[ImageJ-devel] [ImgLib2] The img-metadata branch

Wed Dec 4 15:57:16 CST 2013

Hi Brian & everyone,

> there is currently a bug in ImgSaver preventing things from working
...
> We are working on a fix now and will reply back when the bug is
> resolved.

Just a quick update that ImgSaver of scifio-0.7.3 is working better. The
following code now produces a multi-page TIFF as expected:

--snip--
import io.scif.SCIFIO;
import io.scif.img.ImgOpener;
import io.scif.img.ImgOptions;
import io.scif.img.ImgOptions.ImgMode;
import io.scif.img.ImgSaver;
import net.imglib2.meta.ImgPlus;

public class WriteAnImgPlus {
public static void main(final String... args) throws Exception {
final SCIFIO scifio = new SCIFIO();
 final ImgOpener opener = new ImgOpener(scifio.getContext());

// NB: ImgSaver only supports PlanarImg for now!
 final ImgOptions options = new ImgOptions().setImgModes(ImgMode.PLANAR);
final ImgPlus<?> imgPlus =
 opener.openImg("stack&axes=X,Y,Z&lengths=128,128,10.fake", options);

System.out.println("imgPlus = " + imgPlus);
 System.out.println("numDimensions = " + imgPlus.numDimensions());
for (int d=0; d<imgPlus.numDimensions(); d++) {
 System.out.println("dim #" + d + " = " + imgPlus.dimension(d));
System.out.println("axis #" + d + " = " + imgPlus.axis(d).type());
 }

final ImgSaver saver = new ImgSaver(scifio.getContext());
saver.saveImg("stack.tif", (ImgPlus) imgPlus);
 }
}
--snap--

As of this writing, please note that you will only be able to save as
OME-TIFF if you include the ome-formats library [1] plus dependencies on
your classpath.

