def execute_MLtomo(self):
import os
import launch_job, utils_xmipp
if (self.RestartIter>0):
print '*********************************************************************'
print '* Restarting ml_tomo program :'
restartname = utils_xmipp.composeFileName('ml3d_it',iter,'log')
params= ' -restart ' + restartname
else:
print '*********************************************************************'
print '* Executing ml_tomo program :'
# General parameters
params= ' -i ' + str(self.InSelFile) + \
' -doc ' + str(self.InDocFile) + \
' -o ' + str(self.WorkingDir) + "/" + str(self.OutputRootName) + \
' -iter ' + str(self.NumberOfIterations) + \
' -sym ' + str(self.Symmetry) +\
' -maxres ' + str(self.MaximumResolution)
if (len(self.MissingDocFile) > 0):
params+= ' -missing ' + str(self.MissingDocFile)
if (self.Dimension > 0):
params+= ' -dim ' + str(self.Dimension)
if (self.DoKeepAngles):
params+= ' -keep_angles '
# Alignment parameters
if (self.DoAlign):
params+= ' -ang ' + str(self.AngularSampling)
if (self.AngularSearchRange<360):
params+= ' -ang_search ' + str(self.AngularSearchRange)
if (self.DoPerturb):
params+= ' -perturb '
else:
params+= ' -dont_align '
# Classification parameters
if (len(self.SeedsSelfile)>0):
params+= ' -ref ' + str(self.SeedsSelfile)
else:
params+= ' -nref ' + str(self.NumberOfReferences)
if (self.InitialRegularization>0):
params+= ' -reg0 ' + str(self.InitialRegularization)
params+= ' -reg_steps ' + str(self.NumberRegularizationSteps)
if (len(self.MaskName) > 0):
if (self.DoAlign):
print '********************************************************************************'
print '* ERROR: you can only provide a mask if you do NOT allow orientations to change'
self.close()
else:
params+= ' -mask ' + str(self.MaskName)
# Extra parameters
if (len(self.ExtraParamsMLtomo) > 0):
params+=' ' + str (self.ExtraParamsMLtomo)
# Thread parallelization
if (self.NumberOfThreads > 1):
params+=' -thr ' + str(self.NumberOfThreads)
launchJob("xmipp_ml_tomo",
params,
self.log,
self.DoParallel,
self.NumberOfMpi,
self.NumberOfThreads,
self.SystemFlavour)
def __init__(
self,
SelectClasses,
VisualizeVolZ,
VisualizeVolX,
VisualizeVolY,
VisualizeVolChimera,
MatrixWidth,
VisualizeUntiltedAverages,
VisualizeUntiltedImages,
VisualizeTiltedImages,
VisualizeVols,
VisualizeFilteredVols,
ProtocolName,
):
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 visualization, utils_xmipp
# Import the corresponding protocol, get WorkingDir and go there
pardir = os.path.abspath(os.getcwd())
shutil.copy(ProtocolName, "protocol.py")
import protocol
self.WorkingDir = protocol.WorkingDir
os.chdir(self.WorkingDir)
ShowVolumes = []
ShowSelfiles = []
ShowImages = []
refs = utils_xmipp.getCommaSeparatedIntegerList(SelectClasses)
for ref in refs:
basename = utils_xmipp.composeFileName("rct_ref", ref, "")
if VisualizeUntiltedAverages:
ShowImages.append(basename + "_untilted_avg.xmp")
if VisualizeUntiltedImages:
ShowSelfiles.append(basename + "_untilted.sel")
if VisualizeTiltedImages:
ShowSelfiles.append(basename + "_tilted.sel")
if VisualizeVols:
ShowVolumes.append(basename + "_tilted.vol")
if VisualizeFilteredVols:
ShowVolumes.append(basename + "_tilted_filtered.vol")
visualization.visualize_volumes(ShowVolumes, VisualizeVolZ, VisualizeVolX, VisualizeVolY, VisualizeVolChimera)
visualization.visualize_images(ShowSelfiles, True, MatrixWidth)
visualization.visualize_images(ShowImages)
# Return to parent dir and remove protocol.py(c)
os.chdir(pardir)
if os.path.exists("protocol.py"):
os.remove("protocol.py")
if os.path.exists("protocol.pyc"):
os.remove("protocol.pyc")
