Merge branch 'control-networks' into 'main'

control networks docs

Closes #21

See merge request astrogeology/asc-public-docs!34

docs/concepts/control-networks/automatic-registration.md

+
+# Automatic Registration
+
+## Introduction
+
+Automatic registration is the attempt to match a pattern in an image
+cube. Pattern matching has many different purposes.
+
+Examples:
+
+1.  Register an entire image to a second image. The registration of an
+    image is performed by moving (rubber-sheet) the pixels to output
+    pixel locations that result in pattern matching directly to a second
+    'fixed' or 'truth' image.
+
+    - Use: [coreg](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/coreg/coreg.html)
+
+2.  Relative cartographic registration between a number of overlapping
+    images. Pattern matching is used to build a control point network
+    across a number of overlapping images for solving and adjusting the
+    camera pointing that are then applied to map project the images.
+
+    - Use: [pointreg](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/pointreg/pointreg.html) or [jigsaw](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/jigsaw/jigsaw.html)
+
+3.  Find and record the pixel location(s) of a camera reference mark
+    (e.g., Vidicon reseau mark) across an image
+
+    - Use: [findrx](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/findrx/findrx.html)
+
+
+## Match Algorithm Definition Files (PVL)
+
+Registration of images can be an advanced and complicated process. ISIS3
+is designed to supply a choice of match/registration algorithms to
+handle a variety of image data conditions. An ISIS3 "plugin" algorithm
+expects all match algorithms to supply parameter information through a
+Parameter Value Language (PVL) definition file. Examples of match
+algorithm PVL's can be found in
+
+    $ISIS3DATA/base/templates/autoreg/coreg*.def 
+
+Registration applications (such as coreg) will allow the user to choose
+from this collection of PVL files in the user interface gui.
+
+A PVL file can be generated for a selected match algorithm with 
+[autoregtemplate](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/autoregtemplate/autoregtemplate.html).
+
+## Match Algorithms
+
+### Maximum Correlation
+
+The Maximum Correlation match algorithm is most commonly used. The
+algorithm computes a  
+correlation coefficient that will range from no correlation (zero) to
+perfect correlation (one).
+
+Example templates for Maximum Correlation can be found in:
+
+ 
+    $ISIS3DATA/base/templates/autoreg/coreg.maxcor.p*.s*.def.  
+
+
+An example PVL for the Maximum Correlation follows:
+
+    Object = AutoRegistration
+    
+      Group = Algorithm
+        Name = MaximumCorrelation
+        Tolerance = 0.7
+      End_Group
+    
+    End_Object
+
+!!! tip
+
+    A successful correlation is met if the **Goodness of Fit** is **Greater Than** 
+    the Tolerance parameter value for the Maximum Correlation Algorithm.
+
+### Minimum Difference
+
+The Minimum Difference match algorithm performs a subtraction of the
+Pattern Chip and the sub-region of the Search Chip. The **Goodness of 
+Fit** will range from zero for a perfect match, while larger values 
+indicate a less likely match. The **Goodness of Fit** is measured as an 
+absolute value and will never be negative.
+
+Example templates for Minimum Difference can be found in:
+
+    $ISIS3DATA/base/templates/autoreg/coreg.mindif.p*.s*.def.
+
+An example PVL for the Minimum Difference follows:
+
+    Object = AutoRegistration
+    
+      Group = Algorithm
+        Name = MinimumDifference
+        Tolerance = 100
+      End_Group
+    
+    End_Object
+
+!!! tip
+
+    A successful correlation is met if the **Goodness of Fit** is **Less
+    Than** the Tolerance parameter value for the Minimum Difference Algorithm.
+
+## Tolerance
+
+The Tolerance parameter is used by both Maximum
+Correlation and Minimum
+Difference. Each correlation coefficient result
+(**Goodness of Fit**) is tested against the Tolerance. Tolerance is set
+within the PVL file along with the chosen
+registration algorithm.
+
+Points that fail the Tolerance test are reported by the autoreg
+applications as:
+
+- `FitChipToleranceNotMet`
+
+- `SurfaceModelToleranceNotMet`
+
+## Chips
+
+There are two chips used in automatic registration, the Pattern
+Chip and the Search Chip. The
+two chips are nothing more than sub-areas of the input image cubes,
+generally small in size. An NxM Chip is defined to be an N-Sample by
+M-Line region of an image. Basic elements of a chip are:
+
+  - N and M are natural numbers (1, 2, 3...,50)
+  - Like image cubes, chip coordinates are sample/line and 1-band based
+  - The center of the chips is (N - 1)/2 + 1 and (M - 1)/2 + 1
+
+### Pattern Chip
+
+A Pattern Chip will contain the data you would like to match. This
+Pattern Chip is basically extracted from the 'Reference' image (it is
+also referred to as the 'Truth' image). The Pattern Chip is then walked
+across the Search Chip that has been extracted from
+the other image that is to be modified.
+
+The PVL for a Pattern Chip defined as 25 Samples x 25 Lines (625 pixels)
+is:
+
+    Object = AutoRegistration
+    
+      Group = PatternChip
+        Samples = 25
+        Lines = 25
+      End_Group
+    
+    End_Object
+
+**Pattern Chip Size Requirement:**
+
+N + M \>= 3. This ensures that the pattern is not a single pixel.
+
+???+ tip "Tips"
+
+    1.  The feature to match included in the Pattern Chip does not have to
+        be in the center.
+    2.  The more "bland" the data is within the input images, the larger the
+        Pattern Chip box should be. A larger box will allow for more pixel
+        DN variance.
+    3.  In general, avoid very small box sizes less than 11 Samples X 11
+        Lines
+    4.  The smaller the size of the Pattern Chip, the greater the chance of
+        matching too many areas in the search chip and returning a 'false
+        positive' match.
+
+### Search Chip
+
+A Search Chip is the sub-area of the image cube that the pattern might
+be found in. The Pattern Chip is walked through the
+Search Chip looking for the best match. The Search Chip must be larger
+than the Pattern Chip (at least one pixel bigger on line/sample size).
+
+The PVL for a Search Chip defined as 45 Samples x 45 Lines (2025 pixels)
+is:
+
+    Object = AutoRegistration
+    
+      Group = PatternChip
+        Samples = 25
+        Lines = 25
+      End_Group
+    
+      Group = SearchChip
+        Samples = 45
+        Lines = 45
+      End_Group
+    
+    End_Object
+
+**Search Chip Size Requirement:**
+
+!!! danger "TODO - Update Link"
+
+    TODO: Update **Sub-Pixel Definition** links to new docs once those pages are migrated.
+
+N(search) \>= N(pattern) + 2 and similarly for M. This ensures that the
+Pattern Chip spans at least a 3x3 window within the Search Chip. An
+important requirement for surface fitting in order to compute sub-pixel
+accuracy. (Refer to: [Sub-Pixel Definition](https://DOI-USGS.github.io/ISIS3/gh-pages/ISIS_Cube_Format)).
+
+???+ tip "Tips"
+
+    - The Search Chip must be larger than the Pattern Chip (at least one
+        pixel bigger on line/sample size).
