# Pixel manipulations in C#
**URL:** https://discourse.itk.org/t/pixel-manipulations-in-c/5091
**Category:** Beginner Questions
**Created:** [June 15, 2022, 7:51pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091 "2022-06-15T19:51:00Z")
**Posts on this page:** 15
**Page:** 1
### Author:  [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)
#### Post date: [June 15, 2022, 7:51pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/1 "2022-06-15T19:51:00Z")
Hello,
I am trying to implement the following example from [SimpleITK’s notebook](http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/Python_html/21_Transforms_and_Resampling.html).
The Python code is:
```auto
img = logo
# Generate random samples inside the image, we will obtain the intensity/color values at these points.
num_samples = 10
physical_points = []
for pnt in zip(*[list(np.random.random(num_samples)*sz) for sz in img.GetSize()]):
physical_points.append(img.TransformContinuousIndexToPhysicalPoint(pnt))
# Create an image of size [num_samples,1...1], actual size is dependent on the image dimensionality. The pixel
# type is irrelevant, as the image is just defining the interpolation grid (sitkUInt8 has minimal memory footprint).
interp_grid_img = sitk.Image([num_samples] + [1]*(img.GetDimension()-1), sitk.sitkUInt8)
# Define the displacement field transformation, maps the points in the interp_grid_img to the points in the actual
# image.
displacement_img = sitk.Image([num_samples] + [1]*(img.GetDimension()-1), sitk.sitkVectorFloat64, img.GetDimension())
for i, pnt in enumerate(physical_points):
displacement_img[[i] + [0]*(img.GetDimension()-1)] = np.array(pnt) - np.array(interp_grid_img.TransformIndexToPhysicalPoint([i] + [0]*(img.GetDimension()-1)))
# Actually perform the resampling. The only relevant choice here is the interpolator. The default_output_pixel_value
# is set to 0.0, but the resampling should never use it because we expect all points to be inside the image and this
# value is only used if the point is outside the image extent.
interpolator_enum = sitk.sitkLinear
default_output_pixel_value = 0.0
output_pixel_type = sitk.sitkFloat32 if img.GetNumberOfComponentsPerPixel()==1 else sitk.sitkVectorFloat32
resampled_points = sitk.Resample(img, interp_grid_img, sitk.DisplacementFieldTransform(displacement_img),
interpolator_enum, default_output_pixel_value, output_pixel_type)
# Print the interpolated values per point
for i in range(resampled_points.GetWidth()):
print(str(physical_points[i]) + ': ' + str(resampled_points[[i] + [0]*(img.GetDimension()-1)]) + '\n')
```
The problem is that in C#, neither indexing nor SetPixel work for setting the displacement\_img. I have seen examples of buffer access, but only with Int8, not for vector images. How might you do it?
Also, here interp\_grid\_img is the ReferenceImage and sitk.DisplacementFieldTransform(displacement\_img) is the Transform in the object-oriented interface, right?
Thank you!
---
### Author:  [@blowekamp](https://discourse.itk.org/u/blowekamp)
#### Post date: [June 15, 2022, 8:00pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/2 "2022-06-15T20:00:45Z")
Can you please provide a minimal example in C# to reproduce the problem encountered, and the error message received?
---
### Author:  [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)
#### Post date: [June 15, 2022, 8:13pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/3 "2022-06-15T20:13:06Z")
Of course, here is the code giving me trouble:
```auto
uint[] gridSize = new uint[] { (uint)Math.Floor(insonationWidth * sampleFactor), (uint)Math.Floor(insonationHeight * sampleFactor), 1 };
Image grid = new Image(new VectorUInt32(gridSize), itk.simple.PixelIDValueEnum.sitkUInt8);
grid.SetSpacing(new VectorDouble() { pixel_size / sampleFactor, pixel_size / sampleFactor, pixel_size / sampleFactor });
Image displacement_field = new Image(new VectorUInt32(gridSize), itk.simple.PixelIDValueEnum.sitkVectorFloat64, 3);
for (int i = 0; i < insonationWidth * sampleFactor; i++)
{
for (int j = 0; j < insonationHeight * sampleFactor; j++)
{
VectorDouble gridPoint = grid.TransformIndexToPhysicalPoint(new VectorInt64() { i, j, 1 });
displacement_field[i, j, 1] = physicalSamplePoints[(int)Math.Floor(j + i * insonationHeight * sampleFactor)] - new Vector3((float)gridPoint[0],(float)gridPoint[1],(float)gridPoint[2]);
}
}
```
The error message is “Cannot apply indexing with [] to an expression of type ‘Image’” (when I try to set displacement\_field). If I try SetPixel, it tells me the class Image contains no such method.
