public bool GetIndicatorList(int experimentID)
{
bool success = true;
ObservableCollection <ExperimentIndicatorContainer> indicators;
if (m_db.GetAllExperimentIndicatorsForExperiment(experimentID, out indicators))
{
m_vm.indicators = indicators;
}
else
{
success = false;
}
return(success);
}
private void CreateReportPB_Click(object sender, RoutedEventArgs e)
{
ObservableCollection <ExperimentIndicatorContainer> expIndicatorList;
bool success = m_wgDB.GetAllExperimentIndicatorsForExperiment(VM.CurrentExperiment.ExperimentID, out expIndicatorList);
if (success)
{
ProjectContainer project;
success = m_wgDB.GetProject(VM.CurrentProject.ProjectID, out project);
if (success && project != null)
{
ExperimentContainer experiment;
success = m_wgDB.GetExperiment(VM.CurrentExperiment.ExperimentID, out experiment);
if (success && experiment != null)
{
ReportDialog dlg = new ReportDialog(project, experiment, expIndicatorList);
dlg.ShowDialog();
}
}
}
}
public bool WriteExperimentFile_WaveGuide(string filename, List <AnalysisContainer> analysisList)
{
bool success = true;
if (File.Exists(filename))
{
MessageBoxResult result = MessageBox.Show("File: " + filename + " already exists! Do you want to over write it?", "File Already Exists",
MessageBoxButton.YesNo, MessageBoxImage.Exclamation);
switch (result)
{
case MessageBoxResult.Yes:
File.Delete(filename);
break;
case MessageBoxResult.No:
success = false;
m_lastErrorString = "File already exists";
break;
}
}
if (success)
{
try
{
string delimiter = "\t"; // \t = tab
FileStream fs = new FileStream(filename, FileMode.CreateNew, FileAccess.Write);
using (StreamWriter sw = new StreamWriter(fs))
{
// Start writing HEADER
sw.WriteLine("<HEADER>");
DateTime dt = m_experiment.TimeStamp;
sw.WriteLine("Date" + delimiter + dt.Year.ToString() + "-" + dt.Month.ToString() + "-" + dt.Day.ToString());
sw.WriteLine("Time" + delimiter + dt.Hour.ToString() + ":" + dt.Minute.ToString() + ":" + dt.Second.ToString());
sw.WriteLine("Instrument" + delimiter + "Panoptic");
sw.WriteLine("ProtocolName" + delimiter + m_method.Description);
sw.WriteLine("AssayPlateBarcode" + delimiter + m_plate.Barcode);
success = m_wgDB.GetAllExperimentCompoundPlatesForExperiment(m_experiment.ExperimentID);
if (success)
{
foreach (ExperimentCompoundPlateContainer ecPlate in m_wgDB.m_experimentCompoundPlateList)
{
sw.WriteLine("AddPlateBarcode" + delimiter + ecPlate.Barcode);
}
}
ObservableCollection <ExperimentIndicatorContainer> expIndicatorList = new ObservableCollection <ExperimentIndicatorContainer>();
foreach (AnalysisContainer ac in analysisList)
{
ExperimentIndicatorContainer expIndicator;
success = m_wgDB.GetExperimentIndicator(ac.ExperimentIndicatorID, out expIndicator);
if (success && expIndicator != null)
{
// make sure this experiment indicator isn't already in the list
bool alreadyInList = false;
foreach (ExperimentIndicatorContainer expCont in expIndicatorList)
{
if (expIndicator.ExperimentIndicatorID == expCont.ExperimentIndicatorID)
{
alreadyInList = true;
break;
}
}
if (!alreadyInList)
{
sw.WriteLine("Indicator" + delimiter +
expIndicator.Description + delimiter +
expIndicator.ExcitationFilterDesc + delimiter +
expIndicator.EmissionFilterDesc + delimiter +
expIndicator.Exposure.ToString() + delimiter +
