Provided by: grass-doc_6.4.3-3_all 
NAME
r.le.setup - Interactive tool used to setup the sampling and analysis framework that will
be used by the other r.le programs.
KEYWORDS
raster, landscape structure analysis, patch index
SYNOPSIS
r.le.setup
r.le.setup help
r.le.setup map=name [vect=name] [--verbose] [--quiet]
Parameters:
map=name
Raster map to use to setup sampling
vect=name
Vector map to overlay
DESCRIPTION
r.le.setup program is used to set up the sampling and analysis framework that will be used
by the other r.le programs.
NOTES
Full instructions can be found in the r.le manual (see "REFERENCES" section below).
The first menu allows the user to define a rectangular sampling frame, select how sampling
will be done (regions, sampling units, moving window), setup the limits for groups and
classes, and change the color table. Use the left mouse button to make your choice.
Information about the structure of the landscape is obtained by overlaying a set of
sampling areas on top of a specified part (the sampling frame of a map layer, and then
calculating specific structural measures for the part of the map layer that corresponds to
the area in each sampling area.
To setup a sampling frame click on SAMPLING FRAME in the main menu. The program will ask
"Will the sampling frame (total area within which sampling units are distributed) be the
whole map? (y/n) [y]" Just hit a carriage return to accept the default, which is to use
the whole map. You do not need to setup a sampling frame if you want to use the whole
map, as this is the default. To setup a different sampling frame type "n" in response to
this question. Then use the mouse and a rubber band box to outline a rectangular sampling
frame on screen. This box will be moved to the nearest row and column of the map. You
will be asked last whether you want to "Refresh the screen before choosing more setup?"
If you don't like the sampling frame you just setup, answer yes to this question, then
click on SAMPLING FRAME again to redo this part of the setup. This sampling frame will be
used in all subsequent setup procedures unless you change it. You can change it at any
time by simply clicking on SAMPLING FRAME again.
A sampling area may be one of four things. First, it is possible to treat the entire map
layer as the one (and only) sampling area. Second, if the map layer can be divided into
meaningful geographical regions, then it is possible to treat the regions themselves as
sampling areas. The third option is that the sampling areas may be sampling units of
fixed shape and size (also called scale) that are placed within the map layer as a whole.
The fourth and final option is that the sampling area may be moved systematically across
the map as a moving window.
If regions are to be used as the sampling areas , then the user can use r.le.setup to draw
regions or any existing map of regions can simply be used directly. To draw regions and
create a new regions map in r.le.setup select "REGIONS" from the first r.le.setup menu,
and the user is asked to do the following:
1. "ENTER THE NEW REGION MAP NAME:" Only a new raster map name is acceptable. The user
can type LIST to find out the existing raster map names in this location and mapset.
2. "PLEASE OUTLINE REGION # 1" The user should move the mouse cursor into the graphic
monitor window and use the mouse buttons as instructed:
- Left button: where am I.to display the current coordinates of the cursor.
- Middle button: Mark start (next) point. to enter a vertex of the region boundary.
- Right button: Finish region-connect to 1st point to close the region boundary by setting
the last vertex to be equal to the first one.
3. A "REGION OPTIONS:" menu is displayed and the user should use the mouse to select one
of the options:
- "DRAW MORE": repeat the above process and setup another region.
- "START OVER": abandon the previous setup and start all over again.
- "DONE-SAVE": save the regions outlined so far and exit this procedure.
- "QUIT-NO SAVE": quit the procedure without saving the regions.
Once the "DONE-SAVE" option is selected, the new raster map of the sampling regions is
generated. It is displayed on the monitor window for several seconds, the monitor window
is refreshed, the main menu is displayed again, and the program is ready for other setup
work. Note that you cannot draw regions in areas outside the mask, if a mask is present
(see r.mask command).
The user can also use the GRASS r.digit or v.digit programs to digitize circular or
polygonal regions and to create a sampling regions map without using r.le.setup. Or, as
mention above, an existing raster map can be used as a regions map.
