# Avizo Project 202020
# Avizo
# Generated by Avizo 2020.2
remove -all
remove "grayScale.am" "physics.icol" "labels.am" "HAADF.info" "Ni.info" "HAADF.processed0" "Image Stack Processing" "Ortho Slice" "Color Wash" "Ortho Slice 2"

# Create viewers
viewer setVertical 1

viewer 0 setTransparencyType 6
viewer 0 setAutoRedraw 0
viewer 0 show
viewer 1 setTransparencyType 6
viewer 1 setAutoRedraw 0
viewer 1 show
mainWindow show

_units setUnitsManagementMode 1
_units setDisplayCoordinatesUnit µm
_units setWorkingCoordinatesUnit nm

set hideNewModules 1
[ load ${AMIRA_ROOT}/data/colormaps/grayScale.am ] setLabel "grayScale.am"
"grayScale.am" setIconPosition 0 0
"grayScale.am" setNoRemoveAll 1
"grayScale.am" setVar "CustomHelp" {HxColormap256}
"grayScale.am" fire
"grayScale.am" setMinMax 0 255
"grayScale.am" flags setValue 1
"grayScale.am" shift setMinMax -1 1
"grayScale.am" shift setButtons 0
"grayScale.am" shift setEditButton 1
"grayScale.am" shift setIncrement 0.133333
"grayScale.am" shift setValue 0
"grayScale.am" shift setSubMinMax -1 1
"grayScale.am" scale setMinMax 0 1
"grayScale.am" scale setButtons 0
"grayScale.am" scale setEditButton 1
"grayScale.am" scale setIncrement 0.1
"grayScale.am" scale setValue 1
"grayScale.am" scale setSubMinMax 0 1
"grayScale.am" fire
"grayScale.am" setViewerMask 16383

set hideNewModules 1
[ load ${AMIRA_ROOT}/data/colormaps/physics.icol ] setLabel "physics.icol"
"physics.icol" setIconPosition 0 0
"physics.icol" setNoRemoveAll 1
"physics.icol" fire
"physics.icol" setMinMax 0 1
"physics.icol" flags setValue 1
"physics.icol" shift setMinMax -1 1
"physics.icol" shift setButtons 0
"physics.icol" shift setEditButton 1
"physics.icol" shift setIncrement 0.133333
"physics.icol" shift setValue 0
"physics.icol" shift setSubMinMax -1 1
"physics.icol" scale setMinMax 0 1
"physics.icol" scale setButtons 0
"physics.icol" scale setEditButton 1
"physics.icol" scale setIncrement 0.1
"physics.icol" scale setValue 1
"physics.icol" scale setSubMinMax 0 1
"physics.icol" fire
"physics.icol" setViewerMask 16383

set hideNewModules 1
[ load ${AMIRA_ROOT}/data/colormaps/labels.am ] setLabel "labels.am"
"labels.am" setIconPosition 0 0
"labels.am" setNoRemoveAll 1
"labels.am" setVar "CustomHelp" {HxColormap256}
"labels.am" fire
"labels.am" setMinMax 1 8
"labels.am" flags setValue 1
"labels.am" shift setMinMax -1 1
"labels.am" shift setButtons 0
"labels.am" shift setEditButton 1
"labels.am" shift setIncrement 0.133333
"labels.am" shift setValue 0
"labels.am" shift setSubMinMax -1 1
"labels.am" scale setMinMax 0 1
"labels.am" scale setButtons 0
"labels.am" scale setEditButton 1
"labels.am" scale setIncrement 0.1
"labels.am" scale setValue 1
"labels.am" scale setSubMinMax 0 1
"labels.am" fire
"labels.am" setViewerMask 16383

