From z_stages to helical

myron requested to merge z_stages_2_helical into master

From z_stages to helical

It takes a list of nx files and obtains one whole nx scan that can be reconstructed in helical mode

  • Build a first prototype
  • test
  • integrate in nxtomomill

Example of usage

>...: % ls /data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages*.nx

/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W__0029_0001.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W__0030_0001.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W__0031_0001.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W_REF_B_0000_0001.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W_REF_E_0000_0001.nx

>...: % wd="/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages"

>...: % nxtomomill z-concatenate-scans   
\--filename_template ${wd}/HA-1100\_27.73um_sheep-head_ethanol_W__XXXX_0001.nx   
\--target_file concat.nx   
\--total_nstages 44   
\--first_stage 29   
\--last_stage 31   
\--cors_file cors.txt   
\--pixel_size_m 0.00002737   
\--flats_from_before_after yes   
\--scan_before   
${wd}/HA-1100\_27.73um_sheep-head_ethanol_W_REF_B_0000_0001.nx   
\--scan_after   
${wd}/HA-1100\_27.73um_sheep-head_ethanol_W_REF_E_0000_0001.nx
Edited by payno

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