public static TVEResults Calculate(SliceData sliceData, double factor = 0.3, CalcMode mode = CalcMode.BySum)
{
var data = mode == CalcMode.BySum ? sliceData.DataBySum : sliceData.DataByCount;
var total = data.Sum(x => x);
var tve = new TVEResults
{
SliceData = sliceData,
Factor = factor,
Total = total,
Cutoff = (int)(total * factor),
Mode = mode,
};
var sorted = data.OrderByDescending(x => x).ToArray();
int sum = 0;
int nToExceed = 0;
for (int i = 0; i < sorted.Length; i++)
{
nToExceed++;
sum += sorted[i];
if (sum > tve.Cutoff)
{
break;
}
}
tve.Count = nToExceed;
tve.Percentage = nToExceed * 100.0 / sliceData.Count;
return(tve);
}
public static Histogram Calculate(SliceData sd, CalcMode calcMode = CalcMode.BySum, HistoMode histoMode = HistoMode.Normal)
{
var h = new Histogram
{
SliceData = sd,
Frequency = new int[100],
CalcMode = calcMode,
HistoMode = histoMode,
};
var data = calcMode == CalcMode.ByCount ? sd.DataByCount : sd.DataBySum;
if (h.HistoMode == HistoMode.Normal)
{
var min = calcMode == CalcMode.ByCount ? sd.RollingCountMinValue : sd.RollingSumMinValue;
var max = calcMode == CalcMode.ByCount ? sd.RollingCountMaxValue : sd.RollingSumMaxValue;
double div = Math.Max(1.0, max - min);
foreach (var val in data)
{
int idx = Math.Min(99, (int)Math.Floor((val - min) / div * 100.0));
h.Frequency[idx]++;
}
}
else
{
var min = calcMode == CalcMode.ByCount ? sd.RollingCountMinValue : sd.RollingSumMinValue;
var max = calcMode == CalcMode.ByCount ? sd.RollingCountMaxValue : sd.RollingSumMaxValue;
double div = Math.Max(10.0, max - min);
foreach (var val in data)
{
int idx = Math.Min(99, (int)Math.Floor((Math.Log10(Math.Max(1, val - min)) / Math.Log10(div) * 100.0)));
h.Frequency[idx]++;
}
}
return(h);
}
public static SliceData Calculate(RawData raw, double thresholdPercent = 0.1, int rollingWidth = 100)
{
var sd = new SliceData
{
RawData = raw,
Sums = new int[raw.FrameCount],
PixelsAboveThreshold = new int[raw.FrameCount],
Mins = new int[raw.FrameCount],
Maxs = new int[raw.FrameCount],
RollingSums = new int[raw.FrameCount - rollingWidth + 1],
RollingCounts = new int[raw.FrameCount - rollingWidth + 1],
RollingWidth = rollingWidth,
ThresholdPercent = thresholdPercent,
Count = rollingWidth * raw.PixelsPerFrame,
};
var sorted = raw.Data.OrderByDescending(s => s).ToArray();
sd.MinValue = sorted.Last();
sd.MaxValue = sorted.First();
var nonzero = sorted.Where(s => s > 0).ToArray();
int threshold = nonzero[(int)((1 - thresholdPercent) * nonzero.Length)];
for (int f = 0; f < raw.FrameCount; f++)
{
int min = int.MaxValue;
int max = int.MinValue;
int sum = 0;
int aboveThreshold = 0;
int frameOffset = raw.PixelsPerFrame * f;
for (int p = frameOffset; p < frameOffset + raw.PixelsPerFrame; p++)
{
int val = raw.Data[p];
if (val > max)
{
max = val;
}
else if (val < min)
{
min = val;
}
sum += val;
if (val > threshold)
{
aboveThreshold++;
}
}
sd.Sums[f] = sum;
sd.Mins[f] = min;
sd.Maxs[f] = max;
sd.PixelsAboveThreshold[f] = aboveThreshold;
}
// Rolling Sums
int rs_sum = 0;
for (int i = 0; i < rollingWidth; i++)
{
rs_sum += sd.Sums[i];
}
sd.RollingSums[0] = rs_sum;
int rs_max = rs_sum;
int rs_maxIndex = 0;
for (int i = rollingWidth; i < raw.FrameCount; i++)
{
rs_sum = sd.RollingSums[i - rollingWidth] - sd.Sums[i - rollingWidth] + sd.Sums[i];
