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);
}
}
// Start is called before the first frame update
void Awake()
{
m_CleanPlates = FindObjectOfType <PlateContainer>();
if (m_DirtyPlates.Count < 1)
{
Debug.Log("have no plates!"); // for debugging
}
else
{
changePlatesActiveState(false);
}
}
public bool GetPlateList(int projectID)
{
#if (SIMULATE)
m_vm.plates.Clear();
PlateContainer plate = new PlateContainer();
plate.Barcode = "123456";
plate.BarcodeValid = true;
plate.Description = "plate 1";
plate.IsPublic = true;
plate.OwnerID = 1;
plate.PlateID = 1;
plate.PlateIDResetBehavior = PLATE_ID_RESET_BEHAVIOR.CONSTANT;
plate.PlateTypeID = 1;
plate.ProjectID = 1;
m_vm.plates.Add(plate);
plate = new PlateContainer();
plate.Barcode = "456123";
plate.BarcodeValid = true;
plate.Description = "plate 2";
plate.IsPublic = true;
plate.OwnerID = 2;
plate.PlateID = 2;
plate.PlateIDResetBehavior = PLATE_ID_RESET_BEHAVIOR.CONSTANT;
plate.PlateTypeID = 2;
plate.ProjectID = 2;
m_vm.plates.Add(plate);
return(true);
#else
bool success = true;
if (m_db.GetAllPlatesForProject(projectID))
{
m_vm.plates = m_db.m_plateList;
}
else
{
success = false;
}
return(success);
#endif
}
/////////////////////////////
// Private Constructor
private ExperimentParams()
{
_numFoFrames = 5;
_experimentPlate = new PlateContainer();
_experiment = new ExperimentContainer();
_compoundPlateList = new System.Collections.ObjectModel.ObservableCollection <ExperimentCompoundPlateContainer>();
_controlSubtractionWellList = new System.Collections.ObjectModel.ObservableCollection <Tuple <int, int> >();
_indicatorList = new System.Collections.ObjectModel.ObservableCollection <ExperimentIndicatorContainer>();
_experimentRunPlateCount = 2;
_experimentCurrentPlateNumber = 0;
_writeExcelReport = true;
_writeWaveguideReport = true;
m_wgDB = new WaveguideDB();
bool success = m_wgDB.GetCameraSettingsDefault(out _cameraSettings);
if (!success)
{
_cameraSettings = new CameraSettingsContainer();
}
}
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++;
}
}
