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ISIS 3 Application Documentation


handmos

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Hand place a cube into a mosaic

Description
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Description

This application creates a mosaic by placing an input image in the output by a sample, line, and band pixel position. An input cube can be mosaicked into an existing output mosaic cube or a new output file can be created. If a portion of the input cube falls outside of the dimensions of the mosaic, it will be clipped. The line, sample, band dimensions of the output mosaic are required to be specified at the time of creation. This application does not require a camera model, Instrument Group or Mapping Group keywords as required by the other mosaic applications, mapmos and automos.

Integrity-check Parameters:

MATCHBANDBIN = FALSE, the default is to require all the BandBin group and wavelength keywords of the input cube files exactly match the output mosaic.

MATCHDEM = FALSE, the default does not check the SHAPEMODEL keyword of the input cube files and does not propagate what DEM Shapemodel that was used when the input files were projected.

The PRIORITY parameter will determine how each input cube is combined with the current output mosaic cube. The process involves replacing an output mosaic pixel (or not) with an input pixel at the same location. There are many user options and criteria that influence the pixel replacement. Use of the PRIORITY parameter with and without other options is explained in the tables and descriptions below.

The TRACK feature creates a separate tracking cube in addition to the mosaic cube, and contains information for the source files of every pixel within the output mosaic. This cube will have the same base-name as the mosaic cube, but will end in "_tracking.cub". The tracking cube must always reside in the same directory as the mosaic cube to be properly accessed; this means that if the mosaic cube is copied or moved, then its associated tracking cube must be copied or moved to the same location. The tracking cube will always be of type unsigned integer. Depending on the bit-type of the mosaic cube and/or the number of bands it contains, the tracking cube may be as much as four times the size of the mosaic cube itself.

The tracking cube can be used appropriately through the QVIEW-AdvancedTracking tool. As the user pans across the displayed mosaic, for every mosaic pixel location, QVIEW-AdvancedTracking will interactively report the index, the filename and the serial number of the input cube that was input to handmos for that specific pixel location. Since the tracking cube is of bit-type unsigned integer, the DN values of 0, 1 and 2 are reserved for NULL, LRS and LIS, respectively, so valid pixel DN values will begin at an offset of 3. In other words, a pixel of DN value 3 in the tracking cube means that this same pixel within the mosaic was taken from the first input image. The tracking cube cannot be used outside of the QVIEW-AdvancedTracking tool except as a visual representation of the source cubes for the different pixels.

The TRACK feature works with Priority options ONTOP and BENEATH for single band input cubes. It works for multiband cubes for PRIORITY=ONTOP only when the NULL, HIGHSATURATION and LOWSATURATION options are set to true. It also works for multiband cubes when PRIORITY=BAND. Furthermore, this feature is NOT supported when PRIORITY=AVERAGE.

Please Note: Prior to ISIS version 3.6.0, tracking for the various mosaicking apllications was being handled with an internal tracking band. Tracking is now being handled by an external tracking cube that contains the associated tracking information. This application can no longer add to mosaics of the old format. In order to continue to use these older mosaics with the updated mosaicking applications, you must first use the trackextract utility application to extract the tracking band and the associated tracking information into an external tracking cube.

The following table describes how the program will determine the pixel value in the output mosaic for areas of image overlap.

PRIORITYRESULT
ONTOP This is the default. The current input image will be placed on top of the output mosaic. Thus in any area of overlap, the Valid pixel values for the current input image will appear in the output mosaic (it replaces the output mosaic pixel). Invalid input Special Pixels (NULL,HRS,HIS,LRS,LIS) will NOT replace an existing Valid output mosaic pixel unless the optional flags are set. Refer to parameters HIGHSATURATION,LOWSATURATION, and NULL to override replacement of Valid output mosaic pixels.

NOTE: When using this priority with multi-band mosaics and with the TRACK option set, all Special Pixel flags must be set as well. This is because the same pixel within different bands of a single input image may hold both Valid and Special Pixel values, and since our Tracking capabilities can only track one input image per pixel (as it is a single band), it must accept the values for that particular pixel from every band in the input image being placed on top.

