<div dir="ltr"><div>So if you have multi-series images where the series are of differing resolutions, would the ImageIO::Read populate the image array with itk::CovariantArrays (or some other array type?) and just fill in the positions that exist? Because it's 1 array per position, would that necessitate smaller resolutions being stored after larger resolutions?<br>
<br></div>is there a way, in the ITK API, to request a specific series from the ImageIO?<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jul 2, 2013 at 9:10 AM, Mark Hiner <span dir="ltr"><<a href="mailto:hinerm@gmail.com" target="_blank">hinerm@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Yep, the SCIFIOImageIO is actually a gateway to a Bio-Formats <a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/scifio/src/loci/formats/ImageReader.java" target="_blank">ImageReader</a>, which provides support for all the <a href="http://loci.wisc.edu/bio-formats/formats" target="_blank">Bio-Formats formats</a>... and it allows updates to Bio-Formats (e.g. new formats) to be automatically supported, without duplicating the work in C++.<br>
<br></div>The <a href="https://github.com/scifio/scifio" target="_blank">SCIFIO source</a> (which is in beta) is just a dynamically extensible ImageIO framework, and we're working on refactoring Bio-Formats to use the SCIFIO API.<br>
<br></div>Eventually I plan on creating a high-level C++ mirror of the SCIFIO API, which will greatly simplify the SCIFIOImageIO... but for today I'll be happy just to get multi-series images working :)<br><br></div>
Thanks again.<br>
<div><div><div><br><br></div></div></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jul 2, 2013 at 8:58 AM, Williams, Norman K <span dir="ltr"><<a href="mailto:norman-k-williams@uiowa.edu" target="_blank">norman-k-williams@uiowa.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">That sounds about right. The first step (if you haven't done this<br>
already) is to set up a Gerritt account so you can submit patches for<br>
review: <a href="http://www.itk.org/Wiki/ITK/Git/Develop" target="_blank">http://www.itk.org/Wiki/ITK/Git/Develop</a><br>
<br>
<br>
I hadn't realized until I looked what a crazy thing the SCIFIOImageIO was.<br>
It starts up a java process and passes it commands?<br>
<br>
I'm not volunteering or anything, but I can't imagine that the file format<br>
is so complex that it wouldn't be worth writing a C++ parser for it.<br>
<div><br>
On 7/2/13 8:27 AM, "Mark Hiner" <<a href="mailto:hiner@wisc.edu" target="_blank">hiner@wisc.edu</a>> wrote:<br>
<br>
>The SCIFIOImageIO doesn't currently have knowledge of the series count,<br>
>but it would be simple to pass that information from the Java portion of<br>
>the ImageIO during the ReadImageInformation step.<br>
><br>
><br>
>So it sounds like, if I modify the SCIFIOImageIO to start tracking the<br>
>series count, and use that information to populate the data array<br>
>according to the<br>
><br>
>VectorImage spec<br>
</div>><<a href="http://www.itk.org/Doxygen/html/classitk_1_1VectorImage.html#a62029e56578" target="_blank">http://www.itk.org/Doxygen/html/classitk_1_1VectorImage.html#a62029e56578</a><br>
>31db8bdec71a5b3482964> during ImageIO::Read, everything will just work..<br>
<div><div>>right?<br>
><br>
>Thanks for the help!<br>
><br>
><br>
><br>
><br>
>On Mon, Jul 1, 2013 at 3:34 PM, Williams, Norman K<br>
><<a href="mailto:norman-k-williams@uiowa.edu" target="_blank">norman-k-williams@uiowa.edu</a>> wrote:<br>
><br>
>I haven't worked on the SCIFIO reader, so I'm not sure how it behaves.<br>
><br>
>In a perfect world, you'd specify an itk::VectorImage as the image type<br>
>for the reader. VectorImage is more efficient in cases where all voxels<br>
>have the same number of vector elements. Then, when SCIFIO reads the file<br>
>initially, it should know enough about the image format to deduce the<br>
>series size, and reorganize the raw Image Buffer such that the conversion<br>
>to vector voxels does the right thing.<br>
><br>
>The image type parameter of the ImageFileReader shouldn't need to specify<br>
>the series size.<br>
><br>
><br>
>Looking at the SCIFIOImageIO class, it definitely doesn't look that smart.<br>
> In that case you'll need to read the image in as a 4D image of scalar<br>
>voxels, and build the 3D VectorImage from the 4D Scalar Image.<br>
><br>
>On 7/1/13 3:12 PM, "Mark Hiner" <<a href="mailto:hiner@wisc.edu" target="_blank">hiner@wisc.edu</a>> wrote:<br>
><br>
>>Hi all,<br>
>><br>
>><br>
>>I'm working on a Bio-Formats / ITK bridge that invokes Bio-Formats<br>
>>(SCIFIO) Readers by piping commands from C++ to Java.<br>
>><br>
>> I'm having some issues with multi-image datasets. I have a file that<br>
>>contains 580 2048x2048x11 images. If I use a pure Bio-Formats conversion<br>
>>tool, the images are merged as a single image with 580 T slices.<br>
>><br>
>><br>
>> First of all, how should an image like this be represented in ITK? My<br>
>>assumption is as a VectorImage type and not by using the<br>
>>ImageSeriesReader.. as the latter says it needs multiple files, and I<br>
>>have multiple series in a single file.<br>
>><br>
>><br>
>> Given the proper data structure for this dataset, how do I actually<br>
>>determine (or set) the appropriate series size parameters?<br>
>><br>
>><br>
>>e.g. if I do have a VectorImage does its size have to be declared to even<br>
>>make a Reader/Writer, or is there some way I can set it from my ImageIO<br>
>>during the ReadImageInformation call?<br>
>><br>
>><br>
>>... or if I do have to explicitly declare the size, how can the ImageIO<br>
>>tell which series is currently being queried during ImageIO::Read/Write,<br>
>>so I can pass that series parameter to a Bio-Formats Reader?<br>
>><br>
>><br>
>><br>
>><br>
>>Thanks,<br>
>>Mark<br>
>><br>
><br>
><br>
><br>
><br>
><br>
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