public void GetComponentFromImageNormalCase()
{
PCA p = new PCA();
double[,] matrixArr = new double[10, 2]
{
{ 1.507, 0.988 },
{ 2.107, -9.312 },
{ 1.407, 1.798 },
{ 1.397, 2.098 },
{ -9.563, 1.988 },
{ 0.797, 0.888 },
{ 2.607, 0.488 },
{ -0.493, 1.588 },
{ 0.627, -0.412 },
{ -0.393, -0.112 }
};
double[] expectation = new double[1] {
0.083723606
};
double[,] img = new double[1, 2] {
{ 1, 1 }
};
p.Train(matrixArr);
double[] res = p.GetComponentsFromImage(img, 1);
Console.WriteLine(res.Length);
CollectionAssert.AreEqual(expectation,
res,
new Comparer(floatingPointTolerance));
}
public void GetComponentFromImageException()
{
PCA p = new PCA();
double[,] image = new double[2, 2] {
{ 5, 10 }, { 10, 5 }
};
Assert.Throws <NullReferenceException>(() => p.GetComponentsFromImage(image, 1));
}
public void GetComponentFromImageNormalCaseUShortArray()
{
PCA p = new PCA();
byte[] matrixArr = new byte[16]
{
10, 20, 59, 223,
24, 80, 99, 31,
54, 113, 215, 70,
167, 131, 200, 101
};
byte[] matrixArr2 = new byte[16]
{
10, 20, 59, 223,
24, 80, 99, 31,
54, 113, 215, 70,
167, 131, 200, 101
};
double[] expectation = new double[1] {
5130
};
byte[] imgArr = new byte[16] {
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
};
List <UShortArrayAsImage> img = new List <UShortArrayAsImage>();
img.Add(new UShortArrayAsImage(matrixArr, 4, 4));
img.Add(new UShortArrayAsImage(matrixArr2, 4, 4));
p.Train(img);
double[] res = p.GetComponentsFromImage(img[0], 1);
Console.WriteLine(res.Length);
CollectionAssert.AreEqual(expectation,
res,
new Comparer(floatingPointTolerance));
}
private async Task PerformAnalysis(String path, Rectangle rectangle)
{
UShortArrayAsImage image = null;
double[] pcaComponents = null;
int tasksComplete = 0;
UpdateStatus(path, startingImageStatusStr);
List <Task> tasks = new List <Task>()
{
new Task(() =>
{
var file = db.FileStorage.FindById($"images/{path}");
var ms = new MemoryStream();
file.CopyTo(ms);
ms.Seek(0, 0);
image = DicomFile.Open(ms).GetUshortImageInfo();
UpdateStatus(path, loadedImageStatusStr);
}),
new Task(() =>
{
image = Normalization.GetNormalizedImage(image, rectangle,
int.Parse(Configuration.Get("sizeImageToAnalyze")));
db.FileStorage.Upload($"images/{path}-cropped", $"{path}-cropped",
image.GetPngAsMemoryStream());
UpdateStatus(path, croppedImageStatusStr);
}),
new Task(() =>
{
image = Contrast.ApplyHistogramEqualization(image);
db.FileStorage.Upload($"images/{path}-croppedContrast", $"{path}-croppedContrast",
image.GetPngAsMemoryStream());
UpdateStatus(path, contrastImageStatusStr);
}),
new Task(() =>
{
//PCA
PCA pca = PCA.LoadModelFromFile(Configuration.Get("PcaModelLocation"));
if (!int.TryParse(Configuration.Get("componentsToUse"), out int components))
{
components = pca.Eigenvalues.Length;
}
pcaComponents = pca.GetComponentsFromImage(image, components);
UpdateStatus(path, pcaImageStatusStr);
}),
new Task(() =>
{
//SVM
SVMProblem svmProblem = new SVMProblem();
// add all the components to an SVMNode[]
SVMNode[] nodes = new SVMNode[pcaComponents.Length];
for (int i = 0; i < pcaComponents.Length; i++)
{
nodes[i] = new SVMNode(i + 1, pcaComponents[i]);
}
svmProblem.Add(nodes, 0);
svmProblem = svmProblem.Normalize(SVMNormType.L2);
SVMModel svmModel = SVM.LoadModel(Configuration.Get("ModelLocation"));
double[] results = svmProblem.PredictProbability(svmModel, out var probabilities);
var analysis = db.GetCollection <Analysis>("analysis");
Analysis currentAnalysis = analysis.FindOne(x => x.Id.ToString().Equals(path));
currentAnalysis.Certainty = results[0] == 0 ? probabilities[0][1] * 100 : probabilities[0][0] * 100;
currentAnalysis.Diagnosis = results[0] == 0
? DdsmImage.Pathologies.Benign
: DdsmImage.Pathologies
.Malignant;
analysis.Update(currentAnalysis);
UpdateStatus(path, svmImageStatusStr);
})
};
foreach (Task task in tasks)
{
task.Start();
await task;
// lets set percentage done:
var analysis = db.GetCollection <Analysis>("analysis");
Analysis currentAnalysis = analysis.FindOne(x => x.Id.ToString().Equals(path));
currentAnalysis.PercentageDone = (++tasksComplete * 100) / tasks.Count;
analysis.Update(currentAnalysis);
}
UpdateStatus(path, doneStatusStr);
}