BENEATH The current input image will be placed beneath the output mosaic. Thus in any area of overlap, the Valid pixel values for the current mosaic will remain in the output mosaic. The Valid pixel values for the current input image will only replace the NULL pixels values in the output mosaic. The HRS,HIS,LRS and LIS special pixel values in the output mosaic will NOT be replaced by the Valid input pixel. The parameters HIGHSATURATION, LOWSATURATION and NULL are not supported under this priority.
BAND The input image pixels will be placed in the output mosaic based on the "Lesser" or "Greater" criteria of a priority band defined by the user. Parameters that apply to this priority feature are TYPE, NUMBER, KEYNAME, KEYVALUE, CRITERIA.
AVERAGE Overlapping Valid pixel values from the current input image and output mosaic will be averaged for the new mosaic pixel values. A count-band is created with the output mosaic file. The count-band keeps track of the number of images involved in the averaging of the input DN values for each pixel in the mosaic. Invalid input pixel values will not be included in the average. In the case where only one Valid pixel exists between the input image pixels or the current mosaic pixel, the Valid pixel is retained in the current output mosaic. Refer to parameters HIGHSATURATION, LOWSATURATION, and NULL to override replacement of valid output mosaic pixels.

Choosing this priority will cause the mosaic to have twice the number of bands of the input image. Hence the file (byte) size of the mosaic is increased due to the count-bands.

NOTE: If an existing mosaic does not already contain a count-band, an error will be encountered.

Each of the following priority option tables indicates the resulting output pixel for a particular input pixel, given the selected special pixel options (parameters HIGHSATURATION for HRS, HIS; LOWSATURATION for LRS, LIS; and NULL) in each table row.

PRIORITY=ONTOP
Options Images
High Saturation Low Saturation Null Input Pixel Value Type Current Mosaic Pixel Value Type Output Mosaic Pixel Value Source
False False False Valid Special or Valid Input
False False False Special High Saturation or Low Saturation or Valid Mosaic
False False False Special or Valid Null Input
True or False True or False True Valid Special or Valid Input
True or False True or False True Special Special or Valid Input



PRIORITY=BENEATH
Input Pixel Value Type Current Mosaic Pixel Value Type Output Mosaic Pixel Value Source
Special or Valid Null Input
Special or Valid High Saturation or Low Saturation or Valid Mosaic



PRIORITY=BAND
Options Images
High SaturationLow SaturationNull Input Pixel Value TypeCurrent Mosaic Pixel Value Type Output Mosaic Pixel Value Source
False False False Valid Valid Criteria based
False False False Valid Special Input
False False False Special High Saturation or Low Saturation or Valid Mosaic
False False False Special or Valid Null Input
True or False True or False True Special Special or Valid Input
True or False True or False True Valid Valid Criteria based
True or False True or False True Valid Special Input



PRIORITY=AVERAGE
Options Images
High SaturationLow SaturationNull Input Pixel Value TypeCurrent Mosaic Pixel Value Type Output Mosaic Pixel Value Source Count Band Pixel Value (# of images used for average)
False False False Valid Valid Average increment count by 1
False False False Valid Special Input count = 1
False False False Special Special Mosaic count = 0
False False False Special Valid Mosaic count unchanged
True or False True or False True Special Special or Valid Input count = 0
True or False True or False True Valid Valid Average increment count by 1
True or False True or False True Valid Special Input count = 1


Categories


Related Applications to Previous Versions of ISIS

This program replaces the following application existing in previous versions of ISIS:

Related Objects and Documents

Applications


Parameter Groups

Files

Name Description
FROM Cube to be placed in the mosaic
MOSAIC Mosaic output cube
PRIORITY The priority of pixel placement

Band Priority

Name Description
TYPE Indicate the name or number to use for the comparison
NUMBEREnter the Band Number
KEYNAME Enter the Key name as it appears in the cube labels
KEYVALUE Enter the value associated with the "KEYNAME"
CRITERIA Determines pixel placement given a band

Placement

Name Description
INSAMPLEThis sample in the input cube will be placed at OUTSAMPLE in the mosaic
INLINEThis line in the input cube will be placed at OUTLINE in the mosaic
INBANDThis band in the input cube will be placed at OUTBAND in the mosaic
OUTSAMPLEThe INSAMPLE sample will be placed at this sample in the mosaic
OUTLINEThe INLINE line will be placed at this line in the mosaic
OUTBANDThe INBAND band will be placed at this band in the mosaic

