private void ToolStripMenuItem_DisplayImage(object sender, EventArgs e)
{
List<cImageMetaInfo> ListInfo = cGlobalInfo.ImageAccessor.GetImageInfo(this);
cImage Image = new cImage(ListInfo);
this.BD_BoxMax.Z = this.BD_BoxMin.Z = 0;
// this.BD_BoxMin.Y = Image.Height - this.BD_BoxMin.Y;
// this.BD_BoxMax.Y = Image.Height - this.BD_BoxMax.Y;
if (this.BD_BoxMin.Y > this.BD_BoxMax.Y)
{
double Tmp = this.BD_BoxMin.Y;
this.BD_BoxMin.Y = this.BD_BoxMax.Y;
this.BD_BoxMax.Y = Tmp;
}
cImage CroppedImaged = Image.Crop(this.BD_BoxMin, this.BD_BoxMax);
cDisplaySingleImage IV = new cDisplaySingleImage();
IV.IsUseSavedDefaultDisplayProperties = true;
IV.DefaultZoom = 100;
IV.Title = "[Plate] " + this.AssociatedWell.AssociatedPlate.GetName() + " - [Well] " + this.AssociatedWell.GetPos() + " - [Field] " + this.ImageField + " - " + this.CellularPhenotypeType.Name;
IV.SetInputData(CroppedImaged);
IV.Run();
}
public cFeedBackMessage Run(c3DNewWorld _3DWorld)
{
if (base.Start() == false)
{
base.FeedBackMessage.IsSucceed = false;
return base.FeedBackMessage;
}
#region Properties Management
object _firstValue = base.ListProperties.FindByName("Thresold");
double Thresold = 0.5;
if (_firstValue == null)
{
base.GenerateError("-Thresold- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Thresold = (double)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Thresold- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Split objects ?");
bool IsSplit = false;
if (_firstValue == null)
{
base.GenerateError("-Split objects ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsSplit = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Split objects ?- cast didn't work");
return base.FeedBackMessage;
}
#endregion
ListObjects = new cListGeometric3DObject("");
if (IsSplit == false)
{
c3DMeshObject MyMesh = null;
if (this.VTKInput == null)
{
MyMesh = new c3DMeshObject(this.Input, Thresold);
}
else
{
MyMesh = new c3DMeshObject(this.VTKInput, (int)Thresold);
}
MyMesh.Create(Color.Aqua, this.Pos );
ListObjects.Name = MyMesh.GetName() + " metaobject";
ListObjects.Add(MyMesh);
}
else
{
// ok that's a little bit more complicated now
// first we need to binarize the image
cImageSegmentationThreshold IST = new cImageSegmentationThreshold();
IST.ListProperties.FindByName("Threshold").SetNewValue(Thresold);
cImage SourceImage = new cImage(this.Input, false);
IST.SetInputData(SourceImage);
IST.Run();
// now perform image labeling
cImage BinImage = IST.GetOutPut();
cImage LabeledImage = new cImage(BinImage, false);
ConnectedComponentSet CCS = new ConnectedComponentSet(BinImage,LabeledImage,SourceImage, 0, eConnectivity.THREED_6, 0, float.MaxValue);
Random RD = new Random();
int IdxObj = 1;
// loop over each object
int NumObj = CCS.Count;
ListObjects.Name = "T_" + Thresold + " [" + SourceImage.Name + " Metaobject";
for(int i = 0;i<NumObj;i++)
{
ConnectedVoxels item = CCS[i];
// if (item.Volume <= 1) continue;
List<cPoint3D> ExtremePts = item.GetExtremaPoints();
// crop the labeled image
cImage TmpIm = LabeledImage.Crop(ExtremePts[0], ExtremePts[1]);
// we have to clean the cropped image to prevent any overlapping object to be segmented
for (int Pix = 0; Pix < TmpIm.ImageSize; Pix++)
{
if ((TmpIm.SingleChannelImage[0].Data[Pix] > 0) && (TmpIm.SingleChannelImage[0].Data[Pix] != IdxObj)) TmpIm.SingleChannelImage[0].Data[Pix] = 0;
}
// update the position of the object
cPoint3D NewPos = ExtremePts[0]*SourceImage.Resolution;
c3DMeshObject MyMesh = new c3DMeshObject(TmpIm.SingleChannelImage[0], 0.5);
MyMesh.Create(Color.FromArgb(RD.Next(255), RD.Next(255), RD.Next(255)), NewPos);
MyMesh.SetName(MyMesh.GetName() + "_" + IdxObj);
MyMesh.AssociatedConnectedComponent = item;
ListObjects.AddObject(MyMesh);
IdxObj++;
}
}
return base.FeedBackMessage;
}
private void TSItemSubPopSelectionDataTableImages(object sender, EventArgs e)
{
ToolStripMenuItem ParentTag = (ToolStripMenuItem)(sender);
List<int> MyList = ((List<int>)(ParentTag.Tag));
cExtendedTable ET = new cExtendedTable(this.InputSimpleData.Count, MyList.Count, 0);
for (int i = 0; i < this.InputSimpleData.Count; i++)
{
ET[i].Name = this.InputSimpleData[i].Name;
}
ET.ListRowNames = new List<string>();
for (int i = 0; i < MyList.Count; i++)
{
ET.ListRowNames.Add(i.ToString());
}
if (this.InputSimpleData.ListTags != null) ET.ListTags = new List<object>();
int IdxPt = 0;
FormForProgress FP = new FormForProgress();
FP.Show();
int MaxProgress = MyList.Count;
FP.progressBar.Maximum = MaxProgress;
foreach (var item in MyList)
{
for (int i = 0; i < this.InputSimpleData.Count; i++)
{
ET[i][IdxPt] = this.InputSimpleData[i][MyList[IdxPt]];
}
if ((this.InputSimpleData.ListTags != null) && (this.InputSimpleData.ListTags[IdxPt] != null))
{
if (this.InputSimpleData.ListTags[MyList[IdxPt]].GetType() == typeof(cSingleBiologicalObject))
{
cSingleBiologicalObject TmpBioObj = ((cSingleBiologicalObject)this.InputSimpleData.ListTags[MyList[IdxPt]]);
List<cImageMetaInfo> ListMeta = cGlobalInfo.ImageAccessor.GetImageInfo(TmpBioObj);
if (ListMeta==null) continue;
cImage Image = new cImage(ListMeta);
TmpBioObj.BD_BoxMax.Z = TmpBioObj.BD_BoxMin.Z = 0;
cImage CroppedImaged = Image.Crop(TmpBioObj.BD_BoxMin, TmpBioObj.BD_BoxMax);
if((cGlobalInfo.TmpImageDisplayProperties==null)||(cGlobalInfo.TmpImageDisplayProperties.ListMin.Count != CroppedImaged.GetNumChannels()))
{
ET.ListTags.Add(CroppedImaged.GetBitmap(1f, null, null));
}
else
{
cImageDisplayProperties IP = cGlobalInfo.TmpImageDisplayProperties;
ET.ListTags.Add(CroppedImaged.GetBitmap(1f, IP, null));
}
FP.richTextBoxForComment.AppendText("Object "+ IdxPt +" / "+MyList.Count +"\n");
}
}
FP.progressBar.Value = IdxPt;
FP.Refresh();
IdxPt++;
}
FP.Close();
ET.Name = "Data Table - " + MyList.Count + " Objects";
cDisplayExtendedTable DET = new cDisplayExtendedTable();
DET.SetInputData(ET);
DET.Run();
//DataPoint DP = new DataPoint();
//if (this.InputSimpleData[0].ListTags != null)
//{
// if (j >= this.InputSimpleData[0].ListTags.Count) continue;
// DP.Tag = this.InputSimpleData[0].ListTags[j];
// // if (DP.Tag.GetType() == typeof(cWell))
// // {
// // DP.Color = ((cWell)(DP.Tag)).GetClassColor();
// // DP.ToolTip = ((cWell)(DP.Tag)).GetShortInfo() + Value[0];
// // }
// if (DP.Tag.GetType() == typeof(cSingleBiologicalObject))
// {
// // DP.Color = ((cSingleBiologicalObject)(DP.Tag)).GetColor();
// // DP.ToolTip = ((cSingleBiologicalObject)(DP.Tag)).GetAssociatedPhenotype().Name + "\nValue: (" + DP.XValue.ToString("N2") + ":" + DP.YValues[0].ToString("N2") + ")";
// }
//}
}
private void ToolStripMenuItem_DisplayImages(object sender, EventArgs e)
{
//if (cWell.cGlobalInfo.ImageAccessor.ImagingPlatformType == HCSAnalyzer.Classes.General_Types.eImagingPlatformType.OPERETTA) return;
cGlobalInfo.ImageAccessor.Field = 1;// (int)this.numericUpDownField.Value;
//string FileName = cWell.cGlobalInfo.ImageAccessor.GetImageFileName(this);
foreach (cWell item in this.ListActiveWells)
{
List<cImageMetaInfo> ListMetaInfo = cGlobalInfo.ImageAccessor.GetImageInfo(item);
cImage Image = new cImage(ListMetaInfo);
Image.Name = "Image [" + item.GetShortInfo() + "] - Field [" + cGlobalInfo.ImageAccessor.Field + "]";
cImage FinaleImage = Image.Crop(new cPoint3D(400, 400, 0), new cPoint3D(800 + 400, 800 + 400, 0));
//cImageGeometricResize IR = new cImageGeometricResize();
//IR.SetInputData(Image);
//IR.InterpolationType = Emgu.CV.CvEnum.INTER.CV_INTER_LINEAR;
//IR.ListProperties.UpdateValueByName("Scale", (double)0.25);
//IR.Run();
//cImage FinaleImage = IR.GetOutPut();
//FinaleImage.Name = "Image [" + item.GetShortInfo()+"] - Field ["+ cWell.cGlobalInfo.ImageAccessor.Field + "]";
cDisplaySingleImage IV = new cDisplaySingleImage();
IV.SetInputData(FinaleImage);
IV.Run();
}
//cImage IM = new cImage(this.Info);
//if (IM == null) return;
//cImageViewer IV = new cImageViewer();
//IV.SetImage(IM);
//IV.Show();
//cViewerImage3D VI3D = new cViewerImage3D();
//foreach (cWell item in this.ListActiveWells)
//{
// vtkJPEGReader JPEGReader = vtkJPEGReader.New();
// JPEGReader.SetFileName(item.Info);
// JPEGReader.Update();
// vtkImageData ID0 = JPEGReader.GetOutput();
// VI3D.SetInputData(ID0);
//}
//// cVolume3D Volume3D0 = new cVolume3D(ID0, new HCSAnalyzer.Classes._3D.cPoint3D(0, 0, 0));
//VI3D.Run();
//cDisplayToWindow DTW = new cDisplayToWindow();
//DTW.SetInputData(VI3D.GetOutPut());
//DTW.Run();
//DTW.Display();
}