# Creating a displacement field image from a numpy array

**URL:** https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681
**Category:** Beginner Questions
**Tags:** python
**Created:** [December 6, 2020, 6:21pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681 "2020-12-06T18:21:39Z")
**Posts on this page:** 12
**Page:** 1

<div class="post-metadata">

### Author: ![Alex\_Reimelt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/a/b487fb/32.png) [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)
#### Post date: [December 6, 2020, 6:21pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/1 "2020-12-06T18:21:39Z")

</div>

Hello,

in my PhD project I analyze 3D microCT datasets of lung tissue samples to find out more about the alveolar shape. One topic is the simulation of an atelectasis by warping the image. In order to do that (using the WarpImageFilter or the ResampleImageFilter) I have to create a displacement vector field (with ITK Python). Therefore, I have to convert a 3D numpy array into an itk image using the GetImageFromArray function.

Here´s my code:

```auto
array1 = []

for i in range (-5,5):
    for j in range(-5,5):
        for k in range(-5,5):
            if i == 0 and j == 0 and k == 0:
                array1.append([0, 0, 0])
            else:
                x = (float(i)/float(i **2 + j** 2 + k**2))
                y = (float(j)/float(i **2 + j** 2 + k**2))
                z = (float(k)/float(i **2 + j** 2 + k**2))
                array1.append([x, y, z])

displacementFieldFileName = itk.image_from_array(np.reshape(array1, (10,10,10,3)), is_vector = True)

```

In the last line, I receive the following error message:

Traceback (most recent call last):  
File “Test\_Displacement.py”, line 39, in   
displacementFieldFileName = itk.image\_from\_array(np.reshape(array1, (10,10,10,3)), is\_vector = True)  
File “/home/reimelta/.local/lib/python2.7/site-packages/itkExtras.py”, line 297, in GetImageFromArray  
return \_GetImageFromArray(arr, “GetImageFromArray”, is\_vector)  
File “/home/reimelta/.local/lib/python2.7/site-packages/itkExtras.py”, line 291, in \_GetImageFromArray  
templatedFunction = getattr(itk.PyBuffer[ImageType], function)  
File “/home/reimelta/.local/lib/python2.7/site-packages/itkTemplate.py”, line 340, in **getitem**  
raise TemplateTypeError(self, tuple(cleanParameters))  
itkTemplate.TemplateTypeError: itk.PyBuffer is not wrapped for input type `itk.Image[itk.Vector[itk.D,3],3]`.

A similar topic can be found here:

> [@Importing image from array and axis reorder](https://discourse.itk.org/t/importing-image-from-array-and-axis-reorder/1192):
>
> I am creating image from a numpy array, using itk-python, and I see that it reorders the array axes: print("Array shape: "+str(scanArray.shape)) scanVolume = itk.GetImageFromArray(scanArray) print("Image shape: "+str(scanVolume.GetLargestPossibleRegion().GetSize())) Result: Array shape: (512, 512, 133) Image shape: itkSize3 ([133, 512, 512]) So I then thought I can swap axes to take care of this, but the result is not what I was expected: print("Array shape: "+str(scanArray.shape)) scanArra…

Any help will be highly appreciated!  
Alex

---

<div class="post-metadata">

### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [December 7, 2020, 8:58pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/2 "2020-12-07T20:58:52Z")

</div>

You should make your NumPy array 32-bit floats, by throwing in `.astype(np.float32` or specifying somethere `dtype=np.float32`. Or build ITK yourself and make sure to enable wrapping for 3-dimensional `Vector` images and `double` scalar type.

---

<div class="post-metadata">

### Author: ![Alex\_Reimelt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/a/b487fb/32.png) [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)
#### Post date: [December 8, 2020, 9:01am UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/3 "2020-12-08T09:01:58Z")

</div>

Thank you for your reply! I tried out the first two suggestions but am getting the following error with both of them:

```auto
Traceback (most recent call last):
  File "Test_Displacement.py", line 61, in <module>
    fieldReader.SetFileName(displacementFieldFileName)
TypeError: in method 'itkImageFileReaderIF3_SetFileName', argument 2 of type 'std::string const &'

```

Here is the code in case I did not use the suggestions correctly:

```auto
array1 = []

for i in range (-5,5):
    for j in range(-5,5):
        for k in range(-5,5):
            if i == 0 and j == 0 and k == 0:
                array1.append([0, 0, 0])
            else:
                x = ((float(i)/float(i **2 + j** 2 + k**2)))
                y = ((float(j)/float(i **2 + j** 2 + k**2)))
                z = ((float(k)/float(i **2 + j** 2 + k**2)))
                
                array1.append([x, y, z])

array2 = np.array(array1, dtype = np.float32)

displacementFieldFileName = itk.image_from_array(np.reshape(array2, (10,10,10,3)), is_vector = True)

```

or:

```auto
array1 = []

for i in range (-5,5):
    for j in range(-5,5):
        for k in range(-5,5):
            if i == 0 and j == 0 and k == 0:
                array1.append([0, 0, 0])
            else:
                x = ((float(i)/float(i **2 + j** 2 + k**2)))
                y = ((float(j)/float(i **2 + j** 2 + k**2)))
                z = ((float(k)/float(i **2 + j** 2 + k**2)))
                
                array1.append([x, y, z])

displacementFieldFileName = itk.image_from_array(np.reshape(array1, (10,10,10,3)).astype(np.float32), is_vector = True)

```

What am I doing wrong?

Thanks in advance  
Alex

---

<div class="post-metadata">

### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [December 8, 2020, 1:56pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/4 "2020-12-08T13:56:33Z")

</div>

Where is line 61? I don’t see `ImageFileReader` anywhere in your code. Some other part of your code might be giving you the issue now.

---

<div class="post-metadata">

### Author: ![phcerdan](https://discourse.itk.org/user_avatar/discourse.itk.org/phcerdan/32/286_2.png) [@phcerdan](https://discourse.itk.org/u/phcerdan)
#### Post date: [December 8, 2020, 1:58pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/5 "2020-12-08T13:58:54Z")

</div>

> [@Alex\_Reimelt](#):
>
> ```auto
> File "Test_Displacement.py", line 61, in <module>
> fieldReader.SetFileName(displacementFieldFileName)
> TypeError: in method 'itkImageFileReaderIF3_SetFileName', argument 2 of type 'std::string const &'
> 
> ```

Not sure if that error report is complete, check that your `displacementFieldFileName` is actually a python string. `'....'`

---

<div class="post-metadata">

### Author: ![Alex\_Reimelt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/a/b487fb/32.png) [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)
#### Post date: [December 8, 2020, 2:02pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/6 "2020-12-08T14:02:24Z")

</div>

I´m sorry, the the last line was missing, here you can see the whole script:

```auto
#!/usr/bin/env python
import itk
import numpy as np
import sys

if len(sys.argv) != 3:
    print('Usage: ' + sys.argv[0] +
          ' <InputFileName> <OutputFileName>')
    sys.exit(1)

inputFileName = sys.argv[1]
outputFileName = sys.argv[2]

Dimension = 3

VectorComponentType = itk.F
VectorPixelType = itk.Vector[VectorComponentType, Dimension]

DisplacementFieldType = itk.Image[itk.F, Dimension]

PixelType = itk.UC
ImageType = itk.Image[PixelType, Dimension]

array1 = []

for i in range (-5,5):
    for j in range(-5,5):
        for k in range(-5,5):
            if i == 0 and j == 0 and k == 0:
                array1.append([0, 0, 0])
            else:
                x = ((float(i)/float(i **2 + j** 2 + k**2)))
                y = ((float(j)/float(i **2 + j** 2 + k**2)))
                z = ((float(k)/float(i **2 + j** 2 + k**2)))
                
                array1.append([x, y, z])

displacementFieldFileName = itk.image_from_array(np.reshape(array1, (10,10,10,3)).astype(np.float32), is_vector = True)

reader = itk.ImageFileReader[ImageType].New()
reader.SetFileName(inputFileName)

fieldReader = itk.ImageFileReader[DisplacementFieldType].New()
fieldReader.SetFileName(displacementFieldFileName)
fieldReader.Update()

deformationField = fieldReader.GetOutput()

warpFilter = \
        itk.WarpImageFilter[ImageType, ImageType, DisplacementFieldType].New()

interpolator = itk.LinearInterpolateImageFunction[ImageType, itk.D].New()

warpFilter.SetInterpolator(interpolator)

warpFilter.SetOutputSpacing(deformationField.GetSpacing())
warpFilter.SetOutputOrigin(deformationField.GetOrigin())
warpFilter.SetOutputDirection(deformationField.GetDirection())

warpFilter.SetDisplacementField(deformationField)

warpFilter.SetInput(reader.GetOutput())

writer = itk.ImageFileWriter[ImageType].New()
writer.SetInput(warpFilter.GetOutput())
writer.SetFileName(outputFileName)

writer.Update()

```

---

<div class="post-metadata">

### Author: ![phcerdan](https://discourse.itk.org/user_avatar/discourse.itk.org/phcerdan/32/286_2.png) [@phcerdan](https://discourse.itk.org/u/phcerdan)
#### Post date: [December 8, 2020, 2:12pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/7 "2020-12-08T14:12:23Z")

</div>

In your script, `displacementFieldFileName` is not a FileName, but an ITK image, change its name directly to `deformationField`. You can remove all the `fieldReader` part.

---

<div class="post-metadata">

### Author: ![Alex\_Reimelt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/a/b487fb/32.png) [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)
#### Post date: [December 8, 2020, 2:13pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/8 "2020-12-08T14:13:59Z")

</div>

Thanks for the advice. I will do so!

---

<div class="post-metadata">

### Author: ![Alex\_Reimelt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/a/b487fb/32.png) [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)
#### Post date: [December 8, 2020, 2:53pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/9 "2020-12-08T14:53:31Z")

</div>

The script now delivers an output (and no error message), but only for small arrays. If the given array is 10 by 10 by 10 or larger, the output file is all black. The dataset that I would like to process has 500 voxels in each direction. Could it be that the image origin and the origin of the deformation field do not fit to each other or something similar?

Here´s how the code with the correct size would look like:

```auto
#!/usr/bin/env python
import itk
import numpy as np
import sys

if len(sys.argv) != 3:
    print('Usage: ' + sys.argv[0] +
          ' <InputFileName> <OutputFileName>')
    sys.exit(1)

inputFileName = sys.argv[1]
outputFileName = sys.argv[2]

Dimension = 3

VectorComponentType = itk.F
VectorPixelType = itk.Vector[VectorComponentType, Dimension]

DisplacementFieldType = itk.Image[VectorPixelType, Dimension]

PixelType = itk.UC
ImageType = itk.Image[PixelType, Dimension]

array1 = []

for i in range (-250,250):
    for j in range(-250,250):
        for k in range(-250,250):
            if i == 0 and j == 0 and k == 0:
                array1.append([0, 0, 0])
            else:
                x = (float(i)/float(i **2 + j** 2 + k**2))
                y = (float(j)/float(i **2 + j** 2 + k**2))
                z = (float(k)/float(i **2 + j** 2 + k**2))
                
                array1.append([x, y, z])

deformationField = itk.image_from_array(np.reshape(array1, (500,500,500,3)).astype(np.float32), is_vector = True)

reader = itk.ImageFileReader[ImageType].New()
reader.SetFileName(inputFileName)

warpFilter = \
        itk.WarpImageFilter[ImageType, ImageType, DisplacementFieldType].New()

interpolator = itk.LinearInterpolateImageFunction[ImageType, itk.D].New()

warpFilter.SetInterpolator(interpolator)

warpFilter.SetOutputSpacing(deformationField.GetSpacing())
warpFilter.SetOutputOrigin(deformationField.GetOrigin())
warpFilter.SetOutputDirection(deformationField.GetDirection())

warpFilter.SetDisplacementField(deformationField)

warpFilter.SetInput(reader.GetOutput())

writer = itk.ImageFileWriter[ImageType].New()
writer.SetInput(warpFilter.GetOutput())
writer.SetFileName(outputFileName)

writer.Update()

```

Thank you again for your help.

---

<div class="post-metadata">

### Author: ![phcerdan](https://discourse.itk.org/user_avatar/discourse.itk.org/phcerdan/32/286_2.png) [@phcerdan](https://discourse.itk.org/u/phcerdan)
#### Post date: [December 8, 2020, 3:39pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/10 "2020-12-08T15:39:07Z")

</div>

First, I fail to find a `reader.Update()` after `reader.SetFileName`, so `reader->GetOutput()` is not populated.  
Second, I am not familiar with the `WarpImageFilter`, but I am sure this is not doing what you expect:

> [@Alex\_Reimelt](#):
>
> ```auto
> warpFilter.SetOutputSpacing(deformationField.GetSpacing())
> warpFilter.SetOutputOrigin(deformationField.GetOrigin())
> warpFilter.SetOutputDirection(deformationField.GetDirection())
> 
> ```

You haven’t set the `Spacing`, `Origin` and `Direction` of your `deformationField` image, so those are the default. If you want to copy that metadata from your input image:

```auto
reader = itk.ImageFileReader[ImageType].New()
reader.SetFileName(inputFileName)
reader.Update()
deformationField = itk.image_from_array(np.reshape(array1, (500,500,500,3)).astype(np.float32), is_vector = True)
deformationField.SetSpacing(reader.GetOutput().GetSpacing())
deformationField.SetOrigin(reader.GetOutput().GetOrigin())
deformationField.SetDirection(reader.GetOutput().GetDirection())

```

Hope it helps!

---

<div class="post-metadata">

### Author: ![Alex\_Reimelt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/a/b487fb/32.png) [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)
#### Post date: [December 8, 2020, 3:41pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/11 "2020-12-08T15:41:22Z")

</div>

Thank you! I will try it out.

---

<div class="post-metadata">

### Author: ![Alex\_Reimelt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/a/b487fb/32.png) [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)
#### Post date: [December 8, 2020, 5:06pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681/12 "2020-12-08T17:06:18Z")

</div>

It worked out kind of how I wanted it to be. The only smaller issue is that on the first and last 5 to 6 images of my stack there are empty spaces. But they can be cut out or I will try to use the ResampleImage Filter.

Thank you both!