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);
});
}
}
static int GenomeAlignmentFromCmd(string[] args)
{
string keyFilePath = args[0];
string rCmapFilePath = args[1];
string outputDirPath = args[2];
int projectId = int.Parse(args[3]);
float lengthFilter = float.Parse(args[4]) * 1000;
float confidenceFilter = float.Parse(args[5]);
float alignedLenPercentFilter = float.Parse(args[6]);
string queryLocation = args[7];
bool saveChannel1 = int.Parse(args[8]) == 1 ? true : false;
bool saveChannel2 = int.Parse(args[9]) == 1 ? true : false;
int readKeyChroms = CMAPParser.ReadKeyFile(keyFilePath);
Tuple <List <int>, List <Tuple <int, int, int> > > locations = UserInputParser.getLocations(queryLocation, null);
List <int> chromIdsFilter = locations.Item1;
List <Tuple <int, int, int> > chromStartEndFilter = locations.Item2;
CMAPParser.rCmapPositions = CMAPParser.ParseCmap(rCmapFilePath, 1);
List <Molecule> selectedMolecules = DatabaseManager.SelectMoleculesForGenomeAlignment(projectId, lengthFilter, confidenceFilter, alignedLenPercentFilter, null, chromIdsFilter,
chromStartEndFilter);
foreach (Molecule molecule in selectedMolecules)
{
CMAPParser.FitMoleculeToRef(molecule, saveChannel1, saveChannel2, outputDirPath);
}
return(0);
}
private void filterMolecules_Click(object sender, EventArgs e)
{
alignmentFilter = aligned_filter_ckbx.Checked ? 1 : 0;
lengthFilter = String.IsNullOrEmpty(min_len_txtbx.Text) ? 0 : float.Parse(min_len_txtbx.Text) * 1000;
confidenceFilter = String.IsNullOrEmpty(min_conf_txtbx.Text) ? 0 : float.Parse(min_conf_txtbx.Text);
alignedLenPercentFilter = String.IsNullOrEmpty(min_aligned_len_txtbx.Text) ? 0 : float.Parse(min_aligned_len_txtbx.Text);
molIdsFilterArray = null;
chromIdsFilter = null;
chromStartEndFilter = null;
if (!String.IsNullOrEmpty(mols_ids_txtbx.Text) && !String.IsNullOrEmpty(mol_ids_file_path_txtbx.Text))
{
MessageBox.Show("For molecule IDs filter either input into the text box, or upload a file, but not both", "Error parsing filter options");
return;
}
if (!String.IsNullOrEmpty(mols_ids_txtbx.Text) || !String.IsNullOrEmpty(mol_ids_file_path_txtbx.Text))
{
molIdsFilterArray = UserInputParser.getMolIds(mols_ids_txtbx.Text, mol_ids_file_path_txtbx.Text);
if (molIdsFilterArray == null)
{
MessageBox.Show("Can't open molecule IDs file", "Error parsing filter options");
return;
}
}
if (!String.IsNullOrEmpty(mol_locations_txtbx.Text) && !String.IsNullOrEmpty(mol_locations_file_path_txtbx.Text))
{
MessageBox.Show("For molecule locations filter either input into the text box, or upload a file, but not both", "Error parsing filter options");
return;
}
if (!String.IsNullOrEmpty(mol_locations_txtbx.Text) || !String.IsNullOrEmpty(mol_locations_file_path_txtbx.Text))
{
if (String.IsNullOrEmpty(key_file_path_txtbx.Text))
{
MessageBox.Show("For molecule locations filter you must supply a key file", "Error parsing filter options");
return;
}
else //file and lines are present, parse the input
{
int readKeyChroms = CMAPParser.ReadKeyFile(key_file_path_txtbx.Text); //reading the key file to translate chromosome names to IDs, becaues chromosomes are saved as IDs in DB
if (readKeyChroms == -1)
{
MessageBox.Show("Can't open specified key file", "Error opening file");
return;
}
else
{
//get the locations from user input
Tuple <List <int>, List <Tuple <int, int, int> > > locations = UserInputParser.getLocations(mol_locations_txtbx.Text, mol_locations_file_path_txtbx.Text);
chromIdsFilter = locations.Item1;
chromStartEndFilter = locations.Item2;
}
}
}
}