+    - The Search Chip needs to be large enough to allow a 'best guess' or
+        predicted line and sample mis-registration offset between the images
+        that are to be correlated.  
+        - **SearchChipSize = PatternChipSize + (OffsetPixelEstimate *
+            2)**
+    - BUT, the Search Chip shouldn't be too much larger than the Pattern
+        Chip.  
+        - The difference in size could greatly affect how long the
+            registration application would run.
+    - Refer to PVL example above:
+        - An estimated offset between two input images of 10 Lines by 10
+            Samples will need a Search Chip size (10 Line offset * 2) by
+            (10 Sample offset * 2). The Search Chip size in this example
+            needs to be at least 20*20 Lines/Samples bigger than the pattern
+            chip.
+        - PatternChipSize = 25 * 25
+        - SearchLineDimention = 25 + (10 * 2) = 45 * SearchSampleDimention = 25 + (10 * 2) = 45
+        - SearchChipSize= 45 * 45
+
+## Restricting Input Pixel Ranges
+
+!!! danger "TODO - Update Link"
+
+    TODO: Update **Input Pixels** and **Special Pixel** links to new docs once those pages are migrated.
+
+The validity of the [input pixels](https://DOI-USGS.github.io/ISIS3/gh-pages/ISIS_Cube_Format) 
+of the Pattern Chip is the very first test
+performed. Prior to the match algorithm being invoked during the walk
+process, a simple test is performed to ensure there are enough pixels to
+work with. Pixels are deemed valid if they are in the minimum/maximum
+range and/or they are not [special pixel](https://DOI-USGS.github.io/ISIS3/gh-pages/Special_Pixels.html) values.
+
+The Pattern Chip is only checked once. If it does not contain enough
+valid pixels, the match is deemed to fail. Otherwise, the walk through
+occurs and the sub-area is extracted from the Search
+Chip. If this sub-area does not have enough valid
+pixels a match will be deemed to fail at that search location.
+
+Points that fail the default or specified Valid Minimum/Maximum and/or
+ValidPercent tests are reported by the autoreg applications as:
+
+- `PatternNotEnoughValidData`
+
+- `FitChipNoData`
+
+- `SurfaceModelToleranceNotMet`
+
+### Valid Minimum/Maximum
+
+Input image pixels (DN) values may be excluded from the match
+algorithm if they fall outside of a specific range. The ranges can be
+specified independently for the Search Chip and Pattern Chip. While this
+might not be necessary for a successful registration, excluding pixel
+data could improve the chances depending on the characteristics of the
+input images. (i.e., Eliminating the DN range of deep shadow areas in an
+image).
+
+The ranges are handled via the PVL as follows:
+
+    Object = AutoRegistration
+    
+      Group = PatternChip
+        Samples = 20
+        Lines = 20
+        ValidMinimum = 0.1
+        ValidMaximum = 0.4
+      End_Group
+    
+      Group = SearchChip
+        Samples = 55
+        Lines = 55
+        ValidMinimum = 2.5
+        ValidMaximum = 10.5
+      End_Group
+    
+    End_Group
+
+### Valid Pixel Count (ValidPercent)
+
+`ValidPercent` defines the percentage of valid data that is required
+within the Pattern Chip or Search Chip. The parameter can be set in
+conjunction with Valid Minimum/Maximum.
+
+The Valid Percent would be handled via the PVL as follows:
+
+    Object = AutoRegistration
+    
+      Group = PatternChip
+        Samples = 20
+        Lines = 20
+        ValidPercent = 80
+      End_Group 
+    End_Group
+
+Default for `ValidPercent`: `AutoRegDefaults`
+
+!!! tip
+
+    `ValidPercent` is specified in the Pattern Chip, as the sub-area 
+    chip of the search area will use the same value.
+
+## Fit Chip
+
+As the Pattern Chip walks through the sub-regions
+of the Search Chip , a third chip is generated
+called a Fit Chip. The Fit Chip will have the same line and sample
+dimensions as the Search Chip. The Fit Chip is filled with the resulting
+**Goodness of Fit** values at every position that the Pattern Chip is walked
+across the Search Chip computing a fit correlation value.
+
+The highest or lowest **Goodness of Fit** values within the Fit Chip
+generally represent the position that best matched between the Pattern
+and Search areas. It is only good to a maximum of **ONE pixel accuracy**.
+
+The Fit Chip can be interactively generated and viewed using the image
+display application  
+[qnet](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/qnet/qnet.html).
+
+
+## Sub-Pixel Accuracy
+
+!!! danger "TODO - Update Link"
+
+    TODO: Update **Sub-Pixel Definition** links to new docs once those pages are migrated.
+
+The attempt to reach a registration of sub-pixel accuracy is performed
+on the Fit Chip. The Fit Chip is created as the
+Pattern Chip is walked through Search
+Chip. The Fit Chip contains the resulting
+correlation position between the two chips of a maximum of ONE pixel
+accuracy. In many cases, the actual, ultimate registration may lie
+somewhere between two pixels. (Refer to:
+[Sub-Pixel Definition](https://DOI-USGS.github.io/ISIS3/gh-pages/ISIS_Cube_Format)).
+
+The sub-pixel accuracy can be turned off through the PVL settings as
+follows:
+
+    Group = Algorithm
+      Name = MaximumCorrelation
+      SubPixelAccuracy = False
+    End_Group
+
+When the sub-pixel accuracy is turned off, the whole pixel with the best
+fit is returned.  
+Default for SubPixelAccuracy: AutoRegDefaults
+
+!!! tip
+
+    By default, if an ideal **Goodness of Fit** is found (e.g. Zero (0.0) for
+    Minimum Difference or One (1.0) for Maximum Correlation), we have a perfect 
+    fit and assume that it is the best position. In this case, the sub-pixel 
+    accuracy phase is omitted.
+
+### Surface Modeling
+
+A continuous mathematical surface is modeled based on the data within
+the Fit Chip. A 2nd degree 2-dimensional
+polynomial is calculated given an NxN window of points extracted from
+the Fit Chip surrounding the correlation peak (highest value)-which
+represents the whole pixel registration. An estimate of the true
+sub-pixel registration position of the chip can be reached based on this
+surface model.
+
+A perfect 3D linear fit (global maximum) would be represented by a
+spherical surface with a single high peak.
+
+## AutoRegDefaults
+
+(As of May 20, 2009)
+
+    ValidPercent                  = 50.0
+    MinimumZScore                 = 1.0
+    Tolerance                     = Null (no default)
+    ReductionFactor               = 1.0
+    
+    SubPixelAccuracy              = True
+    SurfaceModelDistanceTolerance = 1.5
+    SurfaceModelWindows           = 5
+    SurfaceModelEccentricityRatio = 2 (2:1)

docs/concepts/control-networks/autoseed.md

+
+# Autoseed
+
+See Also: [autoseed Application
+Documentation](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/autoseed/autoseed.html)
+
+## Introduction
+
+[Autoseed](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/autoseed/autoseed.html)
+is a program that will automatically build a gridded network of evenly
+distributed tiepoints across overlapping polygons. The distance between
+the tiepoints is defined in meters, or number of points along the major
+axis and minor axis. Autoseed requires the success of ISIS3's
+[spiceinit](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/spiceinit/spiceinit.html),
+[footprintinit](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/footprintinit/footprintinit.html)
+and
+[findimageoverlaps](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/findimageoverlaps/findimageoverlaps.html)
+applications. The collection of tiepoints are further refined with other
+ISIS3 programs, and used to improve the geometric accuracy of the input
+images.
+
+## Overlap Polygons
+
+![Colorful polygons overlap each other with varying degrees of transparency.](
+  ../../assets/control-networks/overlap-polygon-example.png 
+  "ISIS3 qmos image footprint plot of Clementine images."){ align=right width=300 }
+
+The automatic seeding program is dependent on the information about how
+all the images to be combined into a single output overlap each other.
+The polygons can be different shapes and sizes. A separate program 
+(**findimageoverlaps**) attempts to find all the polygons and saves the
+information to an output file. This output file is defined as the
+*overlap* parameter in **autoseed**. This image shows the
+overlap polygons in different shades of color.
+
+
+
+## Available Algorithms
+
+| Algorithm | Best for:                                                                     |
+|-----------|-------------------------------------------------------------------------------|
+| **Grid**  | different shapes and sizes of overlap polygon                                 |
+| **Limit** | limiting the number of seeded tiepoints per polygon                           |
+| **Strip** | rectangular shaped overlap polygons such as those for adjacent line scan data |
+
+The standard autoseed templates for the three algorithms are in
+`$ISIS3DATA/base/templates/autoseed/`
+
+## Required Parameters for each Algorithm
+
+The required parameters for each algorithm are provided through a
+separate **Parameter Value Language** (PVL) definition file.
+
+??? abstract "Grid Algorithm PVL File"
+
+        Object = AutoSeed
+          Group = PolygonSeederAlgorithm
+            Name = Grid
+            Minimum Thickness = 0.0
+            MinimumArea = 100000000
+            XSpacing = 10000
+            YSpacing = 10000
+          EndGroup
+        EndObject
+
+
+??? abstract "Limit Algorithm PVL File"
+
+        Object = AutoSeed
+          Group = PolygonSeederAlgorithm
+            Name = Limit
+            Minimum Thickness = 0.0
+            MinimumArea = 100000000
+            MajorAxisPoints = 6
+            MinorAxisPoints = 3
+          EndGroup
+        EndObject
+
+
+??? abstract "Strip Algorithm PVL File"
+
+        Object = AutoSeed
+          Group = PolygonSeederAlgorithm
+            Name = Strip
+            Minimum Thickness = 0.0
+            MinimumArea = 100000000
+            XSpacing = 10000
+            YSpacing = 10000
+          EndGroup
+        EndObject
+
+
+???+ example "Using keywords to specify a set of valid parameters to seed tie points"
+
+        Object = AutoSeed
+          Group = PolygonSeederAlgorithm
+            Name = Grid
+            MinimumThickness = 0.0
+            MinimumArea = 1000 <meters>
+            XSpacing = 20000 <meters>
+            YSpacing = 10000 <meters>
+            PixelsFromEdge = 20.0
+            MinEmission = 20.0
+            MaxEmission = 75.0
+            MinIncidence = 25.0
+            MaxIncidecne = 80.0
+            MinResolution = 255.0
+            MaxResolution = 259.0
+            # MinDN and MaxDN are costly checks
+            MinDN = 0.145
+            MaxDN = 0.175
+          EndGroup
+        EndObject
+
+
+### MinimumThickness
+
+![Vertical slightly tilted rectangles overlap each other. A sliver where two rectangles barely overlap each other is pointed out.](
+  ../../assets/control-networks/ctx-footprint-plot-cropped-demo.png 
+  "Simple Polygons"){ width=250 align=left }
+
+!!! tip
+
+    Setting the **MinimumThickness** parameter will most likely work better 
+    for these polygons. If boxes were drawn around the polygons they would be 
+    similar to the shape of the original polygons.
+
+The MinimumThickness is used to exclude seeding tiepoints within
+polygons that are narrow slivers. If the thickness value is below the
+defined minimum thickness, then no tiepoints are seeded within the
+polygon. The valid values are between 0.0 and 1.0, and the default value
+is 0.0 if nothing is entered. The thickness value is derived by drawing
+a box around the polygon, and calculating the ratio of the short side by
+the long side of the box. The MinimumThickness option works best if the
+polygons are rectangular or square shapes. Use this parameter with
+caution because the calculated value for thickness may not be accurate.
+
+-----
+
+### MinimumArea
+
+![Outlined polygons. Narrow Slivers are pointed out.](
+  ../../assets/control-networks/narrow-sliver-polygon-example.png 
+  "Polygon types"){ width=300 align=left }
+
+The MinimumArea is used to specify what the smallest calculated value
+for the minimum area of an overlap polygon must be in order to seed
+tiepoints. The default value is 0.0 if nothing is entered for
+MinimumArea. This parameter is useful for excluding small and skinny
+overlap polygons from being seeded with tiepoints.
+
+!!! tip
+
+    1. Set the **MinimumArea** to avoid seeding tiepoints in polygons 
+    formed by narrow slivers overlapping.
+    
+    1. **MinimumThickness** might be misleading for these polygons; 
+    its estimate would be too large.
+
+-----
+
+### *XSpacing* & *YSpacing*
+
+The *grid* and *strip* algorithms require the user to define XSpacing
+and YSpacing, and if nothing is entered the program will report an error
+and fail. The XSpacing and YSpacing parameters are defined in meters,
+and determine how the tiepoints will be distributed within each polygon.
+The tiepoints are seeded starting at the center of each polygon, and
+spaced every XSpacing increment along the X-axis, and YSpacing increment
+along the Y-axis. The resolution of the input images will contribute to
+how dense the tiepoints are seeded. See Examples.
+
+### *MajorAxisPoints* & *MinorAxisPoints*
+
+These two parameters are only used for the *Limit* algorithm. The
+MajorAxisPoints is used to specify how many tiepoints to seed along the
+longer side of a box drawn around the polygon. The MinorAxisPoints is
+used to specify how many tiepoints to seed along the shorter side of a
+box drawn around a polygon. So, if you set MajorAxisPoints = 10 and
+MinorAxisPoints = 3, then you would have 30 equally spaced tiepoints (10
+rows by 3 columns or 3 rows by 10 columns) within each of the overlap
+polygons.
+
+
+## Preparing for autoseed (run these programs first)
+#### These must be run on individual input images:
+
+|   | Program           | Purpose                                                               |
+|---|-------------------|------------------------------------------------------------------|
+| 1 | **spiceinit**     | attaches SPICE data to the ISIS3 cube                            |
+| 2 | **footprintinit** | adds image footprint information to ISIS3 cube labels            |
+| 3 | **camstats**      | attaches geometric and image statistics to the ISIS3 cube labels |
+
+#### *findimageoverlaps* needs a list of images as input:
+
+|                       |                                                                            |
+|-----------------------|----------------------------------------------------------------------------|
+| **findimageoverlaps** | determines all the overlap polygons among all the images in the input list |
+
+## Deciding which algorithm to use
+
+The first step is to display the images you have selected to see how
+they overlap each other using either PILOT, qmos, or some other display
+method. The overlap polygons are areas where a unique set of images
+overlap each other. The complexity of the polygons across your mosaic
+area will determine which algorithm is the most appropriate to use.
