# Amira-Script-Object V3.0
# NO DEPRECATION WARNING

# Constructor is called when scro is instantiated
$this proc constructor {} {

    # Threshold port
    "$this" newPortRangeSlider threshold 
    "$this" threshold setLabel "Threshold"
    "$this" threshold setTooltip "Threshold defining the background used for segmentation"
    "$this" threshold setValues 0 255
    
    # Number of objects port
    "$this" newPortIntSlider numberOfObjects
    "$this" numberOfObjects setLabel "Number of Objects"
    "$this" numberOfObjects setTooltip "Defines the Number of Objects that have the biggest volume"
    "$this" numberOfObjects setMinMax 0 100
    "$this" numberOfObjects setValue 1
    
    # Port to hide intermediate objects
    "$this" newPortToggleList hideObjectOption 1
    "$this" hideObjectOption setLabel "Object Visibility"
    "$this" hideObjectOption setLabel 0 "Hide Intermediate Objects"
    "$this" hideObjectOption setValue 0 1

    # Action button
    "$this" newPortButtonList action 1
    "$this" action setLabel 0 "Apply"
    "$this" action setCmd 0 {$this computeDoIt}
    
    # List of all the objects created by "$this"
    "$this" setVar objectInstances {}
}

# Destructor is called when scro is removed
$this proc destructor {} {
    "$this" deleteObjects
}

# Remove created objects
$this proc deleteObjects {} {
    
    # Clean up
    foreach obj ["$this" getVar objectInstances] {
      remove "$obj"
    }
    "$this" setVar objectInstances {}
}

# Append new object
$this proc appendObject {myObject} {
    "$this" setVar objectInstances [concat ["$this" getVar objectInstances] "\{$myObject\}"]
}

# Processing...
$this proc computeDoIt {} {

    # Viewer should clean during processing
    viewer redraw

    # Check if input data is defined
    set data [$this data source] 
    if {$data == ""} {return}
    
    # Clean up before creating anything
    "$this" deleteObjects
    
    # List of all the objects created by "$this"
    "$this" setVar baseIconPositionX [expr "[lindex [$this getIconPosition] 0] + 30"]
    "$this" setVar baseIconPositionY [expr "[lindex [$this getIconPosition] 1] + 50"] 
    
    # Thresholding to detect the pores
    set InteractiveThresholdingObj [create HxInteractiveThreshold]
    "$InteractiveThresholdingObj" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 0]
    "$InteractiveThresholdingObj" fire
    "$InteractiveThresholdingObj" setViewerMask 0
    # --> Interconnect source
    "$InteractiveThresholdingObj" data connect [$this data source]
    "$InteractiveThresholdingObj" fire
    # --> Interconnect threshold
    "$InteractiveThresholdingObj" threshold connect "$this" threshold
    "$InteractiveThresholdingObj" fire
    "$InteractiveThresholdingObj" doIt snap 0 1
    "$InteractiveThresholdingObj" fire
    "$InteractiveThresholdingObj" setViewerMask 65534
    ["$InteractiveThresholdingObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 88] [expr ["$this" getVar baseIconPositionY] + 20]
    ["$InteractiveThresholdingObj" getResult] fire

    "$this" appendObject "$InteractiveThresholdingObj"
    "$this" appendObject ["$InteractiveThresholdingObj" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$InteractiveThresholdingObj" fire
      "$InteractiveThresholdingObj" hideIcon
    }
    
    # Create distance map
    set ChamferDistanceMapObj [create distxxx]
    "$ChamferDistanceMapObj" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 20]
    "$ChamferDistanceMapObj" fire
    "$ChamferDistanceMapObj" doIt snap 0 1
    "$ChamferDistanceMapObj" inputImage connect ["$InteractiveThresholdingObj" getResult]
    "$ChamferDistanceMapObj" faceDistance setValue 0 1
    "$ChamferDistanceMapObj" edgeDistance setValue 0 1.414
    "$ChamferDistanceMapObj" cornerDistance setValue 0 1.73
    "$ChamferDistanceMapObj" fire
    ["$ChamferDistanceMapObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 18] [expr ["$this" getVar baseIconPositionY] + 40]
    ["$ChamferDistanceMapObj" getResult] fire

    "$this" appendObject "$ChamferDistanceMapObj"
    "$this" appendObject ["$ChamferDistanceMapObj" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$ChamferDistanceMapObj" hideIcon
    }

