# THIS IS A COMMAND FILE TO RUN TILTALIGN
#
####CreatedVersion#### 3.10.4
#
# To exclude views, add a line "ExcludeList view_list" with the list of views
#
# To specify sets of views to be grouped separately in automapping, add a line
# "SeparateGroup view_list" with the list of views, one line per group
#
$tiltalign -StandardInput
ModelFile	MTEg5series6D.fid
ImageFile	MTEg5series6D.preali
#ImageSizeXandY	4096,3072
OutputModelFile	MTEg5series6D.3dmod
OutputResidualFile	MTEg5series6D.resid
OutputFidXYZFile	MTEg5series6Dfid.xyz
OutputTiltFile	MTEg5series6D.tlt
OutputXAxisTiltFile	MTEg5series6D.xtilt
OutputTransformFile	MTEg5series6D.tltxf
ImagesAreBinned	2
RobustFitting	
RotationAngle	-3.3
TiltFile	MTEg5series6D.rawtlt
#
# ADD a recommended tilt angle change to the existing AngleOffset value
#
AngleOffset	0.99
RotOption	1
RotDefaultGrouping	5
#
# TiltOption 0 fixes tilts, 2 solves for all tilt angles; change to 5 to solve
# for fewer tilts by grouping views by the amount in TiltDefaultGrouping
#
TiltOption	5
TiltDefaultGrouping	5
MagReferenceView	1
MagOption	1
MagDefaultGrouping	4
#
# To solve for distortion, change both XStretchOption and SkewOption to 3;
# to solve for skew only leave XStretchOption at 0
#
XStretchOption	0
SkewOption	0
XStretchDefaultGrouping	7
SkewDefaultGrouping	11
BeamTiltOption	0
#
# Criterion # of S.D's above mean residual to report (- for local mean)
#
ResidualReportCriterion	-2.0
SurfacesToAnalyze	1
MetroFactor	0.25
MaximumCycles	1000
KFactorScaling	0.9
#
# ADD a recommended amount to shift up to the existing AxisZShift value
#
AxisZShift	-5.5
ShiftZFromOriginal      1
#
# Set to 1 to do local alignments
#
LocalAlignments	0
OutputLocalFile	MTEg5series6Dlocal.xf
#
# Target size of local patches to solve for in X and Y
#
TargetPatchSizeXandY	700,700
MinSizeOrOverlapXandY	0.5,0.5
#
# Minimum fiducials total and on one surface if two surfaces
#
MinFidsTotalAndEachSurface	8,0
FixXYZCoordinates	0
LocalOutputOptions	1,0,1
LocalRotOption	3
LocalRotDefaultGrouping	6
LocalTiltOption	5
LocalTiltDefaultGrouping	6
LocalMagReferenceView	1
LocalMagOption	3
LocalMagDefaultGrouping	7
LocalXStretchOption	0
LocalXStretchDefaultGrouping	7
LocalSkewOption	0
LocalSkewDefaultGrouping	11
ExcludeList	1 
#
# COMBINE TILT TRANSFORMS WITH PREALIGNMENT TRANSFORMS
#
$xfproduct -StandardInput
InputFile1	MTEg5series6D.prexg
InputFile2	MTEg5series6D.tltxf
OutputFile	MTEg5series6D_fid.xf
$b3dcopy -p MTEg5series6D_fid.xf MTEg5series6D.xf
$b3dcopy -p MTEg5series6D.tlt MTEg5series6D_fid.tlt
#
# CONVERT RESIDUAL FILE TO MODEL
#
$if (-e MTEg5series6D.resid) patch2imod -s 10 MTEg5series6D.resid MTEg5series6D.resmod
$if (-e ./savework) ./savework