[ImageJ-devel] [ImgLib2] The img-metadata branch
Mark Hiner
hiner at wisc.edu
Fri Dec 13 08:24:15 CST 2013
Hi Brian,
> On first glance it would seem to me the SAMPLE_FORMAT should be set to 3
> (for float) somehow in the typedTranslate function. However I'm not
> overly familiar with the code.
>
Your fix was absolutely correct. I updated SCIFIO
master<https://github.com/scifio/scifio/commit/ece33ccc7c1b4bfdb13e749dce96b440d66db534>to
account for floats when translating.
Anyway, I really appreciate you taking the time - not just to report the
bug - but to delve into the code! Since it takes extra effort on your part
to debug, if you ever would like your name attached to your work, please
feel welcome to submit pull requests (e.g. to
scifio<https://github.com/scifio/scifio/pulls>
).
Thanks again for reporting this issue - let us know if anything else comes
up!
- Mark
On Thu, Dec 12, 2013 at 8:23 AM, Brian Northan <bnorthan at gmail.com> wrote:
> Hi Curtis
>
> I was testing out the ImgSaver updates and seem to be having trouble
> saving a 32 bit float image. At some point in the chain the format seems
> to be getting set to 32 bit unsigned int.
>
> Not sure if I am doing something wrong... basically my code looks exactly
> like your example. I did step through the scifio code a bit and was
> looking at the translation steps for the meta data. In TiffFormat.java,
> "typedTranslate" the format gets set to either 2 or 1 depending on whether
> it is signed...
>
> firstIFD.putIFDValue(IFD.SAMPLE_FORMAT, FormatTools.isSigned(m
> .getPixelType()) ? 2 : 1);
>
> In the next step where the translated meta data is set for the
> destination, it seems to be looking for a sample format of 3 for float.
> But the sample format was set to 2 in the previous step...
>
> final int bitFormat = getIFDIntValue(SAMPLE_FORMAT);
> ....
> case 32:
> if (bitFormat == 3) return FormatTools.FLOAT;
> return bitFormat == 2 ? FormatTools.INT32 :
> FormatTools.UINT32;
>
> On first glance it would seem to me the SAMPLE_FORMAT should be set to 3
> (for float) somehow in the typedTranslate function. However I'm not
> overly familiar with the code.
>
> Brian
>
>
>
> On Wed, Dec 4, 2013 at 4:57 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
>> 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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