expIndicator.Gain.ToString());
expIndicatorList.Add(expIndicator);
}
}
}
success = m_wgDB.GetAllExperimentIndicatorsForExperiment(m_experiment.ExperimentID, out expIndicatorList);
if (success)
{
foreach (ExperimentIndicatorContainer expIndicator in expIndicatorList)
{
}
}
sw.WriteLine("NumRows" + delimiter + m_plateType.Rows.ToString());
sw.WriteLine("NumCols" + delimiter + m_plateType.Cols.ToString());
List <EventMarkerContainer> eventMarkerList;
success = m_wgDB.GetAllEventMarkersForExperiment(m_experiment.ExperimentID, out eventMarkerList);
if (success)
{
foreach (EventMarkerContainer eventMarker in eventMarkerList)
{
string timeString = String.Format("{0:0.000}", (float)eventMarker.SequenceNumber / 1000);
sw.WriteLine("Event" + delimiter + eventMarker.Name + delimiter +
eventMarker.Description + delimiter +
timeString);
}
}
sw.WriteLine("Operator" + delimiter + m_user.Username + delimiter +
m_user.Lastname + delimiter +
m_user.Firstname);
sw.WriteLine("Project" + delimiter + m_project.Description);
sw.WriteLine("</HEADER>");
// END writing HEADER
if (success)
{
foreach (AnalysisContainer analysis in analysisList)
{
ExperimentIndicatorContainer expIndicator;
success = m_wgDB.GetExperimentIndicator(analysis.ExperimentIndicatorID, out expIndicator);
sw.WriteLine("<INDICATOR_DATA" + delimiter + expIndicator.Description + delimiter + ">");
// START write column headers
sw.Write("Time" + delimiter);
StringBuilder builder = new StringBuilder();
for (int r = 0; r < m_plateType.Rows; r++)
{
for (int c = 0; c < m_plateType.Cols; c++)
{
builder.Append((char)(65 + r)).Append(c + 1).Append(delimiter);
}
}
builder.Remove(builder.Length - delimiter.Length, delimiter.Length); // remove last delimiter
sw.WriteLine(builder.ToString());
// END write column headers
// START writing data frames
success = m_wgDB.GetAllAnalysisFramesForAnalysis(analysis.AnalysisID);
if (success)
{
foreach (AnalysisFrameContainer aFrame in m_wgDB.m_analysisFrameList)
{
string timeString = String.Format("{0:0.000}", (float)aFrame.SequenceNumber / 1000);
sw.Write(timeString + delimiter);
string[] values = aFrame.ValueString.Split(',');
foreach (string val in values)
{
sw.Write(val + delimiter);
}
sw.WriteLine("");
}
}
// END writing data frames
sw.WriteLine("</INDICATOR_DATA>");
}
}
}
if (!success)
{
m_lastErrorString = m_wgDB.GetLastErrorMsg();
}
} // end try
catch (Exception e)
{
success = false;
m_lastErrorString = e.Message;
}
}
return(success);
} // end function
void LoadSimulationConfiguration()
{
// m_iParams = iParams;
// m_project = project;
// m_experimentPlate = plate;
// m_method = method;
// m_mask = mask;
// m_plateType = plateType;
// m_indicatorList = indicatorList;
// m_compoundPlateList = compoundPlateList;
// m_controlSubtractionWellList = controlSubtractionWellList;
//m_numFoFrames = numFoFrames;
//m_dynamicRatioNumerator = dynamicRatioNumerator;
//m_dynamicRatioDenominator = dynamicRatioDenominator;
//ChartArray.BuildChartArray(mask.Rows, mask.Cols, m_indicatorList);
////////////////////////
// set up project
m_project = null;
bool success = m_wgDB.GetAllProjects(false);
foreach (ProjectContainer project in m_wgDB.m_projectList)
{
if (project.Description.Equals("Debug", StringComparison.OrdinalIgnoreCase))
{