Regards,
Curtis

[1] https://github.com/scifio/ome-formats

On Thu, Oct 24, 2013 at 1:14 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Brian,
>
> Apologies for the long delay in reply. It is better to write to a public
> mailing list. I am CCing imagej-devel.
>
> > Is the following code snippet still correct given recent changes??
> >
> > AxisType[] ax = new AxisType[3]; ax[0]=Axes.X; ax[1]=Axes.Y;
> > ax[2]=Axes.Z;
> >
> > ImgPlus<T> imgPlus = new ImgPlus<T>(image, name, ax);
>  >
> > new ImgSaver().saveImg("name.ome.tif", imgPlus);
>
> Firstly, as an aside, please note that ImgSaver has moved from the
> net.imglib2:imglib2-io project into io.scif:scifio core.
>
> But yes, the above code is still supposed to work.
>
> However, in practice there is currently a bug in ImgSaver preventing
> things from working correctly.
>
> Here is a complete (non-)working example:
> https://gist.github.com/ctrueden/6234396
>
> We are working on a fix now and will reply back when the bug is resolved.
>
> Regards,
> Curtis
>
>
> On Tue, Aug 13, 2013 at 5:21 AM, Brian Northan <bnorthan at gmail.com> wrote:
>
>> Hi Curtis
>>
>> So after updating imglib this morning I now get lots of errors.  Which is
>> expected after your changes.  So I suspect after I sort through them and
>> rework my code for the changes that saving the axis types will work again.
>>
>> But one other quick question.  Is the ImageJ2 scripting ready for use??
>> I looked at it a bit a while ago but it didn't seem quite ready.   I have a
>> series of commands I call, so temporarily I just use a bash script calling
>> Imagej2 in headless mode, with a utility I wrote to parse command name and
>> parameters.   Eventually I will switch to the ImageJ scripting...  is it
>> usable yet or should I wait a few more months?
>>
>> Thanks, this stuff is really great.
>>
>> Brian
>>
>> On Tue, Aug 13, 2013 at 4:46 AM, Brian Northan <bnorthan at gmail.com>wrote:
>>
>>> Hi Curtis
>>>
>>> I have some simple code to wrap an 3D Img<T> as an ImgPlus, define the
>>> axis as x,y and z and then save it.  Up until a week or so ago it seemed to
>>> work fine.  But now when I read back the image it come in as x, y, t.   Is
>>> the following code snippet still correct given recent changes??   Thanks-
>>> Brian
>>>
>>> AxisType[] ax = new AxisType[3];
>>>         ax[0]=Axes.X;
>>>         ax[1]=Axes.Y;
>>>         ax[2]=Axes.Z;
>>>
>>> ImgPlus<T> imgPlus = new ImgPlus<T>(image, name, ax);
>>>
>>> new ImgSaver().saveImg("name.ome.tif", imgPlus);
>>>
>>>
>>>
>>> On Mon, Aug 12, 2013 at 1:39 PM, Curtis Rueden <ctrueden at wisc.edu>wrote:
>>>
>>>> Hi all,
>>>>
>>>> > I will merge the img-metadata branch to master on Thursday.
>>>>
>>>> Got a bit busy in the interim, but img-metadata is now merged to
>>>> imglib.git's master branch:
>>>>
>>>>
>>>> https://github.com/imagej/imglib/commit/e4e26aa05e0f42ff1a90e8c6d67235431471de44
>>>>
>>>>  The commit message gives a quick gist of the changes, including future
>>>> directions.
>>>>
>>>> Please let me know of any questions or problems with it!
>>>>
>>>> Regards,
>>>> Curtis
>>>>
>>>>
>>>> On Tue, Jul 30, 2013 at 10:28 AM, Curtis Rueden <ctrueden at wisc.edu>wrote:
>>>>
>>>>> Hi all, and especially ImgLib2 developers,
>>>>>
>>>>> At the ImgLib2 hackathon this past May, I started work on a branch to
>>>>> make it easier to attach per-axis metadata to N-dimensional spaces. I think
>>>>> this branch is finally in a merge-worthy state.
>>>>>
>>>>> It introduces an AnnotatedSpace extension to EuclideanSpace which lets
>>>>> you attach on Axis per dimension. It defines TypedSpace, which declares an
>>>>> AxisType for each Axis, as well as a CalibratedSpace, which in addition
>>>>> adds a calibration value and optional unit name to the mix.
>>>>>
>>>>> This approach is much more flexible than the previous CalibratedSpace,
>>>>> which has been renamed to OldCalibratedSpace and deprecated until we can
>>>>> fully transition all the code away from it. In particular, having the axes
>>>>> attached to the space directly will allows Views to maintain the axis
>>>>> metadata without much additional work.
>>>>>
>>>>> Note that these new classes are defined in the net.imglib2.meta
>>>>> component, which was split into a separate module called imglib2-meta. The
>>>>> ImgPlus class moved there, too (it should have been there all along). So
>>>>> merging this branch will cause some code breakage, but all should be
>>>>> straightforward to fix: rename usages of CalibratedSpace to
>>>>> OldCalibratedSpace, and rename the ImgPlus package from net.imglib2.img to
>>>>> net.imglib2.meta.
>>>>>
>>>>> Going forward, we can also add a CalibratedViews class to the
>>>>> net.imglib2.meta package which has some additional features such as
>>>>> exposing resampled Imgs from a source CalibratedSpace into a target one
>>>>> based on the units used. We can lean on a units library for this, as we
>>>>> have discussed in the past.
>>>>>
>>>>> If interested, you can browse the branch at:
>>>>> https://github.com/imagej/imglib/compare/img-metadata
>>>>>
>>>>> If no one objects, I will merge the img-metadata branch to master on
>>>>> Thursday.
>>>>>
>>>>> Regards,
>>>>> Curtis
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> ImageJ-devel mailing list
>>>> ImageJ-devel at imagej.net
>>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-devel/attachments/20131204/c164d41a/attachment.html>