public void CalculateBackground(Tiff scanTiff, int projectId, int runId)
{
int[] colsForBackground = new int[] { 1, TiffImages.columnPerScan };
IEnumerable <int>[] colsForBackgroundMolFrames = new IEnumerable <int> [colsForBackground.Length];
HashSet <short> framesForBackgroundCalc = new HashSet <short>();
for (int colPos = 0; colPos < colsForBackground.Length; colPos++)
{
colsForBackgroundMolFrames[colPos] = DatabaseManager.SelectColumnRows(projectId, runId, 1, colsForBackground[colPos]);
for (int row = 1; row <= TiffImages.rowsPerColumn; row++)
{
if (!colsForBackgroundMolFrames[colPos].Contains(row))
{
framesForBackgroundCalc.Add(TiffImages.GetFrameNumber(colsForBackground[colPos], row, this.Channel));
}
}
}
this.CalculateAveragePixelValues(scanTiff, framesForBackgroundCalc);
this.CalculateBackgroundStd();
}
private void button1_Click(object sender, EventArgs e)
{
Stopwatch stopWatch = new Stopwatch();
string[] runRootDirs = runs_paths_txtbx2.Text.Split('\n');
if (String.IsNullOrEmpty(runRootDirs[0]))
{
MessageBox.Show("Must provide path to root directory of run files", "Missing file path");
return;
}
stopWatch.Start();
Task newTask = Task.Factory.StartNew(() =>
{
Dictionary <int, Scan[]> selectedMolecules = DatabaseManager.SelectMoleculesForPixelData(projectID, alignmentFilter, lengthFilter, confidenceFilter, alignedLenPercentFilter, molIdsFilterArray, chromIdsFilter,
chromStartEndFilter);
TiffImages.ProcessAllRuns(projectID, runRootDirs, selectedMolecules, updateBox);
});
newTask.ContinueWith(_ => MessageBox.Show(stopWatch.Elapsed.ToString()));
}
private void CalculateAveragePixelValues(Tiff scanTiff, IEnumerable <short> noMoleculeFrames)
{
short[][] framePixels;
foreach (short frame in noMoleculeFrames)
{
framePixels = TiffImages.FramePixelsAsShortArray(scanTiff, frame);
for (int row = 0; row < this.ImageLength; row++)
{
for (int col = 0; col < this.ImageWidth; col++)
{
this.PixelValues[row][col] += framePixels[row][col];
}
}
}
for (int row = 0; row < this.ImageLength; row++)
{
for (int col = 0; col < this.ImageWidth; col++)
{
this.PixelValues[row][col] /= noMoleculeFrames.Count();
this.AverageValue += this.PixelValues[row][col];
}
}
this.AverageValue /= (ImageLength * ImageWidth);
}
