private static TifFileInfo TrackCropToolStripMenuItem_click(ROI roi, string dir, TifFileInfo fi)
{
ROI oldROI = roi;
roi = ROITransformer.ROIEditor.TransformToRect(fi, roi);
if (roi == null)
{
return(null);
}
fi.available = false;
TifFileInfo newFI = null;
//crop the rectangle
newFI = DuplicateFI(fi);
newFI.Dir = newFI.Dir.Substring(0, newFI.Dir.LastIndexOf(".")) + "_ROI"
+ (fi.roiList[fi.cValue].IndexOf(roi) + 1).ToString() + ".tif";
Size size = new Size(roi.Width, roi.Height);
newFI.sizeX = roi.Width;
newFI.sizeY = roi.Height;
newFI.xCompensation = 0;
newFI.yCompensation = 0;
newFI.imageCount = fi.imageCount;
newFI.openedImages = newFI.imageCount;
AddEmptyArraysToFI(newFI);
Point[] locs = roi.GetLocationAll()[0];
switch (fi.bitsPerPixel)
{
case 8:
byte[][][] image8bit = new byte[fi.imageCount][][];
Parallel.For(0, fi.imageCount, frame =>
{
Point location = locs[frame];
Rectangle rect = new Rectangle(location, size);
image8bit[frame] = new byte[rect.Height][];
for (int y = rect.Y, yNew = 0; y < rect.Y + rect.Height; y++, yNew++)
{
image8bit[frame][yNew] = new byte[rect.Width];
for (int x = rect.X, xNew = 0; x < rect.X + rect.Width; x++, xNew++)
{
if (x >= 0 && y >= 0 && x < fi.sizeX && y < fi.sizeY)
{
image8bit[frame][yNew][xNew] = fi.image8bit[frame][y][x];
}
}
}
});
newFI.image8bit = image8bit;
newFI.image8bitFilter = newFI.image8bit;
break;
case 16:
ushort[][][] image16bit = new ushort[fi.imageCount][][];
Parallel.For(0, fi.imageCount, frame =>
{
Point location = locs[frame];
Rectangle rect = new Rectangle(location, size);
image16bit[frame] = new ushort[rect.Height][];
for (int y = rect.Y, yNew = 0; y < rect.Y + rect.Height; y++, yNew++)
{
image16bit[frame][yNew] = new ushort[rect.Width];
for (int x = rect.X, xNew = 0; x < rect.X + rect.Width; x++, xNew++)
{
if (x >= 0 && y >= 0 && x < fi.sizeX && y < fi.sizeY)
{
image16bit[frame][yNew][xNew] = fi.image16bit[frame][y][x];
}
}
}
});
newFI.image16bit = image16bit;
newFI.image16bitFilter = newFI.image16bit;
break;
}
newFI.loaded = true;
newFI.original = false;
//FileEncoder.SaveTif(newFI, dir);
fi.available = true;
RecalculateOriginalROI(oldROI, roi, newFI);
return(newFI);
}
private static string calculateCTTagValue(TifFileInfo fi)
{
List <string> vals = new List <string>();
try
{
vals.Add("seriesCount->" + fi.seriesCount.ToString());
vals.Add("imageCount->" + fi.imageCount.ToString());
vals.Add("sizeX->" + fi.sizeX.ToString());
vals.Add("sizeY->" + fi.sizeY.ToString());
vals.Add("sizeC->" + fi.sizeC.ToString());
vals.Add("sizeZ->" + fi.sizeZ.ToString());
vals.Add("sizeT->" + fi.sizeT.ToString());
vals.Add("umXY->" + fi.umXY.ToString());
vals.Add("umZ->" + fi.umZ.ToString());
vals.Add("bitsPerPixel->" + fi.bitsPerPixel.ToString());
vals.Add("dimensionOrder->" + fi.dimensionOrder);
vals.Add("pixelType->" + fi.pixelType.ToString());
vals.Add("FalseColored->" + fi.FalseColored.ToString());
vals.Add("isIndexed->" + fi.isIndexed.ToString());
vals.Add("MetadataComplete->" + fi.MetadataComplete.ToString());
vals.Add("DatasetStructureDescription->" + fi.DatasetStructureDescription);
vals.Add("Micropoint->" + fi.Micropoint.ToString());
