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+.help fixpix Aug96 proto
+.ih
+NAME
+fixpix -- fix pixels identified by a bad pixel mask, image, or file
+.ih
+USAGE	
+.nf
+fixpix images masks
+.fi
+.ih
+PARAMETERS
+.ls images
+List of two dimensional images to be "fixed" (modified) by
+linear interpolation.
+.le
+.ls masks
+List of bad pixel masks, images, or files (collectively called masks)
+identifying the bad pixels.  The list of masks must either match the
+list of input images in number or a single mask may be specified to apply
+to all images.  The special name "BPM" may be specified to select a mask
+specified by the header keyword "BPM" in the input image.  The possible
+mask formats are given in the DESCRIPTION section.
+.le
+.ls linterp = "INDEF", cinterp = "INDEF"
+Normally interpolation is performed across the narrowest dimension spanning
+the bad pixels with interpolation along image lines if the two dimensions are
+equal.  However specific values in the mask may be used to
+identify the desired interpolation direction.  The value in the mask
+specifying line interpolation is given by the \fIlinterp\fR parameter and
+the value specifying column interpolation is given by the \fIcinterp\fR
+parameter.  Any values which are do not match one of these parameters
+results in interpolation along the narrowest dimension.  Note that a
+text file mask always has 2 for pixels with narrow dimension along
+lines and 3 for pixels with narrow dimension along columns.
+.le
+.ls verbose = no
+If this parameter is set to yes a line identifying each image and
+associated mask is printed.  If the \fIpixels\fR parameter is
+set then a list of the pixels modified is also printed.
+.le
+.ls pixels = no
+List the pixels modified?  This is only done if this parameters and
+the \fIverbose\fR parameter are set.
+.le
+.ih
+DESCRIPTION
+Pixels in a list of images identified by bad pixel masks, images, or text
+files (collectively called masks here) are replaced by linear interpolation
+along lines or columns using the nearest good pixels.  The list of input
+images, specified by the \fIimages\fR parameter, are matched with a list of
+masks, specified by the \fImasks\fR parameter.  The list of masks must
+match the list of input images or a single mask name may be given to apply
+to all input images.  The special mask name "BPM" may be used to
+select a mask name given in the input image header under the keyword
+"BPM".
+
+There are three types of masks which may be used.  The preferred type
+is a bad pixel mask given as a "pixel list" image.  Pixel list images
+have the extension ".pl" signifying a special compact file of integer
+values ideal for identifying sets of pixels.  For a bad pixel mask the
+good pixels have a value of zero and bad pixels have positive integer
+values.
+
+The second type is any image format.  The image will be internally
+converted to a bad pixel mask.  Note that real image values will be
+truncated to integers.  Again good pixels will have values of zero and bad
+pixels will have positive values.
+
+The final format is a text file with lines giving the integer coordinates
+of a single pixel or a rectangular region.  A single pixel is specified by
+a column and line number.  A region is specified by a starting column, an
+ending column, a starting line, and an ending line.  Internally this file
+is turned into a bad pixel mask of the size of the input image with values
+of zero for non-specified pixels, a value of two for pixels with narrowest
+interpolation direction along lines, and three for pixels with narrowest
+interpolation direction along columns.
+
+As noted previously, bad pixels are "fixed" by replacing them with values
+by linear interpolation to the nearest pixels not identified as bad.
+Normally interpolation is performed across the narrowest dimension spanning
+bad pixels with interpolation along image lines if the two dimensions are
+equal.  However specific values in the mask may be used to identify the
+desired interpolation direction.  The value in the mask specifying line
+interpolation is given by the \fIlinterp\fR parameter and the value
+specifying column interpolation is given by the \fIcinterp\fR parameter.
+Any values which are do not match one of these parameters results in
+interpolation along the narrowest dimension.  Note that a text file mask
+always has 1 for pixels with narrow dimension along lines and 2 for pixels
+with narrow dimension along columns.
+
+The \fIverbose\fR allows printing a line giving the task name, the
+image name, and the mask name.  In addition, if the \fIpixels\fR
+parameter is set the pixels modified are listed.  The list of pixels
+consists of the column and line of the pixel, the original
+and replaced pixel values, and the column and line of the one or two
+pixels used for the interpolation.  If the bad pixel region has no
+pixels at one end, that is there are bad pixels all the way to one edge
+of the image, then the single pixel used is printed.
+
+Normally the input images and the masks will have the same dimension.
+However, this task matches bad pixels in the masks with the input images
+based on physical coordinates.  Thus, the mask image may be bigger or
+smaller than the input image and image sections may be used with either
+the input images or the bad pixel mask or image mask images.  If the
+input image is the result of extracting a subsection of a bigger image
+the coordinates of the pixels will be those of the original image
+and the matching coordinates of the mask will be applied.  This has
+the effect of allowing image sections to be applied to images having
+a bad pixel mask specified in the image and still having the bad pixel
+mask be valid.
+
+Mask images may be made in a variety of ways.  Any task which produces
+and modifies image values may be used.  Some useful tasks are
+\fBimexpr, imreplace, imcopy,\fR and \fBmkpattern\fR.  If a new image
+is specified with the explicit ".pl" extension then the pixel mask
+format is produced.  Two other ways to make masks are with the
+tasks \fBtext2mask\fR and \fBccdmask\fR.  The former uses an input
+text file consisting of rectangular region.  This is the old
+"fixpix" format.  The task \fBccdmask\fR is specialized to make a mask
+of bad pixels from flat fields or, even better, from the ratio of
+two flat fields of different exposure levels.
+.ih
+EXAMPLES
+1.  A list of images have bad pixel masks defined in the image header.
+To replace the bad pixels by interpolation along the narrowest
+dimension:
+
+.nf
+    cl> fixpix obj* BPM
+.fi
+
+2.  A simple mask of 0s and 1s defines bad columns in spectral data
+with dispersion along the lines.  To interpolate along the lines:
+
+.nf
+    cl> fixpix spec00*h ccdmask linterp=1 v+
+    FIXPIX: image spec001.imh with mask ccdmask
+    FIXPIX: image spec002.imh with mask ccdmask
+    ...
+.fi
+
+3.  A text file of bad pixels is used and the modified pixels are printed
+with:
+
+.nf
+    cl> type mask.dat
+    1 2 1 1
+    25 26 25 25
+    26 27 27 27
+    49 50 50 50
+    10 10
+    20 21 20 20
+    cl> fixpix myimage mask.dat v+ p+
+    FIXPIX: image myimage with mask mask.dat
+       1    1       1.       1.   1    2
+       2    1       1.       1.   2    2
+      10   10       1.       1.   9   10  11   10
+      20   20       1.       1.  20   19  20   21
+      21   20       1.       1.  21   19  21   21
+      25   25       1.       1.  25   24  25   26
+      26   25       1.       1.  26   26  26   28
+      26   27       1.       1.  26   26  26   28
+      27   27       1.       1.  27   26  27   28
+      49   50       1.       1.  49   49
+      50   50       1.       1.  50   49
+.fi
+
+4.  Because a text file input automatically sets the mask values to
+2 or 3 you may need to set the linterp and cinterp parameters to
+force the direction.  In particular, to apply FIXPIX to a 1D image,
+say a spectrum, if you have regions described by ranges in columns
+the mask interpolation values will be assigned as 3.  This means
+it is trying to interpolation between line 0 and line 2 which is
+obviously not what is intended.  To make this work set linterp to
+3:
+
+.nf
+    cl> fixpix myimage mask.dat linterp=3
+.fi
+.ih
+REVISIONS
+.ls FIXPIX V2.11
+This task replaces the old task (now obsolete.ofixpix) and works with the
+more general pixel mask facilities.  It also provides greater flexibility
+in choosing the interpolation direction.
+.le
+.ih
+SEE ALSO
+epix, imedit, ccdproc, text2mask, obsolete.ofixpix
+.endhelp