If sampling units are to be used as the sampling areas (Fig. 2), then choose "SAMPLING
UNITS" from the first r.le.setup menu. The program checks the r.le.para subdirectory for
an existing "units" file from a previous setup session and allows the user to rename this
file (to save it) before proceeding. The r.le.setup program will otherwise overwrite the
"units" file. Then the following choice is displayed followed by a series of other
choices:
Which do you want to do?
(1) Use the keyboard to enter sampling unit parameters
(2) Draw the sampling units with the mouse
Enter 1 or 2:
When sampling units are defined using the keyboard, the user inputs the shape and size
(scale) of the sampling units by specifying dimensions in pixels using the keyboard. When
sampling units are drawn with the mouse, the user clicks the mouse to define the sampling
units in the GRASS monitor window, and then actually places the sampling units for each
scale onto the map. By placing the units with the mouse the user can directly determine
the method of sampling unit distribution as well as the shape, size, and number of
sampling units.
If the choice is made to define sampling units using the keyboard, the following series of
questions must be answered:
How many different SCALES do you want (1-15)?
The user is asked to specify the number of scales that will be used. The r.le programs
allow the user to simultaneously sample the same map with the same measures using sampling
areas of different sizes. Currently there can be between 1 and 15 scales that can be
sampled simultaneously. Substantial output can be produced if many scales are used.
Sampling units must be placed spatially into the landscape. There are five options for
doing this :
Random nonoverlapping
Sampling units are placed in the landscape by randomly choosing numbers that specify the
location of the upper left corner of each sampling unit, subject to the constraint that
successive sampling units not overlap other sampling units or the edge of the landscape,
and that they must be entirely within the area defined by the mask (see r.mask command) if
one exists.
Systematic contiguous
Sampling units are placed side by side across the rows. The user will be able to enter a
row and column to indicate where the upper left corner of the systematic contiguous
framework should be placed. Rows are numbered from the top down beginning with row 1 of
the sampling frame. Columns are numbered from left to right, beginning with column 1 of
the sampling frame. A random starting location can be obtained by using a standard random
number table to choose the starting row and column. The r.le.setup program does not avoid
placing the set of sampling units over areas outside the mask. The user will have to make
sure that sampling units do not extend outside the mask by choosing a particular starting
row and column or by drawing a sampling frame before placing the set of sampling units.
Systematic noncontiguous
The user must specify the starting row and column as in #2 above and the amount of spacing
(in pixels) between sampling units. Horizontal and vertical spacing are identical.
Sampling units are again placed side by side (but spaced) across the rows. As in #2 the
program does not avoid placing sampling units outside the masked area; the user will have
to position the set of units to avoid areas outside the mask.
Stratified random
The strata are rectangular areas within which single sampling units are randomly located.
The user must first specify the starting row and column as in #2 above. Then the user
must specify the number of strata in the horizontal and vertical directions. As in #2
the program does not avoid placing sampling units outside the masked area; the user will
have to position the set of units to avoid areas outside the mask.
Centered over sites
The user must specify the name of a sitefile containing point locations. A single
sampling unit is placed with its center over each site in the site file. This is a useful
approach for determining the landscape structure around points, such as around the
location of wildlife observations.
The user is prompted to enter a ratio that defines the shape of the sampling units.
Sampling units may have any rectangular shape, including square as a special case of
rectangular. Rectangular shapes are specified by entering the ratio of columns/rows
(horizontal dimension/vertical dimension) as a real number. For example, to obtain a
sampling unit 10 columns wide by 4 rows long specify the ratio as 2.5 (10/4).
Recommended maximum SIZE is m in x cell total area.
What size (in cells) for each sampling unit of scale n?
The user is then given the recommended maximum possible size for a sampling unit (in
pixels) and asked to input the size of sampling units at each scale. Sampling units can
be of any size, but the maximum size is the size of the landscape as a whole. All the
sampling units, that make up a single sampling scale, are the same size. After specifying
the size, the program determines the nearest actual number of rows and columns, and hence
size, that is closest to the requested size, given the shape requested earlier.
The nearest size is x cells wide X y cells high = xy cells
Is this size OK? (y/n) [y]
Maximum NUMBER of units in scale n is p?
What NUMBER of sampling units do you want to try to use?
The maximum number of units that can be placed over the map, given the shape and size of
the units, is then given. The user can then choose the number of sampling units to be
used in the map layer. It may not always be possible to choose the maximum number,
depending upon the shape of the sampling units. In the case of systematic contiguous and
noncontiguous, the program will indicate how many units will fit across the columns and
down the rows. The user can then specify a particular layout (e.g., 6 units could be
placed as 2 rows of 3 per row or as 3 rows of 2 per row).
Is this set of sampling units OK? (y/n) [y]
Finally, the set of sampling units is displayed on the screen (e.g., Fig. 1) and the user
is asked whether it is acceptable. If the answer is no, then the user is asked if the
screen should be refreshed before redisplaying the menu for "Methods of sampling unit
distribution" so that the user can try the sampling unit setup again.
The choice is made to define sampling units using the mouse, then the following menu for
use with the mouse is displayed:
Outline the standard sampling unit of scale n.
Left button: Check unit size
Middle button: Move cursor
Right button: Lower right corner of unit here
The user can then use the mouse and the rubber band box to outline the standard sampling
unit. Once it has been outlined, the number of columns and rows in the unit, the ratio of
width/length and the size of the unit, in cells, will be displayed. After this first unit
is outlined, then a new menu is displayed:
Outline more sampling units of scale n?
Left button: Exit
Middle button: Check unit position
Right button: Lower right corner of next unit here
The user can then place more units identical to the standard unit by simply clicking the
right mouse button where the lower right corner of the unit should be placed. The rest of
the rubber band box can be ignored while placing additional units. The program is set up
so that units cannot be placed so they overlap one another, so they overlap the area
outside the mask, or so they overlap the edge of the sampling frame. Warning messages are
issued for all three of these errors and a sampling unit is simply not placed.
Using this procedure a rectangular "window" or single sampling area is moved
systematically across the map to produce a new map (Fig. 2,3). This sampling procedure
can only be used with the measures that produce a single value or with a single class or
group when measures produce distributions of values (Table 1). The first class or group
specified when defining class or group limits (section 2.3.2.) is used if distributional
measures are chosen with the moving window sampling method. In this case, the user should
manually edit the r.le.para/recl_tb file so that the desired group is listed as the first
group in this file.
Sampling begins with the upper left corner of the window placed over the upper left corner
of the sampling frame. It is strongly recommended that the user read the section on the
GRASS mask (section 2.2.2) prior to setting up the moving window, as this mask can be used
to speed up the moving window operation. The value of the chosen measure is calculated
for the window area. This value is assigned to the location on the new map layer
corresponding to the center pixel in the window if the window has odd (e.g. 3 X 3)
dimensions. The value is assigned to the location on the new map layer corresponding to
the first pixel below and to the right of the center if the window has even dimensions
(e.g. 6 X 10). If this pixel has the value "0," which means "no data" in GRASS, then this
pixel is skipped and a value of "0" is assigned to the corresponding location in the new
map. The window is then moved to the right (across the row) by one pixel, and the process
is repeated. At the end of the row, the window is moved down one pixel, and then back
across the row. This option produces a new map layer, whose dimensions are smaller by
approximately (m-1)/2 rows and columns, where m is the number of rows or columns in the
window.
If the "MOVE-WINDOW" option in the main menu is selected, first the program checks for an
existing "move_wind" file, in the r.le.para subdirectory, containing moving window
specifications from a previous session. The user is given the option to avoid overwriting
this file by entering a new file name for the old "move_wind" file. Users should be aware
that moving window analyses are very slow, because a large number of sampling units are,
in effect, used. See the appendix on "Time needed to complete analyses with the r.le
programs" for some ideas about how moving window size and sampling frame area affect the
needed time to complete the analyses.
The r.le programs r.le.dist and r.le.patch allow the attribute categories in the input map
to be reclassed into several attribute groups, and reports the analysis results by each of
these attribute groups. It is necessary to setup group limits for all measures that say
"by gp" when typing "r.le.dist help" or "r.le.patch help" at the GRASS prompt. The same
reclassing can be done with the measurement indices (e.g., size), except that each
"cohort" (class) of the reclassed indices is called an index class instead of a group. It
is also necessary to setup class limits for all measures that say "by class" when typing
"r.le.dist help" or "r.le.patch help" at the GRASS prompt.
Group/class limits are setup by choosing "GROUP/CLASS LIMITS" from the main menu upon
starting r.le.setup, or you can create the files manually using a text editor. The
program checks for existing group/class limit files in subdirectory r.le.para and allows
the user to rename these files prior to continuing. If the files are not renamed the
program will overwrite them. The files are named recl_tb (attribute group limits), size
(size class limits), shape_PA (shape index class limits for perimeter/area index),
shape_CPA (shape index class limits for corrected perimeter/area index), shape_RCC (shape
index class limits for related circumscribing circle index), and from_to (for the
r.le.dist program distance methods m7-m9).
Attribute groups and index classes are defined in a different way. In the r.le programs
attribute groups are defined as in the following example:
1, 3, 5, 7, 9 thru 21 = 1 (comment)
31 thru 50 = 2 (comment)
end
In this example, the existing categories 1, 3, 5, 7, {9, 10, ... 20, 21} are included in
the new group 1, while {31, 32, 33, ..., 49, 50} are included in the new group 2. The
characters in bold are the "key words" that are required in the definition. Each line is
called one "reclass rule".
The GRASS reclass convention is adopted here with a little modification (see "r.reclass"
command in the GRASS User's Manual). The difference is that r.le only allows one rule for
each group while the GRASS r.reclass command allows more than one. The definition of
"from" and "to" groups is simply the extension of the GRASS reclass rule. The advantage
of using the GRASS reclass convention is that the user can generate a permanent reclassed
map, using GRASS programs, directly from the r.le setup results.
The r.le measurement index classes are defined by the lower limits of the classes, as in
the following example:
0.0, 10.0, 50.0, 200.0, -999
This means:
if v >= 0.0 and v < 10.0 then v belongs to index class 1;
if v >= 10.0 and v < 50.0 then v belongs to index class 2;
if v >= 50.0 and v < 200.0 then v belongs to index class 3;
if v >= 200.0 then v belongs to index class 4;
where v is the calculated index value and -999 marks the end of the index class
definition. The measurement index can be the size index, one of the three shape indices,
or one of the three distance indices. The program is currently designed to allow no more
than 25 attribute groups, 25 size classes, 25 shape index classes, and 25 distance index
classes. As an alternative, the user may want to permanently group certain attributes
prior to entering the r.le programs. For example, the user may want to group attributes
1-10, in a map whose attributes are ages, into a single attribute representing young
patches. The user can do this using the GRASS r.reclass and r.resample commands, which
will create a new map layer that can then be analyzed directly (without setting up group
limits) with the r.le programs.
REFERENCES
Baker, W.L. and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape
structure using the GRASS geographical information system. Landscape Ecology
7(4):291-302.
The r.le manual: Quantitative analysis of landscape structures (GRASS 5; 2001)
SEE ALSO
r.le.patch, r.le.pixel, r.le.trace
AUTHOR
William L. Baker Department of Geography and Recreation University of Wyoming Laramie,
Wyoming 82071 U.S.A.
Last changed: $Date: 2010-01-20 05:26:08 -0800 (Wed, 20 Jan 2010) $
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