Level 2 Help for MARSDEBAYER

INP

Single-band input file containing the Bayer pattern.  Must be byte or
halfword format.  In the case of ZOOM_MODE of NONE, the input need not
have the Bayer pattern, although it must still be a single band of byte
or halfword data.


OUT

Output files containing the color image.

If three filenames are given, three separate 1-band files will be created,
in R,G,B order.  If only one filename is given, a single 3-band file will be
created.  The data type will be the same as the input file.

In the case of ZOOM_MODE of NONE or AVERAGE, the output must be a single
file, which will contain only one band.


NAVTABLE

Corrected navigation filename.
If marsnav was run on the input images it created a table of corrected
pointing parameters. If you refer to this table using NAVTABLE it
will override the pointing parameters (e.g. azimuth and elevation) in the
picture labels, giving different (and presumably better) output coordinates.

This parameter is unlikely to be useful for this program; it is included
because it is standard for the PIG suite.


ZOOM_MODE

Specifies the geometry of the output file(s).  Possible values are:

* NORMAL - No zooming; the output is the same size as the input.  For Red
  and Blue, there is only one-quarter of the data necessary; for Green there
  is only half the data.  The rest is filled in according to the INTERP keyword.
  This is the mode that is used onboard by the MSL MMM cameras.

* HALF_SCALE - The output is half the size of the input.  Each Bayer cell
  this corresponds to a single pixel in the output.  The Green cells are
  oversampled by 2x; they are averaged to produce the output value.

* UPPER - Like HALF_SCALE, but only the "upper" of the two Green pixels is used
  in each Bayer cell, with no averaging.

* LOWER - Like HALF_SCALE, but only the "lower" of the two Green pixels is used
  in each Bayer cell, with no averaging.

* TALL - The result has the same vertical size as the input, but half the
  horizontal size.  This changes the aspect ratio by a factor of 2.  This
  preserves all the Green pixel data without replication.  The Red and Blue
  pixels are doubled per the INTERP parameter.

* AVERAGE - No de-Bayering is done, but the 4 pixels in each Bayer cell are
  averaged together.  The output is thus a single one-band file at half scale
  compared to the input.

* NONE - No de-Bayering is done; the output is a single one-band file looking
  the same as the input.  This mode could be useful to extract a subframe from
  an image (potentially not even a Bayer pattern image) while keeping the
  camera model correct.


SS

Starting sample in the input image for subframing (starting at 1).  This
value must be odd, i.e. you cannot split a Bayer cell by subframing.
If omitted, defaults to 1.


SL

Starting line in the input image for subframing (starting at 1).  This
value must be odd, i.e. you cannot split a Bayer cell by subframing.
If omitted, defaults to 1.


NS

Number of samples from the input image for subframing.  If omitted, defaults
to the size of the input.  Note that this value must be even, i.e. you cannot
split a Bayer cell by subframing.


NL

Number of lines from the input image for subframing.  If omitted, defaults
to the size of the input.  Note that this value must be even, i.e. you cannot
split a Bayer cell by subframing.


INTERP

Specifies the interpolation mode when sizing up (NORMAL mode, or TALL mode
for red and blue pixels).  Ignored in the other modes.

* REPLICATE - Pixel replication.  The output cell is filled with the value
from the input cell, with no interpolation.  Produces a very blocky image.

* BILINEAR - Bilinear interpolation.

* MALVAR - image is demosaicked based on convolution matrices developed by
  Malvar, He, and Cutler at Microsoft.  See METHOD.

The default is BILINEAR.


MIN_DN

Specifies the minimum dn value to use on valid data when using the malvar
interpolation mode.  The malvar algorithm can result in an underflow
(values < 0).  The minumum dn value sets what the undeflow value will
be interpreted as.  Default is 1 since 0 typically means no data.


MAX_DN

Specifies the minimum dn value to use on valid data when using the malvar
interpolation mode.  The malvar algorithm can result in an overflow
(values > 2^n -1, where n = number of bits).  
The maximum dn value sets the overflow value.  Default 255 (8-bit data).


MULT

Specifies the multiplicative factors to use on red, green, and blue
bands respectively.  The factors are applied before demosaicing is
performed.


ROTATE

Specifies the clockwise rotation to apply to the input image before
demosaicing is performed.  Rotate should be used to align the bayer
patterned cells to the correct orientation specified above. Rotations
will always be performed prior to any other image processing. (e.g. MULT,
OFFSET, etc.)  The output image is rotated back to the original orientation.


OFFSET

Specifies a Bayer pattern starting offset of 1 in line, sample, or both.
The offset is applied to the mutiplicative factoring of bands and to
demosaicing.  For simplicity, the offset is handled by shifting the image
1 pixel, truncating the first line or sample (or both). The last line and
sample in the image are then set to 0 DN value.


ONLY_BAND

Specifies which band to write, if only one color output is desired.  The
result will be a single-band file.  It cannot be used in the -none or -average
modes (which are already single-band).


CONFIG_PATH

A colon-separated list of directories in which to look for configuration
and calibration files.  Environment variables are allowed in the list
(and may themselves contain colon-separated lists).  The directories are
searched in order for each config/cal file when it is loaded.  This allows
multiple projects to be supported simultaneously, and allows the user to
override any given config/cal file.  Note that the directory structure below
the directories specified in this path must match what the project expects.
For example, Mars 98 expects flat fields to be in a subdirectory named
"flat_fields" while Mars Pathfinder expects them to be directly in the
directory specified by the path (i.e. no intermediate subdirectories).


POINT_METHOD

Specifies a mission-specific pointing method to use.  Normally this
parameter is not used, in which case the "default" pointing methods
are used.  Some missions may have special, or alternate, pointing
methods available, which are indicated by this string (for example,
backlash models, using arm joint angles instead of x/y/z/az/el, etc).
A substring search is used, so multiple methods (where that makes sense)
can be specified by separating the keywords with commas.

Note that nav files created using one pointing method will most likely
not be compatible with a mosaic created using a different pointing method.

The methods available vary per mission, but some methods available at
the time of this writing are:

BACKLASH : Mars 98 SSI only.  Selects a backlash pointing model,
which adjusts the telemetered azimuth and elevation values based on
knowledge of the camera's mechanical backlash and the direction the
motor was travelling when the image was taken.


NOSITE

Disables all label-derived parameters to the Site mechanism which underlies
coordinate systems.  This forces all sites to be identical, with all rotations
and offsets set the same.  In the case of MPF or Mars 98, this disables
the lander quaternion and offset (sets them to identity and 0, respectively).
This option should not be used with images taken from different vantage
points (e.g. the spacecraft moved, or mixing a lander and a rover) or
invalid results will be obtained.  The use of this option invalidates the
Fixed coordinate frame; any values reported in the Fixed frame will not
correctly reflect the orientation of the lander/rover.

Obviously, this option should be rarely used; it is intended for when the
image labels defining the site are invalid or inconsistent.


DATA_SET_NAME

The DATA_SET_NAME typically identifies the instrument that acquired the
data, the target of that instrument, and the processing level of the data.
This value is copied to the output label, property IDENTIFICATION,
keyword DATA_SET_NAME.


DATA_SET_ID

The DATA_SET_ID value for a given data set or product is constructed
according to flight project naming conventions.  In most cases the
DATA_SET_ID is an abbreviation of the DATA_SET_NAME.
This value is copied to the output label, property IDENTIFICATION,
keyword DATA_SET_ID.


RELEASE_ID

When a data set is released incrementally, such as every three months during
a mission, the RELEASE_ID is updated each time part of the data set is released.
For each mission(or host id if multiple spacecrafts), the first release of a data
set should have a value of "0001".
This value is copied to the output label, property IDENTIFICATION,
keyword RELEASE_ID.


PRODUCT_ID

Specifies a permanent, unique identifier assigned to a data product by
its producer. Most commonly, it is the filename minus the extension.
This value is copied to the output label, property IDENTIFICATION,
keyword PRODUCT_ID.


PRODUCER_ID

Specifies the unique identifier of an entity associated with the
production of a data set. This value is copied to the output label,
property IDENTIFICATION, keyword PRODUCER_ID.


PRODUCER_INST

Specifies the identity of a university, research center, NASA center or other
institution associated with the production of a data set.
This value is copied to the output label, property IDENTIFICATION, keyword
PRODUCER_INSTITUTION_NAME.


TARGET_NAME

Specifies a target.  The target may be a planet, satelite, ring, region, feature,
asteroid or comet.  This value is copied to the output label, property
IDENTIFICATION, keyword TARGET_NAME.


TARGET_TYPE

Specifies the type of a named target. This value is copied to the output
label, property IDENTIFICATION, keyword TARGET_NAME.


RSF

Rover State File.  This is a list of filenames to load containing
Rover State information.  These files contain position and orientation
information for a rover (or other mobile spacecraft) at various sites.
They are in XML format.  See the "Rover Motion Counter (RMC) Master File SIS"
for details on these files.

Rover State Files have a priority order.  The files listed first have
the highest priority.

Environment variables may be used in the list.

For MER, if a directory is specified, then that directory is searched for
RMC Master files and any found are loaded.  The directory structure and
filename convention is covered in the RMC SIS.  The directory specified
is the one containing "master", so if <dir> is the name specified in the
RSF parameter, the following files will be searched for:

<dir>/master/_Master.svf
<dir>/master/_Site__Master.rvf

The name of each file loaded is printed to the stdout log for reference.


DEBUG_RSF

If enabled, this causes the internal database of RMC locations to be
printed out to the stdout log.  This is after the RSF files have been
loaded and the coordinate systems read from the input label(s).


COORD

The coordinate system to use for the output UVW vectors.  The interpretation
of the values is dependent on the mission.  Some representative missions are
listed here:

Fixed - The Fixed frame.  This is the ultimate reference frame
    (see also FIXED_SITE for rover missions).
Instrument - (default) The "natural" frame for the instrument 
    (of the first input image).  MPF: Lander or Rover; M98: MVACS; MER: Rover.
Site - A major Site frame.  For rover missions, COORD_INDEX specifies which
    Site frame to use.  Non-rover missions treat this as Fixed.
Rover - An instance of the Rover frame.  For rover missions, COORD_INDEX
    specifies which instance of the rover frame to use.  Non-rover mission
    use the spacecraft frame (e.g. Lander for M98).  For MSL, this is the
    Rover Nav frame.
Local_Level - An instance of a Local Level frame.  This is typically
    coincident with the Rover frame (in XYZ) but oriented toward North
    like the Site and Fixed frames.  For MER, this is an instance of a
    Drive index move.
RMECH - for MSL, this is the Rover Mechanical frame.  It should not normally
    be used except for testing.


COORD_INDEX

The index specifies which instance of a coordinate system to use.  It is
currently applicable only to rover-based missions, but could have other
uses.  The index is equivalent to the Rover Motion Counter (RMC) for MER
and FIDO.

For MER/FIDO, there are many Site frames.  Each is numbered with a single
index.  For Site Frames, coord_index specifies which to use.  Likewise,
there are many Local_Level and Rover frames, corresponding to values of
the RMC.  The multiple instances of this frame are selected by COORD_INDEX.

Generally COORD_INDEX defaults sensibly so you don't usually need to
specify it.  It will default to the instance used by the first input.


FIXED_SITE

Specifies which major Site is the "Fixed" Site for this run.

Historically, MPF and M98 had a single "Surface Fixed" frame which never
moved, and which all other coordinate system frames were referenced to.
With the advent of long-range rovers (such as MER and FIDO), that became
insufficient.  The rover traverses far enough that errors in knowledge of
coordinate system offset and orientation become unacceptable.

For this reason, a system of major Sites was introduced.  Periodically
during the mission, a Site frame is declared.  This then becomes the
reference frame for all activities until the next Site is declared.
References are kept local, and errors don't propogate across Sites.

However, if images from more than one Site are combined together, the
Site's must be placed relative to each other.  Therefore a single reference
frame is still needed to combine different sites.

The FIXED_SITE parameter controls which of the major Site frames is
the reference ("fixed") site for this program run.  This fixed frame
can vary in different program runs, but is constant throughout one
execution.

If not specified, FIXED_SITE defaults to the minimum Site number (i.e.
lowest numbered, or earliest chronologically) used in all input images.
Normally this default is sufficient; rarely must FIXED_SITE be specified.

One or more Rover State Files must usually be specified in order to combine
image from more than one Site.  These describe the relationship between
sites.  See the RSF parameter.


SOLUTION_ID

Specifies which solution ID to use when specifying the coordinate system.

There are potentially many different definitions for the same coordinate
system.  These are identified via a unique Solution ID.  If this parameter
is given, only the specified solution's definition is searched for.  Without
it, the "best" available solution is chosen.

It is extremely rare that this parameter should be needed.  The default
will be sufficient in almost every case.

Note that the current MER implementation requires that a value for COORD_INDEX
also be provided, in order for this parameter to take effect.