    # Get all the local maxima
    set HMaximaObj [create merge_maxima]
    "$HMaximaObj" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 40]
    "$HMaximaObj" fire
    "$HMaximaObj" inputImage connect ["$ChamferDistanceMapObj" getResult]
    "$HMaximaObj" doIt snap 0 1
    "$HMaximaObj" fire
    ["$HMaximaObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 98] [expr ["$this" getVar baseIconPositionY] + 60]
    ["$HMaximaObj" getResult] fire

    "$this" appendObject "$HMaximaObj"
    "$this" appendObject ["$HMaximaObj" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$HMaximaObj" hideIcon
    }

    # Make a label per local maxima
    set LabelingObj [create label]
    "$LabelingObj" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 60]
    "$LabelingObj" fire
    "$LabelingObj" doIt snap 0 1
    "$LabelingObj" inputImage connect ["$HMaximaObj" getResult]
    "$LabelingObj" fire
    ["$LabelingObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 106] [expr ["$this" getVar baseIconPositionY] + 80]
    ["$LabelingObj" getResult] fire

    "$this" appendObject "$LabelingObj"
    "$this" appendObject ["$LabelingObj" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$LabelingObj" hideIcon
      ["$HMaximaObj" getResult] hideIcon
    }

    # Get the inverse of the distance map
    set NotObj [create logical_not]
    "$NotObj" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 80]
    "$NotObj" fire
    "$NotObj" doIt snap 0 1
    "$NotObj" inputImage connect ["$ChamferDistanceMapObj" getResult]
    "$NotObj" applyTransformToResult 1
    "$NotObj" fire
    ["$NotObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 124] [expr ["$this" getVar baseIconPositionY] + 100]
    ["$NotObj" getResult] fire

    "$this" appendObject "$NotObj"
    "$this" appendObject ["$NotObj" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$NotObj" hideIcon
    }

    # Apply the watershed algorithm using the inverse of the distance map and a set of local maxima labels
    set MarkerBasedWatershedObj [create fastwatershed]
    "$MarkerBasedWatershedObj" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 100]
    "$MarkerBasedWatershedObj" fire
    "$MarkerBasedWatershedObj" doIt snap 0 1
    "$MarkerBasedWatershedObj" inputGrayscaleImage connect ["$NotObj" getResult]
    "$MarkerBasedWatershedObj" inputLabelImage connect ["$LabelingObj" getResult]
    "$MarkerBasedWatershedObj" fire
    ["$MarkerBasedWatershedObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 92] [expr ["$this" getVar baseIconPositionY] + 120]
    ["$MarkerBasedWatershedObj" getResult] fire

    "$this" appendObject "$MarkerBasedWatershedObj"
    "$this" appendObject ["$MarkerBasedWatershedObj" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$MarkerBasedWatershedObj" hideIcon
      ["$LabelingObj" getResult] hideIcon
      ["$NotObj" getResult] hideIcon
    }

    # Compose the pores thresholding with the watershed result
    set AndNotImageObj [create logical_subimage]
    "$AndNotImageObj" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 120]
    "$AndNotImageObj" fire
    "$AndNotImageObj" doIt snap 0 1
    "$AndNotImageObj" inputImage1 connect ["$InteractiveThresholdingObj" getResult]
    "$AndNotImageObj" inputImage2 connect ["$MarkerBasedWatershedObj" getResult]
    "$AndNotImageObj" fire
    ["$AndNotImageObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 66] [expr ["$this" getVar baseIconPositionY] + 140]
    ["$AndNotImageObj" getResult] fire

    "$this" appendObject "$AndNotImageObj"
    "$this" appendObject ["$AndNotImageObj" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$AndNotImageObj" hideIcon
      ["$InteractiveThresholdingObj" getResult] hideIcon
      ["$MarkerBasedWatershedObj" getResult] hideIcon
    }

    # Get individual labels from the composition of the pores thresholding and the watershed result
    set LabelingObj2 [create label]
    "$LabelingObj2" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 140]
    "$LabelingObj2" fire
    "$LabelingObj2" interpretation setValue 0
    "$LabelingObj2" outputLocation setIndex 0 0
    "$LabelingObj2" neighborhood setValue 2
    "$LabelingObj2" doIt snap 0 1
    "$LabelingObj2" inputImage connect ["$AndNotImageObj" getResult]
    "$LabelingObj2" applyTransformToResult 1
    "$LabelingObj2" fire
    ["$LabelingObj2" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 96] [expr ["$this" getVar baseIconPositionY] + 160]
    ["$LabelingObj2" getResult] fire

