f32 images

[nilgoyette]

Hi, thank you for working on this. It's the only nifti loader in rust! I tried using it to test an image denoising algo but it's not possible to load a f32 image. I know it's only a side project for you and I won't be waiting for a fix.

I tried with the simple InMemNiftiObject and by creating a NiftiHeader with the right values. Both give really sparse data. A whole lot of zeros with some random floats.

[Enet4]

Hello! Thank you for reporting. It's true that f32 volumes should be supported, they're pretty common. Can you provide the code that you tried? I might look into this at some point.

[nilgoyette]

I created a test image with this python code

import nibabel as nib
import numpy as np

data = np.zeros((11, 11, 11), dtype=np.float32)
data[5, :, :] = np.arange(0, 1.1, 0.1)
data[:, 5, :] = np.arange(0, 1.1, 0.1)
data[:, :, 5] = np.arange(0, 1.1, 0.1)
data[5, 5, 5] = 1.0

img = nib.Nifti1Image(data, np.eye(4))
nib.save(img, '/path/to/f32.nii.gz')

And I tried to load it with

fn main() {
    let obj = InMemNiftiObject::from_file(
        "/path/to/f32.nii.gz").expect("Can't load file.");
    let header = obj.header();
    let volume = obj.volume();
    println!("{:?}", header);
    println!("{:?}", volume.dim());
    for x in 0..11 {
        for y in 0..11 {
            print!("{:?}", volume.get_f32(&[x, y, 5]).unwrap());
        }
    }
}

The header and dimension are right but the data is wrong.

[nilgoyette]

I checked InMemNiftiVolume::from_stream and I see nothing wrong with it. Must be the get_f32 then.

if self.datatype == NiftiType::Uint8 { 
    // this is working
} else { ... }

Do you already know what's missing/broken in the code for f32 images? I'm totally not a Rust expert but I would prefer fixing your lib than coding my own!

[Enet4]

Thanks for the MCVE, I certainly wish to fix this, and I believe I have a clue of what's wrong.

[Enet4]

All right, I just pushed some neat changes to the master branch, tests included. This latest version also allows you to convert f32 volumes to an ndarray, although it always requires a full copy right now.

@nilgoyette Would you like to try it out? There should be no breaking changes from 0.1.0.

nifti = { git = "https://github.com/Enet4/nifti-rs" }

[nilgoyette]

Whoah, thank you for working on this so fast. I'll test your branch today.

[nilgoyette]

GJ, it's working with an InMemNiftiVolume. However, it's panicking as soon as I use a ndarray:

let volume = obj.into_volume().to_ndarray::<f32>().unwrap();
thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: UnsupportedDataType(Float32)', /checkout/src/libcore/result.rs:860:4

[Enet4]

@nilgoyette Oops, that was all me. I forgot to remove an old check for the data type. The fix is in the master branch now, can you try again?

[nilgoyette]

It's compiling and there's no panic... but there's only 0.0 everywhere. You might want to add a "values test" like you did in tests/volumes.rs :)

I load an non-blank image (same as before) and the ndarray is always returning 0.0:

let volume = obj.into_volume().to_ndarray::<f32>().unwrap();
for x in 0..11 {
    for y in 0..11 {
        for z in 0..11 {
            let val = volume[[x, y, z]];
            if val != 0.0 {
                print!("{} ", val);
            }
        }
    }
}
println!("{:?}", volume.slice(s![4..7, 1..10, 1..10]));

[Enet4]

You are right, I should indeed make a few more tests. I'll get back to this (and hopefully make a new release) in a few hours. In the mean time, can you check whether using the volume API directly works as intended?

[nilgoyette]

Yes, what I meant in my last message by "GJ, it's working with an InMemNiftiVolume" was that the values are ok. I even tested with a real brain image and I think it's right. In fact, I'm testing with

• MITK: the values and direction fit with nifti-rs
• nibabel: the values are ok but the directions doesn't fit with nifti-rs

Probably a LPS/RAS "problem". In fact, it's not actually a problem, I just want you to know. Does nifti-rs revert the directions or simply ignore them?

[Enet4]

Does nifti-rs revert the directions or simply ignore them?

You are correct, orientation information stated in the header file is currently ignored (that could earn a separate issue here). Thank you for the checks, I'll try to release 0.2.0 tonight.

[Enet4]

@nilgoyette Just to let you know that the bug has been fixed, and I will throw in a new release soon-ish.

Update: It's in.

[nilgoyette]

Sorry, I never saw your update. I'm testing with f32 images and everything seems right. I'll update this issue if I found anything.

I have a question though. The to_ndarray function only accept a pixel type and return a ndarray<T, Dyn>. If we know the image dimension, what's the proper way (or what would you do) to get a Array3<T> Do you suggest a ndarray solution, like using an ArrayView<A, 3>, or would asking a specific dimension to to_ndarray<T, D> be better?

In fact, my goal is to write something like:

let volume = ...;
if volume is in 3D
    call f(volume)
else // 4D
    for t in 0..volume.dim()[3]
        call f(volume[:, :, :, t])

fn f<A>(
    data: &Array3<A>,
    ...

[Enet4]

Good point. I have used a dynamic shape because this one is sure to work for volumes of any dimensionality. Right now, one can use into_shape to turn it into an array with a known rank:

let a = v.to_ndarray::<f32>()?; // D = IxDyn
let shape = a.shape();
assert_eq!(shape.len(), 3);
let new_shape = [shape[0], shape[1], shape[2]];
let a = a.into_shape(new_shape)?; // D = Dim<[Ix; 3]>

On the other hand, there sure may be room for improvements in this API, and integrating a second type parameter for the dimension type might indeed work. Let's make this a separate issue. :)