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ABBA, controlled from python

License: Other

Makefile 1.72% Jupyter Notebook 35.21% Python 63.07%

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abba_python's Issues

Import issues on python > 3.7

For some reasons, using python > 3.7 makes abba fails on
from abba_python import abba

I do not know why.

Can't put license file in standalone installer

Cf NicoKiaru/ABBA-Python#14 and conda/constructor#657

abba_python do not work on Mac OSX

Why ?

Because abba_python specify DeepSlice as a required dependency
DeepSlice requires tensorflow 1.15
Tensorflow 1.15 requires python 3.7
There's no build for python 3.7 on mac (M1)

-> DeepSlice should be optional.

Python dependency is missing in the Getting Started section

Hi,
Thank you for developing Abba, it's a very nice tool.

I have a concern about the getting started section.
The instructions are as follows:

create an environment without python
activate it
call pip install abba-python

On my system, this results in installing all abba-python dependencies in system's pip.

I assume this is not the intended behavior and it may result in very unexpected problems.

I would suggest adding python and using a YML file that can be passed to conda, such as:

# Run conda env create -f <path to this file> to create the environment
# Run conda env update -f <path to this file> to update the environment
name: abba-env
channels:
  - conda-forge
dependencies:
  - openjdk=8
  - python=3.10 
  - pip
  - ipykernel
  - ipywidgets
  - maven
  - pip:
    - abba-python

(i had to install maven)

Adds support to DeepSlice Rat brain

Related to NicoKiaru/ABBA-Python#18

Adds supports to DeepSlice rat model - probably needs to be implemented on the Java side first, and also by updating to Json instead of XML.

Run python elastix wrappers instead of separate standalone application

This would simplify the installation process.

cf NicoKiaru/ABBA-Python#5

Investigate debugging pyimagej with intellij

See:

https://imagej.net/develop/debugging#attaching-to-imagej-instances

Export to Qupath does not work in headless mode from a script

ABBA Python version: 0.3.0
Python version: 3.7.16
Operating System: Windows 10

Description

I want to export registration to the Qupath project programmatically from python.
To do this, I launch an ABBA instance in headless mode, I load a state file and run the export registration command :

aligner = abba.Abba('Adult Mouse Brain - Allen Brain Atlas V3p1', headless=True)
aligner.state_load(os.path.join(inputdir, inputfile))
aligner.select_all_slices()
aligner.export_registration_to_qupath(erase_previous_file=True)

The following line is printed :
Exporting slice img_001.ome.tiff registration to QuPath
But there is nothing written in the Qupath project.

There is an error raised during the loading of the state file (see below), but this error did not prevent me from doing things with abba_python previously (eg. converting coordinates).

Doing the same thing not in headless mode (eg. aligner = abba.Abba('Adult Mouse Brain - Allen Brain Atlas V3p1')), the output is more talkative, those lines are also printed :

Multipositioner : Save slice ROI to quPath project path\to\qproj\data\1\ABBA-RoiSet-Adult Mouse Brain - Allen Brain Atlas V3p1.zip
Multipositioner : Save transformation to quPath project path\to\qproj\data\1\ABBA-Transform-Adult Mouse Brain - Allen Brain Atlas V3p1.json

And the files are indeed exported.

So it seems the multipositionner does not really exist in headless mode and Qupath export relies on it (but converting coordinates does not so that is why the latter works) ?

Output

[java.lang.Enum.toString] [ERROR] Multipositioner : null
[ERROR] Command errored: ABBA - Load State
java.awt.HeadlessException
        at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
        at java.awt.Window.<init>(Window.java:536)
        at java.awt.Frame.<init>(Frame.java:420)
        at java.awt.Frame.<init>(Frame.java:385)
        at javax.swing.JFrame.<init>(JFrame.java:189)
        at ch.epfl.biop.atlas.aligner.MultiSlicePositioner.lambda$new$2(MultiSlicePositioner.java:134)
        at ch.epfl.biop.atlas.aligner.MultiSlicePositioner.lambda$new$4(MultiSlicePositioner.java:144)
        at ch.epfl.biop.atlas.aligner.MultiSlicePositioner.loadState(MultiSlicePositioner.java:1181)
        at ch.epfl.biop.atlas.aligner.command.ABBAStateLoadCommand.run(ABBAStateLoadCommand.java:27)
        at org.scijava.command.CommandModule.run(CommandModule.java:196)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
        at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
[java.lang.Enum.toString] [ERROR] Command errored: ABBA - Load State
java.awt.HeadlessException
        at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
        at java.awt.Window.<init>(Window.java:536)
        at java.awt.Frame.<init>(Frame.java:420)
        at java.awt.Frame.<init>(Frame.java:385)
        at javax.swing.JFrame.<init>(JFrame.java:189)
        at ch.epfl.biop.atlas.aligner.MultiSlicePositioner.lambda$new$2(MultiSlicePositioner.java:134)
        at ch.epfl.biop.atlas.aligner.MultiSlicePositioner.lambda$new$4(MultiSlicePositioner.java:144)
        at ch.epfl.biop.atlas.aligner.MultiSlicePositioner.loadState(MultiSlicePositioner.java:1181)
        at ch.epfl.biop.atlas.aligner.command.ABBAStateLoadCommand.run(ABBAStateLoadCommand.java:27)
        at org.scijava.command.CommandModule.run(CommandModule.java:196)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
        at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)

DeepSlice fails on certain QuPath projects

ABBA Python version: 0.1.14
Python version: 3.7
Operating System: Win11

Description

Try to run DeepSlice in the omero test project.

What I Did

The results are done but are not applied. Probably an error on the Java side with no log.

Adds standalone installer

Use conda constructor to make stand alone installer for:

Windows
Mac
Linux

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