m_project = project;
break;
}
}
if (m_project == null) // not found in database, so create it
{
m_project = new ProjectContainer();
m_project.Description = "Debug";
m_project.TimeStamp = DateTime.Now;
m_project.Archived = false;
success = m_wgDB.InsertProject(ref m_project);
}
////////////////////////
// set up plateType
m_plateType = null;
success = m_wgDB.GetAllPlateTypes();
if (m_wgDB.m_plateTypeList.Count() > 0)
{
m_plateType = m_wgDB.m_plateTypeList.ElementAt(0);
}
else
{
// create a new plateType
m_plateType = new PlateTypeContainer();
m_plateType.Cols = 24;
m_plateType.Description = "Debug";
m_plateType.IsDefault = false;
m_plateType.Rows = 16;
success = m_wgDB.InsertPlateType(ref m_plateType);
}
////////////////////////
// set up experiment plate
m_experimentPlate = null;
success = m_wgDB.GetAllPlatesForProject(m_project.ProjectID);
if (m_wgDB.m_plateList.Count() > 0)
{
m_experimentPlate = m_wgDB.m_plateList.ElementAt(0);
}
else
{
// create a new plate
m_experimentPlate = new PlateContainer();
m_experimentPlate.Barcode = "12345678";
m_experimentPlate.Description = "Debug";
m_experimentPlate.IsPublic = true;
m_experimentPlate.OwnerID = GlobalVars.UserID;
m_experimentPlate.PlateTypeID = m_plateType.PlateTypeID;
m_experimentPlate.ProjectID = m_project.ProjectID;
success = m_wgDB.InsertPlate(ref m_experimentPlate);
}
////////////////////////
// set up method
m_method = null;
success = m_wgDB.GetAllMethodsForUser(GlobalVars.UserID);
foreach (MethodContainer method in m_wgDB.m_methodList)
{
if (method.Description.Equals("Debug", StringComparison.OrdinalIgnoreCase))
{
m_method = method;
break;
}
}
if (m_method == null)
{
m_method = new MethodContainer();
m_method.BravoMethodFile = "";
m_method.Description = "Debug";
m_method.IsPublic = true;
m_method.OwnerID = GlobalVars.UserID;
success = m_wgDB.InsertMethod(ref m_method);
}
success = m_wgDB.GetAllIndicatorsForMethod(m_method.MethodID);
if (m_wgDB.m_indicatorList.Count < 1)
{
// create indicators for this new method
IndicatorContainer ind = new IndicatorContainer();
ind.Description = "Debug";
ind.EmissionsFilterPosition = 6;
ind.ExcitationFilterPosition = 4;
ind.MethodID = m_method.MethodID;
ind.SignalType = SIGNAL_TYPE.UP;
success = m_wgDB.InsertIndicator(ref ind);
}
////////////////////////
// set up experiment
m_experiment = null;
ObservableCollection <ExperimentContainer> expList;
success = m_wgDB.GetAllExperimentsForPlate(m_experimentPlate.PlateID, out expList);
if (expList.Count() > 0)
{
m_experiment = expList.ElementAt(0);
}
else
{
m_experiment = new ExperimentContainer();
m_experiment.Description = "Debug";
m_experiment.HorzBinning = 1;
m_experiment.MethodID = m_method.MethodID;
m_experiment.PlateID = m_experimentPlate.PlateID;
m_experiment.ROI_Height = GlobalVars.PixelHeight;
m_experiment.ROI_Width = GlobalVars.PixelWidth;
m_experiment.ROI_Origin_X = 1;
m_experiment.ROI_Origin_Y = 1;
m_experiment.TimeStamp = DateTime.Now;
m_experiment.VertBinning = 1;
success = m_wgDB.InsertExperiment(ref m_experiment);
}
////////////////////////
// set up mask
m_mask = null;
success = m_wgDB.GetAllMasksForPlateType(m_experimentPlate.PlateTypeID);
if (m_wgDB.m_maskList.Count() > 0)
{
m_mask = m_wgDB.m_maskList.ElementAt(0);
}
else
{
// create a new mask
m_mask = new MaskContainer();
