Ignore:
Timestamp:
Jan 12, 2022 8:35:30 PM (9 months ago)
Author:
ilavsky
Message:

12IDB fix instructions

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/User Procedures/Nika/NI1_InstrumentSupport.ipf

    r1176 r1177  
    25322532        else
    25332533        String nb = "APS12IDB_Instructions"
    2534         NewNotebook/N=$nb/F=1/V=1/K=1/ENCG={1,1}/W=(930,427,1644,1205) as "APS12IDB_Instructions"
     2534        NewNotebook/N=$nb/F=1/V=1/K=1/ENCG={1,1}/W=(130,170,1236,1000) as "APS12IDB_Instructions"
    25352535        Notebook $nb defaultTab=10, magnification=125
    25362536        Notebook $nb showRuler=1, rulerUnits=2, updating={1, 1}
     
    25402540        Notebook $nb ruler=Normal, text="\r"
    25412541        Notebook $nb text="\r"
    2542         Notebook $nb text="1. Find path to your tif images. Pick folder with raw tiff images, not the average folder. \r"
     2542        Notebook $nb text="1. Find path to your data images. Pick folder - either \"SAXS\" or \"WAXS\" - with raw tiff or hdf5/Nexus im"
     2543        Notebook $nb text="ages, not the average folder. \r"
    25432544        Notebook $nb text="\r"
    2544         Notebook $nb text="2. Code will find available masks and present dialog to select:\r"
    2545         Notebook $nb text="\ta. Data reduction method (see below)\r"
    2546         Notebook $nb text="\tb. Proper (SAXS/WAXS mask)\r"
     2545        Notebook $nb text="2. Code will find available data, calibrations, masks and present dialog to choose to :\r"
    25472546        Notebook $nb text="\r"
    2548         Notebook $nb text="3. Configuration and calibration should be read from meta files with metadata for each file automaticall"
    2549         Notebook $nb text="y. \r"
     2547        Notebook $nb text="\ta. ", fStyle=1, text="Subtract Empty/background?", fStyle=-1
     2548        Notebook $nb text=" - this is basically data reduction method (see below)\r"
     2549        Notebook $nb text="\r"
     2550        Notebook $nb text="\tb. ", fStyle=1, text="Load calibration from appropriate calibration file", fStyle=-1
     2551        Notebook $nb text=". If you choose not to, you need to calibrate everything yourself. \r"
     2552        Notebook $nb text="\r"
     2553        Notebook $nb text="   c. ", fStyle=1, text="Choose to reload calibration from metadata with each loaded image", fStyle=-1
     2554        Notebook $nb text=". Rarely needed... This is useful when you may have data from different calibrations in the same folder. Do "
     2555        Notebook $nb text="NOT choose this oiption if you need to overwrite original calibration.  \r"
     2556        Notebook $nb text="\r"
     2557        Notebook $nb text="   d. ", fStyle=1, text="Load appropriate mask", fStyle=-1
     2558        Notebook $nb text=", SAXS or WAXS, if found. If you choose not to, you need to design your own mask and switch masking on y"
     2559        Notebook $nb text="ourself. \r"
     2560        Notebook $nb text="\r"
     2561        Notebook $nb text="With default choices you will : choose \"bioSAXS\" data processing, load calibration from xxxx_calibration"
     2562        Notebook $nb text="_parameters.txt file, not reload calibration with each loaded image, and load appropriate existing mask."
    25502563        Notebook $nb text="\r"
    25512564        Notebook $nb text="\r"
    2552         Notebook $nb text="*** Data reduction methods ***\r"
    2553         Notebook $nb text="1. Subtract Empty/Background NO: reduces each image separately, normalized by transmitted counts (flux an"
    2554         Notebook $nb text="d transmission normalization), masked. Solvent/background sutraction needs to be done later, for example"
    2555         Notebook $nb text=" in BioSAXS Irena tools, but you can average many data sets together. This is default beamline and bioSAXS setting.\r"
    25562565        Notebook $nb text="\r"
    2557         Notebook $nb text="2. Subtract Empty/Background : YES. This is typical Nika processing - solvent/background image is subtr"
    2558         Notebook $nb text="acted in Nika directly, with flux normalization for sample and background, transmission calculation etc."
    2559         Notebook $nb text=" In this case only ONE background image can be used at time, which may not be suitable if you have multiple images. \r"
     2566        Notebook $nb fStyle=5, text="*** Data reduction methods ***\r"
     2567        Notebook $nb fStyle=-1, text="1. ", fStyle=1, text="Subtract Empty/Background - NO", fStyle=-1
     2568        Notebook $nb text=": reduces each image separately, normalized by transmitted counts (flux and transmission normalization) "
     2569        Notebook $nb text="and normalization factor, masked. Solvent/background sutraction needs to be done later. This is typical "
     2570        Notebook $nb text="for BioSAXS data when multiple images are collected per sample. Using Irena bioSAXS tools you can then a"
     2571        Notebook $nb text="verage multiple data together, subtracted these averaged data etc. This is default beamline processing a"
     2572        Notebook $nb text="nd typical for bioSAXS data.\r"
     2573        Notebook $nb text="\r"
     2574        Notebook $nb text="2. ", fStyle=1, text="Subtract Empty/Background - YES", fStyle=-1
     2575        Notebook $nb text=". This is typical Nika processing for materials SAXS - solvent/background image is subtracted in Nika di"
     2576        Notebook $nb text="rectly, with flux normalization for sample and background, transmission calculation etc. In this case on"
     2577        Notebook $nb text="ly ONE background image can be used at time, which may not be suitable if you have multiple images. \r"
    25602578        Notebook $nb text="\r"
    25612579        Notebook $nb text="\r"
    2562         Notebook $nb text="Jan Ilavsky, 1/5/2021\r"
     2580        Notebook $nb text="Jan Ilavsky, 1/12/2021\r"
    25632581        Notebook $nb text="\r"
    25642582        Notebook $nb fStyle=2, text="Hint: watch history area for notes on what Nika has found and done. \r"
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