public void Configure(ImagingParameters iParams, ProjectContainer project, PlateContainer plate, ExperimentContainer experiment,
MethodContainer method,
MaskContainer mask, PlateTypeContainer plateType,
ObservableCollection <ExperimentIndicatorContainer> indicatorList,
ObservableCollection <ExperimentCompoundPlateContainer> compoundPlateList,
ObservableCollection <Tuple <int, int> > controlSubtractionWellList,
int numFoFrames,
ExperimentIndicatorContainer dynamicRatioNumerator,
ExperimentIndicatorContainer dynamicRatioDenominator)
{
m_iParams = iParams;
m_project = project;
m_experimentPlate = plate;
m_experiment = experiment;
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;
m_vworksProtocolFilename = m_method.BravoMethodFile;
ChartArray.BuildChartArray(mask.Rows, mask.Cols, m_iParams.HorzBinning, m_iParams.VertBinning, m_indicatorList);
Dictionary <int, ImageDisplay> idDictionary = ChartArray.GetImageDisplayDictionary();
m_displayPipeline = m_imager.CreateDisplayPipeline(m_uiTask, idDictionary);
m_storagePipeline = m_imager.CreateImageStoragePipeline(GlobalVars.CompressionAlgorithm, m_iParams.imageWidth, m_iParams.imageHeight);
int numerID = 0;
int denomID = 0;
if (m_dynamicRatioNumerator != null)
{
numerID = m_dynamicRatioNumerator.ExperimentIndicatorID;
}
if (m_dynamicRatioDenominator != null)
{
denomID = m_dynamicRatioDenominator.ExperimentIndicatorID;
}
m_analysisPipeline = m_imager.CreateAnalysisPipeline(ChartArray, m_mask, m_iParams.imageWidth,
m_iParams.imageHeight, m_iParams.HorzBinning, m_iParams.VertBinning,
m_iParams.ExperimentIndicatorID, m_controlSubtractionWellList, m_numFoFrames,
numerID, denomID);
if (m_histogram != null)
{
m_histogramPipeline = m_imager.CreateHistogramPipeline(m_uiTask, m_histogram);
}
}
public async void StartVideo(int numberOfImagesToTake)
{
if (m_imager == null)
{
return;
}
VM.StatusString = "Imaging";
if (numberOfImagesToTake == 1)
{
SnapShotPB.Content = "Cancel";
VideoPB.IsEnabled = false;
}
else
{
SnapShotPB.IsEnabled = false;
VideoPB.Content = "Cancel";
}
GainSpin.IsEnabled = false;
ExposureSpin.IsEnabled = false;
Optimize1PB.IsEnabled = false;
//ExcitationFilterCombo.IsEnabled = false;
//EmissionFilterCombo.IsEnabled = false;
m_uiTask = TaskScheduler.FromCurrentSynchronizationContext();
m_iParams = new ImagingParameters();
m_iParams.NumIndicators = 1;
m_iParams.NumImages = numberOfImagesToTake;
m_iParams.Exposure[0] = ((float)VM.Exposure) / 1000;
m_iParams.CycleTime[0] = VM.Exposure + 250;
m_iParams.ExcitationFilter[0] = (byte)VM.ExFilter.PositionNumber;
m_iParams.EmissionFilter[0] = (byte)VM.EmFilter.PositionNumber;
m_iParams.ExcitationFilterChangeSpeed = 5;
m_iParams.EmissionFilterChangeSpeed = 5;
m_iParams.Gain[0] = VM.Gain;
m_iParams.HorzBinning = VM.HorzBinning;
m_iParams.VertBinning = VM.VertBinning;
m_iParams.LampShutterIsOpen[0] = true;
m_iParams.LightIntensity = 100;
m_iParams.SyncExcitationFilterWithImaging = true;
m_iParams.Image_StartCol = VM.RoiX;
m_iParams.Image_EndCol = VM.RoiX + VM.RoiW - 1;
m_iParams.Image_StartRow = VM.RoiY;
m_iParams.Image_EndRow = VM.RoiY + VM.RoiH - 1;
m_iParams.imageWidth = VM.RoiW;
m_iParams.imageHeight = VM.RoiH;
m_iParams.maxPixelValue = (2 ^ m_imager.m_camera.BitDepth) - 1;
m_iParams.ExperimentIndicatorID[0] = 0; // 0 here indicates that images will not be saved
