[Neuroimaging] RGB Nifti

[Fernando Pérez-García]

Hi Ariel,

data.shape is (5256, 3216, 3) at that point.

If I do just
nii = nib.Nifti1Image(data, np.eye(4))
nib.save(nii, p.replace('png', 'nii')),

I'll get a 3D nifti image with three slices, with one value per pixel. I
want a 2D nifti image with one slice, three values per pixel. I do
accomplish what I want with my code, but it's not very efficient. Do you
think I should ask in the NumPy or SciPy mailing list?


Cheers,

Fernando

2016-02-16 17:46 GMT+01:00 Ariel Rokem <arokem at gmail.com>:

> Hi Fernando,
>
> Just trying to understand what you are trying to achieve:
>
> On Tue, Feb 16, 2016 at 8:44 AM, Fernando Pérez-García <fepegar at gmail.com>
> wrote:
>
>> Hi Paulo,
>>
>> Thanks for your response. It seems that ConvertScalarImageToRGB reads a
>> gray nifti and makes an RGB nifti (using ITK) with a certain colormap. The
>> image I'm reading is a PNG file already RGB, as you can see in my code, so
>> I think ANTS won't help here.
>>
>>
>> Cheers,
>>
>> Fernando
>>
>> 2016-02-16 17:32 GMT+01:00 paulo rodrigues <khamael at gmail.com>:
>>
>>> Hi Fernando,
>>>
>>> Did you have a look at ants? It has some tools for that kind of
>>> operations: check ConvertScalarImageToRGB
>>>
>>> Cheers,
>>> Paulo
>>>
>>> On Tue, Feb 16, 2016 at 5:05 PM, Fernando Pérez-García <
>>> fepegar at gmail.com> wrote:
>>>
>>>> Dear Nibabel experts,
>>>>
>>>> I'm trying to create an RGB nifti image from a PNG file. I've been
>>>> messing around with a working RGB nifti, in order to mimic the datatype
>>>> found in its header. So far I've managed to convert the image pixel-wise
>>>> with for loops, which is very slow. Do you know how this could be done in a
>>>> faster way?
>>>>
>>>>
>>>> My code:
>>>>
>>>> import numpy as np
>>>> import Image
>>>> import nibabel as nib
>>>>
>>>> p = '/home/fernando/test/nii_rgb/TC1.png'
>>>> im = Image.open(p)
>>>>
>>>> data = np.array(im)
>>>> data = np.rot90(data)
>>>>
>>>
> What is `data.shape` at this point?
>
> Why wouldn't the following work?
>
>     nii = nib.Nifti1Image(data, np.eye(4))
>     nib.save(nii, p.replace('png', 'nii'))
>
> Cheers,
>
> Ariel
>
>
>> rgb = np.zeros((data.shape[0], data.shape[1], 1, 1), [('R', 'u1'), ('G',
>>>> 'u1'), ('B', 'u1')])
>>>>
>>>> for i in range(data.shape[0]):
>>>>     for j in range(data.shape[1]):
>>>>         rgb[i, j] = tuple(data[i, j, :])
>>>>
>>>> nii = nib.Nifti1Image(rgb, np.eye(4))
>>>> nib.save(nii, p.replace('png', 'nii'))
>>>>
>>>>
>>>>
>>>> Thanks in advance,
>>>>
>>>> Fernando
>>>>
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>>>>
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