private void AddCommonInfo2RunResult(RunResult runResult)
{
runResult.buffySlice = pipettingSetting.dstbuffySlice;//ResultReader.Instance.HasBuffyCoat() ? 1 : 0;
runResult.buffyVolume = pipettingSetting.buffyVolume;
runResult.plasmaVolume = pipettingSetting.plasmaGreedyVolume;
runResult.plasmaTotalSlice = pipettingSetting.dstPlasmaSlice;
}
private void AddEachSampleInfo2RunResult(int srcRackIndex, int startSampleIndex,List<DetectedHeight> heightsThisTime, RunResult runResult)
{
double r = pipettingSetting.r_mm;
double area = 3.14159265 * r * r;
for (int i = 0; i < heightsThisTime.Count; i++)
{
double z1 = heightsThisTime[i].Z1;
double z2 = heightsThisTime[i].Z2;
double totalPlasmaVolume = (z1 - z2 - pipettingSetting.safeDelta) * area;
int plasmaSlice = pipettingSetting.dstPlasmaSlice;
if (pipettingSetting.plasmaGreedyVolume != 0)
{
int maxPlasmaSlice = (int)Math.Ceiling(totalPlasmaVolume / pipettingSetting.plasmaGreedyVolume);
plasmaSlice = Math.Min(plasmaSlice, maxPlasmaSlice);
}
int startSampleID = srcRackIndex * labwareSettings.sourceWells + i + startSampleIndex + 1;
runResult.plasmaRealSlices.Add(plasmaSlice);
//sw.WriteLine(string.Format("{0};{1};{2};{3}{4}", startSampleID, plasmaSlice, pipettingSetting.dstPlasmaSlice, buffySlice, pipettingSetting));
}
}
private void SaveRunResult(RunResult runResult)
{
string sRunResultPath = Utility.GetOutputFolder() + "runResult.xml";
if (File.Exists(sRunResultPath))
File.Delete(sRunResultPath);
string sContent = Utility.Serialize(runResult) ;
File.WriteAllText(sRunResultPath, sContent);
}
public bool DoJob()
{
SettingsHelper settingHelper = new SettingsHelper();
log.Info("load settings");
settingHelper.LoadSettings(ref pipettingSetting, ref labwareSettings);
heights = ResultReader.Instance.Read();
log.Info("read heights");
//PreparePlasmaDestPositions();
positionGenerator = new PositionGenerator(pipettingSetting, labwareSettings,heights.Count);
string errMsg = "";
bool bok = settingHelper.IsValidSetting(labwareSettings,pipettingSetting,ref errMsg);
if (!bok)
{
throw new Exception("Invalid setting:" + errMsg);
}
int maxSampleAllowed = positionGenerator.AllowedSamples();
if (maxSampleAllowed < heights.Count)
throw new Exception(string.Format("max allowed sample is: {0}",maxSampleAllowed));
string sOutput = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location) + "\\output\\";
//create folders
if (!Directory.Exists(sOutput))
Directory.CreateDirectory(sOutput);
RunResult runResult = new RunResult();
int sourceRackCount = (int)Math.Ceiling((double)heights.Count / labwareSettings.sourceWells);
WriteRacksCount(sourceRackCount);
string sOrgOutPut = sOutput;
for (int srcRack = 0; srcRack < sourceRackCount; srcRack++)
{
sOutput = sOrgOutPut + "\\srcRack" + (srcRack + 1).ToString() + "\\";
if (!Directory.Exists(sOutput))
Directory.CreateDirectory(sOutput);
int thisRackSamples = srcRack == sourceRackCount - 1 ? (heights.Count - srcRack * labwareSettings.sourceWells) : labwareSettings.sourceWells;
Utility.Write2File(sOutput + "totalSample.txt", thisRackSamples.ToString());
int batchNum = (int)Math.Ceiling((double)thisRackSamples / labwareSettings.tipCount);
Utility.Write2File(sOutput + "batchCount.txt", batchNum.ToString());
for (int startSample = 0; startSample < thisRackSamples; startSample += labwareSettings.tipCount)
{
List<DetectedHeight> heightsThisTime = new List<DetectedHeight>();
for (int tip = 0; tip < labwareSettings.tipCount; tip++)
{
if (tip + startSample >= thisRackSamples)
break;
heightsThisTime.Add(heights[srcRack*labwareSettings.sourceWells+ startSample + tip]);
}
GenerateForBatch(sOutput,srcRack, startSample, heightsThisTime);
AddEachSampleInfo2RunResult(srcRack, startSample,heightsThisTime, runResult);
}
}
AddCommonInfo2RunResult(runResult);
SaveRunResult(runResult);
//runResultSw.Close();
return true;
}
public bool DoJob()
{
detectInfos = ResultReader.Instance.Read();
patientInfos = ResultReader.Instance.ReadPatientInfos();
if (patientInfos != null)
{
patientInfos = patientInfos.Take(detectInfos.Count).ToList();
Console.WriteLine(string.Format("{0} samples", patientInfos.Count));
}
if (GlobalVars.Instance.TrackBarcode)
{
barcodeTracker = new BarcodeTracker(pipettingSettings, labwareSettings, patientInfos);
}
log.Info("read heights");
mappingCalculator = new MappingCalculator(Settings.Utility.GetExeFolder() + Settings.stringRes.calibFileName);
//PreparePlasmaDestPositions();
positionGenerator = new PositionGenerator(pipettingSettings, labwareSettings, detectInfos.Count);
int maxSampleAllowed = positionGenerator.AllowedSamples();
if (maxSampleAllowed < detectInfos.Count)
{
throw new Exception(string.Format("max allowed sample is: {0}", maxSampleAllowed));
}
string sOutput = Utility.GetOutputFolder();
int sourceRackCount = (int)Math.Ceiling((double)detectInfos.Count / labwareSettings.sourceWells);
WriteRacksCount(sourceRackCount);
string sOrgOutPut = sOutput;
RunResult runResult = new RunResult();
for (int srcRack = 0; srcRack < sourceRackCount; srcRack++)
{
sOutput = sOrgOutPut + "\\srcRack" + (srcRack + 1).ToString() + "\\";
if (!Directory.Exists(sOutput))
{
Directory.CreateDirectory(sOutput);
}
int thisRackSamples = srcRack == sourceRackCount - 1 ? (detectInfos.Count - srcRack * labwareSettings.sourceWells) : labwareSettings.sourceWells;
Utility.Write2File(sOutput + "totalSample.txt", thisRackSamples.ToString());
int batchNum = (int)Math.Ceiling((double)thisRackSamples / labwareSettings.tipCount);
Utility.Write2File(sOutput + "batchCount.txt", batchNum.ToString());
for (int startSample = 0; startSample < thisRackSamples; startSample += labwareSettings.tipCount)
{
List <DetectedInfo> heightsThisTime = new List <DetectedInfo>();
for (int tip = 0; tip < labwareSettings.tipCount; tip++)
{
if (tip + startSample >= thisRackSamples)
{
break;
}
heightsThisTime.Add(detectInfos[srcRack * labwareSettings.sourceWells + startSample + tip]);
}
GenerateForBatch(sOutput, srcRack, startSample, heightsThisTime);
AddEachSampleInfo2RunResult(srcRack, startSample, heightsThisTime, runResult);
}
}
if (GlobalVars.Instance.TrackBarcode)
{
barcodeTracker.WriteResult();
}
AddCommonInfo2RunResult(runResult);
SaveRunResult(runResult);
Thread.Sleep(1000);
return(true);
}
private void AddEachSampleInfo2RunResult(int srcRackIndex, int startSampleIndex, List <DetectedInfo> heightsThisTime, RunResult runResult)
{
double area = mappingCalculator.GetArea();
for (int i = 0; i < heightsThisTime.Count; i++)
{
double z1 = heightsThisTime[i].Z1;
double z2 = heightsThisTime[i].Z2;
double totalPlasmaVolume = mappingCalculator.GetVolumeFromHeight(z1) -
mappingCalculator.GetVolumeFromHeight(z2) - pipettingSettings.safeDelta * area;
int plasmaSlice = pipettingSettings.dstPlasmaSlice;
if (pipettingSettings.plasmaGreedyVolume != 0)
{
int maxPlasmaSlice = (int)Math.Ceiling(totalPlasmaVolume / pipettingSettings.plasmaGreedyVolume);
plasmaSlice = Math.Min(plasmaSlice, maxPlasmaSlice);
}
int startSampleID = srcRackIndex * labwareSettings.sourceWells + i + startSampleIndex + 1;
runResult.plasmaRealSlices.Add(plasmaSlice);
//sw.WriteLine(string.Format("{0};{1};{2};{3}{4}", startSampleID, plasmaSlice, pipettingSetting.dstPlasmaSlice, buffySlice, pipettingSetting));
}
}
public bool DoJob()
{
detectInfos = ResultReader.Instance.Read();
patientInfos = ResultReader.Instance.ReadPatientInfos();
if(GlobalVars.Instance.TrackBarcode)
barcodeTracker = new BarcodeTracker(pipettingSetting, labwareSettings, patientInfos);
log.Info("read heights");
mappingCalculator = new MappingCalculator(Settings.Utility.GetExeFolder() + Settings.stringRes.calibFileName);
//PreparePlasmaDestPositions();
positionGenerator = new PositionGenerator(pipettingSetting, labwareSettings,detectInfos.Count);
int maxSampleAllowed = positionGenerator.AllowedSamples();
if (maxSampleAllowed < detectInfos.Count)
throw new Exception(string.Format("max allowed sample is: {0}",maxSampleAllowed));
string sOutput = Utility.GetOutputFolder();
int sourceRackCount = (int)Math.Ceiling((double)detectInfos.Count / labwareSettings.sourceWells);
WriteRacksCount(sourceRackCount);
string sOrgOutPut = sOutput;
RunResult runResult = new RunResult();
for (int srcRack = 0; srcRack < sourceRackCount; srcRack++)
{
sOutput = sOrgOutPut + "\\srcRack" + (srcRack + 1).ToString() + "\\";
if (!Directory.Exists(sOutput))
Directory.CreateDirectory(sOutput);
int thisRackSamples = srcRack == sourceRackCount - 1 ? (detectInfos.Count - srcRack * labwareSettings.sourceWells) : labwareSettings.sourceWells;
Utility.Write2File(sOutput + "totalSample.txt", thisRackSamples.ToString());
int batchNum = (int)Math.Ceiling((double)thisRackSamples / labwareSettings.tipCount);
Utility.Write2File(sOutput + "batchCount.txt", batchNum.ToString());
for (int startSample = 0; startSample < thisRackSamples; startSample += labwareSettings.tipCount)
{
List<DetectedInfo> heightsThisTime = new List<DetectedInfo>();
for (int tip = 0; tip < labwareSettings.tipCount; tip++)
{
if (tip + startSample >= thisRackSamples)
break;
heightsThisTime.Add(detectInfos[srcRack*labwareSettings.sourceWells+ startSample + tip]);
}
GenerateForBatch(sOutput,srcRack, startSample, heightsThisTime);
AddEachSampleInfo2RunResult(srcRack, startSample, heightsThisTime, runResult);
}
}
if(GlobalVars.Instance.TrackBarcode)
barcodeTracker.WriteResult();
AddCommonInfo2RunResult(runResult);
SaveRunResult(runResult);
return true;
}
