoFilter
self.Highpass=Highpass
self.Lowpass=Lowpass
self.NumberOfMpi=NumberOfMpi
self.SystemFlavour=SystemFlavour
# Setup logging
self.log=log.init_log_system(self.ProjectDir,
LogDir,
sys.argv[0],
self.WorkingDir)
# Create directory if does not exist
if not os.path.exists(self.WorkingDir):
os.makedirs(self.WorkingDir)
self.doStep1=True
self.doStep2=True
# Save parameters and compare to possible previous runs
self.saveAndCompareParameters([
"InSelFile",
"ReferenceImage",
"NumberOfIterations",
"DoFilter",
"Highpass",
"Lowpass"]);
# Backup script
log.make_backup_of_script_file(sys.argv[0],
os.path.abspath(self.WorkingDir))
# Update status
fh=open(self.WorkingDir + "/status.txt", "a")
fh.write("Step 0: Process started at " + time.asctime() + "\n")
fh.close()
# Run
self.preprocess()
self.execute_CLalign2D()
self.postprocess()
fh=open(self.WorkingDir + "/status.txt", "a")
fh.write("Step F: Process finished at " + time.asctime() + "\n")
fh.close()
