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<div class="">That is a little complicated of a directory structure.</div>
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<div class="">I would separate the arguments to run the test and defining the data dependency. First `ExternalData_Expand_Arguments` is called with the path to “acquisition” in the source directory, which contains the MD5. Something like:</div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">ExternalData_Expand_Arguments(ITKData</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> ExpandedData # ignores output variable</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> DATA{Input/acquisition/,</span><span style="color: rgb(68, 68, 68); font-family: monospace; font-size: 12.34999942779541px; text-align: justify; background-color: rgb(236, 240, 243);" class="">RECURSE:,REGEX:.*</span>}</div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> )</span></div>
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<div class="">Then add the test :</div>
<div class=""> itk_add_test( NAME itkBurkerTest1 COMMAND ITKBurkerTestDirver DATA{<span style="font-family: Menlo; font-size: 11px; background-color: rgb(255, 255, 255);" class="">Input/acquisition/1/2dseq}"</span></div>
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<div class="">You can find an example of this here:</div>
<div class=""><a href="https://github.com/InsightSoftwareConsortium/ITK/blob/c5c879ad54778ce3b514fd35c197ed4340ccd976/Modules/Filtering/FFT/test/CMakeLists.txt#L138-L150" class="">https://github.com/InsightSoftwareConsortium/ITK/blob/c5c879ad54778ce3b514fd35c197ed4340ccd976/Modules/Filtering/FFT/test/CMakeLists.txt#L138-L150</a></div>
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<div class="">Please note I have not tried those lines, but I expect them to be close to the proper things to do.</div>
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<div class="">Brad</div>
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<div class="">On Jun 14, 2017, at 9:13 AM, Wood, Tobias <<a href="mailto:tobias.wood@kcl.ac.uk" class="">tobias.wood@kcl.ac.uk</a>> wrote:</div>
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<div class="">Thanks very much Brad. Individual responses below.<br class="">
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<blockquote type="cite" class="">If you need an entire folder, you can create it here. I am not sure what problem you encountered with this layout.<br class="">
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To be honest, I didn’t try it. I assumed it would cause problems. I will try it.<br class="">
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<blockquote type="cite" class="">There are quite a number of options for referencing files series, file pair, and associated directories. I would expect this to meet you needs.<br class="">
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Again thanks - I had completely missed this documentation.<br class="">
<br class="">
<blockquote type="cite" class=""> It’s not clear to me what files are needed when reading, if you need recommendation on using `DATA{}` please be specific with the files needed by the IO, and their locations.<br class="">
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The bare minimum required to read the image are the ‘2dseq’ and ‘visu_pars’ file. I have kept the convention of the old Bruker reader which is to specify the ‘2dseq’ file as the input, and then to work out the paths to ‘visu_pars’ and the other headers.<br class="">
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The Bruker format is a bit complex. The issue is that each acquisition can be reconstructed multiple times. The directory structure goes something like this:<br class="">
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acquistion/<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>method<span class="Apple-tab-span" style="white-space:pre">
</span><- An important header file<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>acqp<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"></span><- Another important header<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>fid<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"></span><- Raw data<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>***bunch of other stuff***<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>pdata/<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>1/<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>2dseq<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"></span><- Reconstructed data<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"></span>visu_pars<span class="Apple-tab-span" style="white-space:pre">
</span><- Most important header<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"></span>reco<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"></span><- Less important header, mostly duplicated in visu_pars<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>procs<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"></span><- Unimportant header<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>id<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"></span><- Unimportant header<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>2/<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"></span>2dseq<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>visu_pars<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>reco<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"></span>procs<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>id<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>...<br class="">
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I hope the indentation survives transmission. Here, 1 and 2 are different reconstructed images, for instance magnitude and phase, or for diffusion it might be raw images and a multi-volume file containing FA, MD etc. as calculated by ParaVision.<br class="">
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From Paravision 6 onwards, the bare minimum to read an image seems to be 2dseq + visu_pars. However, some important meta-data like diffusion b-values and b-vectors is only present in the method header. Hence I’m not entirely sure what should be considered a
valid “image” by ITK - just 2dseq + visu_pars, or the entire data structure?<br class="">
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For my uses, I think the best approach would be to consider 2dseq + visu_pars the minimum, but if the other headers are present read them in to get the meta-data. Is that acceptable?<br class="">
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Best wishes,<br class="">
Toby<br class="">
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