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;
}
}
void BuildFromListTable(cListExtendedTable ListSources)
{
if (ListSources.Count == 0) return;
if (ListSources[0].Count == 0) return;
if (ListSources[0][0].Count == 0) return;
//this.NumChannels = ListSources.Count;
this.Width = ListSources[0].Count;
this.Height = ListSources[0][0].Count;
this.Depth = 1;
this.SliceSize = this.Height * this.Width;
this.SingleChannelImage = new cListSingleChannelImage();
for (int IdxChannel = 0; IdxChannel < ListSources.Count; IdxChannel++)
{
this.SingleChannelImage.Add(new cSingleChannelImage(this.Width, this.Height, 1, new cPoint3D(1, 1, 1)));
for (int i = 0; i < this.Width; i++)
for (int j = 0; j < this.Height; j++)
{
this.SingleChannelImage[IdxChannel].Data[i + j * this.Width] = (float)ListSources[IdxChannel][i][j];
}
}
this.Name = ListSources.Name;
}
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 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);
}
}
public cImage(Image<Gray, byte> CVImage)
{
//this.output = new cImage(this.input);
this.Width = CVImage.Width;
this.Height = CVImage.Height;
this.SliceSize = this.Height * this.Width;
this.ImageSize = SliceSize * Depth;
this.SingleChannelImage = new cListSingleChannelImage();
//for (int IdxChannel = 0; IdxChannel < NumChannels; IdxChannel++)
this.SingleChannelImage.Add(new cSingleChannelImage(Width, Height, 1, new cPoint3D(1, 1, 1)));
for (int j = 0; j < CVImage.Height; j++)
for (int i = 0; i < CVImage.Width; i++)
this.SingleChannelImage[0].Data[i + j * this.Width] = CVImage.Data[j, i, 0];
//this.NumChannels = 1;
}
public cImage(int Width, int Height, int Depth, int NumChannels)
{
//this.NumChannels = NumChannels;
this.Width = Width;
this.Height = Height;
this.Depth = Depth;
this.SliceSize = this.Height * this.Width;
this.ImageSize = SliceSize * Depth;
this.SingleChannelImage = new cListSingleChannelImage();
for (int IdxChannel = 0; IdxChannel < NumChannels; IdxChannel++)
{
this.SingleChannelImage.Add(new cSingleChannelImage(Width, Height, Depth, new cPoint3D(this.Resolution)));
this.SingleChannelImage[this.SingleChannelImage.Count - 1].Name = "Channel " + IdxChannel;
}
}
