# Amira-Script-Object V3.0
# Master script object to load density files (amiramesh) for different clones

# To use this:
# 1) Prepare a directory containing density files for the clones
#    Give them short names (eg aSP3g_F.am)
#    and make sure they all have the same suffix
# 2) Load in a copy of the script which makes a little object
# 3) Specify a filename - one of the density files in your directory
# 4) Click LoadAll
# 5) HideAll/ShowAll will show hide the volume renderings
# 6) You can also use the checkboxes
# 7) You can use the setCloneColour function in the TCL window 
#    e.g. ShowClones.scro setCloneColour "aSP3-c_F" 0 1 0.843137254901961
# 8) you can put a bunch of these commands into a tcl script (name ends in .hx)
#    See: setCloneColourExampleScript.hx for an example
# 9) You can also use R to set colours, see RainbowColourCloneScript() in FruMARCMCode
#    R can even do the equivalent of dragging and dropping the script onto Amira 
#    for you by system(paste("open",hxscriptfilename))
# 10) You can have multiple script objects referring to multiple directories if you want
#     so long as none of the density files have the same name
# 11) You may want to change the name of each script object if you have more than 1 eg
#     ShowClones.scro setLabel "Dimorphic"
#     ShowClones2.scro setLabel "Regular"

$this proc constructor { } {
	global this

	$this newPortFilename filename

	$this filename setValue /Volumes/JData/JPeople/Sebastian/fruitless/Registration/IS2Reg/CanonicalClones-resampled/M/AL-a_M.am
	
    $this newPortButtonList Action 5
	$this Action setLabel Action:
	$this Action setLabel 0 LoadAll
	$this Action setLabel 1 Remove
	$this Action setLabel 2 Flip
	$this Action setLabel 3 HideAll
	$this Action setLabel 4 Male
	
	$this newPortFloatSlider red
	$this red setMinMax 0 1
	$this newPortFloatSlider green
	$this green setMinMax 0 1
	$this newPortFloatSlider blue
	$this blue setMinMax 0 1
	
	# $this newPortFloatSlider width
	# $this width setMinMax 0 2.5
	# $this width setValue 1
	# 
	# $this newPortIntSlider ScoreThreshold
	# $this ScoreThreshold setMinMax 0 4
	# $this ScoreThreshold setValue 4
	
	$this setVar dirName ""
	$this setVar lafObjectList ""
	$this setVar fileList ""
	$this setVar glomTogList ""
	$this setVar glomActive ""

	# the default axis to flip over (0=X, 1=Y ...)
	$this setVar flipAxis 0
	# $this setVar thresholds ""
	# $this setVar widths ""
	
	# $this newPortInfo numObjects
	# $this updateNumObjects
}

$this proc compute { } {
	
	if { [ $this Action isNew  ] && [$this Action getValue]==0 } {
		$this makeFileListFromDir
		$this loadFiles
		# $this updateNumObjects
	}
	if { [ $this Action isNew  ] && [$this Action getValue]==1} {
		$this removeAllData
	}
	if { [ $this Action isNew  ] && [$this Action getValue]==2} {
		# flip
		$this flipActiveClones [$this getVar flipAxis]
	}
	if { [ $this Action isNew  ] && [$this Action getValue]==3} {		
		if { [ $this Action getLabel 3]=="ShowAll" } {
			$this showLineViews 1
		} elseif {[ $this Action getLabel 3]=="HideAll" } {
			$this showLineViews 0
		}
		# $this updateNumObjects
	}
	if { [ $this Action isNew  ] && [$this Action getValue]==4} {
		if { [ $this Action getLabel 4]=="Male" } {
			$this showMale 1
			$this Action setLabel 4 Female
		} elseif {[ $this Action getLabel 4]=="Female" } {
			$this showMale 0
			$this Action setLabel 4 Male
		}
	}
	# if { [ $this ScoreThreshold isNew ] } {
	# 	# $this updateLafObjectsThreshold
	# 	$this updateNumObjects
	# }
	if { [ $this red isNew ] || [ $this green isNew ] || [ $this blue isNew ] } {
		$this updateLafObjectsColor
	}
	if {[$this Action getValue] != 4} {
		set glomActive ""
		foreach glomTog [$this getVar glomTogList] {
			for {set i 0} {$i < 6} {incr i} {
				set obj [$this $glomTog getLabel $i]
				#echo "checking obj $obj"
				if {[exists $obj]} {
					#echo "obj $obj exists"
					if {[ $this $glomTog isNew ]} {
						$obj setViewerMask [$this $glomTog getValue $i]
					}
					if {[$this $glomTog getValue $i]} {
						lappend glomActive [$this $glomTog getLabel $i]
						#echo [concat "added " [$this $glomTog getLabel $i]]
					}
				}
			}
		} 
		$this setVar glomActive $glomActive		
	}
	# echo $glomActive
	# uncomment to turn on continuous update
	# $this myupdate
}

$this proc showLineViews {mask} {
	set glomActive ""
	foreach glomTog [$this getVar glomTogList] {
		for {set i 0} {$i < 6} {incr i} {
			set obj [$this $glomTog getLabel $i]
			#echo "checking obj $obj"
			if {[exists $obj]} {
				#echo "obj $obj exists"
				$this $glomTog setValue $i $mask
				if {$mask} {
					lappend glomActive [$this $glomTog getLabel $i]
					#echo [concat "added " [$this $glomTog getLabel $i]]
				}
			}
		}
	} 
	$this setVar glomActive $glomActive
	if {$mask == 0} { $this Action setLabel 3 ShowAll}
	if {$mask == 1} { $this Action setLabel 3 HideAll}
}

# $this proc updateNumObjects {} {
# 	set numObjects 0
# 	foreach lafObject [$this getVar lafObjectList] {
# 		if {[exists $lafObject]} {
# 			set numObjects [expr $numObjects + 1]
# 		}
# 	}
# 	$this setVar numObjects $numObjects
# }	



# $this proc updateLafObjectsThreshold {} {
# 	foreach glom [$this getVar glomActive] {
# 		if {[exists $glom]} {
# 			$glom ScoreThreshold setValue [$this ScoreThreshold getValue]
# 			$glom fire
# 		}
# 	} 
# }

$this proc updateLafObjectsColor {} {
	foreach clone [$this getVar glomActive] {
		$this setCloneColour $clone [$this red getValue] [$this green getValue] [$this blue getValue]
	} 
}

$this proc setCloneColour { clone r g b } {
	if {[exists $clone]} {
		# change upper range to trick amira into updating colours
		set upperrange [$clone range getValue 1]
		$clone range setValue 1 [expr $upperrange - 1]
		$clone range setValue 1 $upperrange
		$clone colormap setDefaultColor $r $g $b
		$clone colormap setDefaultAlpha 0.35
		$clone fire
	}
}

$this proc flipClone { clone axis } {
	set data [$clone data source]
	if {[exists $data]} {
		$data flip $axis
		$clone doIt hit
		$clone fire
	}
}

$this proc flipActiveClones { axis } {
	set glomActive ""
	foreach clone [$this getVar glomActive] {
		$this flipClone $clone $axis
	}
}

$this proc setCloneVoltexRange { clone lower upper } {
	if {[exists $clone]} {
		$clone range setValue 0 $lower
		$clone range setValue 1 $upper
		$clone fire
	}
}

$this proc setAllCloneVoltexRanges { lower upper } {
	set glomActive ""
	foreach clone [$this getVar glomActive] {
		$this setCloneVoltexRange $clone $lower $upper
	}
}

$this proc setCloneAlphaScale { clone alpha } {
	if {[exists $clone]} {
		$clone setAlphaScale $alpha
		$clone fire
	}
}

$this proc setAllCloneAlphaScales { alpha } {
	set glomActive ""
	foreach clone [$this getVar glomActive] {
		$this setCloneAlphaScale $clone $alpha
	}
}

$this proc setCloneColormapAlpha { clone alpha } {
	if {[exists $clone]} {
		$clone colormap setDefaultAlpha $alpha
		$clone fire
	}
}

$this proc setAllCloneColormapAlphas { alpha } {
	set glomActive ""
	foreach clone [$this getVar glomActive] {
		$this setCloneColormapAlpha $clone $alpha
	}
}

$this proc showClone { clone mask } {
	if {[exists $clone]} {
		$clone setViewerMask $mask
	}
}

$this proc updateTogglesFromList {glomActive} {
	foreach glomTog [$this getVar glomTogList] {
		for {set i 0} {$i < 6} {incr i} {
			set obj [$this $glomTog getLabel $i]
			if {[exists $obj]} {
				if {[lsearch -exact $glomActive $obj] > -1} {
					# echo "found $obj, turning it on"
					$obj setViewerMask 1
					$this $glomTog setValue $i 1
				} else {
					# echo "Didn't find $obj, turning it off"
					$obj setViewerMask 0
					$this $glomTog setValue $i 0
				}
			}
		}
	}	
}

