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napari-j's Introduction

napari-J

License PyPI Python Version tests codecov

A plugin to exchange data with FIJI and to use FIJI image analysis from napari. Current features are:

  • get the active image from FIJI
  • send a screenshot to FIJI
  • get a set of points from the FIJI results table
  • filter the points in napari
  • send the filtered points back to FIJI

Known problems:

  • Crashes on linux when the file-dialog is opened. Workaround: Set the option Use JFileChooser to open/save from the Edit>Options>Input/Output menu.
  • 03.05.2022 - Currently you need to have the range of the quality values for point between 0 and 255, in the new version they can have any range, but we are waiting for the bug in napari 0.4.15 to be fixed to release this.

This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-J via pip:

pip install napari-J

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the MIT license, "napari-J" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

napari-j's People

Contributors

jaimergp avatar l-tellez avatar volker-baecker avatar

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napari-j's Issues

Error message

Thank you for generating the plugin. When I tried to run, I got the following error message:

ModuleNotFoundError Traceback (most recent call last)
File ~/miniconda3/envs/napari-env/lib/python3.9/site-packages/napari_j/image.py:80, in Image._on_click_get_image(self=<napari_j.image.Image object>)
79 def _on_click_get_image(self):
---> 80 self.getImage()
self = <napari_j.image.Image object at 0x1971c1e50>

File ~/miniconda3/envs/napari-env/lib/python3.9/site-packages/napari_j/image.py:105, in Image.getImage(self=<napari_j.image.Image object>)
103 def getImage(self):
104 print("Fetching the active image from IJ")
--> 105 self.getBridge().getActiveImageFromIJ()
self = <napari_j.image.Image object at 0x1971c1e50>

File ~/miniconda3/envs/napari-env/lib/python3.9/site-packages/napari_j/image.py:98, in Image.getBridge(self=<napari_j.image.Image object>)
97 def getBridge(self):
---> 98 from .bridge import Bridge
99 if not self.bridge:
100 self.bridge = Bridge(self.viewer)

File ~/miniconda3/envs/napari-env/lib/python3.9/site-packages/napari_j/bridge.py:9
7 from jpype.types import *
8 import numpy as np
----> 9 from ij.measure import ResultsTable
10 from ij import IJ, ImagePlus, WindowManager
11 from ij.plugin import HyperStackConverter

File ~/miniconda3/envs/napari-env/lib/python3.9/site-packages/ij/init.py:15
12 from itertools import chain
13 from operator import add
---> 15 from ut.ml.sk.feature_extraction.text import TreeTokenizer
16 from functools import reduce
18 path_separator_pattern = re.compile('/+')

ModuleNotFoundError: No module named 'ut'

Relationship with `ImageJ-Python-Bridge`?

Hello!

A part of the napari team is migrating the plugin ecosystem to conda-forge. We are reviewing this specific project here, where I stumbled upon the two packages being distributed in this repo:

  • napari_j
  • ijpb

It looks like the latter refers to another project in this organization, ImageJ-Python-Bridge, and I would like to clarify what's the status/relationship of both projects:

  • Can people use them separately or are they tightly coupled?
  • Are they developed at the same pace or do they have different release schedules?
  • Will ImageJ-Python-Bridge be distributed on its own on PyPI at some point?
  • In essence, should we package napari_j together with ijpb or not?

Thanks!

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