Options

Name Description
MATCHBANDBINInput and mosaic BandBin Groups must match
MATCHDEMEnforce DEM Match
HIGHSATURATIONCopy Input HS (Instrument and Representation) values
LOWSATURATIONCopy Input LS (Instrument and Representation) values
NULLCopy Input NULL values

Initialization

Name Description
CREATECreate the output mosaic
TRACK Track the source filenames for each mosaic pixel
PROPAGATE Propagate the labels, tables, and BLOBs from the input cube
NSAMPLESThe number of samples to allocate in the mosaic
NLINESThe number of lines to allocate in the mosaic
NBANDSThe number of bands to allocate in the mosaic

Files: FROM

Description

This cube will be placed into the mosaic. It must have the same ProjectionName, PixelResolution, EquatorialRadius, PolarRadius, LatitudeType, and LongitudeDirection as the mosaic. The projection specific keywords, such as CenterLatitude and CenterLongitude, must match as well.

Type cube
File Mode input
Filter *.cub

Files: MOSAIC

Description

The mosaic cube which will have the input cube placed in it. If the selected cube does not already exist as a mosaic, the CREATE option must be selected and it will be created. In this case NSAMPLES, NLINES, and NBANDS must be entered.

Type cube
File Mode output
Filter *.cub

Files: PRIORITY

Description

This parameter determines how the pixels from the input cube will overlap with the pixels in the mosaic.

Type string
Default ONTOP
Option List:
Option Brief Description
ONTOP Input cube is placed on top of the mosaic Valid input pixels will always be copied onto the mosaic. Any input pixel will be placed onto a NULL mosaic pixel. If the mosaic pixel is not NULL and the input pixel is special, it will only be copied onto the mosaic if the special pixel flags are set.

Exclusions

  • TYPE
  • CRITERIA
  • NUMBER
  • KEYNAME
  • KEYVALUE
BENEATH Input cube is placed beneath the mosaic If the mosaic pixel is NULL, then the input pixel will be placed on top of the mosaic. Otherwise, it remains unchanged.

Exclusions

  • TYPE
  • CRITERIA
  • NUMBER
  • KEYNAME
  • KEYVALUE
  • HIGHSATURATION
  • LOWSATURATION
  • NULL

Inclusions

  • TRACK
BAND Input pixel is placed on top of the mosaic based on the criteria in the selected band If the input and mosaic pixel of the priority band, specified by NUMBER or KEYNAME and KEYVALUE are valid, a less than or greater than comparison is done. Depending on the CRITERIA selected, the lower or higher of the two pixels is placed on top. Special and NULL pixels are not placed on top unless their flags are set. So, if the comparison of the priority band says that the input pixel should be on top but the input pixel on any other band is null, without the null option being selected, the mosaic pixel will remain unchanged for that band.

Inclusions

  • TYPE
  • CRITERIA
AVERAGEAverage of valid input and the mosaic pixels If the Input and Mosaic pixels are valid, the output will be the average of the 2 values. A count band is created for each corresponding band in the mosaic and holds the count of the images corresponding to the Average DN value of each pixel in the mosaic.

Exclusions

  • TYPE
  • CRITERIA
  • NUMBER
  • KEYNAME
  • KEYVALUE
  • TRACK

Band Priority: TYPE

Description

This option allows the user to select the method in which they want to specify the band to use for the pixel comparison.

Type string
Default BANDNUM
Option List:
Option Brief Description
BANDNUMBERBand Number The band number to use in the pixel comparison.

Exclusions

  • KEYNAME
  • KEYVALUE

Inclusions

  • NUMBER
KEYWORD PVL Keyword in "BandBin" group Selecting this option allows the user to enter the Keyword name and value corresponding to the band to use in the pixel comparison.

Exclusions

  • NUMBER

Inclusions

  • KEYNAME
  • KEYVALUE

Band Priority: NUMBER

Description

This is the ban dnumber selected for the pixel comparison.

Type integer
Default 1

Band Priority: KEYNAME

Description

The entered keyword name must match the name in the BandBin group.