set hideNewModules 0
[ load -unit nm ${SCRIPTDIR}/NiParticles-files/HAADF.info ] setLabel "HAADF.info"
"HAADF.info" setIconPosition 20 10
"HAADF.info" setVar "CustomXML" {HAADF.info_config.xml}
"HAADF.info" sharedColormap disconnect
"HAADF.info" sharedColormap setDefaultColor 0.8 0.8 0.8
"HAADF.info" sharedColormap setDefaultAlpha 0.500000
"HAADF.info" sharedColormap activateLocalRange 1
"HAADF.info" sharedColormap setLocalMinMax 0.000000 1.000000
"HAADF.info" sharedColormap enableAlpha 1
"HAADF.info" sharedColormap enableAlphaToggle 1
"HAADF.info" sharedColormap setAutoAdjustRangeMode 1
"HAADF.info" sharedColormap setColorbarMinMax 0 51490
"HAADF.info" fire
"HAADF.info" setViewerMask 16383

set hideNewModules 0
[ load -unit nm ${SCRIPTDIR}/NiParticles-files/Ni.info ] setLabel "Ni.info"
"Ni.info" setIconPosition 20 44
"Ni.info" setVar "CustomXML" {Ni.info_config.xml}
"Ni.info" sharedColormap disconnect
"Ni.info" sharedColormap setDefaultColor 0.8 0.8 0.8
"Ni.info" sharedColormap setDefaultAlpha 0.500000
"Ni.info" sharedColormap activateLocalRange 1
"Ni.info" sharedColormap setLocalMinMax 0.000000 1.000000
"Ni.info" sharedColormap enableAlpha 1
"Ni.info" sharedColormap enableAlphaToggle 1
"Ni.info" sharedColormap setAutoAdjustRangeMode 1
"Ni.info" sharedColormap setColorbarMinMax 0 35158
"Ni.info" fire
"Ni.info" setViewerMask 16383

set hideNewModules 0
create HxISPModule "Image Stack Processing"
"Image Stack Processing" setIconPosition 160 10
"Image Stack Processing" setVar "CustomHelp" {HxISPModule}
"Image Stack Processing" setVar "CustomXML" {HxISPModule_config.xml}
"Image Stack Processing" data connect "HAADF.info"
"Image Stack Processing" filename setState "${SCRIPTDIR}/NiParticles_Recipe.hxisp"
"Image Stack Processing" fire
"Image Stack Processing" input1 connect "Ni.info"
"Image Stack Processing" applyTransformToResult 1
"Image Stack Processing" fire
"Image Stack Processing" setViewerMask 16383
"Image Stack Processing" setPickable 1

set hideNewModules 0
[ load -unit nm ${SCRIPTDIR}/NiParticles-files/HAADF.processed0 ] setLabel "HAADF.processed0"
"HAADF.processed0" setIconPosition 18 95
"HAADF.processed0" setVar "CustomXML" {HAADF.processed0_config.xml}
"HAADF.processed0" master connect "Image Stack Processing" "result" 0
"HAADF.processed0" sharedColormap connect "labels.am"
"HAADF.processed0" sharedColormap setDefaultColor 0.8 0.8 0.8
"HAADF.processed0" sharedColormap setDefaultAlpha 0.500000
"HAADF.processed0" sharedColormap activateLocalRange 1
"HAADF.processed0" sharedColormap setLocalMinMax 1.000000 8.000000
"HAADF.processed0" sharedColormap enableAlpha 1
"HAADF.processed0" sharedColormap enableAlphaToggle 1
"HAADF.processed0" sharedColormap setAutoAdjustRangeMode 1
"HAADF.processed0" sharedColormap setColorbarMinMax 1 8
"HAADF.processed0" fire
"HAADF.processed0" primary setIndex 0 0
"HAADF.processed0" fire
"HAADF.processed0" setViewerMask 16383

