[Potential Bug] No such input: slicing_mode at initiation

[aaronbwong]

I wanted to run abba programatically using python, and have successfully installed a conda environment as described in the Readme. I then used the following code to import and initiate Abba:

from abba_python.abba import Abba
abba = Abba('Adult Mouse Brain - Allen Brain Atlas V3p1')

However, I noticed that I keep running into the following error:

[WARNING] Unmatched input: slicing_mode
Traceback (most recent call last):
File "DefaultCommandService.java", line 168, in org.scijava.command.DefaultCommandService.run
Exception: Java Exception

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

Traceback (most recent call last):
File "", line 1, in
File "C:\Users________\miniconda3\envs\abba-env\lib\site-packages\abba_python\abba.py", line 274, in init
self.mp = ij.command().run(ABBAStartCommand, True,
java.lang.java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: No such input: slicing_mode

Seems like the java code that was called do not expect the input parameter slicing_mode. So I traced back to the abba.py file and removed the line (line 275) containing the input:

        self.mp = ij.command().run(ABBAStartCommand, True,
                                   'slicing_mode', self.slicing_mode, # I removed this line
                                   'ba', self.atlas
                                   ).get().getOutput('mp')

Abba then seems to start properly, but I would need to click a button in the popup window.

Could it be a bug? Maybe there's an updated to the BIOP atlas aligner code (here) that was not accommodated?

My specs:
OS: Windows 10
python version: 3.10.16
abba version: 0.9.11
conda environment created in miniconda3 with conda version 23.1.0
abba-python installed with pip

[NicoKiaru]

Ah indeed you're right, I did not update the python API to match the Java one, thanks for the issue! I'll make a new release

[aaronbwong]

Thanks for the quick response.
Is this something I can bypass when initiating ABBA programmatically? It would be nice if I can already specify when calling...

[NicoKiaru]

    @Parameter(choices = {
            "AP (Anterior-Posterior)",
            "PA (Posterior-Anterior)",
            "SI (Superior-Inferior)",
            "IS (Inferior-Superior)",
            "RL (Right-Left)",
            "LR (Left-Right)"})
    String x_axis;

    @Parameter(choices = {
            "AP (Anterior-Posterior)",
            "PA (Posterior-Anterior)",
            "SI (Superior-Inferior)",
            "IS (Inferior-Superior)",
            "RL (Right-Left)",
            "LR (Left-Right)"})
    String y_axis;

    @Parameter(choices = {
            "AP (Anterior-Posterior)",
            "PA (Posterior-Anterior)",
            "SI (Superior-Inferior)",
            "IS (Inferior-Superior)",
            "RL (Right-Left)",
            "LR (Left-Right)"})
    String z_axis;

If you need a quick hot fix, can you try to edit the installed abba.py file ?

Please try for instance:

        self.mp = ij.command().run(ABBAStartCommand, True,
                                  'x_axis', 'RL',
                                  'y_axis', 'SI',
                                  'z_axis', 'AP',
                                  'ba', self.atlas
                                   ).get().getOutput('mp')

This is for coronal sectioning. See other basic modes here: https://github.com/BIOP/ijp-imagetoatlas/blob/master/src/main/java/ch/epfl/biop/atlas/aligner/command/ABBAStartCommand.java

Let me know!

[aaronbwong]

I have indeed tried that, but it just showed a smaller version of the popup.

and crashes after clicking OK.

java.lang.StringIndexOutOfBoundsException: begin 0, end 3, length 2
at java.base/java.lang.String.checkBoundsBeginEnd(String.java:3319)
at java.base/java.lang.String.substring(String.java:1874)
at ch.epfl.biop.atlas.aligner.command.ABBAStartCommand.run(ABBAStartCommand.java:74)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
Traceback (most recent call last):
File "Thread.java", line 829, in java.lang.Thread.run
java.lang.java.lang.StringIndexOutOfBoundsException: java.lang.StringIndexOutOfBoundsException: begin 0, end 3, length 2

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

Traceback (most recent call last):
File "Thread.java", line 829, in java.lang.Thread.run
java.lang.java.lang.RuntimeException: java.lang.RuntimeException: Module threw exception

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

Traceback (most recent call last):
File "FutureTask.java", line 191, in java.util.concurrent.FutureTask.get
Exception: Java Exception

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

Traceback (most recent call last):
File "", line 1, in
File "C:\Users\972021\miniconda3\envs\abba-env\lib\site-packages\abba_python\abba.py", line 279, in init
).get().getOutput('mp')
java.util.concurrent.java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception

[NicoKiaru]

Ah, damned! Then sorry, there's no quick and easy solution right now, but I'll try to get this fixed later in the afternoon

[NicoKiaru]

The crash is probably because I split wrongly the String to 3 characters instead of 2, you can bypass it probably with an extra space:

        self.mp = ij.command().run(ABBAStartCommand, True,
                                  'x_axis', 'RL ',
                                  'y_axis', 'SI ',
                                  'z_axis', 'AP ',
                                  'ba', self.atlas
                                   ).get().getOutput('mp')

But that won't fix the popup, I'll get back to you

[NicoKiaru]

Well it's not completed yet

[NicoKiaru]

@aaronbwong please try the version 0.10.1.dev0 which should arrive in pypi in a few minutes. And please close the issue if you can confirm that it is fixed

Thanks a lot for the report!

[imagesc-bot]

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

https://forum.image.sc/t/fiji-friends-weekly-dev-update-thread/103718/53