public cImage GetMontage()
{
cImage MyIm = new cImage((int)this.MontageDimensions.X, (int)this.MontageDimensions.Y, (int)this.MontageDimensions.Z,this.NumberOfChannels);
MyIm.Resolution = new cPoint3D(this.Resolution);
return MyIm;
}
/// <summary> 3D connected components detector
/// Computes various information on the detected objects
/// </summary>
/// <param name="labeledInputimage">Gray level input image (background value must be 0)</param>
/// <param name="labeledOutputImage">Empty input image of same size that labeledInput image (can be null)</param>
/// <param name="image">Original greyscale image (can be null)</param>
/// <param name="band">the image band</param>
/// <param name="connectivity">Connectivity. MUST be 6 or 26</param>
/// <param name="minVolume">Minimum object volume to consider</param>
/// <param name="maxVolume">Maximum object volume to consider</param>
public ConnectedComponentSet(cImage labeledInputimage, cImage labeledOutputImage, cImage image, int band, eConnectivity connectivity, float minVolume, float maxVolume)
{
if (image != null && (image.Width != labeledInputimage.Width || image.Height != labeledInputimage.Height || image.Depth != labeledInputimage.Depth))
{
if (connectivity == eConnectivity.THREED_6 || connectivity == eConnectivity.THREED_26)
{
// throw new DescriptorException("Uncompatible Image sizes");
}
}
if (labeledOutputImage != null && (labeledOutputImage.Width != labeledInputimage.Width || labeledOutputImage.Height != labeledInputimage.Height || labeledOutputImage.Depth != labeledInputimage.Depth))
{
if (connectivity == eConnectivity.THREED_6 || connectivity == eConnectivity.THREED_26)
{
// throw new DescriptorException("Uncompatible Image sizes");
}
if (labeledOutputImage.GetNumChannels() != 1)
{
// throw new DescriptorException("Output label image must be single band");
}
}
if (labeledInputimage.Depth == 1)
{
if (connectivity == eConnectivity.THREED_6 || connectivity == eConnectivity.THREED_26)
{
// throw new DescriptorException("Given connectivity is incompatible with the image depth");
}
}
else if (connectivity == eConnectivity.TWOD_4 || connectivity == eConnectivity.TWOD_8 || connectivity == eConnectivity.TWOD_24)
{
// throw new DescriptorException("Given connectivity is incompatible with the image depth");
}
this.min = minVolume;
this.max = maxVolume;
this.connectivity = connectivity;
this.width = labeledInputimage.Width;
this.height = labeledInputimage.Height;
this.depth = labeledInputimage.Depth;
this.scanSliceSize = width * height;
this.twoTimesWidth = 2 * width;
if (labeledOutputImage == null)
{
this.labeledOutputImage = new cImage(labeledInputimage.Width, labeledInputimage.Height, labeledInputimage.Depth, 1);
}
else
{
this.labeledOutputImage = labeledOutputImage;
}
this.labeledOutput = this.labeledOutputImage.SingleChannelImage[0].Data;
this.labeledInputimage = labeledInputimage;
this.labeledInput = labeledInputimage.SingleChannelImage[band].Data;
this.image = image;
FindConnectedComponents();
}
public cFeedBackMessage Run()
{
if (this.Input == null)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data defined.";
return FeedBackMessage;
}
this.OutPut = new cImage(this.Input);
this.OutPut.Name = "Image(" + this.Input.Name + ")";
return FeedBackMessage;
}
private void exctractSliceToolStripMenuItem_Click(object sender, EventArgs e)
{
int CurrentZ = (int)this.numericUpDownZPos.Value;
cDisplaySingleImage NewView = new cDisplaySingleImage();
cImage NewImage = new cImage(this.Sender.AssociatedImage.Width, this.Sender.AssociatedImage.Height, 1, this.Sender.AssociatedImage.GetNumChannels());
NewImage.Name = this.Sender.AssociatedImage.Name + " [Z=" + CurrentZ + "]";
NewImage.Resolution = new _3D.cPoint3D(this.Sender.AssociatedImage.Resolution);
for (int i = 0; i < this.Sender.AssociatedImage.GetNumChannels(); i++)
{
Array.Copy(this.Sender.AssociatedImage.SingleChannelImage[i].Data, CurrentZ * this.Sender.AssociatedImage.SliceSize,
NewImage.SingleChannelImage[i].Data, 0,
NewImage.ImageSize);
}
NewView.SetInputData(NewImage);
NewView.Run();
}
/// <summary>
/// Add a new image to the montage
/// </summary>
/// <param name="NewIm">New image to be integrated</param>
/// <param name="IsForceInconsistencies">if set to TRUE then we'll try to force the image integration within the montage even if there are some inconsistencies with the last image (resolution, number of channels)</param>
public bool Add(cImage NewIm, bool IsForceInconsistencies)
{
if (ListImage == null)
{
ListImage = new List<cImage>();
ListImage.Add(NewIm);
}
if ((ListImage[ListImage.Count - 1].GetNumChannels() != NewIm.GetNumChannels()) && (!IsForceInconsistencies))
{
return false;
}
else
{
if (this.NumberOfChannels < NewIm.GetNumChannels())
this.NumberOfChannels = NewIm.GetNumChannels();
this.ListImage.Add(NewIm);
}
if (((ListImage[ListImage.Count - 1].Resolution.X != NewIm.Resolution.X) && (!IsForceInconsistencies)) ||
((ListImage[ListImage.Count - 1].Resolution.Y != NewIm.Resolution.Y) && (!IsForceInconsistencies)) ||
((ListImage[ListImage.Count - 1].Resolution.Z != NewIm.Resolution.Z) && (!IsForceInconsistencies)))
{
return false;
}
else
{
this.Resolution.X = NewIm.Resolution.X;
this.Resolution.Y = NewIm.Resolution.Y;
this.Resolution.Z = NewIm.Resolution.Z;
this.ListImage.Add(NewIm);
}
return true;
}
private void ToolStripMenuItem_SplitByChannels(object sender, EventArgs e)
{
for (int i = 0; i < this.AssociatedImage.GetNumChannels(); i++)
{
cDisplaySingleImage NewView = new cDisplaySingleImage();
cImage NewImage = new cImage(this.AssociatedImage.Width, this.AssociatedImage.Height, this.AssociatedImage.Depth, 1);
NewImage.Name = this.AssociatedImage.Name + " [" + this.AssociatedImage.SingleChannelImage[i].Name + "]";
NewImage.Resolution = new cPoint3D(this.AssociatedImage.Resolution);
Array.Copy(this.AssociatedImage.SingleChannelImage[i].Data, NewImage.SingleChannelImage[0].Data, NewImage.ImageSize);
NewView.SetInputData(NewImage);
NewView.Run();
}
}
private void ToolStripMenuItem_BitmapToImage(object sender, EventArgs e)
{
cDisplaySingleImage NewView = new cDisplaySingleImage();
Bitmap BMP = this.GetBitmap();
if (BMP == null) return;
cImage NewImage = new cImage(BMP.Width, BMP.Height, 1, 3);
NewImage.Name = "RGB_Bitmap(" + this.AssociatedImage.Name + ")";
NewImage.Resolution = new cPoint3D(this.AssociatedImage.Resolution);
for (int j = 0; j < BMP.Height; j++)
{
for (int i = 0; i < BMP.Width; i++)
{
Color C = BMP.GetPixel(i, j);
NewImage.SingleChannelImage[0].Data[i + j * NewImage.Width] = C.R;
NewImage.SingleChannelImage[1].Data[i + j * NewImage.Width] = C.G;
NewImage.SingleChannelImage[2].Data[i + j * NewImage.Width] = C.B;
}
}
NewView.SetInputData(NewImage);
NewView.Run();
}
/// <summary> 3D connected components detector
/// Computes various information on the detected objects
/// </summary>
/// <param name="labeledInputimage">Gray level input image (background value must be 0)</param>
/// <param name="band">the image band</param>
/// <param name="connectivity">Connectivity. MUST be 6 or 26</param>
/// <param name="minVolume">Minimum object volume to consider</param>
/// <param name="maxVolume">Maximum object volume to consider</param>
public ConnectedComponentSet(cImage labeledInputimage, int band, eConnectivity connectivity, float minVolume, float maxVolume)
: this(labeledInputimage, null, null, band, connectivity, minVolume, maxVolume)
{
}
protected VoxelList(int label, cImage labeledImage, cImage image, eConnectivity connectivity)
{
this.label = label;
surfacePoints = new List<int[]>();
points = new List<int[]>();
indices = new List<int>();
values = new List<float[]>();
this.labeledImage = labeledImage;
this.labeledImageData = labeledImage.SingleChannelImage[0].Data;
this.image = image;
if (image != null)
{
int NumChannels = image.GetNumChannels();
this.numBands = NumChannels;
this.intensity = new float[NumChannels];
this.surfaceIntensity = new float[NumChannels];
this.maxIntensity = new float[NumChannels];
this.minIntensity = new float[NumChannels];
for (int b = 0; b < NumChannels; b++)
{
maxIntensity[b] = float.MinValue;
minIntensity[b] = float.MaxValue;
}
}
this.imageWidth = labeledImage.Width;
this.imageHeight = labeledImage.Height;
this.imageDepth = labeledImage.Depth;
this.scanSliceSize = labeledImage.SliceSize;
this.connectivity = connectivity;
}
cImage Rescale(cImage input, int inputChannel, cImage output, int outputChannel, float minBound, float maxBound)
{
float min = input.SingleChannelImage[inputChannel].Data.Min();
float max = input.SingleChannelImage[inputChannel].Data.Max();
if (min == max)
{
for (int i = 0; i < input.Height*input.Width; i++) output.SingleChannelImage[outputChannel].Data[i] = minBound;
}
else
for (int i = 0; i < input.Width*input.Height; i++)
output.SingleChannelImage[outputChannel].Data[i] = ((maxBound - minBound) * (input.SingleChannelImage[inputChannel].Data[i] - min) / (max - min)) + minBound;
return output;
}
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") + ")";
// }
//}
}
public cFeedBackMessage Run()
{
base.Start();
object _firstValue = base.ListProperties.FindByName("Width");
int Width = 0;
if (_firstValue == null)
{
base.GenerateError("-Width- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Width = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Width- Size cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Height");
int Height = 0;
if (_firstValue == null)
{
base.GenerateError("-Height- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Height = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Height- Size cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Depth");
int Depth = 0;
if (_firstValue == null)
{
base.GenerateError("-Depth- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Depth = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Depth- Size cast didn't work");
return base.FeedBackMessage;
}
cImage NewImage = new cImage(Width, Height, Depth, 1);
NewImage.Name = "Image [" + Width + ", " + Height + ", " + Depth + "]";
cDisplaySingleImage DSI = new cDisplaySingleImage();
DSI.SetInputData(NewImage);
DSI.Run();
base.End();
return FeedBackMessage;
}
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 CommonInit(Sequence BinarySubImageSeq)
//{
// vtkImageData ImageData1 = new vtkImageData();
// ImageData1.SetDimensions(BinarySubImageSeq.Width, BinarySubImageSeq.Height, BinarySubImageSeq.Depth);
// ImageData1.SetNumberOfScalarComponents(1);
// ImageData1.SetSpacing(BinarySubImageSeq.XResolution, BinarySubImageSeq.YResolution, BinarySubImageSeq.ZResolution);
// ImageData1.SetScalarTypeToFloat();
// vtkFloatArray array1 = new vtkFloatArray();
// for (int i = 0; i < BinarySubImageSeq.ImageSize; i++)
// array1.InsertTuple1(i, BinarySubImageSeq[0].Data[0][i]);
// ImageData1.GetPointData().SetScalars(array1);
// vtkExtractVOI VOI = new vtkExtractVOI();
// VOI.SetInput(ImageData1);
// VOI.SetSampleRate(1, 1, 1);
// vtkMarchingCubes ContourObject = vtkMarchingCubes.New();
// vtk_PolyDataMapper = vtkPolyDataMapper.New();
// //ContourActor = new vtkActor();
// VOI.SetVOI(0, BinarySubImageSeq.Width - 1, 0, BinarySubImageSeq.Height - 1, 0, BinarySubImageSeq.Depth - 1);
// ContourObject.SetInput(VOI.GetOutput());
// ContourObject.SetValue(0, 0.5);
// vtk_PolyDataMapper.SetInput(ContourObject.GetOutput());
// vtk_PolyDataMapper.ScalarVisibilityOn();
// vtk_PolyDataMapper.SetScalarModeToUseFieldData();
//}
///// <summary>
///// Generate a 3D mesh using marching-cubes algorithm. If voxel value is lower than 1 it is consider as background, else as object
///// </summary>
///// <param name="BinarySubImageSeq">The binary image</param>
///// <param name="Colour">Mesh color</param>
///// <param name="Pos">Postion of the object in the world</param>
//public void Generate(Sequence BinarySubImageSeq, Color Colour, cPoint3D Pos)
//{
// vtkImageData ImageData1 = new vtkImageData();
// ImageData1.SetDimensions(BinarySubImageSeq.Width, BinarySubImageSeq.Height, BinarySubImageSeq.Depth);
// ImageData1.SetNumberOfScalarComponents(1);
// ImageData1.SetSpacing(BinarySubImageSeq.XResolution, BinarySubImageSeq.YResolution, BinarySubImageSeq.ZResolution);
// ImageData1.SetScalarTypeToFloat();
// vtkFloatArray array1 = new vtkFloatArray();
// for (int i = 0; i < BinarySubImageSeq.ImageSize; i++)
// array1.InsertTuple1(i, BinarySubImageSeq[0].Data[0][i]);
// ImageData1.GetPointData().SetScalars(array1);
// vtkExtractVOI VOI = new vtkExtractVOI();
// VOI.SetInput(ImageData1);
// VOI.SetSampleRate(1, 1, 1);
// vtkMarchingCubes ContourObject = vtkMarchingCubes.New();
// vtk_PolyDataMapper = vtkPolyDataMapper.New();
// //ContourActor = new vtkActor();
// VOI.SetVOI(0, BinarySubImageSeq.Width - 1, 0, BinarySubImageSeq.Height - 1, 0, BinarySubImageSeq.Depth - 1);
// // perform the amrching cubes
// ContourObject.SetInput(VOI.GetOutput());
// ContourObject.SetValue(0, 0.5);
// //vtkDecimatePro deci
// //deci SetInputConnection [fran GetOutputPort]
// //deci SetTargetReduction 0.9
// //deci PreserveTopologyOn
// if (MeshSmoother!=null)
// {
// vtkSmoothPolyDataFilter smoother = new vtkSmoothPolyDataFilter();
// smoother.SetInputConnection(ContourObject.GetOutputPort());// [deci GetOutputPort]
// smoother.SetNumberOfIterations(50);
// vtk_PolyData = smoother.GetOutput();
// }
// else
// {
// vtk_PolyData = ContourObject.GetOutput();
// }
// vtk_PolyDataMapper.SetInput(vtk_PolyData);
// vtk_PolyDataMapper.ScalarVisibilityOn();
// vtk_PolyDataMapper.SetScalarModeToUseFieldData();
// this.Position = new cPoint3D(Pos.X, Pos.Y, Pos.Z);
// this.Colour = Colour;
// CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// // compute convex hull
// hullFilter = vtkHull.New();
// hullFilter.SetInputConnection(ContourObject.GetOutputPort());
// hullFilter.AddRecursiveSpherePlanes(1);
// hullFilter.Update();
// // this.BackfaceCulling(false);
// Information = new cInformation(ContourObject, this, hullFilter);
//}
public void Generate(cImage BinarySubImageSeq, Color Colour, cPoint3D Pos/*, List<cBiological3DObject> Containers, int ContainerMode*/)
{
vtkImageData ImageData1 = new vtkImageData();
ImageData1.SetDimensions(BinarySubImageSeq.Width, BinarySubImageSeq.Height, BinarySubImageSeq.Depth);
ImageData1.SetNumberOfScalarComponents(1);
ImageData1.SetSpacing(BinarySubImageSeq.Resolution.X, BinarySubImageSeq.Resolution.Y, BinarySubImageSeq.Resolution.Z);
ImageData1.SetScalarTypeToFloat();
vtkFloatArray array1 = new vtkFloatArray();
for (int i = 0; i < BinarySubImageSeq.ImageSize; i++)
array1.InsertTuple1(i, BinarySubImageSeq.SingleChannelImage[0].Data[i]);
ImageData1.GetPointData().SetScalars(array1);
vtkExtractVOI VOI = new vtkExtractVOI();
VOI.SetInput(ImageData1);
VOI.SetSampleRate(1, 1, 1);
vtkMarchingCubes ContourObject = vtkMarchingCubes.New();
vtk_PolyDataMapper = vtkPolyDataMapper.New();
//ContourActor = new vtkActor();
VOI.SetVOI(0, BinarySubImageSeq.Width - 1, 0, BinarySubImageSeq.Height - 1, 0, BinarySubImageSeq.Depth - 1);
ContourObject.SetInput(VOI.GetOutput());
ContourObject.SetValue(0, 0.5);
vtkAlgorithmOutput AlgoOutPut = null;
if (MeshSmoother != null)
{
//vtkSmoothPolyDataFilter smoother = new vtkSmoothPolyDataFilter();
vtkWindowedSincPolyDataFilter smoother = new vtkWindowedSincPolyDataFilter();
smoother.SetInputConnection(ContourObject.GetOutputPort());// [deci GetOutputPort]
smoother.SetNumberOfIterations(MeshSmoother.NumberOfIterations);
vtk_PolyData = smoother.GetOutput();
//smoother.GetOutputPort();
AlgoOutPut = smoother.GetOutputPort();
}
else
{
vtk_PolyData = ContourObject.GetOutput();
AlgoOutPut = ContourObject.GetOutputPort();
}
vtk_PolyDataMapper.SetInput(vtk_PolyData);
vtk_PolyDataMapper.ScalarVisibilityOn();
vtk_PolyDataMapper.SetScalarModeToUseFieldData();
vtkActor TmpActor = vtkActor.New();
TmpActor.SetMapper(vtk_PolyDataMapper);
TmpActor.SetPosition(Pos.X, Pos.Y, Pos.Z);
//Console.WriteLine("PosX"+Pos.X+" PosY"+Pos.Y+" PosZ"+Pos.Z);
#region deal with the containers
if (this.Containers != null)
{
if (this.Containers.ContainerMode == 0)
{
cPoint3D Centroid = new cPoint3D((float)TmpActor.GetCenter()[0], (float)TmpActor.GetCenter()[1], (float)TmpActor.GetCenter()[2]);
bool IsInside = false;
for (int Idx = 0; Idx < Containers.Containers.Count; Idx++)
{
cBiological3DVolume CurrentContainer = (cBiological3DVolume)(Containers.Containers[Idx]);
if (CurrentContainer.IsPointInside(Centroid))
{
IsInside = true;
ContainerIdx = Idx;
break;
}
}
if (IsInside)
{
this.SetPosition(new cPoint3D(Pos.X, Pos.Y, Pos.Z));
this.Colour = Colour;
CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// compute convex hull
hullFilter = vtkHull.New();
hullFilter.SetInputConnection(AlgoOutPut);
hullFilter.AddRecursiveSpherePlanes(0);
hullFilter.Update();
Information = new cInformation(AlgoOutPut, this, hullFilter);
this.Detected = true;
}
else
{
this.Detected = false;
}
}
else if (Containers.ContainerMode == 1)
{
this.Detected = true;
//bool IsInside = false;
for (int Idx = 0; Idx < Containers.Containers.Count; Idx++)
{
cBiological3DVolume CurrentContainer = (cBiological3DVolume)(Containers.Containers[Idx]);
if (CurrentContainer.IsPointInside(Pos))
{
//IsInside = false;
this.Detected = false;
return;
}
}
this.SetPosition(new cPoint3D(Pos.X, Pos.Y, Pos.Z));
this.Colour = Colour;
CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// compute convex hull
hullFilter = vtkHull.New();
hullFilter.SetInputConnection(AlgoOutPut);
hullFilter.AddRecursiveSpherePlanes(0);
hullFilter.Update();
Information = new cInformation(AlgoOutPut, this, hullFilter);
this.Detected = true;
}
}
else
{
this.SetPosition(new cPoint3D(Pos.X, Pos.Y, Pos.Z));
this.Colour = Colour;
CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// compute convex hull
hullFilter = vtkHull.New();
hullFilter.SetInputConnection(AlgoOutPut);
hullFilter.AddRecursiveSpherePlanes(1);
hullFilter.Update();
// this.BackfaceCulling(false);
Information = new cInformation(AlgoOutPut, this, hullFilter);
}
#endregion
}
cFeedBackMessage Process()
{
if (base.Start() == false)
{
base.FeedBackMessage.IsSucceed = false;
return base.FeedBackMessage;
}
object _field = base.ListProperties.FindByName("Field");
int Field = 0;
if (_field == null)
{
base.GenerateError("-Field- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_field;
Field = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Field- cast didn't work");
return base.FeedBackMessage;
}
//this.Output = this.Input[0].GetImage(Field);
cGlobalInfo.ImageAccessor.Field = Field;// (int)this.numericUpDownField.Value;
List<cImageMetaInfo> ImageMetaInfo = cGlobalInfo.ImageAccessor.GetImageInfo(this.Input[0]);
if(ImageMetaInfo==null)
{
FeedBackMessage.IsSucceed = false;
base.End();
return FeedBackMessage;
}
//string FileName = ImageMetaInfo[0].FileName;
this.Output = new cImage(ImageMetaInfo);
//this.Output = new cImage(30000, 5000, 1, 1);
//for (int i = 0; i < this.Output.SliceSize; i++)
//{
// this.Output.SingleChannelImage[0].Data[i] = i;
//}
base.End();
return FeedBackMessage;
}
public void SetInputData(cImage InputImage)
{
base.Title += ": " + InputImage.Name;
this.InputImage = InputImage;
}
//public void DrawPic()
//{
// if (this.LUTManager == null) return;
// if (this.ZNavigator == null) return;
// int ZPos = ZNavigator.trackBarForZPos.Value;
// ThisGraph = this.CreateGraphics();
// float ZoomFactor = Zoom / 100.0f;
// int NewWidth = (int)(AssociatedImage.Width * ZoomFactor);
// int NewHeight = (int)(AssociatedImage.Height * ZoomFactor);
// this.Width = NewWidth;
// this.Height = NewHeight;
// if ((NewHeight == 0) || (NewWidth == 0)) return;
// int PosViewX = (this.Width - NewWidth) / 2;
// int PosViewY = (this.Height - NewHeight) / 2;
// // this.Location = new Point(PosViewX,PosViewY);
// BT = new Bitmap(NewWidth, NewHeight, System.Drawing.Imaging.PixelFormat.Format24bppRgb);
// // Lock the bitmap's bits.
// Rectangle rect = new Rectangle(0, 0, NewWidth, NewHeight);
// System.Drawing.Imaging.BitmapData bmpData = BT.LockBits(rect, System.Drawing.Imaging.ImageLockMode.ReadWrite, BT.PixelFormat);
// // Get the address of the first line.
// IntPtr ptr = bmpData.Scan0;
// int scanline = Math.Abs(bmpData.Stride);
// byte CurrentRed;
// byte CurrentGreen;
// byte CurrentBlue;
// int RealX;
// int RealY;
// int NewStartX = (int)(this.StartViewX / ZoomFactor);
// int NewStartY = (int)(this.StartViewY / ZoomFactor);
// List<float> Min = new List<float>();
// List<float> Max = new List<float>();
// List<double> GammaList = new List<double>();
// for (int IdxChannel = 0; IdxChannel < this.AssociatedImage.GetNumChannels(); IdxChannel++)
// {
// if (this.LUTManager != null)
// {
// UserControlSingleLUT SingleLUT = (UserControlSingleLUT)this.LUTManager.panelForLUTS.Controls[IdxChannel];
// Min.Add((float)SingleLUT.numericUpDownMinValue.Value);
// Max.Add((float)SingleLUT.numericUpDownMaxValue.Value);
// GammaList.Add((double)SingleLUT.trackBarGamma.Value / 100.0);
// }
// }
// #region Obsolete
// // test for new display
// //List<byte[][]> ListLut = new List<byte[][]>();
// //for (int IdxChannel = 0; IdxChannel < this.AssociatedImage.NumChannels; IdxChannel++)
// //{
// // UserControlSingleLUT SingleLUT = (UserControlSingleLUT)this.LUTManager.panelForLUTS.Controls[IdxChannel];
// // if (SingleLUT.checkBoxIsActive.Checked == false) continue;
// // ListLut.Add(SingleLUT.SelectedLUT);
// //}
// //ConvertImageFloatToRGB(AssociatedImage, 0, 255, ListLut, 0);
// #endregion
// // Declare an array to hold the bytes of the bitmap.
// int bytes = scanline * NewHeight;
// byte[] rgbValues = new byte[bytes];
// // Copy the RGB values into the array.
// System.Runtime.InteropServices.Marshal.Copy(ptr, rgbValues, 0, bytes);
// for (int IdxChannel = 0; IdxChannel < this.AssociatedImage.GetNumChannels(); IdxChannel++)
// {
// UserControlSingleLUT SingleLUT = (UserControlSingleLUT)this.LUTManager.panelForLUTS.Controls[IdxChannel];
// if (SingleLUT.checkBoxIsActive.Checked == false) continue;
// byte[][] CurrentLUT = SingleLUT.SelectedLUT;
// //ConvertImageFloatToRGB(AssociatedImage, 0, 255, SingleLUT.SelectedLUT, 0);
// if (GammaList[IdxChannel] != 1)
// {
// for (int FullY = 0; FullY < NewHeight; FullY++)
// {
// RealY = (int)(FullY / ZoomFactor) + NewStartY;
// if (RealY >= AssociatedImage.Height) RealY = AssociatedImage.Height - 1;
// for (int FullX = 0; FullX < NewWidth; FullX++)
// {
// RealX = (int)(FullX / ZoomFactor) + NewStartX;
// if (RealX >= AssociatedImage.Width) RealX = AssociatedImage.Width - 1;
// float Value = AssociatedImage.SingleChannelImage[IdxChannel].Data[RealX + RealY * AssociatedImage.Width + ZPos * AssociatedImage.SliceSize];
// Value = (float)Math.Pow(Value, GammaList[IdxChannel]);
// int ConvertedValue = (int)((((CurrentLUT[0].Length - 1) * (Value - Min[IdxChannel])) / (Max[IdxChannel] - Min[IdxChannel])));
// if (ConvertedValue < 0) ConvertedValue = 0;
// if (ConvertedValue >= CurrentLUT[0].Length) ConvertedValue = CurrentLUT[0].Length - 1;
// CurrentRed = (byte)CurrentLUT[0][ConvertedValue];
// CurrentGreen = (byte)CurrentLUT[1][ConvertedValue];
// CurrentBlue = (byte)CurrentLUT[2][ConvertedValue];
// double NewValue = rgbValues[3 * FullX + FullY * scanline] + CurrentBlue;
// if (NewValue > 255)
// rgbValues[3 * FullX + FullY * scanline] = 255;
// else
// rgbValues[3 * FullX + FullY * scanline] += CurrentBlue;
// NewValue = rgbValues[3 * FullX + 1 + FullY * scanline] + CurrentGreen;
// if (NewValue > 255)
// rgbValues[3 * FullX + 1 + FullY * scanline] = 255;
// else
// rgbValues[3 * FullX + 1 + FullY * scanline] += CurrentGreen;
// NewValue = rgbValues[3 * FullX + 2 + FullY * scanline] + CurrentRed;
// if (NewValue > 255)
// rgbValues[3 * FullX + 2 + FullY * scanline] = 255;
// else
// rgbValues[3 * FullX + 2 + FullY * scanline] += CurrentRed;
// }
// }
// }
// else
// {
// for (int FullY = 0; FullY < NewHeight; FullY++)
// {
// RealY = (int)(FullY / ZoomFactor) + NewStartY;
// if (RealY >= AssociatedImage.Height) RealY = AssociatedImage.Height - 1;
// for (int FullX = 0; FullX < NewWidth; FullX++)
// {
// RealX = (int)(FullX / ZoomFactor) + NewStartX;
// if (RealX >= AssociatedImage.Width) RealX = AssociatedImage.Width - 1;
// float Value = AssociatedImage.SingleChannelImage[IdxChannel].Data[RealX + RealY * AssociatedImage.Width + ZPos * AssociatedImage.SliceSize];
// int ConvertedValue = (int)((((CurrentLUT[0].Length - 1) * (Value - Min[IdxChannel])) / (Max[IdxChannel] - Min[IdxChannel])));
// if (ConvertedValue < 0) ConvertedValue = 0;
// if (ConvertedValue >= CurrentLUT[0].Length) ConvertedValue = CurrentLUT[0].Length - 1;
// CurrentRed = (byte)CurrentLUT[0][ConvertedValue];
// CurrentGreen = (byte)CurrentLUT[1][ConvertedValue];
// CurrentBlue = (byte)CurrentLUT[2][ConvertedValue];
// double NewValue = rgbValues[3 * FullX + FullY * scanline] + CurrentBlue;
// if (NewValue > 255)
// rgbValues[3 * FullX + FullY * scanline] = 255;
// else
// rgbValues[3 * FullX + FullY * scanline] += CurrentBlue;
// NewValue = rgbValues[3 * FullX + 1 + FullY * scanline] + CurrentGreen;
// if (NewValue > 255)
// rgbValues[3 * FullX + 1 + FullY * scanline] = 255;
// else
// rgbValues[3 * FullX + 1 + FullY * scanline] += CurrentGreen;
// NewValue = rgbValues[3 * FullX + 2 + FullY * scanline] + CurrentRed;
// if (NewValue > 255)
// rgbValues[3 * FullX + 2 + FullY * scanline] = 255;
// else
// rgbValues[3 * FullX + 2 + FullY * scanline] += CurrentRed;
// }
// }
// }
// }
// // Copy the RGB values back to the bitmap
// System.Runtime.InteropServices.Marshal.Copy(rgbValues, 0, ptr, bytes);
// // Unlock the bits.
// BT.UnlockBits(bmpData);
// // Draw the modified image.
// ThisGraph.DrawImage(BT, this.StartViewX, this.StartViewY);
// DrawLayers(ZoomFactor);
//}
public Bitmap ConvertImageFloatToRGB(cImage ImageFloat, float Min, float Max, List<byte[][]> ListSelectedLUTs, int Z)
{
Bitmap BMP = new Bitmap(ImageFloat.Width, ImageFloat.Height, PixelFormat.Format24bppRgb);
BitmapData bData = BMP.LockBits(new Rectangle(0, 0, ImageFloat.Width, ImageFloat.Height), ImageLockMode.ReadWrite, PixelFormat.Format24bppRgb);
/*the size of the image in bytes */
int size = bData.Stride * bData.Height;
/*Allocate buffer for image*/
byte[] ConvertedValues = new byte[size];
int Zpos = Z * ImageFloat.Width * ImageFloat.Height;
int Ypos;
float MAXMIN = Max - Min;
double NewValue;
byte CurrentRed;
byte CurrentGreen;
byte CurrentBlue;
for (int Channel = 0; Channel < ImageFloat.GetNumChannels(); Channel++)
{
byte[][] SelectedLUT = ListSelectedLUTs[Channel];
int LUTLength = SelectedLUT[0].Length - 1;
for (int j = 0; j < ImageFloat.Height; j++)
{
Ypos = j * AssociatedImage.Width;
for (int i = 0; i < ImageFloat.Width; i++)
{
float Value = ImageFloat.SingleChannelImage[Channel].Data[i + Ypos + Zpos];
int ConvertedValue = (int)((LUTLength * (Value - Min)) / MAXMIN);
if (ConvertedValue < 0) ConvertedValue = 0;
else if (ConvertedValue > LUTLength) ConvertedValue = LUTLength;
CurrentRed = (byte)SelectedLUT[0][ConvertedValue];
CurrentGreen = (byte)SelectedLUT[1][ConvertedValue];
CurrentBlue = (byte)SelectedLUT[2][ConvertedValue];
NewValue = ConvertedValues[i * 3 + j * bData.Stride] + CurrentBlue;
if (NewValue > 255)
ConvertedValues[i * 3 + j * bData.Stride] = 255;
else
ConvertedValues[i * 3 + j * bData.Stride] += CurrentBlue;
NewValue = ConvertedValues[i * 3 + j * bData.Stride + 1] + CurrentGreen;
if (NewValue > 255)
ConvertedValues[i * 3 + j * bData.Stride + 1] = 255;
else
ConvertedValues[i * 3 + j * bData.Stride + 1] += CurrentGreen;
NewValue = ConvertedValues[i * 3 + j * bData.Stride + 2] + CurrentRed;
if (NewValue > 255)
ConvertedValues[i * 3 + j * bData.Stride + 2] = 255;
else
ConvertedValues[i * 3 + j * bData.Stride + 2] += CurrentRed;
//for (int RGBIdx = 0; RGBIdx < 3; RGBIdx++)
//{
// NewValue = (ConvertedValues[i * 3 + j * bData.Stride + RGBIdx] + ConvertedValue);
// if (NewValue >= LUTLength) NewValue = LUTLength - 1;
// // now go through the LUT
// //ConvertedValues[i * 3 + j * bData.Stride + 0] = SelectedLUT[2][NewValue];
// //ConvertedValues[i * 3 + j * bData.Stride + 1] = SelectedLUT[1][NewValue];
// ConvertedValues[i * 3 + j * bData.Stride + RGBIdx] = SelectedLUT[RGBIdx][NewValue];
//}
//ConvertedValues[i * 3 + j * bData.Stride + Channel] = (byte)NewValue;
}
}
}
//for (int j = 0; j < ImageFloat.Height; j++)
//{
// Ypos = j * AssociatedImage.Width;
// for (int i = 0; i < ImageFloat.Width; i++)
// {
// BMP.SetPixel(i, j, Color.FromArgb(SelectedLUT[0][ConvertedValues[i+Ypos]],
// SelectedLUT[1][ConvertedValues[i + Ypos]],
// SelectedLUT[2][ConvertedValues[i + Ypos]]));
// }
//}
/*This overload copies data of /size/ into /data/ from location specified (/Scan0/)*/
//System.Runtime.InteropServices.Marshal.Copy(bData.Scan0, ConvertedValues, 0, size);
//for (int i = 0; i < size; i += bitsPerPixel / 8)
//{
// double magnitude = 1 / 3d * (ConvertedValues[i] + ConvertedValues[i + 1] + ConvertedValues[i + 2]);
// //data[i] is the first of 3 bytes of color
//}
/* This override copies the data back into the location specified */
System.Runtime.InteropServices.Marshal.Copy(ConvertedValues, 0, bData.Scan0, ConvertedValues.Length);
BMP.UnlockBits(bData);
Form1 F = new Form1();
F.pictureBox1.Image = BMP;
F.ShowDialog();
return BMP;
}
public void SetInputData(cImage input, int inputBand)
{
this.Input = input;
this.ListChannelsToBeProcessed.Add(inputBand);
}
public void CurrentPanel_DragDrop(object sender, DragEventArgs e)
{
cImage SourceImage = (cImage)e.Data.GetData(typeof(cImage));
cDisplaySingleImage NewView = new cDisplaySingleImage();
cImage NewIm = new cImage(SourceImage.Width, SourceImage.Height, SourceImage.Depth, SourceImage.GetNumChannels() + this.AssociatedImage.GetNumChannels());
int IdxChannel = 0;
for (int i = 0; i < SourceImage.GetNumChannels(); i++)
Array.Copy(SourceImage.SingleChannelImage[i].Data, NewIm.SingleChannelImage[IdxChannel++].Data, NewIm.SliceSize);
for (int i = 0; i < this.AssociatedImage.GetNumChannels(); i++)
Array.Copy(this.AssociatedImage.SingleChannelImage[i].Data, NewIm.SingleChannelImage[IdxChannel++].Data, NewIm.SliceSize);
NewView.SetInputData(NewIm);
NewView.Run();
cGlobalInfo.WindowHCSAnalyzer.richTextBoxConsole.AppendText("DragNDrop: from " + SourceImage.Name + " to " + this.AssociatedImage.Name + "\n");
}
public void SetInputData(cImage input)
{
this.Input = input;
this.ListChannelsToBeProcessed.AddRange(input.GetListChannels());
}
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();
}
// Image ImageToDisp = new Bitmap(@"C:\Workspace\IM3\IM3 Plugin3\bin\Background.png");
///// <summary>
///// Optional method to override. Init() is called before the loop of Process() call
///// </summary>
//public override void Init()
//{
//}
/// <summary>
/// Process() is called in a loop when the user start a process.
/// </summary>
/// <param name="experiment"></param>
//public override void Process(Experiment experiment)
//{
// // Use Experiment as you wish!
// //Experiment e = experiment;
// for (int i = 0; i < experiment.Sequences;i++)
// {
// Sequence SeqToProcess = experiment.SequenceList[i];
// AnalyseSequence(experiment, SeqToProcess);
// }
//}
///// <summary>
///// Optional method to override. Conclude() is called after the loop of Process() call
///// </summary>
//public override void Conclude()
//{
//}
public Plugin3D(cImage AssociatedImage)
{
InitializeComponent();
this.AssociatedImage = AssociatedImage;
Show();
}
public void Run()
{
// first we have to convert the image with the right number of color
cImage RescaledInput = new cImage(Input.Width, Input.Height, Input.Depth, 1);
int[] Histo = new int[HistoSize];
// Rescale(Input, inputBand, RescaledInput, 0, 0, HistoSize - 1);
float[] inp = RescaledInput.SingleChannelImage[0].Data;
float[] outp = Output.SingleChannelImage[outputBand].Data;
int PosX, PosY;
for (int depth = 0; depth < Input.Depth; depth++)
{
int i, j, ki, kj;
int Value = 0;
int IdxFinal = 0;
int Threshold = ((2 * Radius + 1) * (2 * Radius + 1)) / 2;
#region main loop
for (j = 0; j < Input.Height; j++)
{
for (int Idx = 0; Idx < HistoSize; Idx++)
Histo[Idx] = 0;
for (kj = -Radius; kj <= Radius; kj++)
for (ki = -Radius; ki <= Radius; ki++)
{
PosX = ki;
if (PosX < 0) PosX = -PosX - 1;
else if (PosX >= Input.Width) PosX = 2 * Input.Width - PosX - 1;
PosY = kj + j;
if (PosY < 0) PosY = -PosY - 1;
else if (PosY >= Input.Height) PosY = 2 * Input.Height - PosY - 1;
Histo[(int)inp[PosX + PosY * Input.Width + depth * Input.SliceSize]]++;
}
Value = 0;
IdxFinal = 0;
while (Value < Threshold)
{
Value += Histo[IdxFinal];
IdxFinal++;
}
outp[Radius + 1 + j * Input.Width + depth * Input.SliceSize] = IdxFinal;
//for (i = 0; i < input.Width; i++)
for (i = 0; i < Input.Width/* - (radius + 1)*/; i++)
{
// remove the first column
for (int Idx = -Radius; Idx <= Radius; Idx++)
{
PosX = i - Radius - 1;
if (PosX < 0) PosX = -PosX - 1;
else if (PosX >= Input.Width) PosX = 2 * Input.Width - PosX - 1;
PosY = j + Idx;
if (PosY < 0) PosY = -PosY - 1;
else if (PosY >= Input.Height) PosY = 2 * Input.Height - PosY - 1;
Histo[(int)inp[PosX + PosY * Input.Width + depth * Input.SliceSize]]--;
}
// add the new column
for (int Idx = -Radius; Idx <= Radius; Idx++)
{
PosX = i + Radius;
if (PosX < 0) PosX = -PosX - 1;
if (PosX >= Input.Width) PosX = Input.Width - (PosX - Input.Width + 1);
PosY = j + Idx;
if (PosY < 0) PosY = -PosY - 1;
if (PosY >= Input.Height) PosY = 2 * Input.Height - PosY - 1;
Histo[(int)inp[PosX + PosY * Input.Width + depth * Input.SliceSize]]++;
}
Value = 0;
IdxFinal = 0;
while (Value < Threshold)
{
Value += Histo[IdxFinal];
IdxFinal++;
}
//return;
outp[i + j * Input.Width + depth * Input.SliceSize] = IdxFinal;
}
}
#endregion
}
return;
}
public cFeedBackMessage Run()
{
if (base.Start() == false)
{
base.FeedBackMessage.IsSucceed = false;
return base.FeedBackMessage;
}
#region parameters initilization
object _firstValue = base.ListProperties.FindByName("Kernel size");
int KernelSize = 0;
if (_firstValue == null)
{
base.GenerateError("Kernel size not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
KernelSize = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("Kernel size cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Image width");
int ImWidth = 0;
if (_firstValue == null)
{
base.GenerateError("Image width not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
ImWidth = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("Image width cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Image height");
int ImHeight = 0;
if (_firstValue == null)
{
base.GenerateError("Image height not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
ImHeight = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("Image height cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Image depth");
int ImDepth = 0;
if (_firstValue == null)
{
base.GenerateError("Image depth not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
ImDepth = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("Image depth cast didn't work");
return base.FeedBackMessage;
}
#endregion
if (this.Input[0].Count == 2) ImDepth = 1;
if (this.Input[0].Count == 1)
{
ImDepth = 1;
ImHeight = 1;
}
this.Output = new cImage(ImWidth, ImHeight, ImDepth, this.Input.Count);
cImageDrawKernel GK = new cImageDrawKernel();
GK.sigma_x = KernelSize;
GK.sigma_y = KernelSize;
GK.sigma_z = KernelSize;
GK.Run();
cImage K = GK.GetOutPut();
for (int IdxChannel = 0; IdxChannel < this.Input.Count; IdxChannel++)
{
cExtendedTable CurrentTable = this.Input[IdxChannel];
cExtendedList ListVolumes = new cExtendedList();
double MaxX = CurrentTable[0].Max();
double MinX = CurrentTable[0].Min();
double MaxY = CurrentTable[1].Max();
double MinY = CurrentTable[1].Min();
double MaxZ = 0;
double MinZ = 0;
if (CurrentTable.Count>2)
{
MaxZ = CurrentTable[2].Max();
MinZ = CurrentTable[2].Min();
}
this.Output.SingleChannelImage[IdxChannel].Resolution.X = (MaxX - MinX) / (double)ImWidth;
this.Output.SingleChannelImage[IdxChannel].Resolution.Y = (MaxY - MinY) / (double)ImHeight;
this.Output.SingleChannelImage[IdxChannel].Resolution.Z = (MaxZ - MinZ) / (double)ImDepth;
if (CurrentTable.Count > 2)
{
for (int j = 0; j < CurrentTable[0].Count; j++)
{
double TmpValueX = (ImWidth * (CurrentTable[0][j] - MinX)) / (MaxX - MinX) - K.Width / 2;
double TmpValueY = (ImHeight * (CurrentTable[1][j] - MinY)) / (MaxY - MinY) - K.Height / 2;
double TmpValueZ = (ImDepth * (CurrentTable[2][j] - MinZ)) / (MaxZ - MinZ) - K.Depth / 2;
this.Output.AddInto(K, (int)TmpValueX, (int)TmpValueY, (int)TmpValueZ, IdxChannel);
}
}
else
{
for (int j = 0; j < CurrentTable[0].Count; j++)
{
double TmpValueX = (ImWidth * (CurrentTable[0][j] - MinX)) / (MaxX - MinX) - K.Width / 2;
double TmpValueY = ImHeight - (ImHeight * (CurrentTable[1][j] - MinY)) / (MaxY - MinY) - K.Height / 2;
this.Output.AddInto(K, (int)TmpValueX, (int)TmpValueY, 0, IdxChannel);
}
}
cListExtendedTable TablesForDensity = new cListExtendedTable(this.Output);
for (int idxChannel = 0; idxChannel < this.Output.GetNumChannels(); idxChannel++)
{
this.Output.SingleChannelImage[idxChannel].Name = this.Input.Name;//cGlobalInfo.ListCellularPhenotypes[idxChannel].Name;
float Sum = 1;
if (IsNormalized)
{
Sum = (float)TablesForDensity[idxChannel].Sum();
if (Sum <= 0.0) continue;
for (int i = 0; i < this.Output.SingleChannelImage[idxChannel].Data.Length; i++)
{
this.Output.SingleChannelImage[idxChannel].Data[i] = (10000000 * this.Output.SingleChannelImage[idxChannel].Data[i]) / Sum;
}
}
//else
//{
// for (int i = 0; i < this.Output.SingleChannelImage[idxChannel].Data.Length; i++)
// {
// // if (ClassPopulations[idxChannel] > 0)
// this.Output.SingleChannelImage[idxChannel].Data[i] = this.Output.SingleChannelImage[idxChannel].Data[i];
// }
//}
}
}
this.Output.SingleChannelImage[0].UpDateMax();
this.Output.SingleChannelImage[0].UpDateMin();
base.End();
return FeedBackMessage;
}
public void SetInputData(cImage input, List<int> ListChannelsToBeProcessed)
{
this.Input = input;
this.ListChannelsToBeProcessed.AddRange(ListChannelsToBeProcessed);
}
internal ConnectedVoxels(int label, cImage labeledImage, cImage image, eConnectivity connectivity)
: base(label, labeledImage, image, connectivity)
{
}
private void AnalyseSequence(cImage SeqToAnalyse)
{
// //FormForThumbnails WindThumbnail = new FormForThumbnails();
// //for (int k = 0; k < ListFormForControl.Count; k++)
// //{
// // FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k-1);
// // Obj.DisplayThumbnail(WindThumbnail);
// //}
// //WindThumbnail.Show();
// //return;
#region initialization
if (SeqToAnalyse == null) return;
// create World
if (Current3DWorld == null)
{
Current3DWorld = new c3DNewWorld(new cPoint3D(SeqToAnalyse.Width, SeqToAnalyse.Height, SeqToAnalyse.Depth),
new cPoint3D(SeqToAnalyse.Resolution));
}
else
{
// // Current3DWorld.ren1.
// Current3DWorld.Terminate();
Current3DWorld = null;
Current3DWorld = new c3DNewWorld(new cPoint3D(SeqToAnalyse.Width, SeqToAnalyse.Height, SeqToAnalyse.Depth),
new cPoint3D(SeqToAnalyse.Resolution));
}
for (int k = 0; k < ListFormForControl.Count; k++)
{
FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k-1);
if (Obj.numericUpDownChannel.Value >= SeqToAnalyse.GetNumChannels())
{
MessageBox.Show("Wrong number of channels", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
}
// // Current3DWorld.ListObjControl = ListFormForControl;
// // dataGridViewForClassif.DataSource = CurrentTable;
// if (DataGrid == null)
// {
// DataGrid = new FormForDataGridView();
// DataGrid.Show();
// }
// Current3DWorld.SetLinkToDataGridView(DataGrid.dataGridViewForResults);
Current3DWorld.ListMetaObjectList = new List<cMetaBiologicalObjectList>();
cMetaBiologicalObjectList ListMetacells = new cMetaBiologicalObjectList("List Meta Objects");
Current3DWorld.ListMetaObjectList.Add(ListMetacells);
#endregion
#region Detection
for (int k = 0; k < ListFormForControl.Count; k++)
{
FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k -1);
if (Obj.radioButtonIsVolume.Checked) // we have to detect a volume !
{
cVolumeDetection Detection = new cVolumeDetection(SeqToAnalyse, (int)Obj.numericUpDownChannel.Value, Obj.WindowForVolumeDetection.checkBoxIsBorderKill.Checked);
Detection.SetShift(new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value));
if ((Obj.checkBoxPreProcessings.Checked == false) || (Obj.WindowForPreProcessing.checkBoxMedianIsDisabled.Checked))
{
Detection.SetMedian(-1);
Detection.SetShift(new cPoint3D(0, 0, 0));
}
else
{
Detection.SetMedian((int)Obj.WindowForPreProcessing.numericUpDownMedianKernel.Value);
Detection.SetShift(new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value));
}
if (Obj.WindowForVolumeDetection.checkBoxVolumeSmooth.Checked)
Detection.MeshSmoother = new cMeshSmoother((int)Obj.WindowForVolumeDetection.numericUpDownSmoothIterations.Value);
if ((Obj.comboBoxContainer.SelectedItem !=null) && (Obj.comboBoxContainer.SelectedItem.ToString() != ""))
{
Detection.SetContainers(Current3DWorld.GetListBiologicalObjectsOfType(Obj.comboBoxContainer.Items[0].ToString()));
if (Obj.InOrOut.radioButtonIn.Checked) Detection.SetContainersMode(0);
else Detection.SetContainersMode(1);
}
else
Detection.SetContainers(null);
if (Obj.WindowForVolumeDetection.checkBoxIsRegionGrowing.Checked == false) // no region growing direct detection
{
Obj.AssociatedBiologicalObjectList = Detection.IntensityThreshold((float)Obj.WindowForVolumeDetection.numericUpDownIntensityThreshold.Value,
(float)Obj.WindowForVolumeDetection.numericUpDownVolumeMinVol.Value,
(float)Obj.WindowForVolumeDetection.numericUpDownVolumeMaxVol.Value);
}
else // region growing
{
if (Obj.WindowForVolumeDetection.radioButtonRegionsBased.Checked) // start from a segmentation
{
if (Obj.WindowForVolumeDetection.radioButtonVolumeDetectionNew.Checked) // a new segmentation has to be performed
{
// // Image3D CurrentPatch = new Image3D(2 * Radius, 2 * Radius, 1, CurrentImageToProcess.NumBands);
cImage CurrentBinary = new cImage(SeqToAnalyse.Width, SeqToAnalyse.Height, SeqToAnalyse.Depth, 1);
for (int i = 0; i < CurrentBinary.ImageSize; i++)
{
if (SeqToAnalyse.SingleChannelImage[(int)Obj.numericUpDownChannel.Value].Data[i] >= (float)Obj.WindowForVolumeDetection.numericUpDownIntensityThreshold.Value)
CurrentBinary.SingleChannelImage[0].Data[i] = 1;
}
eConnectivity CurrentConnectivity = eConnectivity.TWOD_4;
if (CurrentBinary.Depth > 1)
CurrentConnectivity = eConnectivity.THREED_6;
ConnectedComponentSet OFNucleus = new ConnectedComponentSet(CurrentBinary, null, null, 0, CurrentConnectivity, (int)Obj.WindowForVolumeDetection.numericUpDownRegionBasedMinArea.Value, (int)Obj.WindowForVolumeDetection.numericUpDownRegionBasedMaxArea.Value);
// // RegionGrowing = new cRegionGrowing(OFNucleus, NewSeq[0], (int)numericUpDownChannelForRegionGrowing.Value, (float)numericUpDownIntensityForRegionGrowing.Value, (int)numericUpDownMaxNucleusArea.Value);
int NumIterations = -1;
if (Obj.WindowForVolumeDetection.checkBoxIsConvergence.Checked == false) NumIterations = (int)Obj.WindowForVolumeDetection.numericUpDownIterationNumber.Value;
float MergingRatio = (float)((Obj.WindowForVolumeDetection.trackBarMergingStrength.Maximum - Obj.WindowForVolumeDetection.trackBarMergingStrength.Value) / 100.0);
Obj.AssociatedBiologicalObjectList = Detection.RegionGrowing(OFNucleus,
(float)Obj.WindowForVolumeDetection.numericUpDownIntensityForRegionGrowing.Value,
(float)Obj.WindowForVolumeDetection.numericUpDownVolumeMinVol.Value,
(float)Obj.WindowForVolumeDetection.numericUpDownVolumeMaxVol.Value, NumIterations, MergingRatio);
}
// else
// {
// throw new System.ArgumentException("Not implemented", "Error");
// }
// }
// else // start from seeds points
// {
// // first gather the seeds
// if (Obj.WindowForVolumeDetection.comboBoxExistingSpotsDetected.Items.Count == 0) break;
// List<cBiological3DObject> ListSeeds = Current3DWorld.GetListBiologicalObjectsOfType(Obj.WindowForVolumeDetection.comboBoxExistingSpotsDetected.Items[0].ToString());
// int NumIterations = -1;
// if (Obj.WindowForVolumeDetection.checkBoxIsConvergence.Checked == false) NumIterations = (int)Obj.WindowForVolumeDetection.numericUpDownIterationNumber.Value;
// float MergingRatio = (float)((Obj.WindowForVolumeDetection.trackBarMergingStrength.Maximum - Obj.WindowForVolumeDetection.trackBarMergingStrength.Value) / 100.0);
// Obj.AssociatedBiologicalObjectList = Detection.RegionGrowing(ListSeeds,
// (float)Obj.WindowForVolumeDetection.numericUpDownIntensityForRegionGrowing.Value,
// (float)Obj.WindowForVolumeDetection.numericUpDownVolumeMinVol.Value,
// (float)Obj.WindowForVolumeDetection.numericUpDownVolumeMaxVol.Value, NumIterations, MergingRatio);
}
}
if (Obj.AssociatedBiologicalObjectList != null)
{
Obj.richTextBoxInfo.AppendText(Obj.AssociatedBiologicalObjectList.Count + " objects detected.");
for (int i = 0; i < Obj.AssociatedBiologicalObjectList.Count; i++)
{
cBiological3DVolume TmpVol = (cBiological3DVolume)Obj.AssociatedBiologicalObjectList[i];
Obj.AssociatedBiologicalObjectList[i].SetType(Obj.textBoxName.Text);
// TmpVol.ThumbnailnewImage = imageListForThumbnail.Images[Obj.AssociatedBiologicalObjectList[i].GetType() + ".jpg"];
Obj.AssociatedBiologicalObjectList[i].Name = Obj.textBoxName.Text + " " + i;
// Obj.AssociatedBiologicalObjectList[i].IsMaster = Obj.IsMasterObject();
// List<double> Res = TmpVol.Information.GetInformation();
if (Obj.checkBoxIsDisplayName.Checked)
{
cGeometric3DObject AssociatedText = TmpVol.AttachText(TmpVol.Name, 10, Color.White);
AssociatedText.IsStayInFrontOfCamera = true;
Current3DWorld.AddGeometric3DObject(AssociatedText);
// TmpVol.AddText(TmpVol.Name, Current3DWorld, (double)Obj.ForText.numericUpDownArrowScale.Value, Obj.ForText.buttonChangeColorPositive.BackColor);
}
if (Obj.checkIsBoxPointingArrow.Checked)
{
cGeometric3DObject AssociatedArrow = TmpVol.AttachPointingArrow((double)Obj.ForArrow.numericUpDownArrowScale.Value,
Obj.ForArrow.buttonChangeColorPositive.BackColor);
Current3DWorld.AddGeometric3DObject(AssociatedArrow);
}
Obj.AssociatedBiologicalObjectList[i].SetOpacity((double)Obj.ColorOpacity.numericUpDownValue.Value);
// if the object it the Master then create a meta-object and put it inside
if (Obj.IsMasterObject())
{
cMetaBiologicalObject Cell = new cMetaBiologicalObject(Obj.WindowForMaster.textBoxName.Text + i, Current3DWorld.ListMetaObjectList[0], Obj.AssociatedBiologicalObjectList[i]);
// // Cell.AddObject(Obj.AssociatedBiologicalObjectList[i]);
Current3DWorld.ListMetaObjectList[0].Add(Cell);
}
}
if (Obj.radioButtonColorSingle.Checked)
Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Regular);
else if (Obj.radioButtonColorRandom.Checked)
Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Random);
else if (Obj.radioButtonColorIndexed.Checked)
Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Indexed);
}
}
else if (Obj.RadioButtonIsSpot.Checked)
{
cSpotDetection Detection = new cSpotDetection(SeqToAnalyse, (int)Obj.numericUpDownChannel.Value);
if ((Obj.checkBoxPreProcessings.Checked == false) || (Obj.WindowForPreProcessing.checkBoxMedianIsDisabled.Checked))
{
Detection.SetMedian(-1);
Detection.SetShift(new cPoint3D(0, 0, 0));
}
else
{
Detection.SetMedian((int)Obj.WindowForPreProcessing.numericUpDownMedianKernel.Value);
Detection.SetShift(new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value));
}
if ((Obj.comboBoxContainer.Items.Count > 0) && (Obj.comboBoxContainer.SelectedItem != null))
{
Detection.SetContainers(Current3DWorld.GetListBiologicalObjectsOfType(Obj.comboBoxContainer.SelectedItem.ToString()));
if (Obj.InOrOut.radioButtonIn.Checked) Detection.SetContainersMode(0);
else Detection.SetContainersMode(1);
}
Obj.AssociatedBiologicalObjectList = Detection.HessianDetection((float)Obj.WindowForSpotDetection.numericUpDownSpotRadius.Value,
(float)Obj.WindowForSpotDetection.numericUpDownIntensityThreshold.Value,
(int)Obj.WindowForSpotDetection.numericUpDownSpotLocality.Value,
(double)Obj.WindowForSpotDetection.numericUpDownSphereDisplayRadius.Value);
Obj.richTextBoxInfo.AppendText(Obj.AssociatedBiologicalObjectList.Count + " objects detected.");
for (int i = 0; i < Obj.AssociatedBiologicalObjectList.Count; i++)
{
cBiologicalSpot TmpSpot = (cBiologicalSpot)Obj.AssociatedBiologicalObjectList[i];
TmpSpot.Name = Obj.textBoxName.Text + " " + i;
TmpSpot.SetType(Obj.textBoxName.Text);
// TmpSpot.ThumbnailnewImage = imageListForThumbnail.Images[Obj.AssociatedBiologicalObjectList[i].GetType() + ".jpg"];
// if (Obj.checkBoxIsDisplayName.Checked)
// TmpSpot.AddText(TmpSpot.Name, Current3DWorld, (double)Obj.ForText.numericUpDownArrowScale.Value, Obj.ForText.buttonChangeColorPositive.BackColor);
if (Obj.checkIsBoxPointingArrow.Checked)
{
cGeometric3DObject AssociatedArrow = TmpSpot.AttachPointingArrow((double)Obj.ForArrow.numericUpDownArrowScale.Value, Obj.ForArrow.buttonChangeColorPositive.BackColor);
Current3DWorld.AddGeometric3DObject(AssociatedArrow);
}
// TmpSpot.SetOpacity((double)Obj.ColorOpacity.numericUpDownValue.Value);
// // if the object it the Master then create a meta-object and put it inside
if (Obj.IsMasterObject())
{
cMetaBiologicalObject Cell = new cMetaBiologicalObject("Cell " + i, Current3DWorld.ListMetaObjectList[0], Obj.AssociatedBiologicalObjectList[i]);
// // Cell.AddObject(Obj.AssociatedBiologicalObjectList[i]);
Current3DWorld.ListMetaObjectList[0].Add(Cell);
}
// /*cMetaBiologicalObject Cell = */
// //Current3DWorld.ListMetaObjectList[0].AssociateWith(Current3DWorld.ListMetaObjectList[0].FindTheClosestVolumeFrom(TmpSpot.GetCentroid(), 20), TmpSpot);
}
// if (Obj.radioButtonColorSingle.Checked)
// Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Regular);
// else if (Obj.radioButtonColorRandom.Checked)
// Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Random);
// else if (Obj.radioButtonColorIndexed.Checked)
// Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Indexed);
}
else if (Obj.radioButtonIsVolumeRendering.Checked)
{
Current3DWorld.AddVolume3D(new cVolumeRendering3D(this.AssociatedImage.SingleChannelImage[(int)Obj.numericUpDownChannel.Value],
new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value),
null, Current3DWorld));
// cVolume3D Volume = new cVolume3D(SeqToAnalyse, (int)Obj.numericUpDownChannel.Value, new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value));
// Current3DWorld.AddVolume3D(Volume, Color.Black, Obj.buttonChangeColorPositive.BackColor);
}
// Thread oThread = new Thread(new ThreadStart(Obj.DisplayDone));
}
#endregion
#region Objects Association
cMetaBiologicalObjectList MetaCellList = Current3DWorld.ListMetaObjectList[0];
// let's associate the objects
for (int k = 0; k < ListFormForControl.Count; k++)
{
FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k -1);
// that's a volume rendering ... no connection
if (Obj.radioButtonIsVolumeRendering.Checked) continue;
// the object is the master
if (Obj.IsMasterObject()) continue;
// this object has not connections ... is not associated to the master
if (Obj.comboBoxLinkToTheMaster.SelectedIndex == 0) continue;
cPoint3D ClosestPt = new cPoint3D(0, 0, 0);
foreach (cBiological3DVolume CurrentSubObj in Obj.AssociatedBiologicalObjectList)
{
cBiological3DVolume ObjectToIdentify = null;
switch (Obj.comboBoxLinkToTheMaster.SelectedIndex)
{
case 1: // association by distance to the master centroid
ObjectToIdentify = MetaCellList.FindTheClosestVolumeCentroidFrom(CurrentSubObj.GetCentroid(), (double)Obj.WindowDistanceToMaster.numericUpDownDistanceMaxToMaster.Value);
break;
case 2:
// //cBiological3DVolume CurrentVolume
ObjectToIdentify = MetaCellList.FindTheClosestVolumeFrom(CurrentSubObj, (double)Obj.WindowDistanceToMaster.numericUpDownDistanceMaxToMaster.Value, out ClosestPt);
break;
default:
break;
}
if (ObjectToIdentify == null) continue;
cMetaBiologicalObject Cell = MetaCellList.AssociateWith(ObjectToIdentify, CurrentSubObj);
// // -------------- draw information and links between the objects ---------------------
if (Obj.WindowDistanceToMaster.checkBoxDrawLinkToMasterCenter.Checked)
{
c3DLine CurrLine = new c3DLine(CurrentSubObj.GetCentroid(), ObjectToIdentify.GetCentroid());
Current3DWorld.AddGeometric3DObject(CurrLine);
//if (Obj.WindowDistanceToMaster.checkBoxDisplayBranchToCenterDistance.Checked)
// CurrLine.DisplayLenght(Current3DWorld, 0.4);
}
// // -------------- draw information and links between the objects ---------------------
if (Obj.WindowDistanceToMaster.checkBoxDrawLinkToMasterEdges.Checked)
{
c3DLine CurrLine1 = new c3DLine(CurrentSubObj.GetCentroid(), ClosestPt);
Current3DWorld.AddGeometric3DObject(CurrLine1);
//if(Obj.WindowDistanceToMaster.checkBoxDisplayBranchToEdgesDistance.Checked)
// CurrLine1.DisplayLenght(Current3DWorld, 0.4);
}
}
}
#endregion
#region Post Processings
for (int k = 0; k < ListFormForControl.Count; k++)
{
FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k - 1);
// the object is the master
// // if (!Obj.IsMasterObject()) continue;
if (!Obj.WindowForMaster.checkBoxDrawAssociatedDelaunay.Checked) continue;
foreach (cMetaBiologicalObject CurrentMeta in MetaCellList)
{
Current3DWorld.AddGeometric3DObject(CurrentMeta.GenerateDelaunay(2.0f,true));
}
}
if (PostProcessWindow.checkBoxRemoveUnAssociatedObjects.Checked)
{
int RemovedObjects = Current3DWorld.RemoveNonAssociatedObjects();
Console.WriteLine(RemovedObjects + " objects removed.");
}
// if (PostProcessWindow.checkBoxExportMetaObjectSignatures.Checked)
// {
// if (CurrentTable == null)
// {
// CurrentTable = new DataTable();
// if (CurrentExperiment == null)
// CurrentTable.Columns.Add(new DataColumn("Image Idx", typeof(int)));
// else
// {
// CurrentTable.Columns.Add(new DataColumn("Image Col.", typeof(int)));
// CurrentTable.Columns.Add(new DataColumn("Image Row", typeof(int)));
// }
// CurrentTable.Columns.Add(new DataColumn("Meta Object Name", typeof(string)));
// foreach (string DescName in MetaCellList[0].GetSignatureNames())
// CurrentTable.Columns.Add(new DataColumn(DescName, typeof(double)));
// CurrentTable.Columns.Add(new DataColumn("Class", typeof(double)));
// }
// foreach (cMetaBiologicalObject CurrentMeta in MetaCellList)
// {
// List<double> CurrentSignature = CurrentMeta.GetSignature();
// CurrentTable.Rows.Add();
// if (CurrentExperiment == null)
// {
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][0] = IdxImageProcessed;
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][1] = CurrentMeta.Name;
// for (int Idx = 0; Idx < CurrentSignature.Count; Idx++)
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][Idx + 2] = CurrentSignature[Idx];
// }
// else
// {
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][0] = CurrentExperiment.Column;
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][1] = CurrentExperiment.Row;
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][2] = CurrentMeta.Name;
// for (int Idx = 0; Idx < CurrentSignature.Count; Idx++)
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][Idx + 3] = CurrentSignature[Idx];
// }
// // Current3DWorld.CopyMetaObjectSignatureToTable(CurrentMeta, 0);
// }
// if (DataGrid != null)
// {
// DataGrid.dataGridViewForResults.DataSource = CurrentTable;
// DataGrid.Update();
// IdxImageProcessed++;
// }
// }
#endregion
// //CurrentTable = new DataTable();
// if (CurrentExperiment == null)
// {
// if (PostProcessWindow.checkBoxDisplayBottomPlate.Checked) Current3DWorld.DisplayBottom(Color.FromArgb(255, 255, 255));
// Current3DWorld.SetBackgroundColor(PostProcessWindow.buttonChangeColorPositive.BackColor);
// Current3DWorld.Render();
// }
// // Current3DWorld.SetLinkToDataGridView(dataGridViewForClassif);
cViewer3D V3D = new cViewer3D();
V3D.SetInputData(Current3DWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Run();
DTW.Display();
}
public void SetInputData(cImage MyData)
{
this.Input = MyData;
}
public void SetInputData(cImage Input)
{
this.Input = Input;
}
// protected override void on
//protected override void OnFormClosing(FormClosingEventArgs e)
//{
// AssociatedImage.Dispose();
// // base.OnFormClosing(e);
//}
public void Unsafe_SetAssociatedImage(cImage Im)
{
this.AssociatedImage = Im;
}