Type string
Default OriginalBand

Band Priority: KEYVALUE

Description

This value must match the value associated with the KEYNAME parameter.

Type string
Default 1

Band Priority: CRITERIA

Description

Select which type of comparison to do on the pixels. You can choose whether the lesser or greater of the two pixels will be placed on top of the mosaic.

Type string
Default LESSER
Option List:
Option Brief Description
LESSER The lower DN value between the input and mosaic pixels will be placed on top The lower DN value between the input and mosaic pixels will be placed on top of the mosaic.
GREATER The larger DN value between the input and mosaic pixels will be placed on top The larger DN value between the input and mosaic pixels will be placed on top of the mosaic.

Placement: INSAMPLE

Description

This is a sample in the input image. This sample in the input cube will be placed at OUTSAMPLE in the mosaic.

Type integer
Default 1

Placement: INLINE

Description

This is a line in the input image. This line in the input cube will be placed at OUTLINE in the mosaic.

Type integer
Default 1

Placement: INBAND

Description

This is a band in the input image. This band in the input cube will be placed at OUTBAND in the mosaic.

Type integer
Default 1

Placement: OUTSAMPLE

Description

This parameter is used to select the starting sample where the input cube will be placed. The sample INSAMPLE will be placed at this sample in the output mosaic.

Type integer
Default 1

Placement: OUTLINE

Description

This parameter is used to select the starting line where the input cube will be placed. The line INLINE will be placed at this line in the output mosaic.

Type integer
Default 1

Placement: OUTBAND

Description

This parameter is used to select the starting band where the input cube will be placed. The band INBAND will be placed at this band in the output mosaic.

Type integer
Default 1

Options: MATCHBANDBIN

Description

This option causes the application to fail if the input bandbin group does not match the mosaic bandbin group. This parameter will only apply when the input labels contain a BandBin Group with wavelength keywords.

Type boolean
Default FALSE

Options: MATCHDEM

Description

This option causes the application to fail if the input DEM shapemodel does not match the mosaic's' shapemodel. This parameter will only apply when the input labels contain a ShapeModel keyword in the Kernels Group.

Type boolean
Default FALSE

Options: HIGHSATURATION

Description

This option causes High Saturation values (both Instrument and Representation) in the input image to be automatically copied to the mosaic regardless of the priority.

Type boolean
Default FALSE

Options: LOWSATURATION

Description

This option causes Low Saturation values (both Instrument and Representation) in the input image to be automatically copied to the mosaic regardless of the priority.

Type boolean
Default FALSE

Options: NULL

Description

This option causes NULL values in the input image to be automatically copied to the mosaic regardless of the priority.

Type boolean
Default FALSE

Initialization: CREATE

Description

This parameter is used to specify whether the mosaic needs to be created.

Type string
Default NO
Option List:
Option Brief Description
NO The output mosaic already exists Choose this option if the output mosaic already exists.

Exclusions

  • NSAMPLES
  • NLINES
  • NBANDS
  • TRACK
  • PROPAGATE
YESCreate the output mosaic The output mosaic does not exist and will be created.

Inclusions

  • NSAMPLES
  • NLINES
  • NBANDS
  • PROPAGATE

Initialization: TRACK

Description

The Track feature creates a separate tracking cube containing the index values for the source of every pixel in the output mosaic. The tracking cube can only be used appropriately through the QVIEW-AdvancedTracking tool. As the user pans across the displayed mosaic, for every mosaic pixel location QVIEW-AdvancedTracking will interactively report the filename, the serial number and the index of the input cube that was input to handmos for that specific pixel location. The tracking cube cannot be used outside the QVIEW-AdvancedTracking tool except as a visual representation of the source cubes for the different pixels. TRACK must be set to TRUE at the time of mosaic creation only and cannot be turned on after the mosaic is created. When a mosaic is created with TRACK=TRUE, all subsequent runs will default to TRACK=TRUE. When a mosaic is created with TRACK=FALSE, an error will be encountered if subsequent runs have TRACK=TRUE. The tracking cube will always be of type unsigned integer. Depending on the bit-type of the mosaic cube and/or the number of bands it contains, the tracking cube may be as much as four times the size of the mosaic cube itself.

WARNING: If Tracking is turned on in a mosaic, any subsequent applications that modify DN values, such as the applicationreduce, will corrupt the DN values in the tracking cube.

Type boolean
Default FALSE

Initialization: PROPAGATE

Description

If selected the application will transfer the labels, tables, and BLOBs from the input cube to the output mosaic. If not selected only the Band Bin information will be transferred. This option can only be used when the mosaic is being created (i.e., CREATE=YES).

Type boolean
Default TRUE

Initialization: NSAMPLES

Description

This parameter is used to specify the number of samples in the output mosaic.

Type integer
Minimum 1 (inclusive)

Initialization: NLINES

Description

This parameter is used to specify the number of lines in the output mosaic.

Type integer
Minimum 1 (inclusive)

Initialization: NBANDS

Description

This parameter is used to specify the number of bands in the output mosaic.

Type integer
Minimum 1 (inclusive)

History

Jeff Anderson2003-07-14 Original version
Stuart Sides2003-07-29 Modified filename parameters to be cube parameters where necessary
Jeff Anderson2003-09-19 Added option to initialize the base mosaic
Jeff Anderson2004-02-17 Updated progress text and made output create use input cube attributes
Elizabeth Miller2006-09-01 Added the MATCHBANDBIN option that checks to make sure the input cube bandbin group matches the mosaic bandbin group. The default is true.
Elizabeth Miller2006-09-28 Added history entry to the output cube
Steven Lambright2008-05-06 Expanded upon position parameters
Eric Hyer2009-06-11 Parameter "INPUT" now called "PRIORITY" to be consistent with the mapmos app
Sharmila Prasad2009-09-04 Added option "TRACK" to track pixel origin. Also added new priority called BAND where specified input and mosaic band is compared for moving input to mosaic and to track the pixel origin. Added parameter "TYPE" to choose Band "NUMBER" or PVL "KEYWORD" from the BandBin group. If "BANDNUMBER" is chosen, then "NUMBER" is activated to enter band number. If "KEYWORD" is chosen then parameter "KEYNAME" and "KEYVALUE" are activated to enter key name and value from the BandBin group for band comparison. Band comparison "CRITERIA" are "LESSER" or "GREATER" than. Also there are options "HIGHSATURATION", "LOWSATURATION" and "NULL", set to true will cause HS, LS and NULL input pixels to be copied to the mosaic regardless of the priorities and criteria. These options are not supported for "BENEATH" priority.
Sharmila Prasad2009-12-16 Always place an input pixel over a NULL mosaic pixel. Track the origin for multiband ONTOP priority if all the Special Pixel flags are set. Store the Serial numbers of the input mosaic in the mosaic along with the file name.
Sharmila Prasad2010-10-27 Process Input Image's Attributes
Sharmila Prasad2011-01-19 Added "AVERAGE" priority where the mosaic will be average of valid input and mosaic pixels.
Sharmila Prasad2011-01-24 Option to match DEM and also added new group "mosaic" to hold ShapeModel attributes for the mosaic
Steven Lambright2011-10-19 Output cube when CREATE=yes no longer propagates labels other than the band bin information.
Sharmila Prasad2011-11-07 Updated documentation for Average priority. Fixes #553
Stuart Sides2012-01-19 Added option to have the BLOBs and labels transferred from the input cube transferred to the output mosaic from the input cube.
Kimberly Oyama2012-09-18 When an image is placed twice (usually because the longitude range is greater than 360 and encompasses the image more than once) only the last occurance was written to the log file. This has been fixed so that there is an entry in the log file for every image placement. References #976.
Kimberly Oyama2014-03-28 Added an app test for the error check when PRIORITY=AVERAGE and the mosaic does not have a count band. References #746.
Tammy Becker and Kimberly Oyama2014-04-07 Updated user documentation. Backward Compatibility Issue: The MATCHBANDBIN parameter now defaults to FALSE because the input cubes for handmos are not required to have the BandBin group in the cube labels which could impact processing scripts/pipelines. Fixes #1620. References #1623.
Summer Stapleton2018-08-13 Updated code and documentation to reflect new handling of tracking capabilities with an external tracking cube as well as clarify why special pixel flags are required when priority=ontop for multiband mosaics. References #2092