# GMT C API

## Introduction

### Preamble

GMT 4 programs contain all the high-level functionality.

Prior to version 5, the bulk of GMT functionality was coded directly in the standard GMT C program modules (e.g., `surface.c`, `grdimage.c`, etc.). The GMT library only offered access to low-level functions from which those high-level GMT programs were built. The standard GMT programs have been very successful, with tens of thousands of users world-wide. However, the design of the main programs prevented developers from leveraging GMT functionality from within other programming environments since access to GMT tools could only be achieved via system calls [1]. Consequently, all data i/o had to be done via temporary files. The design also prevented the GMT developers themselves from taking advantage of these modules directly. For instance, the tool legend needed to make extensive use of system calls to plot and text in order to plot the lines, symbols and text that make up a map legend, making it a very awkward program to maintain.

GMT 5 programs contain all the high-level functionality.

Starting with GMT version 5, all standard GMT programs have been rewritten into separate function “modules” invoked by a single driver program called `gmt.c`. The gmt executable simply calls the corresponding GMT modules; it is these modules that do all the work. These new functions have been placed in a new GMT high-level API library and can be called from a variety of environments (C/C++, FORTRAN, Julia, Python, MATLAB, Visual Basic, R, etc.) [2]. For example, the main program `blockmean.c` has been reconfigured as a high-level function `GMT_blockmean()`, which does the actual spatial averaging and can pass the result back to the calling program (or write it to file). The previous behavior of `blockmean.c` is achieved by calling `gmt blockmean`, i.e., the module is now just the first argument to the gmt executable. For backwards compatibility with older GMT (4) scripts we optionally install numerous symbolic links to the gmt executable with names such as blockmean, plot, surface, etc. The gmt executable is smart enough to understand when it is being invoked via one of these links and then knows which module to call upon. Consequently, `blockmean.c` and other files do in fact no longer exist.

GMT 5 API showing current and future external environments.

### The i/o abstraction layer

In order for the API to be as flexible as possible we have generalized the notions of input and output. Data that already reside in an application’s memory may serve as input to a GMT module and we refer to such data as “Virtual Files”. Other sources of input may be file pointers and file descriptors (as well as the standard mechanism for passing file names). For standard data table i/o, the GMT API takes care of the task of assembling any combination of files, pointers, and memory locations into a single virtual data set from which the GMT module may read (a) all records at once into memory, or (b) read one record at a time. Likewise, GMT functions may write their output to a virtual destination, which might be a memory location in the user’s application (another Virtual File), a file pointer or descriptor, or an output file. The GMT modules are unaware of these details and simply read from a “source” and write to a “destination”. Thus, the standard concept of file-based input/output so familiar to any GMT user carries over to the API, except for the generalization that files can be virtual files already in memory. Because of this design we will see that we need to associate these virtual files with special filenames that we may pass to modules, and the modules will faithfully treat these as real files. However, under the hood the API layer will take care of the differences between real and virtual files.

Users who wish to maintain their own data types and memory management can also use the GMT modules, but some limitations and requirements do apply: The user’s data can either be provided as (1) a 2-D matrix (of any data type, e.g., float, integer, etc.) and in any memory layout configuration (e.g., row-major or column-major layout) or as (2) a set of column vectors that each may be of any type. These custom arrays will need to be hooked onto the GMT containers GMT_MATRIX and GMT_VECTOR, respectively. Such objects can then be treated as virtual files for either input of output.

### Our audience

Here, we document the new functions in the GMT API library for application developers who wish to call these functions from their own custom programs. At this point, only the new high-level GMT API is fully documented and intended for public use. The structure and documentation of the under-lying lower-level GMT library is not finalized. Developers using these functions may risk disruption to their programs due to changes we may make in the library in support of the GMT API. However, developers who wish to make supplemental packages to be distributed as part of GMT will (other than talk to us) probably want to access the entire low-level GMT library as well. It is unlikely that the low-level library will ever be fully documented.

There are two classes of development that users can pursue:

1. Building stand-alone custom executables that link with the shared GMT API. Our examples in this documentation are of this kind. There programs are likely to address a user’s special data formats or processing needs by leveraging high-level GMT modules to do some of the heavy lifting.

2. Building shared library plugins to extend the breath of GMT. Users who wish to build one or more new modules and distributed then via a plugin that is dynamically loaded at run-time can now do so. At the present, all the modules in the official GMT supplement are compiled into a single plugin that can be accessed at run-time. Similarly, developers may add additional plugin libraries with any number of GMT-like modules and these will then be available from the gmt command (as well as from derived interfaces such as the GMT/MATLAB toolbox and the Python module). An example of plugin development is given by the GSFML extension to GMT.

### Definitions

For the purpose of this documentation a few definitions are needed:

1. “Standard GMT program” refers to one of the traditional stand-alone command-line executables known to all GMT users, e.g., blockmean, plot, grdimage, etc. Prior to version 5, these were the only GMT executables available. In GMT 5 and up, these are accessed via the gmt executable.

2. “GMT module” refers to the function in the GMT API library that is responsible for all the action taken by the corresponding standard GMT program. All such modules are given the same names as the corresponding programs e.g., “blockmean”, but are invoked via the `GMT_Call_Module` function.

3. “GMT application” refers to a new application written by any developer. It uses the API, perhaps for custom i/o, and may call one or more GMT functions to create a new GMT-compatible executable.

4. “GMT plugin library” refers to a collection of one or more new custom GMT-like modules that are presented as a plugin library. It such libraries are placed in the official GMT plugin directory or their path is added to the GMT defaults parameter GMT_CUSTOM_LIBS then the gmt executable can find them.

5. “Family” refers to one of the many high-level GMT data types (e.g., grids, CPTs) and is typically a required argument to some API functions.

6. “Method” refers to one of several ways in which data can be read or written in the API, including from existing memory variables.

7. “Direction” is typically either GMT_IN (for reading) or GMT_OUT (for writing).

8. In the API description that follows we will use the type `int` to mean a 4-byte integer. All integers used in the API are 4-byte integers with the exception of one function where an 8-byte integer is used. Since different operating systems have their own way of defining 8-byte integers we use C99’s `int64_t` for this purpose; it is guaranteed to yield the correct type that the GMT function expects.

In version 5, the standard GMT programs are themselves simple invocations of the gmt application with the function name as argument. However, some of these modules, such as legend, gmtconvert, grdblend, grdfilter and others may call several additional modules.

### API changes from GMT5 to GMT 6

The API released with GMT5 was considered experimental as our usage of it in GMT proper as well as in the GMT/MATLAB toolbox and the GMT/Python package would undoubtably lead to revisions. We developed API to enable GMT access from other environments hence we want the library to address the needs of such developers. Here are the changes in the GMT 6 API that are not backwards compatible with GMT 5:

1. There is no longer a GMT_TEXTSET resource. Data records are now generalized to contain an optional leading numerical array followed by an optional trailing text. A “TEXTSET” in this context is simply a DATASET that has no leading numerical array. This change was necessary so that all modules reading tables expect the same fundamental GMT_DATASET resource. The alternative (which we lived to regret) was that developers calling modules from their environment would have to format their data in different ways depending on the module, and in some case depending on module options. Now, all table modules expect GMT_DATASET.

2. The function GMT_Alloc_Segment no longer takes the family of the segment (since there are now only DATASET segments) but the family variable has been reused as a mode which is passed as either GMT_WITH_STRINGS or GMT_NO_STRINGS so that data segments can be allocated with or without the optional string array.

3. We introduce a new structure GMT_RECORD which is used by GMT_Get_Record and GMT_Put_Record. Because such records may have both leading numerical columns and a trailing string these functions needed to work with such a structure rather than either an array or string.

4. The unused function GMT_Set_Columns needed to accept direction so it could be used for either input or output. It is rarely needed but some tools that must only read N numerical columns and treat anything beyond that as trailing text (even if numbers) must set the fixed input columns before reading. We also added one more mode (GMT_COL_FIX_NO_TEXT) to enforce reading of a fixed number of numerical columns and skip any trailing text.

5. The GMT_DATASET structure has gained a new (hidden) enum GMT_enum_read `type` which indicates what record types were read to produce this dataset (GMT_READ_DATA, GMT_READ_TEXT, GMT_READ_MIXED). We also changed the geometry from unsigned int to enum GMT_enum_geometry.

6. The long obsolete enums GMT_READ_DOUBLE and GMT_WRITE_DOUBLE have now fully been removed; use GMT_READ_DATA and GMT_WRITE_DATA instead.

7. The GMT_Convert_Data function’s flag array is now of length 2 instead of 3 (because there are no longer any TEXTSET settings), with what used to be flag3 now being given as flag2.

### GMT resources

The GMT API knows how to create, duplicate, read and write six types of data objects common to GMT operations: Pure data tables (ASCII or binary), grids, images, cubes, color palette tables (also known as CPT), PostScript documents, and text tables (ASCII, usually a mix of data and free-form text). In addition, we provide two data objects to facilitate the passing of simple user arrays (one or more equal-length data columns of any data type, e.g., double, char) and 2-D or 3-D user matrices (of any data type and column/row organization). We refer to these data types as GMT resources. There are many attributes for each of these resources and therefore we use a top-level structure for each object to keep them all within one container. These containers are given or returned by GMT API functions using opaque pointers (`void *`). Below we provide a brief overview of these containers, listing only the most critical members. For complete details, see Appendix A. We will later present how they are used when importing or exporting them to or from files, memory locations, or streams. The first six are the standard GMT objects, while the latter two are special data containers to facilitate the passing of user data in and out of GMT modules. These resources are defined in the include file `gmt_resources.h`; please consult this file to ensure correctness in case the documentation is not up-to-date. Note than in all instances the fundamental data variable is called “data”.

#### Data tables

Much data processed in GMT come in the form of ASCII, netCDF, or native binary data tables. These may have any number of header records (ASCII files only) and perhaps segment headers that separate groups of points or lines and polygons. GMT programs will read one or more such tables when importing data. However, to avoid memory duplication or data limitations some programs may prefer to read such records one at the time. The GMT API has functions that let you read your data record-by-record by presenting a virtual data set that combines all the data tables specified as input. This simplifies record processing considerably. Programs reading an entire data set will encounter several structures: A data set (`struct` GMT_DATASET) may contain any number of tables (`struct` GMT_DATATABLE), each with any number of segments (`struct` GMT_DATASEGMENT), each segment with any number of records, and each record with any number of (fixed) columns. Thus, the arguments to GMT API functions that handle such data sets expect a struct GMT_DATASET. All segments are expected to have the same number of columns.

    struct GMT_DATASET { /* Single container for an array of GMT tables (files) */
        uint64_t  n_tables;     /* The total number of tables contained */
        uint64_t  n_columns;    /* The number of data columns */
        uint64_t  n_segments;   /* The total number of segments across all tables */
        uint64_t  n_records;    /* The total number of data records across all tables */
        double   *min;         /* Minimum coordinate for each column */
        double   *max;         /* Maximum coordinate for each column */
        struct GMT_DATATABLE **table;    /* Pointer to array of tables */
    };

The top-level dataset structure for pure data tables contains the table structure, as defined below:

    struct GMT_DATATABLE {  /* Single container for an array of data segments */
        unsigned int n_headers;    /* Number of table header records (0 if no header) */
        uint64_t     n_columns;    /* Number of columns (fields) in each record */
        uint64_t     n_segments;   /* Number of segments in the array */
        uint64_t     n_records;    /* Total number of data records across all segments */
        double      *min;          /* Minimum coordinate for each column */
        double      *max;          /* Maximum coordinate for each column */
        char       **header;       /* Array with all table header records, if any) */
        struct GMT_DATASEGMENT **segment; /* Pointer to array of segments */
    };

Finally, the table structure depends on a structure for individual data segments:

    struct GMT_DATASEGMENT {       /* For holding segment lines in memory */
        uint64_t n_rows;           /* Number of points in this segment */
        uint64_t n_columns;        /* Number of fields in each record (>= 2) */
        double  *min;              /* Minimum coordinate for each column */
        double  *max;              /* Maximum coordinate for each column */
        double **data;             /* Data x,y, and possibly other columns */
        char  **text;              /* trailing text strings beyond the data */
        char    *label;            /* Label string (if applicable) */
        char    *header;           /* Segment header (if applicable) */
     };

Data sets may have different geometries, such as representing a set of points, one or more lines, or closed polygons.

#### GMT grids

GMT grids are used to represent equidistant and organized 2-D surfaces. These can be processed or plotted as contour maps, color images, or perspective surfaces. Because the native GMT grid is simply a 1-D float array with metadata kept in a separate `struct` GMT_GRID_HEADER header, we pass this information via a `struct` GMT_GRID, which is a container that holds both items. Thus, the arguments to GMT API functions that handle GMT grids expect this type of variable.

    struct GMT_GRID {                        /* A GMT float grid and header in one container */
        struct GMT_GRID_HEADER *header;      /* The full GMT header for the grid */
        float                  *data;        /* Pointer to the float grid array */
    };

The top-level grid structure, holding both header and data array, depends on the grid header structure:

    struct GMT_GRID_HEADER {
        uint32_t n_columns;                     /* Number of columns */
        uint32_t n_rows;                        /* Number of rows */
        uint32_t registration;                  /* GMT_GRID_NODE_REG (0) for node grids,
                                                   GMT_GRID_PIXEL_REG (1) for pixel grids */
        double wesn[4];                         /* Min/max x and y coordinates */
        double z_min;                           /* Minimum z value */
        double z_max;                           /* Maximum z value */
        double inc[2];                          /* The x and y increments */
        double z_scale_factor;                  /* Grid values must be multiplied by this factor */
        double z_add_offset;                    /* After scaling, add this */
        char   x_units[GMT_GRID_UNIT_LEN80];    /* Units in x-direction */
        char   y_units[GMT_GRID_UNIT_LEN80];    /* Units in y-direction */
        char   z_units[GMT_GRID_UNIT_LEN80];    /* Grid value units */
        char   title[GMT_GRID_TITLE_LEN80];     /* Name of data set */
        char   command[GMT_GRID_COMMAND_LEN320];/* Name of generating command */
        char   remark[GMT_GRID_REMARK_LEN160];  /* Comments regarding this data set */
    };

The basic grid header holds the metadata written to grid files.

#### GMT images

GMT images are used to represent bit-mapped images typically obtained via the GDAL bridge. These can be reprojected internally, such as when used in grdimage. Since images and grids share the concept of a header, we use the same header structure for grids as for images; however, some additional metadata attributes are also needed. Finally, the image itself may be of any data type and have more than one band (channel). Both image and header information are passed via a `struct` GMT_IMAGE, which is a container that holds both items. Thus, the arguments to GMT API functions that handle GMT images expect this type of variable. Unlike the other objects, writing images has only partial support via grdimage [3]. For the full definition, see GMT_IMAGE.

    struct GMT_IMAGE {     /* A GMT char image, header, and colormap in one container */
        enum GMT_enum_type      type;             /* Data type, e.g. GMT_FLOAT */
        int                    *colormap;         /* Array with color lookup values */
        int                     n_indexed_colors; /* Number of colors in a color-mapped image */
        struct GMT_GRID_HEADER *header;           /* Pointer to full GMT header for the image */
        unsigned char          *data;             /* Pointer to actual image */
    };

#### GMT cubes

GMT cubes are used to represent 3-D grids where all the horizontal layers are represented by a single grid header. Thus, all nodes along the third dimension are coregistered and in the horizontal plane they are, like all GMT grids, equidistant. However, the spacing in the third dimension (which is typically depth or time) does not have to be equidistant. At this moment, only greenspline and grdinterpolate can produce 3-D cubes while the latter can also read them (other grid modules can read individual layers of a cube as a single grid). We use the same header structure as for grids. However, some additional metadata attributes are needed for the third dimension. Both the cube and header information are passed via a `struct` GMT_CUBE, which is a container that holds all items. Thus, the arguments to GMT API functions that handle GMT cubes expect this type of variable. For the full definition, see GMT_CUBE.

    struct GMT_CUBE {     /* A GMT 3-D cube in one container */
         struct GMT_GRID_HEADER *header;      /* The full GMT header for the grid */
         float                  *data;        /* Pointer to the float 3-D array */
    };

#### Color palette tables (CPT)

The color palette table files, or just CPTs, contain colors and patterns used for plotting data such as surfaces (i.e., GMT grids) or symbols, lines and polygons (i.e., GMT tables). GMT programs will generally read in a color palette table, make it the current palette, do the plotting, and destroy the table when done. The information is accessed via a pointer to `struct` GMT_PALETTE. Thus, the arguments to GMT API functions that handle palettes expect this type of variable. It is not expected that users will wish to manipulate the CPT directly, but rather use this mechanism to hold them in memory and pass as arguments to GMT modules. Developers are unlikely to actually manipulate the contents of CPT structures but if needed then the full definition can be found in GMT_PALETTE.

    struct GMT_PALETTE { /* Holds color-related parameters for look-up */
        unsigned int          n_headers;     /* Number of CPT header records (0 if no header) */
        unsigned int          n_colors;      /* Number of colors in the data array */
        unsigned int          mode;          /* Flags controlling use of BFN colors */
        struct GMT_LUT       *data;          /* CPT lookup data with color information */
        struct GMT_BFN        bfn[3];        /* Structures with back/fore/nan fills */
        char                **header;        /* Array with all CPT header records, if any) */
    };

#### PostScript document

Normally, GMT modules producing PostScript will write to standard output or a designated file. Alternatively, you can tell the API to write to a memory buffer instead and then receive a structure with the final plot (or partial plot) represented as a long text string. The full structure definition can be found in GMT_POSTSCRIPT.

    struct GMT_POSTSCRIPT {      /* Single container for a chunk of PostScript text */
        unsigned int n_headers;          /* Number of PostScript header records (0 if no header) */
        size_t n_bytes;                  /* Length of data array so far */
        unsigned int mode;               /* Bit-flag for header (1) and trailer (2) */
        char *data;                      /* Pointer to actual PostScript text */
        char **header;                   /* Array with all PostScript header records, if any) */
    };

#### User data matrices

Users may write programs that need to call GMT modules but may keep their data in separate 2-D arrays that the allocate and maintain independent of GMT. For instance, a program may have built an integer 2-D matrix in memory and wish to use that as the input grid to the `grdfilter` module, which normally expects a `struct` GMT_GRID with floating point data via an actual or virtual file. To handle this case we create a `struct` GMT_MATRIX container (see Create empty resources), assign the appropriate union pointer to your data matrix and provide information on dimensions and data type. We then open this container as a virtual file and pass its filename to any module. The full structure definition can be found in GMT_MATRIX.

    struct GMT_MATRIX {  /* Single container to hold a user matrix */
       uint64_t             n_rows;        /* Number of rows in the matrix */
       uint64_t             n_columns;     /* Number of columns in the matrix */
       uint64_t             n_layers;      /* Number of layers in a 3-D matrix */
       enum GMT_enum_fmt    shape;         /* 0 = C (rows) and 1 = FORTRAN (cols) */
       enum GMT_enum_reg    registration;  /* 0 for gridline and 1 for pixel registration  */
       size_t               dim;           /* Allocated length of longest C or FORTRAN dim */
       size_t               size;          /* Byte length of data */
       enum GMT_enum_type   type;          /* Data type, e.g. GMT_FLOAT */
       double               range[6];      /* Contains xmin/xmax/ymin/ymax[/zmin/zmax] */
       union GMT_UNIVECTOR  data;          /* Pointer to actual matrix of the chosen type */
       char               **text;          /* Pointer to optional array of strings [NULL] */
    };

The `enum` types referenced in GMT_VECTOR and Table GMT_MATRIX and summarized in Table types.

#### User data columns

Likewise, programs may instead be manipulating a set of custom column vectors. For instance, the user’s program may have allocated and populated three column arrays of type float and wishes to use these as the input source to the `surface` module, which normally expects double precision triplets via a `struct` GMT_DATASET read from an actual or virtual file Simply create a new GMT_VECTOR container (see section Create empty resources) and assign the union array pointers (see univector) to your data columns and provide the required information on length, data types, and optionally range. Again, once we open this data as a virtual file we can pass its filename to any module expecting such data. The full structure definition can be found in GMT_VECTOR.

    struct GMT_VECTOR {   /* Single container to hold user vectors */
        uint64_t             n_columns;     /* Number of vectors */
        uint64_t             n_rows;        /* Number of rows in each vector */
        enum GMT_enum_reg    registration;  /* 0 for gridline and 1 for pixel registration */
        enum GMT_enum_type  *type;          /* Array with data type for each vector */
        union GMT_UNIVECTOR *data;          /* Array with unions for each column */
        double               range[2];      /* The min and max limits on t-range (or 0,0) */
        char               **text;          /* Pointer to optional array of strings [NULL] */
    };

#### Data record

For record-by-record i/o we use the GMT_RECORD structure.

    struct GMT_RECORD {  /* Single container for an array of GMT tables (files) */
        double  *data;   /* Pointer to array of double-precision numbers [NULL] */
        char  *text;     /* Pointer to the trailing string [NULL] */
    };

## Overview of the GMT C Application Program Interface

Users who wish to create their own GMT application based on the API must make sure their program goes through the steps below. The details for each step will be revealed in the following chapter. We have kept the API simple: In addition to the GMT modules, there are only 57 public functions to become familiar with, but most applications will only use a very small subset of this selection. Functions either return an integer error code (when things go wrong; otherwise it is set to `GMT_NOERROR (0)`), or they return a void pointer to a GMT resource (or NULL if things go wrong). In either case, the API will report what the error is. The layout here assumes you wish to use virtual files as input sources (i.e., data you already have in memory); if the data must be read from actual data files then things simplify considerably.

To keep things as simple as possible we will assume you are writing an application that will read in table data, call a module using the data in memory as input, and then save the output from the module back into another memory location. No actual processing of the data or further calculation will be done here (so a bit of a boring program, but the point is to develop something short we can test). Also, to keep the code short we completely ignore the return codes of the modules for now. We will call our program example1.c. Here are the steps:

1. Initialize a new GMT session with GMT_Create_Session, which allocates a hidden GMT API control structure and returns an opaque pointer to it. This pointer is a required argument to all subsequent GMT API function calls within the session.

2. Read a data set (or grid, etc.) into memory with GMT_Read_Data, which, depending on data type, returns one of the data structures discussed earlier.

3. Associate your data with a virtual file using GMT_Open_VirtualFile. This steps returns a special filename that you can use to tell a module where to read its input. No actual file is created.

4. Open a new virtual file to hold the output using GMT_Open_VirtualFile. This step also returns a special filename for the module to send its output.

5. Prepare required arguments (including the two virtual file names) and call the GMT module you wish to use via GMT_Call_Module.

6. Obtain the desired output object via GMT_Read_VirtualFile, which returns a data structure of requested type.

7. Close the virtual files you have been using with GMT_Close_VirtualFile.

8. We terminate the GMT session by calling GMT_Destroy_Session.

### Example code

For the example code to run you must have Internet access. Compile and run this program:

    #include "gmt.h"
    int main (int argc, char *argv[]) {
        void *API;                        /* The API control structure */
        struct GMT_DATASET *D = NULL;     /* Structure to hold input dataset */
        struct GMT_GRID *G = NULL;        /* Structure to hold output grid */
        char input[GMT_VF_LEN] = {""};    /* String to hold virtual input filename */
        char output[GMT_VF_LEN] = {""};   /* String to hold virtual output filename */
        char args[128] = {""};            /* String to hold module command arguments */

        /* Initialize the GMT session */
        API = GMT_Create_Session ("test", 2U, 0, NULL);
        /* Read in our data table to memory */
        D = GMT_Read_Data (API, GMT_IS_DATASET, GMT_IS_FILE, GMT_IS_PLP, GMT_READ_NORMAL, NULL,
            "@Table_5_11.txt", NULL);
        /* Associate our data table with a virtual file */
        GMT_Open_VirtualFile (API, GMT_IS_DATASET, GMT_IS_PLP, GMT_IN, D, input);
        /* Create a virtual file to hold the resulting grid */
        GMT_Open_VirtualFile (API, GMT_IS_GRID, GMT_IS_SURFACE, GMT_OUT, NULL, output);
        /* Prepare the module arguments */
        sprintf (args, "-R0/7/0/7 -I0.2 -D1 -St0.3 %s -G%s", input, output);
        /* Call the greenspline module */
        GMT_Call_Module (API, "greenspline", GMT_MODULE_CMD, args);
        /* Obtain the grid from the virtual file */
        G = GMT_Read_VirtualFile (API, output);
        /* Close the virtual files */
        GMT_Close_VirtualFile (API, input);
        GMT_Close_VirtualFile (API, output);
        /* Write the grid to file */
        GMT_Write_Data (API, GMT_IS_GRID, GMT_IS_FILE, GMT_IS_SURFACE, GMT_READ_NORMAL, NULL,
            "junk.nc", G);
        /* Destroy the GMT session */
        GMT_Destroy_Session (API);
    };

### Compilation

To compile this program (we assume it is called example1.c), we use the gmt-config script to determine the correct compile and link flags and then run gcc:

    inc=`gmt-config --cflags`
    lib=`gmt-config --libs`
    gcc example1.c $inc $lib -o example1
    ./example1

This obviously assumes you have already installed GMT and that it is in your path. If you run example1 it will take a moment (this is mostly due to the gridding performed by greenspline) and then it stops. You should find the resulting grid junk.nc in the current directory. Plot it to see if it makes sense, e.g.

    gmt grdimage junk.nc -Jx1:50 -Bafg > junk.ps

If you intend to write applications that take any number of data files via the command line then there will be more book-keeping to deal with, and we will discuss those steps later. Likewise, if you need to process a file record-by-record then more lines of code will be required.

### Plugins

Developers who wish to make custom plugin libraries that are compatible with GMT should examine the fully functioning examples of more involved code, available from the repository gmt-custom, obtainable via

    git clone https://github.com/GenericMappingTools/custom-supplements.git

### List of API functions

The following is an alphabetical listing of all the public API functions in GMT. Click on any of them to see the full syntax of each function.

The C/C++ API is deliberately kept small to make it easy to use.

> constant | description
> --- | ---
> GMT_Alloc_Segment | Allocate data segments
> GMT_Append_Option | Append new option structure to linked list
> GMT_Begin_IO | Enable record-by-record i/o
> GMT_Call_Module | Call any of the GMT modules
> GMT_Convert_Data | Convert between compatible data types
> GMT_Close_VirtualFile | Close a virtual file
> GMT_Create_Args | Convert linked list of options to text array
> GMT_Create_Cmd | Convert linked list of options to command line
> GMT_Create_Data | Create an empty data resource
> GMT_Create_Options | Convert command line options to linked list
> GMT_Create_Session | Initialize a new GMT session
> GMT_Delete_Option | Delete an option structure from the linked list
> GMT_Destroy_Args | Delete text array of arguments
> GMT_Destroy_Cmd | Delete text command of arguments
> GMT_Destroy_Data | Delete a data resource
> GMT_Destroy_Group | Delete a group of data resources
> GMT_Destroy_Options | Delete the linked list of option structures
> GMT_Destroy_Session | Terminate a GMT session
> GMT_Duplicate_Data | Make an identical copy of a data resources
> GMT_Encode_Options | Encode option arguments for external interfaces
> GMT_Error_Message | Return character pointer to last API error message
> GMT_Expand_Option | Expand option with explicit memory references
> GMT_End_IO | Disable further record-by-record i/o
> GMT_FFT | Take the Fast Fourier Transform of data object
> GMT_FFT_1D | Take the Fast Fourier Transform of 1-D float data
> GMT_FFT_2D | Take the Fast Fourier Transform of 2-D float data
> GMT_FFT_Create | Initialize the FFT machinery
> GMT_FFT_Destroy | Terminate the FFT machinery
> GMT_FFT_Option | Explain the FFT options and modifiers
> GMT_FFT_Parse | Parse argument with FFT options and modifiers
> GMT_FFT_Reset | Manually demultiplex output of inverse FFT
> GMT_FFT_Wavenumber | Return wavenumber given data index
> GMT_Find_Option | Find an option in the linked list
> GMT_Free | Free GMT-allocated non-container memory
> GMT_Get_Common | Determine if a GMT common option was set
> GMT_Get_Coord | Create a coordinate array
> GMT_Get_Default | Obtain one of the API or GMT default settings
> GMT_Get_Enum | Obtain one of the API enum constants
> GMT_Get_FilePath | Verify input file exist and replace with full path
> GMT_Get_Index | Convert row, col into a grid or image 1-D index
> GMT_Get_Index3 | Convert row, col, layer into a cube 1-D index
> GMT_Get_Info | Obtain meta data (range, dimension), … from object
> GMT_Get_Matrix | Obtain pointer to user matrix from container
> GMT_Get_Pixel | Get grid or image node
> GMT_Get_Record | Import a single data record
> GMT_Get_Row | Import a single grid row
> GMT_Get_Status | Check status of record-by-record i/o
> GMT_Get_Strings | Obtain pointer to user strings from matrix or vector
> GMT_Get_Values | Convert string into coordinates or dimensions
> GMT_Get_Vector | Obtain pointer to user vector from container
> GMT_Get_Version | Return the current lib version as a float
> GMT_Init_IO | Initialize i/o given registered resources
> GMT_Init_VirtualFile | Reset a virtual file for reuse
> GMT_Inquire_VirtualFile | Get family of a virtual file
> GMT_Make_Option | Create an option structure
> GMT_Message | Issue a message, optionally with time stamp
> GMT_Open_VirtualFile | Select memory location as input or output for module
> GMT_Option | Explain one or more GMT common options
> GMT_Parse_Common | Parse the GMT common options
> GMT_Put_Levels | Put user level coordinates into cube container
> GMT_Put_Matrix | Put user matrix into container
> GMT_Put_Record | Export a data record
> GMT_Put_Row | Export a grid row
> GMT_Put_Strings | Put user strings into various containers
> GMT_Put_Vector | Put user vector into container
> GMT_Read_Data | Import a data resource or file
> GMT_Read_Group | Import a group of data resources or files
> GMT_Read_VirtualFile | Access the output from a module via memory
> GMT_Register_IO | Register a resources for i/o
> GMT_Report | Issue a message contingent upon verbosity level
> GMT_Set_AllocMode | Set allocation mode of object to external
> GMT_Set_Default | Set one of the API or GMT default settings
> GMT_Set_Comment | Assign a comment to a data resource
> GMT_Set_Columns | Specify how many columns to use for rec-by-rec i/o
> GMT_Set_Geometry | Specify data geometry for rec-by-rec i/o
> GMT_Set_Index | Convert row, col into a grid or image index
> GMT_Update_Option | Modify an option structure
> GMT_Write_Data | Export a data resource

> Summary of all the API functions and their purpose.

## The GMT C Application Program Interface

### Initialize a new GMT session

Advanced programs may be calling more than one GMT session and thus run several sessions, perhaps concurrently as different threads on multi-core machines. We will now discuss these steps in more detail. Throughout, we will introduce upper-case GMT C enum constants in lieu of simple integer constants. These are considered part of the API and are available for developers via the `gmt_resources.h` include file.

Most applications will need to initialize only a single GMT session. This is true of all the standard GMT programs since they only call one GMT module and then exit. Most user-developed GMT applications are likely to only initialize one session even though they may call many GMT modules. However, the GMT API supports any number of simultaneous sessions should the programmer wish to take advantage of it. This might be useful when you have access to several CPUs and want to spread the computing load [4]. In the following discussion we will simplify our treatment to the use of a single session only.

To initiate the new GMT session we use

>     void *GMT_Create_Session (const char *tag, unsigned int pad, unsigned int mode,
>         int (*print_func) (FILE *, const char *));

and you will typically call it like this:

>     void *API = NULL;   /* Opaque pointer to GMT controls */
>     API = GMT_Create_Session ("Session name", 2, 0, NULL);

where `API` is an opaque pointer to the hidden GMT API control structure. You will need to pass this pointer to all subsequent GMT API functions; this is how essential internal information is passed around. The key task of this initialization is to set up the GMT machinery and internal variables used for map projections, plotting, i/o, etc. The initialization also allocates space for internal structures used to keep track of data. The `pad` argument specifies how many rows and columns should be used as padding for grids and images so that boundary conditions can be applied. GMT uses 2 and we strongly recommend that you use that value. In particular, if you choose 0 or 1 there may be certain GMT modules that will be unable to do their work properly as they count on those boundary rows and columns in the grids. Note that this setting has no effect on what is written to a grid file; the padding is an internal feature. The `mode` argument is only used for external APIs that need to communicate their special needs during the session creation. This integer argument is a sum of bit flags and the various bits control the following settings:

1. Bit 1 (1 or GMT_SESSION_NOEXIT): If set, then GMT will not call the system exit function when a serious problem has been detected but instead will simply return control to the calling environment. For instance, this is required by the GMT/MATLAB toolbox since calling exit would also exit MATLAB itself. Unless your environment has this feature you should leave this bit alone.

2. Bit 2 (2 or GMT_SESSION_EXTERNAL): If set, then it means we are calling the GMT API from an external API, such as MATLAB, Octave, or Python. Normal C/C++ programs should leave this bit alone. Its effect is to enable two additional modules for reading and writing GMT resources from these environments (those modules would not make any sense in a Unix command-line environment).

3. Bit 3 (4 or GMT_SESSION_COLMAJOR): If set, then it means the external API uses a column-major format for matrices (e.g., MATLAB, FORTRAN). If not set we default to row-major format (C/C++, Python, etc.).

4. Big 4 (8 or GMT_SESSION_LOGERRORS): If set, we redirect all error messages to a log file based on the session name (we append “.log”).

5. Bit 5 (16 or GMT_SESSION_RUNMODE): If set, the we enable GMT’s modern run-mode (where -O -K are not allowed and PostScript is written to hidden temp file). Default is the GMT classic run-mode.

6. Bit 6 (32 or GMT_SESSION_NOHISTORY): If set, then we disable GMT’s command shorthand via gmt.history files. The default is to allow this communication between GMT modules.

7. Bit 7 (64 or GMT_SESSION_NOGDALCLOSE): If set with GMT_SESSION_EXTERNAL, then we do not close the GDAL connection as the calling environment requires it to stay open.

The `print_func` argument is a pointer to a function that is used to print messages from GMT via GMT_Message or GMT_Report from external environments that cannot use the standard printf function (this is the case for the GMT/MATLAB toolbox, for instance). For all other uses you should simply pass NULL for this argument. You can also access the last cached error message by calling GMT_Error_Message which returns a pointer to the internal character buffer with that message. Pass NULL and set the mode bit if you want writing to a log file instead. Should something go wrong during the API initialization then `API` will be returned as `NULL`. Finally, GMT_Create_Session will examine the environmental parameter TMPDIR (TEMP on Windows) to set the GMT temporary directory [/tmp on Unix, current directory on Windows].

Below is a bare-bones minimalistic GMT program hello.c that initializes and destroys a GMT session:

    #include "gmt.h"
    int main (int argc, char *argv[]) {
          void *API;      /* The API control structure */
          /* Initialize the GMT session */
          API = GMT_Create_Session ("test", 2U, 0, NULL);
          /* And now for something original: */
          GMT_Message (API, GMT_TIME_NONE, "hello, world\n");
          /* Destroy the GMT session */
          GMT_Destroy_Session (API);
    };

While not super-exiting, this code demonstrates the two essential API calls required to initiate and later terminate a GMT session. In between we do what all basic programs are supposed to do: print “Hello, world”. The user is of course allowed to do whatever custom processing before the GMT session is created and can do all sorts of stuff after the GMT session is destroyed, as long as no GMT functions or resources are accessed. It may be convenient to isolate the GMT-specific processing from the custom part of the program and only maintain an active GMT session when needed.

### Get full path to local or remote files

If given a filename, GMT will look in several directories to find the given input file. However, GMT can also look for files remotely, either via the remote file mechanism or URLs. When you have a remote file (@filename) you may wish to have GMT automatically download the file and provide you with the local path. This is a job for GMT_Get_FilePath, whose prototype is

>     int GMT_Get_FilePath (void *API, unsigned int family, unsigned int direction,
>       unsigned int mode, char **ptr);

where family and `direction` set the data file type and whether it is for input or output, `mode` modifies the behavior of the function, and `*ptr` is a pointer to a character string with the filename in question. Normally, we only look for local files (GMT_FILE_LOCAL [0]), but if `mode` contains the bit flag GMT_FILE_REMOTE [1] we will try to download any remote files given to the function. By default, we will replace the filename with the full path. Add the bit flag GMT_FILE_CHECK [2] to only check for the files and return error codes but leave `*ptr` alone.

### Register input or output resources

When using the standard GMT programs, it is common to specify input files on the command line or via special program options (e.g., -I intensity.nc). The outputs of the programs are either written to standard output (which you may redirect to files or pipes into other programs) or to files specified by specific program options (e.g., -G output.nc). Alternatively, the GMT API allows you to specify input (and output) to be associated with open file handles or virtual files. We will examine this more closely below. Registering a resource is a required step before attempting to import or export data that do not come from files or standard input/output.

#### Resource initialization

All GMT programs dealing with input or output files given on the command line, and perhaps defaulting to the standard input or output streams if no files are given, must call the i/o initializer function GMT_Init_IO once for each direction required (i.e., input and output separately). For input it determines how many input sources have already been registered. If none has been registered then it scans the program arguments for any filenames given on the command line and register these input resources. Finally, if we still have found no input sources we assign the standard input stream as the single input source. For output it is similar: If no single destination has been registered we specify the standard output stream as the output destination. Only one main output destination is allowed to be active when a module writes data (some modules also write additional output via program-specific options). The prototype for this function is

>     int GMT_Init_IO (void *API, unsigned int family, unsigned int geometry,
>         unsigned int direction, unsigned int mode, unsigned int n_args, void *args);

where family specifies what kind of resource is to be registered, geometry specifies the geometry of the data, `direction` is either `GMT_IN` or `GMT_OUT`, and `mode` is a bit flag that determines what we do if no resources have been registered. The choices are

> GMT_ADD_FILES_IF_NONE (1) means “add command line (option) files if none have been registered already”.

> GMT_ADD_FILES_ALWAYS (2) means “always add any command line files”.

> GMT_ADD_STDIO_IF_NONE (4) means “add std* if no other input/output have been specified”.

> GMT_ADD_DEFAULT (6) means “always add any command line files first, and then add std* if no other input/output were specified”.

> GMT_ADD_STDIO_ALWAYS (8) means “always add std* even if resources have been registered”.

> GMT_ADD_EXISTING (16) means “only use already registered resources”.

The standard behavior is `GMT_ADD_DEFAULT` (6). Next, `n_args` is 0 if `args` is the head of a linked list of options (further discussed in Prepare modules opts); otherwise `args` is an array of `n_args` strings (i.e., the int argc, char *argv[] model)

Many programs will register an export location where results of a GMT function (say, a filtered grid) should be returned, but may then wish to use that variable as an input resource in a subsequent module call. This is accomplished by re-registering the resource as an input source, thereby changing the direction of the data set. The function returns 1 if there is an error; otherwise it returns 0. Example

X

## Resource initialization example

#### Resource registration

Should your program need to add additional sources (or a destination) to the list of items to be considered you will need to register them manually. This is considered a low-level activity and most applications are unlikely to have to resort to this step. We document it here in case your situation calls for such action. Registration involves a direct or indirect call to

>     int GMT_Register_IO (void *API, unsigned int family, unsigned int method,
>         unsigned int geometry, unsigned int direction, double wesn[], void *ptr);

where family specifies what kind of resource is to be registered, method specifies how we to access this resource (see Table methods for recognized methods), geometry specifies the geometry of the data, `ptr` is the address of the pointer to the named resource. If `direction` is `GMT_OUT` and the `method` is not related to a file (filename, stream, or handle), then `ptr` must be NULL. Note there are some limitations on when you may pass a file pointer as the method. Many grid file formats cannot be read via a stream (e.g., netCDF files) so in those situations you cannot pass a file pointer [and GMT_Register_IO would have no way of knowing this]. For grid (and image) resources you may request to obtain a subset via the wesn array; otherwise, pass NULL (or an array with at least 4 items all set to 0) to obtain the entire grid (or image). The `direction` indicates input or output and is either `GMT_IN` or `GMT_OUT`. Finally, the function returns a unique resource ID, or `GMT_NOTSET` if there was an error.

> family | source points to
> --- | ---
> GMT_IS_DATASET | A [multi-segment] data file
> GMT_IS_GRID | A grid file
> GMT_IS_IMAGE | An image
> GMT_IS_CUBE | A 3-D cube
> GMT_IS_PALETTE | A color palette table [CPT]
> GMT_IS_POSTSCRIPT | A GMT PostScript object
> GMT_IS_MATRIX | A custom user data matrix
> GMT_IS_VECTOR | A custom user data vector
> GMT_VIA_MATRIX | Modifier for grids and datasets
> GMT_VIA_VECTOR | Modifier for grids and datasets

> GMT constants used to specify a data family.

> method | how to read/write data
> --- | ---
> GMT_IS_FILE | Pointer to name of a file
> GMT_IS_STREAM | Pointer to open stream (or process)
> GMT_IS_FDESC | Pointer to integer file descriptor
> GMT_IS_DUPLICATE | Pointer to memory we may duplicate data from
> GMT_IS_REFERENCE | Pointer to memory we may reference data from

> GMT constants used to specify how data will be read or written.

> geometry | description
> --- | ---
> GMT_IS_NONE | Not a geographic feature
> GMT_IS_POINT | Multi-dimensional point data
> GMT_IS_LINE | Geographic or Cartesian line segments
> GMT_IS_POLY | Geographic or Cartesian closed polygons
> GMT_IS_LP | Either lines or polygons
> GMT_IS_PLP | Either points, lines, or polygons
> GMT_IS_SURFACE | 2-D gridded surface
> GMT_IS_VOLUME | 3-D gridded volume

> GMT constants used to specify the geometry of the data object.

> index | description
> --- | ---
> GMT_XLO | x_min (west) boundary of grid subset
> GMT_XHI | x_max (east) boundary of grid subset
> GMT_YLO | y_min (south) boundary of grid subset
> GMT_YHI | y_max (north) boundary of grid subset
> GMT_ZLO | z_min (bottom) boundary of 3-D matrix subset
> GMT_ZHI | z_max (top) boundary of 3-D matrix subset

> GMT constants used for domain array indexing.

### Create empty resources

If your application needs to build and populate GMT resources in ways that do not depend on external resources (files, memory locations, etc.), or you have data read in separately and you wish to build a GMT resource from scratch, then you can obtain an empty object by calling

>     void *GMT_Create_Data (void *API, unsigned int family, unsigned int geometry,
>          unsigned int mode, uint64_t par[], double *wesn, double *inc,
>          unsigned int registration, int pad, void *data)

which returns a pointer to the allocated resource. Pass a valid family selection. Also pass a compatible geometry. Depending on the family and your particular way of representing dimensions you may pass the additional parameters in one of two ways:

1. Actual integer dimensions of items needed (which depends on the `family`).

2. Physical distances and increments of each dimension.

For the first case you should pass both `wesn` and `inc` as NULL (or as arrays with elements all set to 0), and pass the `par` array with contents as indicated below:

> GMT_IS_GRID.

>   An empty GMT_GRID structure with a header is allocated; the data array is NULL. Use `registration` to choose either gridline (`GMT_GRID_PIXEL_REG`) or pixel (`GMT_GRID_NODE_REG`) registration. The domain can be prescribed on one of two ways: (1) The `par` argument is NULL. Then `wesn` and `inc` can also be NULL but only if the common GMT options -R and -I have been set because they are required to get the necessary info. If they were not set, then `wesn` and `inc` must in fact be transmitted. If `wesn` and `inc` are set (directly or indirectly) then `par` is ignored, even if not NULL. (2) The `par` argument is not NULL but both `wesn` and `inc` are NULL. Now, `par[0]` must have the number of columns and `par[1]` must have the number of rows in the grid. Internally, `inc` will be set to 1/1 and `wesn` will be set to 0/n_columns/0/n_rows. As an option, add `GMT_GRID_XY` to `mode` and we also allocate the grids’s x and y coordinate vectors.

> GMT_IS_IMAGE.

>   Same procedure as for GMT_IS_GRID but we return an empty GMT_IMAGE object. In either way of specification you may use `par[2]` to pass the number of image bands [1].

> GMT_IS_CUBE.

>   Same procedure as for GMT_IS_GRID but both `wesn`, `inc` and `par` have one extra dimension for the depth or time axis. For non-equidistant layers you need to use `par[2]` to sets the number of layers and use `inc[2] = 0`, otherwise `wesn` and `inc` can set it all.

> GMT_IS_DATASET.

>   We allocate an empty GMT_DATASET structure consisting of `par[0]` tables, each with `par[1]` segments, each with `par[2]` rows, all with `par[3]` columns. The `wesn`, `inc`, and `registration` argument are ignored. The `data` argument should be NULL. As an option, add `GMT_WITH_STRINGS` to `mode` and we also allocate the segments’ text field.

> GMT_IS_PALETTE.

>   We allocate an empty GMT_PALETTE structure with `par[0]` palette entries. The `wesn`, `inc`, and `registration` arguments are ignored and should be NULL/0. The `data` argument should be NULL.

> GMT_IS_POSTSCRIPT.

>   We allocate an empty GMT_POSTSCRIPT structure with a text buffer of length `par[0]`. Give `par[0]` = 0 if the PostScript string is allocated or obtained by other means. The `wesn`, `inc`, and `registration` arguments are ignored and should be NULL/0. The `data` argument should be NULL.

> GMT_IS_VECTOR.

>   We allocate an empty GMT_VECTOR structure with `par[0]` column entries. The number of rows can be specified in one of two ways: (1) Set the number of rows via `par[1]`. Then, `wesn`, `inc`, and `registration` arguments are ignored. (2) Specify `wesn`, `inc`, and `registration` and the number of rows will be computed from these parameters instead. Finally, `par[2]` holds the data type of all vectors, if you are allocating them here. The `data` argument should be NULL. If you have custom vectors you wish to use then pass `par` but make sure to select mode GMT_CONTAINER_ONLY so that no memory is allocated. Furthermore, if you are manually setting up output containers then pass mode as GMT_IS_OUTPUT instead. Use GMT_Put_Vector to hook up your vectors.

> GMT_IS_MATRIX.

>   We allocate an empty GMT_MATRIX structure. The domain can be prescribed on one of two ways: (1) Here, `par[0]` is the number of columns while `par[1]` has the number of rows. Also, `par[2]` indicates the number of layers for a 3-D matrix, or pass 0, 1, or NULL for a 2-D matrix. Finally, `par[3]` holds the data type of the matrix, if you are allocating one. (2) Pass `wesn`, `inc`, `registration` and we compute the dimensions of the matrix. The `data` argument should be NULL. As for vectors, to use custom data you must (for input) pass the mode as GMT_CONTAINER_ONLY and hook your custom matrix in via a call to GMT_Put_Matrix. The matrix may either be row- or column-oriented and this is normally determined when you created the session with GMT_Create_Session (see the bit 3 setting). However, you can pass `pad` = 1 (GMT_IS_ROW_FORMAT; set row major) or `pad` = 2 (GMT_IS_COL_FORMAT; set col major) to override the default. As for vectors, if this container is for output then pass mode as GMT_IS_OUTPUT instead.

Users wishing to pass their own data matrices and vectors to GMT modules will need to do so via the GMT_IS_MATRIX and GMT_IS_VECTOR containers. However, no module deals with such containers directly (they either expect GMT_IS_GRID or GMT_IS_DATASET, for instance). The solution is to specify the container type the GMT module expects but add in the special flags GMT_VIA_MATRIX or GMT_VIA_VECTOR. This will create the GMT_IS_MATRIX or GMT_IS_VECTOR container the user needs to add the user data, but will also tell GMT how they should be considered by the module. Note: When creating your own geographic data (dataset, grid, image, matrix, or vector) you may add `GMT_DATA_IS_GEO` to `mode` so that the structure that is created will retain this information.

For grids and images you may pass `pad` to set the padding, or -1 to accept the prevailing GMT default. The `mode` determines what is actually allocated when you have chosen grids or images. As for GMT_Read_Data you can pass `GMT_CONTAINER_AND_DATA` to initialize the header and allocate space for the array; here `data` must be NULL. Alternatively, you can pass `GMT_CONTAINER_ONLY` to just initialize the grid or image header, and later call GMT_Create_Data a second time, now passing `GMT_DATA_ONLY`, to allocate space for the array. In that second call you pass the pointer returned by the first call as `data` and specify the family; all other arguments should be NULL or 0. Normally, resources created by this function are considered to be input (i.e., have a direction that is `GMT_IN`). The exception to this is for containers to hold results from GMT which need have a direction set to `GMT_OUT`. Such empty containers are requested by passing mode = `GMT_IS_OUTPUT` and setting all dimension arguments to 0 or NULL. The function returns a pointer to the data container. In case of an error we return a NULL pointer and pass an error code via `API->error`. Your C code will have to include “gmt_private.h” to be able to dereference the API pointer.

#### Hooking user arrays to objects

If you have custom column vector or matrices and you want them to be used as input to GMT modules, you will need to create a GMT_VECTOR or GMT_MATRIX container and hook your items to them. Likewise, if you want to receive the output of GMT modules into user arrays or matrices then you will need to access those data. The following utility functions are used for these tasks:

>     int GMT_Put_Matrix (void *API, struct GMT_MATRIX *M, unsigned int type, int pad, void *matrix);

where `M` is a GMT_MATRIX created by GMT_Create_Data, the `type` is one of the recognized data types, `pad` indicates if the matrix has or should have padding, and `matrix` is your custom matrix. The `pad` entry is typically 0 (no pad present), but if you intend the matrix to serve as grid input to a module then GMT will expect 2. If your matrix already has been extended by 2 extra rows and columns then pass `pad` = 2. To extract a custom matrix from an output GMT_MATRIX you can use

>     void *GMT_Get_Matrix (void *API, struct GMT_MATRIX *M);

which simply returns a pointer to the right union pointer. For vectors the same principles apply:

>     int GMT_Put_Vector (void *API, struct GMT_VECTOR *V, unsigned int col,
>         unsigned int type, void *vector);

where `V` is the GMT_VECTOR created by GMT_Create_Data, `col` is the vector column in question, `type` is one of the recognized data types used for this vector, and `vector` is a pointer to the user’s read-only custom vector. In addition, `type` may also be GMT_TEXT, in which case we expect an array of strings with numbers, longitudes, latitudes, or ISO datetime strings and we do the conversion to internal numerical values and allocate a vector to hold the result in the given `col`. By default that vector will be assigned to type GMT_DOUBLE but you can add another primary data type for the conversion if you prefer (e.g., GMT_TEXT|GMT_LONG to get final internal absolute time in integer seconds). For the special data type GMT_TEXT GMT allocates internal memory to hold the converted data and `vector` is not used any further.

To extract a custom vector from an output GMT_VECTOR you can use

>     void *GMT_Get_Vector (void *API, struct GMT_VECTOR *V, unsigned int col);

where `col` is the vector number you wish to obtain a pointer to.

>     int GMT_Put_Levels (void *API, struct GMT_CUBE *C, double *levels, uint64_t n_levels);

where `C` is the GMT_CUBE created by GMT_Create_Data, `levels` is an array with the (probably) non-equidistant coordinates for the third cube dimension, and `n_levels` is their number. This function is typically used when we are creating a cube whose spacing between layers is not equidistant and hence cannot be computed internally from range and increment.

>     void *GMT_Get_Version (void *API, unsigned int *major, unsigned int *minor, unsigned int *patch);

Returns the current lib version as a float, e.g. 6.0, and optionally its constituints. Either one or all of in *major, *minor, *patch args can be NULL. If they are not, one gets the corresponding version component. The API pointer is actually not used in this function, so passing NULL is the best option.

Finally, for either vectors, matrices or palettes you may optionally add a pointer to an array of text strings, one per row (or CPT slice). This is done via

>     int GMT_Put_Strings (void *API, unsigned int family, void *X, char **array);

where `family` is either GMT_IS_VECTOR, GMT_IS_MATRIX, or GMT_IS_PALETTE, `X` is either a GMT_VECTOR, GMT_MATRIX or GMT_MATRIX, and `array` is the a pointer to your string array. You may add `GMT_IS_DUPLICATE` to `family` to indicate you want the array of strings to be duplicated; the default is to just set a pointer to `array`. For GMT_IS_PALETTE you must also add GMT_IS_PALETTE_LABEL or GMT_IS_PALETTE_KEY to indicate which strings are being set.

To access the string array from an output vector or matrix container you will use

>     char **GMT_Get_Strings (void *API, unsigned int family, void *X);

where again `family` is either GMT_IS_VECTOR or GMT_IS_MATRIX and `X` is either a GMT_VECTOR or GMT_MATRIX.

#### Manually add segments

If you do not know the number of rows in the segments or you expect different segments to have different lengths then you should set the row dimension to zero in GMT_Create_Data and add the segments manually with `GMT_Alloc_Segment`, which allocates a new GMT_DATASET segment for such multi-segment tables.

>     void *GMT_Alloc_Segment (void *API, unsigned int mode,
>         uint64_t n_rows, uint64_t n_columns, char *header, void *S);

where `header` is the segment’s desired header (or NULL) and mode determines if the segment should allocate a string array, which in this case should either be `GMT_NO_STRINGS` or `GMT_WITH_STRINGS`. If `S` is not NULL then we simply reallocate the lengths of the segment; otherwise a new segment is first allocated.

There is also the option of controlling the allocation of the segment array by setting n_rows = 0. This would allow external arrays (double-precision only) to connect to the S->data[col] arrays and not be freed by GMT’s garbage collector.

#### Get information (meta data) about object

If you are creating objects in an environment where the objects are opaque pointers, then it may be necessary to inquire about an objects dimension, range, registration, padding, etc. We can do this with

>     void *_GMT_Get_Info (void *API, unsigned int family, void *data, unsigned int *geometry,
>         uint64_t dim[], double *range, double *inc, unsigned int *registration, int *pad)

where `family` is the type of object referenced by `data`. Depending on the type of object, one or more of `dim`, `range`, `inc`, `registration`, and `pad` will be initialized, but only if they do not point to NULL. The function returns an error code if an invalid family was selected.

### Duplicate resources

Often you have read or created a data resource and then need an identical copy, presumably to make modifications to. Or, you want a copy with the same dimensions and allocated memory, except data values should not be duplicated. Alternatively, perhaps you just want to duplicate the header and skip the allocation and duplication of the data entirely. These tasks are addressed by

>     void *GMT_Duplicate_Data (void *API, unsigned int family, unsigned int mode,
>         void *data);

which returns a pointer to the allocated resource. Specify which family and select `mode` from `GMT_DUPLICATE_DATA`, `GMT_DUPLICATE_ALLOC`, and `GMT_DUPLICATE_NONE`, as discussed above (also see `mode` discussion above). For GMT_GRID you may add `GMT_DUPLICATE_RESET` which will ensure the duplicate grid will have normal padding (useful when the original has non-standard padding). For GMT_DATASET you can add modifiers `GMT_ALLOC_VERTICAL` or `GMT_ALLOC_HORIZONTAL` to the `mode` if you wish to put all the data into a single long table or to paste all tables side-by-side, respectively (thus getting one wide table instead). Additional note for GMT_DATASET: Normally we allocate the output given the corresponding input dimensions. You can override these by specifying your alternative dimensions in the input dataset’s variable `dim[]`. The `data` is a pointer to the resource you wish to duplicate. In case of an error we return a NULL pointer and pass an error code via `API->error`.

### Convert between resource types

Having a resource in memory you may want to convert it to an alternative representation. For instance, you may have a GMT_DATASET but need to strip the information from the data into a VECTOR format, dropping all the segment header information, so that your custom algorithm or other non-GMT functions can be used on the data. In this case you will use

>     void *GMT_Convert_Data (void *API, void *In, unsigned int family_in,
>                 void *Out, unsigned int family_out, unsigned int flag[]);

which returns a pointer to the converted resource. Specify the needed family for both the input and output resources and set the (up to) two flags passed via the `flag` array. The first `flag[0]` determines how table headers and segment headers should be handled. By default (`flag[0]` = 0) they are preserved (to the extent possible). E.g., converting a GMT_DATASET to MATRIX always means table headers are skipped whereas segment headers are converted to NaN-records. Other values for this flag is 1 (Table headers are not copied, segment headers are preserved), 2 (Headers are preserved, segment headers are reset to blank), or 3 (All headers headers are eliminated). Note that this flag only affects duplication of headers. If the new object is written to file at a later stage then it is up to the GMT default setting if headers are written to file or not. The second `flag[1]` controls restructuring of tables and segments within a set. For `flag[1]` = 0 we retain the original layout. Other selections are `GMT_WRITE_TABLE_SEGMENT` (combine all segments into a single segment in a single table), `GMT_WRITE_TABLE` (collect all segments into a single table), and `GMT_WRITE_SEGMENT` (combine segments into one segment per table). Many family combinations are simply not allowed, such as grid to color palette, dataset to image, etc.

### Import Data Sets

If your program needs to import any of the six recognized data types (data table, grid, image, cube, CPT, or PostScript) you will use the GMT_Read_Data or GMT_Read_VirtualFile functions. The former is typically used when reading from files, streams (e.g., `stdin`), or an open file handle, while the latter is only used to read from memory. Because of the similarities of these six import functions we use an generic form that covers all of them.

All input functions takes a parameter called `mode`. The `mode` parameter generally has different meanings for the different data types and will be discussed below. However, one bit setting is common to all types: By default, you are only allowed to read a data source once; the source is then flagged as having been read and subsequent attempts to read from the same source will result in a warning and no reading takes place. In the unlikely event you need to re-read a source you can override this default behavior by adding `GMT_IO_RESET` to your `mode` parameter. Note that this override does not apply to sources that are streams or file handles, as it may not be possible to re-read their contents.

#### Import from a file, stream, or handle

To read an entire resource from a file, stream, or file handle, use

>     void *GMT_Read_Data (void *API, unsigned int family, unsigned int method,
>         unsigned int geometry, unsigned int mode, double wesn[], const char *input, void *ptr);

- API

- family

- method

- geometry

- mode -- see below

- wesn

- input -- a pointer to char holding the file name to read, or NULL if `stdin`

- ptr -- NULL or the pointer returned by this function after a first call (when reading grids in two steps)

- Return: Pointer to data container, or NULL if there were errors (passed back via API->error)

where `ptr` is NULL except when reading grids in two steps (i.e., first get a grid structure with a header, then read the data). Most of these arguments have been discussed earlier. This function can be called in three different situations:

1. If you have a single source (filename, stream pointer, etc.) you can call GMT_Read_Data directly; there is no need to first register the source with GMT_Register_IO or gather the sources with GMT_Init_IO. Furthermore, for GMT_DATASET you can also specify a filename that contains UNIX wildcards (e.g., “all_*_[ab]?.txt”) and these will all be read to produce a single multi-table GMT_DATASET (for other datatypes, see GMT_Read_Group instead).

2. If you want to specify `stdin` as source then pass `input` as NULL.

3. If you already registered all desired sources with GMT_Init_IO then you indicate this choice by passing the invalid `geometry` = 0.

Space will be allocated to hold the results, as needed, and a pointer to the object is returned. If there are errors we simply return NULL and report the error. Note that you can read in a GMT_IS_MATRIX either from a text table (passing `geometry` as GMT_IS_POINT) or from a grid (passing `geometry` as GMT_IS_SURFACE). The `mode` parameter has different meanings for different data types.

Color palette table.

  `mode` contains bit-flags that control how the CPT’s back-, fore-, and NaN-colors should be initialized. Select 0 to use the CPT resource’s back-, fore-, and NaN-colors, 2 to replace these with the current GMT default values, or 4 to replace them with the color table’s entries for highest and lowest value.

Data table.

  `mode` is currently not used.

Text table.

  `mode` is currently not used.

GMT grid or image.

  Here, `mode` determines how we read the grid: To read the entire grid and its header, pass `GMT_CONTAINER_AND_DATA`. However, if you may need to extract a sub-region you must first read the header by passing `GMT_CONTAINER_ONLY` with `wesn` = NULL, then examine the header structure range attributes, specify a subset via the array `wesn`, and finally call GMT_Read_Data a second time, now with `mode` = `GMT_DATA_ONLY`, passing your `wesn` array and the grid structure returned from the first call as `ptr`. In the event your data array should be allocated to hold both the real and imaginary parts of a complex data set you must add either `GMT_GRID_IS_COMPLEX_REAL` or `GMT_GRID_IS_COMPLEX_IMAG` to `mode` so as to allow for the extra memory needed and to stride the complex value-pairs correctly. If your grid is huge and you must read it row-by-row, set `mode` to `GMT_CONTAINER_ONLY` | `GMT_GRID_ROW_BY_ROW`. You can then access the grid row-by-row using GMT_Get_Row. By default, the rows will be automatically processed in sequential order. To completely specify which row to be read, pass `GMT_GRID_ROW_BY_ROW_MANUAL` instead. Finally, as an option you may add `GMT_GRID_XY` to the mode and we also allocate the x and y coordinate vectors for the grid or image.

PostScript.

  `mode` is currently not used.

If you need to read the same resource more than once you should add the bit flag `GMT_IO_RESET` to the given `mode`.

#### Import a group of data sets

To read a group of resources, you may instead use

>     void *GMT_Read_Group (void *API, unsigned int family, unsigned int method,
>         unsigned int geometry, unsigned int mode, double wesn[],
>         void *input, unsigned int *n_items, void *ptr);

- API

- family

- method

- geometry

- mode -- see below

- wesn

- input -- Contents depends on the value of n_items. If it is zero then we expect a pointer to char holding UNIX wildcard file name(s) to read, otherwise we expect a pointer to an array of character strings (n_items in total) with names of all the files to read. If n_items is NULL then we assume 0 but cannot return the number found.

- ptr -- NULL or the pointer returned by this function after a first call (applies when reading grids or images in two steps)

- Return: Pointer to array of data container, or NULL if there were errors (passed back via API->error)

where `ptr` is NULL except when reading grids in two steps (i.e., first get a grid structures with a header, then read the data arrays). Most of these arguments have been discussed earlier. It is useful when you need to read a series of files (e.g., from a list with filenames) or want to specify the items to read using a UNIX wildcard specification. Note: If used with GMT_DATASET then you will receive an array of structures as well. Typically, many data files are read into separate tables that all form part of a single SET (this is what GMT_Read_Data does), but if GMT_Read_Group is used on the same arguments then an array of one-table sets will be returned instead. The purpose of your application will dictate which form is more convenient.

#### Using user arrays in GMT

If your program uses a matrix or a set of column vectors to hold data and you wish to use such data in a GMT module, you must first create a GMT_MATRIX (for matrices) or GMT_VECTOR (for vectors) to hold your arrays. In this situation you must pass `dim` with the final dimensions of your rows and columns when you call GMT_Create_Data to make the empty containers. You can then use GMT_Put_Matrix and GMT_Put_Vector to hook up your own allocated arrays. It is then these containers that you will pass to GMT via virtual files. For receiving output from GMT it is normal to simply use Open_VirtualFile and have GMT allocate the space needed. However, if you want the result to be written to your own arrays or matrix then you must call GMT_Create_Data yourself with mode = GMT_IS_OUTPUT and specify the dimensions of your array, then (as for input) assign your memory to the container using GMT_Put_Matrix or GMT_Put_Vector. Finally, if you also need to pass record of strings then see GMT_Put_Strings and GMT_Get_Strings.

#### Open a virtual file (memory location)

If you have read in or otherwise obtained a data object in memory and you now wish for it to serve as input to a GMT module, you will have to associate that object with a “Virtual File”. This step assigns a special filename to the memory location and you can then pass this filename to any module that needs to read that data. It is similar for writing, except you may pass NULL as the object to have GMT automatically allocate the output resource. If you want GMT to write to your preallocated memory then you must instead create a suitable container first (and pass the dimensions of the arrays) and then attach your array(s) using GMT_Put_Matrix or GMT_Put_Vector. The full syntax is

>     int GMT_Open_VirtualFile (void *API, unsigned int family, unsigned int geometry,
>                 unsigned int direction, void *data, char *filename);

Here, `data` is the pointer to your memory object. The function returns the desired filename via `filename`. This string must be at least `GMT_VF_LEN` bytes (16). The other arguments have been discussed earlier. Specifically for direction, use GMT_IN for reading and GMT_OUT for writing. Simply pass this filename in the calling sequence to the module you want to use to indicate which file should be used for reading or writing. Note that if you plan to pass a matrix or vectors instead of grids or dataset you must add the modifiers GMT_IS_MATRIX or GMT_IS_VECTOR to `family` so that the module knows what to do. Finally, in the case of passing `data` as NULL you may also control what type of matrix or vector will be created in GMT for the output by adding in the modifiers GMT_VIA_type, as listed in types. Note: GMT tries to minimize data duplication if possible, so if your input arrays are compatible with the data type used by the modules then we could use your array directly. This may have the side-effect that your input array is modified by the module, especially if the module writes the results to a netCDF grid file. If that is a price you are willing to pay then you can add GMT_IS_REFERENCE to the `direction` argument and we will pass the array internally to avoid duplicating memory. For output it is best to pass GMT_IS_REFERENCE as well.

#### Import from a virtual file

Once the module completes it will have written its output to the virtual file you initialized with GMT_Open_VirtualFile. To use the actual data you will need to “read” it into your program. Of course, the data are already in memory but to access it you need to use GMT_Read_VirtualFile, which expects the output filename you obtained from GMT_Open_VirtualFile. The syntax is

>     void *GMT_Read_VirtualFile (void *API, char *filename);

The function requires the output filename via `filename` and then returns the data object, similar to what GMT_Read_Data does.

#### Inquire a virtual file for family

If you do not know what family is being represented by a virtual file then you should first obtain the family via GMT_Inquire_VirtualFile. The syntax is

>     int GMT_Inquire_VirtualFile (void *API, const char *filename);

The function requires the virtual file’s `filename` and then returns the family of the data object.

#### Reset a virtual file for reuse

Should you need to read a virtual file again then you must first reset it to its original state with GMT_Init_VirtualFile. The syntax is

>     int GMT_Init_VirtualFile (void *API, unsigned int mode, const char *filename);

The function requires the virtual file’s `filename` and then resets the internal counters (e.g., record numbers and other book-keeping parameters). The `mode` is presently not used.

#### Close a virtual file

Once you have finished using a virtual file you need to close it. This will reset its internal settings back to what it was before you used it as a virtual file. The syntax is

>     int GMT_Close_VirtualFile (void *API, char *filename);

where `filename` is the name of the virtual file.

### Record-by-record input

In the case of data tables you have the option of selecting record-by-record reading or writing. As a general rule, your program development simplifies if you can read entire resources into memory with GMT_Read_Data or GMT_Read_VirtualFile. However, if this leads to unacceptable memory usage or if the program logic is particularly simple, you may obtain one data record at the time via GMT_Get_Record and write one at a time with GMT_Put_Record. For row-by-row i/o for grids there is the corresponding function GMT_Get_Row. There are additional overhead involved in setting up record-by-record processing, which is the topic of this section.

#### Enable Data Import

Once all input resources have been registered, we signal the API that we are done with the registration phase and are ready to start the actual data import. This step is only required when reading one record at the time. We initialize record-by-record reading by calling GMT_Begin_IO. This function enables data record-by-record reading and prepares the registered sources for the upcoming import. The prototype is

>     int GMT_Begin_IO (void *API, unsigned int family, unsigned int direction,
>         unsigned int header);

where family specifies the resource type to be read or written (only `GMT_IS_DATASET` is available for record-by-record handling). The `direction` is either `GMT_IN` or `GMT_OUT`, so for import we obviously use `GMT_IN`. The function determines the first input source and sets up procedures for skipping to the next input source in a virtual data set. The GMT_Get_Record function will not be able to read any data before GMT_Begin_IO has been called. As you might guess, there is a companion GMT_End_IO function that completes, then disables record-by-record data access. You can use these several times to switch modes between registering data resources, doing the importing/exporting, and disabling further data access, perhaps to do more registration. We will discuss GMT_End_IO once we are done with the data import. The final `header` argument determines if the common header-block should be written during initialization; choose between `GMT_HEADER_ON` and `GMT_HEADER_OFF`. The function returns 1 if there is an error; otherwise it returns 0.

#### Set data geometry

Typically only done for output data written record by record, we designate the data set’s geometry by calling

>     int _GMT_Set_Geometry (void *API,  unsigned int direction, unsigned int geometry);

where `direction` is either `GMT_IN` or `GMT_OUT` and geometry sets the geometry that will be produced (or read).

#### Importing a data record

If your program will read data table records one-by-one you must first enable this input mechanism with GMT_Begin_IO and then read the records within a loop, repeatedly using

>     void *GMT_Get_Record (void *API, unsigned int mode, int *nfields);

where the returned value is a pointer to a GMT_RECORD structure, whose member pointers data and text point to ephemeral memory internal to GMT and should be considered read-only. When we reach end-of-file, encounter conversion problems, read header comments, or identify segment headers we instead return a NULL pointer. The `nfields` integer pointer will return the number of fields returned; pass NULL if your program should ignore this information.

Normally (i.e., `mode` = `GMT_READ_DATA`), we return a pointer to a double array. To read text records, supply instead `mode` = `GMT_READ_TEXT` and we will return a pointer to the text record. However, if you have input records that mixes organized floating-point columns with text items you could pass `mode` = `GMT_READ_MIXED`. Then, GMT will attempt to extract the floating-point values from as many columns as needed; you can still access the original record string, as discussed below. Finally, if your application needs to be notified when GMT closes one file and opens the next, add `GMT_FILE_BREAK` to `mode` and check for the status code `GMT_IO_NEXT_FILE` (by default, we treat the concatenation of many input files as a single virtual file). Using GMT_Get_Record requires you to first initialize the source(s) with GMT_Init_IO. For certain records, GMT_Get_Record will return NULL and sets status codes that your program will need to examine to take appropriate response. Table IO-status lists the various status codes you can check for, using the `GMT_Get_Status` function (see next section).

#### Examining record status

Programs that read record-by-record must be aware of what the current record represents. Given the presence of headers, data gaps, NaN-record, etc., the developer may want to check the status after reading the current record. The internal i/o status mode can be interrogated with the function

>     int GMT_Get_Status (void *API, unsigned int mode);

which returns 0 (false) or 1 (true) if the current status is reflected by the specified `mode`. There are 11 different modes available to programmers; for a list see Table IO-status For an example of how these may be used, see the test program `testgmtio.c`. Developers who plan to import data on a record-by-record basis may also consult the source code of, say, blockmean or text, to see examples of working code.

> mode | description and return value
> --- | ---
> GMT_IO_DATA_RECORD | 1 if we read a data record
> GMT_IO_TABLE_HEADER | 1 if we read a table header
> GMT_IO_SEGMENT_HEADER | 1 if we read a segment header
> GMT_IO_ANY_HEADER | 1 if we read either header record
> GMT_IO_MISMATCH | 1 if we read incorrect number of columns
> GMT_IO_EOF | 1 if we reached the end of the file (EOF)
> GMT_IO_NAN | 1 if we only read NaNs
> GMT_IO_GAP | 1 if this record implies a data gap
> GMT_IO_NEW_SEGMENT | 1 if we enter a new segment
> GMT_IO_LINE_BREAK | 1 if we encountered a segment header, EOF, NaNs or gap
> GMT_IO_NEXT_FILE | 1 if we finished one file but not the last

> The various modes used to test the status of the record-by-record machinery.

#### Importing a grid row

If your program must read a grid file row-by-row you must first enable row-by-row reading with GMT_Read_Data and then use the GMT_Get_Row function in a loop; the prototype is

>     int GMT_Get_Row (void *API, int row_no, struct GMT_GRID *G, float *row);

where `row` is a pointer to a pre-allocated single-precision array to receive the current row, `G` is the grid in question, and `row_no` is the number of the current row to be read. Note this value is only considered if the row-by-row mode was initialized with `GMT_GRID_ROW_BY_ROW_MANUAL`. The user must allocate enough space to hold the entire row in memory.

#### Disable Data Import

Once the record-by-record input processing has completed we disable further input to prevent accidental reading from occurring (due to poor program structure, bugs, etc.). We do so by calling GMT_End_IO. This function disables further record-by-record data import; its prototype is

>     int GMT_End_IO (void *API, unsigned int direction, unsigned int mode);

and we specify `direction` = `GMT_IN`. At the moment, `mode` is not used. This call will also reallocate any arrays obtained into their proper lengths. The function returns 1 if there is an error (whose code is passed back with `API->error`), otherwise it returns 0 (`GMT_NOERROR`).

### Manipulate data

Once you have created and allocated empty resources, or read in resources from the outside, you may wish to manipulate their contents. This section discusses how to set up loops and access the important variables for each of the supported families. For grids and images it may in addition be required to determine what the coordinates are at each node point. This information can be obtained via arrays of coordinates for each dimension, obtained by

>     double *GMT_Get_Coord (void *API, unsigned int family, unsigned int dim,
>         void *data);

where family must be `GMT_IS_GRID` or `GMT_IS_DATASET`, `dim` is either `GMT_IS_X` or `GMT_IS_Y`, and `data` is the grid or image pointer. This function will be used below in our example on grid manipulation.

Another aspect of dealing with grids and images is to convert a row and column 2-D reference to our 1-D array index. Because of grid and image boundary padding the relationship is not straightforward, hence we supply

>     uint64_t GMT_Get_Index (struct GMT_GRID_HEADER *header, int row, int col);

where the `header` is the header of either a grid or image, and `row` and `col` is the 2-D position in the grid or image. We return the 1-D array position; again this function is used below in our example. Likewise, for images with many layers we also define

>     uint64_t GMT_Get_Pixel (struct GMT_GRID_HEADER *header, int row,
>         int col, int layer);

where the `header` is the header of an image, and `row`, `col` and `layer` (= 1 for grids) is the position in the grid or image.

For data cubes we need to also supply the `level` in the cube. Because each layer is basically a padded grid, we supply

>     uint64_t GMT_Get_Index3 (struct GMT_GRID_HEADER *header, int row, int col, int level);

where we return the 1-D array position.

#### Manipulate grids

Most applications wishing to manipulate grids will want to loop over all the nodes, typically in a manner organized by rows and columns. In doing so, the coordinates at each node may also be required for a calculation. Below is a snippet of code that shows how to do visit all nodes in a grid and assign each node the product x * y:

>     int row, col, node;
>     double *x_coord = NULL, *y_coord = NULL;
>     /*... create a grid G or read one ... */
>     x_coord = GMT_Get_Coord (API, GMT_IS_GRID, GMT_X, G);
>     y_coord = GMT_Get_Coord (API, GMT_IS_GRID, GMT_Y, G);
>     for (row = 0; row < G->header->n_rows) {
>         for (col = 0; col < G->header->n_columns; col++) {
>             node = GMT_Get_Index (G->header, row, col);
>             G->data[node] = x_coord[col] * y_coord[row];
>         }
>     }

Note the use of GMT_Get_Index to get the grid node number associated with the `row` and `col` we are visiting. Because GMT grids have padding (for boundary conditions) the relationship between rows, columns, and node indices is more complicated and hence we hide that complexity in GMT_Get_Index. Note that for trivial procedures such setting all grid nodes to a constant (e.g., -9999.0) where the row and column does not enter you can instead do a single loop:

>     int node;
>     /*... create a grid G or read one ... */
>     for (node = 0; node < G->header->size) G->data[node] = -9999.0;

Note we must use `G->header->size` (size of allocated array) and not `G->header->nm` (number of nodes in grid) since the latter is smaller due to the padding and a single loop like the above treats the pad as part of the “inside” grid. Replacing `size` by `nm` would be a bug.

#### Manipulate data tables

Another common application is to process the records in a data table. Because GMT considers the GMT_DATASET resources to contain one or more tables, each of which may contain one or more segments, all of which may contain one or more columns, you will need to have multiple nested loops to visit all entries. The following code snippet will visit all data records and add 1 to all columns beyond the first two (x and y), and if the data has a trailing string it will print it to stdout:

>     uint64_t tbl, seg, row, col;
>     struct GMT_DATATABLE *T = NULL;
>     struct GMT_DATASEGMENT *S = NULL;

>     /* ... create a dataset D or read one ... */
>     for (tbl = 0; tbl < D->n_tables; tbl++) {       /* For each table */
>       T = D->table[tbl];       /* Convenient shorthand for current table */
>       for (seg = 0; seg < T->n_segments; seg++) {   /* For all segments */
>         S = T->segment[seg];   /* Convenient shorthand for current segment */
>         for (row = 0; row < S->n_rows; row++) { /* For all rows in segment */
>           for (col = 2; col < T->n_columns; col++) {    /* For all cols > 1 */
>             S->data[col][row] += 1.0;   /* Just add one */
>           }
>                   if (S->text) printf ("Row %d has string: %s\n", (int)row, S->text[row]);
>         }
>       }
>     }

### Message and Verbose Reporting

The API provides two functions for your program to present information to the user during the run of the program. One is used for messages that are always written (optionally with a time stamp) while the other is used for reports whose verbosity level must exceed the verbosity settings specified via -V.

#### Verbose reporting

>     int GMT_Report (void *API, unsigned int level, const char *message, ...);

This function takes a verbosity level and a multi-part message (e.g., a format statement and zero or more variables as required by the format string). The verbosity `level` is an integer in the 0–5 range; these levels are listed in Table timemodes You assign an appropriate verbosity level to your message, and depending on the chosen run-time verbosity level set via -V your message may or may not be reported. Only messages whose stated verbosity level is lower or equal to the -V level will be printed. These messages are typically progress reports, etc., and are sent to standard error.

> constant | description
> --- | ---
> GMT_MSG_QUIET | Quiet; no messages whatsoever
> GMT_MSG_ERROR | Error messages only
> GMT_MSG_WARNING | Warnings
> GMT_MSG_TICTOC | Time usage for slow algorithms
> GMT_MSG_INFORMATION | Informational messages
> GMT_MSG_COMPAT | Compatibility warnings
> GMT_MSG_DEBUG | Debug messages for developers mostly

> The different levels of verbosity that can be selected.

#### Error string

>     char * GMT_Error_Message (void *API);

This function simply returns a character pointer to the internal error message buffer holding the last error message generated.

#### User messages

For custom messages to the user that should always be printed, we use

>     int GMT_Message (void *API, unsigned int mode, const char *format, ...);

This function always prints its message to the standard output. Use the `mode` value to control if a time stamp should preface the message, and if selected how the time information should be formatted. See Table timemodes for the various modes.

> constant | description
> --- | ---
> GMT_TIME_NONE | Display no time information
> GMT_TIME_CLOCK | Display current local time
> GMT_TIME_ELAPSED | Display elapsed time since last reset
> GMT_TIME_RESET | Reset the elapsed time to 0

> The different types of message modes.

### Special GMT modules

There are some differences between calling modules on the command line and using them via the API. These are discussed here.

#### API-only modules

There are two general-purpose modules that are not part of the command-line version of GMT. These are the read and write modules. Both take an option to specify what GMT resource is being read of written: -Tc|d|g|i|p, which selects CPT, dataset, grid, image, or PostScript, respectively. In addition both modules accept the infile and outfile argument for source and destination. These may be actual files of memory locations, of course.

#### PostScript Access

The GMT module psconvert is normally given one or more PostScript files that may be converted to other formats. When accessed by the API it may also be given the special file name “=”, which means we are to use the internal PostScript string produced by the latest GMT plotting instead of any actual file name. The module can access this string which must be a complete plot (i.e., it must have header, middle, and trailer and thus be a valid PostScript file). This allows the API to convert plots to a suitable image format without any duplication and manipulation of the PostScript itself.

### Adjusting headers and comments

All header records in incoming datasets are stored in memory. You may wish to replace these records with new information, or append new information to the existing headers. This is achieved with

>     int GMT_Set_Comment (void *API, unsigned int family, unsigned int mode,
>         void *arg, void *data)

Again, family selects which kind of resource is passed via `data`. The `mode` determines what kind of comment is being considered, how it should be included, and in what form the comment passed via `arg` is provided. Table comments lists the available options, which may be combined by adding (bitwise “or”). The GMT_Set_Comment function does not actually output anything but sets the relevant comment and header records in the relevant structure. When a file is written out the information will be output as well (Note: Users can always decide if they wish to turn header output on or off via the common GMT option `-h`. For record-by-record writing you must enable the header block output when you call GMT_Begin_IO.

> constant | description
> --- | ---
> GMT_COMMENT_IS_TEXT | Comment is a text string
> GMT_COMMENT_IS_OPTION | Comment is a linked list of GMT_OPTION structures
> GMT_COMMENT_IS_COMMAND | Comment is the command
> GMT_COMMENT_IS_REMARK | Comment is the remark
> GMT_COMMENT_IS_TITLE | Comment is the title
> GMT_COMMENT_IS_NAME_X | Comment is the x variable name (grids only)
> GMT_COMMENT_IS_NAME_Y | Comment is the y variable name (grids only)
> GMT_COMMENT_IS_NAME_Z | Comment is the z variable name (grids only)
> GMT_COMMENT_IS_COLNAMES | Comment is the column names header
> GMT_COMMENT_IS_RESET | Comment replaces existing information

> The modes for setting various comment types.

The named modes (command, remark, title, name_x|y|z and colnames are used to distinguish regular text comments from specific fields in the header structures of the data resources, such as GMT_GRID. For the various table resources (e.g., GMT_DATASET) these modifiers result in a specially formatted comments beginning with “Command: ” or “Remark: “, reflecting how this type of information is encoded in the headers.

### Export Data Sets

If your program needs to write any of the six recognized data types (CPTs, data tables, grids, images, cubes or PostScript) you can use the GMT_Write_Data function.

Both of these output functions takes a parameter called `mode`. The `mode` parameter generally takes on different meanings for the different data types and will be discussed below. However, one bit setting is common to all types: By default, you are only allowed to write a data resource once; the resource is then flagged to have been written and subsequent attempts to write to the same resource will quietly be ignored. In the unlikely event you need to re-write a resource you can override this default behavior by adding `GMT_IO_RESET` to your `mode` parameter.

#### Exporting a data set

To have your program accept results from GMT modules and write them separately requires you to use the GMT_Write_Data function. It is very similar to the GMT_Read_Data function encountered earlier.

##### Exporting a data set to a file, stream, or handle

The prototype for writing to a file (via name, stream, or file handle) is

>     int GMT_Write_Data (void *API, unsigned int family, unsigned int method,
>         unsigned int geometry, unsigned int mode, double wesn[], void *output, void *data);

- API

- family

- method

- geometry

- mode -- specific to each data type (see below)

- wesn

- output --

- data -- A pointer to any of the six families.

- Return: 0 on success, otherwise return -1 and set API->error to reflect to cause.

where `data` is a pointer to any of the four structures discussed previously.

Color palette table

  `mode` controls if the CPT’s back-, fore-, and NaN-colors should be written (1) or not (0).

Data table

  If `method` is `GMT_IS_FILE`, then the value of `mode` affects how the data set is written:

  GMT_WRITE_SET

    The entire data set will be written to the single file [0].

  GMT_WRITE_TABLE

    Each table in the data set is written to individual files [1]. You can either specify an output file name that must contain one C-style format specifier for an int variable (e.g., “New_Table_%06d.txt”), which will be replaced with the table number (a running number from 0) or you must assign to each table i a unique output file name via the `D->table[i]->file[GMT_OUT]` variables prior to calling the function.

  GMT_WRITE_SEGMENT

    Each segment in the data set is written to an individual file [2]. Same setup as for `GMT_WRITE_TABLE` except we use sequential segment numbers to build the file names.

  GMT_WRITE_TABLE_SEGMENT

    Each segment in the data set is written to an individual file [3]. You can either specify an output file name that must contain two C-style format specifiers for two int variables (e.g., “New_Table_%06d_Segment_%03d.txt”), which will be replaced with the table and segment numbers, or you must assign to each segment j in each table i a unique output file name via the `D->table[i]->segment[j]->file[GMT_OUT]` variables prior to calling the function.

  GMT_WRITE_OGR

    Writes the dataset in OGR/GMT format in conjunction with the `-a` setting [4].

Text table

  The `mode` is used the same way as for data tables.

GMT grid

  Here, `mode` may be `GMT_CONTAINER_ONLY` to only update a file’s header structure, but normally it is simply `GMT_CONTAINER_AND_DATA` so the entire grid and its header will be exported (a subset is not allowed during export). However, in the event your data array holds both the real and imaginary parts of a complex data set you must add either `GMT_GRID_IS_COMPLEX_REAL` or `GMT_GRID_IS_COMPLEX_IMAG` to `mode` so as to export the corresponding grid values correctly. Finally, for native binary grids you may skip writing the grid header by adding `GMT_GRID_NO_HEADER`; this setting is ignored for all other grid formats. If your output grid is huge and you are building it row-by-row, set `mode` to `GMT_CONTAINER_ONLY` | `GMT_GRID_ROW_BY_ROW`. You can then write the grid row-by-row using GMT_Put_Row. By default the rows will be automatically processed in order. To completely specify which row to be written, use `GMT_GRID_ROW_BY_ROW_MANUAL` instead; this requires a file format that supports direct writes, such as netCDF. Finally, if you are preparing a geographic grid outside of GMT you need to add the mode `GMT_GRID_IS_GEO` to ensure that the proper metadata will be written to the netCDF header, thus letting the grid be recognized as such.

Note: If `method` is GMT_IS_FILE, family is `GMT_IS_GRID`, and the filename implies a change from NaN to another value then the grid is modified accordingly. If you continue to use that grid after writing please be aware that the changes you specified were applied to the grid.

### Record-by-record output

In the case of data tables, you may also consider the GMT_Put_Record function for record-by-record writing. As a general rule, your program organization may simplify if you can write the entire resource with GMT_Write_Data. However, if the program logic is simple or already involves using GMT_Get_Record, it may be better to export one data record at the time via GMT_Put_Record. For grids there is the corresponding GMT_Put_Row function.

#### Enable Data Export

Similar to the data import procedures, once all output destinations have been registered, we signal the API that we are done with the registration phase and are ready to start the actual data export. As for input, this step is only needed when dealing with record-by-record writing. Again, we enable record-by-record writing by calling GMT_Begin_IO, this time with `direction` = `GMT_OUT`. This function enables data export and prepares the registered destinations for the upcoming writing.

##### Specifying the number of output columns

For record-based ASCII input/output you will need to specify the number of columns, unless for output it equals the number of input columns. This is done with the GMT_Set_Columns function:

>     void *GMT_Set_Columns (void *API, unsigned int direction, unsigned int n_columns, unsigned int mode);

The `n_columns` is a number related to the number of columns you plan to read/write, while `mode` controls what that number means. For input, `mode` = `GMT_COL_FIX` sets the actual number of numerical columns to read. Anything beyond is considered trailing text and is parsed unless you use `GMT_COL_FIX_NO_TEXT` instead. If your records have variable number of numerical columns then you may use `GMT_COL_VAR`. For output, you can also select from other modes. Here, `mode` = `GMT_COL_ADD` means it should be added to the known number of input columns to arrive at the number of final output columns, while `mode` = `GMT_COL_SUB` means this value should be subtracted from the number of input columns to find the number of output columns.

#### Exporting a data record

If your program must write data table records one-by-one you must first enable record-by-record writing with GMT_Begin_IO and then use the `GMT_Put_Record` function in a loop; the prototype is

>     int GMT_Put_Record (void *API, unsigned int mode, void *rec);

where `rec` is a pointer to (a) a GMT_RECORD structure for the current row. Alternatively (b), `rec` points to a text string. The `mode` parameter must be set to reflect what is passed. Using GMT_Put_Record requires you to first initialize the destination with GMT_Init_IO. Note that for `GMT_IS_DATASET` the methods `GMT_IS_DUPLICATE` and `GMT_IS_REFERENCE` are not supported since you can simply populate the GMT_DATASET structure directly. As mentioned, `mode` affects what is actually written:

GMT_WRITE_DATA.

  Normal operation that builds the current output record from the numerical values in `rec`.

GMT_WRITE_TABLE_HEADER.

  For ASCII output mode we write the text string `rec`. If `rec` is NULL then we write the last read header record. If binary output mode we quietly skip writing this record.

GMT_WRITE_SEGMENT_HEADER.

  For ASCII output mode we use the text string `rec` as the segment header. If `rec` is NULL then we use the current (last read) segment header record. If binary output mode instead we write a record composed of NaNs.

The function returns 1 if there was an error associated with the writing (which is passed back with `API->error`), otherwise it returns 0 (`GMT_NOERROR`).

#### Exporting a grid row

If your program must write a grid file row-by-row you must first enable row-by-row writing with GMT_Read_Data and then use the GMT_Put_Row function in a loop; the prototype is

>     int GMT_Put_Row (void *API, int row_no, struct GMT_GRID *G, float *row);

where `row` is a pointer to a single-precision array with the current row, `G` is the grid in question, and `row_no` is the number of the current row to be written. Note this value is only considered if the row-by-row mode was initialized with `GMT_GRID_ROW_BY_ROW_MANUAL`.

#### Disable Data Export

Once the record-by-record output has completed we disable further output to prevent accidental writing from occurring (due to poor program structure, bugs, etc.). We do so by calling GMT_End_IO. This function disables further record-by-record data export; here, we obviously pass `direction` as `GMT_OUT`.

### Destroy allocated resources

If your session imported any data sets into memory then you may explicitly free this memory once it is no longer needed and before terminating the session. This is done with the GMT_Destroy_Data function, whose prototype is

>     int GMT_Destroy_Data (void *API, void *data);

where `data` is the address of the pointer to a data container, i.e., not the pointer to the container but the address of that pointer (e.g. &pointer). Note that when each module completes it will automatically free memory created by the API; similarly, when the session is destroyed we also automatically free up memory. Thus, `GMT_Destroy_Data` is therefore generally only needed when you wish to directly free up memory to avoid running out of it. The function returns 1 if there is an error when trying to free the memory (the error code is passed back with `API->error`), otherwise it returns 0 (`GMT_NOERROR`).

### Destroy groups of allocated resources

If you obtained an array of resources via GMT_Read_Group then you will need to destroy these resources with GMT_Destroy_Group instead, whose prototype is

>     int GMT_Destroy_Group (void *API, void *data, unsigned int n);

where `data` is the address of the array with data containers, i.e., not the array to the containers but the address of that array (e.g. &array), and `n` is the number of containers.

### Free other allocated memory

Some GMT functions may allocate memory that is not part of the containers and thus cannot be freed with GMT_Destroy_Data. For these cases there is the GMT_Free function, whose prototype is

>     int GMT_Free (void *API, void *ptr);

where `ptr` is the address of the pointer to arbitrary data allocated by the GMT API. The most common use of this function is to free the resources returned by GMT_Encode_Options.

### Terminate a GMT session

Before your program exits it should properly terminate the GMT session, which involves a call to

>     int GMT_Destroy_Session (void *API);

which simply takes the pointer to the GMT API control structure as its only arguments. It terminates the GMT machinery and deallocates all memory used by the GMT API book-keeping. It also unregisters any remaining resources previously registered with the session. The GMT API will only close files that it was responsible for opening in the first place. Finally, the API structure itself is freed so your main program does not need to do so. The function returns 1 if there is an error when trying to free the memory (the error code is passed back with `API->error`), otherwise it returns 0 (`GMT_NOERROR`).

### Presenting and accessing GMT options

As you develop a program you may wish to rely on some of the GMT common options. For instance, you may wish to have your program present the `-R` option to the user, let GMT handle the parsing, and examine the values. You may also wish to encode your own custom options that may require you to parse user text into the corresponding floating point dimensions, constants, coordinates, absolute time, etc. The API provides several functions to simplify these tedious parsing tasks. This section is intended to show how the programmer will obtain information from the user that is necessary to do the task at hand (e.g., special options to provide values and settings for the program). In the following section we will concern ourselves with preparing arguments for calling any of the GMT modules.

#### Display usage syntax for GMT common options

You can have your program menu display the standard usage message for a GMT common option by calling the function

>     int GMT_Option (void *API, const char *options);

where `options` is a comma-separated list of GMT common options (e.g., “R,J,O,X”). You can repeat this function with different sets of options in order to intersperse your own custom options within an overall alphabetical order; see any GMT module for examples of typical layouts.

#### Parsing the GMT common options

The parsing of all GMT common option is done by on call to

>     int GMT_Parse_Common (void *API, const char *args, struct GMT_OPTION *list);

where `args` is a string of the common GMT options your program is allowed to use. An error will be reported if any of the common GMT options fail to parse, and if so we return 1; if no errors we return 0. All other options, including file names, will be silently ignored. The parsing will update the internal GMT information structure that affects module operations.

#### Inquiring about the GMT common options

The API provide only a limited window into the full GMT machinery accessible to the modules. You can determine if a particular common option has been parsed and in some cases determine the values that were set with

>     int GMT_Get_Common (void *API, unsigned int option, double *par);

where `option` is a single option character (e.g., ‘R’) and `par` is a double array with at least a length of 6. If the particular option has been parsed then the function returns the number of parameters passed back via `par`; otherwise we return -1. For instance, to determine if the `-R` was set and to obtain the specified region you may call

>     if (GMT_Get_Common (API, 'R', wesn)) != -1) {
>         /* wesn now contains the boundary information */
>     }

The `wesn` array could now be passed to the various read and create functions for GMT resources.

#### Parsing text values

Your program may need to request values from the user, such as distances, plot dimensions, coordinates, date/time strings and other data. The conversion from such text to actual distances, taking units into account, is tedious to program. You can simplify this by using

>     int GMT_Get_Values (void *API, const char *arg, double par[], int maxpar);

where `arg` is the text item with one or more values that are separated by commas, spaces, tabs, semi-colons, or slashes, and `par` is an array of length `maxpar` long enough to hold all the items you are parsing. The function returns the number of items parsed with a maximum of `maxpar`, or -1 if there is an error. For instance, assume the character string `origin` was given by the user as two geographic coordinates separated by a slash (e.g., `"35:45W/19:30:55.3S"`). We obtain the two coordinates in decimal degrees by calling

>     n = GMT_Get_Values (API, origin, pair, 2);

Your program can now check that `n` equals 2 and then use the values in `pairs` separately. Note: Dimensions given with units of inches, cm, or points are converted to the current default unit set via PROJ_LENGTH_UNIT, while distances given in km, nautical miles, miles, feet, or survey feet are returned in meters. Arc lengths in minutes and seconds are returned in decimal degrees, and date/time values are returned in seconds since the current epoch [1970].

#### Get or set an API or GMT default parameter

If your program needs to determine one or more of the current API or GMT default settings you can do so via

>     int GMT_Get_Default (void *API, const char *keyword, char *value);

where `keyword` is one such keyword (e.g., PROJ_LENGTH_UNIT) and `value` must be a character string long enough to hold the answer. In addition to the long list of GMT defaults you can also inquire about the following API parameters:

> - `API_PAD` - the current pad setting

> - `API_IMAGE_LAYOUT` - the order and structure of image memory storage

> - `API_GRID_LAYOUT` - order of grid memory storage

> - `API_VERSION` - the API version string

> - `API_CORES` - the number of cores seen by the API

> - `API_BINDIR` - the API (GMT) executable path

> - `API_SHAREDIR` - the API (GMT) shared directory path

> - `API_DATADIR` - the API (GMT) data directory path

> - `API_PLUGINDIR` - the API (GMT) plugin path

> - `API_BIN_VERSION` - the API version string with Git commit information

Depending on what parameter you selected you could further convert it to a numerical value with GMT_Get_Values or just use it in a text comparison.

To change any of the API or GMT default settings programmatically you would use

>     int GMT_Set_Default (void *API, const char *keyword, const char *value);

where as before `keyword` is one such keyword (e.g., PROJ_LENGTH_UNIT) and `value` must be a character string with the new setting. Note that all settings must be passed as text strings even if many are inherently integers or floats.

#### Get an API enum constant

The GMT API enum constants that are part of the API are defined in the include file gmt_resources.h, which is included by gmt.h. So, if you are writing an application in C/C++ you are including gmt.h and thus have access to all the API enums directly. However, if your application is written in other languages and you are perhaps just interfacing with the shared GMT API library, then you can access any GMT enum via

>     int GMT_Get_Enum (void *API, const char *enumname);

where `enumname` is the name of one such enum (e.g., GMT_SESSION_EXTERNAL, GMT_IS_DATASET, etc.), including the ones listed in types and types; see gmt_resources.h for the full listing. The function returns the corresponding integer value. For unrecognized names we return -99999. Note: You may pass a NULL pointer as API if you need to obtain enum values prior to calling GMT_Create_Session.

For indexed access to custom grids and images we may need to know the internal matrix layout. You can change this information via

>     int64_t GMT_Set_Index (struct GMT_GRID_HEADER *header, char *code);

where the `header` is the header of either a grid or image, and `code` is a three-character code indication …

#### Change allocation mode

When external programs supply their own allocated memory (e.g., grid arrays, matrices) that are then hooked into the GMT containers data pointer, we need to flag the allocation mode as being external to GMT via

>     int GMT_Set_AllocMode (void *API, unsigned int family, void *object);

where family sets the object type and and `object` is the container. This change prevents GMT from trying to free memory it did not allocate.

### Call a module

One of the advantages of programming with the API is that you have access to the high-level GMT modules. For example, if your program must compute the distance from a node to all other nodes in the grid then you can simply set up options and call grdmath to do it for you and accept the result back as an input grid. All the module interfaces are identical and are called via

>     int GMT_Call_Module (void *API, const char *module, int mode, void *args);

Here, `module` is the name of any of the GMT modules, such as plot or grdvolume. All GMT modules may be called with one of three sets of `args` depending on `mode`. The three modes differ in how the options are passed to the module:

> mode = `GMT_MODULE_EXIST`.

>   Return GMT_NOERROR (0) if the module exists, nonzero otherwise.

> mode = `GMT_MODULE_PURPOSE`.

>   Just print the one-line purpose of the module; args must be NULL.

> mode = `GMT_MODULE_LIST`.

>   Just prints a list of all modules (including those given as plugins); args must be NULL.

> mode = `GMT_MODULE_OPT`.

>   Expects `args` to be a pointer to a doubly-linked list of objects with individual options for the current program. We will see how API functions can help prepare and maintain such lists.

> mode = `GMT_MODULE_CMD`.

>   Expects `args` to be a single text string with all needed options.

> mode > 0.

>   Expects `args` to be an array of text strings and `mode` to be a count of how many options are passed (i.e., the `argc, argv[]` model used by the GMT programs themselves).

From external interfaces and with a debug verbosity level set, `GMT_Call_Module` will also print out the equivalent command line to standard error (or its substitute).

#### Set program options via text array arguments

When `mode > 0` we expect an array `args` of character strings that each holds a single command line option (e.g., “-R120:30/134:45/8S/3N”) and interpret `mode` to be the count of how many options are passed. This, of course, is almost exactly how the stand-alone GMT programs are called (and reflects how they themselves are activated internally). We call this the “argc-argv” mode. Depending on how your program obtains the necessary options you may find that this interface offers all you need.

#### Set program options via text command

If `mode =` 0 then `args` will be examined to see if it contains several options within a single command string. If so we will break these into separate options. This is useful if you wish to pass a single string such as “-R120:30/134:45/8S/3N -JM6i mydata.txt -Sc0.2c”. We call this the “command” mode and it is extensively used by the modules themselves.

#### Set program options via linked structures

The third, linked-list interface allows developers using higher-level programming languages to pass all command options via a pointer to a NULL-terminated, doubly-linked list of option structures, each containing information about a single option. Here, instead of text arguments we pass the pointer to the linked list of options mentioned above, and `mode` must be passed as `GMT_MODULE_OPT`. Using this interface can be more involved since you need to generate the linked list of program options; however, utility functions exist to simplify its use. This interface is intended for programs whose internal workings are better suited to generate such arguments -- we call this the “options” mode. The order in the list is not important as GMT will sort it internally according to need. The option structure is defined below.

>     struct GMT_OPTION {
>         char               option;  /* Single option character (e.g., 'G' for -G) */
>         char              *arg;     /* String with arguments (NULL if not used) */
>         struct GMT_OPTION *next;    /* Next option pointer (NULL for last option) */
>         struct GMT_OPTION *prev;    /* Previous option (NULL for first option) */
>     };

#### Convert between text and linked structures

To assist programmers there are also two convenience functions that allow you to convert between the two argument formats. They are

>     struct GMT_OPTION *GMT_Create_Options (void *API, int argc, void *args);

This function accepts your array of text arguments (cast via a void pointer), allocates the necessary space, performs the conversion, and returns a pointer to the head of the linked list of program options. However, in case of an error we return a NULL pointer and set `API->error` to indicate the nature of the problem. Otherwise, the pointer may now be passed to the relevant GMT module. Note that if your list of text arguments were obtained from a C `main()` function then `argv[0]` will contain the name of the calling program. To avoid passing this as a bad file name option, call GMT_Create_Options with `argc-1` and `argv+1` instead. If you wish to pass a single text string with multiple options (in lieu of an array of text strings), then pass `argc` = 0. When no longer needed you can remove the entire list by calling

>     int GMT_Destroy_Options (void *API, struct GMT_OPTION **list);

The function returns 1 if there is an error (which is passed back with `API->error`), otherwise it returns 0 (`GMT_NOERROR`).

The inverse function prototype is

>     char **GMT_Create_Args (void *API, int *argc, struct GMT_OPTION *list);

which allocates space for the text strings and performs the conversion; it passes back the count of the arguments via `argc` and returns a pointer to the text array. In the case of an error we return a NULL pointer and set `API->error` to reflect the error type. Note that `argv[0]` will not contain the name of the program as is the case the arguments presented by a C `main()` function. When you no longer have any use for the text array, call

>     int GMT_Destroy_Args (void *API, int argc, char **argv[]);

to deallocate the space used. This function returns 1 if there is an error (which is passed back with `API->error`), otherwise it returns 0 (`GMT_NOERROR`).

Finally, to convert the linked list of option structures to a single text string command, use

>     char *GMT_Create_Cmd (void *API, struct GMT_OPTION *list);

Developers who plan to import and export GMT shell scripts might find it convenient to use these functions. In case of an error we return a NULL pointer and set `API->error`, otherwise a pointer to an allocated string is returned. When you no longer have any use for the text string, call

>     int GMT_Destroy_Cmd (void *API, char **string);

to deallocate the space used. This function returns 1 if there is an error (which is passed back with `API->error`), otherwise it returns 0 (`GMT_NOERROR`).

#### Manage the linked list of options

Several additional utility functions are available for programmers who wish to manipulate program option structures within their own programs. These allow you to create new option structures, append them to the linked list, replace existing options with new values, find a particular option, and remove options from the list. Note: The order in which the options appear in the linked list is of no consequence to GMT. Internally, GMT will sort and process the options in the manner required. Externally, you are free to maintain your own order.

##### Make a new option structure

GMT_Make_Option will allocate a new option structure, assign values given the `option` and `arg` parameters (pass NULL if there is no argument for this option), and return a pointer to the allocated structure. The prototype is

>     struct GMT_OPTION *GMT_Make_Option (void *API, char option, const char *arg);

Should memory allocation fail the function will print an error message pass an error code via `API->error`, and return NULL.

##### Append an option to the linked list

GMT_Append_Option will append the specified `option` to the end of the doubly-linked `list`. The prototype is

>     struct GMT_OPTION *GMT_Append_Option (void *API, struct GMT_OPTION *option,
>         struct GMT_OPTION *list);

We return the list back, and if `list` is given as NULL we return `option` as the start of the new list. Any errors result in a NULL pointer with `API->error` holding the error type.

