#Tue May 28 13:11:53 MDT 2013 Setup.Post.Trimvol.ScaleXMax=1244 Setup.AxisB.TiltAngle.TiltAngleFilename= ScreenState.TomoGen.Sirt.Header.AdvancedBasic=basic Setup.AxisA.TiltAngle.TiltAngleFilename= Setup.tiltalign.TargetPatchSizeXandY=700,700 ScreenState.FidModel.mb.expert-parameters.open=false Setup.Binning=2 ScreenState.Combine.bn.restart-at-patchcorr.done=false ScreenState.CoarseAlign.mb.tiltxcorr.advanced=false ScreenState.Combine.bn.create-combine-scripts.done=false ScreenState.FinalStack.bn.create-full-aligned-stack.done=true Setup.UseLocalAlignmentsB=true Setup.Combine.FiducialMatchListB= Setup.UseLocalAlignmentsA=true Setup.Combine.FiducialMatchListA= ScreenState.FidModel.bn.seed-fiducial-model.done=true Setup.Track.A.OverlapOfPatchesXandY=.33,.33 Setup.Gen.A.Scale.Factor.Linear=0.1 ReconstructionState.nullTomoPos.tilt.Fiducialess=false Setup.Combine.PatchBoundaryYMin=0 ScreenState.PostProc.bn.run-flattenwarp-to-assess-smoothing.done=false ScreenState.PreProc.bn.use-fixed-stack.done=true ScreenState.TomoGen.bn.use-current-trial-tomogram.done=false LogPanel.Visible=true ScreenState.TomoGen.Tilt.Header.OpenClose=open ProcessTrack.FinalAlignedStack-B=Not started ProcessTrack.FinalAlignedStack-A=Complete Setup.Post.Trimvol.SectionScaleMax=170 ScreenState.PostProc.bn.squeeze-volume.done=false ScreenState.FineAlign.BeamTilt.Header.AdvancedBasic=basic Setup.Post.Trimvol.YMax=1856 ScreenState.TomoGen.bn.delete-intermediate-image-stacks.done=false ScreenState.CoarseAlign.mb.newstack.open=true ReconstructionState.Stack.A.UseLinearInterpolation=false ReconstructionState.Pre.A.UseFixedStack.Warning=false Setup.Stack.A.EraseGold.ModelUseFid=false Setup.DataSource=CCD ProcessTrack.CoarseAlignment-B=Not started Setup.AxisB.TiltAngle.RangeStep=1.0 ReconstructionState.UsedLocalAlignmentsB=no result ScreenState.FinalStack.bn.use-filtered-stack.done=false ProcessTrack.CoarseAlignment-A=Complete ReconstructionState.TrimvolFlipped=true Setup.DefaultParallel=true Setup.Post.LambdaForSmoothingList=1,1.5,2,2.5,3 ReconstructionState.UsedLocalAlignmentsA=false Setup.Combine.RevisionNumber=1.2 Setup.Combine.TempDirectory= Setup.AxisB.TiltAngle.RangeMin=-60.0 Setup.FinalStack.a.FiducialDiameter=14.8 Setup.Post.Trimvol.ScaleYMax=1368 ReconstructionState.a.sample.AxisZShift=0.0 ScreenState.Combine.bn.restart-combine.done=false ScreenState.FineAlign.bn.compute-alignment.done=true Setup.a.FineAlign.FixedBeamTiltSelected=false ScreenState.FinalStack.Mtffilter.Header.AdvancedBasic=basic ReconstructionState.MadeZFactorsB=no result ReconstructionState.MadeZFactorsA=false Setup.PixelSize=0.674 ReconstructionState.PostProc.TrimVol.Input.NColumns=1852 Setup.WholeTomogramSampleB=false Setup.WholeTomogramSampleA=true Setup.a.FineAlign.NoBeamTiltSelected=true Setup.Combine.MaxPatchBoundaryZMax=0 Setup.FiducialessAlignmentB=false Setup.FiducialessAlignmentA=false Setup.Combine.Transfer=true Setup.FinalStack.a.ExpandCircleIterations=2 Setup.Post.CurTab=0 Setup.Gen.A.Subarea=false Setup.Gen.A.Scale.Offset.Log=0.0 ProcessTrack.FineAlignment-B=Not started ProcessTrack.FineAlignment-A=Complete ScreenState.FinalStack.bn.run-findbeads3d.done=false ScreenState.TomoGen.Tilt.Header.AdvancedBasic=basic Setup.Combine.PatchBoundaryZMin=0 