m_mask.Angle = 0.0;
m_mask.Cols = 24;
m_mask.Description = "Debug";
m_mask.IsDefault = false;
m_mask.NumEllipseVertices = 24;
m_mask.PlateTypeID = m_experimentPlate.PlateTypeID;
m_mask.ReferenceImageID = 0;
m_mask.Rows = 16;
m_mask.Shape = 0;
m_mask.XOffset = 28;
m_mask.XSize = 28;
m_mask.XStep = 41.522;
m_mask.YOffset = 190;
m_mask.YSize = 28;
m_mask.YStep = 41.467;
success = m_wgDB.InsertMask(ref m_mask);
}
////////////////////////////////////
// setup test indicator(s)
m_indicatorList = new ObservableCollection <ExperimentIndicatorContainer>();
ObservableCollection <ExperimentIndicatorContainer> expIndList;
success = m_wgDB.GetAllExperimentIndicatorsForExperiment(m_experiment.ExperimentID, out expIndList);
if (expIndList.Count > 0)
{
foreach (ExperimentIndicatorContainer ex in expIndList)
{
m_indicatorList.Add(ex);
}
}
else
{
success = m_wgDB.GetAllIndicatorsForMethod(m_method.MethodID);
foreach (IndicatorContainer ind in m_wgDB.m_indicatorList)
{
ExperimentIndicatorContainer exInd = new ExperimentIndicatorContainer();
exInd.Description = ind.Description;
FilterContainer filter;
success = m_wgDB.GetExcitationFilterAtPosition(ind.ExcitationFilterPosition, out filter);
exInd.ExcitationFilterDesc = filter.Description;
success = m_wgDB.GetEmissionFilterAtPosition(ind.EmissionsFilterPosition, out filter);
exInd.EmissionFilterDesc = filter.Description;
exInd.EmissionFilterPos = ind.EmissionsFilterPosition;
exInd.ExcitationFilterPos = ind.ExcitationFilterPosition;
exInd.ExperimentID = m_experiment.ExperimentID;
exInd.Exposure = 150;
exInd.Gain = 5;
exInd.MaskID = m_mask.MaskID;
exInd.SignalType = SIGNAL_TYPE.UP;
exInd.Verified = true;
success = m_wgDB.InsertExperimentIndicator(ref exInd);
m_indicatorList.Add(exInd);
}
}
////////////////////////////////////
// compound plates
m_compoundPlateList = new ObservableCollection <ExperimentCompoundPlateContainer>();
////////////////////////////////////
// control subtraction well list
m_controlSubtractionWellList = new ObservableCollection <Tuple <int, int> >();
// all wells in last row = control wells
for (int c = 0; c < m_mask.Cols; c++)
{
m_controlSubtractionWellList.Add(Tuple.Create(m_mask.Rows - 1, c));
}
////////////////////////////////////
//m_numFoFrames = numFoFrames;
m_numFoFrames = 5;
if (m_indicatorList.Count() > 1)
{
////////////////////////////////////
//m_dynamicRatioNumerator = dynamicRatioNumerator;
m_dynamicRatioNumerator = m_indicatorList.ElementAt(0);
////////////////////////////////////
//m_dynamicRatioDenominator = dynamicRatioDenominator;
m_dynamicRatioDenominator = m_indicatorList.ElementAt(1);
}
else
{
m_dynamicRatioNumerator = new ExperimentIndicatorContainer();
m_dynamicRatioNumerator.ExperimentIndicatorID = 0;
m_dynamicRatioDenominator = new ExperimentIndicatorContainer();
m_dynamicRatioDenominator.ExperimentIndicatorID = 0;
}
if (m_iParams == null)
{
m_iParams = new ImagingParameters();
}
m_iParams.maxPixelValue = GlobalVars.MaxPixelValue;
m_iParams.imageWidth = GlobalVars.PixelWidth;
m_iParams.imageHeight = GlobalVars.PixelHeight;
m_iParams.Image_StartCol = 1;
m_iParams.Image_EndCol = GlobalVars.PixelWidth;
m_iParams.Image_StartRow = 1;
m_iParams.Image_EndRow = GlobalVars.PixelHeight;
m_iParams.BravoMethodFilename = "";
