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 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;
}