vals.Add("autoDetectBandC->" + fi.autoDetectBandC.ToString());
vals.Add("applyToAllBandC->" + fi.applyToAllBandC.ToString());
vals.Add("xCompensation->" + fi.xCompensation.ToString());
vals.Add("yCompensation->" + fi.yCompensation.ToString());
vals.Add("DataSourceInd->" + fi.DataSourceInd.ToString());
vals.Add("LutList->" + TagValueToString(fi.LutList));
vals.Add("TimeSteps->" + TagValueToString(fi.TimeSteps));
if (fi.MinBrightness != null)
{
vals.Add("MinBrightness->" + TagValueToString(fi.MinBrightness));
}
else
{
int[] a = new int[fi.sizeC];
vals.Add("MinBrightness->" + TagValueToString(a));
}
if (fi.MaxBrightness != null)
{
vals.Add("MaxBrightness->" + TagValueToString(fi.MaxBrightness));
}
else
{
int[] a = new int[fi.sizeC];
int c1 = 250;
if (fi.bitsPerPixel != 8)
{
c1 = 16000;
}
for (int i = 0; i < a.Length; i++)
{
a[i] = c1;
}
vals.Add("MaxBrightness->" + TagValueToString(a));
}
vals.Add("tracking_MaxSize->" + TagValueToString(fi.tracking_MaxSize));
vals.Add("tracking_MinSize->" + TagValueToString(fi.tracking_MinSize));
vals.Add("tracking_Speed->" + TagValueToString(fi.tracking_Speed));
vals.Add("SegmentationProtocol->" + TagValueToString(fi.SegmentationProtocol));
vals.Add("SegmentationCBoxIndex->" + TagValueToString(fi.SegmentationCBoxIndex));
vals.Add("thresholdsCBoxIndex->" + TagValueToString(fi.thresholdsCBoxIndex));
vals.Add("SelectedSpotThresh->" + TagValueToString(fi.SelectedSpotThresh));
vals.Add("typeSpotThresh->" + TagValueToString(fi.typeSpotThresh));
vals.Add("SpotThresh->" + TagValueToString(fi.SpotThresh));
vals.Add("spotSensitivity->" + TagValueToString(fi.spotSensitivity));
vals.Add("thresholds->" + TagValueToString(fi.thresholds));
vals.Add("SpotColor->" + TagValueToString(fi.SpotColor));
vals.Add("RefSpotColor->" + TagValueToString(fi.RefSpotColor));
vals.Add("sumHistogramChecked->" + TagValueToString(fi.sumHistogramChecked));
vals.Add("SpotTailType->" + string.Join("\t", fi.SpotTailType));
vals.Add("thresholdColors->" + TagValueToString(fi.thresholdColors));
vals.Add("RefThresholdColors->" + TagValueToString(fi.RefThresholdColors));
vals.Add("thresholdValues->" + TagValueToString(fi.thresholdValues));
vals.Add("FileDescription->" + fi.FileDescription);
vals.Add("xAxisTB->" + fi.xAxisTB.ToString());
vals.Add("yAxisTB->" + fi.yAxisTB.ToString());
//Roi part
int c = 0;
foreach (List <ROI> roiList in fi.roiList)
{
if (roiList != null)
{
foreach (ROI roi in roiList)
{
string str = "roi.new->" + roi_new(c, roi);
vals.Add(str);
}
}
c++;
}
//it is important FilterHistory to be the last
vals.Add("FilterHistory->" + TagValueToString(fi.FilterHistory.ToArray()));
}
catch { System.Windows.Forms.MessageBox.Show(vals[vals.Count - 1]); }
return(string.Join(";\n", vals));
}
private static TifFileInfo CropToolStripMenuItem_click(ROI roi, string dir, TifFileInfo fi)
{
if (roi.Type == 1)
{
return(TrackCropToolStripMenuItem_click(roi, dir, fi));
}
return(null);
fi.available = false;
TifFileInfo newFI = null;
Rectangle rect = Rectangle.Empty;
//find rectangles
switch (roi.Type)
{
case 0:
if (roi.Shape == 1 | roi.Shape == 0)
{
Point p = roi.GetLocation(fi.cValue)[0];
Size size = new Size(roi.Width, roi.Height);
rect = new Rectangle(p, size);
}
else if (roi.Shape == 2 || roi.Shape == 3 || roi.Shape == 4 || roi.Shape == 5)
{
Point[] pList = roi.GetLocation(fi.cValue);
int X = int.MaxValue;
int Y = int.MaxValue;
int W = int.MinValue;
int H = int.MinValue;
foreach (Point p1 in pList)
{
if (p1.X < X)
{
X = p1.X;
}
if (p1.Y < Y)
{
Y = p1.Y;
}
if (p1.X > W)
{
W = p1.X;
}
if (p1.Y > H)
{
H = p1.Y;
}
}
Point p = new Point(X, Y);
Size size = new Size(W - X, H - Y);
rect = new Rectangle(p, size);
}
break;
case 1:
if (roi.Shape == 1 | roi.Shape == 0)
{
Point[] pList = roi.GetLocationAll()[0];
int X = int.MaxValue;
int Y = int.MaxValue;
int W = int.MinValue;
int H = int.MinValue;
for (int i = fi.cValue; i < fi.imageCount; i += fi.sizeC)
{
Point p1 = pList[i];
if (p1 != null)
{
if (p1.X < X)
{
X = p1.X;
}
if (p1.Y < Y)
{
Y = p1.Y;
}
if (p1.X > W)
{
W = p1.X;
}
if (p1.Y > H)
{
H = p1.Y;
}
}
}
Point p = new Point(X, Y);
Size size = new Size(W - X + roi.Width, H - Y + roi.Height);
rect = new Rectangle(p, size);
}
else if (roi.Shape == 2 || roi.Shape == 3 || roi.Shape == 4 || roi.Shape == 5)
{
int X = int.MaxValue;
int Y = int.MaxValue;
int W = int.MinValue;
int H = int.MinValue;
Point[] pList;
for (int i = fi.cValue; i < fi.imageCount; i += fi.sizeC)
{
pList = roi.GetLocation(i);
foreach (Point p1 in pList)
{
if (p1.X < X)
{
X = p1.X;
}
if (p1.Y < Y)
{
Y = p1.Y;
}
if (p1.X > W)
{
W = p1.X;
}
if (p1.Y > H)
{
H = p1.Y;
}
}
}
Point p = new Point(X, Y);
Size size = new Size(W - X, H - Y);
rect = new Rectangle(p, size);
}
break;
}
//crop the rectangle
newFI = DuplicateFI(fi);
newFI.Dir = newFI.Dir.Substring(0, newFI.Dir.LastIndexOf(".")) + "_ROI"
+ (fi.roiList[fi.cValue].IndexOf(roi) + 1).ToString() + ".tif";
newFI.sizeX = rect.Width;
newFI.sizeY = rect.Height;
newFI.xCompensation = rect.X;
newFI.yCompensation = rect.Y;
newFI.imageCount = fi.imageCount;
newFI.openedImages = newFI.imageCount;
AddEmptyArraysToFI(newFI);
switch (fi.bitsPerPixel)
{
case 8:
byte[][][] image8bit = new byte[fi.imageCount][][];
Parallel.For(0, fi.imageCount, frame =>
{
image8bit[frame] = new byte[rect.Height][];
for (int y = rect.Y, yNew = 0; y < rect.Y + rect.Height; y++, yNew++)
{
image8bit[frame][yNew] = new byte[rect.Width];
for (int x = rect.X, xNew = 0; x < rect.X + rect.Width; x++, xNew++)
{
if (x >= 0 && y >= 0 && x < fi.sizeX && y < fi.sizeY)
{
image8bit[frame][yNew][xNew] = fi.image8bit[frame][y][x];
}
}
}
});
newFI.image8bit = image8bit;
newFI.image8bitFilter = newFI.image8bit;
break;
case 16:
ushort[][][] image16bit = new ushort[fi.imageCount][][];
Parallel.For(0, fi.imageCount, frame =>
{
image16bit[frame] = new ushort[rect.Height][];
for (int y = rect.Y, yNew = 0; y < rect.Y + rect.Height; y++, yNew++)
{
image16bit[frame][yNew] = new ushort[rect.Width];
for (int x = rect.X, xNew = 0; x < rect.X + rect.Width; x++, xNew++)
{
if (x >= 0 && y >= 0 && x < fi.sizeX && y < fi.sizeY)
{
image16bit[frame][yNew][xNew] = fi.image16bit[frame][y][x];
}
}
}
});
newFI.image16bit = image16bit;
newFI.image16bitFilter = newFI.image16bit;
break;
}
newFI.loaded = true;
newFI.original = false;
//FileEncoder.SaveTif(newFI, dir);
fi.available = true;
return(newFI);
}