+
+### Examples:
+
+![PILOT Webpage showing overlapping long blue rectangles on a map of Mars.  
+  The rectangles criss-cross and are not all pointed the same way.](
+  ../../assets/control-networks/upc-ctx-search-for-footprint-reduced.png 
+  "Astrogreology UPC image search"){ align=left width=300 }
+
+#### Non-uniform order and size → *Grid*
+
+The image footprints are not in a uniform order, and the size of the images 
+varies. The `Grid` algorithm would be the best to use for this data.
+
+(This image shows rendered footprints in [PILOT](http://pilot.wr.usgs.gov/).)
+
+-----
+
+![Overlapping colored rectangles on white. The rectangles are taller 
+  than they are wide.  Some rectangles are shorter than others.  The 
+  rectangles are all pointed the same way.](
+  ../../assets/control-networks/ctx-footprint-plot.png 
+  "ISIS3 qmos image footprint plot"){ align=left width=300 }
+
+#### Same resolution but different sizes → *Limit* or maybe *Strip*
+
+The resolution of the images are about the same, but
+the ground area that was imaged varies in size. The strips of CTX
+linescan data are adjacent to each other, and the overlap polygons are
+simple and easily identified. The `Limit` algorithm would be the easiest
+to use. You would need to decide how many points to seed along the
+longest side of the overlap polygon and how many points across the
+shorter side. The `Strip` algorithm will provide more evenly distributed
+set of tiepoints, but you will need to figure out the most appropriate X
+and Y spacing.
+
+-----
+
+![Overlapping colored rectangle outlines on white. They are oriented 
+  like an Asian paper fan or seats in an auditorium towards an unmarked 
+  point in the bottom left. The rectangles are more concentrated closer
+  to the point. The rectangles are all similar in size.](
+    ../../assets/control-networks/clem-footprint-plot.png 
+    "Clem footprint Plot"){ align=left width=300 }
+
+#### Same resolution and size, varying overlaps → *MinimumArea* + *Grid* or *Strip*
+
+The resolution of the images are about the same. The
+size of the overlap polygons vary in shape, orientation, and sizes. It
+would be best to specify the `MinimumArea` to eliminate many of the
+smaller polygons from getting seeded. The best option would be to use
+either `Grid` or `Strip` algorithm to avoid clustered points in the smaller
+polygons. The `MinimumArea` can be increased if there are too many points
+clustered together in the smaller polygons, and the spacing can also be
+increased to put a greater distance between the seeded tiepoints.
+
+-----
+
+![A cluster of overlapping colored rectangle outlines around an unmarked 
+  centerpoint.  The rectangles are more concentrated towards the center.](
+  ../../assets/control-networks/clem-polar-footprints.png 
+  "Clem Plar Footprints"){ align=left }
+
+#### Complex overlaps → Manual Approach with *seedgrid*
+
+The overlap polygons here are so complex that
+`findimageoverlaps` will fail, and `autoseed` cannot be run. In this
+case, the only option is to use the program `seedgrid` to generate a
+network of seeded tiepoints. The `seedgrid` program does not require
+prior knowledge of the overlap polygons, but does require latitude
+range, longitude range, and a map template.
+
+-----
+
+## Determining XSpacing and YSpacing
+
+It is important to know the range of resolutions for the images you wish
+to include. Decide how many tiepoints you want to seed across the longer
+side and shorter side of the overlap polygons. For example, let’s say
+most of the polygons have 50 pixels of overlap along the shortest width
+and 5000 pixels along the longest length and the median resolution is 6
+meters/pixel, and you have decided to seed 3 points across the shorter
+side and 10 points along the longer side of the polygons. The
+calculation for the spacing would be the following:
+
+    X-spacing = (50/(3 + 1)) * 6  =  75m
+    y-spacing = (5000/(10 + 1)) * 6 = ~2727m (round up to 2800m)
+
+The second option is to display two images whose overlap pattern is
+representative of most of the images in the mosaic using ISIS3 **qview**
+program. The following is an example of the **qview** measurement tool,
+depicted as a ruler on the right side, to measure the distance of the
+widest overlap area:
+
+!!! danger "TODO - Update link"
+
+    TODO: Update **Using Qview to view cubes** link once that page is migrated.
+
+See [Using Qview to view cubes](https://github.com/DOI-USGS/ISIS3/wiki/Introduction_to_Isis) for more
+information about **qview**.
+
+![Measurement tool on two side-by-side Clementine images to show the overlap area](
+  ../../assets/control-networks/qview-moreoverlap-measure-for-spacing-calculation.png "Clem overlap 1")
+
+The tool measured approximately 278 pixels. The resolution of these two
+images are around 190 meters/pixel. So, the calculation for XSpacing
+would be ((278 pixels/6) \* 190 m/pixel) resulting in 8803.3 meters. You
+could start with XSpacing and YSpacing equal to 8800 meters as a
+starting point, and then increase or decrease the number based on
+whether you want to increase or decrease the distance between the seeded
+tiepoints.
+
+![Measurement tool on two side-by-side Clementine images to show the overlap area](
+  ../../assets/control-networks/qview-measure-for-spacing-calculation-indexcolor.png "Clem overlap 2")
+
+This example shows the measurement for the shorter side of the polygon,
+which is about 86 pixels. Sometimes the spacing increments you select
+may need to be different in the x and y directions, especially for line
+scan data where the image has a lot more lines than samples. If the
+desire is to seed only two tiepoints along the shorter side then your
+calculation would be ((86 pixels/3) \* 190 m/pixel) giving an xspacing
+of 5446 meters. You could use 5500 meters for x-spacing and 8800 meters
+for y-spacing.
+
+## Required Parameters
+
+Autoseed parameters:
+
+| Parameter     | Description                                                                                                               |
+|---------------|---------------------------------------------------------------------------------------------------------------------------|
+| `fromlist`    | List of all the filenames to be included in a control solution                                                            |
+| `deffile`     | PVL file containing the seeding algorithm and spacing between the tiepoints                                               |
+| `overlaplist` | Output file from **findimageoverlaps** program                                                                            |
+| `cnet`        | Filename of existing control network to add to (optional)                                                                 |
+| `onet`        | Output filename for control network generated by  **autoseed**                                                            |
+| `errors`      | Output filename for error tracking                                                                                        |
+| `networkid`   | ID name assigned to the control network file                                                                              |
+| `pointid`     | Starting string to be assigned to the **PointId**s, with question </br>marks for the number of digits needed (like "`C?????`") |
+| `description` | Description of the contents of the output control net file                                                                |
+
+## Running Autoseed
+
+!!! example "Command Line Interface"
+
+    In your terminal, type `autoseed` followed by `parameter=value` for each parameter as shown:
+    ```sh
+        autoseed fromlist=lev1.lis deffile=clem_grid2_autoseed.def overlaplist=overlaps.lis onet=autoseed_grid.net errors=autoseed_grid.err networkid=Clementine1 pointid=C?????? description="Clementine grid1"
+    ```
+
+??? example "Graphical Interface"
+
+    ![A form with an input space for each parameter.](../../assets/control-networks/autoseed-gui-2012.png "Autoseed GUI")
+
+## Output
+
+The output file is a binary control network (cnet) file that contains
+the control pointids and control measurements of all the images that
+overlap each seeded tiepoint. The program **qmos** can be used to
+display the images, image footprints, and the control network to see how
+the tiepoints are distributed. If the distribution of tiepoints is too
+dense, increase the spacing between the tie points to spread them apart
+and to reduce the number of tiepoints. If the tiepoints are too sparse
+then decrease the spacing to add more tiepoints. Rerun **autoseed** each
+time the parameters in the PVL definition file are changed. When you
+have reached an acceptable solution then use the program **qnet** to
+evaluate and refine the tiepoints by loading the control network file.
