public CalPAP(UISettings ui, FileData file, ref ConcurrentBag <double> AreaBag) : base(ui, file)
{
try {
MulticolorComponentsLabeling mclabel = new MulticolorComponentsLabeling()
{
Low = (int)Math.Round(Low_Threshold / ui.um2px2),
High = (int)Math.Round(Math.Min(int.MaxValue, High_Threshold / ui.um2px2))
};
Invert AFinvert = new Invert();
UnmanagedResult = mclabel.Apply(AFinvert.Apply(UnmanagedBlackWhite));
foreach (Blobx blob in mclabel.BlobCounter.blobs)
{
//if (blob.Area<mclabel.Low) {
// Low_count++; Low_sumArea+=blob.Area;
//} else if (blob.Area<=mclabel.High) {
Normal_count++; Normal_SumArea += ui.um2px2 * blob.Area; AreaBag.Add(ui.um2px2 * blob.Area);
//} else {
// High_count++; High_sumArea+=blob.Area;
//}
}
Total_SumArea = ui.um2px2 * (UnmanagedMarkup.Width * UnmanagedMarkup.Height); // total area
Lung_SumArea = Total_SumArea - Low_SumArea - High_SumArea; // lung area
Paren_SumArea = Lung_SumArea - NonParen_SumArea; // parenchymal area
Tis_SumArea = Paren_SumArea - Normal_SumArea; // septum tissue
Normal_Count = 1000.0d * 1000.0d * Normal_count / Paren_SumArea; // counts per reference area
StringBuilder header = new StringBuilder();
header.Append($"{FileName} ps: {ui.PixelScale:G2}/{ui.ResizeValue:G2} px/um"
+ $"\nlung: {Lung_SumArea:G2}µm\xB2, {Lung_SumArea/Total_SumArea:0%} image (blw: {Low_SumArea/Total_SumArea:0%} ovr: {High_SumArea/Total_SumArea:0%})"
+ $"\nparenchyma: {Paren_SumArea:G2}µm\xB2, {Paren_SumArea/Lung_SumArea:0%} lung (exc: {NonParen_SumArea/Total_SumArea:0%})"
+ $"\nseptum: {Tis_SumArea:G2}µm\xB2, {Tis_SumArea/Paren_SumArea:0%} paren (airspace: {Normal_SumArea/Total_SumArea:0%})");
StringBuilder footer = new StringBuilder();
footer.Append($"Total #: {mclabel.BlobCounter.blobs.Count}");
UnmanagedMarkup = UnmanagedImage.FromManagedImage(AddBlobText(UnmanagedMarkup.ToManagedImage(false), Color.Black, $"{header}", $"{footer}", null, null, (int)Math.Round(0.02d * UnmanagedMarkup.Width * Math.Sqrt(ui.ExportDetailRatio))));
UnmanagedResult = UnmanagedImage.FromManagedImage(AddBlobText(UnmanagedResult.ToManagedImage(false), Color.PaleGreen, $"{header}", $"{footer}", null, null, (int)Math.Round(0.02d * UnmanagedMarkup.Width * Math.Sqrt(ui.ExportDetailRatio))));
} catch { throw new Exception("Error Occured During Airspace Profiling"); }
}
public CalPAQ1(UISettings ui, FileData f, CalPAC categ = null) : base(ui, f)
{
try {
// low-alv-des-high cut
if (categ != null) // use alv des cutoffs from categorize class
{
Alv_Log_Size = categ.p1Mean;
//Sac_Log_Size=categ.p2Mean;
//Des_Log_Size=categ.p3Mean;
Alv_Size = Math.Pow(10.0d, categ.p1Mean) - 1;
//Sac_size=Math.Pow(10.0d, categ.p2Mean)-1;
//Des_size=Math.Pow(10.0d, categ.p3Mean)-1;
//Alv_Cut=Math.Pow(10.0d, categ.Alv_Log_Cut)-1;
DucDes_Threshold = Math.Pow(10.0d, categ.c1_DucDes_CI95_1tail) - 1;
//Alv_cut=Alv_Cut/px2um2;
}
else // alv des cutoffs from ui
{
DucDes_Threshold = Math.Pow(10.0d, ui.BlobDes) - 1;
}
DucDes_Log_Threshold = Math.Log10(DucDes_Threshold + 1);
AreaComponentsLabeling aclabel = new AreaComponentsLabeling()
{
Low = (int)Math.Round(Low_Threshold / ui.um2px2),
High = (int)Math.Round(Math.Min(int.MaxValue, High_Threshold / ui.um2px2)),
Alv = (int)Math.Round(DucDes_Threshold / ui.um2px2), // use Des_cut to elliminate Sac color
Des = (int)Math.Round(DucDes_Threshold / ui.um2px2)
};
Invert AFinvert = new Invert();
UnmanagedResult = aclabel.Apply(AFinvert.Apply(UnmanagedBlackWhite));
//Low_count = Low_sumArea = High_count = High_sumArea = 0;
foreach (Blobx blob in aclabel.BlobCounter.blobs)
{
if (blob.Area <= aclabel.Des) // alv/sac
{
AlvSac_count++; AlvSac_SumArea += ui.um2px2 * blob.Area; AlvSac_SumBoundary += ui.umpx * blob.Perimeter;
}
else // duct/des
{
DucDes_count++; DucDes_SumArea += ui.um2px2 * blob.Area; DucDes_SumBoundary += ui.umpx * blob.Perimeter;
}
}
Total_SumArea = ui.um2px2 * (UnmanagedMarkup.Width * UnmanagedMarkup.Height); // total area
Lung_SumArea = Total_SumArea - Low_SumArea - High_SumArea; // lung area
Paren_SumArea = Lung_SumArea - NonParen_SumArea; // parenchymal area
Tis_SumArea = Paren_SumArea - AlvSac_SumArea - DucDes_SumArea; // septum tissue
AlvSac_Count = 1000.0d * 1000.0d * AlvSac_count / Paren_SumArea;
DucDes_Count = 1000.0d * 1000.0d * DucDes_count / Paren_SumArea;
AlvSac_Boundary = 1.0d * AlvSac_SumBoundary / Paren_SumArea;
DucDes_Boundary = 1.0d * DucDes_SumBoundary / Paren_SumArea;
AlvSac_Fraction = 1.0d * AlvSac_SumArea / Paren_SumArea;
DucDes_Fraction = 1.0d * DucDes_SumArea / Paren_SumArea; // is still better to divide by paren area
Tis_Fraction = 1.0d - AlvSac_Fraction - DucDes_Fraction;
DucDes_Alv_Ratio = DucDes_Fraction / AlvSac_Fraction;
StringBuilder header = new StringBuilder();
header.Append($"{FileName} ps: {ui.PixelScale:G2}/{ui.ResizeValue:G2} px/um" + $"\nduc/des thres:{DucDes_Log_Threshold:0.00} log\x2081\x2080µm\xB2");
header.Append($"\nlung: {Lung_SumArea:G2}µm\xB2, {(1.0d*Lung_SumArea/Total_SumArea):0%} image (blw: {Low_SumArea/Total_SumArea:0%} ovr: {1.0d*High_SumArea/Total_SumArea:0%})");
header.Append($"\nparenchyma: {Paren_SumArea:G2}µm\xB2, {(Paren_SumArea/Lung_SumArea):0%} lung (exc: {1.0d*NonParen_SumArea/Total_SumArea:0%})");
header.Append($"\nseptum: {Tis_SumArea:G2}µm\xB2, {Tis_SumArea/Paren_SumArea:0%} paren (airspace: {(AlvSac_SumArea+DucDes_SumArea)/Total_SumArea:0%})");
StringBuilder footer = new StringBuilder();
if (Math.Abs(Alv_Size) > 0.01d)
{
footer.Append($" AS:{Alv_Size:G2} (Size, µm\xB2)");
}
footer.Append($"\nASC:{AlvSac_Count:G2} DC:{DucDes_Count:G2} (Count\x2090: 1/mm\xB2)"
+ $"\nASB:{AlvSac_Boundary:G2} DB:{DucDes_Boundary:G2} (Boundary\x2090, 1/µm)"
+ $"\nASF:{AlvSac_Fraction:0%} DF:{DucDes_Fraction:0%} (Area\x2090 Fraction, %)"
+ $"\nTF:{Tis_Fraction:0.0%} D2A:{DucDes_Alv_Ratio:F2} (Fraction, Ratio)");
UnmanagedMarkup = UnmanagedImage.FromManagedImage(AddBlobText(UnmanagedMarkup.ToManagedImage(false), Color.Black, $"{header}", $"{footer}", null, null, // ,blobs, blobDes.ToArray()
(int)Math.Round(0.02d * UnmanagedMarkup.Width * Math.Sqrt(ui.ExportDetailRatio))));
UnmanagedResult = UnmanagedImage.FromManagedImage(AddBlobText(UnmanagedResult.ToManagedImage(false), Color.PaleGreen, $"{header}", $"{footer}", null, null, // ,blobs, blobDes.ToArray()
(int)Math.Round(0.02d * UnmanagedMarkup.Width * Math.Sqrt(ui.ExportDetailRatio))));
} catch { throw new Exception("Error Occured During Airspace Quantification"); }
}