/// <summary>
/// Compares the increase in values from the reference Nifti (prior) to the input Nifti (current).
/// The inputs should be pre-registered and normalised.
/// </summary>
/// <param name="input">Current example</param>
/// <param name="reference">Prior example</param>
/// <returns>Nifti who's values are the meaningful increase between prior and current.</returns>
public static INifti <float> CompareMSLesionIncrease(INifti <float> input, INifti <float> reference)
{
INifti <float> output = Compare.GatedSubract(input, reference, backgroundThreshold: 10, minRelevantStd: -1, maxRelevantStd: 5, minChange: 0.8f, maxChange: 5);
for (int i = 0; i < output.Voxels.Length; ++i)
{
if (output.Voxels[i] < 0)
{
output.Voxels[i] = 0;
}
}
output.RecalcHeaderMinMax(); // This will update the header range.
output.ColorMap = ColorMaps.RedScale();
return(output);
}
private Histogram DoCompare(INifti <float> currentnii, INifti <float> priornii)
{
_log.Info("Starting normalization...");
currentnii = Normalization.ZNormalize(currentnii, priornii);
_log.Info($@"..done.");
currentnii.RecalcHeaderMinMax();
priornii.RecalcHeaderMinMax();
var tasks = new List <Task>();
var histogram = new Histogram
{
Prior = priornii,
Current = currentnii
};
var cs = _recipe.CompareSettings;
if (cs.CompareIncrease)
{
var t = Task.Run(() =>
{
_log.Info("Comparing increased signal...");
var increase = Compare.GatedSubract(currentnii, priornii, cs.BackgroundThreshold, cs.MinRelevantStd, cs.MaxRelevantStd, cs.MinChange, cs.MaxChange);
for (int i = 0; i < increase.Voxels.Length; ++i)
{
increase.Voxels[i] = increase.Voxels[i] > 0 ? increase.Voxels[i] : 0;
}
increase.RecalcHeaderMinMax();
increase.ColorMap = ColorMaps.RedScale();
histogram.Increase = increase;
var increaseOut = currentnii.AddOverlay(increase);
var outpath = _currentPath + ".increase.nii";
increaseOut.WriteNifti(outpath);
Metrics.ResultFiles.Add(new ResultFile()
{
FilePath = outpath, Description = "Increased Signal", Type = ResultType.CURRENT_PROCESSED
});
});
tasks.Add(t);
}
if (cs.CompareDecrease)
{
_log.Info("Comparing decreased signal...");
// I know the code in these two branches looks similar but there's too many inputs to make a function that much simpler...
var t = Task.Run(() =>
{
var decrease = Compare.GatedSubract(currentnii, priornii, cs.BackgroundThreshold, cs.MinRelevantStd, cs.MaxRelevantStd, cs.MinChange, cs.MaxChange);
for (int i = 0; i < decrease.Voxels.Length; ++i)
{
decrease.Voxels[i] = decrease.Voxels[i] < 0 ? decrease.Voxels[i] : 0;
}
decrease.RecalcHeaderMinMax();
decrease.ColorMap = ColorMaps.ReverseGreenScale();
histogram.Decrease = decrease;
var decreaseOut = currentnii.AddOverlay(decrease);
var outpath = _currentPath + ".decrease.nii";
decreaseOut.WriteNifti(outpath);
Metrics.ResultFiles.Add(new ResultFile()
{
FilePath = outpath, Description = "Decreased Signal", Type = ResultType.CURRENT_PROCESSED
});
});
tasks.Add(t);
}
Task.WaitAll(tasks.ToArray());
_log.Info("...done.");
return(histogram);
}
