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mscotfflat mscred


On-The-Fly (OTF) Calibration


MSCDISPLAY and the real-time display based on this task applies an on-the-fly (OTF) calibration to raw mosaic exposures as they are being displayed. This does not change the actual data files and the calibration is intended to be quick and approximate. The calibration steps performed are a line-by-line bias subtraction using the overscan region of the data and a division by a flat field. If the data have been overscan corrected or flat field corrected by CCDPROC then the task will automatically skip those steps. The title of the display will indicate if the data have been calibrated by adding "[bias]" for bias subtraction and "[bias,flat=XXX]" for bias subtraction and flat fielding using an OTF flat field called XXX.

The bias subtraction is performed by averaging the overscan pixels in a line and subtracting this average from all the pixels in the line. This removes the amplifier bias and line-by-line patterns.

The flat field or response calibration is performed by reading special flat field calibration data which provides an approximate relative response for each pixel in each amplifier readout. Depending on how the calibration file is derived this will approximately correct for pixel sensitivity variations, gain variations between the amplifiers, sky illumination variations, and any pupil ghost pattern (as occurs with NOAO Mosaic data from the KPNO 4meter telescope). Note that this is not the correct way to remove the pupil ghost but for the purposes of flattening the display in order to see faint objects this is useful.

The other display related tasks, MSCEXAMINE and MSCFOCUS, must perform the same correction when the display and cursor are used to select data to measure. Currently they do not know if the data have been calibrated in the display. Instead, one must make sure to use the same parameters relating to the display in the MIMPARS parameter set.

Creating and Installing OTF Flat Fields at NOAO

1. Take one or more flat fields. The count levels have to be below 30000. If not divide the values by a number either before or after processing using MSCARITH. Since the OTF flats are spatially binned and digitized to reduce size it probably is not very useful to create a high quality flat from multiple exposures, a single exposure should be fine.

2. Process the flat(s). The processing should be only overscan and trim. If combining multiple flats with FLATCOMBINE set the processing as noted. The processing should save the raw exposures in the Raw subdirectory (or whatever is set for the "backup" parameter in MSCRED).

3. Run MSCOTFFLAT with the default values. The output name must be one word (that is an acceptible directory name) and should be the standard identifier for the filter. Typically this would be the first word of the filter name recorded in the header (with any characters which are not letters, numbers, or . replaced with _). The template name is one of the raw exposures.

    ms> mscotfflat flat001 B Raw/flat001

This will create a subdirectory, B in this example, with the number of pl files equal to the number of extensions.

3a. You can check if things make sense by the size of the pl files being approximately 0.6-1.6Mb. You can also display the files and compare with the original data using:

    ms> display B/flat1 1 fill+ ...
    ms> display flat00[1] 2 fill+ ...

They should be very similar to the flat from which they were derived.

4. To use during your run with the real-time DCA display you would set the calibration directory in the DCA GUI to point to the parent directory containing the subdirectories of pl files (the directory you were in when you ran MSCOTFFLAT). This is done from the "Edit" menu, selecting "Path Params", editing the "Calibration Dir" field, and finally clicking "Apply". Also if you are going to use MSCDISPLAY with "process=yes" then go to the "mimpars" parameters and set the "caldir" directory parameter there too. Remember that directories in IRAF must end with / (or $ for logical directories).

If you do nothing else the software will look in the specified calibration directory for a subdirectory which matches the first word of the filter string in the image header (with any characters that are not letters, numbers, or . changed to _). If you want to translate the header filter name to some other (directory) name you can add a "" file where the first column is the filter name (quoted if there are blanks) and the second column is the directory name. This file is also used to set the override choices for the filter in the DCA GUI.

The following is done to install the OTF directory for general use and requires the IRAF login.

5. Login as IRAF and go to the standard calibration directory:

/iraf/extern/mscdb/noao/ctio/4meter/caldir/Mosaic2A     # CTIO 4m (8 A amps)
/iraf/extern/mscdb/noao/ctio/4meter/caldir/Mosaic2B     # CTIO 4m (8 B amps)
/iraf/extern/mscdb/noao/ctio/4meter/caldir/Mosaic2      # CTIO 4m (16 amps)
/iraf/extern/mscdb/noao/kpno/4meter/caldir              # KPNO 4m
/iraf/extern/mscdb/noao/kpno/36inch/caldir              # KPNO 36inch
/iraf/extern/mscdb/noao/kpno/wiyn/caldir                # KPNO WIYN

Transfer the OTF directory to that calibration directory. One way is

    % (cd /md1/4meter/nite1; wtar B) | rtar -xv

6. Edit the file. The first column is the filter name as given in the data files under the FILTER keyword. The second name is the directory name. The order of the entries in the order in which the filters will appear in the DCA list. Note the DCA list is only used to override the automatic filter selection based on the filter keyword.

7. Remove the OTF directory in your data area. One way is with "!rm -rf <dir>". You can also restore the original raw flats for taping by moving the files from the Raw subdirectory back to the data directory.

8. I am maintaining a master MSCDB directory that includes current OTF flats. This serves the purpose of a backup, the source to generate installation files, and the source to generate distribution files for users who might want them. So if you create OTF files please notify me.

OTF Flat Field Calibration Format

The flat field calibration is a special, more compact format than a regular mosaic flat field. The small size is important both to save disk space in a standard calibration directory with lots of filters and to allow more efficient I/O and in-memory storage of the flat field data. For instance, the NOAO Mosaic has 14 filters and two telescopes.

The compression relies on two factors. First is that pixel values can be quantized and still produce a good approximate calibration. The second is that the quantized values often have the same values over contiguous regions. These factors allow use of the IRAF pixel list format which represents integer values which are constant over segments of each line by fewer bytes than the individual values.

The algorithm for creating the compressed flat field format consists of two simple steps with two parameters. The first step is to block average the original real-valued flat field specified by a block average factor. This brings neighboring values to the same value which aids the pixel list representation. Then the quantization is performed using the equation:

    quantized integer value = int (nint (value / scale) * scale)

where "value" is the real flat field pixel value and "scale" is a quantization factor. The nint function takes the nearest integer value of its argument and the int function truncates its argument to an integer. The scale factor is defined by

    scale = <value> * resolution

where "<value>" is the mean flat field value and "resolution" is a parameter of the algorithm. The resolution is then a fractional resolution of the mean flat field.

For example, suppose the mean flat field value is 5001.23 and the resolution is 0.5%. The digitization quantum is then 25.006. A flat field value of 5123.45 would be quantized to 5126 and all values between 5113.8 to 5138.8 also quantize to 5126.

The NOAO Mosaic has significant flat field variations, which prompted the development of the OTF calibration. The variations are on the order of 10%. The size of a full flat field exposure, reduced to real values, is 256 Mb. Applying the algorithm above with a 2x2 block average and a 0.5% resolution produces an IRAF pixel list format, OTF flat field which is ~5 Mb. Application of this OTF flat field shows virtually no artifacts.

MIMPARS Parameters

The parameters controlling the OTF calibration are set in the MIMPARS parameter set. This parameter set is a subset of the MSCDISPLAY, MSCEXAMINE, and MSCFOCUS tasks. As such they can be edited from EPAR on these task by typing ":e" when over the "mimpars" parameter or the values can be given on the command line for those tasks. Typing "mimpars" or "epar mimpars" will also let you edit these parameters and "lpar mimpars" will display the parameters. The EPAR display looks like

    ms> mimpars
			       I R A F  
		Image Reduction and Analysis Facility
    PACKAGE = mscred
       TASK = mimpars

    (extname=             ) extension name pattern
    (exttmpl= _![1-9]![1-9]![1-9].*) extension template for ...

    (xgap   =           72) minimum X gap between images
    (ygap   =           36) minimum Y gap between images

    (process=           no) do calibration processing?
    (oversca=          yes) do line-by-line overscan subtraction?
    (flatfie=          yes) do flat field correction?
    (caldir =             ) calibration directory
    (filter =             ) filter

The first two groups of parameters have to do with selecting data to be displayed and the gaps between the mosaic pieces added during display. It is the last set of parameters that deal with the OTF calibration.

For the NOAO Mosaic, running SETINSTRUMENT or using the parameters set at the telescope will set some of these parameters appropriately to reference a calibration directory supplied by the instrument team. For example, at the Kitt Peak 4meter telescope the parameters would be

    (caldir = mscdb$noao/kpno/4meter/caldir/) cal...
    (filter =              !filter) filter

The process parameter selects whether to turn on or off the OTF processing. If it is no then regardless of the overscan or flatfield values no calibration will be done. If it is yes then one or both calibration operations can be selected.

The flat field calibration requires special calibration files. The caldir parameter defines a directory containing the calibration files. This can be a standard directory or a user directory. Note that if a directory is specified it must end with $ or /. In this directory, which could include other files, the calibrations are given by some set of names. Currently these are the names of directories containing pixel list files for each amplifier. Creating these files is done with the task MSCOTFFLAT which is described below. The filter parameter can be set to one of these names.

For more automatic selection of calibrations, the calibrations can be selected by the filter string in the header (or by giving the same filter string in the filter parameter). To use the filter string in the header the value of the filter parameter is set to "!<keyword>" where <keyword> is the keyword for the filter string. The filter string often contains some general description. The OTF calibration software goes through the following steps to resolve the string to a calibration file in the calibration directory.

If the file "" is present in the calibration directory it is read to find translations between the filter string and the calibration name. The translations consist of two columns with the full filter string and the calibration name. If either contains spaces then it must be quoted. For example:

    "OIII Mosaic N2"    O3
If the file is not present or a match to the filter string is not found then the first word of the filter string is used with non-alphanumeric characters replaced by _. For example, "OIII Mosaic N2" is mapped to OIII.
If the name arrived at by the first two methods fails then a calibration called "default" in the calibration directory is sought.

Note that one may use the "" file or not and one can use logical links to provide explicit mappings between filters for which a calibration has been generated and those which have not in addition to making "default" link to some particular filter calibration.

Real-time Display with the DCA

At the telescope with the NOAO Mosaic, the data capture agent (DCA) has controls to select processing during the readout automatic display. One toggle is equivalent to the process parameter. If the processing is turned on the DCA automatically selects only overscan bias subtraction for non-object exposures and selects both bias subtraction and flat field division for object exposures. The filter parameter is set by passing through the filter string from the data acquisition system or by overriding this and using the filter menu to select one of the available calibrations.

Creation of OTF Flat Fields

Begin by reducing the flat field data. This could be from combining a sequence of dome flat exposures or it could be more ambitious super sky flat field. The reduced flat field would normally be trimmed to remove the bias. A template raw flat field exposure needs to be kept to define the final OTF flat field size and keywords. The OTF flat field needs to be the same size as the common raw exposures for efficiency since if the OTF flat field is a different size it will be adjusted to match the data being calibrated but at some computation expense.

The OTF flat field is prepared from a real flat field using the task MSCOTFFLAT. The parameters are

			       I R A F  
		Image Reduction and Analysis Facility
    PACKAGE = mscred
       TASK = mscotfflat

    input   =               Input processed mosaic flat field
    output  =               Output OTF flat field
    template=               Template raw mosaic flat field
    (bin    =            2) Binning size
    (resolut=        0.005) Resolution

The input is the name of the reduced flat field exposure. The output name is typically an abbreviated version of the filter name though it could be anything. The template parameter is the name of a raw exposure. Finally the two algorithm parameters described previously.

An example showing the reduction of a sequence of flat field exposures to an OTF flat field for the "V Mosaic" filter follows. This assumes the MSCRED, CCDPROC, and FLATCOMBINE parameters have been set as desired ( basically the default values).

    ms> flatcombine flat*
    ms> mscotfflat FlatV V Raw/flat001
    ms> dir V     

Note that the individual pixel list (pl files) can be examined using IRAF image tasks. In particular, they can be display with display .

To use this OTF flat field in the current directory

    ms> mscdisplay obj123 1 proc+ caldir="" filter=V

To use a standard directory and setup the filter name translation create or move the OTF directory and contents in the desired standard directory. In that directory create a file "" which has the filter name followed by the OTF calibration directory names.

To place the OTF flat field in a standard directory and setup the filter name translation

    ms> dir home$otfdir
    V       B
    ms> page home$otfdir/
    "V Mosaic"      V
    "B Mosaic"      B
    ms> mscdisplay obj123 1 proc+ caldir=home$otfdir/ filter=!filter

If you are creating OTF flat field for users of the NOAO Mosaic at Kitt Peak the calibration directories are mscdb$noao/kpno/4meter/caldir/ and mscdb$noao/kpno/36inch/caldir/.

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