Contents

Step 4. Specifying Common Tables [optional]

 

Once a new model has been created (Fig. 3) and the input grids have been added or imported from a batch file, the next optional step is to specify common tables (in the bottom left pane of the model dialog, figure 3) used to describe and attribute the classes (patch types) and assign edge depths, edge contrasts, and similarity coefficients used in the corresponding functional metrics, as described below:

  • Class descriptors [Optional] -- Click on the corresponding browse button and navigate to and select the desired file. Note, FRAGSTATS uses the file extension .fcd for class descriptor files and will look for files with this extension by default when navigating. The .fcd extension is not mandatory, but using it can help keep files organized. Each record in the file should contain a numeric class (patch type) value, the character descriptor for that patch type, a logical status indicator, and a local background indicator. The syntax for this comma-delimited ASCII file is as follows:

    ID, Name, Enabled, Background

    • ID -- is an integer value corresponding to a class value in the landscape.
    • Name -- is a descriptive name of the class; descriptive names can be any length and contain any characters, including spaces, but cannot include commas. This descriptive name is reported in all patch and class output files for the variable TYPE.
    • Enabled -- can take on the values: "true", or "t"; and "false", or "f" (upper or lower case), and determines whether the corresponding class should be processed and added to the results or simply ignored in the output files. A "true" or "t" indicates that the class is enabled and should be output in the patch and class output files. A "false" or "f" indicates that the class is disabled and should not be output. Note, enabling or disabling a class does not effect the computation of landscape metrics; disabled classes are still included, as necessary, in the computation of landscape metrics. Although there is some savings of computer processing by disabling a class, the primary effect is on the output. This feature allows you to "turn off" classes that you are not interested in so that you don't have to view their statistics in the output files.
    • Background -- can take on the values: true, or t; and false, or f (upper or lower case), and determines whether the corresponding class should be reclassified and treated as background (i.e., assigned the background value specified in the grid attributes). Note, classifying a class as background will have an effect on many landscape metrics (see Overview).

    The class descriptors file should contain a record for each class in the input landscape, and all arguments should be separated by a comma or space(s). For example:

    1, shrubs, true, false
    2, conifers, true, false
    3, deciduous, true, false
    4, other, false, true
    Etc.

    Importantly, the class descriptors file can contain additional classes that do not exist in the input landscape, but all classes that exist should be listed in this file.

    In summary, the class descriptors file allows you to do three things: (1) specify character descriptors for each class in order to facilitate interpretation of the output files, (2) limit the output files to only the classes of interest, and (3) reclassify classes to background.

    NOTE, if the class descriptors file is provided, the class names will be written to the output files. Otherwise, the class IDs (numeric patch type codes) will be written to the output files.

  • Edge depth [Optional] -- The Edge depth table displays the "depth-of-edge" values to use in determining what constitutes the core of a patch in the core area metrics and is only relevant if one or more core area metrics are selected (see below). There are two options:
    1. Fixed edge depth -- If you wish to treat all edges the same, then check the corresponding check box (Use fixed depth), click the (...) button and enter a non-zero distance (in meters). By default this box contains a zero, but you should enter a non-zero distance because a zero depth-of-edge would result in the core area being equal to patch area, and thus would be redundant.

    2. Variable edge depths -- Alternatively, you can specify separate edge depths for each edge type (i.e., each pairwise combination of patch types). Click on the corresponding browse button and navigate to and select the desired file. Note, FRAGSTATS uses the file extension .fsq for edge depth files and will look for files with this extension by default when navigating. The .fsq extension is not mandatory, but using it can help keep files organized. The syntax for this comma-delimited ASCII file is as follows:

      FSQ_TABLE
      CLASS_LIST_LITERAL(1stClassName, 2ndClassName, etc.)
      CLASS_LIST_NUMERIC(1stClassID, 2ndClassID, etc.)
      EdgeDepth_1-1, EdgeDepth_1-2, etc.
      EdgeDepth_2-1, EdgeDepth_2-2, etc.
      Etc.

      • Comment lines start with # and are allowed anywhere in the table.
      • FSQ_TABLE must be specified in the first line.
      • Two types of class lists are allowed CLASS_LIST_LITERAL() and CLASS_LIST_NUMERIC(), but only the first one encountered is considered, so you only need one of these lines.
      • Literal class names (1stClassName, 2ndClassName, etc.,) are character strings and cannot contain spaces.
      • Class Ids (1stClassID, 2ndClassID, etc.) are integer values corresponding to class values in the grid.
      • With regards to the edge depths, the order of rows and column is the one specified in the CLASS_LIST_LITERAL() or CLASS_LIST_NUMERIC(), whichever comes first. EdgeDepth_i-j is an integer value giving the depth-of-edge (in meters) for the corresponding edge type (i.e., for the focal class designated by the ith ClassID and the adjacent class designated by the jth ClassID). Note, it is advisable but not necessary to provide edge depths in increments equal to the cell size, because FRAGSTATS will always round up or down to the nearest cell when applying the edge mask (see Overview).

      The edge depth entries must be a square matrix (i.e., same number of rows and columns), must have the same list and order of ClassIDs as given in the CLASS_LIST_LITERAL or CLASS_LIST_NUMERIC, should contain a record for each unique pairwise combination of patch types (classes) in the input landscape (any missing class must be missing in both the rows and columns and will be assigned a zero edge depth for all edges involving that class), and all arguments should be separated by a comma. For example, given four classes, the following file would be suitable:

      FSQ_TABLE
      CLASS_LIST_LITERAL(A, B, BG, C, D)
      CLASS_LIST_NUMERIC(2, 3, 4, 5, 6)
      0, 30, 30, 30, 30
      70, 0, 40, 40, 40
      30, 40, 0, 50, 50
      30, 40, 50, 0, 60
      30, 40, 50, 60, 0

      NOTE, this table can be created and managed using any text editor and then simply saved as a comma delimited file (.csv).

      NOTE, the edge depth matrix can be asymmetrical; that is, upper right and lower left triangles do not need to mirror each other. Accordingly, it is important to realize that the rows represent the focal class and the columns represent the adjacent or abutting class. Let's consider the edge depths for focal class A (or ID=2) in the example above, given in the first row of the edge depth matrix. An adjacent patch of class B (or ID=3) has an edge depth of 30 m; i.e., has an edge effect that penetrates 30 m into the patch of class A. Conversely, class A penetrates 70 m into class B (row 2, column 1). Thus, the edge effect penetrates less into class A than into class B. This asymmetry may be important in some applications; for example, when urban edge effects penetrate deeply into forest, but forest edge effects penetrate very little, if at all, into urban areas.

      NOTE, the diagonals are typically given a zero edge depth, but it is possible to specify a non-zero diagonal. However, the only situation in which a patch can abut a patch of the same class is along the landscape boundary when a landscape border is present (see Overview). In this case, it is possible to specify a non-zero edge depth, although in most cases it would not be logical to do so.

      NOTE, if you have background in the image, you need to include the background class value specified in the grid properties during data import, otherwise all background edges will be given a zero edge depth.

     

  • Edge contrast [Optional] -- The Edge contrast table displays the "edge contrast" values to use in determining the magnitude of contrast for each edge type (i.e., each pairwise combination of patch types) and is only relevant if one or more edge contrast metrics are selected (see below). Click on the corresponding browse button and navigate to and select the desired file. Note, FRAGSTATS uses the file extension .fsq for edge contrast files and will look for files with this extension by default when navigating. The .fsq extension is not mandatory, but using it can help keep files organized. The syntax for this comma-delimited ASCII file is as follows:

    FSQ_TABLE
    CLASS_LIST_LITERAL(1stClassName, 2ndClassName, etc.)
    CLASS_LIST_NUMERIC(1stClassID, 2ndClassID, etc.)
    ContrastWeight_1-1, ContrastWeight_1-2, etc.
    ContrastWeight_2-1, ContrastWeight_2-2, etc.
    Etc.

    • Comment lines start with # and are allowed anywhere in the table.
    • FSQ_TABLE must be specified in the first line.
    • Two types of class lists are allowed CLASS_LIST_LITERAL() and CLASS_LIST_NUMERIC(), but only the first one encountered is considered.
    • Literal class names (1stClassName, 2ndClassName, etc.,) are character strings and cannot contain spaces.
    • Class Ids (1stClassID, 2ndClassID, etc.) are integer values corresponding to class values in the grid.
    • With regards to the contrast weights, the order of rows and column is the one specified in the CLASS_LIST_LITERAL() or CLASS_LIST_NUMERIC(), whichever comes first. ContrastWeight_i-j is an integer value giving the depth-of-edge (in meters) for the corresponding edge type (i.e., for the focal class designated by the ith ClassID and the adjacent class designated by the jth ClassID).
    • Contrast weights must range from 0 (no contrast) to 1 (maximum contrast).