m_iParams.CameraTemperature = GlobalVars.CameraTargetTemperature;
m_iParams.HorzBinning = 1;
m_iParams.VertBinning = 1;
m_iParams.EmissionFilterChangeSpeed = GlobalVars.FilterChangeSpeed;
m_iParams.ExcitationFilterChangeSpeed = GlobalVars.FilterChangeSpeed;
m_iParams.LightIntensity = 100;
m_iParams.NumImages = 1000000; // artificial limit on number of images
m_iParams.NumIndicators = m_indicatorList.Count;
m_iParams.SyncExcitationFilterWithImaging = true;
m_iParams.CycleTime = new int[m_indicatorList.Count];
m_iParams.EmissionFilter = new byte[m_indicatorList.Count];
m_iParams.ExcitationFilter = new byte[m_indicatorList.Count];
m_iParams.Exposure = new float[m_indicatorList.Count];
m_iParams.Gain = new int[m_indicatorList.Count];
m_iParams.ExperimentIndicatorID = new int[m_indicatorList.Count];
m_iParams.IndicatorName = new string[m_indicatorList.Count];
m_iParams.LampShutterIsOpen = new bool[m_indicatorList.Count];
int i = 0;
foreach (ExperimentIndicatorContainer ind in m_indicatorList)
{
m_iParams.CycleTime[i] = 1000;
m_iParams.EmissionFilter[i] = (byte)ind.EmissionFilterPos;
m_iParams.ExcitationFilter[i] = (byte)ind.ExcitationFilterPos;
m_iParams.Exposure[i] = (float)ind.Exposure / 1000;
m_iParams.Gain[i] = ind.Gain;
m_iParams.ExperimentIndicatorID[i] = 0; // created by the RunExperiment object when the experiment is run
m_iParams.IndicatorName[i] = ind.Description;
m_iParams.LampShutterIsOpen[i] = true;
m_iParams.ExperimentIndicatorID[i] = ind.ExperimentIndicatorID;
i++;
}
}
public bool GetIndicatorList(int experimentID)
{
#if (SIMULATE)
m_vm.indicators.Clear();
ExperimentIndicatorContainer indicator = new ExperimentIndicatorContainer();
indicator.CycleTime = 100;
indicator.DarkFieldRefImageID = 1;
indicator.Description = "indicator 1";
indicator.EmissionFilterDesc = "filter 1";
indicator.EmissionFilterPos = 1;
indicator.ExcitationFilterDesc = "filter 2";
indicator.ExcitationFilterPos = 2;
indicator.ExperimentID = 1;
indicator.ExperimentIndicatorID = 1;
indicator.Exposure = 50;
indicator.FlatFieldCorrection = FLATFIELD_SELECT.NONE;
indicator.FlatFieldRefImageID = 1;
indicator.Gain = 10;
indicator.MaskID = 1;
indicator.OptimizeWellList = null;
indicator.PreAmpGain = 1;
indicator.SignalType = SIGNAL_TYPE.UP;
indicator.Verified = true;
m_vm.indicators.Add(indicator);
indicator = new ExperimentIndicatorContainer();
indicator.CycleTime = 100;
indicator.DarkFieldRefImageID = 1;
indicator.Description = "indicator 2";
indicator.EmissionFilterDesc = "filter 1";
indicator.EmissionFilterPos = 1;
indicator.ExcitationFilterDesc = "filter 2";
indicator.ExcitationFilterPos = 2;
indicator.ExperimentID = 2;
indicator.ExperimentIndicatorID = 2;
indicator.Exposure = 50;
indicator.FlatFieldCorrection = FLATFIELD_SELECT.NONE;
indicator.FlatFieldRefImageID = 1;
indicator.Gain = 10;
indicator.MaskID = 1;
indicator.OptimizeWellList = null;
indicator.PreAmpGain = 1;
indicator.SignalType = SIGNAL_TYPE.UP;
indicator.Verified = true;
m_vm.indicators.Add(indicator);
return(true);
#else
bool success = true;
ObservableCollection <ExperimentIndicatorContainer> indicators;
if (m_db.GetAllExperimentIndicatorsForExperiment(experimentID, out indicators))
{
m_vm.indicators = indicators;
}
else
{
success = false;
}
return(success);
#endif
}