rmfringe: Remove fringe pattern

Package: msctools

Parameters

input: List of input images or multiextension files.

output: List of corrected output images or multiextension files. If no list is specified then the input list is used, otherwise the output list must match the input list. If an input and output file are the same the output is created in a temporary file and the input is replaced after the output is completed.

fringe: List of fringe images or multiextension files. The list must either match the input list or be a single file to be used for all the input files. The fringe pattern is assumed to have a flat mean background. This is usually zero though this task will determine and ignore any constant mean in the data.

masks: List of masks identifying pixels to ignore in the input data. Pixels to ignore have non-zero mask values. An empty list applies no bad pixel mask, a single mask applies to all input data, and a list is matched with the input list. A mask is specified by a filename or by reference to a filename given by the value of a header keyword in the input image. A header keyword reference is made with the syntax "!<keyword>" where <keyword> is the desired keyword with case ignored. For multiextension files the masks may be either a multiextension file with matching extension names or a directory of pixel list files with the extension names as the filenames.

fringemasks: List of masks identifying pixels to ignore in the fringe image. This mask is primarily intended to restrict the amplitude calculation to the region of the fringe pattern. Pixels to ignore have non-zero mask values. The same options for specifying the masks apply as for the masks parameter. Keyword references will sought in the fringe pattern image header.

background = "": List of backgrounds for the input data. If no list is given then the mean of the data, excluding masked pixels, is used for the background. The list may be either a single value which applies to all the input data or match the input list in number. The background may be specifed as an image or constant value. Images are linearly interpolated to the size of the data images if the sizes do not match.

ncblk = 5, nlblk = 5: Moving average block sizes for the input and fringe images. The block average size for columns and for lines are specified separately.

extfit = "": Extensions to use for fitting the fringe amplitude. A null string matches all extension names. Otherwise the parameter is a comma separated list of patterns which match the entire extension name. Thus, a list of extension names may be given or the pattern matching characters '?' for any character or [] for a set of characters. The set may include ranges in ascii order by using hyphens; i.e. 1-3 matches the characters 1, 2, and 3. All the selected extensions in the input files must also exist in the fringe and mask files.

logfile = "": Filename for appending log information. If no name is specified then no log is written. Note that there is no need to use "STDOUT" since the same information is written when the verbose parameter is set.

verbose = yes: If set to yes, log information is written to the standard output. Note that this is the same information as written to the logfile specified by the logfile parameter.

Description

RMFRINGE determines the fringe amplitude that minimizes the weighted mean difference between an input image and a fringe image given in equation 1. The input images, specified by the input parameter, may be individual images (which includes images selected from multiextension files as explicit image extensions) or multiextension files specified by a root filename. In the latter case the image extension names selected by the extfit parameter are used for computing a global fringe amplitude for all the extensions.

The output of this task are fringe corrected images or multiextension files and log information with the computed fringe amplitude. When the input is a multiextension file the output is a multiextension file with all the same extensions. Note that all extensions are used for the output regardless of which extensions are selected for fitting. The fringe correction is "A - s * (F - <F>)" where the quantities are defined below.

The statistic used to compute the scale is

(1)  <(((A - B) - s (F - <F>)) (F - <F>))> = 0

where

A           Input image               (input parameter)
B           Input image background    (background parameter)
F           Fringe image              (fringe parameter)
s           Fringe amplitude scale factor

The solution of equation 1 is determined over all pimels in the image or extensions selected by the extfit parameter which are not flagged in the pixel mask specified by the masks parameter. For multiextension files equation 1 is also solved separately for each extension and estimates of the fringe scale are shown in the log output (see examples 2 and 3). However, the final fringe amplitude is not the average of these values but the solution over all pixels. To treat image extensions as independent images the various file lists must be explicit images rather than multiextension file rootnames (see example 4).

The fitting defined by equation 1 is improved by smoothing when the data and fringe pattern include noise, such as occurs when it is derived from observational data. The images may be smoothed by a moving block average with block sizes specified by the parameters ncblk and nlblk.

There are three types of backgrounds, B, which may be specified. An image, a constant, and the mean value. The image may be a fully sampled image of the same size as the image to which it applies or a smaller sampled image that is interpolated to match the size of the image. If there is a background gradient in the input data it is useful to supply a background image otherwise the mean may be used by specifying a null string, "".

A key to obtaining the best match between the fringe and the input data is to use masks for the input and fringe pattern. The masks will identify bad data and the objects in the input image. The task nproto.objmasks is recommended for creating the object masks.

The masks specified by the masks parameter may be in any of the supported masks formats. As of IRAF V2.12 this includes pixel list (.pl) files and FITS "type=mask" extensions. When the input is a multiextension file, the selected extension names are appended to the mask filename to select masks with the same extension name. If a mask file of the form "name[ext]" is not found the task will treat the filename as a directory of pixel list files and select the filename corresponding to the extension name; i.e. "name/ext.pl".

In addition to the fringe corrected image, log output to the terminal is produced when verbose is "yes" and log output to a specified file is produced by setting logfile. The output is the same for both. Because this task is a simple script calling the task patfit the log output contains some additional information not described here. See the help page for patfit for details.

The output image will also contain a record of the operation performed under the keyword RMFRINGE as in the following example.

RMFRINGE  = 'o262 - 0.80696 (fringe - 0.15538)'

Examples

1. Fringe removal from a single image, "o262". The fringe image, "fringe", is created by combining many exposures during the night to eliminate the objects. A smooth background, averaged on scales larger than the fringe pattern, is subtracted. The input image is processed to produce a mask, "objmask262", of the objects and bad pixels (see nproto.objmasks) and also a low frequency sky map to account for gradients in the background.

cl> rmfringe o262 fo262 fringe objmask262 background=sky262
RMFRINGE: NOAO/IRAF V2.11EXPORT ... 18-Jan-2002
  input = o262
  pattern = fringe
  weight = fringe
  input background = sky262
  pattern background = <pattern>
  weight background = <weight>
  input mask = objmask262
  output = fo262
  outtype = pdiff
  <pattern> = 0.1554
  <weight> = 0.1554
  scale = 0.807
    fo262 = o262 - 0.80696 (fringe - 0.15538)

2. The same fringing example but with multiextension files. In this case the object mask may either be a multiextension file of mask type extensions (V2.12 and later) or a directory "objmask262" with files im1.pl, im2.pl, etc.

cl> rmfringe o262 fo262 fringe objmask262 background=sky262
RMFRINGE: NOAO/IRAF V2.11EXPORT ... 15-Jan-2002
  input = o262
  pattern = fringe
  weight = fringe
  input background = sky262
  pattern background = <pattern>
  weight background = <weight>
  input mask = objmask262
  output = fo262
  outtype = pdiff
    o262[im1]: 0.8127
    o262[im2]: 0.8103
    o262[im3]: 0.8235
    o262[im4]: 0.8177
    o262[im5]: 0.8161
    o262[im6]: 0.8365
    o262[im7]: 0.7584
    o262[im8]: 0.7979
  <pattern> = 0.5208
  <weight> = 0.5208
  scale = 0.8095
    fo262[im1] = o262[im1] - 0.80953 (fringe[im1]...
    fo262[im2] = o262[im2] - 0.80953 (fringe[im2]...
    fo262[im3] = o262[im3] - 0.80953 (fringe[im3]...
    fo262[im4] = o262[im4] - 0.80953 (fringe[im4]...
    fo262[im5] = o262[im5] - 0.80953 (fringe[im5]...
    fo262[im6] = o262[im6] - 0.80953 (fringe[im6]...
    fo262[im7] = o262[im7] - 0.80953 (fringe[im7]...
    fo262[im8] = o262[im8] - 0.80953 (fringe[im8]...

3. The same fringing example with multiextension files with fitting extensions specified. This artificial example shows fitting one set of extensions and outputing a different set. A more likely situation would be fitting a subset of extensions (for speed) but outputing all the extensions.

cl> rmfringe o262 fo262 fringe objmask262 background=sky262 \
>>> extfit=im[123]
RMFRINGE: NOAO/IRAF V2.11EXPORT ... 18-Jan-2002
  input = o262
  pattern = fringe
  weight = fringe
  input background = sky262
  pattern background = <pattern>
  weight background = <weight>
  input mask = objmask262
  output = fo262
  outtype = pdiff
    o262[im1]: 0.8127
    o262[im2]: 0.8103
    o262[im3]: 0.8235
  <pattern> = 0.1554
  <weight> = 0.1554
  scale = 0.8153
    fo262[im4] = o262[im4] - 0.81534 (fringe[im4]...
    fo262[im5] = o262[im5] - 0.81534 (fringe[im5]...
    fo262[im6] = o262[im6] - 0.81534 (fringe[im6]...

4. The same multextension fringing example treating the extensions as independent images. Note that in this case the mask is actually objmask262/im1.pl but is referenced as objmask262[im1] (the other form could also be used).

cl> dpar rmfringe
rmfringe.input = "o262[im1],o262[im2],o262[im3]"
rmfringe.output = "fo262[im1],fo262[im2,append],...
rmfringe.fringe = "fringe[im1],fringe[im2],...
rmfringe.masks = "objmask262[im1],objmask262[im2],objmask262[im3]"
rmfringe.background = ""
rmfringe.extfit = ""
rmfringe.logfile = "logfile"
rmfringe.verbose = yes
rmfringe.mode = "ql"
# EOF
cl> rmfringe
List of input images (o262[im1],o262[im2],o262[im3]):
List of output corrected images (fo262[im1],fo262[im2,append],...
Fringe or list of fringe patterns (fringe[im1],...
List of object/bad data masks (objmask262[im1],...
RMFRINGE: NOAO/IRAF V2.11EXPORT ... 18-Jan-2002
  input = o262[im1]
  pattern = fringe[im1]
  weight = fringe[im1]
  input background = <input>
  pattern background = <pattern>
  weight background = <weight>
  input mask = objmask262[im1]
  output = fo262[im1]
  outtype = pdiff
  <input> = 7340.
  <pattern> = 0.1587
  <weight> = 0.1587
  scale = 0.8088
    fo262[im1] = o262[im1] - 0.80883 (fringe[im1]...
RMFRINGE: NOAO/IRAF V2.11EXPORT ... 18-Jan-2002
  input = o262[im2]
  pattern = fringe[im2]
  weight = fringe[im2]
  input background = <input>
  pattern background = <pattern>
  weight background = <weight>
  input mask = objmask262[im2]
  output = fo262[im2,append]
  outtype = pdiff
  <input> = 7299.
  <pattern> = -0.3147
  <weight> = -0.3147
  scale = 0.7948
    fo262[im2,append] = o262[im2] - 0.79481 (fringe[im2]...
RMFRINGE: NOAO/IRAF V2.11EXPORT ... 18-Jan-2002
  input = o262[im3]
  pattern = fringe[im3]
  weight = fringe[im3]
  input background = <input>
  pattern background = <pattern>
  weight background = <weight>
  input mask = objmask262[im3]
  output = fo262[im3,append]
  outtype = pdiff
  <input> = 7260.
  <pattern> = 0.634
  <weight> = 0.634
  scale = 0.8185
    fo262[im3,append] = o262[im3] - 0.81849 (fringe[im3]...

Note that in this case an output multiextension file is built from the individual outputs by using the "append" syntax of the FITS image kernel.

rmfringe: Remove fringe pattern

Parameters

Description

Examples

See also