private static void ProcessRunTiffs(int projectId, string[] runsDirectoryPaths, int runId, Scan[] runMoleculesByScanByCol, UpdateBox updateBox)
{
BackgroundFOV[] allChannelsBackgroundFOVs;
string[] runNameMonth = DatabaseManager.GetRunNameMonth(runId);
int rootDirIdx = UserInputParser.GetRunRootDir(runsDirectoryPaths, runNameMonth[1], runNameMonth[0]);
if (rootDirIdx >= 0)
{
string runDir = Path.Combine(runsDirectoryPaths[rootDirIdx], runNameMonth[1], runNameMonth[0]);
string backgroundTiffPath = Path.Combine(runDir, runNameMonth[0] + "_Scan001.tiff");
using (Tiff backgroundTiff = Tiff.Open(backgroundTiffPath, "r"))
{
FieldValue[] width = backgroundTiff.GetField(TiffTag.IMAGEWIDTH);
FieldValue[] height = backgroundTiff.GetField(TiffTag.IMAGELENGTH);
imageLength = height[0].ToInt();
imageWidth = width[0].ToInt();
scanlineSize = backgroundTiff.ScanlineSize();
allChannelsBackgroundFOVs = GetAllChannelsBackgroundFOVs(backgroundTiff, projectId, runId);
}
Parallel.ForEach(runMoleculesByScanByCol.Where(scan => scan != null), scan =>
{
ProcessScanTiff(runDir, runNameMonth[0], scan, allChannelsBackgroundFOVs, updateBox);
});
}
}
public static void ProcessAllRuns(int projectId, string[] runsDirectoryPaths, Dictionary <int, Scan[]> selectedMolecules, UpdateBox updateBox)
{
DatabaseManager.SetConnection();
DatabaseManager.sql_con.Open();
using (DatabaseManager.sql_con)
{
foreach (KeyValuePair <int, Scan[]> moleculesByRun in selectedMolecules)
{
ProcessRunTiffs(projectId, runsDirectoryPaths, moleculesByRun.Key, moleculesByRun.Value, updateBox);
}
}
}
public static void ProcessScanTiff(string runPath, string runName, Scan scan, BackgroundFOV[] allChannelsBackgroundFOVs, UpdateBox updateBox)
{
const string scanFilesSubDir = "Detect Molecules";
const string FOVFilePrefix = "Stitch";
const string FOVFileExtension = ".fov";
string scanTiffFilePath = Path.Combine(runPath, runName + "_Scan" + scan.ScanNumber.ToString("D3") + ".tiff");
string FOVFilePath = Path.Combine(runPath, scanFilesSubDir, FOVFilePrefix + scan.ScanNumber.ToString() + FOVFileExtension);
using (Tiff scanImages = Tiff.Open(scanTiffFilePath, "r"))
{
FieldValue[] width = scanImages.GetField(TiffTag.IMAGEWIDTH);
FieldValue[] height = scanImages.GetField(TiffTag.IMAGELENGTH);
FieldValue[] bitsPerSample = scanImages.GetField(TiffTag.BITSPERSAMPLE);
FieldValue[] samplesPerPixel = scanImages.GetField(TiffTag.SAMPLESPERPIXEL);
imageLength = height[0].ToInt();
imageWidth = width[0].ToInt();
bitsPerPixel = bitsPerSample[0].ToShort();
spp = samplesPerPixel[0].ToShort();
scanlineSize = scanImages.ScanlineSize();
Dictionary <Tuple <int, int>, FOV> FOVData = ParseFOVFile(FOVFilePath);
using (var transaction = DatabaseManager.sql_con.BeginTransaction())
{
for (int currColumn = 1; currColumn <= columnPerScan; currColumn++)
{
if (scan.ColumnMolecules[currColumn - 1].Count > 0)
{
ProcessColumnImages(scanImages, currColumn, FOVData, allChannelsBackgroundFOVs, scan.ColumnMolecules[currColumn - 1]);
}
updateBox(currColumn.ToString());
}
transaction.Commit();
}
scan.ColumnMolecules = null;
}
}