Thanks for the announcement! Can you expand on how you see the eco-system of scikit-image, imread and imageio interacting?

Since imageio has a pretty good plugin system, it could be a good place to implement io for all the weird scientific file formats that exist. Next to imread(), volread(), etc. imageio also provides the read() function, which returns a reader object specific to the plugin. This reader object can have additional methods and may yield other data then just 2D/3D numpy arrays if this makes sense for the format.

So I suppose I am hoping for skimage devs to embrace imageio and help move it further.

With that, I suppose skimage could focus on the processing rather than the io, since ideally, we'd have one library for processing images, and one for reading/saving images.

<rant> Developers tend to have a fear for dependencies. I understand this, and I try to minimize dependencies myself, but reading/writing images is a task that warrants a standalone package IMO. It troubles me a bit that different libraries are each rolling their own image io functionalities. </rant>

As for the imread package: Zach and I considered it when discussing plans for imageio, but imread is based on C++, which is harder to maintain and makes it a harder dependency. imageio is pure Python with ctypes bindings to some libs that are auto-downloaded.

- Almar

PS: some fancy stuff that imageio can do which might be interesting for skimage users: stream images from webcam, export visualizations to animated gif or mp4.

Hi Almar

On 2014-11-14 00:40:37, Almar Klein almar.klein@gmail.com wrote:

With that, I suppose skimage could focus on the processing rather than the io, since ideally, we'd have one library for processing images, and one for reading/saving images.

That is certainly the direction we're aiming for. At the moment, we try to have a minimal setup that works in 80% of use-cases. Once imageio is distributed widely in the main distributions, we can even make it a default dependency.

In the mean time, let's talk about integrating it as a plugin, or perhaps add a page to the skimage docs on how to read more exotic formats (especially cross-platform video would be a big win!).

Stéfan

We included a copy of Christophe's `tifffile.py` in our repo and are using that within our PIL plugin for loading TIFF files.

Ah great, in that case I suspect making an imageio plugin would be easy.

I could see perhaps *vendoring* ImageIO to replace `skimage.io` and requiring FreeImage as the only external dependency.

What do you mean by "vendoring"?

BTW: the freeimage lib is auto-downloaded. Imageio also has its own version of that lib for Linux, since I found some Linux's have a rather old version of FreeImage, which was causing bugs.

Also good to know: Ghislain Vaillant is currently making a debian package for imageio.

Regards, Almar

Stéfan would have to weigh in on that.

Regards,

Steve

On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote:

Hi all,

I'm pleased to announce version 1.0 of imageio - a library for reading
and writing images. This library started as a spin-off of the freeimage
plugin in skimage, and is now a fully-fledged library with unit tests
and all.

Imageio provides an easy interface to read and write a wide range of
image data, including animated images, volumetric data, and scientific
formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy
to install.

Imageio is plugin-based, making it easy to extend. It could probably
use
more scientific formats. I welcome anyone who's interested to
contribute!

install: pip install imageio
website: http://imageio.github.io
release notes:
http://imageio.readthedocs.org/en/latest/releasenotes.html
<http://imageio.readthedocs.org/en/latest/releasenotes.html>

Regards,
    Almar

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By vendoring I meant including a snapshot of the imageio project in the scikit-image repo, and using it if there is not a system version available (which is how we handle `tifffile.py`).

I suppose you'd like imageio to use relative imports throughout for this to work? It does not yet, but that's easy enough to fix from my end.

I agree with Stéfan that we should include imageio as an optional plugin in the short term and then once an imageio Debian package and conda mainline package are available, more toward making it a requirement instead of PIL.

That sounds like a reasonable plan.

I will implement the imageio scikit-image plugin (unless you'd rather), but I've got a few other commitments lined up prior to getting more involved in the short term.

Great. I am involved in a few other things now as well, so I was hoping someone would pick this up.

As someone who has worked in a lab with no internet connection, I am wary of requiring an external library to be downloaded upon install

Actually, it's downloaded at runtime. Which is even worse, I guess :) The motivation for this is that a) it made the code simpler; 2) some dependencies like the ffmpeg exe are rather large, and installing these by default (or shipping them along in the dist package) seemed like something that might irritate users who just want to read a png image.