+
+The output network can no longer be viewed by a text editor unless the
+network file has been converted to a PVL format with **cnetbin2pvl** ,
+but use caution if the file size is large. The second option is to use
+**cneteditor** to view the network file in the binary format.
+
+**Converting binary control network to PVL format:**
+
+```sh
+cnetbin2pvl from=hirise_set1_autoseed.net to=hirise_set1_autoseed_pvl.net
+```
+
+??? abstract "Contents of an example HiRISE cnet file (first 66 lines)"
+
+        Object = ControlNetwork
+          NetworkId    = Hirise_set1
+          TargetName   = Mars
+          UserName     = elee
+          Created      = 2012-05-08T10:38:21
+          LastModified = 2012-05-08T10:38:21
+          Description  = "HiRise set1 images autoseed with hirise_ccd_sets_seed.def"
+          Version      = 3
+
+          Object = ControlPoint
+            PointType   = Free
+            PointId     = hirise_set1_00001
+            ChooserName = autoseed
+            DateTime    = 2012-05-08T10:38:45
+
+            Group = ControlMeasure
+              SerialNumber  = MRO/HIRISE/867676384:40724/RED0/2
+              MeasureType   = Candidate
+              ChooserName   = autoseed
+              DateTime      = 2012-05-08T10:38:45
+              Sample        = 2040.423603891
+              Line          = 20.242382897271
+              AprioriSample = 2040.423603891
+              AprioriLine   = 20.242382897271
+            End_Group
+
+            Group = ControlMeasure
+              SerialNumber  = MRO/HIRISE/867676384:40724/RED1/2
+              MeasureType   = Candidate
+              ChooserName   = autoseed
+              DateTime      = 2012-05-08T10:38:45
+              Sample        = 43.186441092459
+              Line          = 13.357872143126
+              AprioriSample = 43.186441092459
+              AprioriLine   = 13.357872143126
+            End_Group
+          End_Object
+
+          Object = ControlPoint
+            PointType   = Free
+            PointId     = hirise_set1_00002
+            ChooserName = autoseed
+            DateTime    = 2012-05-08T10:38:45
+
+            Group = ControlMeasure
+              SerialNumber  = MRO/HIRISE/867676384:40724/RED0/2
+              MeasureType   = Candidate
+              ChooserName   = autoseed
+              DateTime      = 2012-05-08T10:38:45
+              Sample        = 2011.1452341621
+              Line          = 16.380977898313
+              AprioriSample = 2011.1452341621
+              AprioriLine   = 16.380977898313
+            End_Group
+
+            Group = ControlMeasure
+              SerialNumber  = MRO/HIRISE/867676384:40724/RED1/2
+              MeasureType   = Candidate
+              ChooserName   = autoseed
+              DateTime      = 2012-05-08T10:38:45
+              Sample        = 13.917053834296
+              Line          = 9.5400377909342
+              AprioriSample = 13.917053834296
+              AprioriLine   = 9.5400377909342
+            End_Group
+          End_Object
+
+
+**Run this command to display the control network with cneteditor:**
+
+```sh
+cneteditor hirise_set1_autoseed.net
+```
+
+??? info "A control network in cneteditor"
+
+    ![A partial listing of a control network file using
+    cneteditor](../../assets/control-networks/cneteditor-2012.png)
+
+## Examples
+
+Examples of image footprint and tiepoints plotted with different parameter settings.
+
+??? example "Coarse *Grid*"
+
+    ![Autoseed automatically seeded tiepoints for Clementine images](
+      ../../assets/control-networks/clem-grid1-autoseed.png 
+      "Clem grid1 Autoseed"){ align=right width=450 }
+
+    **Autoseed PVL definition file for *Grid* algorithm**
+
+        Name = Grid
+        MinimumThickness = 0.0
+        MinimumArea = 10000000
+        XSpacing = 10000
+        YSpacing = 10000
+
+    The spacing increment for both X and Y directions are the same due to
+    the similar shapes of the overlap polygons. The `MinimumArea` was defined
+    to limit clustered tiepoints.
+
+??? example "Fine *Grid*"
+
+    ![Autoseed automatically seeded tiepoints for Clementine images](
+      ../../assets/control-networks/clem-grid2-autoseed.png 
+      "Clem_grid2_autoseed"){ align=right width=450 }
+
+    **Autoseed PVL definition file for *Grid* algorithm**
+
+        Name = Grid
+        MinimumThickness = 0.0
+        MinimumArea = 10000000
+        XSpacing = 5000
+        YSpacing = 5000
+
+    The spacing increment decreased by a factor of two so more tiepoints can
+    be automatically seeded. It was desirable to have more tiepoints due to
+    the fact that we are working with data near the South Pole where there
+    are more areas in shadows than normal.
+
+??? example "Coarse *Strip*"
+
+    ![Autoseed automatically seeded tiepoints for Clementine images](
+      ../../assets/control-networks/clem-strip1-autoseed.png 
+      "Clem_strip1_autoseed"){ align=right width=450 }
+
+    **Autoseed PVL definition file for *Strip* algorithm**
+
+        Name = Strip
+        MinimumThickness = 0.0
+        MinimumArea = 10000000
+        XSpacing = 10000
+        YSpacing = 10000
+
+    The spacing increment for both X and Y directions are the same due to
+    the similar shapes of the overlap polygons. The `MinimumArea` was defined
+    to limit clustered tiepoints. The result is very similar to the grid
+    algorithm and some of the tiepoints are seeded in difference locations.
+
+??? example "Fine *Strip*"
+
+    ![Autoseed automatically seeded tiepoints for Clementine images](
+      ../../assets/control-networks/clem-strip2-autoseed.png 
+      "Clem_strip2_autoseed"){ align=right width=450}
+
+    **Autoseed PVL definition file for *Strip* algorithm**
+
+        Name = Strip
+        MinimumThickness = 0.0
+        MinimumArea = 10000000
+        XSpacing = 5000
+        YSpacing = 5000
+
+    The spacing increment decreased by a factor of two so more tiepoints can
+    be automatically seeded. It was desirable to have more tiepoints due to
+    the fact that we are working with data near the South Pole where there
+    are more areas in shadows than normal. There are more tiepoints
+    clustered along polygon boundaries for this test.