ScreenState.FinalStack.bn.filter.done=false ScreenState.TomoGen.TrialTilt.Header.OpenClose=open Setup.Combine.PatchSize=Medium Setup.Post.Trimvol.XMin=359 Setup.Post.Trimvol.FixedScaling=false ReconstructionState.Track.A.LightBeads=0 ScreenState.CoarseAlign.bn.make-distortion-corrected-stack.done=false ScreenState.TomoGen.bn.use-sirt-output-file.done=false Setup.AxisA.ExcludeProjections= ReconstructionState.A.AdjustOrigin=true Setup.Gen.A.Scale.Offset.Linear=0.0 Setup.AxisA.TiltAngle.RangeStep=1.0 ReconstructionState.SqueezevolFlipped=no result ScreenState.FinalStack.bn.correct-ctf.done=true Setup.AxisB.TiltAngle.Type=Extract Setup.Combine.FiducialMatch=BothSides Setup.Combine.PatchRegionModel= ScreenState.FinalStack.bn.use-ctf-correction.done=true Setup.Track.A.LengthAndOverlap=16,4 Setup.Post.Trimvol.ZMax=216 ScreenState.CoarseAlign.bn.fix-alignment-with-midas.done=false ScreenState.Combine.bn.restart-at-matchvol1.done=false Setup.PostTrimvol.Scaling.NewStyleZ=true Setup.AxisType=Single Axis ScreenState.PostProc.bn.trim-volume.done=true Setup.FinalStack.a.PolynomialOrder=0 Setup.Post.Trimvol.ScaleXMin=697 ScreenState.FidModel.bn.run-raptor.done=false ReconstructionState.a.sample.XAXISTILT=0.0 ReconstructionState.a.align.AxisZShift=-26.6 ScreenState.FidModel.bn.fix-fiducial-model.done=true Setup.PostTrimvol.NewStyleZ=true Setup.Stack.A.Tilt.Parallel=true ScreenState.PreProc.bn.create-fixed-stack.done=true Setup.DistortionFile= ScreenState.FidModel.bn.track-patches.done=false Setup.FinalStack.a.UseExpandCircleIterations=true ScreenState.FinalStack.CtfCorrection.Header.AdvancedBasic=basic Setup.Pos.A.Exists=true Setup.Gen.A.BackProjection=true Setup.FinalStackA.CtfCorrection.Parallel=true ReconstructionState.Stack.A.UseErasedStack.Warning=false Setup.Combine.PatchBoundaryXMax=0 ScreenState.CoarseAlign.bn.fix-edges-with-midas.done=false Setup.AxisB.ExcludeProjections= Setup.Track.A.TrackMethod=Seed Setup.Post.Trimvol.SectionScaleMin=77 ProcessTrack.FiducialModel-B=Not started ProcessTrack.FiducialModel-A=Complete ScreenState.TomoPos.bn.create-sample-tomograms.done=true Setup.Post.Trimvol.YMin=7 ScreenState.ParallelProcess.Header.OpenClose=open Setup.Squeezevol.LinearInterpolation=false ReconstructionState.Combine.ScriptsCreated=no result Setup.Stack.EraseBeadsInitialized=true Setup.Post.SqueezeVol.InputTrimVol=true Setup.RevisionNumber=1.12 Setup.Stack.A.3dFind.Binning=3 ScreenState.FinalStack.bn.transform-fiducial-model.done=false Setup.FinalStackBinningA=1 Setup.Post.Trimvol.ScaleYMin=845 ReconstructionState.a.FixedFiducials=true ScreenState.FinalStack.bn.erase-beads.done=true Setup.DefaultGpuProcessing=false ScreenState.Combine.bn.restart-at-matchorwarp.done=false ScreenState.FinalStack.bn.align-and-build-tomogram.done=true Setup.Post.Trimvol.ConvertToBytes=true ProcessTrack.PostProcessing=Complete ReconstructionState.Track.A.UsingNewstOrBlend3dFindOutput=true ReconstructionState.PostProc.TrimVol.Input.NRows=266 ProcessTrack.RevisionNumber=2.0 Setup.TomoGenA.Tilt.Parallel=true ScreenState.CoarseAlign.bn.generate-coarse-aligned-stack.done=true ScreenState.Combine.bn.restart-at-volcombine.done=false Setup.Post.Exists=true ProcessTrack.TomogramCombination=Not started Setup.DatasetName=WTI042413_1series4 Setup.Gen.A.Exists=true ScreenState.PostProc.bn.flatten.done=false Setup=/ Setup.Combine.UseList= Setup.ImageRotationB=0.0 Setup.MagGradientFile= Setup.ImageRotationA=168.0 LogPanel.FrameSize.Width=649 Setup.Combine.PatchBoundaryYMax=0 ScreenState.Stack.FindBeads3dHeader.AdvancedBasic=basic Setup.Post.Trimvol.SwapYZ=false Setup.First.sample.THICKNESS=600 ProcessTrack.TomogramPositioning-B=Not started ProcessTrack.TomogramPositioning-A=Complete ReconstructionState.a.align.AngleOffset=0.48 ScreenState.CoarseAlign.mb.newstack.advanced=false ScreenState.TomoPos.bn.create-final-alignment.done=true Setup.Post.Trimvol.ZMin=29 ScreenState.FidModel.bn.transfer-fiducials-from-other-axis.done=false ScreenState.CoarseAlign.bn.calculate-cross-correlation.done=true ScreenState.TomoGen.bn.generate-tomogram.done=true ScreenState.FinalStack.bn.reproject-model.done=true Setup.Fine.A.Exists=true ScreenState.TomoGen.Sirt.Header.OpenClose=open ScreenState.Stack.FindBeads3dHeader.OpenClose=open ReconstructionState.Stack.A.ImageRotation=168.0 ProcessTrack.Setup=Complete ProcessTrack.CleanUp=Complete Setup.A.Fiducialess=false Setup.Track.A.Raptor.UseRawStack=false ScreenState.TomoPos.bn.compute-z-shift-&-pitch-angles.done=true LogPanel.FrameSize.Height=251 Setup.Combine.ModelBased=false ReconstructionState.PostProc.TrimVol.Input.NSections=1856 ScreenState.Stack.AlignAndTiltHeader.OpenClose=open Setup.Post.Flatten.InputTrimVol=true Setup.Track.A.Raptor.Diam=15 Setup.ViewType=Single View Setup.Combine.PatchBoundaryXMin=0 ScreenState.Combine.bn.start-combine.done=false ReconstructionState.InvalidEdgeFunctionsB=no result ReconstructionState.InvalidEdgeFunctionsA=no result ScreenState.FinalStack.Newst.Header.AdvancedBasic=basic Setup.Gen.A.Log=0.0 ReconstructionState.a.sample.AngleOffset=0.0 Setup.TomoPosBinningA=3 Setup.Combine.ManualCleanup=false Setup.Post.FlattenWarp.ContoursOnOneSurface=false ScreenState.CoarseAlign.mb.tiltxcorr.open=true ProcessTrack.TomogramGeneration-B=Not started ProcessTrack.TomogramGeneration-A=Complete Setup.UseZFactorsA=true ProcessTrack.PreProcessing-B=Not started Setup.Post.Trimvol.RotateX=true ProcessTrack.PreProcessing-A=Complete Setup.Combine.PatchBoundaryZMax=0 Setup.Post.Trimvol.XMax=1612 ScreenState.FinalStack.bn.use-erased-stack.done=true ReconstructionState.NewstFiducialessAlignmentB=no result ReconstructionState.NewstFiducialessAlignmentA=false Setup.AxisA.TiltAngle.Type=Extract Setup.B.SizeToOutputInXandY=/ Setup.BackupDirectory= Setup.tiltalign.NumberOfLocalPatchesXandY=5,5 Setup.AxisA.TiltAngle.RangeMin=-60.0 Setup.Squeezevol.ReductionFactorZ=1.25 Setup.Squeezevol.ReductionFactorY=1.25 ScreenState.FidModel.mb.beadtracker.advanced=false Setup.Squeezevol.ReductionFactorX=1.25 ScreenState.TomoGen.bn.run-sirt.done=false ScreenState.FidModel.mb.beadtracker.open=true ScreenState.ParallelProcess.Header.MoreLess=more Setup.FiducialDiameter=10.0 ScreenState.FidModel.bn.use-raptor-result-as-fiducial-model.done=false Setup.Gen.A.Scale.Factor.Log=700.0 ScreenState.FidModel.bn.track-seed-model.done=true LogPanel.FrameLocation.Y=546 LogPanel.FrameLocation.X=995 Setup.Stack.B.CTF.AutoFit.RangeAndStep=/ ReconstructionState.a.track.LastModified=1367011160000 ReconstructionState.Stack.A.UseCtfCorrection.Warning=false Setup.A.SizeToOutputInXandY=/