napari: Cannot open .tif files after #1061

🐛 Bug

I believe after delaying the loading of image reading library(ies) in #1061, you can no longer drag and drop .tifs into napari, when launching the GUI from the command line. It also doesn’t seem to work loading the image from “Open image(s):” and get error:

No plugin found capable of reading XXX.tif.

To Reproduce

Steps to reproduce the behavior:

Drag .tif into Napari
Open .tif in File menu

Expected behavior

Switching back to commit 434d54e fixes the problem

@jni @sofroniewn @Czaki

About this issue

Original URL
State: closed
Created 4 years ago
Comments: 18 (13 by maintainers)

Commits related to this issue

Update dependencies - jupyter client no longer needs to be pinned, see https://github.com/napari/napari/pull/1240 - we need to depend on tifffile for our built-in IO plugin, see https://github.co... — committed to jni/napari-feedstock by jni 4 years ago

Most upvoted comments

Ah, sorry everyone. I’m on 391cfd572, but the issue is that I did not update the dependencies after updating to the latest commit, namely tifffile wasn’t actually installed. All good now! I hate when that happens when installed in developer mode.

hectormz on Apr 10, 2020

It worked like a charm! Thank you all for the fast fix!

Just to leave a note for people like me: conda update --all doesn’t seem to bring the latest build, do conda remove napari && conda install -y -c conda-forge napari instead.

hungyiwu on May 26, 2020

The latest napari build on conda-forge depends on tifffile. Hopefully that is enough to fix your problem @hywu0110! btw, if your tiffs aren’t supported by that version, you can either:

pip install imagecodecs, or
conda install -c conda-forge tiffffile=2019.7.26.2, ie get an earlier version of tifffile, see https://github.com/conda-forge/tifffile-feedstock/issues/39. The earlier version should still have built-in support for most common codecs.

jni on May 26, 2020

Thanks @hywu0110 - looks like @tlambert03 might have identified the issue here https://github.com/napari/napari/issues/1129#issuecomment-633772534 which we can work to fix

sofroniewn on May 26, 2020

@sofroniewn Here’s what I got when running napari --info:

napari: 0.3.1
Platform: Linux-5.4.0-7629-generic-x86_64-with-debian-bullseye-sid
Python: 3.7.7 (default, Mar 26 2020, 15:48:22)  [GCC 7.3.0]
Qt: 5.12.5
PyQt5: 5.12.3
NumPy: 1.18.1
SciPy: 1.4.1
Dask: 2.16.0
VisPy: 0.6.4

GL version:  4.6 (Compatibility Profile) Mesa 20.0.4
MAX_TEXTURE_SIZE: 16384

Plugins:
  - napari-plugin-engine: 0.1.5
  - svg: 0.1.2

hungyiwu on May 26, 2020

This likely relates to https://github.com/napari/napari/pull/1061#issuecomment-612061394

sofroniewn on Apr 10, 2020