set hideNewModules 0
create HxOrthoSlice "Ortho Slice"
"Ortho Slice" setIconPosition 632 10
"Ortho Slice" setVar "CustomHelp" {HxOrthoSlice}
"Ortho Slice" setVar "CustomXML" {HxOrthoSlice_config.xml}
"Ortho Slice" data connect "HAADF.info"
"Ortho Slice" fire
"Ortho Slice" sliceOrientation setValue 0
"Ortho Slice" fire
"Ortho Slice" origin  setBoundingBox -3.40282e+038 3.40282e+038 -3.40282e+038 3.40282e+038 -3.40282e+038 3.40282e+038
"Ortho Slice" origin  setImmediateMode 0
"Ortho Slice" origin  setOrtho 0
"Ortho Slice" origin  showDragger 0
"Ortho Slice" origin  showPoints 0
"Ortho Slice" origin  setPointScale 1
"Ortho Slice" origin  showOptionButton 1
"Ortho Slice" origin  setNumPoints 1 1 1
"Ortho Slice" origin  setCoord 0 1.17645 1.17645 0
"Ortho Slice" normal  setBoundingBox -3.40282e+038 3.40282e+038 -3.40282e+038 3.40282e+038 -3.40282e+038 3.40282e+038
"Ortho Slice" normal  setImmediateMode 0
"Ortho Slice" normal  setOrtho 0
"Ortho Slice" normal  showDragger 0
"Ortho Slice" normal  showPoints 0
"Ortho Slice" normal  setPointScale 1
"Ortho Slice" normal  showOptionButton 1
"Ortho Slice" normal  setNumPoints 1 1 1
"Ortho Slice" normal  setCoord 0 0 0 0.001
"Ortho Slice" options setValue 0 1
"Ortho Slice" options setToggleVisible 0 1
"Ortho Slice" options setValue 1 0
"Ortho Slice" options setToggleVisible 1 1
"Ortho Slice" options setValue 2 0
"Ortho Slice" options setToggleVisible 2 1
"Ortho Slice" mappingType setIndex 0 0
"Ortho Slice" contrastLimit setMinMax 0 -16777216 16777216
"Ortho Slice" contrastLimit setValue 0 7
"Ortho Slice" colormap connect "grayScale.am"
"Ortho Slice" colormap setDefaultColor 1 0.8 0.5
"Ortho Slice" colormap setDefaultAlpha 1.000000
"Ortho Slice" colormap activateLocalRange 1
"Ortho Slice" colormap setLocalMinMax 8957.000000 51490.000000
"Ortho Slice" colormap enableAlpha 1
"Ortho Slice" colormap enableAlphaToggle 1
"Ortho Slice" colormap setAutoAdjustRangeMode 1
"Ortho Slice" colormap setColorbarMinMax 8957 51490
"Ortho Slice" sliceNumber setMinMax 0 0
"Ortho Slice" sliceNumber setButtons 1
"Ortho Slice" sliceNumber setEditButton 1
"Ortho Slice" sliceNumber setIncrement 1
"Ortho Slice" sliceNumber setValue 0
"Ortho Slice" sliceNumber setSubMinMax 0 0
"Ortho Slice" transparency setValue 0
"Ortho Slice" alpha setMinMax 0 -16777216 16777216
"Ortho Slice" alpha setValue 0 0
"Ortho Slice" alpha setMinMax 1 -16777216 16777216
"Ortho Slice" alpha setValue 1 255
"Ortho Slice" frameSettings setState {item 0 1 item 2 1 color 3 1 0.5 0 }
"Ortho Slice" embossingOnOff setValue 0
"Ortho Slice" depth setMinMax -60 60
"Ortho Slice" depth setButtons 0
"Ortho Slice" depth setEditButton 1
"Ortho Slice" depth setIncrement 8
"Ortho Slice" depth setValue 2
"Ortho Slice" depth setSubMinMax -60 60
"Ortho Slice" fire

"Ortho Slice" fire
"Ortho Slice" setViewerMask 16381
"Ortho Slice" setShadowStyle 3
"Ortho Slice" setPickable 1

