private void CalculateConvolution(ComputeContext computeContext)
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
float dx;
bool shiftXParse = float.TryParse(textBoxShiftX.Text, NumberStyles.Float, CultureInfo.InvariantCulture.NumberFormat, out dx);
if (!shiftXParse)
{
throw new SyntaxErrorException(", needs to be .");
}
float dy;
bool shiftYParse = float.TryParse(textBoxShiftX.Text, NumberStyles.Float, CultureInfo.InvariantCulture.NumberFormat, out dy);
if (!shiftYParse)
{
throw new SyntaxErrorException(", needs to be .");
}
float dz;
bool shiftZParse = float.TryParse(textBoxShiftX.Text, NumberStyles.Float, CultureInfo.InvariantCulture.NumberFormat, out dz);
if (!shiftZParse)
{
throw new SyntaxErrorException(", needs to be .");
}
int pixelCount = _imageDimensionX * _imageDimensionY * _imageDimensionZ;
Console.WriteLine("Computing...");
Console.WriteLine("Reading kernel...");
String kernelPath = Directory.GetParent(Directory.GetCurrentDirectory()).Parent.Parent.FullName;
String kernelString;
using (var sr = new StreamReader(kernelPath + "\\convolution.cl"))
kernelString = sr.ReadToEnd();
Console.WriteLine("Reading kernel... done");
float[] selectedTransformation = Transformations.GetTransformation((TransformationType)comboBoxTransform.SelectedItem, 1.0f / float.Parse(textBoxPixelSize.Text), 1.0f / float.Parse(textBoxPixelSize.Text), 1.0f / float.Parse(textBoxPixelSize.Text), dx, dy, dz);
//create openCL program
ComputeProgram computeProgram = new ComputeProgram(computeContext, kernelString);
computeProgram.Build(computeContext.Devices, null, null, IntPtr.Zero);
ComputeProgramBuildStatus computeProgramBuildStatus = computeProgram.GetBuildStatus(_selectedComputeDevice);
Console.WriteLine("computeProgramBuildStatus\n\t" + computeProgramBuildStatus);
String buildLog = computeProgram.GetBuildLog(_selectedComputeDevice);
Console.WriteLine("buildLog");
if (buildLog.Equals("\n"))
{
Console.WriteLine("\tbuildLog is empty...");
}
else
{
Console.WriteLine("\t" + buildLog);
}
float[] fluorophores = CsvData.ReadFluorophores(_sourceFilename);
/////////////////////////////////////////////
// Create a Command Queue & Event List
/////////////////////////////////////////////
ComputeCommandQueue computeCommandQueue = new ComputeCommandQueue(computeContext, _selectedComputeDevice, ComputeCommandQueueFlags.None);
////////////////////////////////////////////////////////////////
// Create Buffers Transform
////////////////////////////////////////////////////////////////
ComputeBuffer <float> fluorophoresCoords = new ComputeBuffer <float>(computeContext, ComputeMemoryFlags.ReadWrite, fluorophores.LongLength);
ComputeBuffer <float> transformationMatrix = new ComputeBuffer <float>(computeContext, ComputeMemoryFlags.ReadOnly, selectedTransformation.LongLength);
/////////////////////////////////////////////
// Create the transformFluorophoresKernel
///////////////////////////////////////////////////////////
ComputeKernel transformFluorophoresKernel = computeProgram.CreateKernel("transform_fluorophores");
/////////////////////////////////////////////
// Set the transformFluorophoresKernel arguments
/////////////////////////////////////////////
transformFluorophoresKernel.SetMemoryArgument(0, fluorophoresCoords);
transformFluorophoresKernel.SetMemoryArgument(1, transformationMatrix);
/////////////////////////////////////////////
// Configure the work-item structure
/////////////////////////////////////////////
long[] globalWorkOffsetTransformFluorophoresKernel = null;
long[] globalWorkSizeTransformFluorophoresKernel = new long[] { fluorophores.Length / 4 };
long[] localWorkSizeTransformFluorophoresKernel = null;
////////////////////////////////////////////////////////
// Enqueue the transformFluorophoresKernel for execution
////////////////////////////////////////////////////////
computeCommandQueue.WriteToBuffer(fluorophores, fluorophoresCoords, true, null);
computeCommandQueue.WriteToBuffer(selectedTransformation, transformationMatrix, true, null);
computeCommandQueue.Execute(transformFluorophoresKernel, globalWorkOffsetTransformFluorophoresKernel, globalWorkSizeTransformFluorophoresKernel, localWorkSizeTransformFluorophoresKernel, null);
// computeCommandQueue.ExecuteTask(transformFluorophoresKernel, transformFluorophoresEvents);
float[] transformedFluorophores = new float[fluorophores.Length];
computeCommandQueue.ReadFromBuffer(fluorophoresCoords, ref transformedFluorophores, true, null);
computeCommandQueue.Finish();
//TODO remove, only for testing
// for (int i = 0; i < transformedFluorophores.Length; i++)
// {
// Console.WriteLine(transformedFluorophores[i]);
// }
// /TODO remove, only for testing
stopwatch.Stop();
Console.WriteLine("Transform fluophores duration:\n\t" + stopwatch.Elapsed);
stopwatch.Reset();
stopwatch.Start();
// fluorophoresCoords are now transformed (done in place)
////////////////////////////////////////////////////////////////
// Create Buffers Convolve Fluorophores
////////////////////////////////////////////////////////////////
const int convolve_kernel_lwgs = 16;
int totalBuffer = (int)Math.Ceiling(pixelCount / (float)convolve_kernel_lwgs) * convolve_kernel_lwgs;
ComputeBuffer <float> resultImage = new ComputeBuffer <float>(computeContext, ComputeMemoryFlags.WriteOnly, totalBuffer);
/////////////////////////////////////////////
// Create the transformFluorophoresKernel
/////////////////////////////////////////////
ComputeKernel convolveFluorophoresKernel = computeProgram.CreateKernel("convolve_fluorophores");
/////////////////////////////////////////////
// Set the convolveFluorophoresKernel arguments
/////////////////////////////////////////////
convolveFluorophoresKernel.SetMemoryArgument(0, resultImage);
convolveFluorophoresKernel.SetValueArgument(1, _imageDimensionX);
convolveFluorophoresKernel.SetValueArgument(2, _imageDimensionY);
convolveFluorophoresKernel.SetMemoryArgument(3, fluorophoresCoords);
convolveFluorophoresKernel.SetLocalArgument(4, convolve_kernel_lwgs);
convolveFluorophoresKernel.SetValueArgument(5, fluorophores.Length / 4);
/////////////////////////////////////////////
// Configure the work-item structure
/////////////////////////////////////////////
long[] globalWorkOffsetTransformConvolveFluorophoresKernel = null;
long[] globalWorkSizeTransformConvolveFluorophoresKernel = new long[] { pixelCount };
long[] localWorkSizeTransformConvolveFluorophoresKernel = new long[] { convolve_kernel_lwgs };
////////////////////////////////////////////////////////
// Enqueue the convolveFluorophoresKernel for execution
////////////////////////////////////////////////////////
computeCommandQueue.Execute(convolveFluorophoresKernel, globalWorkOffsetTransformConvolveFluorophoresKernel, globalWorkSizeTransformConvolveFluorophoresKernel, localWorkSizeTransformConvolveFluorophoresKernel, null);
float[] resultImageData = new float[totalBuffer];
computeCommandQueue.ReadFromBuffer(resultImage, ref resultImageData, true, null);
computeCommandQueue.Finish();
for (int i = 0; i < pixelCount; i++)
{
Console.WriteLine(resultImageData[i]);
}
Console.WriteLine("Writing data to file...");
// CsvData.WriteToDisk("..\\..\\..\\output.csv", resultImageData);
TiffData.WriteToDisk(resultImageData, _saveFilename, _imageDimensionX, _imageDimensionY);
Bitmap bitmap = new Bitmap(_imageDimensionX, _imageDimensionY);
float max = resultImageData.Max();
float scale = 255 / (float)max;
// for (int r = 0; r < _imageDimensionY; r++)
// {
// for (int c = 0; c < _imageDimensionX; c++)
// {
// float value = resultImageData[c*(r + 1)];
// Color newColor = Color.FromArgb((int)(value * scale), (int)(value * scale), (int)(value * scale));
// bitmap.SetPixel(c,r, newColor);
// }
// }
ushort[] ushortdata = new ushort[resultImageData.Length];
for (int i = 0; i < resultImageData.Length; i++)
{
ushortdata[i] = (ushort)resultImageData[i];
}
uint[] convertGray16ToRgb = ConvertGray16ToRGB(ushortdata, 16);
byte[] bytes = new byte[convertGray16ToRgb.Length * 4];
//
// int[] resultImageData2 = new int[resultImageData.Length];
//
for (int index = 0; index < convertGray16ToRgb.Length; index++)
{
// resultImageData2[index] = (int)(scale*resultImageData[index]);
byte[] bytes1 = BitConverter.GetBytes(convertGray16ToRgb[index]);
bytes[index] = bytes1[0];
bytes[4 * index + 1] = bytes1[1];
bytes[4 * index + 2] = bytes1[2];
bytes[4 * index + 3] = bytes1[3];
}
//
// for (int r = 0; r < _imageDimensionY; r++)
// {
// for (int c = 0; c < _imageDimensionX; c++)
// {
// float value = resultImageData2[c*(r + 1)];
// Color newColor = Color.FromArgb((int)(value), (int)(value), (int)(value));
// bitmap.SetPixel(c,r, newColor);
// }
// }
// bitmap.Save("c:\\temp.bmp");
using (MemoryStream ms = new MemoryStream(bytes))
{
Image image = Bitmap.FromStream(ms);
image.Save("c:\\temp.bmp");
}
Console.WriteLine("Writing data to file... done");
stopwatch.Stop();
Console.WriteLine("Convolve fluophores duration:\n\t" + stopwatch.Elapsed);
Console.WriteLine("Computing... done");
}
