Provenance Challenge 1 workflow -- mockup version

Value

Value

Script

// align warp shell wrapper

// mockup: creates output string based in input string values

String header = AnatomyInput.get(0);
String image  = AnatomyInput.get(1);

WarpParameters = "warp("+header+","+image+")";

Script

// reslice based on calculated warp parameters

List resliced = new ArrayList();

resliced.add("reslice("+warpParameters+".H");
resliced.add("reslice("+warpParameters+".I");

Script

// softmean

// combines list of pairs (header, image) into an average (header, image)

// it naively concats the headers together and the images together just to trace its input values

List atlasAverage = new ArrayList();

String averageHeader = "softmean(";
String averageImage  = "softmean(";

for (List reslicedEntry: resliced) {
       averageHeader = averageHeader+reslicedEntry.get(0)+"/";
       averageImage = averageImage+reslicedEntry.get(1)+"/";
}

atlasAverage.add(averageHeader.substring(0,averageHeader.length()-1)+")");
atlasAverage.add(averageImage.substring(0,averageImage.length()-1)+")");

Script

// slicer

// takes a pair [header, image] and an axis
// and slices the image along that axis

atlasSlice  = new ArrayList();

atlasSlice.add(axis+"-slice("+atlasAverage.get(0)+")");
atlasSlice.add(axis+"-slice("+atlasAverage.get(1)+")");

Script

// converter  (header, image) -> (header, image)

List atlasGraphic = new ArrayList();

atlasGraphic.add("convert("+atlasSlice.get(0)+")");
atlasGraphic.add("convert("+atlasSlice.get(1)+")");

Script

axes = new ArrayList();

axes.add("x");
axes.add("y");
axes.add("z");