fiber tracto tools update

QMRITools/Kernel/CardiacTools.wl

@@ -2217,7 +2217,7 @@ MakeECVBloodMask[pre_, post_, OptionsPattern[]] := Block[{
 (*MakeECVBloodMask*)
 
 
-ECVCalc[mappre_, mappost_, hema_?RealQ] := Block[{z, x, y, mask},
+ECVCalc[mappre_, mappost_, hema_?NumberQ] := Block[{z, x, y, mask},
 	mask = MakeECVBloodMask[mappre, mappost, OutputCheckImage -> False];
 	ECVCalc[mappre, mappost, mask, hema]
 ]

QMRITools/Kernel/ElastixTools.wl

@@ -657,7 +657,7 @@ SplitRegInput[input_] := Which[
 (*RegisterData*)
 
 
-Options[RegisterData]={
+Options[RegisterData] = {
 	Iterations->250,
 	Resolutions->1,
 	HistogramBins->32,

QMRITools/Kernel/GeneralTools.wl

@@ -1136,9 +1136,7 @@ MakeIntFunction[dat_, int_?IntegerQ, opts:OptionsPattern[]] := MakeIntFunction[d
 
 MakeIntFunction[dat_, vox_, int_?IntegerQ, opts:OptionsPattern[]] := Block[{dim, def, range},
 	dim = Dimensions[dat][[;;3]];
-
 	range = Thread[{vox, vox dim}] - If[OptionValue[CenterVoxel], 0.5, 0] vox - If[OptionValue[CenterRange], 0.5, 0] dim;
-
 	def = 0. dat[[1,1,1]];
 	def =If[ListQ[def], Flatten@def, def];
 
@@ -1149,13 +1147,13 @@ MakeIntFunction[dat_, vox_, int_?IntegerQ, opts:OptionsPattern[]] := Block[{dim,
 		InterpolatingFunction[
 			range,
 			{5,If[ArrayDepth[dat]===3, 6, 2],0, dim,
-			{int,int,int}+1,0,0,0,0,ex&,{},{},False},
-			Range[range[[#,1]],range[[#,2]],vox[[#]]]&/@{1,2,3},
+			{int, int, int} + 1, 0, 0, 0, 0, ex&, {}, {}, False},
+			Range[range[[#, 1]], range[[#, 2]], vox[[#]]]& /@ {1, 2, 3},
 			If[ArrayDepth[dat] === 3 && $VersionNumber >= 13.3, 
 				{PackedArrayForm, Range[0,Length[fdat]], fdat}, 
 				ToPackedArray@N@dat
 			],
-			{Automatic,Automatic,Automatic}]
+			{Automatic, Automatic, Automatic}]
 	]
 ]
 
@@ -1936,15 +1934,18 @@ MakeFunctionGraph[func_, opts:OptionsPattern[]] := Block[{
 	Graph[edges, 
 		VertexLabels -> vertLab, VertexShapeFunction -> vertFunc, VertexStyle -> vertCol,
 		VertexLabelStyle -> Directive[Black, Bold, Automatic], EdgeStyle -> Directive[Black, Thick], 
-		VertexSize -> Automatic]
+		VertexSize -> Automatic, ImageSize -> {Automatic, 600}]
 ]
 
 
 (* ::Subsubsection::Closed:: *)
 (*GetDependencies*)
 
 
-GetDependencies[sym_String] := If[SymbolQ[ToExpression[sym]], SelectFunctions[(Union@Level[(Hold @@ DownValues[sym])[[All, 2]], {-1}, Hold, Heads -> True])], Nothing]
+GetDependencies[sym_String] := If[
+	Head[ToExpression[sym]] === Symbol,
+	(*SymbolQ[ToExpression[sym]],*) 
+	SelectFunctions[(Union@Level[(Hold @@ DownValues[sym])[[All, 2]], {-1}, Hold, Heads -> True])], Nothing]
 
 
 SelectFunctions[func_] := Select[StringSplit[ToString /@ Pick[List @@ Defer /@ func, List@ReleaseHold[FunctionQC /@ func], 1],"[" | "]"][[All, 2]], Context[#] =!= "System`" &]

QMRITools/Kernel/MuscleBidsTools.wl

@@ -136,6 +136,7 @@ VersionCheck::usage =
 (* ::Subsection::Closed:: *)
 (*Error Messages*)
 
+
 CheckDataDiscription::key = "Datasets have duplicate names which is not allowed.";
 