+
+??? example "Limit example"
+
+    #### Starting Point
+
+    ![Clem_limit1_autoseed](
+      ../../assets/control-networks/clem-limit1-autoseed.png 
+      "Clem_limit1_autoseed"){align=right width=450 }
+
+        MinimumThickness = 0.0
+        MinimumArea = 10000000
+        MajorAxisPoints = 6
+        MinorAxisPoints = 3
+
+    -----
+
+    #### Step 1
+
+    ![Clem_limit2_autoseed](
+      ../../assets/control-networks/clem-limit2-autoseed.png 
+      "Clem_limit2_autoseed"){ align=right width=450 }
+
+        MinimumThickness = 0.0
+        MinimumArea = 10000000
+        MajorAxisPoints = 3
+        MinorAxisPoints = 1
+
+    The number of points for the major and minor axis were reduced to seed
+    fewer tiepoints.
+
+    -----
+
+    #### Step 2
+
+    ![Clem_limit3_autoseed](
+      ../../assets/control-networks/clem-limit3-autoseed.png 
+      "Clem_limit3_autoseed"){ align=right width=450 }
+
+        MinimumThickness = 0.0
+        MinimumArea = 20000000
+        MajorAxisPoints = 3
+        MinorAxisPoints = 1
+
+    The MinimumArea was doubled to eliminate tiepoints in the small
+    polygons.
+
+    -----
+
+    #### Step 3
+
+    ![Clem_limit4_autoseed](
+      ../../assets/control-networks/clem-limit4-autoseed.png 
+      "Clem_limit4_autoseed"){ align=right width=450 }
+
+        MinimumThickness = 0.0
+        MinimumArea = 50000000
+        MajorAxisPoints = 3
+        MinorAxisPoints = 1
+
+    The MinimumArea was increased again to remove more tiepoints from the
+    small polygons.
+
+    -----
+
+    #### Step 4
+
+    ![Clem_limit5_autoseed](
+      ../../assets/control-networks/clem-limit5-autoseed.png 
+    "Clem_limit5_autoseed"){ align=right width=450 }
+
+        MinimumThickness = 0.0
+        MinimumArea = 75000000
+        MajorAxisPoints = 3
+        MinorAxisPoints = 1
+
+    The MinimumArea was increased even further to eliminate tiepoints that
+    were still too close together especially along the polygon boundaries.
+
+## Seedgrid
+
+The last option is to utilize **seedgrid** instead of **autoseed** if
+**findimageoverlaps** fails. This method seeds tiepoints without relying
+on the overlap polygons. The program will seed tiepoints across a
+specified area based solely on the spacing provided by the user, either
+in x/y spacing or lat/lon increment. The output file will contain the
+PointId and the latitude and longitude coordinate associated with each
+pointid. This option is also useful if your data set includes images
+with a wide range of resolutions, or if the limb or terminator in the
+image.
+
+!!! example "Running seedgrid on the command line"
+
+    ```
+    seedgrid target=Mars minlat=0 maxlat=5 minlon=0 maxlon=6 spacing=latlon latstep=1 lonstep=1 networkid=Seedgrid1 pointid=Mars_seedgrid_??? onet=seedgrid.net description="Seedgrid latinc=1 loninc=1"
+    cnetbin2pvl from=seedgrid.net to=seedgrid_pvl.net
+    ```
+    
+
+??? abstract "Partial contents of seedgrid control network file"
+
+        Object = ControlNetwork
+          NetworkId    = Seedgrid1
+          TargetName   = Mars
+          UserName     = elee
+          Created      = 2012-06-01T11:07:49
+          LastModified = 2012-06-01T11:07:49
+          Description  = "Seedgrid latinc=1 loninc=1"
+          Version      = 3
+
+          Object = ControlPoint
+            PointType   = Free
+            PointId     = Mars_seedgrid_001
+            ChooserName = seedgrid
+            DateTime    = 2012-06-01T11:07:49
+            Ignore      = True
+
+            # AprioriLatitude = 0.0 <degrees>
+            AprioriX    = 3396190.0 <meters>
+
+            # AprioriLongitude = 0.0 <degrees>
+            AprioriY    = 0.0 <meters>
+
+            # AprioriRadius = 3396190.0 <meters>
+            AprioriZ    = 0.0 <meters>
+          End_Object
+
+          Object = ControlPoint
+            PointType   = Free
+            PointId     = Mars_seedgrid_002
+            ChooserName = seedgrid
+            DateTime    = 2012-06-01T11:07:49
+            Ignore      = True
+
+            # AprioriLatitude = 1.0 <degrees>
+            AprioriX    = 3395672.7438132 <meters>
+
+            # AprioriLongitude = 0.0 <degrees>
+            AprioriY    = 0.0 <meters>
+
+            # AprioriRadius = 3396190.0 <meters>
+            AprioriZ    = 59271.688218238 <meters>
+          End_Object
+
+The next step would be to run **cnetadd** to add new control measurement
+for the images in your input list.
+
+    ls *lev1.cub > lev1.lis
+    cnetadd cnet=seedgrid.net addlist=lev1.lis onet=seedgrid_cnetadd.net tolist=cnetadd_output.lis log=seedgrid_cnetadd.log modifiedpoints=modified.lis polygon=yes retrieval=point
+
+Continue with control registration with **pointreg** or other cnet
+programs.
