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update release 3.24.0
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@mfroeling
mfroeling committed Jul 16, 2024
1 parent c92b51f commit abc3689
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Showing 5 changed files with 20,164 additions and 14,451 deletions.
142 changes: 101 additions & 41 deletions QMRITools/Kernel/MaskingTools.wl
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,10 @@ SmoothMask::usage =
MaskData::usage =
"MaskData[data, mask] applies a mask to data. mask can be 2D or 3D, data can be 2D, 3D or 4D."

MaskSegmentation::usage =
"MaskSegmentation[seg, mask] applies a mask to a splited segmentation seg from SplitSegmentations.
The mask is 3D, seg is 4D."

GetMaskData::usage =
"GetMaskData[data, mask] retruns the data selected by the mask."

Expand Down Expand Up @@ -107,7 +111,8 @@ maskdim is the dimensions of the output {zout,xout,yout}."


NormalizeMethod::usage =
"NormalizeMethod is an option for NormalizeData. Can be \"Set\" or \"Volumes\" wichi normalizes to the firs volume or normalizes each volume individually, respectively."
"NormalizeMethod is an option for NormalizeData. Can be \"Set\" or \"Volumes\" wich normalizes to the first volume or normalizes each volume individually, respectively.
If \"Uniform\" normalizes the histogram of the data to have a uniform distribution between 0 and 1 where 0 is treated as background of the data."

FitOrder::usage =
"FitOrder is an option for HomogenizeData. It specifies the order of harmonics to be used for the homogenization."
Expand Down Expand Up @@ -177,9 +182,13 @@ Options[NormalizeData] = {NormalizeMethod -> "Set"}
SyntaxInformation[NormalizeData] = {"ArgumentsPattern" -> {_, _., OptionsPattern[]}};

NormalizeData[data_, opts : OptionsPattern[]] := Block[{ndat, mask},
ndat = Switch[ArrayDepth[data], 3, data, 4, Mean@Transpose@data];
mask = Mask[NormDat[ndat - Min@ndat, 0.]];
NormalizeData[data, mask, opts]
If[OptionValue[NormalizeMethod]=!="Uniform",
ndat = Switch[ArrayDepth[data], 3, data, 4, Mean@Transpose@data];
mask = Mask[NormDat[ndat - Min@ndat, 0.]];
NormalizeData[data, mask, opts]
,
NormDatC[data]
]
]

NormalizeData[data_, msk_, opts : OptionsPattern[]] := Block[{dat, mn, min, dato, mask},
Expand All @@ -196,6 +205,19 @@ NormalizeData[data_, msk_, opts : OptionsPattern[]] := Block[{dat, mn, min, dato
]


(*normalization towards uniform distribution*)
NormDatC = Compile[{{dat, _Real, 3}}, Block[{fl, flp, min, max, bins, cdf, n},
n = 512;
fl = Flatten[dat];
flp = Pick[fl, Unitize[fl], 1];
{min, max} = MinMax[flp];
bins = BinCounts[flp, {min, max, (max - min)/n}];
cdf = Prepend[N[Accumulate[bins]/Total[bins]], 0.];
Map[cdf[[# + 1]] &, Clip[Floor[(dat - min)/(max - min) n], {0, n}, {0, n}], {-2}]
], RuntimeAttributes -> {Listable}, RuntimeOptions -> "Speed", Parallelization -> True];


(*normalization towards median of given valueue*)
NormDat[dat_, mn_] := ToPackedArray[100. Which[
mn===0., dat/MedianNoZero[Flatten@dat],
ListQ[mn],Transpose[Transpose[dat]/mn],
Expand Down Expand Up @@ -330,23 +352,26 @@ SmoothMask[msk_, OptionsPattern[]] := Block[{itt, dil, pad, close, obj, filt, ma

SyntaxInformation[DilateMask] = {"ArgumentsPattern" -> {_, _}};

DilateMask[seg_, size_] := Which[
(*dilation*)
size > 0,
If[ArrayDepth[seg]>3,
Transpose[SparseArray[SparseArray[ImageData@Dilation[Image3D[#], Round[size]]] & /@ Transpose[seg]]],
SparseArray[Dilation[Normal[seg], Round[size]]]
],
(*erosion*)
size < 0,
If[ArrayDepth[seg]>3,
Transpose[SparseArray[SparseArray[ImageData@Erosion[Image3D[#], Round[Abs[size]]]] & /@ Transpose[seg]]],
SparseArray[Erosion[Normal[seg], Round[Abs[size]]]]
],
True,
SparseArray[seg]
DilateMask[seg_, size_] := Block[{sz, fun},
sz = Abs[Round[size]];

If[sz =!= 0,
(*see if dilation of erosion*)
fun = If[size > 0, Dilation, Erosion];

(*3D or 4D data*)
SparseArray@Switch[ArrayDepth[seg],
3, DilateMaskI[seg, fun, sz],
4, Transpose[DilateMaskI[#, fun, sz] & /@ Transpose[seg]]
]
,
(*if size is 0 dont do anything*)
SparseArray@seg
]
]

DilateMaskI[seg_, fun_, size_] := Round[SparseArray[ReverseCrop[fun[#[[1]], size], Dimensions[seg], #[[2]]]] &[AutoCropData[seg]]]


(* ::Subsubsection::Closed:: *)
(*MaskData*)
Expand All @@ -366,19 +391,34 @@ MaskData[data_, mask_]:=Block[{dataD, maskD,dimD,dimM,out},
{2,2}, If[dimD == dimM, mask data, 1],
{3,3}, If[dimD == dimM, mask data, 1],
{3,2}, If[dimD[[2;;]] == dimM, mask # &/@ data, 1],
{4,3}, Which[dimD[[2;;]] == dimM, mask # & /@ data, dimD[[{1,3,4}]] == dimM, Transpose[mask # & /@ Transpose[data]], True, 1],
_, 2
{4,3}, Which[
dimD[[2;;]] == dimM, mask # & /@ data,
dimD[[{1,3,4}]] == dimM, Transpose[mask # & /@ Transpose[data]],
True, Return[Message[MaskData::dim, dimD, dimM];$Failed]],
_, Return[Message[MaskData::dep, dataD, maskD];,$Failed]
];

(*check for errors*)
If[out === 1, Message[MaskData::dim, dimD, dimM]];
If[out === 2, Message[MaskData::dep, dataD, maskD]];

(*make the output*)
ToPackedArray@N@Normal@out
]


(* ::Subsubsection::Closed:: *)
(*MaskSegmentation*)


SyntaxInformation[MaskSegmentation] = {"ArgumentsPattern" -> {_, _}};

MaskSegmentation[seg_, mask_] := Block[{dim, sc, cr},
msk = Normal@mask;
dim = Dimensions[seg[[All, 1]]];
Transpose[(
{sc, cr} = AutoCropData[#];
Round@SparseArray@ReverseCrop[ApplyCrop[msk, cr] sc, dim, cr]
) & /@ Transpose[seg]]
]


(* ::Subsubsection::Closed:: *)
(*GetMaskData*)

Expand All @@ -390,19 +430,26 @@ SyntaxInformation[GetMaskData] = {"ArgumentsPattern" -> {_, _, OptionsPattern[]}
GetMaskData[data_?ArrayQ, mask_, opts:OptionsPattern[]] := Block[{out},
Which[
ArrayDepth[data]===4&&ArrayDepth[mask]===3,
GetMaskData[#,mask, opts]&/@Transpose[data]
GetMaskData[#, mask, opts]&/@Transpose[data]
,
ArrayDepth[data]===3&&ArrayDepth[mask]===4,
GetMaskData[data,#, opts]&/@Transpose[mask]
GetMaskData[data, #, opts]&/@Transpose[mask]
,
True,
If[!(Dimensions[data]=!=Dimensions[mask] || Drop[Dimensions[data], {2}]=!=Dimensions[mask]),
Message[GetMaskData::dim,Dimensions[data],Dimensions[mask]],
Retrun[Message[GetMaskData::dim,Dimensions[data],Dimensions[mask]];$Failed]
,
out = Switch[OptionValue[GetMaskOutput],
"Slices", MapThread[Pick[Chop[Flatten[N[#1]]], Unitize[Flatten[Normal@#2]], 1]&, {data, mask}, ArrayDepth[data]-2],
"Sparse", (data mask)["ExplicitValues"],
_, Pick[Flatten[N[data]], Unitize[Flatten[Normal@mask]], 1]
];

