imagej / imagej/pyimagej

Support conversion of complex-valued ImgLib2 images to Python

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#78 2 comments 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
Python
Stars
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Forks
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Description

I'm not able to print FFT results with ij.py.show!

```python
import skimage
import imagej
import numpy as np
from skimage import io
import imagej
import imglyb
from jnius import cast
from jnius import autoclass

ij = imagej.init('sc.fiji:fiji:2.0.0-pre-10')

img = io.imread('https://www.fi.edu/sites/fi.live.franklinds.webair.com/files/styles/featured_large/public/General_EduRes_Heart_BloodVessels_0.jpg')

img = np.mean(img, axis=2)
print(ij.op().help('filter.fft'))
result= ij.op().filter().fft(ij.py.to_java(img))

```

Error 'JavaException: JVM exception occurred: java.util.concurrent.ExecutionException: java.lang.ClassCastException: net.imglib2.type.numeric.complex.ComplexFloatType cannot be cast to net.imglib2.type.numeric.real.AbstractRealType java.lang.RuntimeException'

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Research direction

Start by running the Python reproduction using ij.py.to_java(img) and the FFT operation shown in the issue. Trace how complex-valued ImgLib2 results are converted for Python, then verify that FFT output can be displayed without the ComplexFloatType/ClassCastException reported here.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
api
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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