MAKEFLAT

Produces a flatfield calibration image

Description:

This routine combines a set of frames into a flatfield. The input data should be of a photometrically flat source, and should be corrected for any instrumental effects. The output calibration frame is normalised to have an average value of one or can be left unnormalised if a larger scaled normalisation is more appropriate (over a CCD mosaic).

The input data are filtered in an attempt to remove any small blemishes etc. before combination. This is achieved by smoothing using a boxfilter and then comparing with the original data. An estimate of the standard deviation of each pixel from its surroundings is made. Pixels deviating by more than GAMMA standard deviations are rejected. This procedure is then iterated ITER times. In this way, all image features with a scale size comparable with, or smaller than, the smoothing area size are rejected.

Usage:

makeflat in out 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]
BOXSIZE(2) = _INTEGER (Read)
The X and Y sizes (in pixels) of the rectangular box to be applied to smooth the input images. If only a single value is given, then it will be duplicated so that a square filter is used. The values given will be rounded up to positive odd integers if necessary. The values should be adjusted to be larger than the size of any expected defects. [15,15]
CLEAN = _LOGICAL (Read)
Whether or not to attempt to clean the input images of any defects. For some data types (i.e. spectra) small scale strutures and sharp edges may be real and can be protected against removal by setting this parameter FALSE. [TRUE]
GAMMA = _REAL (Read)
The number of standard deviations by which a value has to deviate from the local mean (defined by the mean within a box of BOXSIZE(1) by BOXSIZE(2) pixels) before it is considered to be in error. Aberrant pixels are removed from the data before the next "cleaning" iteration is performed. [3.0]

GENVAR = _LOGICAL (Read)

If TRUE and USEVAR is also FALSE, then “variances” for the output image will be generated using the natural variation in the input images. These values can be used to estimate the quality of the output flatfield.

Note that for this option to work well you should have many images and that any output pixels that only have one input image contributing to their value will have their variances set bad. [FALSE]

IN = LITERAL (Read)

A list image names. These contain the flatfield data. The image names should be separated by commas and may include wildcards.
ITER = _INTEGER (Read)
The number of defect rejecting iterations. [3]
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 should probably only be used if this program is part of a sequence of commands and the intermediary data used by it are not important.

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 the data. This limit applies to the output data range.
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. This limit applies to the output data range.
MINPIX = _INTEGER (Read)
The minimum number of good (ie. not BAD) pixels required which are required to contribute to the value of an output pixel. Output pixels not meeting this requirement are set BAD. [1|2]
NITER = _INTEGER (Read)
The number of refining iterations performed if METHOD = "MODE". [7]
NORM = _LOGICAL (Read)
Whether to normalise the output NDF to have a mean of one. [TRUE]
OUT = LITERAL (Write)
Name of an image to contain the output flatfield data. Note this image will have a precision of at least _REAL. 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. [TRUE]
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 pixel variance if one exists, otherwise one is etimated from the population of values. [4.0]
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 flatfield 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 flatfields, they will be written as separate NDF structures into a single HDS container file. If no Set header information is present in the input files, then flatfielding is done on all the input files together, 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]

USEVAR = _LOGICAL (Read)
If TRUE and all the input images contain error information (variances), then these will be used as weights during image combination and will be propagated to the output image. [TRUE]
TITLE = LITERAL (Read)
Title for the output image. [Output from MAKEFLAT]

Examples:

makeflat in=’"f1,f2,f3,f4,f5"’ method=median out=mflat
This forms a master flat field from images f1 to f5. The input data are first cleaned using the default values for the GAMMA and ITER parameters. The combination mode chosen is the median. The output image is mflat. Note the quotes when entering a comma separated list on the command line.
makeflat in=^flat_frames.lis out=master_flat
In this example the list of images is read from the file flat_frames.lis. This file may contain indirection to other files up to a depth of 7.
makeflat in=’flatr/∗’ out=’flatr/master_flat’ gamma=2.5 iter=5
In this example all the images in the subdirectory bias/ are used. The input data are severely cleaned using a noise cut of 2.5 standard deviations (current) and 5 iterations. Such severe cleaning is only recommended when many input frames are given, if this is not the case then BAD areas may be seen in the output image.
makeflat in=’ff*’ out=master_flat gamma=10 iter=1
In this example all the frames "ff*" are combined into a master flatfield. Defect rejection is still performed but with gamma set so high and by performing only one iteration almost no bad data will be detected.

See also

“Flatfielding”, FLATCOR.

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 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.

Implementation Status: