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Command analogous to 'unu head' for im files #15

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cpoczatek opened this issue Jun 20, 2016 · 0 comments
Open

Command analogous to 'unu head' for im files #15

cpoczatek opened this issue Jun 20, 2016 · 0 comments
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@cpoczatek
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cpoczatek commented Jun 20, 2016

The command unu head file.nrrd prints the header (which is text) of file.nrrd to standard out. This is very useful when looking over the metadata for an experiment. Right now you have to do the file conversion to .nrrd to do this. It would be nice if we could do this with .im files.

Since the header of an .im file is binary we have to do a fair amount of work to parse it. We have a few options how to do this:

  • fork out the Opener/MIMSReader classes into a stand alone utility outside of IJ/Fiji. This has the drawback of parsing each time we call it on a file and JVM startup time. unu head is fast since it's just reading/printing till the end of the header (an empty line).
  • Run within Fiji. Since there's a lot of things going to std out I don't think we can just print the header. We'd have to write it to a file. It might make sense to write detached nrrd headers (.nhdr files) with an empty data field.

Not sure which way is better at the moment. Though there's no reason the 1st option couldn't have both behaviors.

@taylorwrt taylorwrt self-assigned this Sep 26, 2016
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