/// <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 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 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 AddInto(cImage SubImage, int Dest_PosX, int Dest_PosY, int Dest_PosZ, int Dest_Channel)
{
if (SubImage.GetNumChannels() > 1) return;
for (int Z = 0; Z < SubImage.Depth; Z++)
{
int OriginalPosZ = Dest_PosZ + Z;
if ((OriginalPosZ < 0) || (OriginalPosZ > this.Depth - 1)) continue;
for (int Y = 0; Y < SubImage.Height; Y++)
{
int OriginalPosY = Dest_PosY + Y;
if ((OriginalPosY < 0) || (OriginalPosY > this.Height - 1)) continue;
for (int X = 0; X < SubImage.Width; X++)
{
int OriginalPosX = Dest_PosX + X;
if ((OriginalPosX < 0) || (OriginalPosX > this.Width - 1)) continue;
this.SingleChannelImage[Dest_Channel].Data[OriginalPosX + OriginalPosY * this.Width + OriginalPosZ * this.SliceSize] += SubImage.SingleChannelImage[0].Data[X + Y * SubImage.Width + Z * SubImage.SliceSize];
}
}
}
}
public cImage(cImage Source, bool IsCopyData)
{
//Source.GetNumChannels();
this.Width = Source.Width;
this.Height = Source.Height;
this.Depth = Source.Depth;
this.SliceSize = this.Height * this.Width;
this.ImageSize = SliceSize * Depth;
this.Resolution = new cPoint3D(Source.Resolution);
this.SingleChannelImage = new cListSingleChannelImage();
for (int IdxChannel = 0; IdxChannel < Source.GetNumChannels(); IdxChannel++)
{
this.SingleChannelImage.Add(new cSingleChannelImage(Source.Width, Source.Height, Source.Depth, new cPoint3D(Source.Resolution)));
this.SingleChannelImage[IdxChannel].Name = Source.SingleChannelImage[IdxChannel].Name;
this.SingleChannelImage[IdxChannel].Data = new float[Source.SingleChannelImage[IdxChannel].Data.Length];
if (IsCopyData)
Array.Copy(Source.SingleChannelImage[IdxChannel].Data, this.SingleChannelImage[IdxChannel].Data, Source.SingleChannelImage[IdxChannel].Data.Length);
}
}
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;
}
/// <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();
}
private void buttonProcess_Click(object sender, EventArgs e)
{
ImageWidth = (int)numericUpDownMapWidth.Value;
ImageHeight = (int)numericUpDownMapHeight.Value;
if (this.radioButton2D.Checked) ImageDepth = 1;
else
ImageDepth = (int)numericUpDownMapDepth.Value;
//GlobalInfo.ListCellularPhenotypes[(int)MachineLearning.Classes[j]]
cImageDrawKernel GK = new cImageDrawKernel();
GK.sigma_x = (int)numericUpDownKernelSize.Value;
GK.sigma_y = (int)numericUpDownKernelSize.Value;
GK.sigma_z = (int)numericUpDownKernelSize.Value;
GK.Run();
cImage K = GK.GetOutPut();
if (Parent.comboBoxAxeY.SelectedIndex == -1) return;
if (Parent.comboBoxVolume.SelectedIndex == -1) return;
cExtendedList ListVolumes = new cExtendedList();
ListX.Clear();
ListY.Clear();
ListZ.Clear();
cExtendedTable TableForDataToBeAnalyzed = Parent.GetActiveSignatures(false);
for (int j = 0; j < TableForDataToBeAnalyzed[0].Count; j++)
{
ListX.Add(TableForDataToBeAnalyzed[Parent.comboBoxAxeX.SelectedIndex][j]);
ListY.Add(TableForDataToBeAnalyzed[Parent.comboBoxAxeY.SelectedIndex][j]);
}
//MaxX = ListX.Max();
//MinX = ListX.Min();
//MaxY = ListY.Max();
//MinY = ListY.Min();
MaxX = Parent.chartForPoints.ChartAreas[0].AxisX.Maximum;
MinX = Parent.chartForPoints.ChartAreas[0].AxisX.Minimum;