    "$this" appendObject "$LabelingObj2"
    "$this" appendObject ["$LabelingObj2" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$LabelingObj2" hideIcon
      ["$AndNotImageObj" getResult] hideIcon
    }

    # Filter the previous labels according to their volume (keep the biggest ones only)
    set FilterByMeasure [create measurefilter]
    "$FilterByMeasure" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 160]
    "$FilterByMeasure" fire
    # --> Interconnect threshold
    "$FilterByMeasure" numberOfPatterns connect "$this" numberOfObjects
    "$FilterByMeasure" fire
    "$FilterByMeasure" doIt snap 0 1
    "$FilterByMeasure" inputImage connect ["$LabelingObj2" getResult]
    "$FilterByMeasure" inputIntensityImage connect ["$ChamferDistanceMapObj" getResult]
    "$FilterByMeasure" measure setValue Volume
    "$FilterByMeasure" fire
    ["$FilterByMeasure" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 60] [expr ["$this" getVar baseIconPositionY] + 180]
    ["$FilterByMeasure" getResult] fire
    
    "$this" appendObject "$FilterByMeasure"
    "$this" appendObject ["$FilterByMeasure" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$FilterByMeasure" hideIcon
      ["$ChamferDistanceMapObj" getResult] hideIcon
      ["$LabelingObj2" getResult] hideIcon
    }

    # Create surfaces from the filtered labels using the previous measure
    set GenerateSurfaceObj [create HxGMC]
    "$GenerateSurfaceObj" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [expr ["$this" getVar baseIconPositionY] + 180]
    "$GenerateSurfaceObj" fire
    "$GenerateSurfaceObj" data connect ["$FilterByMeasure" getResult]
    "$GenerateSurfaceObj" fire
    "$GenerateSurfaceObj" border setValue 0 0
    "$GenerateSurfaceObj" action snap 0 1
    "$GenerateSurfaceObj" fire

    "$this" appendObject "$GenerateSurfaceObj"
    "$this" appendObject ["$GenerateSurfaceObj" getResult]
    if { ["$this" hideObjectOption getValue  0] == 1} {
      "$GenerateSurfaceObj" hideIcon
      ["$FilterByMeasure" getResult] hideIcon
      ["$GenerateSurfaceObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 126] [expr ["$this" getVar baseIconPositionY] + 0]
      ["$GenerateSurfaceObj" getResult] fire
    } else {
      ["$GenerateSurfaceObj" getResult] setIconPosition [expr ["$this" getVar baseIconPositionX] - 260 + 126] [expr ["$this" getVar baseIconPositionY] + 200]
      ["$GenerateSurfaceObj" getResult] fire
    }
    
    # Display the surfaces
    set SurfaceView [create HxDisplaySurface]
    "$SurfaceView" setIconPosition [expr ["$this" getVar baseIconPositionX] + 0] [lindex [["$GenerateSurfaceObj" getResult] getIconPosition] 1]
    "$SurfaceView" data connect ["$GenerateSurfaceObj" getResult]
    "$SurfaceView" fire
    "$SurfaceView" Patch setMinMax 0 120
    "$SurfaceView" Patch setSubMinMax 0 120
    "$SurfaceView" BoundaryId setIndex 0 -1
    "$SurfaceView" materials setIndex 0 1
    "$SurfaceView" drawStyle setNormalBinding 1
    "$SurfaceView" fire
    # "$SurfaceView" selectTriangles zab HIJMONNKMNANIDDAAMAGNAEPMKAAIMNEPNLHGBAACEBDNEDDPEFAGIFKPKJOJEKLBFJPPMCDFHABAAAAAAMALOGEOKOPDKFLPANBDJACAAJPNHKKCOONDBPGCMHKAPAAAAAAAAIANLEIDCOFLJPHJNEHPPAFAAAAIAHDOEHBPOFNFBAPLLIMMOALAALOMJFGBNAPOKKGFLFLAAPIGBEHHFHOJENCFPAAAAAADHNGMHJOPGNOMMDEJLJJAAAAAAAAOAIPCFONOFKNMHAKELNHLGII
    # "$SurfaceView" fire
    "$SurfaceView" setShadowStyle 0
    "$this" appendObject "$SurfaceView"

    viewer 0 viewAll
    viewer 0 setAutoRedraw 1
    viewer 0 redraw
}