m_iParams.IndicatorName[0] = VM.IndicatorName;
m_tokenSource = new CancellationTokenSource();
m_cancelToken = m_tokenSource.Token;
Progress <int> progress = new Progress <int>();
progress.ProgressChanged += (sender1, num) =>
{
VM.StatusString = "Completed " + num.ToString() + " images";
};
ImageDisplayControl.SetImageSize(m_iParams.imageWidth, m_iParams.imageHeight, m_iParams.maxPixelValue);
m_bitmap = ImageDisplayControl.m_imageBitmap;
Task ImagingTask = Task.Factory.StartNew(() => m_imager.StartImaging(m_iParams,
null, // no analysis parameters needed here
m_cancelToken, m_uiTask, progress,
ImageDisplayControl, m_colorModel.m_colorMap,
m_histogram), m_cancelToken);
try
{
await ImagingTask;
}
catch (AggregateException aggEx)
{
StringBuilder sb = new StringBuilder();
sb.Append("Exception(s) occurred: ");
foreach (Exception ex in aggEx.InnerExceptions)
{
sb.Append(ex.Message);
sb.Append(", ");
}
MessageBoxResult result = MessageBox.Show(sb.ToString(), "Exception(s) Occurred", MessageBoxButton.OK, MessageBoxImage.Error);
}
catch (OperationCanceledException)
{
VM.StatusString = "Canceled";
}
catch (Exception ex)
{
MessageBoxResult result = MessageBox.Show(ex.Message, "Unknown Exception Occurred", MessageBoxButton.OK, MessageBoxImage.Error);
}
finally
{
ImagingTask.Dispose();
OnImagingStopped(EventArgs.Empty);
VideoPB.Content = "Video";
SnapShotPB.Content = "Snap Shot";
VideoPB.IsEnabled = true;
SnapShotPB.IsEnabled = true;
GainSpin.IsEnabled = true;
ExposureSpin.IsEnabled = true;
Optimize1PB.IsEnabled = true;
//ExcitationFilterCombo.IsEnabled = true;
//EmissionFilterCombo.IsEnabled = true;
VM.IsImaging = false;
VM.StatusString = "Ready";
}
}
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 async void StartVideo(ImagingParameters iParams)
{
if (m_imager == null)
{
return;
}
//m_uiTask = TaskScheduler.FromCurrentSynchronizationContext();
m_tokenSource = new CancellationTokenSource();
m_cancelToken = m_tokenSource.Token;
Progress <int> progress = new Progress <int>();
progress.ProgressChanged += (sender1, num) =>
{
VM.MessageText = num.ToString() + " images";
};
Dictionary <int, ImageDisplay> imageDisplayDictionary = ChartArray.GetImageDisplayDictionary();
foreach (KeyValuePair <int, ImageDisplay> entry in imageDisplayDictionary)
{
ImageDisplay imageDisplay = entry.Value;
imageDisplay.SetImageSize(iParams.imageWidth, m_iParams.imageHeight, m_iParams.maxPixelValue);
}
Task ImagingTask = Task.Factory.StartNew(() => m_imager.StartImaging(m_iParams,
Tuple.Create(m_mask, m_controlSubtractionWellList, m_numFoFrames,
m_dynamicRatioNumerator.ExperimentIndicatorID,
m_dynamicRatioDenominator.ExperimentIndicatorID),
m_cancelToken, m_uiTask, progress,
null, m_colorModel.m_colorMap, m_histogram, ChartArray), m_cancelToken);
try
{
await ImagingTask;
}
catch (AggregateException aggEx)
{
StringBuilder sb = new StringBuilder();
sb.Append("Exception(s) occurred: ");
foreach (Exception ex in aggEx.InnerExceptions)
{
sb.Append(ex.Message);
sb.Append(", ");
}
MessageBoxResult result = MessageBox.Show(sb.ToString(), "Exception(s) Occurred", MessageBoxButton.OK, MessageBoxImage.Error);
}
catch (OperationCanceledException)
{
}
catch (Exception ex)
{
MessageBoxResult result = MessageBox.Show(ex.Message, "Unknown Exception Occurred", MessageBoxButton.OK, MessageBoxImage.Error);
}
finally
{
ImagingTask.Dispose();
}
}
