static void Train()
{
List <LabeledTomogram> tomograms = LabeledTomogramsFromPaintedFiles();
DecisionTreeOptions options = new DecisionTreeOptions
{
// TODO: Fill in
MaximumNumberOfRecursionLevels = 25,
NumberOfFeatures = 300,
NumberOfThresholds = 35,
OffsetXMax = 40,
OffsetXMin = -40,
OffsetYMax = 40,
OffsetYMin = -40,
OutOfRangeValue = 1000000,
SplittingThresholdMax = .2f,
SufficientGainLevel = 0,
PercentageOfPixelsToUse = .9f,
//DistanceThreshold = .1f,
};
DecisionTreeNode node = DecisionTreeBuilder.Train(tomograms, new Random(1234), options);
BinaryFormatter bf = new BinaryFormatter();
using (FileStream fs = File.Create("serialized.dat"))
{
bf.Serialize(fs, node);
}
return;
}
private static List <LabeledPoint> TomogramsToPoints(List <LabeledTomogram> tomograms,
Random random, DecisionTreeOptions options)
{
List <LabeledPoint> points = new List <LabeledPoint>();
foreach (LabeledTomogram tomogram in tomograms)
{
for (int y = 0, i = 0; y < tomogram.Height; y++)
{
for (int x = 0; x < tomogram.Width; x++, i++)
{
float value = tomogram.Data[i];
if (random != null)
{
int label = (int)tomogram.Labels[i];
if (label == 1)
{
points.Add(new LabeledPoint
{
X = x,
Y = y,
Z = value,
Label = tomogram.Labels != null ? (int)tomogram.Labels[i] : -1,
SourceTomogram = tomogram,
});
}
else
{
if (random.NextDouble() < options.PercentageOfPixelsToUse)
{
points.Add(new LabeledPoint
{
X = x,
Y = y,
Z = value,
Label = tomogram.Labels != null ? (int)tomogram.Labels[i] : -1,
SourceTomogram = tomogram,
});
}
}
}
else
{
points.Add(new LabeledPoint
{
X = x,
Y = y,
Z = value,
SourceTomogram = tomogram,
});
}
}
}
}
return(points);
}
public static float[] Predict(LabeledTomogram image, DecisionTreeNode node, DecisionTreeOptions options)
{
List <LabeledPoint> points = TomogramsToPoints(
new List <LabeledTomogram>(new LabeledTomogram[] { image }), null, null);
List <float> labels = new List <float>();
foreach (LabeledPoint point in points)
{
labels.Add(RecurseAndPredict(point, node, options));
}
return(labels.ToArray());
}
private static SplitDirection ComputeSplitDirection(LabeledPoint point, SplittingQuestion question,
DecisionTreeOptions options)
{
int frameHeight = point.SourceTomogram.Height;
int frameWidth = point.SourceTomogram.Width;
int uY = point.Y + question.OffsetUY;
if (uY >= frameHeight)
{
uY = -1;
}
int uX = point.X + question.OffsetUX;
if (uX >= frameWidth)
{
uX = -1;
}
int vY = point.Y + question.OffsetVY;
if (vY >= frameHeight)
{
vY = -1;
}
int vX = point.X + question.OffsetVX;
if (vX >= frameWidth)
{
vX = -1;
}
int u = uY * frameWidth + uX;
int v = vY * frameWidth + vX;
int z = point.Y * frameWidth + point.X;
float uVal = 0f, vVal = 0f, zVal = point.SourceTomogram.Data[z];
if (u < 0 || v < 0)
{
uVal = vVal = options.OutOfRangeValue;
}
else
{
uVal = point.SourceTomogram.Data[u];
//if(Math.Abs(zVal - uVal) > options.DistanceThreshold)
//{
// uVal = options.OutOfRangeValue;
//}
vVal = point.SourceTomogram.Data[v];
//if(Math.Abs(zVal - vVal) > options.DistanceThreshold)
//{
// vVal = options.OutOfRangeValue;
//}
}
if ((uVal - vVal) < question.Threshold)
{
return(SplitDirection.Left);
}
else
{
return(SplitDirection.Right);
}
}
private static int RecurseAndPredict(LabeledPoint point, DecisionTreeNode node, DecisionTreeOptions options)
{
if (node.IsLeaf)
{
return(node.Class);
}
else
{