set hideNewModules 0
create HxColorwash "Color Wash"
"Color Wash" setIconPosition 632 34
"Color Wash" setVar "CustomHelp" {HxColorwash}
"Color Wash" setVar "CustomXML" {HxColorwash_config.xml}
"Color Wash" data connect "HAADF.processed0"
"Color Wash" module connect "Ortho Slice"
"Color Wash" colormap connect "labels.am"
"Color Wash" colormap setDefaultColor 1 0.8 0.5
"Color Wash" colormap setDefaultAlpha 0.500000
"Color Wash" colormap activateLocalRange 1
"Color Wash" colormap setLocalMinMax 1.000000 8.000000
"Color Wash" colormap enableAlpha 1
"Color Wash" colormap enableAlphaToggle 1
"Color Wash" colormap setAutoAdjustRangeMode 1
"Color Wash" colormap setColorbarMinMax 1 8
"Color Wash" fire
"Color Wash" mode setIndex 0 7
"Color Wash" weightFactor setMinMax 0 1
"Color Wash" weightFactor setButtons 0
"Color Wash" weightFactor setEditButton 1
"Color Wash" weightFactor setIncrement 0.1
"Color Wash" weightFactor setValue 0.5
"Color Wash" weightFactor setSubMinMax 0 1
"Color Wash" lenseWidth setMinMax 5 80
"Color Wash" lenseWidth setButtons 1
"Color Wash" lenseWidth setEditButton 1
"Color Wash" lenseWidth setIncrement 1
"Color Wash" lenseWidth setValue 30
"Color Wash" lenseWidth setSubMinMax 5 80
"Color Wash" overlayRange setMinMax 0 -3.40282346638529e+038 3.40282346638529e+038
"Color Wash" overlayRange setValue 0 100
"Color Wash" overlayRange setMinMax 1 -3.40282346638529e+038 3.40282346638529e+038
"Color Wash" overlayRange setValue 1 1000
"Color Wash" transparency setMinMax 0 1
"Color Wash" transparency setButtons 0
"Color Wash" transparency setEditButton 1
"Color Wash" transparency setIncrement 0.1
"Color Wash" transparency setValue 0.3
"Color Wash" transparency setSubMinMax 0 1
"Color Wash" options setValue 0 0
"Color Wash" options setToggleVisible 0 1
"Color Wash" options setValue 1 1
"Color Wash" options setToggleVisible 1 1
"Color Wash" generalOptions setValue 0 0
"Color Wash" generalOptions setToggleVisible 0 1
"Color Wash" fire
"Color Wash" setViewerMask 16383
"Color Wash" setPickable 1

set hideNewModules 0
create HxOrthoSlice "Ortho Slice 2"
"Ortho Slice 2" setIconPosition 397 38
"Ortho Slice 2" setVar "CustomHelp" {HxOrthoSlice}
"Ortho Slice 2" setVar "CustomXML" {HxOrthoSlice_config.xml}
"Ortho Slice 2" data connect "Ni.info"
"Ortho Slice 2" fire
"Ortho Slice 2" sliceOrientation setValue 0
"Ortho Slice 2" fire
"Ortho Slice 2" origin  setBoundingBox -3.40282e+038 3.40282e+038 -3.40282e+038 3.40282e+038 -3.40282e+038 3.40282e+038
"Ortho Slice 2" origin  setImmediateMode 0
"Ortho Slice 2" origin  setOrtho 0
"Ortho Slice 2" origin  showDragger 0
"Ortho Slice 2" origin  showPoints 0
"Ortho Slice 2" origin  setPointScale 1
"Ortho Slice 2" origin  showOptionButton 1
"Ortho Slice 2" origin  setNumPoints 1 1 1
"Ortho Slice 2" origin  setCoord 0 1.17645 1.17645 0
"Ortho Slice 2" normal  setBoundingBox -3.40282e+038 3.40282e+038 -3.40282e+038 3.40282e+038 -3.40282e+038 3.40282e+038
"Ortho Slice 2" normal  setImmediateMode 0
"Ortho Slice 2" normal  setOrtho 0
"Ortho Slice 2" normal  showDragger 0
"Ortho Slice 2" normal  showPoints 0
"Ortho Slice 2" normal  setPointScale 1
"Ortho Slice 2" normal  showOptionButton 1
"Ortho Slice 2" normal  setNumPoints 1 1 1
"Ortho Slice 2" normal  setCoord 0 0 0 0.001
"Ortho Slice 2" options setValue 0 0
"Ortho Slice 2" options setToggleVisible 0 1
"Ortho Slice 2" options setValue 1 0
"Ortho Slice 2" options setToggleVisible 1 1
"Ortho Slice 2" options setValue 2 0
"Ortho Slice 2" options setToggleVisible 2 1
"Ortho Slice 2" mappingType setIndex 0 0
"Ortho Slice 2" contrastLimit setMinMax 0 -16777216 16777216
"Ortho Slice 2" contrastLimit setValue 0 7
"Ortho Slice 2" colormap connect "grayScale.am"
"Ortho Slice 2" colormap setDefaultColor 1 0.8 0.5
"Ortho Slice 2" colormap setDefaultAlpha 1.000000
"Ortho Slice 2" colormap activateLocalRange 1
"Ortho Slice 2" colormap setLocalMinMax 1.000000 35158.000000
"Ortho Slice 2" colormap enableAlpha 1
"Ortho Slice 2" colormap enableAlphaToggle 1
"Ortho Slice 2" colormap setAutoAdjustRangeMode 1
"Ortho Slice 2" colormap setColorbarMinMax 1 35158
"Ortho Slice 2" sliceNumber setMinMax 0 0
"Ortho Slice 2" sliceNumber setButtons 1
"Ortho Slice 2" sliceNumber setEditButton 1
"Ortho Slice 2" sliceNumber setIncrement 1
"Ortho Slice 2" sliceNumber setValue 0
"Ortho Slice 2" sliceNumber setSubMinMax 0 0
"Ortho Slice 2" transparency setValue 0
"Ortho Slice 2" alpha setMinMax 0 -16777216 16777216
"Ortho Slice 2" alpha setValue 0 0
"Ortho Slice 2" alpha setMinMax 1 -16777216 16777216
"Ortho Slice 2" alpha setValue 1 255
"Ortho Slice 2" frameSettings setState {item 0 1 item 2 1 color 3 1 0.5 0 }
"Ortho Slice 2" embossingOnOff setValue 0
"Ortho Slice 2" depth setMinMax -60 60
"Ortho Slice 2" depth setButtons 0
"Ortho Slice 2" depth setEditButton 1
"Ortho Slice 2" depth setIncrement 8
"Ortho Slice 2" depth setValue 2
"Ortho Slice 2" depth setSubMinMax -60 60
"Ortho Slice 2" fire

"Ortho Slice 2" fire
"Ortho Slice 2" setViewerMask 16382
"Ortho Slice 2" select
"Ortho Slice 2" setShadowStyle 3
"Ortho Slice 2" setPickable 1

set hideNewModules 0

viewer 0 setCameraOrientation 1 0 0 3.14159
viewer 0 setCameraPosition 1176.45 1176.45 -4026.36
viewer 0 setCameraFocalDistance 4026.36
viewer 0 setCameraNearDistance 4022.33
viewer 0 setCameraFarDistance 4030.38
viewer 0 setCameraType perspective
viewer 0 setCameraHeightAngle 44.9023
viewer 0 setAutoRedraw 1
viewer 0 redraw

viewer 1 setCameraOrientation 1 0 0 3.14159
viewer 1 setCameraPosition 1176.45 1176.45 -4026.36
viewer 1 setCameraFocalDistance 4026.36
viewer 1 setCameraNearDistance 4022.33
viewer 1 setCameraFarDistance 4030.38
viewer 1 setCameraType perspective
viewer 1 setCameraHeightAngle 44.9023
viewer 1 setAutoRedraw 1
viewer 1 redraw

"Ortho Slice 2" colormap interconnect "PermanentColormapEditor" colormap
correlationPanel closeTabs
correlationPanel setTabName 0 "Correlation 1"
correlationPanel 0 setLogScalingOnAxis 0 0
correlationPanel 0 setLogScalingOnAxis 1 0

histogramPanel closeTabs
histogramPanel setTabName 0 "Histogram 1"
histogramPanel 0 setLogScalingOnAxis 0 0
histogramPanel 0 setLogScalingOnAxis 1 1

theObjectPool setSelectionOrder {Ortho Slice 2}