---
### Author:  [@blowekamp](https://discourse.itk.org/u/blowekamp)
#### Post date: [June 16, 2022, 1:02pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/4 "2022-06-16T13:02:09Z")
Thank you for the code.
Since C# is a typed language you need to use `SetPixelAsVectorUInt32` method.
I’ll need to look into the [] operator further…
---
### Author:  [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)
#### Post date: [June 16, 2022, 1:40pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/5 "2022-06-16T13:40:00Z")
Thank you! That worked.
Also, this code is very slow. Is that to be expected? As I said, I’m trying to resample at a given set of points.
---
### Author:  [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [June 16, 2022, 1:58pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/6 "2022-06-16T13:58:55Z")
Hello @Ale_Ballester,
If the goal is to resample at a set of points, the next version of SimpleITK will have new methods for the `Image` class `EvaluateAtPhysicalPoint` and `EvaluateAtContinuousIndex` (get the compiled release candidate from [github](https://github.com/SimpleITK/SimpleITK/releases)). A Python notebook [illustrating the use is here](https://github.com/zivy/SimpleITK-Notebooks/blob/sitk2.2.0/Python/21_Transforms_and_Resampling.ipynb) relevant section **Resampling at a set of locations**.
---
### Author:  [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)
#### Post date: [June 16, 2022, 2:10pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/7 "2022-06-16T14:10:20Z")
I am trying to construct a 2D image from an arbitrary slice of a 3D image. Since I have the 4x4 transformation matrix that can give me arbitrary points in my plane of interest, I thought resampling at a particular set of sample points within the plane and setting a default pixel value was the easiest way to do it. It was easy, but way too slow (I am writing real time software).
---
### Author:  [@mauigna06](https://discourse.itk.org/u/mauigna06)
#### Post date: [June 16, 2022, 2:20pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/8 "2022-06-16T14:20:10Z")
I think it is possible to do this operation fast enough with numpy arrays. I think you would need to operate in the indices preserving the scalar values of the CT, then you should do a trivial threshold operation. The transform should be something like SliceToRAS on Slicer or it’s inverse
---
### Author:  [@dchen](https://discourse.itk.org/u/dchen)
#### Post date: [June 16, 2022, 2:25pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/9 "2022-06-16T14:25:25Z")
Could you use the Resample function and to resample the 3d image onto your 2d target image?
---
### Author:  [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)
#### Post date: [June 16, 2022, 3:47pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/10 "2022-06-16T15:47:07Z")
Yes, but I need to implement it on C#/Unity for a standalone application (no slicer).
---
### Author:  [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)
#### Post date: [June 16, 2022, 3:48pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/11 "2022-06-16T15:48:32Z")
I am trying to do it using Resample with identity transform, setting the origin, direction and output size, and then use ExtractImageFilter to get my slice. So far no success.
---
### Author:  [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)
#### Post date: [June 16, 2022, 3:59pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/12 "2022-06-16T15:59:51Z")
Keep in mind I am generating 192,000 points per frame. Do you really think this can be made fast enough?
---
### Author:  [@mauigna06](https://discourse.itk.org/u/mauigna06)
#### Post date: [June 16, 2022, 4:01pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/13 "2022-06-16T16:01:48Z")
Yeah
(If I understood your question well)
---
### Author:  [@dchen](https://discourse.itk.org/u/dchen)
#### Post date: [June 22, 2022, 3:39pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/14 "2022-06-22T15:39:52Z")
I made a simple example (in Python) on how to do an oblique 2d cut through a 3d volume using SimpleITK’s Resample function. Here’s how I do it:
```
import SimpleITK as sitk
# Example volume: https://raw.githubusercontent.com/dave3d/dicom2stl/main/examples/Data/ct_example.nii.gz
img = sitk.ReadImage("ct_example.nii.gz")
cut = sitk.Image([300,300,1], sitk.sitkUInt16)
rotate = sitk.Euler3DTransform()
# 15 degree rotation about X axis
rotate.SetRotation(.2618, 0.0, 0.0)
cut.SetDirection(rotate.GetMatrix())
cut2 = sitk.Resample(img, cut)
```
I made a Jupyter notebook that uses ITKWidgets to show the result, if you want to try it yourself:
[Cut-resample.ipynb · GitHub](https://gist.github.com/dave3d/6e9a0f37929e63bdc982e7c69bed3f87)
---
### Author:  [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)
#### Post date: [June 22, 2022, 3:49pm UTC](https://discourse.itk.org/t/pixel-manipulations-in-c/5091/15 "2022-06-22T15:49:00Z")
Thank you!
I ended up solving it using resample with an identity transform. But this is great!