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MAKEBIAS

Produces a master from a set of bias frames

Description:

This routine processes a series of bias frames (stored in images), so as to produce a single "master bias" frame in which the noise levels are reduced. This master bias frame can then be used to de-bias other CCD frames (using DEBIAS). Using the given readout noise an, optional, variance component may be produced for the output data. The use of a variance component allows the effects of noise in bias subtraction to be properly monitored.

MAKEBIAS also performs other functions during processing, such as estimating the readout noise (which it displays for comparison with the nominal value), estimating the data levels, zeroing the average value of the input data before combination (to more closely follow any drifts in the zero level) and also supports many different methods for performing the bias-frame data combination. The combination methods offer a mixture of very robust (median) to very efficient (mean) estimators.

Usage:

makebias in out rnoise method
  {
alpha=? sigmas=? niter=? niter=? min=? max=?

  method

Parameters:

ALPHA = _REAL (Read)
The fraction of extreme values to remove before combining the data at any pixel. This fraction is removed from each extreme so can only take a value in the range 0 to 0.5. Only used if METHOD="TRIMMED" [0.2]
GENVAR = _LOGICAL (Read)
If TRUE then a variance component representative of the readout noise will be generated. If FALSE then no variance component will be generated. If a variance component is not generated then any future estimates of variance made using the output image will be underestimates, however, disk space savings can be made using this option, if future error analyses are not important. If this parameter is set FALSE then a readout noise estimate will not be requested.

If a global value has been set using CCDSETUP this value will be used, and will be shown as the default. [FALSE]

IN = LITERAL (Read)
A list of image names which contain the raw bias frame data. The image names should be separated by commas and may include wildcards.
KEEPIN = _LOGICAL (Read)
Whether to keep (i.e. not delete) the input images or not. Deleting the input images has the advantage of saving disk space, but since the images input to this routine are raw data files (rather than processed intermediary files) they should be always be keep unless space considerations are at a very high premium.

The default for this parameter is TRUE and this cannot be overridden except by assignment on the command line or in response to a forced prompt. [TRUE]

LOGFILE = FILENAME (Read)
Name of the CCDPACK logfile. If a null (!) value is given for this parameter then no logfile will be written, regardless of the value of the LOGTO parameter.

If the logging system has been initialised using CCDSETUP then the value specified there will be used. Otherwise, the default is "CCDPACK.LOG". [CCDPACK.LOG]

LOGTO = LITERAL (Read)
Every CCDPACK application has the ability to log its output for future reference as well as for display on the terminal. This parameter controls this process, and may be set to any unique abbreviation of the following:

  • TERMINAL – Send output to the terminal only

  • LOGFILE – Send output to the logfile only (see the LOGFILE parameter)

  • BOTH – Send output to both the terminal and the logfile

  • NEITHER – Produce no output at all

If the logging system has been initialised using CCDSETUP then the value specified there will be used. Otherwise, the default is "BOTH". [BOTH]

MAX = _REAL (Read)
If METHOD = "THRESH" then this value defines the upper limit for values which can be used when combining data. Note that the value used for this parameter will not be corrected for zero pointing. Hence if the output image is to be zeroed then the maximum value should be a offset from zero (say some positive number 2 or 3 sigmas large). This could be used as a form of sigma clipping if no variances are to be generated.
METHOD = LITERAL (Read)
The method to be used to combine the data components of the input images. This may be set to any unique abbreviation of the following:

  • MEAN – Mean of the input data values

  • MEDIAN – Weighted median of the input data values

  • TRIMMED – An "alpha trimmed mean" in which a fraction alpha of the values are removed from each extreme

  • MODE – An iteratively "sigma clipped" mean which approximates to the modal value

  • SIGMA – A sigma clipped mean

  • THRESHOLD – Mean with values above and below given limits removed

  • MINMAX – Mean with the highest and lowest values removed

  • BROADENED – A broadened median (the mean of a small number of central values)

  • CLIPMED – A sigma clipped median

  • FASTMED – Unweighted median of the input data values

See also “Image combination techniques”.

[MEDIAN]

MIN = _REAL (Read)
If METHOD = "THRESH" then this value defines the lower limit for values which can be used when combining the data. Note that the value used for this parameter will not be corrected for zero pointing. Hence if the output image is to be zeroed then the minimum value should be a offset from zero (say some negative number 2 or 3 sigmas large). This could be used as a form of sigma clipping if no variances are to be generated.
MINPIX = _INTEGER (Read)
The minimum number of good (i.e. not BAD) pixels required to contribute to the value of an output pixel. Output pixels not meeting this requirement are set BAD. [1]
NITER = _INTEGER (Read)
The number of refining iterations performed if METHOD = "MODE". [7]
OUT = LITERAL (Read)
Name of the output image. This has the master bias frame and the estimated variances. If USESET is true and multiple Sets are represented in the IN list, then this name will be used as the name of an HDS container file containing one NDF structure for each Set Index value. This name may be specified using indirection through a file.
PRESERVE = _LOGICAL (Read)
If TRUE then this indicates that the input data type is to be used for processing. If not then the output type will either be _REAL or _DOUBLE, the precision at which the combinations are performed.

If a global value has been set using CCDSETUP then this will be used. [TRUE]

RNOISE = _DOUBLE (Read)
The readout-noise standard deviation. This should be in the input data units (ADUs). A value for this will be worked out for each frame and reported at the end of the task. The average of these values is reported immediately before this parameter is accessed and can be used if a better estimate is not known. Note that the supplied estimate has some resilience to large-scale structure in the input frames, but will be incorrect if the input-frame backgrounds are severely sloped. If variances are not generated then this value will not be accessed.

The value of this parameter may not be used if the USEEXT parameter is TRUE and will not be used if GENVAR is FALSE (i.e. no variances are being generated). If USEEXT is TRUE then readout noise values will be extracted from the images CCDPACK extensions. Only if a suitable value is not present will the value associated with this parameter be used.

If a global value has been set up using CCDSETUP this value will be used, and will be shown as the default. If USESET is true, a global value specific to each image’s Set Index value will be sought. [Dynamically derived value]

SIGMAS = _REAL (Read)
Number of standard deviations to reject data at. Used for "MODE", "SIGMA" and "CLIPMED" methods. For METHOD = "MODE" the standard deviation is estimated from the population of values. For METHOD = "SIGMA" and "CLIPMED" this value is the readout noise. [4]
TITLE = LITERAL (Read)
Title for the output image [Output from MAKEBIAS].
USEEXT = _LOGICAL (Read)
If TRUE then the parameter RNOISE of this program will not be used and the required values will be obtained from the CCDPACK extensions of the input images instead. This method can only be used if the images have been "imported" using the programs PRESENT or IMPORT. Typically it is used when processing using CCDPACK’s "automated" methods.

Values obtained from the CCDPACK extension are identified in the output log by the presence of a trailing asterisk (∗). [FALSE]

USESET = _LOGICAL (Read)
Whether to use Set header information or not. If USESET is false then any Set header information will be ignored. If USESET is true, then input files will be considered in groups; a separate master bias frame will be constructed for each group of corresponding input frames (i.e. those sharing the same Set Index attribute). If this results in multiple output master bias frames, they will be written as separate NDFs into a single HDS container file. If no Set header information is present in the input files, then all the input files are combined together to form the master bias, so USESET can usually be safely set to TRUE.

If a global value for this parameter has been set using CCDSETUP then that value will be used. [FALSE]

ZERO = _LOGICAL (Read)
Flag indicating whether the output master bias is to have a mean value of zero or not. If TRUE the input data components are ZERO-ed before combination, of the data. Note that if this option is chosen then it will be necessary to offset the master bias to the data before subtraction. This option is not allowed for unsigned input data type (unless PRESERVE is FALSE) as zeroing will make around half the data values invalid. [TRUE]

Examples:

makebias in=’"b1,b2,b3,b4,b5"’ method=median out=mbias rnoise=10
This forms a master bias from the data components of the images b1-b5. The combination mode chosen is the median. The output image is mbias whose variance has values based on a readout noise of 10 data units. Note the quotes when entering a comma separated list on the command line.
makebias in=^bias_frames.lis out=master_bias
In this example the list of images is read from the file bias_frames.lis. This file may contain indirection to other files up to a depth of 7.
makebias in=’∗’ out=master_bias
In this example all the images in the directory are used.

See also

“Making a bias calibration frame”, DEBIAS.

Notes:

Behaviour of parameters

Most parameters retain their current value as default. The "current" value is the value assigned on the last run of the application. If the application has not been run then the "intrinsic" defaults, as shown in the parameter help, apply. The exceptions to this rule are:

Retaining parameter values has the advantage of allowing you to define the default behaviour of the application but does mean that additional care needs to be taken when using the application on new datasets/different devices, or after a break of sometime. The intrinsic default behaviour of the application may be restored by using the RESET keyword on the command line.

Certain parameters (LOGTO, LOGFILE, RNOISE, GENVAR, PRESERVE and USESET) have global values. These global values will always take precedence, except when an assignment is made on the command line. Global values may be set and reset using the CCDSETUP and CCDCLEAR commands. If USESET is true then a global value of RNOISE specific to the Set Index of each image will be used if one is available.

The parameter RNOISE will not be used if the USEEXT parameter is set TRUE. In this case values will be obtained from the input images CCDPACK extensions.

Implementation Status: