Once a new model has been created (Fig. 3), the next step is to select input layers (i.e., input grids). Note, if you opened a saved model, you can modify the input parameters as well.
In the left pane of the model dialog window make sure the Input layers tab is selected. The top half of the left pane is labeled Batch management and this is where you select the input grids either singly (Add layer) or as a previously defined batch file (Import batch), and/or edit or modify the input layers (Edit layer info), as follows:
- Add layer -- Click Add layer to add a grid to the model (to be analyzed). This will open the dialog shown in figure 4.
Figure 4. Dialog for adding a grid to the model.
First, select a Data type by clicking on the corresponding line in the left pane. FRAGSTATS accepts several types of input image data formats. See Overview--Data Formats section for details. Briefly, all input images should be integer grids (i.e., each cell should be assigned an integer value corresponding to its class membership or patch type). Note, assigning the value 0 to a class is problematic if that class exists in the landscape border, since negative zeros are not allowed. In addition, all input grids should consist of square cells with the measurement units in meters.
Choose one of the following:
- Geotiff grid -- geotiff file (contains header).
- Raw ASCII grid -- ascii file without header.
- Raw 8-bit integer grid -- binary file without header.
- Raw 16-bit integer grid -- binary file without header.
- Raw 32-bit integer grid -- binary file without header.
Second, select a dataset by entering the full path and file name of the input grid in the Dataset name box, or click the navigate to button (...) and navigate to and select the desired input grid of the corresponding data type. Note, the navigation window is context sensitive, so that only show files that have the appropriate extension will be displayed by default: (1) geotiff file: *.tif or *.tiff; (2) raw ASCII file: *.asc; and (3) raw 8-, 16-, and 32-bit binary files: *.raw. However, you can change the extension filter to "all types" in the navigation dialog by clicking the drop-down arrow to the right of the file name. Importantly, see the discussion on Data Formats above before trying to import data layers.
Lastly, depending on the Data type, you will need to enter some information about the grid. Note, only the text boxes that are required for the corresponding Data type will be active; all others will be grayed out. Fill in all text boxes that are active.
- Row count (y) -- Enter the number of rows in the input image. This is only required if the input Data type is ASCII or Binary.
- Column count (x) -- Enter the number of columns in the input image. This is only required if the input Data type is ASCII or Binary.
- Cell size(in meters) -- Enter the size of cells in meters in the input image. Cells must be square. The length of 1 side of a cell should be input. This is only required if the input Data type is ASCII or Binary.
- Background value -- [Optional] Enter the value to be used for background cells. This is only required if there are cells interior or exterior to the landscape of interest that you want to treat as background (see Overview). Note, it is possible to specify multiple class values as background, but this must be done in the Class descriptors table (see below). When this is done, the designated classes are reclassified to the background value specified here in the grid attributes. Note, all background cells are assigned this cell value, and this can have important implications if you select core area metrics, edge contrast metrics, or the similarity metric. Specifically, if you wish to specify a non-zero edge depth or edge contrast weight to background edges or a non-unity similarity weight, you must include this background class value in the pairwise combination of classes given in the edge depth, edge contrast, and similarity weight files (see below).
- Edit layer info -- Click Edit layer info> to reopens the dialog shown in figure 4 and edit any of the grid parameters.
- Remove layer -- Click Remove layer to remove the selected grid from the batch manager.
- Remove all layers -- Click Remove all layers to remove all the grids from the batch manager.
- Export batch -- Click Export batch to export the loaded grids as a batch file (.fbt) in the format described below.
- Import batch -- Click Import batch to load a batch file that already contains a list of input grids to be analyzed. The batch file option is convenient if you want to analyze many landscapes. If you select this option, you must specify a properly formatted batch file by navigating to the appropriate file. Note, FRAGSTATS uses the file extension .fbt for batch files and will look for files with this extension by default when navigating. The .fbt extension is not mandatory, but using it can help keep files organized.
The batch file must be a comma-delimited ASCII file. Each line should specify the input landscape file name, cell size, background value, number of rows, number of columns, and input data type, in that order. The syntax for this file is as follows:
InputFileName, CellSize, Background, Rows, Columns, InputDataType
- InputFileName is the full path and file name of the input landscape.
- CellSize is an integer value corresponding to the cell size (in meters).
- Background is an integer value corresponding to the designated background value. Note, any class designated as background in the Class descriptors file (see below) will be reclassified to this class value and treated as background.
- Rows is an integer value corresponding to the number of rows in the input image.
- Columns is an integer value corresponding to the number of columns in the input image.
- InputDataType is a character string identifying the input data format, with the following options corresponding to the various input data format types:
The batch file should contain a record for each input landscape, and all arguments should be separated by a comma. The parameter values should reflect the input Data type for each input landscape; if is ASCII or BINARY, then the record must contain all of the parameters specified above. However, if it is GeoTIFF, then the record need only contain the input landscape file name and the background value; the remaining parameters should be assigned "x", as illustrated in the following example:
D:\Foo\Bar\ASCIIfilename, 25, 999, 250, 300, IDF_ASCII
D:\Foo\Bar\ASCIIfilename, 25, 999, 250, 300, IDF_8BIT
D:\Foo\Bar\16BITfilename, 25, 999, 250, 300, IDF_16BIT
D:\Foo\Bar\32BITfilename, 25, 999, 250, 300, IDF_32BIT
D:\Foo\Bar\GeoTIFFfilename, x, 999, x, x, IDF_GeoTIFF
NOTE, regardless of input data type, the cell size, background value, rows and columns can be different for each input landscape. Also, running from a batch file does not eliminate the necessity of completing the parameterization of FRAGSTATS; it only provides a mechanism for running FRAGSTATS on more than one landscape without having to parameterize and run each landscape separately. Specifically, you still must set analysis parameters and select and parameterize the individual metrics, as described below. The batch file only specifies the file name, input data type, and grid attributes for each input landscape; all other parameters must be specified according to the directions below.