SplitDirection direction = ComputeSplitDirection(point, node.Question, options);
if (direction == SplitDirection.Left)
{
return(RecurseAndPredict(point, node.LeftBranch, options));
}
else
{
return(RecurseAndPredict(point, node.RightBranch, options));
}
}
}
public static DecisionTreeNode Train(List <LabeledTomogram> trainingImages, Random random, DecisionTreeOptions options)
{
Console.WriteLine("Building points...");
List <LabeledPoint> trainingPoints = TomogramsToPoints(trainingImages, random, options);
Console.WriteLine("Build splitting questions...");
List <SplittingQuestion> splittingQuestions =
GenerateSplittingQuestions(random, options);
DecisionTreeNode root = new DecisionTreeNode();
Console.WriteLine("Recurse and partition...");
RecurseAndPartition(trainingPoints, splittingQuestions,
1, options, root, random);
return(root);
}
private static void RecurseAndPartition(List <LabeledPoint> trainingPoints, List <SplittingQuestion> splittingQuestions,
int currentRecursionLevel, DecisionTreeOptions options, DecisionTreeNode currentNode, Random random)
{
Console.WriteLine($"{new String('-', currentRecursionLevel)}{currentRecursionLevel}");
if (currentRecursionLevel >= options.MaximumNumberOfRecursionLevels)
{
// create leaf node
MakeLeafNode(currentNode, trainingPoints);
}
else
{
double currentShannonEntropy = ComputeShannonEntropy(trainingPoints);
double highestGain = double.MinValue;
SplittingQuestion bestSplittingQuestion = null;
//for (int s = 0; s < splittingQuestions.Count; s++)
Parallel.For(0, splittingQuestions.Count, s =>
{
//Console.Write(".");
//Interlocked.Increment(ref t);
//Console.WriteLine($"{t}/{splittingQuestions.Count}");
//List<LabeledPoint> leftBucket1 = new List<LabeledPoint>();
//List<LabeledPoint> rightBucket1 = new List<LabeledPoint>();
List <LabeledPointGroup> leftBucket = new List <LabeledPointGroup>();
leftBucket.Add(new LabeledPointGroup
{
Count = 0,
Class = 0
});
leftBucket.Add(new LabeledPointGroup
{
Count = 0,
Class = 1
});
List <LabeledPointGroup> rightBucket = new List <LabeledPointGroup>();
rightBucket.Add(new LabeledPointGroup
{
Count = 0,
Class = 0
});
rightBucket.Add(new LabeledPointGroup
{
Count = 0,
Class = 1
});
SplittingQuestion splittingQuestion = splittingQuestions[s];
for (int p = 0; p < trainingPoints.Count; p++)
{
//if (random.NextDouble() < .1 || trainingPoints.Count < 1000)
{
LabeledPoint trainingPoint = trainingPoints[p];
SplitDirection split = ComputeSplitDirection(trainingPoint, splittingQuestion, options);
if (split == SplitDirection.Left)
{
leftBucket[trainingPoint.Label].Count++;
//leftBucket1.Add(trainingPoint);
}
else
{
//rightBucket1.Add(trainingPoint);
rightBucket[trainingPoint.Label].Count++;
}
}
}
//double gain = ComputeGain(currentShannonEntropy, leftBucket1, rightBucket1);
double gain = ComputeGain(currentShannonEntropy, leftBucket, rightBucket);
lock (typeof(DecisionTreeBuilder))
{
if (gain > highestGain)
{
highestGain = gain;
bestSplittingQuestion = splittingQuestion;
}
}
});
if (highestGain > options.SufficientGainLevel)
{
List <LabeledPoint> bestLeftBucket = new List <LabeledPoint>();
List <LabeledPoint> bestRightBucket = new List <LabeledPoint>();
for (int p = 0; p < trainingPoints.Count; p++)
{
LabeledPoint trainingPoint = trainingPoints[p];
SplitDirection split = ComputeSplitDirection(trainingPoint, bestSplittingQuestion, options);
if (split == SplitDirection.Left)
{
bestLeftBucket.Add(trainingPoint);
}
else
{
bestRightBucket.Add(trainingPoint);
}
}
currentNode.Question = bestSplittingQuestion;
currentNode.LeftBranch = new DecisionTreeNode();
currentNode.RightBranch = new DecisionTreeNode();
currentNode.IsLeaf = false;
//System.Console.WriteLine("left: " + bestLeftBucket.Count.ToString());
//System.Console.WriteLine("right: " + bestRightBucket.Count.ToString());
//splittingQuestions =
// GenerateSplittingQuestions(random, options);
RecurseAndPartition(bestLeftBucket, splittingQuestions,
currentRecursionLevel + 1, options, currentNode.LeftBranch, random);
RecurseAndPartition(bestRightBucket, splittingQuestions,
currentRecursionLevel + 1, options, currentNode.RightBranch, random);
}
else
{
MakeLeafNode(currentNode, trainingPoints);
}
}
}
private static List <SplittingQuestion> GenerateSplittingQuestions(Random random, DecisionTreeOptions options)
{
List <SplittingQuestion> ret = new List <SplittingQuestion>();
for (int c = 0; c < options.NumberOfFeatures; c++)
{
int uX = random.Next(options.OffsetXMin, options.OffsetXMax);
int uY = random.Next(options.OffsetXMin, options.OffsetXMax);
int vX = random.Next(options.OffsetXMin, options.OffsetXMax);
int vY = random.Next(options.OffsetXMin, options.OffsetXMax);
for (int d = 0; d < options.NumberOfThresholds; d++)
{
float threshold = (float)random.NextDouble() *
options.SplittingThresholdMax * Math.Sign(random.Next(-1, 1));
ret.Add(new SplittingQuestion
{
OffsetUX = uX,
OffsetUY = uY,
OffsetVX = vX,
OffsetVY = vY,
Threshold = threshold
});
}
}
return(ret);
}
static void Test()
{
BinaryFormatter bf = new BinaryFormatter();
using (FileStream fs = File.OpenRead("serialized.dat"))
{
DecisionTreeNode node = bf.Deserialize(fs) as DecisionTreeNode;
DecisionTreeOptions options = new DecisionTreeOptions
{
// TODO: Fill in
MaximumNumberOfRecursionLevels = 25,
NumberOfFeatures = 300,
NumberOfThresholds = 35,
OffsetXMax = 40,
OffsetXMin = -40,
OffsetYMax = 40,
OffsetYMin = -40,
OutOfRangeValue = 1000000,
SplittingThresholdMax = .2f,
SufficientGainLevel = 0,
PercentageOfPixelsToUse = .9f,
//DistanceThreshold = .1f,
};
MRCFile file = MRCParser.Parse(Path.Combine("/home/brush/tomography2_fullsirtcliptrim.mrc"));
MRCFrame frame = file.Frames[145];
LabeledTomogram tom = new LabeledTomogram();
tom.Width = frame.Width;
tom.Height = frame.Height;
tom.Data = new float[frame.Width * frame.Height];
for (int i = 0; i < frame.Data.Length; i++)
{
tom.Data[i] = frame.Data[i];
}
//for (int y = 264, i = 0; y < 364; y++)
//{
// for (int x = 501; x < 601; x++, i++)
// {
// tom.Data[i] = frame.Data[y * frame.Width + x];
// }
//}
float[] labels = DecisionTreeBuilder.Predict(tom, node, options);
//Bitmap bmp = DataManipulator.Tomogram2Bitmap(tom);
Bitmap bmp = Drawing.TomogramDrawing.PaintClassifiedPixelsOnTomogram(tom, labels);
bmp.Save("/var/www/html/static/labeled_real.png", System.Drawing.Imaging.ImageFormat.Png);
LabeledTomogram tom2 = DataReader.ReadDatFile("/home/brush/tom4/0.dat");
labels = DecisionTreeBuilder.Predict(tom2, node, options);
//Bitmap bmp = DataManipulator.Tomogram2Bitmap(tom);
bmp = Drawing.TomogramDrawing.PaintClassifiedPixelsOnTomogram(tom2, labels);
bmp.Save("/var/www/html/static/labeled_simulated.png", System.Drawing.Imaging.ImageFormat.Png);
}
}