I'd be happy to work towards a solution for that. At least to get freeimage working. Perhaps you can help find a solution, as having been in such a situation, you might have a good idea of what could work and what not. See: https://github.com/imageio/imageio/issues/42

Regards, Almar

On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote:

Hi all,

I'm pleased to announce version 1.0 of imageio - a library for reading
and writing images. This library started as a spin-off of the freeimage
plugin in skimage, and is now a fully-fledged library with unit tests
and all.

Imageio provides an easy interface to read and write a wide range of
image data, including animated images, volumetric data, and scientific
formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy
to install.

Imageio is plugin-based, making it easy to extend. It could probably
use
more scientific formats. I welcome anyone who's interested to
contribute!

install: pip install imageio
website: http://imageio.github.io
release notes:
http://imageio.readthedocs.org/en/latest/releasenotes.html
<http://imageio.readthedocs.org/en/latest/releasenotes.html>

Regards,
    Almar

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FYI:

imageio v1.1 is available now.

Release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html

- Almar

On 19-11-14 13:01, Steven Silvester wrote:

Yes, all imports would have to be relative. I've chimed in on #42, but posting my thoughts here:

"I'd vote to have a source-only version, and wheels for 64 bit Linux, Windows, and OSX with just the freeimage support. Rather that auto-downloading, it would be nice to present the user with the option of whether to download an external lib, perhaps as a simple Tk dialog. I think partial functionality is fine in this case given the nature of the library."

Regards,

Steve

On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote:

Hi all,

I'm pleased to announce version 1.0 of imageio - a library for reading
and writing images. This library started as a spin-off of the freeimage
plugin in skimage, and is now a fully-fledged library with unit tests
and all.

Imageio provides an easy interface to read and write a wide range of
image data, including animated images, volumetric data, and scientific
formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy
to install.

Imageio is plugin-based, making it easy to extend. It could probably
use
more scientific formats. I welcome anyone who's interested to
contribute!

install: pip install imageio
website: http://imageio.github.io
release notes:
http://imageio.readthedocs.org/en/latest/releasenotes.html
<http://imageio.readthedocs.org/en/latest/releasenotes.html>

Regards,
    Almar

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Congratulations, and thanks for the nudge. Here's a PR to add a plugin to scikit-image: https://github.com/scikit-image/scikit-image/pull/1575.

On Friday, July 3, 2015 at 8:11:15 AM UTC-5, Almar Klein wrote:

Hi,

imageio v1.3 is available now: http://imageio.readthedocs.org

Imageio is growing in popularity and a user just suggested that skimage should use it as the default plugin, which reminded me of this thread. Time to revive this discussion?

• Almar

On 04-02-15 15:45, Almar Klein wrote:

...

FYI:

imageio v1.1 is available now.

Release notes:

http://imageio.readthedocs.org/en/latest/releasenotes.html

...

• Almar

On 19-11-14 13:01, Steven Silvester wrote:

...

Yes, all imports would have to be relative. I've chimed in on #42, but posting my thoughts here:

"I'd vote to have a source-only version, and wheels for 64 bit Linux, Windows, and OSX with just the freeimage support. Rather that auto-downloading, it would be nice to present the user with the option of whether to download an external lib, perhaps as a simple Tk dialog. I think partial functionality is fine in this case given the nature of the library."

Regards,

Steve

On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote:

Hi all, 

I'm pleased to announce version 1.0 of imageio - a library for 

reading and writing images. This library started as a spin-off of the freeimage plugin in skimage, and is now a fully-fledged library with unit

tests

...

...

and all. 

Imageio provides an easy interface to read and write a wide range 

of

...

...

image data, including animated images, volumetric data, and 

scientific formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy to install.

Imageio is plugin-based, making it easy to extend. It could 

probably

...

...

use 
more scientific formats. I welcome anyone who's interested to 
contribute! 

install: pip install imageio 
website: http://imageio.github.io 
release notes: 
http://imageio.readthedocs.org/en/latest/releasenotes.html 
<http://imageio.readthedocs.org/en/latest/releasenotes.html> 

Regards, 
    Almar 

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