public static void segmentation_pipeline(out List <vtkImageData> outputs, Rendering.renderPipeLine volume, int[] batch_d, int[] extent, int[] axes, string wpath, int bs = 2)
{
//Outputs
outputs = new List <vtkImageData>();
//Get input dimensions
int[] dims = volume.getDims();
// Initialize UNet
UNet model = new UNet();
try
{
model.Initialize(24, batch_d, wpath, false);
}
catch (FileNotFoundException)
{
Console.WriteLine("Model not found");
return;
}
for (int k = 0; k < axes.Length; k++)
{
outputs.Add(vtkImageData.New());
}
//Segment BCI from axis
for (int k = 0; k < axes.Length; k++)
{
//Inference
IList <IList <float> > result = segment_sample(volume, model, extent, axes[k], bs, (float)108.58790588378906, (float)47.622276306152344);
//Copy result to vtkImagedata
vtkImageData _tmp = IO.inference_to_vtk(result, new int[] { dims[1] + 1, dims[3] + 1, dims[5] + 1 }, extent, axes[k]);
outputs.ElementAt(k).DeepCopy(_tmp);
_tmp.Dispose();
result = null;
}
model.Dispose();
}
public static void segmentation_pipeline(out List <vtkImageData> outputs, Rendering.renderPipeLine volume, int[] batch_d, int[] extent, int[] axes, int bs = 2)
{
//Outputs
outputs = new List <vtkImageData>();
//Get input dimensions
int[] dims = volume.getDims();
//Initialize unet
string wpath = "Z:\\Tuomas\\UNetE3BN.h5";
UNet model = new UNet();
model.Initialize(24, batch_d, wpath, false);
//Segment BCI from axis
foreach (int axis in axes)
{
IList <IList <float> > result = segment_sample(volume, model, extent, axis, bs, (float)113.05652141, (float)39.87462853);
//Convert back to vtkimage data
vtkImageData tmp = IO.inference_to_vtk(result, new int[] { dims[1] + 1, dims[3] + 1, dims[5] + 1 }, extent, axis);
outputs.Add(tmp);
}
}
public static IList <IList <float> > segment_sample(Rendering.renderPipeLine vtkObject, UNet model, int[] extent, int axis,
int step = 1, float mu = 0, float sd = 0)
{
//Segmentation range
int[] bounds = new int[] { extent[axis * 2], extent[axis * 2 + 1] };
//Output list
IList <IList <float> > output = null;
//Iterate over vtk data
for (int k = 0; k < (bounds[1] - bounds[0]) / step; k++)
{
//Set current VOI and orientation
int[] _curext = new int[6];
int[] _ori = new int[3];
if (axis == 0)
{
int start = extent[0] + k * step;
int stop = Math.Min(extent[0] + (k + 1) * step - 1, extent[1]);
_curext = new int[] { start, stop, extent[2], extent[3], extent[4], extent[5] };
_ori = new int[] { 2, 1, 0 };
}
if (axis == 1)
{
int start = extent[2] + k * step;
int stop = Math.Min(extent[2] + (k + 1) * step - 1, extent[3]);
_curext = new int[] { extent[0], extent[1], start, stop, extent[4], extent[5] };
_ori = new int[] { 2, 0, 1 };
}
if (axis == 2)
{
int start = extent[4] + k * step;
int stop = Math.Min(extent[4] + (k + 1) * step - 1, extent[5]);
_curext = new int[] { extent[0], extent[1], extent[2], extent[3], start, stop };
_ori = new int[] { 0, 1, 2 };
}
//Extract VOI to float array
float[] input_array = DataTypes.byteToFloat(DataTypes.vtkToByte(vtkObject.getVOI(_curext, _ori)), mu, sd);
//Segment current slice
IList <IList <float> > _cur = model.Inference(input_array);
//Append results to output list
if (output == null)
{
output = _cur;
}
else
{
//Loop over slices
foreach (IList <float> item in _cur)
{
output.Add(item);
}
}
GC.Collect();
}
//Return output list
return(output);
}
