VMBICAL-AIR Operator Instructions


NOTE: This assumes that the latest version of VMBICAL-AIR has been installed on a local machine for the operator to use. If VMBICAL-AIR has not been installed please see the installation instructions and do so.

  1. It is necessary to create a resource file that is sourced for paths to input and output files and directories. To create this file, copy the vmbicalrc file in /vmbical_air/templates/Startup to the operator's home directory.
      > cd vmbical_air/templates/Startup
      > cp vmbicalrc $HOME
      > cd $HOME
      > mv vmbicalrc .vmbicalrc
      

    Note: Once the file has been renamed to .vmbicalrc it will not be visible when a simple ls command is used. To see .files a ls -a is necessary.

  2. Parameters in the .vmbicalrc will need to be edited.
    • edit parm_path to the path of the vmbical_air/params directory
    • edit copy_path to the path of the field.tape.copies directory
    • edit cal_path to the path of the averaged calibration images needed for processing
    • edit ftr_path to the path of the VSN directories containing the raw data
    • edit disk_path to the directories to which the calibrated data will be copied after the output tape has been written
    • edit dsds_path to the path of the directory that holds or to be created to hold the toc and lbl files to be written to the calibrated data (output) tape
    • edit COPIPE_path to the directory to which the calibrated and compressed velocity images will be sent for COPIPE processing
    • edit tapehost to the machine name that tapes will be read from or written to
    • edit tpdrive_in to the tape drive that will be used to write the final tape
    • edit vmbical_soft to the path of the vmbical_air directory
    • edit iraf_home to the path of the vmbical_iraf directory
    • edit VGRASPBIN to the path to the local installation of GRASP executables
    • edit VIRAFBIN to the path to the local installation of IRAF executables

    NOTE: For Operator's not running in production mode it is not necessary to have the COPIPE_path, infact it can be commented out by placing a pound sign in front of it (#COPIPE_path).

  3. Create a control directory in a desired location for data to be processed on. Typically a control directory is named wa0.ssyymmdd where ss indicates the GONG site and yymmdd represents the first date of the data being processed.

  4. It is necessary to have a copy of run_vmbical and a parameter.rc file to the created control directory from the /vmbical_air/templates/Startup directory. It is not necessary to edit the run_vmbical file, but the parameter.rc file will need to be edited. The parameter.rc should be renamed to SSparyymmdd.rc where SS indicates the GONG site and yymmdd represents the first date of the data being processed.

  5. The following parameters will need to be edited in the parameter.rc for processing:
    • edit SITE to the two-letter upper case site designation for the data being processed
    • edit wa1 to the directory path where the initial and intermediate (stz, raw, vmbi and geom) directories for each siteday will be created
    • edit wa2 to the directory path where the output (int, mag, mod, vel and vel.gz) directories for each siteday will be created
    • edit VSN_ins to the VSN numbers of the raw data tapes to be processed
    • edit VSN_ot to the VSN number that will be assigned to the calibrated data (output) tape written at the end of the processing
    • edit tpdrive_ot to the tape drive that will be used to write the final tape

    Check to make sure the run_vmbical script is executable. If it is not executable, change the permissions on the file by typing

    chmod u+x run_vmbical
    at the prompt.

  6. To begin processing, type run_vmbical SSparyymmdd.rc at the prompt.

  7. Hit the Enter key at the Prepare the siteday directories prompt

      to begin setting up the directories for processing. If this step has been completed previously, enter s at the prompt to move on to the second stage of processing data. The second stage of processing data starts in step (15).

  8. Hit the Enter key at the get_site_days for VSN_in prompt
      to begin copying information for each VSN to be processed.

  9. Hit the Enter key at the Enter to process all days from VSN, or enter anything else for no prompt.

      in order to process all of the sitedays on the raw data tape. Or if the operator wishes to choose specific days to process, enter anything other than the Enter key at the prompt. The run_vmbical script will then prompt the operator to hit the Enter key for each day to be processed or s to skip the processing of a specific day. This is most useful when it's obvious to the operator, judging from the instrumental profiles prepared by the FTR operator, that a given siteday is completely clouded out or that the instrument did not guide all day for any other reason.

  10. Hit the Enter key at the Edit tapedata prompt

      if the operator would like to edit the sitedays to be processed. At this point in the processing, after lists of images for each siteday are created, the operator has another opportunity to remove a day, or days, from processing. A vi editor environment is then opened and the tapedata file, which defines for the program which days to process, can be edited using vi commands. Otherwise, the operator enters s at the prompt to process the data as previously defined.

      NOTE: If a siteday has 00 listed for filenumbers that siteday should be deleted from further processing. If the operator does not remove this siteday from processing problems will arise later on in the processing.

  11. Hit the Enter key at the Use the edited file no. ranges in tapedata to copy subsets of hour_ang, phase, net_rad, guider, itime, rawlist prompt

      to create the hour_ang, phase, net_rad, guider, itime and rawlist files required by VMBICAL-AIR for the processing.

  12. Hit the Enter key at the Prepare disk directories (s to skip) prompt

      to create the necessary siteday directories for processing. The operator will then be prompted to hit the Enter key to create a set of directories for each siteday to be processed. Also at this point the operator is asked if the first day on the tape is a continuation from a previous tape, or if the last day is continued on a succeeding tape. The program makes the required files or file edits to accommodate the split day, but at this date the operator is responsible for deleting references to the split day in the VSN directory for the first tape and, at least for the time being, the operator also needs to go into an external window and cd to the hdr_parms directory of the split day's siteday directory and make a copy of the raw_list file in that directory, with the new file being named raw_list_cont.

  13. Hit the Enter key at the Transfer calibration correction images prompt

      to copy them into the control directories for all sitedays to be processed. This is the last step in prepping the data for processing.

  14. Steps 4 - 8 will be repeated for each raw data tape entered on the VSN_ins line of the parameter.rc file.

  15. The second part of the VMBICAL-AIR processing is the staging and calibrating of the siteday data. To begin, hit the Enter key at the Stage all and then process all sitedays prompt.

  16. Hit the Enter key at the Copy All Files from /input/ftr, run UNRICE and run DAYSCAN from VSNs prompt

      to create symlinks to the location of the online data to the siteday stz directories and then to be efficient with processing time, in this version of VMBICAL-AIR all of the sitedays are first decompressed using UNRICE and then the first step in the automatic image rejection (AIR) software, DAYSCAN, is run on all of the siteday images.

  17. Hit the Enter key at the Open the iraf session to run VIEWLOG prompt

      to begin the interactive portion of the AIR software, VIEWLOG. An xgterm window will open with IRAF already started. To load the VMBICAL scripts type

      vmbical
      at the prompt. Click here to see a screen shot of what the IRAF window should look like with the VMBICAL scripts loaded.

    Change directories to the control directory created for the data set in step (1).

    Type run_viewlog at the IRAF prompt to begin VIEWLOG.

      The operator is then prompted for the upper case site code and the VSN number. The operator is then prompted to process each siteday day-by-day, type y or hit the Enter key at the view the log files prompt.

    In the IRAF window the operator is prompted ENTER if ok, (r)edraw, (c)hange mod limits, (p)rint, (v)erbose. Click here to see a screen shot of the IRAF window when a day has been chosen to process and is prompted as above.

      If the plot window is not large enough, the operator can manually resize the window (usually done by clicking and dragging on one of the corners of the graphics window) and then type r at the prompt. If the modulator values need to be changed, type c at the prompt. The operator will then be prompted to enter a new minimum value first and then a new maximum modulator value. If the modulator values do not need to be changed, hit the Enter key.

    A single screen of plots is produced for the siteday. Click here to see a sample of the screen plots produced.

    Calculated values for the whole disk average of the modulator difference images (pseudomagnetograms), standard deviation of the modulator images, whole disk average of one-minute difference between images and the standard deviation of the one-minute difference images are plotted versus time. The values used for rejection criterion are plotted as red lines. See the sample image to become familiar with the plot layout.

    The values of the image rejection criterion (the plotted red lines) were determined empirically. For most of these values there is no reason to expect them to vary over time. The exception is the whole disk modulator average (the top plot in the graphics window). This can change over time, either from periodic seasonal changes (which are probably not significant) or due to changes in the instrument.

    On a good siteday, the plot of the whole disk average modulator state difference should be a smooth but fuzzy line. There can be gradual shifts during the course of the day and the width of the line is generally no more than 20 units. These pseudomagnetograms are highly sensitive to even very thin clouds and may even respond to variations in seeing, so images should not be rejected too aggressively. Deviations from the trend line of 150 or more units may be acceptable and if not one of the other tests will most likely reject them.

    When the modulator average line undergoes one of these intermediate to long term shifts, either approaching the high or low threshold value, that limit should be adjusted to allow for 100 to 150 units of margin between it and the data curve. There is enough redundancy between the various tests that the other limit probably doesn't need to be adjusted until it is more than 300 or 400 units from the data curve. When one of these long term shifts occurs it will be preferable to modify the default copy of the reject.dat file in the VMBICAL installation which holds the rejection criterion values rather than adjusting those values day after day.

    After viewing the plots, if the operator would like to mark a siteday for deletion, type mark at the press RETURN to keep the day or enter 'mark' to delete it prompt.

      Sometimes it may be immediately obvious to the operator that the siteday being viewed contains no useful data. Either the siteday may consist of very poor data (all points fall outside of the rejection criterian) or there is very little data. If a siteday is not to be deleted hit the Enter key at the prompt.

    The operator will need to run run_viewlog individually for each VSN entered on the VSN_ins line. After VIEWLOG has been run on all of the VSNs type

    logout
    at the prompt to close the IRAF window.

  18. Hit the Enter key at the Run REJECT and USEDS on sitedays from VSNs prompt

      to finish the AIR portion of the processing. REJECT and USEDS are run to determine which images should be moved to a "rej" directory and not processed any further. The determination of which images are moved into the rej directory is based on the modulator values set in the VIEWLOG step as well as a few other parameters.

  19. Hit the 'Enter key at the Begin calibration on staged sitedays from VSNs prompt

      to start the calibration process. One press of the Enter key is all that's needed to process the data of all VSNs listed in the parameter.rc file.

  20. Hit the Enter key at the QA the sitedays and Open an iraf window to run getqa prompts

      and an xgterm window will open with IRAF already started to begin the QA portion of the processing. To load the VMBICAL scripts type

      vmbical
      at the prompt. Click here to see a screen shot of what the IRAF window should look like with the VMBICAL scripts loaded.

    Change directories to the control directory created for the data set in step (1).

    Type getqa at the prompt to begin the QA.

      The getqa script then prompts the operator to enter the path to the vmbical_air directory, the upper case site code, the VSN number and the printer to which to send send any plots.

    Then for each siteday getqa will prompt process the qa plot files.

      If the siteday is to be processed, type either y at the prompt or hit the Enter key.

    To print a copy of the good images plot, hit the Enter key at the prompt or type s to skip the plotting. To print a copy of the all images plot hit the Enter key at the prompt of type s to skip the plotting. In general, the operator will skip the plotting at this point until the QA plot has been examined, as discussed below.

    An IMAGE FLAGGING MENU will then be displayed in the IRAF window.

      At this point in the processing, in the original version of VMBICAL, the operator would begin flagging bad images. In the AIR era of VMBICAL, the operator will likely not need to do much additional image flagging.

    At the enter l, ln, r, pg, pgp, pa, pap, x, quit prompt, type in pg and hit the Enter key to check the QA plots onscreen. The velocity plot line can be more easily seen by also taking a look at the pgv plot option.

      Assuming all looks fine, just type x in the menu and the Enter key to print the edited good image plot to keep for the files.

    On the other hand, if the plots, especially the pgv plot, show a wayward point or two, type in l and hit the Enter key in the Flagging Menu. Enter the approximate wayward image time, to get the stats for the 15 images around the suspect minute(s). In this way the operator can pinpoint the images requiring flagging and enter the errant image with the f (flag) option in the Menu, or a range of images with the r option, before executing the x option. The operator can then re-check the pg or pgv plots onscreen before the final x Menu option which ends the flag process and produces the edited hardcopy plot before moving on to the next siteday for that VSN.

    The getqa script will need to be run individually for each VSN being processed in this job. After getqa has been run on all of the VSN's type

    logout
    at the prompt to close the IRAF window.

  21. Hit the Enter key at the Split the images and Split the images from VSN_inprompts

      for the calibrated images to be split into the vzi, bzi, izi and mzi data products.

    The operator will need to hit the Enter key at each Split the images from VSN_in prompt or just type ahead by hitting another Enter for all tapes being processed in the job.

  22. Hit the Enter key at the Prepare the ancillary files to be written to tape prompt

      for all of the ancillary files to be prepared to be written to tape and copied to a remote location.

  23. Hit the Enter key at the Write the vmbical output volume VSN_ot prompt

      to begin writing an output tape of the calibrated data products and ancillary files. The calibrated data products and ancillary files will also be copied to the remote location identified in the disk_path line in the .vmbicalrc file.


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