+
+-----
+
+??? quote "Images on this page"
+
+    [autoseed-gui-2012.png](../../assets/control-networks/autoseed-gui-2012.png)
+    [View](../../assets/control-networks/autoseed-gui-2012.png "View")
+    (79.3 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-grid1-autoseed.png](../../assets/control-networks/clem-grid1-autoseed.png)
+    [View](../../assets/control-networks/clem-grid1-autoseed.png "View")
+    (83.8 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-grid2-autoseed.png](../../assets/control-networks/clem-grid2-autoseed.png)
+    [View](../../assets/control-networks/clem-grid2-autoseed.png "View")
+    (104 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-footprint-plot.png](../../assets/control-networks/clem-footprint-plot.png)
+    [View](../../assets/control-networks/clem-footprint-plot.png "View")
+    (141 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-limit1-autoseed.png](../../assets/control-networks/clem-limit1-autoseed.png)
+    [View](../../assets/control-networks/clem-limit1-autoseed.png "View")
+    (115 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-limit3-autoseed.png](../../assets/control-networks/clem-limit3-autoseed.png)
+    [View](../../assets/control-networks/clem-limit3-autoseed.png "View")
+    (67.7 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-limit2-autoseed.png](../../assets/control-networks/clem-limit2-autoseed.png)
+    [View](../../assets/control-networks/clem-limit2-autoseed.png "View")
+    (68.7 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-limit4-autoseed.png](../../assets/control-networks/clem-limit4-autoseed.png)
+    [View](../../assets/control-networks/clem-limit4-autoseed.png "View")
+    (82.4 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-polar-footprints.png](../../assets/control-networks/clem-polar-footprints.png)
+    [View](../../assets/control-networks/clem-polar-footprints.png "View")
+    (148 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-strip1-autoseed.png](../../assets/control-networks/clem-strip1-autoseed.png)
+    [View](../../assets/control-networks/clem-strip1-autoseed.png "View")
+    (82.6 KB)  Jesse Mapel,
+    2016-05-31 12:58 PM 
+
+    [clem-strip2-autoseed.png](../../assets/control-networks/clem-strip2-autoseed.png)
+    [View](../../assets/control-networks/clem-strip2-autoseed.png "View")
+    (108 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [cneteditor-2012.png](../../assets/control-networks/cneteditor-2012.png)
+    [View](../../assets/control-networks/cneteditor-2012.png "View")
+    (77.5 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [ctx-footprint-plot.png](../../assets/control-networks/ctx-footprint-plot.png)
+    [View](../../assets/control-networks/ctx-footprint-plot.png "View")
+    (114 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [ctx-footprint-plot-cropped-demo.png](../../assets/control-networks/ctx-footprint-plot-cropped-demo.png)
+    [View](../../assets/control-networks/ctx-footprint-plot-cropped-demo.png "View")
+    (47 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [overlap-polygon-example.png](../../assets/control-networks/overlap-polygon-example.png)
+    [View](../../assets/control-networks/overlap-polygon-example.png "View")
+    (22.9 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [narrow-sliver-polygon-example.png](../../assets/control-networks/narrow-sliver-polygon-example.png)
+    [View](../../assets/control-networks/narrow-sliver-polygon-example.png "View")
+    (84.4 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [qview-measure-for-spacing-calculation-indexcolor.png](../../assets/control-networks/qview-measure-for-spacing-calculation-indexcolor.png)
+    [View](../../assets/control-networks/qview-measure-for-spacing-calculation-indexcolor.png "View")
+    (94.5 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [qview-moreoverlap-measure-for-spacing-calculation.png](../../assets/control-networks/qview-moreoverlap-measure-for-spacing-calculation.png)
+    [View](../../assets/control-networks/qview-moreoverlap-measure-for-spacing-calculation.png "View")
+    (126 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [upc-ctx-search-for-footprint-reduced.png](../../assets/control-networks/upc-ctx-search-for-footprint-reduced.png)
+    [View](../../assets/control-networks/upc-ctx-search-for-footprint-reduced.png "View")
+    (170 KB)  Jesse Mapel,
+    2016-05-31 01:00 PM 
+
+    [clem-limit5-autoseed.png](../../assets/control-networks/clem-limit5-autoseed.png)
+    [View](../../assets/control-networks/clem-limit5-autoseed.png "View")
+    (79 KB)  Jesse Mapel,
+    2016-05-31 02:25 PM 

docs/concepts/control-networks/image-registration.md

+
+# Image Registration
+
+There two alternative paths to automatically creating a tie-point
+control network.
+
+1.  **Autoseed Path**
+      - This path will distribute and establish tie-points based on
+        polygon overlaps of a collection of images.
+      - The image coordinates for each point are immediately measured
+        with the **autoseed** application.
+      - The **footprintinit** and **findimageoverlaps** are required by
+        **autoseed**
+1.  **Seedgrid Path**
+      - A gridded pattern of tie-points are established based on
+        specified latitude/longitude values and spacing.
+      - The image coordinates for each "seeded" point are measured with
+        the **cnetadd** application.
+
+## Creating a Tie-Point Control Network
+
+| autoseed Path     | seedgrid Path |
+| ----------------- | ------------- |
+| spiceinit         | spiceinit     |
+| footprintinit     |               |
+| findimageoverlaps | seedgrid      |
+| autoseed          | cnetadd       |
+| cnetref           | cnetref       |
+| pointreg          | pointreg      |
+
+## Related ISIS3 Applications
+
+[**spiceinit**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/spiceinit/spiceinit.html)  
+[**footprintinit**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/footprintinit/footprintinit.html)  
+[**findimageoverlaps**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/findimageoverlaps/findimageoverlaps.html)  
+[**autoseed**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/autoseed/autoseed.html)  
+[**seedgrid**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/seedgrid/seedgrid.html)  
+[**cnetadd**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/cnetadd/cnetadd.html)  
+[**cnetref**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/cnetref/cnetref.html)  
+[**pointreg**](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/pointreg/pointreg.html)

docs/concepts/control-networks/multi-instrument-registration.md

+
+# Multi-Instrument Registration
+
+## Reasons for merging datasets
+
+List of useful reasons:
+
+  - Change detection
+  - Spatial / Spectral merges
+  - Understanding instrument calibration (optical distortion,
+    radiometric similarities)
+  - Multivariate statistical analysis
+  - Principal component analysis
+  - Etc., etc., etc.
+
+## Choosing the "truth"
+
+Datasets from different instruments often do not register using the raw,
+native pointing. In order to merge these datasets, they must be brought
+together by selecting one dataset as having the correct pointing or
+“truth”. The pointing for the other datasets is then adjusted to match
+the truth.
+
+Choosing the truth is dependent on the datasets being merged. First, the
+data with the known best pointing could be chosen, such as the Mars
+Global Surveyor’s MOLA. Or if simply merging HiRISE and CTX, HiRISE
+pointing is considered to be more accurate than CTX pointing.
+
+The differing resolution of the datasets is something to keep in mind.
+You will not want to attempt to register HiRISE directly to MOLA as the
+difference in resolution is too large to find a common point. In
+general, you will want to build up in resolution.
+
+
+| Resolution: | Lowest | -      | -      | -      | -   | Highest |
+| ----------  |:------:|:------:|:------:|:------:|:---:|:-------:|
+| Dataset:    | MOLA   | MOC WA | Themis | MOC NA | CTX | HiRISE  |
+
+Registering to MOLA can be difficult. Using a shaded relief version of
+MOLA (program – **shade**), and running either
+[map2map](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/map2map/map2map.html)
+or
+[map2cam](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/map2cam/map2cam.html)
+to bring MOLA into the local ground area will help.
+
+| CTX                                                                          | MOLA                                                                         |
+| ---------------------------------------------------------------------------- | -----------------------------------------------------------------------------|
+| ![CTX High Res](../../assets/control-networks/ctx-high-res.png){ width=200 } | ![MOLA Low Res](../../assets/control-networks/mola-low-res.png){ width=200 } |
+
+### Registration Tools
+
+[**deltack**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/deltack/deltack.html)
+
+  - Updates camera pointing for a single image
+  - Tie one image to another
+  - THEMIS to MOLA, HiRISE to MOC NA, HiRISE to CTX, etc.
+
+[**jigsaw**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/jigsaw/jigsaw.html)
+
+  - Simultaneously updates camera pointing for multiple images
+  - Typically used for regional or global mosaics
+
+### Initial Datasets
+
+Start with Experiment Data Records (EDRs) if possible to ensure
+consistency among the datasets for SPICE and mapping parameters such as
+planetocentric vs planetographic and positive longitude east vs west.
+
+## Merging THEMIS / CTX / HiRISE (controlled to MOLA)
+
+### Controlling THEMIS to MOLA
+
+Start with the lowest resolution dataset, which in this case is THEMIS.