    The edge contrast entries must be a square matrix (i.e., same number of rows and columns), must have the same list and order of ClassIDs as given in the CLASS_LIST_LITERAL or CLASS_LIST_NUMERIC, should contain a record for each unique pairwise combination of patch types (classes) in the input landscape (any missing class must be missing in both the rows and columns and will be assigned an edge contrast weight of one (maximum)), and all arguments should be separated by a comma. For example, given four classes the following file would be suitable:

    FSQ_TABLE
    CLASS_LIST_LITERAL(A, B, BG, C, D)
    CLASS_LIST_NUMERIC(2, 3, 4, 5, 6)
    0, 0.2, 0, 0.4, 0.6
    0.2, 0, 0, 0.2, 0.4
    0, 0, 0, 0, 0
    0.4, 0.2, 0, 0, 0.2
    0.6, 0.4, 0, 0.2, 0

    NOTE, this table can be created and managed using any text editor and then simply saved as a comma delimited file (.csv).

    NOTE, this matrix must be symmetrical; that is, upper right and lower left triangles must be mirror images, because edge contrast is a property of the edge itself.

    NOTE, the diagonals are typically given a zero edge contrast since there is no contrast between patches of the same type, although any value can be specified. However, the only situation in which a patch can abut a patch of the same class is along the landscape boundary when a landscape border is present (see Overview). In this case, it is possible to specify a nonzero edge contrast, although in most cases it would not be logical to do so.

    NOTE, if you have background in the image, you need to include the background class value specified in the grid properties during data import, otherwise all background edges will be given a zero edge contrast.

  • Similarity [Optional] -- The Similarity table displays the "similarity" values to use in determining the similarity between each pairwise combination of patch types and is only relevant if the similarity index is selected (see below). Click on the corresponding browse button and navigate to and select the desired file. Note, FRAGSTATS uses the file extension .fsq for similarity weights files and will look for files with this extension by default when navigating. The .fsq extension is not mandatory, but using it can help keep files organized. The syntax for this comma-delimited ASCII file is as follows:

    FSQ_TABLE
    CLASS_LIST_LITERAL(1stClassName, 2ndClassName, etc.)
    CLASS_LIST_NUMERIC(1stClassID, 2ndClassID, etc.)
    SimilarityWeight_1-1, SimilarityWeight_1-2, etc.
    SimilarityWeight_2-1, SimilarityWeight_2-2, etc.
    Etc.

    • Comment lines start with # and are allowed anywhere in the table.
    • FSQ_TABLE must be specified in the first line.
    • Two types of class lists are allowed CLASS_LIST_LITERAL() and CLASS_LIST_NUMERIC(), but only the first one encountered is considered.
    • Literal class names (1stClassName, 2ndClassName, etc.,) are character strings and cannot contain spaces.
    • Class Ids (1stClassID, 2ndClassID, etc.) are integer values corresponding to class values in the grid.
    • With regards to the similarity weights, the order of rows and column is the one specified in the CLASS_LIST_LITERAL() or CLASS_LIST_NUMERIC(), whichever comes first. SimilarityWeight_i-j is an integer value giving the similarity weight for the for the focal class designated by the ith ClassID and the adjacent class designated by the jth ClassID).
    • Similarity weights must range from 0 (minimum similarity) to 1 (maximum similarity).

    The similarity entries must be a square matrix (i.e., same number of rows and columns), must have the same list and order of ClassIDs as given in the CLASS_LIST_LITERAL or CLASS_LIST_NUMERIC, should contain a record for each unique pairwise combination of patch types (classes) in the input landscape (any missing class must be missing in both the rows and columns and will be assigned a zero similarity (minimum) for all comparisons involving that class), and all arguments should be separated by a comma. For example, given four classes the following file would be suitable:

    FSQ_TABLE
    CLASS_LIST_LITERAL(A, B, BG, C, D)
    CLASS_LIST_NUMERIC(2, 3, 4, 5, 6)
    1, 0.8, 0, 0.6, 0.4
    0.2, 1, 0, 0.8, 0.6
    0, 0, 1, 0, 0
    0.6, 0.8, 0, 1, 0.8
    0.4, 0.6, 0, 0.8, 1

    NOTE, this table can be created and managed using any text editor and then simply saved as a comma delimited file (.csv).

    NOTE, the similarity matrix can be asymmetrical; that is, upper right and lower left triangles do not need to mirror each other. Accordingly, it is important to realize that the rows represent the focal class and the columns represent the adjacent or abutting class. Let's consider the similarity weights for focal class A (or ID=2) in the example above, given in the first row of the similarity matrix. Given a focal patch of class A, a neighboring patch of type B (or ID=3) has a similarity of 0.8. Conversely, given a focal patch of class B, a neighboring patch of class A has a similarity of 0.2. In most cases, however, it is more logical to think of similarity in terms of symmetrical weights.

    NOTE, the diagonals are typically given a similarity weight of one, because the similarity of two patches of the same class is generally assumed to be maximum, but it is possible to specify a different value.

    NOTE, if you have background in the image, you need to include the background class value specified in the grid properties during data import, otherwise all background edges will be given a zero weight.