 CheckDataDiscription::type = "Unknown Muscle-BIDS type: `1`, using folder \"miss\".";
@@ -2011,15 +2012,15 @@ MuscleBidsTractographyI[foli_, folo_, datType_, allType_, verCheck_, met_]:=Bloc
 		tracto, tractType, tractSeg, tractStopLab, tractStopVal, tractStopLabNam, trkFile,
 		tractTypeLab, fol, parts, checkFile, outfile, seed, lenS, segBone, tractSegLab,
 		datfile, stopfile, tens, vox, dim, stop, ang, step, tracts, seeds, len, seg,
-		segfile, muscles, mlabs, mus, bones, con, leng, dens, flip, per
+		segfile, muscles, mlabs, mus, bones, con, leng, dens, flip, per, duplicate, key
 	}, 
 
 	debugBids["Starting MuscleBidsTractographyI"];
 	debugBids[foli, folo];
 	debugBids[datType];
 
 	(*!!options!!*)
-	{len, ang, step, seed} = {{15, 500}, 25, 1.5, Scaled[.35]};
+	{len, ang, step, seed} = {{15, 500}, 25, 1.5, Scaled[.30]};
 	{lenS, segBone} = {{15, 500}, 100};
 
 	(*figure out if duplicate handeling is needed.*)
@@ -2111,7 +2112,7 @@ MuscleBidsTractographyI[foli_, folo_, datType_, allType_, verCheck_, met_]:=Bloc
 			{tracts, seeds} = FiberTractography[tens, vox, stop,
 				InterpolationOrder -> 0, StepSize -> step, Method -> "Euler", MaxSeedPoints -> seed, 
 				FiberLengthRange -> len, FiberAngle -> ang, TracMonitor -> False,
-				TensorFilps -> flip, TensorPermutations -> per
+				TensorFilps -> flip, TensorPermutations -> per, Parallelization -> True
 			];
 
 			(* Export the tractography results *)

QMRITools/Kernel/PlottingTools.wl

@@ -65,6 +65,9 @@ PlotSegmentations[seg, bone, vox] same but also generates an extra contour with
 Link3DGraphic::usage =
 "Link3DGraphic[3Dgraphics] creates a 3D graphic with a linked view options between all 3D graphics that have been linked."
 
+ShowLink::usage =
+"ShowLink[] shows the linked view options between all 3D graphics that have been linked."
+
 GenerateRotationFrames::usage =
 "GenerateRotationFrames[3Dgraphics, nFrames] generates nFrames of the 3D graphics rotating around the z-axis."
 
@@ -104,6 +107,9 @@ ContourColor::usage =
 ContourOpacity::usage = 
 "ContourOpacity is an option for PlotContour and PlotSegmentations. It specifies the opacity of the contour."
 
+ContourSpecularity::usage =
+"ContourSpecularity is an option for PlotContour. It specifies the specularity of the contour."
+
 ContourColorRange::usage = 
 "ContourColorRange is an option for PlotContour. If the ContourColor is an array this values gives the plot range."
 
@@ -1813,6 +1819,7 @@ GetSlicePositions[data_,vox_,OptionsPattern[]]:=Block[{
 Options[PlotContour] = {
    ContourColor -> Gray,
    ContourOpacity -> 0.5,
+   ContourSpecularity -> 50,
    ContourColorRange -> Automatic,
    ColorFunction -> "SunsetColors",
    ContourSmoothRadius -> None,
@@ -1839,6 +1846,7 @@ PlotContour[dati_, vox_, opts:OptionsPattern[]] := Block[{
 		scale = OptionValue[ContourScaling];
 		color = OptionValue[ContourColor];
 		opac = OptionValue[ContourOpacity];
+		spec = OptionValue[ContourSpecularity];
 
 		If[N[Max[dati]] === 0., 
 			Graphics3D[],
@@ -1853,7 +1861,7 @@ PlotContour[dati_, vox_, opts:OptionsPattern[]] := Block[{
 			data = SparseArray[data];
 
 			col = If[ColorQ[color], color, If[color==="Random", RandomColor[], GrayLevel[1.]]];
-			style = Directive[{Opacity[opac], col, Specularity[Lighter@Lighter@col, 5]}];
+			style = Directive[{Opacity[opac], col, Specularity[Lighter@col, spec]}];
 
 			colfunc = If[!ArrayQ[color],
 				Automatic,
@@ -1864,7 +1872,7 @@ PlotContour[dati_, vox_, opts:OptionsPattern[]] := Block[{
 					ran];
 				coldat = Clip[Rescale[color, ran], {0, 1}];
 				cdim = Dimensions[coldat];
-				style = Directive[{Opacity[opac],Specularity[Red,0]}];
+				style = Directive[{Opacity[opac], Specularity[Red, 0]}];
 				Function[{z, y, x},
 					ColorData[cfunc][coldat[[
 						Clip[Round[x/vox[[1]] + 0.5], {1, cdim[[1]]}],
@@ -1904,7 +1912,7 @@ PlotContour[dati_, vox_, opts:OptionsPattern[]] := Block[{
 
 viewPoint = {1.3, -2.4, 2.0};
 viewVertical = {0., 0., 1.};
-viewAngle = 35. Degree;
+viewAngle = 20. Degree;
 viewCenter = {0.5, 0.5, 0.5};
 