sd.RollingSums[i - rollingWidth + 1] = rs_sum;
if (rs_sum > rs_max)
{
rs_max = rs_sum;
rs_maxIndex = i - rollingWidth + 1;
}
}
sd.RollingSumMaxStartIndex = rs_maxIndex;
sd.RollingSumMinValue = sd.DataBySum.Min();
sd.RollingSumMaxValue = sd.DataBySum.Max();
// Rolling Counts
int rc_sum = 0;
for (int i = 0; i < rollingWidth; i++)
{
rc_sum += sd.PixelsAboveThreshold[i];
}
sd.RollingCounts[0] = rc_sum;
int rc_max = rc_sum;
int rc_maxIndex = 0;
for (int i = rollingWidth; i < raw.FrameCount; i++)
{
rc_sum = sd.RollingCounts[i - rollingWidth] - sd.PixelsAboveThreshold[i - rollingWidth] + sd.PixelsAboveThreshold[i];
sd.RollingCounts[i - rollingWidth + 1] = rc_sum;
if (rc_sum > rc_max)
{
rc_max = rc_sum;
rc_maxIndex = i - rollingWidth + 1;
}
}
sd.RollingCountMaxStartIndex = rc_maxIndex;
sd.RollingCountMinValue = sd.DataByCount.Min();
sd.RollingCountMaxValue = sd.DataByCount.Max();
return(sd);
}
static int Main(string[] args)
{
var lcArgs = args.Select(arg => arg.ToLower());
if (args.Length == 0 || lcArgs.Any(arg => arg == "/?" || arg == "help"))
{
Console.WriteLine($"Usage: dotnet {Assembly.GetEntryAssembly().GetName().Name} commands DICOM.file");
Console.WriteLine("Valid commands are: PixelData SliceData Rolling TVEBySum TVEByCount HistoBySum HistoByCount HistoLogBySum HistoLogByCount");
Console.WriteLine("Call with --version to get version info");
return(0);
}
if (lcArgs.Any(arg => arg == "--version"))
{
Console.WriteLine(Assembly.GetEntryAssembly().GetName().Version);
return(0);
}
// Check if last arg is a valid file.
var path = Path.GetFullPath(args.LastOrDefault() ?? @"\");
FileInfo fileInfo = new FileInfo(path);
if (!fileInfo.Exists)
{
Console.WriteLine("No valid path supplied. Aborting.");
return(1);
}
// Read and parse the DICOM file.
var raw = RawData.FromDicom(fileInfo.FullName);
if (raw == null)
{
Console.WriteLine("Failed to parse DICOM file. Aborting.");
return(1);
}
// Output raw pixel data?
if (lcArgs.Any(arg => arg == "pixeldata"))
{
Console.WriteLine(raw.DumpPixelData());
}
var sd = SliceData.Calculate(raw);
// Output slice data?
if (lcArgs.Any(arg => arg == "slicedata"))
{
Console.WriteLine(sd.Dump());
}
// Output rolling data?
if (lcArgs.Any(arg => arg == "rolling"))
{
Console.WriteLine(sd.DumpRolling());
}
// Calculate and output TVE by sums?
if (lcArgs.Any(arg => arg == "tvebysum"))
{
var tveSum = TVEResults.Calculate(sd);
Console.WriteLine(tveSum.Dump());
}
// Calculate and output TVE by counts?
if (lcArgs.Any(arg => arg == "tvebycount"))
{
var tveCount = TVEResults.Calculate(sd, mode: CalcMode.ByCount);
Console.WriteLine(tveCount.Dump());
}
// Calculate and output histogram data?
if (lcArgs.Any(arg => arg == "histobysum"))
{
var histo = Histogram.Calculate(sd, CalcMode.BySum, HistoMode.Normal);
Console.WriteLine(histo.Dump());
}
if (lcArgs.Any(arg => arg == "histobycount"))
{
var histo = Histogram.Calculate(sd, CalcMode.ByCount, HistoMode.Normal);
Console.WriteLine(histo.Dump());
}
if (lcArgs.Any(arg => arg == "histologbysum"))
{
var histo = Histogram.Calculate(sd, CalcMode.BySum, HistoMode.Log10);
Console.WriteLine(histo.Dump());
}
if (lcArgs.Any(arg => arg == "histologbycount"))
{
var histo = Histogram.Calculate(sd, CalcMode.ByCount, HistoMode.Log10);
Console.WriteLine(histo.Dump());
}
#if DEBUG
Console.ReadKey();
#endif
return(0);
}
