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Json cor file for concatenate in nightrail

Merged myron requested to merge json_cor_file_for_concatenate_in_nightrail into master

For easiness of use within a workflow, the provided cor position can be read from a json file using the cors_file option

  • example of usage, generated by night_rail_bm18 :
 nxtomomill z-concatenate-scans \\\
 --filename_template sessionIN1173_Bliss2NxMultiZScript_output_dir/sessionIN1173_Bliss2NxMultiZScript_output_XXXX.nx \\\
 --target_file sessionIN1173_ConcatenateToHeliScanScript_concatenated.nx \\\
 --entry_name entry0000 \\\
 --total_nstages 35 \\\
 --first_stage 0 \\\
 --last_stage 5 \\\
 --cors_file  sessionIN1173_CompositeCorSimpleScript_cors.json  \\\
 --flats_from_before_after yes \\\
 --scan_before sessionIN1173_Bliss2NxMultiZScript_output_dir/sessionIN1173_Bliss2NxMultiZScript_output_begin.nx \\\
 --scan_after sessionIN1173_Bliss2NxMultiZScript_output_dir/sessionIN1173_Bliss2NxMultiZScript_output_end.nx 
Edited by payno

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