 Link3DGraphic[graphics_]:=Show[graphics, SphericalRegion -> True, 
@@ -1915,6 +1923,16 @@ Link3DGraphic[graphics_]:=Show[graphics, SphericalRegion -> True,
 ]
 
 
+ShowLink[]:=Dynamic[Grid[{
+	{"ViewPoint: ", Round[viewPoint,.01]}, 
+	{"ViewVertical: ", Round[viewVertical,.01]}, 
+	{"ViewAngle: ", Round[viewAngle/Degree,.01]}, 
+	{"ViewCenter: ", Round[viewCenter,.01]}}, Alignment -> Left]]
+
+(* ::Subsection::Closed:: *)
+(*GenerateRotationFrames*)
+
+
 Options[GenerateRotationFrames] = {
 	ImageSize -> 500
 };
@@ -1944,6 +1962,7 @@ Table[Rasterize[Show[gr,(*Graphics3D[InfiniteLine[{0,0,0}, {0,0,1}]]*) ViewPoint
 Options[PlotSegmentations] = {
 	ImageSize -> 400, 
 	ContourOpacity->0.6,
+	ContourSpecularity -> 5,
 	ColorFunction -> "DarkRainbow", 
 	ContourSmoothRadius -> 2,
 	RandomizeColor->True,
@@ -1955,9 +1974,10 @@ SyntaxInformation[PlotSegmentations] = {"ArgumentsPattern" -> {_, _, _., Options
 PlotSegmentations[seg_, vox_, opts : OptionsPattern[]] := PlotSegmentations[seg, None, vox, opts]
 
 PlotSegmentations[seg_, bone_, vox_, opts : OptionsPattern[]] := Block[{
-		smooth, size, plotb, segM, nSeg, rSeg, cols, plotm, ranCol, op, res
+		smooth, size, plotb, segM, nSeg, rSeg, cols, plotm, ranCol, op, res, spec
 	},
-	{smooth, cols, size, ranCol, op, res} = OptionValue[{ContourSmoothRadius, ColorFunction, ImageSize, RandomizeColor, ContourOpacity, ContourResolution}];
+	{smooth, cols, size, ranCol, op, res, spec} = OptionValue[{ContourSmoothRadius, ColorFunction, ImageSize, 
+		RandomizeColor, ContourOpacity, ContourResolution, ContourSpecularity}];
 
 	plotb = If[bone === None, Graphics3D[],
 		PlotContour[If[ArrayDepth[bone]===3, Unitize@bone, Unitize@Total@Transpose@bone], vox, 
@@ -1976,7 +1996,8 @@ PlotSegmentations[seg_, bone_, vox_, opts : OptionsPattern[]] := Block[{
 			cols = Reverse[ColorData[OptionValue[ColorFunction]] /@ Rescale[rSeg]];
 			If[ranCol, SeedRandom[1234]; cols = cols[[RandomSample[rSeg]]]];
 		];
-		Show[Table[PlotContour[segM[[All, i]], vox, ContourColor -> cols[[i]], ContourOpacity -> op, ContourSmoothRadius -> smooth, ContourResolution->res], {i, 1, nSeg}]]
+		Show[Table[PlotContour[segM[[All, i]], vox, ContourColor -> cols[[i]], ContourOpacity -> op, 
+			ContourSpecularity -> spec, ContourSmoothRadius -> smooth, ContourResolution->res], {i, 1, nSeg}]]
 	];
 
 	Show[plotm, plotb, ViewPoint -> Front, ImageSize -> size, Boxed -> False, Axes -> False, SphericalRegion -> False]

QMRITools/Kernel/SegmentationTools.wl

@@ -2328,7 +2328,9 @@ MakeChannelImage[data_, vox_]:=Block[{dat, imdat, rat},
 (*ImportITKLabels*)
 
 
-SyntaxInformation[ImportITKLabels] = {"ArgumentsPattern"->{_}};
+SyntaxInformation[ImportITKLabels] = {"ArgumentsPattern"->{_.}};
+
+ImportITKLabels[] := ImportITKLabels[GetAssetLocation["MusclesLegLabels"]];
 
 ImportITKLabels[file_] := Block[{lines, muscleNames, muscleLabels},
 	(*import*)