out = Switch[OptionValue[GetMaskOutput],
"Mean", Mean[out],
"Median", Median[out],
_, out
];
(*select only non zero values if mask only to false*)
If[OptionValue[GetMaskOnly],out,Pick[out, Unitize[out], 1]]
]
Expand Down Expand Up @@ -445,10 +492,16 @@ SyntaxInformation[SplitSegmentations] = {"ArgumentsPattern" -> {_}};

SplitSegmentations[segI_]:=SplitSegmentations[segI, True]

SplitSegmentations[segI_, sparse_] := Block[{vals, seg},
SplitSegmentations[segI_, sparse_] := Block[{seg, dim, exVals, exPos, vals},
seg = SparseArray[Round[segI]];
vals = Sort[DeleteDuplicates[seg["ExplicitValues"]]];
seg = Transpose[1 - SparseArray[(Unitize[seg - #] & /@ vals)]];
dim = Dimensions[seg];

exVals = seg["ExplicitValues"];
exPos = seg["ExplicitPositions"];
vals = Sort@DeleteDuplicates@exVals;

seg = Transpose[SparseArray[Pick[exPos, Unitize[exVals - #], 0] -> 1, dim] & /@ vals];

{If[sparse, seg, Normal@seg], vals}
]

Expand All @@ -457,7 +510,7 @@ SplitSegmentations[segI_, sparse_] := Block[{vals, seg},
(*GetSegmentationLabels*)


GetSegmentationLabels[seg_]:= DeleteCases[Sort@Round[DeleteDuplicates[Flatten[seg]]],0];
GetSegmentationLabels[segI_]:= Sort[DeleteDuplicates[SparseArray[Round[segI]]["ExplicitValues"]]];


(* ::Subsubsection::Closed:: *)
Expand All @@ -466,9 +519,12 @@ GetSegmentationLabels[seg_]:= DeleteCases[Sort@Round[DeleteDuplicates[Flatten[se

SyntaxInformation[MergeSegmentations] = {"ArgumentsPattern" -> {_,_}};

MergeSegmentations[seg_, lab_] := Block[{mt},
mt = Transpose[SparseArray[seg]];
Normal[Total[lab mt](1 - UnitStep[Total[mt] - 2])]
MergeSegmentations[seg_, lab_] := Block[{mt,nv},
mt = Transpose[SparseArray[Round[seg]]];
nv = Range[Length@lab];

(*mapping over sparce is quicker than direct multiplication and total*)
Normal[Total[mt[[#]] lab[[#]] & /@ nv] (1 - UnitStep[Total[mt[[#]] & /@ nv] - 2])]
]


Expand All @@ -494,13 +550,17 @@ ReplaceSegmentations[segm_, labSel_, labNew_] := SelectReplaceSegmentations[segm
(*SelectReplaceSegmentations*)


SelectReplaceSegmentations[segm_, labSel_, labNew_] := Block[{seg, lab, sel},
{seg, lab} = SplitSegmentations[segm];
SelectReplaceSegmentations[segm_, labSel_, labNew_] := Block[{split, seg, lab, sel},
split = If[Length[segm] == 2, False, True];

{seg, lab} = If[split, SplitSegmentations[segm], segm];

sel = MemberQ[labSel, #] & /@ lab;
MergeSegmentations[
Transpose[Pick[Transpose[seg], sel, True]],
Pick[lab /. Thread[labSel->labNew], sel, True]
]
seg = Transpose[Pick[Transpose[seg], sel, True]];
lab = Pick[lab /. Thread[labSel->labNew], sel, True];
or = Ordering[lab];

If[split, MergeSegmentations[seg, lab], {seg[[All,or]], lab[[or]]}]
]


Expand Down
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