MaxY = Parent.chartForPoints.ChartAreas[0].AxisY.Maximum;
MinY = Parent.chartForPoints.ChartAreas[0].AxisY.Minimum;
//MaxY = Parent.MaxY;
//MinY = Parent.MinY;
if (this.radioButton3D.Checked)
{
for (int j = 0; j < TableForDataToBeAnalyzed[0].Count; j++)
{
ListZ.Add(TableForDataToBeAnalyzed[Parent.comboBoxVolume.SelectedIndex][j]);
}
MaxZ = ListZ.Max();
MinZ = ListZ.Min();
}
DensityMaps = new cImage(ImageWidth, ImageHeight, ImageDepth, cGlobalInfo.ListCellularPhenotypes.Count);
int[] ClassPopulations = new int[cGlobalInfo.ListCellularPhenotypes.Count];
if (this.radioButton3D.Checked)
{
int Idx = 0;
for (int j = 0; j < Parent.InputTable[0].Count; j++)
{
if (Parent.PanelPhenotypeSelection.GetListSelectedClass()[(int)Parent.MachineLearning.Classes[j]])
{
double TmpValueX = (ImageWidth * (ListX[Idx] - MinX)) / (MaxX - MinX) - K.Width / 2;
double TmpValueY = ImageHeight - (ImageHeight * (ListY[Idx] - MinY)) / (MaxY - MinY) - K.Height / 2;
double TmpValueZ = ImageDepth - (ImageDepth * (ListZ[Idx] - MinZ)) / (MaxZ - MinZ) - K.Depth / 2;
DensityMaps.AddInto(K, (int)TmpValueX, (int)TmpValueY, (int)TmpValueZ, (int)Parent.MachineLearning.Classes[j]);
ClassPopulations[(int)Parent.MachineLearning.Classes[j]]++;
Idx++;
}
}
}
else
{
int Idx = 0;
for (int j = 0; j < Parent.InputTable[0].Count; j++)
{
if (Parent.PanelPhenotypeSelection.GetListSelectedClass()[(int)Parent.MachineLearning.Classes[j]])
{
double TmpValueX = (ImageWidth * (ListX[Idx] - MinX)) / (MaxX - MinX) - K.Width / 2;
double TmpValueY = ImageHeight - (ImageHeight * (ListY[Idx] - MinY)) / (MaxY - MinY) - K.Height / 2;
DensityMaps.AddInto(K, (int)TmpValueX, (int)TmpValueY, 0, (int)Parent.MachineLearning.Classes[j]);
ClassPopulations[(int)Parent.MachineLearning.Classes[j]]++;
Idx++;
}
}
}
cListExtendedTable TablesForDensity = new cListExtendedTable(DensityMaps);
for (int idxChannel = 0; idxChannel < DensityMaps.GetNumChannels(); idxChannel++)
{
DensityMaps.SingleChannelImage[idxChannel].Name = cGlobalInfo.ListCellularPhenotypes[idxChannel].Name;
float Sum = 1;
if (checkBoxNormalized.Checked)
{
Sum = (float)TablesForDensity[idxChannel].Sum();
if (Sum <= 0.0) continue;
for (int i = 0; i < DensityMaps.SingleChannelImage[idxChannel].Data.Length; i++)
{
//if (ClassPopulations[idxChannel] > 0)
DensityMaps.SingleChannelImage[idxChannel].Data[i] = (100 * DensityMaps.SingleChannelImage[idxChannel].Data[i]) / Sum;
}
}
else
{
for (int i = 0; i < DensityMaps.SingleChannelImage[idxChannel].Data.Length; i++)
{
// if (ClassPopulations[idxChannel] > 0)
DensityMaps.SingleChannelImage[idxChannel].Data[i] = DensityMaps.SingleChannelImage[idxChannel].Data[i];
}
}
}
cDisplaySingleImage IV = new cDisplaySingleImage();
DensityMaps.Name = "Density Maps. K["+ this.numericUpDownKernelSize.Value +"]";
if (this.checkBoxModifyColors.Checked)
IV.ListLinearMaxColor = new List<Color>();
int RealIdxChannel = 0;
for (int idxChannel = 0; idxChannel < ClassPopulations.Length; idxChannel++)
{
if (ClassPopulations[idxChannel] == 0)
DensityMaps.SingleChannelImage.RemoveAt(RealIdxChannel--);
else
{
if (this.checkBoxModifyColors.Checked)
IV.ListLinearMaxColor.Add(cGlobalInfo.ListCellularPhenotypes[idxChannel].ColourForDisplay);
}
RealIdxChannel++;
}
IV.SetInputData(DensityMaps);
IV.Run();
this.buttonApply.Enabled = true;
}