Add conversion for BitType and BoolType imgs

[gselzer]

Using PyImageJ, functionality that returns boolean type images, like thresholds and morphology Ops, returns those images as images of BitType and/or BoolType. PyImageJ normally converts these to DataArrays of float64, which seems suboptimal.

This change, utilizing imagej/imagej-ops#651, allows those BitType and/or BoolType images to become boolean arrays instead. Of course, we will need to wait for that PR to make its way into release before we can merge this PR.

@elevans is there a better place to put the tests I wrote?

[elevans]

@gselzer This looks great to me, very clean and simple. I think it makes sense to put your tests in tests/test_image_conversion.py. Just as a heads up, since JPype 1.0.0 you can create Java arrays like this:

from jpype import JLong
jarray = JLong[:] @ [15, 20, 30]

Instead of calling the JArray constructor!

[elevans]

@gselzer It looks like I can't convert BitType to NativeBoolType. What am I doing wrong?

Operating in headless mode - the original ImageJ will have limited functionality.
Traceback (most recent call last):
  File "Thread.java", line 829, in java.lang.Thread.run
java.lang.java.lang.ClassCastException: java.lang.ClassCastException: class net.imglib2.type.logic.BitType cannot be cast to class net.imglib2.type.logic.NativeBoolType (net.imglib2.type.logic.BitType and net.imglib2.type.logic.NativeBoolType are in unnamed module of loader 'app')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "OpEnvironment.java", line 136, in net.imagej.ops.OpEnvironment.run
java.util.concurrent.java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.ClassCastException: class net.imglib2.type.logic.BitType cannot be cast to class net.imglib2.type.logic.NativeBoolType (net.imglib2.type.logic.BitType and net.imglib2.type.logic.NativeBoolType are in unnamed module of loader 'app')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "OpEnvironment.java", line 136, in net.imagej.ops.OpEnvironment.run
Exception: Java Exception

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/edward/Documents/repos/loci/pyimagej/src/imagej/__init__.py", line 193, in from_java
    return sj.to_python(data)
           ^^^^^^^^^^^^^^^^^^
  File "/home/edward/Documents/repos/loci/scyjava/src/scyjava/_convert.py", line 553, in to_python
    return _convert(data, py_converters)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edward/Documents/repos/loci/scyjava/src/scyjava/_convert.py", line 104, in _convert
    return converter.convert(obj, **hints)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edward/Documents/repos/loci/scyjava/src/scyjava/_convert.py", line 74, in convert
    else self.converter(obj)
         ^^^^^^^^^^^^^^^^^^^
  File "/home/edward/Documents/repos/loci/pyimagej/src/imagej/__init__.py", line 663, in <lambda>
    converter=lambda obj: convert.java_to_ndarray(self._ij, obj),
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edward/Documents/repos/loci/pyimagej/src/imagej/convert.py", line 203, in java_to_ndarray
    images.copy_rai_into_ndarray(ij, rai, narr)
  File "/home/edward/Documents/repos/loci/pyimagej/src/imagej/images.py", line 166, in copy_rai_into_ndarray
    ij.op().run("copy.rai", sj.to_java(narr), rai)
java.lang.java.lang.RuntimeException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ClassCastException: class net.imglib2.type.logic.BitType cannot be cast to class net.imglib2.type.logic.NativeBoolType (net.imglib2.type.logic.BitType and net.imglib2.type.logic.NativeBoolType are in unnamed module of loader 'app')

[gselzer]

Hmm, fails on my machine too @elevans. Looks like the object sj.to_java(narr) is a DefaultDataset with NativeBoolType elements, while rai is an ArrayImg<BitType>. Naturally, the matching copy Op doesn't handle that, because the Ops there require elements be of the same type.
Options:

1. Write a better Op that can copy between BooleanTypes. Would take a little while to get dependable releases but probably the most correct option.
2. Find some more explicit way to copy the images, where you can make use of the fact that the element types may be different. Unfortunately, ImgUtil.copy can't handle different booleanType implementations either...

I'd prefer (1).

[elevans]

This branch passes test successfully with imagej-ops version 2.1.0 which contains the necessary patch for the BitType and BoolType to be converted directly to boolean arrays. A new release of pom-scijava is needed to bumps the imagej ops version requirements.

[elevans]

Looks good!

[ctrueden]

@gselzer Better would be to use: sj.jarray('j', [10, 10, 10]) because then it doesn't depend on the JPype backend.

[gselzer]

@elevans I rewrote the support for imglib2 boolean types to only be present if the Ops version is there, however this is still smelly to me:

• On one hand, the previous behavior is restored for old versions of ImageJ (Ops), and the correct behavior is now in place for new (enough) versions of ImageJ Ops. I feel like this current revision imposes the least surprising behavior.
• On the other hand, I feel like this revision could have unintended consequences i.e. the behavior of conversion from imglib2 boolean type to bool_ ndarrays is tied to Ops when the actual conversion is not necessarily so.

All of this is to say I'm not sure whether I like that last commit, so it's up to your discretion.

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-friends-weekly-dev-update-thread/103718/39

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-friends-weekly-dev-update-thread/103718/41

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-friends-weekly-dev-update-thread/103718/48