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Hello,
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<div class="">Thank you for your work on this.</div>
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<div class="">Re 1:</div>
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<div class="">The Bruker ImageIO should be moved out of the review directory an placed in own ITK module under "Modules/IO/Bruker2DSEQ”, which you appear to have already done in your branch. Outstanding! I would place the data in this modules under the “test/Input”
subdirectory. If you need an entire folder, you can create it here. I am not sure what problem you encountered with this layout.</div>
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<div class="">Re 2:</div>
<div class="">You can find the CMake documentation for that here:</div>
<div class=""><a href="https://cmake.org/cmake/help/v3.3/module/ExternalData.html#referencing-file-series" class="">https://cmake.org/cmake/help/v3.3/module/ExternalData.html#referencing-file-series</a></div>
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<div 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.</div>
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<div class="">I glanced at the contents: <a href="https://github.com/spinicist/ITK/commit/541411449a9538b758507672583c88db949d90cb" class="">https://github.com/spinicist/ITK/commit/541411449a9538b758507672583c88db949d90cb</a> 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.</div>
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<div class="">HTH,</div>
<div class="">Brad</div>
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<div class="">On Jun 14, 2017, at 6:19 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="">Hello,<br class="">
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I have been slowly working on my updated Bruker2DSEQ file reader. It’s not quite ready for formal review, but it is available here:
<a href="https://github.com/spinicist/ITK" class="">https://github.com/spinicist/ITK</a> (On the Bruker branch)<br class="">
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I have reached a problem writing a suitable test, because the Bruker data format consists of multiple files. I previously discussed this issue with Jon Haitz, but despite his help I am stuck.<br class="">
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I have added a new example Bruker file in Testing/Data/Input/Bruker2DSEQ. There was already a Bruker dataset in Testing/Data/Input/DCB120604.t61, but this is from (I think) ParaVision 3. Bruker made a *lot* of changes when they released ParaVision 6, one of
which was the introduction of a new header file called “visu_pars”. The actual image data is still in the “2dseq” file.<br class="">
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My problem is that the itk Test Driver only transfers the 2dseq file to build/ExternalData/Testing/Data/Input/Bruker2DSEQ/... , and not the “visu_pars” file, and hence trying to read the file fails.<br class="">
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So, questions:<br class="">
1 - Is this the correct place to put the test data? Because of the Bruker directory structure, I assumed the recommended way of requesting an MD5 hash and putting the data in the module’s test directory won’t work?<br class="">
2 - How do I indicate to the test driver that it needs to copy the whole directory structure, and not just the 2dseq file? Eventually, I would like the reader to read all the header files (there are several of them) because they contain useful meta-data that
users might want to extract.<br class="">
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I was hoping to do a bit more polishing before putting this out for any kind of review, but I guess now is as a good a time as any. Let me know if you need more information. Note - I moved the module out of Nonunit/Review, I hope this was a good idea but I
can always move it back if necessary.<br class="">
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Thanks,<br class="">
Toby<br class="">
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