##### Find an option in the linked list

GMT_Find_Option will return a pointer `ptr` to the first option in the linked list starting at `list` whose option character equals `option`. If not found we return NULL. While this is not necessarily an error we still set `API->error` accordingly. The prototype is

>     struct GMT_OPTION *GMT_Find_Option (void *API, char option,
>         struct GMT_OPTION *list);

If you need to look for multiple occurrences of a certain option you will need to call GMT_Find_Option again, passing the option following the previously found option as the `list` entry, i.e.,

>     list = *ptr->next;

##### Update an existing option in the list

GMT_Update_Option will replace the argument of `current` with the new argument `arg` and otherwise leave the option at its place in the list. The prototype is

>     int GMT_Update_Option (void *API, struct GMT_OPTION *current, const char *arg);

An error will be reported if (a) `current` is NULL or (b) `arg` is NULL. The function returns 1 if there is an error, otherwise it returns 0 (`GMT_NOERROR`).

##### Delete an existing option in the linked list

You may use GMT_Delete_Option to remove the `current` option from the linked `list`. The prototype is

>     int GMT_Delete_Option (void *API, struct GMT_OPTION *current, struct GMT_OPTION **head);

We return 1 if the option is not found in the list and set `API->error` accordingly. Note: Only the first occurrence of the specified option will be deleted. If you need to delete all such options you will need to call this function in a loop until it returns a non-zero status.

##### Specify a file via a linked option

To specify an input file name via an option, simply use < as the option (this is what GMT_Create_Options does when it finds filenames on the command line). Likewise, > can be used to explicitly indicate an output file. In order to append to an existing file, use ). For example the following command would read from file.A and append to file.B:

>     gmt convert -<file.A -)file.B

These options also work on the command line but usually one would have to escape the special characters <, > and ) as they are normally used for file redirection.

##### Encode option arguments for external interfaces

Developers writing interfaces between GMT and external platforms such as other languages (Python, Java, Julia, etc.) or tools (MATLAB, Octave, etc.) need to manipulate linked options in a special way. For instance, a GMT call in the MATLAB or Octave application might look like

    table = gmt('blockmean -R30W/30E/10S/10N -I2m', [x y z]);
    grid  = gmt('surface -R -I2m -Lu', table, high_limit_grid);
    grid2 = gmt('grdmath ? LOG10 ? MUL', grid, grid);

Most of the time our implicit rules will take care of the ordering. The rule says that all required input data items must be listed before any secondary input data items, and all primary output items must be listed on the left hand side before any secondary output items. There are three situations where the parsing will need further help; (1) Specifying the positions of memory arguments given to gmtmath, (2) specifying the positions of memory arguments given to grdmath, and (3) using -R? when passing a memory grid to the -R option (since just -R means use the previous region in the command history). Thus, in the gmtmath call we we needed to specify where the specific arguments should be placed among the operators. API developers will rely on GMT_Open_VirtualFile to convert the above syntax to correct options for GMT_Call_Module. The prototype is

>     struct GMT_RESOURCE *GMT_Encode_Options (void *API, const char *module, int n_in,
>                                                struct GMT_OPTION **head, int *n_items);

where `module` is the name of the module whose linked options are pointed to by `*head`, `n_in` contains the number of input objects we have to connect (or -1 if not known) and we return an array that contains specific information for those options that (after processing) contain explicit memory references. The number of items in the array is returned via the `n_items` variable. The function returns NULL if there are errors and sets `API->error` to the corresponding error number. The GMT_RESOURCE structure is defined below:

    struct GMT_RESOURCE {        /* Information for passing external resources */
        enum GMT_enum_family family;     /* GMT data family */
        enum GMT_enum_geometry geometry; /* One of the recognized GMT geometries */
        enum GMT_enum_std direction;     /* Either GMT_IN or GMT_OUT */
        struct GMT_OPTION *option;       /* Pointer to the corresponding module option */
        int object_ID;                   /* Object ID returned by GMT_Register_IO */
        int pos;                         /* Index into external object in|out arrays */
        int mode;                        /* 0 means primary i/o object, 1 means secondary */
        void *object;                    /* Pointer to the registered GMT object */
    };

API developers will need to provide specific code to handle the registration of native structures in their language or application and to translate between the GMT resources and the corresponding native items. Developers should look at an existing and working interface such as the GMT/MATLAB toolbox to see the required steps. Note: The array of structures returned by GMT_Encode_Options should be freed by GMT_Free.

##### Expand an option with explicit memory references

When the external tool or application knows the name of the special file names used for memory references the developer should replace the place-holder `?` character in any option string with the actual reference name. This is accomplished by calling GMT_Expand_Option, with prototype

>     int GMT_Expand_Option (void *API, struct GMT_OPTION *option, const char *name);

where `option` is the current option and `name` is the special file name for the memory reference.

## The GMT FFT Interface

While the i/o options presented so far lets you easily read in a data table or grid and manipulate them, if you need to do the manipulation in the wavenumber domain then this chapter is for you. Here, we outline how to take the Fourier transform of such data, perform calculations in the wavenumber domain, and take the inverse transform before writing the results. To assist programmers we also distribute fully functioning demonstration programs that takes you through the steps we are about to discuss; these demo programs may be used as your starting point for further development and can be found in the gmt-custom repository.

### Presenting and parsing the FFT options

Several GMT programs that use the FFTs present the same unified option and modifier sets to the user. The API makes these available as well. If your program needs to present the FFT option usage you can call

>     unsigned int GMT_FFT_Option (void *API, char option, unsigned int dim,
>                                    const char *string);

Here, `option` is the unique character used for this particular program option (most GMT programs have standardized on using ‘N’ but you are free to choose whatever letter you want except existing GMT common options). The `dim` sets the dimension of the transform; currently you must choose 1 or 2, while `string` is a one-line message that states what the option does; you should tailor this to your program. If NULL then a generic message is placed instead.

To parse the user’s selection you call

>     void *GMT_FFT_Parse (void *API, char option, unsigned int dim, const char *arg);

which accepts the user’s string option via `arg`; the other arguments are the same as those above. The function returns an opaque pointer to a structure with the chosen parameters.

### Initializing the FFT machinery

Before your can take any transforms you must initialize the FFT machinery. This process involves a series of preparatory steps that are conveniently performed for you by

>     void *GMT_FFT_Create (void *API, void *X, unsigned int dim,
>                             unsigned int mode, void *F);

Here, `X` is either your dataset or grid pointer, `dim` is the dimension of the transform (1 or 2 only), `mode` passes various flags to the setup, such as whether the data is real, imaginary, or complex, and `F` is the opaque pointer previously returned by GMT_FFT_Parse. Depending on the option string you passed to GMT_FFT_Parse, the data may have a constant level or a trend removed, mirror reflected and extended by various symmetries, padded and tapered to desired transform dimensions, and possibly temporary files are written out before the transform takes place. See the grdfft man page for a full explanation of the options presented by GMT_FFT_Option.

### Taking the FFT

Now that everything has been set up you can perform the transform with

>     void *GMT_FFT (void *API, void *X, int direction, unsigned int mode, void *K);

which takes as `direction` either `GMT_FFT_FWD` or `GMT_FFT_INV`. The `mode` is used to specify if we pass a real (`GMT_FFT_REAL`) or complex (`GMT_FFT_COMPLEX`) data set, and `K` is the opaque pointer returned by GMT_FFT_Create. The transform is performed in place and returned via `X`. When done with your manipulations (below) you can call it again with the inverse direction to recover the corresponding space-domain version of your data. The FFT is fully normalized so that calling forward followed by inverse yields the original data set. The information passed via `K` determines if a 1-D or 2-D transform takes place; the key work is done via `GMT_FFT_1D` or `GMT_FFT_2D`, as explained below. Note: When `direction` is `GMT_FFT_INV` we will remove the space for the temporary imaginary components so that the result is real-valued only; this is the most common use in spectral analysis. However, you can add `GMT_FFT_NO_DEMUX` to `mode` which will prevent this adjustment.

### Taking the 1-D FFT

A lower-level 1-D FFT is also available via the API, i.e.,

>     int GMT_FFT_1D (void *API, float *data, uint64_t n, int direction,
>         unsigned int mode);

which takes as `direction` either `GMT_FFT_FWD` or `GMT_FFT_INV`. The `mode` is used to specify if we pass a real (`GMT_FFT_REAL`) or complex (`GMT_FFT_COMPLEX`) data set, and `data` is the 1-D data array of length `n` that we wish to transform. The transform is performed in place and returned via `data`. When done with your manipulations (below) you can call it again with the inverse direction to recover the corresponding space-domain version of your data. The 1-D FFT is fully normalized so that calling forward followed by inverse yields the original data set.

### Taking the 2-D FFT

A lower-level 2-D FFT is also available via

>     int GMT_FFT_2D (void *API, float *data, unsigned int n_columns,
>                       unsigned int n_rows, int direction, unsigned int mode);

which takes as `direction` either `GMT_FFT_FWD` or `GMT_FFT_INV`. The `mode` is used to specify if we pass a real (`GMT_FFT_REAL`) or complex (`GMT_FFT_COMPLEX`) data set, and `data` is the 2-D data array in row-major format, with row length `n_columns` and column length `n_rows`. The transform is performed in place and returned via `data`. When done with your manipulations (below) you can call it again with the inverse direction to recover the corresponding space-domain version of your data. The 2-D FFT is fully normalized so that calling forward followed by inverse yields the original data set.

### Wavenumber calculations

As your data have been transformed to the wavenumber domain you may wish to operate on the various values as a function of wavenumber. We will show how this is done for datasets and grids separately. First, we present the function that returns an individual wavenumber:

>     double GMT_FFT_Wavenumber (void *API, uint64_t k, unsigned int mode, void *K);

where `k` is the index into the array or grid, `mode` specifies which wavenumber we want (it is not used for 1-D transform but for the 2-D transform we can select either the x-wavenumber (0), the y-wavenumber (1), or the radial wavenumber (2)), and finally the opaque vector created by GMT_FFT_Create.

#### 1-D FFT manipulation

[To be added after gmtfft has been added as new module, probably in 5.4.]

#### 2-D FFT manipulation

The number of complex pairs in the grid is given by the header’s `nm` variable, while `size` will be twice that value as it holds the number of components. To visit all the complex values and obtain the corresponding wavenumber we simply need to loop over `size` and call GMT_FFT_Wavenumber. This code snippet multiples the complex grid by the radial wavenumber:

>     uint64_t k;
>     for (k = 0; k < Grid->header->size; k++) {
>         wave = GMT_FFT_Wavenumber (API, k, 2, K);
>         Grid->data[k] *= wave;
>     }

Alternatively, you may choose to be more specific about which components are real and imaginary (especially if they are to be treated differently), and set up the loop this way:

>     uint64_t re, im;
>     for (re = 0, im = 1; re < Grid->header->size; re += 2, im += 2) {
>         wave = GMT_FFT_Wavenumber (API, re, 2, K);
>         Grid->data[re] *= wave;
>         Grid->data[im] *= 2.0 * wave;
>     }

### Manual demultiplexing

For almost all applications this step will be done automatically for you when you take the inverse FFT. However, if you need to have the result of the inverse transform still occupy a real/imaginary layout you will need to pass the special mode flag `GMT_FFT_NO_DEMUX` to `GMT_FFT` and then call

>     int GMT_FFT_Reset (void *API, void *data, unsigned int dim, unsigned int mode);

which does the delayed demultiplexing of the data.

### Destroying the FFT machinery

When done you terminate the FFT machinery with

>     int GMT_FFT_Destroy (void *API, void *K);

which simply frees up the memory allocated by the FFT machinery with GMT_FFT_Create.

## FORTRAN Support

FORTRAN 90 developers who wish to use the GMT API may use the same API functions as discussed in Chapter 2. As we do not have much (i.e., any) experience with modern FORTRAN we are not sure to what extent you are able to access the members of the various structures, such as the GMT_GRID structure. Thus, this part will depend on feedback and for the time being is to be considered preliminary and subject to change. We encourage you to take contact should you wish to use the API with your FORTRAN 90 programs.

### FORTRAN 77 Grid i/o

Because of a lack of structure pointers we can only provide a low level of support for FORTRAN 77. This API is limited to help you inquire, read and write GMT grids directly from FORTRAN 77. To inquire about the range of information in a grid, use

>     int gmt_f77_readgrdinfo (unsigned int dim[], double limits[], double inc[],
>                                char *title, char *remark, const char *file)

where `dim` returns the grid width, height, and registration, `limits` returns the min and max values for x, y, and z as three consecutive pairs, `inc` returns the x and y increments, while the `title` and `remark` return the values of these strings. The `file` argument is the name of the file we wish to inquire about. The function returns 0 unless there is an error. Note that you must declare your variables so that `limits` has at least 6 elements, `inc` has at least 2, and `dim` has at least 4.

To actually read the grid, we use

>     int gmt_f77_readgrd (float *array, unsigned int dim[], double wesn[],
>                            double inc[], char *title, char *remark, const char *file)

where `array` is the 1-D grid data array, `dim` returns the grid width, height, and registration, `limits` returns the min and max values for x, y, and z, `inc` returns the x and y increments, and the `title` and `remark` return the values of the corresponding strings. The `file` argument is the name of the file we wish to read from. The function returns 0 unless there is an error. Note on input, `dim[2]` can be set to 1, which means we will allocate the array for you; otherwise we assume space has already been secured. Also, if `dim[3]` is set to 1 we will in-place transpose the array from C-style row-major array order to FORTRAN column-major array order.

Finally, to write a grid to file you can use

>     int gmt_f77_writegrd_(float *array, unsigned int dim[], double wesn[], double inc[],
>                             const char *title, const char *remark, const char *file)

where `array` is the 1-D grid data array, `dim` specifies the grid width, height, and registration, `limits` may be used to specify a subset (normally, just pass zeros), `inc` specifies the x and y increments, while the `title` and `remark` supply the values of these strings. The `file` argument is the name of the file we wish to write to. The function returns 0 unless there is an error. If `dim[3]` is set to 1 we will in-place transpose the array from FORTRAN column-major array order to C-style row-major array order before writing. Note this means `array` will have been transposed when the function returns.

## External Interfaces

Developers may want to access GMT modules from external programming environments, such as MATLAB, Octave, Julia, Python, R, IDL, etc., etc. These all face similar challenges and hence this section will speak in somewhat abstract terms. Specific language addressing the challenges for some of the above-mentioned environments will follow below.

The C/C++ API for GMT makes it possible to call any of the ~100 core modules, the 40 or so supplemental modules, and any number of custom modules provided via shared libraries (e.g., the gsfml modules). Many of the external interfaces come equipped with methods to call C functions directly. The key challenges pertain to specifying the input to use in the module and to receive what is produced by the module. As we know from GMT command line usage, all GMT modules expect input to be given via input files (or stdin, except for sources like grids and images). Similarly, output will be written to a specified output file (or stdout if the data type supports it). Clearly, external interfaces could do the same thing. The problem is that most of the time we already will have the input data in memory and would prefer the output to be returned back to memory, thus avoiding using temporary files. Here, we will outline the general approach for using the GMT API. We will describe a relatively low-level approach to calling GMT modules. Once such an interface exists it is simpler to build a more flexible and user-friendly layer on top that can handle argument parsing in a form that makes the interface seem more of a natural extension of your external environment than a forced fit to GMT’s command-line heritage. Before we describe the interface it is important to understand that the GMT modules, since the beginning or time, have done the i/o inside the modules. While these steps are helped by i/o library functions, the i/o activities all take place inside the modules. This means that external environments in which the desired input data already reside in memory and the desired results should be returned back to memory pose a trickier challenge. We will see the solution to this involves the concept of virtual files.

GMT Modules can read and write information in may ways. The GMT command line modules can only access the methods in white, while all methods are available via the C API. External interfaces will preferentially want the methods in orange.

### Plain interface

While the syntax of your external environment’s language will dictate the details of the implementation, we will in general need to build a function (or class, or method) that allows you to issue a call like this:

[results] = gmt (module, options, inputs)

where results (i.e., objects returned back to memory) is optional and may be one or more items grouped together, depending on language syntax. If no output is required then no left-hand side assignment will be present. Likewise, inputs is optional and may be one or more comma-separated objects present in memory. In most cases, options will be required and this is a string with options very similar to the arguments given on the GMT command line. Finally, module is required since you must specify which one you want to call. The coding of the gmt method, class, or function above may be written entirely in C, partly in C and the external scripting language, or entirely in the scripting language, depending on restrictions on what needs to be done and where this is most easily accomplished. How this is accomplished may vary from environment to environment.

Data pass in and out of the gmt interface which may be written in the scripting language used by the external interface. The native data will need to be encapsulated by GMT containers and this step may be done by a C parser but could also be done by the gmt interface directly. Either of these communicate directly with the C functions in the GMT API.

### Data containers

The external interface developer will need to create native data classes or structures that are capable of containing the information associated with the six GMT objects: data tables, grids, images, cubes, color palette tables, and PostScript documents. In other words, how your external environment will represent these data in memory. Some of these “containers” may already exist, while others may need to be designed. Most likely, you will end up with a set of six containers that can hold the various GMT data objects and related metadata. In addition, it may be convenient to also consider the two GMT helper objects MATRIX and VECTOR, which may be closer to the native representation of your data than, for instance, the native GMT_DATASET.

### Input from memory

Whether input comes from memory or from external files, the call to a GMT module is the same: we have to specify filenames to provide the input data. Thus, the game is to provide virtual file names that represent our in-memory data. The process is relatively simple and may need to be done in a snippet of C code that can be called by a function written in your environments scripting language. The steps go like this:

1. Create a GMT C container marked for input and copy or reference your data provided by your external environment into this container.

2. Open a virtual file using this container to represent the input source.

3. Insert this virtual file name in the appropriate location in the GMT option string. If the module imports data from stdin then we can use the hidden option -<filename.

When the GMT module is run it will know how to make the connections between the virtual file names and the actual data via information stored inside the C API. When the module completes you should close any open virtual files that were used by the module.

### Output to memory

As the case for selecting input, GMT modules only know about writing results to a file (or stdout). Hence, we must follow the same paradigm as we did for input and identify virtual files to represent the output destinations. The steps are:

1. Create an empty GMT C container of the right type marked for output.

2. Create a virtual file name to represent this output destination.

3. Place this file name in the appropriate location in the GMT option string. If the module exports data to stdout then we can use the hidden option ->filename.

When the GMT module is run it will know how to make the connections between the memory allocated by the module and the virtual file names stored inside the C API. Once the module call has completed you can access the results in the external environment by using GMT_Read_VirtualFile with the virtual filename you created earlier. This will return a GMT C container with the results, and you can now populate you external data containers with data produced by the GMT module.

### The magic of knowing

External developers have access to the two extra API functions GMT_Encode_Options and GMT_Expand_Option. Your gmt will need to call GMT_Encode_Options to obtain information about what the selected module expects, what its options are, which were selected, and what data types are expected. It may possibly modify the options, such as adding the filename “?” to options that set required input and output files and returns an array of structures with specific information about all inputs and outputs. If sources and destinations were missing from your options string it is taken to mean that you want to associate these sources and destinations with memory locations rather than actual files. The second function GMT_Expand_Option can then then used to replace these place-holder names with the virtual filenames you created earlier.

#### The MATLAB interface

We have built a MATLAB/Octave interface to GMT called the toolbox. It was our first attempt to use the C API from an external environment and its development influenced how we designed the final GMT C API. MATLAB represents most data as matrices but there are also structures that can hold many different items, including several matrices and text strings. Thus, we designed several native mex structures that represent the six GMT objects. The main gmt function available in MATLAB derives from a small MATLAB script (gmt.m) which handles basic argument testing and then passes the arguments to our C function gmtmex.c. Most of the high-level parsing of options and arguments is done in this function, but we also rely on a C library (gmtmex_parser.c) that hides the details of the implementation. It is this library that does most of the work in translating between the GMT and MATLAB object layouts. Knowing what types are represented by the different sources and destinations is provided by the array of structures returned by GMT_Encode_Options.

#### The Julia interface

Unlike the MATLAB interface, the Julia interface GMT.jl is written entirely in the Julia language.

#### The Python interface

Unlike the MATLAB interface, the Python interface PyGMT is written entirely in the Python language.

### Appendix A: GMT resources

We earlier introduced the six standard GMT resources (dataset, grid, image, cube, color palette table, PostScript) as well as the user vector and matrix. Here are the complete definitions of these structures, including all variables accessible via the structures.

#### Data set

Each data set is represented by a GMT_DATASET that consists of one or more data tables represented by a GMT_DATATABLE, and each table consists of one or more segments represented by a GMT_DATASEGMENT, and each segment contains one or more rows of a fixed number of columns.

    struct GMT_DATASET { /* Single container for an array of GMT tables (files) */
        /* Variables we document for the API: */
        uint64_t               n_tables;       /* Total number of tables (files) contained */
        uint64_t               n_columns;      /* Number of data columns */
        uint64_t               n_segments;     /* Total number of segments across all tables */
        uint64_t               n_records;      /* Total number of data records across all tables */
        double                 *min;           /* Minimum coordinate for each column */
        double                 *max;           /* Maximum coordinate for each column */
        struct GMT_DATATABLE   **table;        /* Pointer to array of tables */
        unsigned int           type;           /* The data record type of this dataset */
        unsigned int           geometry;       /* The geometry of this dataset */
        const char             *ProjRefPROJ4;  /* To store a referencing system string in PROJ.4 format */
        const char             *ProjRefWKT;    /* To store a referencing system string in WKT format */
        int                    ProjRefEPSG;    /* To store a referencing system EPSG code */
        void                   *hidden;        /* ---- Variables "hidden" from the API ---- */
    };

Here is the full definition of the `GMT_DATATABLE` structure:

    struct GMT_DATATABLE {  /* To hold an array of line segment structures and header information in one container */
        /* Variables we document for the API: */
        unsigned int n_headers;           /* Number of file header records (0 if no header) */
        uint64_t n_columns;               /* Number of columns (fields) in each record */
        uint64_t n_segments;              /* Number of segments in the array */
        uint64_t n_records;               /* Total number of data records across all segments */
        double *min;                      /* Minimum coordinate for each column */
        double *max;                      /* Maximum coordinate for each column */
        char **header;                    /* Array with all file header records, if any) */
        struct GMT_DATASEGMENT **segment; /* Pointer to array of segments */
        void *hidden;                     /* ---- Variables "hidden" from the API ---- */
    };

Here is the full definition of the `GMT_DATASEGMENT` structure:

    struct GMT_DATASEGMENT {     /* For holding segment lines in memory */
        /* Variables we document for the API: */
        uint64_t n_rows;         /* Number of points in this segment */
        uint64_t n_columns;      /* Number of fields in each record (>= 2) */
        double *min;             /* Minimum coordinate for each column */
        double *max;             /* Maximum coordinate for each column */
        double **data;           /* Data x,y, and possibly other columns */
        char **text;             /* trailing text strings beyond the data */
        char *label;             /* Label string (if applicable) */
        char *header;            /* Segment header (if applicable) */
        void *hidden;            /* ---- Variables "hidden" from the API ---- */
     };

#### GMT grid

A grid is represented by a GMT_GRID that consists of a header structure represented by a GMT_GRID_HEADER and an float array `data` that contains the grid values.

    struct GMT_GRID {                        /* To hold a GMT float grid and its header in one container */
        struct GMT_GRID_HEADER *header;      /* Pointer to full GMT header for the grid */
        float                  *data;        /* Pointer to the float grid */
        double                 *x, *y;       /* Vector of coordinates */
        void *hidden;                        /* ---- Variables "hidden" from the API ---- */
    };

The full definition of the `GMT_GRID_HEADER` structure. Most of these members are only used internally:

    struct GMT_GRID_HEADER {
        /* Variables we document for the API:
           They are copied verbatim to the native grid header and must be 4-byte unsigned ints. */
        uint32_t n_columns;                   /* Number of columns */
        uint32_t n_rows;                      /* Number of rows */
        uint32_t registration;                /* GMT_GRID_NODE_REG (0) or GMT_GRID_PIXEL_REG (1) */

        /* == The types of the following 12 elements must not be changed.
           == They are also copied verbatim to the native grid header. */
        double wesn[4];                         /* Min/max x and y coordinates */
        double z_min;                           /* Minimum z value */
        double z_max;                           /* Maximum z value */
        double inc[2];                          /* x and y increment */
        double z_scale_factor;                  /* grd values must be multiplied by this */
        double z_add_offset;                    /* After scaling, add this */
        char   x_units[GMT_GRID_UNIT_LEN80];    /* units in x-direction */
        char   y_units[GMT_GRID_UNIT_LEN80];    /* units in y-direction */
        char   z_units[GMT_GRID_UNIT_LEN80];    /* grid value units */
        char   title[GMT_GRID_TITLE_LEN80];     /* name of data set */
        char   command[GMT_GRID_COMMAND_LEN320];/* name of generating command */
        char   remark[GMT_GRID_REMARK_LEN160];  /* comments re this data set */
        /* == End of "untouchable" header.       */

        /* This section is flexible.  It is not copied to any grid header
           or stored in any file. It is considered private */
        unsigned int type;               /* Grid format */
        unsigned int bits;               /* Bits per value (e.g., 32 for ints/floats; 8 for bytes) */
        unsigned int complex_mode;       /* 0 = normal, GMT_GRID_IS_COMPLEX_REAL = real part of complex
                                                                                                        grid, GMT_GRID_IS_COMPLEX_IMAG = imag part of complex grid */
        unsigned int mx, my;             /* Actual dimensions of the grid in memory, allowing for the padding */
        size_t       nm;                 /* Number of data items in this grid (n_columns * n_rows) [padding is excluded] */
        size_t       size;               /* Actual number of items (not bytes) required to hold this grid (= mx * my), per band */
        size_t       n_alloc;            /* Bytes allocated for this grid */
        unsigned int n_bands;            /* Number of bands [1]. Used with IMAGE containers and macros to get ij index from row,col, band */
        unsigned int pad[4];             /* Padding on west, east, south, north sides [2,2,2,2] */
        const char  *ProjRefPROJ4;       /* To store a referencing system string in PROJ.4 format */
        const char  *ProjRefWKT;         /* To store a referencing system string in WKT format */
        float        nan_value;          /* Missing value as stored in grid file */
        double       xy_off;             /* 0.0 (registration == GMT_GRID_NODE_REG) or 0.5 ( == GMT_GRID_PIXEL_REG) */
        void        *hidden;             /* ---- Variables "hidden" from the API ---- */
    };

#### GMT image

An image is similar to a grid except it may have more than one layer (i.e., band). It is represented by a GMT_IMAGE structure that consists of the GMT_GRID_HEADER structure and an char array `data` that contains the image values. The type of the array is determined by the value of `type`. Note: The header size value reflects number of nodes per band, so the actual memory allocated will be size * n_bands.

    struct GMT_IMAGE {
        enum GMT_enum_type      type;             /* Data type, e.g. GMT_FLOAT */
        int                    *colormap;         /* Array with color lookup values */
        int                     n_indexed_colors; /* Number of colors in a color-mapped image */
        struct GMT_GRID_HEADER *header;           /* Pointer to full GMT header for the image */
        unsigned char          *data;             /* Pointer to actual image */
        unsigned char          *alpha;            /* Pointer to an optional transparency layer */
        const char             *color_interp;     /* Color interpretation name */
        double                 *x, *y;            /* Vector of coordinates */
        void                   *hidden;           /* ---- Variables "hidden" from the API ---- */
    };

#### GMT cube

A 3-D cube is similar to a grid but typically has more than one layer. It is represented by a GMT_CUBE structure that consists of the GMT_GRID_HEADER structure and an float array `data` that contains the cube values. Note: The header size value reflects number of nodes per layer, so the actual memory allocated will be size * n_bands, where the latter is one of the parameters in the header.

     struct GMT_CUBE {
          struct GMT_GRID_HEADER *header;      /* The full GMT header for the cube */
          float                  *data;        /* Pointer to the float 3-D array */
          unsigned int           mode;         /* Indicates data originated as a list of 2-D grids rather than a cube */
          double                 z_range[2];   /* Minimum/maximum z-dimension values (complements header->wesn) */
          double                 z_inc;        /* z-dimension increment (complements header->inc) (0 if variable z spacing) */
          double                 *x, *y, *z;   /* Arrays of x,y,z coordinates */
          char name[GMT_GRID_UNIT_LEN80];      /* Name of variable, if read from file (empty if default) */
          char units[GMT_GRID_UNIT_LEN80];     /* Units in 3rd direction (complements x_units, y_units, z_units)  */
          void                   *hidden;      /* ---- Variables "hidden" from the API ---- */
    };

#### CPT palette table

A CPT is represented by a GMT_PALETTE structure that contains several items, such as a GMT_LUT structure `data` that contains the color information per interval. The background, foreground and Nan-color values have colors specified by the GMT_BFN array structure `bfn`. As each actual color may be specified in different ways, including as an image, each color slice is represented by the GMT_FILL structure.

    struct GMT_PALETTE {         /* Holds all pen, color, and fill-related parameters */
        /* Variables we document for the API: */
        struct GMT_LUT       *data;               /* CPT lookup data read by GMT_read_cpt */
        struct GMT_BFN        bfn[3];             /* Structures with back/fore/nan fills */
        unsigned int          n_headers;          /* Number of CPT header records (0 if no header) */
        unsigned int          n_colors;           /* Number of colors in CPT lookup table */
        unsigned int          mode;               /* Flags controlling use of BFN colors */
        unsigned int          model;              /* RGB, HSV, CMYK */
        unsigned int          is_wrapping;        /* true if a cyclic colortable */
        unsigned int          is_gray;            /* true if only grayshades are needed */
        unsigned int          is_bw;              /* true if only black and white are needed */
        unsigned int          is_continuous;      /* true if continuous color tables have been given */
        unsigned int          has_pattern;        /* true if CPT contains any patterns */
        unsigned int          has_hinge;          /* true if CPT has a hinge */
        unsigned int          has_range;          /* true if CPT has a natural range */
        unsigned int          categorical;        /* true if CPT applies to categorical data */
        double                minmax[2];          /* The default range, if has_range is true */
        double                hinge;              /* The default hinge, if is_wrapping is true */
        double                wrap_length;        /* The default period, if has_hinge is true */
        char                **header;             /* Array with all CPT header records, if any) */
        void                 *hidden;             /* ---- Variables "hidden" from the API ---- */
    };

The full definition of the `GMT_LUT` structure.

    struct GMT_LUT {         /* For back-, fore-, and nan-colors */
        double                z_low, z_high, i_dz;
        double                rgb_low[4], rgb_high[4], rgb_diff[4];
        double                hsv_low[4], hsv_high[4], hsv_diff[4];
        unsigned int          annot;              /* 1 for Lower, 2 for Upper, 3 for Both */
        unsigned int          skip;               /* true means skip this slice */
        struct GMT_FILL      *fill;               /* For patterns instead of color */
        char                 *label;              /* For non-number labels */
    };

The full definition of the `GMT_BFN` structure:

    struct GMT_BFN {   /* For back-, fore-, and nan-colors */
        double                rgb[4];             /* Red, green, blue, and alpha */
        double                hsv[4];             /* Hue, saturation, value, alpha */
        unsigned int          skip;               /* true means skip this slice */
        struct GMT_FILL      *fill;               /* For patterns instead of color */
    };

The full definition of the `GMT_FILL` structure. Note: Not part of the GMT API:

    struct GMT_FILL {        /*! Holds fill attributes */
        double                rgb[4];             /* Chosen color if no pattern + Transparency 0-1 [0 = opaque] */
        double                f_rgb[4], b_rgb[4]; /* Colors applied to unset and set bits in 1-bit image */
        bool                  use_pattern;        /* true if pattern rather than rgb is set */
        int                   pattern_no;         /* Number of a predefined pattern, or -1 if not set */
        unsigned int          dpi;                /* Desired dpi of image building-block if use_pattern is true */
        char                  pattern[GMT_BUFSIZ];/* Full filename of user-defined raster pattern */
    };

#### PostScript text

Bulk PostScript is represented by a GMT_POSTSCRIPT structure that contains `data` that points to the text array containing `n_bytes` characters of raw PostScript code. The `mode` parameter reflects the status of the PostScript document.

    struct GMT_POSTSCRIPT {      /* Single container for a chunk of PostScript code */
        /* Variables we document for the API: */
        unsigned int n_headers;          /* Number of PostScript header records (0 if no header) */
        size_t n_bytes;                  /* Length of data array so far */
        unsigned int mode;               /* Bit-flag for header (1) and trailer (2) */
        char *data;                      /* Pointer to PostScript code */
        char **header;                   /* Array with all PostScript header records, if any) */
        void *hidden;                    /* ---- Variables "hidden" from the API ---- */
    };

#### Matrix

User matrices are represented by a GMT_MATRIX structure that contains `data` that points to an array of size `n_columns` by `n_rows`. The `type` indicates the memory type of the matrix, which is represented by the GMT_UNIVECTOR union.

    struct GMT_MATRIX {
        uint64_t             n_rows;        /* Number of rows in the matrix */
        uint64_t             n_columns;     /* Number of columns in the matrix */
        uint64_t             n_layers;      /* Number of layers in a 3-D matrix */
        enum GMT_enum_fmt    shape;         /* 0 = C (rows) and 1 = FORTRAN (cols) */
        enum GMT_enum_reg    registration;  /* 0 for gridline and 1 for pixel registration  */
        size_t               dim;           /* Allocated length of longest C or FORTRAN dim */
        size_t               size;          /* Byte length of data */
        enum GMT_enum_type   type;          /* Data type, e.g. GMT_FLOAT */
        double               range[6];      /* Contains xmin/xmax/ymin/ymax[/zmin/zmax] */
        union GMT_UNIVECTOR  data;          /* Union with pointer to actual matrix of the chosen type */
        char               **text;          /* Pointer to optional array of strings [NULL] */
        char               **header;        /* Array with all Vector header records, if any) */
        char command[GMT_GRID_COMMAND_LEN320]; /* name of generating command */
        char remark[GMT_GRID_REMARK_LEN160];   /* comments re this data set */
        const char          *ProjRefPROJ4;  /* To store a referencing system string in PROJ.4 format */
        const char          *ProjRefWKT;    /* To store a referencing system string in WKT format */
        int                  ProjRefEPSG;   /* To store a referencing system EPSG code */
        void                *hidden;        /* ---- Variables "hidden" from the API ---- */
    };

#### Vectors

User vectors are represented by a GMT_VECTOR structure that contains `data` that points to an array of `n_columns` individual vectors. The `type` array indicates the memory type of each vector. Each vector is represented by the GMT_UNIVECTOR union which can accommodate any data type.

    struct GMT_VECTOR {
        uint64_t             n_columns;     /* Number of vectors */
        uint64_t             n_rows;        /* Number of rows in each vector */
        enum GMT_enum_reg    registration;  /* 0 for gridline and 1 for pixel registration */
        enum GMT_enum_type  *type;          /* Array with data type for each vector */
        union GMT_UNIVECTOR *data;          /* Array with unions for each column */
        double               range[2];      /* The min and max limits on t-range (or 0,0) */
        char               **text;          /* Pointer to optional array of strings [NULL] */
        char               **header;        /* