public void SetInputData(cSingleChannelImage InputImage)
{
this.Input = InputImage;
base.Title += ": " + Input.Name;
this.InputVolume = new cVolumeRendering3D(InputImage, new Classes._3D.cPoint3D(0, 0, 0),null, null);
}
public UserControlSingleLUT(cImagePanel CurrentFormForImageDisplay, cSingleChannelImage AssociatedImageBand, int InitialIdx)
{
this.AssociatedImageBand = AssociatedImageBand;
this.CurrentFormForImageDisplay = CurrentFormForImageDisplay;
this.GlobalInfo = CurrentFormForImageDisplay.GlobalInfo;
this.SelectedLUT = ListLUT.LUT_LINEAR;
InitializeComponent();
if (InitialIdx == 0)
{
this.MaxColorForLinear = Color.FromArgb(255, 255, 0, 0);
}
else if (InitialIdx == 1)
{
this.MaxColorForLinear = Color.FromArgb(255, 0, 255, 0);
}
else if (InitialIdx == 2)
{
this.MaxColorForLinear = Color.FromArgb(255, 0, 0, 255);
}
else
{
this.MaxColorForLinear = Color.FromArgb(255, 255, 0, 0);
}
UpDateLinearLUT();
comboBoxForLUT.Text = "Linear ";
UpDateColorSampleImage();
AssociatedImageBand.UpDateMin();
AssociatedImageBand.UpDateMax();
// this.numericUpDownMinValue.ValueChanged -= new EventHandler(numericUpDownMinValue_ValueChanged);
this.numericUpDownMinValue.Value = (decimal)AssociatedImageBand.Min;
this.numericUpDownMinValue.ValueChanged += new EventHandler(numericUpDownMinValue_ValueChanged);
// this.numericUpDownMaxValue.ValueChanged -= new EventHandler(numericUpDownMaxValue_ValueChanged);
this.numericUpDownMaxValue.Value = (decimal)AssociatedImageBand.Max;
this.numericUpDownMaxValue.ValueChanged += new EventHandler(numericUpDownMaxValue_ValueChanged);
this.trackBarOpacity.ValueChanged += new System.EventHandler(this.trackBarOpacity_ValueChanged);
this.checkBoxIsActive.CheckedChanged += new System.EventHandler(this.checkBoxIsActive_CheckedChanged);
this.comboBoxForLUT.SelectedIndexChanged += new System.EventHandler(this.comboBoxForLUT_SelectedIndexChanged);
this.trackBarGamma.ValueChanged += new System.EventHandler(this.trackBarGamma_ValueChanged);
this.comboBoxForLUT.SelectedValueChanged += new System.EventHandler(this.comboBoxForLUT_SelectedValueChanged);
this.pictureBoxForColorSample.DoubleClick += new System.EventHandler(this.pictureBoxForColorSample_DoubleClick);
this.MouseDown += new System.Windows.Forms.MouseEventHandler(this.UserControlSingleLUT_MouseDown);
this.toolStripMenuItemGammaDefault.Click += new System.EventHandler(this.toolStripMenuItemGammaDefault_Click);
this.textBoxForName.TextChanged += new System.EventHandler(this.textBoxForName_TextChanged);
this.BringToFront();
}
public void SetInputData(cSingleChannelImage Input)
{
this.Input = Input;
}
void LoadFromPath(/*string Path, string FileName*/List<cImageMetaInfo> ListImageMetaInfo)
{
if (ListImageMetaInfo == null) return;
int ChannelStart = 0;
for (int IdxName = 0; IdxName < ListImageMetaInfo.Count; IdxName++)
{
string CurrentName = ListImageMetaInfo[IdxName].FileName;
if (CurrentName == "") continue;
if (CurrentName.Contains("http://"))
{
try
{
using (WebClient Client = new WebClient())
{
string[] ListForExt = CurrentName.Split('.');
Client.DownloadFile(CurrentName, "Tmp." + ListForExt[ListForExt.Length - 1]);
CurrentName = "Tmp." + ListForExt[ListForExt.Length - 1];
}
}
catch (Exception)
{
continue;
}
}
if ((File.Exists(CurrentName) == false)) continue;
string[] ListSplits = CurrentName.Split('.');
string Extension = ListSplits[ListSplits.Length - 1].ToLower();
byte[] rgbValues = null;
int NumBytePerPixel = 0;
int NumBitsPerPixel = 0;
int NumChannels = 0;
object ResMeta = null;
switch (Extension)
{
#region Cellomics c01 - BioFormats
case "c01":
[email protected] MyCellomicsReader = new [email protected]();
MyCellomicsReader.setId(CurrentName);
int SerieCurr = -1;
for (int IdxSerie = 0; IdxSerie < MyCellomicsReader.getSeriesUsedFiles().Count(); IdxSerie++)
{
if (MyCellomicsReader.getSeriesUsedFiles()[IdxSerie] == CurrentName)
{
SerieCurr = IdxSerie;
break;
}
}
MyCellomicsReader.setSeries(SerieCurr);
rgbValues = MyCellomicsReader.openBytes(0);
//int ImC = MyCellomicsReader.getImageCount();
this.Width = MyCellomicsReader.getSizeX();
// ImageProcessorReader r = new ImageProcessorReader(
//new ChannelSeparator(LociPrefs.makeImageReader()));
this.Height = MyCellomicsReader.getSizeY();
this.Depth = MyCellomicsReader.getSizeZ();
NumChannels = MyCellomicsReader.getSizeC();
NumBitsPerPixel = MyCellomicsReader.getBitsPerPixel();
MyCellomicsReader.close();
break;
#endregion
#region tiff - BioFormats
case "tiff":
[email protected] MyTiffReader = new [email protected]();
MyTiffReader.setId(CurrentName);
rgbValues = MyTiffReader.openBytes(0);
this.Width = MyTiffReader.getSizeX();
this.Height = MyTiffReader.getSizeY();
this.Depth = MyTiffReader.getSizeZ();
NumChannels = MyTiffReader.getSizeC();
NumBitsPerPixel = MyTiffReader.getBitsPerPixel();
MyTiffReader.close();
break;
#endregion
#region LSM - BioFormats
case "lsm":
[email protected] MyLSMReader = new [email protected]();
MyLSMReader.setId(CurrentName);
this.Width = MyLSMReader.getSizeX();
this.Height = MyLSMReader.getSizeY();
NumChannels = MyLSMReader.getSizeC();
this.Depth = MyLSMReader.getSizeZ();
this.Name = CurrentName;
this.SliceSize = this.Width * this.Height;
this.ImageSize = SliceSize * Depth;
if (IdxName == 0)
this.SingleChannelImage = new cListSingleChannelImage();
#region GetMetaData
ResMeta = MyLSMReader.getSeriesMetadataValue("VoxelSizeX");
if (ResMeta == null)
this.Resolution.X = 1;
else
this.Resolution.X = ((java.lang.Double)ResMeta).doubleValue();
ResMeta = MyLSMReader.getSeriesMetadataValue("VoxelSizeY");
if (ResMeta == null)
this.Resolution.X = 1;
else
this.Resolution.Y = ((java.lang.Double)ResMeta).doubleValue();
ResMeta = MyLSMReader.getSeriesMetadataValue("VoxelSizeZ");
if (ResMeta == null)
this.Resolution.Z = 1;
else
this.Resolution.Z = ((java.lang.Double)ResMeta).doubleValue();
#endregion
for (int IdxChannel = 0; IdxChannel < NumChannels; IdxChannel++)
this.SingleChannelImage.Add(new cSingleChannelImage(this.Width, this.Height, this.Depth, new cPoint3D(this.Resolution)));
float TmpValue = 0;
byte[] TmpTable;
for (int IdxZ = 0; IdxZ < this.Depth; IdxZ++)
{
for (int IdxChannel = 0; IdxChannel < NumChannels; IdxChannel++)
{
TmpTable = MyLSMReader.openBytes(IdxZ * NumChannels + IdxChannel);
for (int IdxY = 0; IdxY < this.Height; IdxY++)
for (int IdxX = 0; IdxX < this.Width; IdxX++)
{
TmpValue = TmpTable[IdxX + IdxY * this.Width];
this.SingleChannelImage[IdxChannel + ChannelStart].Data[IdxX + IdxY * this.Width + IdxZ * this.SliceSize] = TmpValue;
}
}
}
NumBitsPerPixel = MyLSMReader.getBitsPerPixel();
// if the meta data are ok, take the name
for (int IdxChannel = 0; IdxChannel < NumChannels; IdxChannel++)
{
ResMeta = MyLSMReader.getSeriesMetadataValue("DataChannel #" + (IdxChannel + 1) + " Name");
if (ResMeta != null)
this.SingleChannelImage[IdxChannel + ChannelStart].Name = (string)ResMeta;
}
goto NEXTLOOP;
#endregion
#region tif - FreeImage
case "tif":
//Image<Gray, Single> myImage = new Image<Gray, Single>(@CurrentName);
//var watch = Stopwatch.StartNew();
int PageCount = 1;
this.Depth = PageCount;
NumChannels = 1;
Mat myImage = new Mat(CurrentName, Emgu.CV.CvEnum.LoadImageType.AnyDepth);
//watch.Stop();
//cGlobalInfo.WindowHCSAnalyzer.richTextBoxConsole.AppendText("Opencv = " + watch.ElapsedMilliseconds + "\n");
for (int IDxPlane = 0; IDxPlane < PageCount; IDxPlane++)
{
if (IDxPlane == 0)
{
this.Width = myImage.Width;
this.Height = myImage.Height;
this.Resolution.X = 1;
this.Resolution.Y = 1;
NumBitsPerPixel = 16;
for (int IdxChannel = 0; IdxChannel < NumChannels; IdxChannel++)
{
cSingleChannelImage TmpChannelImage = new cSingleChannelImage(this.Width, this.Height, this.Depth, new cPoint3D(1, 1, 1));
if (ListImageMetaInfo[IdxName].Name != "") TmpChannelImage.Name = ListImageMetaInfo[IdxName].Name;
if (ListImageMetaInfo[IdxChannel].ResolutionX != -1) this.Resolution.X = ListImageMetaInfo[IdxChannel].ResolutionX;
if (ListImageMetaInfo[IdxChannel].ResolutionY != -1) this.Resolution.Y = ListImageMetaInfo[IdxChannel].ResolutionY;
if (ListImageMetaInfo[IdxChannel].ResolutionZ != -1) this.Resolution.Z = ListImageMetaInfo[IdxChannel].ResolutionZ;
Image<Gray, float> myImage2 = myImage.ToImage<Gray, float>();
//var watch2 = Stopwatch.StartNew();
TmpChannelImage.SetNewDataFromOpenCV(myImage2);
//watch2.Stop();
//cGlobalInfo.WindowHCSAnalyzer.richTextBoxConsole.AppendText("Convert = " + watch2.ElapsedMilliseconds + "\n");
this.SingleChannelImage.Add(TmpChannelImage);
}
}
}
this.Name = CurrentName;
this.SliceSize = this.Width * this.Height;
this.ImageSize = SliceSize * Depth;
//goto NEXTLOOP;
break;
}
#endregion
#endregion
NEXTLOOP:;
ChannelStart += NumChannels;
}
}
public cImage(cSingleChannelImage Source, bool CopyData)
{
// this.NumChannels = 1;
this.Width = Source.Width;
this.Height = Source.Height;
this.Depth = Source.Depth;
this.Resolution = new cPoint3D(Source.Resolution);
this.SliceSize = this.Height * this.Width;
this.ImageSize = SliceSize * Depth;
if (CopyData == true)
{
this.SingleChannelImage = new cListSingleChannelImage();
this.SingleChannelImage.Add(new cSingleChannelImage(Source.Width, Source.Height, Source.Depth, Source.Resolution));
this.SingleChannelImage[0].Name = Source.Name;
this.SingleChannelImage[0].Data = new float[Source.Data.Length];
Array.Copy(Source.Data, this.SingleChannelImage[0].Data, Source.Data.Length);
}
else
{
this.SingleChannelImage.Add(Source);
}
this.Name = Source.Name;
}
public cVolumeRendering3D(cSingleChannelImage SingleChannelImage, cPoint3D Pos, byte[][] NewLUT, c3DNewWorld AssociatedWorld)
{
if (SingleChannelImage.Data == null) return;
baseInit(AssociatedWorld);
this.SetName("Volume 3D [" + SingleChannelImage.Name + "]");
this.LUT = NewLUT;
vtk_volume = vtkVolume.New();
vtkImageData imageData = vtkImageData.New();
vtkUnsignedShortArray UshortArray = vtkUnsignedShortArray.New();
voi = vtkExtractVOI.New();
ColorTransferFunction = vtkColorTransferFunction.New();
for (int i = 0; i < SingleChannelImage.Width * SingleChannelImage.Height * SingleChannelImage.Depth; i++)
{
UshortArray.InsertTuple1(i, (ushort)SingleChannelImage.Data[i]); // data are converted to UShort
}
imageData = vtkImageData.New();
imageData.SetDimensions(SingleChannelImage.Width, SingleChannelImage.Height, SingleChannelImage.Depth);
imageData.SetOrigin(0, 0, 0);
if ((SingleChannelImage.Resolution.X == 0) || (SingleChannelImage.Resolution.Y == 0) || (SingleChannelImage.Resolution.Z == 0))
imageData.SetSpacing(1.0, 1.0, 1.0);
else
imageData.SetSpacing(SingleChannelImage.Resolution.X, SingleChannelImage.Resolution.Y, SingleChannelImage.Resolution.Z);
imageData.GetPointData().SetScalars(UshortArray);
voi = vtkExtractVOI.New();
voi.SetInput(imageData);
voi.SetVOI(0, SingleChannelImage.Width - 1, 0, SingleChannelImage.Height - 1, 0, SingleChannelImage.Depth - 1);
voi.SetSampleRate(1, 1, 1);
opacityTransferFunction = vtkPiecewiseFunction.New();
range = imageData.GetScalarRange();
opacityTransferFunction.AddPoint(range[0], 0.0);
opacityTransferFunction.AddPoint(range[1], 0.3);
//opacityTransferFunction.AddPoint(2000, 0.1);
//opacityTransferFunction.AddPoint(range[0] + (range[1]-range[0])/2.0, 0.0);
//opacityTransferFunction.AddPoint(range[1], 0.7);
if (LUT == null)
{
//cLUT MyLut = new cLUT();
//LUT = MyLut.LUT_JET;
ColorTransferFunction.AddRGBPoint(0, 0 , 0, 0);
ColorTransferFunction.AddRGBPoint(1, 1, 1, 1);
}
//double LUTSize = LUT[0].Length;
//for (int i = 0; i < (int)LUTSize; i++)
//{
// colorTransferFunction.AddRGBPoint(i, LUT[0][i] / LUTSize, LUT[1][i] / LUTSize, LUT[2][i] / LUTSize);
//}
ColorTransferFunction.Build();
volumeProperty = vtkVolumeProperty.New();
volumeProperty.SetColor(ColorTransferFunction);
volumeProperty.SetScalarOpacity(opacityTransferFunction);
volumeProperty.SetInterpolationTypeToNearest();
volumeProperty.ShadeOff();
vtkVolumeTextureMapper3D volumeTextureMapper = vtkVolumeTextureMapper3D.New();
volumeTextureMapper.SetInputConnection(voi.GetOutputPort());
//vtkVolumeRayCastCompositeFunction compositeFunction = vtkVolumeRayCastCompositeFunction.New();
//vtkVolumeRayCastMapper volumeMapper = vtkVolumeRayCastMapper.New();
//volumeMapper.SetVolumeRayCastFunction(compositeFunction);
//volumeMapper.SetInputConnection(voi.GetOutputPort());
vtk_volume = vtkVolume.New();
vtk_volume.SetMapper(volumeTextureMapper);
vtk_volume.SetProperty(volumeProperty);
vtk_volume.PickableOn();
vtk_volume.SetPosition(Pos.X, Pos.Y, Pos.Z);
}
public cVolumeRendering3D(cSingleChannelImage SingleChannelImage, cPoint3D Pos, byte[][] NewLUT)
{
this.LUT = NewLUT;
vtk_volume = vtkVolume.New();
vtk_volume.PickableOn();
vtkImageData imageData = vtkImageData.New();
vtkUnsignedShortArray UshortArray = vtkUnsignedShortArray.New();
vtkExtractVOI voi = vtkExtractVOI.New();
vtkPiecewiseFunction opacityTransferFunction = vtkPiecewiseFunction.New();
vtkColorTransferFunction colorTransferFunction = vtkColorTransferFunction.New();
vtkVolumeProperty volumeProperty = vtkVolumeProperty.New();
for (int i = 0; i < SingleChannelImage.Width * SingleChannelImage.Height * SingleChannelImage.Depth; i++)
{
UshortArray.InsertTuple1(i, (ushort)SingleChannelImage.Data[i]);
}
imageData = vtkImageData.New();
imageData.SetDimensions(SingleChannelImage.Width, SingleChannelImage.Height, SingleChannelImage.Depth);
imageData.SetOrigin(0, 0, 0);
if ((SingleChannelImage.Resolution.X == 0) || (SingleChannelImage.Resolution.Y == 0) || (SingleChannelImage.Resolution.Z == 0))
imageData.SetSpacing(1.0, 1.0, 1.0);
else
imageData.SetSpacing(SingleChannelImage.Resolution.X, SingleChannelImage.Resolution.Y, SingleChannelImage.Resolution.Z);
imageData.GetPointData().SetScalars(UshortArray);
voi = vtkExtractVOI.New();
voi.SetInput(imageData);
voi.SetVOI(0, SingleChannelImage.Width - 1, 0, SingleChannelImage.Height - 1, 0, SingleChannelImage.Depth - 1);
voi.SetSampleRate(1, 1, 1);
opacityTransferFunction = vtkPiecewiseFunction.New();
range = imageData.GetScalarRange();
opacityTransferFunction.AddPoint(0, 0.0);
opacityTransferFunction.AddPoint(255, 1);
//opacityTransferFunction.AddPoint(range[0] + (range[1]-range[0])/2.0, 0.0);
//opacityTransferFunction.AddPoint(range[1], 0.7);
if (LUT == null)
{
cLUT MyLut = new cLUT();
LUT = MyLut.LUT_JET;
}
double LUTSize = LUT[0].Length;
for (int i = 0; i < (int)LUTSize - 1; i++)
{
colorTransferFunction.AddRGBPoint(i, this.LUT[0][i] / LUTSize, this.LUT[1][i] / LUTSize, this.LUT[2][i] / LUTSize);
}
colorTransferFunction.Build();
volumeProperty = vtkVolumeProperty.New();
volumeProperty.SetColor(colorTransferFunction);
volumeProperty.SetScalarOpacity(opacityTransferFunction);
volumeProperty.SetInterpolationTypeToLinear();
volumeProperty.ShadeOff();
volumeProperty.SetAmbient(0.6);
volumeProperty.SetDiffuse(0.6);
volumeProperty.SetSpecular(0.1);
vtkVolumeTextureMapper3D volumeTextureMapper = vtkVolumeTextureMapper3D.New();
volumeTextureMapper.SetInputConnection(voi.GetOutputPort());
//vtkVolumeRayCastCompositeFunction compositeFunction = vtkVolumeRayCastCompositeFunction.New();
//vtkVolumeRayCastMapper volumeMapper = vtkVolumeRayCastMapper.New();
//volumeMapper.SetVolumeRayCastFunction(compositeFunction);
//volumeMapper.SetInputConnection(voi.GetOutputPort());
vtk_volume = vtkVolume.New();
vtk_volume.SetMapper(volumeTextureMapper);
vtk_volume.SetProperty(volumeProperty);
vtk_volume.PickableOn();
vtk_volume.SetPosition(Pos.X, Pos.Y, Pos.Z);
}
