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Add a 'nx-copy' application

Merged payno requested to merge fix_157 into main

TODO

  • Add application to copy an NXtomo from one file to another (or to a folder)
    • add a simple option to remove link and embed all in the NXtomo (loading it all in memory for now). If some more advanced option is required will be done in another PR
  • Add test
  • Add doc
  • Update tomwer doc once done (user corner / python script - how to copy an NXtomo)

API

copy a single file (with potentially several NXtomo):

nxtomomill nx-copy /path/to/nxomofile.nx .
nxtomomill nx-copy /path/to/nxomofile.nx new.nx

copy a single NXtomo (potentially contained in a file with several NXtomo):

nxtomomill nx-copy /path/to/nxomofile.nx --entry entry0000  .
nxtomomill nx-copy /path/to/nxomofile.nx --entries entry0000,entry0001  .

copy a set of file:

for file in *.nx
do
    nxtomomill nx-copy "$file" /new/path/"$file"
done

To replace HDF5 virtual datasets by a standard dataset you can also use the --remove-vds option. In this case the full dataset will be load in memory before dumping it.

related to nxtomo!8 (merged)

Edited by payno

Merge request reports

Pipeline #135687 passed

Pipeline passed for f5a3cfa8 on fix_157

Test coverage 77.00% from 1 job

Merged by paynopayno 1 year ago (Sep 25, 2023 1:39pm UTC)

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Pipeline #135704 passed

Pipeline passed for c43a4c32 on main

Test coverage 77.00% from 1 job

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    • 0dc2f326 - add nxtomomill 'copy' application

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  • payno changed title from Draft: Fix 157 to Add a 'nx-copy' application

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  • payno marked the checklist item Add application to copy an NXtomo from one file to another (or to a folder) as completed

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    • 7326d7b1 - add nxtomomill 'copy' application
    • 1d9f2f38 - nx-copy: add `remove-vds` option
    • f5a3cfa8 - doc: add documentation for nx-copy usage

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  • payno marked the checklist item add a simple option to remove link and embed all in the NXtomo (loading it all in memory for now). If some more advanced option is required will be done in another PR as completed

    marked the checklist item add a simple option to remove link and embed all in the NXtomo (loading it all in memory for now). If some more advanced option is required will be done in another PR as completed

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