$this proc showMale {mask} {
	# mask = 1 for male, 0 for female
	set glomActive ""
	foreach clone [$this getVar glomActive] {
		if {[exists $clone]} {
			set cloneToAdd $clone
			set sex [string index $clone end]
			# echo "clone $clone exists with sex $sex"
			if {$sex eq "M"} {
				# echo "clone $clone is male"
				if {$mask == 0} {
					# we want to change to the female version
					set trimmedName [string trimright $clone "M"]
					append trimmedName "F"
					set cloneToAdd $trimmedName
				}			
			} elseif {$sex eq "F"} {
				# echo "clone $clone is female"
				if {$mask == 1} {
					# we want to change to the male version
					set trimmedName [string trimright $clone "F"]
					append trimmedName "M"
					set cloneToAdd $trimmedName
				}			
			}
			lappend glomActive $cloneToAdd
			# echo "Appending $cloneToAdd"
		}
	}
	$this updateTogglesFromList $glomActive
	$this setVar glomActive $glomActive	
}

$this proc removeAllData {} {
	# remove all data files and viewers that we actually loaded/made
	foreach datafile [$this getVar fileList] {
		if {[exists $datafile]} { remove $datafile }
		set glom [file rootname datafile] 
		if {[exists $glom]} { remove $glom }
	}
	# Delete toggles and list of active clones
	$this setVar glomActive "" 
	foreach glomTog [$this getVar glomTogList] {
		$this deletePort $glomTog
	}
	# Clear state variables
	$this setVar lafObjectList ""
	$this setVar fileList ""
	$this setVar glomTogList ""
	$this setVar glomActive ""
}

$this proc makeFileListFromDir {} {
	set filename [ $this filename getValue ] 
	set fileList [glob [file dirname $filename]/*[file extension $filename]]
	# set the instance variable fileList to the value of the local fileList
	$this setVar fileList $fileList
	$this setVar dirName [file dirname $filename]
}

$this proc loadFiles {} {
	set fileList [$this getVar fileList]
	set filesActuallyLoaded ""
	set lafObjectList [$this getVar lafObjectList]
	# set thresholds [$this getVar thresholds]
	# set widths [$this getVar widths]
	
	set xstart [lindex [$this getIconPosition] 0]
	set ystart [lindex [$this getIconPosition] 1]
	
	#echo $fileList
	foreach file $fileList {
		if {[file size $file] > 0} {
			set splitFile [file split $file]
			set justfilename [lindex $splitFile [expr [llength $splitFile]-1]]
			if { [file isfile $file] == 0 } { continue }
	
			set glom [file rootname $justfilename]
			lappend lafObjectList $glom
			set ypos [expr $ystart + [expr [llength $filesActuallyLoaded] * 20 ] + 20]

			if { ![exists $justfilename] } { 
				set newModule [load $file]
				# $newModule Action setValue 4
				lappend filesActuallyLoaded $newModule
				$newModule hideIcon
				$newModule setIconPosition [expr $xstart + 50 ] $ypos
				$newModule fire
			}

			if { ![exists $glom] } {
				set lineView [create HxVoltex]
				$lineView setIconPosition [expr $xstart] $ypos
				$lineView data connect $newModule
				# this removes the volume rendering type colour map (which is always attached)
				$lineView colormap disconnect
				$lineView doIt hit
				$lineView fire
				# this sets the constant colour settings (in the absence of attached colormap)
				$lineView colormap disconnect
				$lineView slices setValue 256
				$lineView range setValue 0 15
				$lineView range setValue 1 255
				$lineView colormap setDefaultColor [$this red getValue] [$this green getValue] [$this blue getValue]
				$lineView colormap setDefaultAlpha 0.35
				# this is required to update the Voltex
				$lineView doIt hit
				$lineView fire
				$lineView setLabel "$glom"
				# lappend widths [$this width getValue]
			}
		}
	}
	#set hideNewModules 0
	$this setVar lafObjectList $lafObjectList
	# replace input file list with the ones that we actually loaded
	$this setVar fileList $filesActuallyLoaded
	$this makeCloneToggles
}

$this proc makeCloneToggles {} {
	set lafObjectList [$this getVar lafObjectList]
	set glomTogList ""
	for {set i 0} {$i<[llength $lafObjectList]} { set i [expr $i + 6]} {
		set j [expr $i / 6]
		$this newPortToggleList "Clone$j" 6
		lappend glomTogList "Clone$j"
		for {set k 0} {[expr $k + $i] < [llength $lafObjectList]} { incr k} {
			$this "Clone$j" setLabel $k [lindex $lafObjectList [expr $k + $i]] 
			$this "Clone$j" setValue $k 1
		}
	}		
	$this setVar glomTogList $glomTogList
}