Posted by
ctrueden on
Jun 30, 2014; 3:59pm
URL: http://imagej.273.s1.nabble.com/Non-Uniform-X-Y-Z-Units-Patch-tp5008492p5008496.html
Hi Alan,
> Is there interest in fixing this?
The ImageJ2 team is definitely interested in making support for non-linear
calibration and units better in ImageJ2. And actually, the data structures
are already in place on the ImgLib2 side of things.
> I developed a start at some patches that improve the non-uniform
> handling and submitted them to the imagej-dev mailing list last week (
>
http://imagej.net/pipermail/imagej-devel/2014-June/002140.html),
> but didn't hear back as of yet.
Changes to ImageJ1 are at Wayne Rasband's discretion, as he is ImageJ1's
sole developer. Historically, he has taken patch submissions and reworked
them to his liking before merging them.
For ImageJ2 code changes, we prefer Pull Requests on GitHub, and public
discussion on the ImageJ and imagej-devel mailing lists.
> Perhaps there is a better way to submit ImageJ1 patches and report
> bugs?
For ImageJ1, sending a patch to imagej-devel, or as a PR on GitHub, or to
Wayne via private mail, all work. The important part is that Wayne receive
the patch, since he is the only one with the authority to merge it. Note
that Wayne typically replies via private mail, especially for long
back-and-forth threads, so current status is often opaque to the rest of
the community.
> Or maybe it is better to have a discussion first before sending out a
> patch.
Having a public discussion is almost always worthwhile; otherwise, you are
a working in a vacuum and not receiving any feedback on your development
directions.
In this particular case, I would caution against hacking on ImageJ1's
calibration logic too much. Firstly, it needs to remain backwards
compatible with existing macros and plugins. And secondly, anything which
makes ImageJ1's calibration logic more complex at this point will also make
ImageJ2's job of backwards compatibility more complex -- and we have enough
on our hands already, there. I would rather see developers start migrating
to the ImageJ2 data structures when they need things like nonlinear
calibration, so that ImageJ1 does not have to worry about that problem at
all, and we can all move forward together as a community.
> Although I have been developing plugins and using ImageJ for years,
> this is my first attempt to engage with the community. I admit I am
> confused about the proper path for that, perhaps because much of the
> community's work seems to be focused on ImageJ2 development at the
> moment.
Hopefully the above clarifies things a bit. If you have further questions,
please feel free to ask! And if you want to benefit the community along
these lines, I encourage you to edit the Community section of the ImageJ
wiki's FAQ to add a question about community contributions, so that others
will not have to ask on the mailing list next time!
http://wiki.imagej.net/FAQ#CommunityRegards,
Curtis
On Mon, Jun 30, 2014 at 10:04 AM, Alan Brooks <
[hidden email]> wrote:
> My company's systems often acquire image data using a linear
> one-dimensional detector, building up an image over time by scanning. The
> raw data files that come from this process naturally have time as one axis
> and pixel as the other axis. In our raw file reader for ImageJ, I have
> found it useful to preserve these units when reading the raw data by using
> the setX/YUnits() methods in Calibration. This allows our teams to analyze
> the raw time axis for sampling and/or noise artifacts and the raw pixel
> axis for any problems related to individual detectors.
>
> A problem with the current ImageJ handling of non-uniform x, y, and z units
> is that even though the units are set, many of the supporting functions
> just use getUnit() which returns getXUnit() even when getY/ZUnit() might
> differ. For example, the Image->Show Info function display the x-units for
> all dimensions when displaying XResolution and YResolution.
>
> Is there interest in fixing this?
>
> I developed a start at some patches that improve the non-uniform handling
> and submitted them to the imagej-dev mailing list last week (
>
http://imagej.net/pipermail/imagej-devel/2014-June/002140.html), but
> didn't
> hear back as of yet.
>
> Perhaps there is a better way to submit ImageJ1 patches and report bugs? Or
> maybe it is better to have a discussion first before sending out a patch.
> Although I have been developing plugins and using ImageJ for years, this is
> my first attempt to engage with the community. I admit I am confused about
> the proper path for that, perhaps because much of the community's work
> seems to be focused on ImageJ2 development at the moment.
>
> Cheers,
> Alan
>
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> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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