+Pick a matching point between THEMIS and MOLA using qview. (Hint: It is
+easier to use a crater as a match point.)  
+Write down the latitude / longitude of the point on MOLA and the sample
+/ line of the point on the THEMIS image. Update the THEMIS pointing by
+running the ISIS3 program `deltack`.
+
+    deltack from=themis.cub lat1=molaLat lon1=molaLon samp1=themisSamp line1=themisLine
+
+This will update the themis pointing to the MOLA.
+
+### Controlling CTX to THEMIS
+
+Next, control the CTX image to the THEMIS image by picking a match point
+the same as was done between the MOLA and THEMIS. Use the THEMIS image
+that has the updated pointing (after
+[deltack](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/deltack/deltack.html)).
+
+    deltack from=ctx.cub lat1=themisLat lon1=themisLon samp1=ctxSamp line1=ctxLine
+
+### Controlling HiRISE to CTX
+
+![](../../assets/control-networks/ctx-hirise-blink.gif){ align=right width=350 }
+
+[Image: CTX/HiRISE Misregistration. Errors: ~40 samples, ~20 lines]
+
+First, control the HiRISE red ccds locally by running the ISIS3 program,
+[autoseed](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/autoseed/autoseed.html), 
+which will automatically pick match points among the red ccd’s. Then run the ISIS3 program,
+[pointreg](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/pointreg/pointreg.html), 
+which will sub-pixel register the points that autoseed picked.
+
+Next, pick a matching point between HiRISE RED5 and the CTX image with
+the updated pointing (after deltack). Record the CTX latitude /
+longitude and the red5 sample / line. This will be used as a ground
+point when running jigsaw on the red CCDs to adjust the pointing.  
+In order to use this point as a ground point, the radius is needed. Run
+the ISIS3 program,
+[campt](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/campt/campt.html)
+to get this radius.
+
+    campt from=ctx.cub lat=cxtLat lon=ctxLon type=ground
+
+This ground point can now be added to the control net file that was
+output from pointreg using any editor.
+
+    Object              = ControlPoint
+       PointType        = Ground
+       PointId          = Ground_1
+       Latitude         = -5.3320739040534
+       Longitude        = 213.71209674872
+       Radius           = 3394090.9408245
+    
+       Group            = ControlMeasure
+         SerialNumber   = MRO/HIRISE/RED5/848376111:51904/2
+         MeasureType    = Automatic
+         Sample         = 1131.92
+         Line           = 18555.3
+         ErrorLine      = 0
+         ErrorSample    = 0
+         ErrorMagnitude = 0
+         DateTime       = 2007-05-25T09:24:50
+         ChooserName    = "TLS"
+         GoodnessOfFit  = 0
+         Reference      = True
+       End_Group
+     End_Object
+
+Finally, run
+[jigsaw](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/jigsaw/jigsaw.html)
+on the HiRISE red cubes.
+
+See Also:
+
+  - controlled mosaics
+  - [jigsaw](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/jigsaw/jigsaw.html)
+
+| MOC Registered with HiRISE Red CCDs                     | MOC Registered with HiRISE Red CCDs (zoomed)                     |
+| ------------------------------------------------------- | ---------------------------------------------------------------- |
+| ![](../../assets/control-networks/moc-hirise-blink.gif) | ![](../../assets/control-networks/moc-hirise-zoomedin-blink.gif) |
+
+## Projecting all
+
+Project the THEMIS, CTX and HiRISE red images using the CTX resolution
+and latitude/longitude range.
+
+    cam2map from=ctx.cub to=ctx.equi.cub pixres=mpp resolution=5.0 
+      map=$base/templates/maps/equirectangular.map
+    
+    cam2map from=themis.cub to=themis.equi.cub map=ctx.equi.cub pixres=map defaultrange=map
+    
+    /bin/ls *RED* | sed s/.balance.cub// > red.lis
+    
+    cam2map from=\$1.balance.cub to=\$1.equi.cub map=ctx.equi.cub pixres=map defaultrange=map
+      -batch=res.lis
+    
+    /bin/ls *RED*.equi.cub > redEqui.lis
+    
+    automos fromlist=redEqui.lis mosaic=redMos.cub match=no
+
+More Information: [Learning About Map Projections](../camera-geometry-and-projections/learning-about-map-projections.md)
+
+## Problems and Issues
+
+  - Registering to MOLA can be difficult:
+    
+      - Use shaded relief if possible ([shade](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/shade/shade.html))
+      - Use
+        [map2cam](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/map2cam/map2cam.html)
+        or
+        [map2map](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/map2map/map2map.html)
+        to bring MOLA image into local ground area to help with the
+        smaller MOLA image size
+
+  - Simultaneous CTX and HiRISE observations do not register
+    
+      - Inconsistent sample/line offsets
+      - Probably have timing issues
+      - Maybe some boresight misalignment
+      - Will research this problem as more CTX data becomes available
+
+  - MOC Narrow Angle does not align with HiRISE or CTX
+    
+      - Update the MOC NA focal length
+      - MOC NA camera model has no distortion model
+      - More research needed in this area
+
+  - MRO CRISM
+    
+      - Unable to fully decipher the PDS IMAGE_PROJECTION_OBJECT
+      - No CRISM camera model in ISIS3
+      - Unable to compare HiRISE, MOC, and THEMIS to CRISM
+
+## Images on this page
+
+[mola-low-res.png](../../assets/control-networks/mola-low-res.png)
+(31.9 KB) Jesse Mapel,
+2016-05-31 02:59 PM 
+
+[ctx-high-res.png](../../assets/control-networks/ctx-high-res.png)
+(243 KB) Jesse Mapel,
+2016-05-31 02:59 PM 
+
+[ctx-hirise-blink.gif](../../assets/control-networks/ctx-hirise-blink.gif)
+(213 KB) Jesse Mapel,
+2016-05-31 03:06 PM 
+
+[moc-hirise-zoomedin-blink.gif](../../assets/control-networks/moc-hirise-zoomedin-blink.gif)
+(118 KB) Jesse Mapel,
+2016-05-31 03:12 PM 
+
+[moc-hirise-blink.gif](../../assets/control-networks/moc-hirise-blink.gif)
+(39.9 KB) Jesse Mapel,
+2016-05-31 03:12 PM 
\ No newline at end of file

mkdocs.yml

@@ -77,6 +77,11 @@ nav:
       - The Power of Spatial Filters:        concepts/image-processing/the-power-of-spatial-filters.md
       - Overview of Noise and Artifacts:     concepts/image-processing/overview-of-noise-and-artifacts.md
       - Overview of Radiometric Calibration: concepts/image-processing/overview-of-radiometric-calibration.md
+    - Control Networks:
+      - Automatic Registration:         concepts/control-networks/automatic-registration.md
+      - Autoseed:                       concepts/control-networks/autoseed.md
+      - Image Registration:             concepts/control-networks/image-registration.md
+      - Multi-Instrument Registration:  concepts/control-networks/multi-instrument-registration.md
   - Manuals: manuals/index.md
 
 extra_css: