DecodeNumpy via BufferAccess classes.

[bioimage-io]

DecodeNumpy via BufferAccess classes.

[carlosuc3m]

Hello @mkitti , I am trying to use your code and I am encountering a couple of problems.
When trying to create imglib2 images from npy files that contain 3D images the reconstruction doe snot work well. I think it is because ImgLib2 indexes flat arrays in a different way to numpy. This is why with 2D images it works well.

Is there a way to go around this problem using ImgLib2 code?

[ctrueden]

Meanwhile, pom-scijava 37.0.0 has been released and now manages imglib2 at 6.2.0...

[mkitti]

xref: scijava/pom-scijava#229

[carlosuc3m]

Awesome, I will implement it then.
Is it possible to get a reference to the imglib2 buffer too?
Does the cursor.get().getByte() already return a reference?

[mkitti]

I am uncertain what you mean by doss not work well.

My guess is that you need to reorder or permute the dimensions. Numpy is usually row major, and I believe imglib2 is column major.

Numpy does support Fortran order.

https://numpy.org/doc/stable/reference/generated/numpy.asfortranarray.html

You could try that. Otherwise, you will need to permite the dimensions on the ImgLib2 side.

[carlosuc3m]

This is what I was trying to refer to:

My guess is that you need to reorder or permute the dimensions. Numpy is usually row major, and I believe imglib2 is column major.

But I did not know how ImgLib2 dimensions are organised.

Permuting the axes might be the best option.
Thanks a lot @mkitti !

[mkitti]

Numpy has dimensions (y,x) where the last dimension is the fastest varying dimension. ImgLib2 has dimensions (x,y) where the first dimension is the fastest varying dimension.

For 3D, Numpy would be (z,y,x) and ImgLib2 would be (x, y, z).

[carlosuc3m]

Finally implemented for numpy file reading. Also improved the tensor<->imglib2 RAI conversion accross all the Deep Learning engines with the help of @tpietzsch at Brno's Hackaton Oct 2023

JDLL/src/main/java/io/bioimage/modelrunner/numpy/DecodeNumpy.java

Line 325 in ec14b9d

public static <T extends NativeType<T>> RandomAccessibleInterval<T> build(ByteBuffer buf, ByteOrder byteOrder, String dtype, long[] shape, boolean fortranOrder) throws IllegalArgumentException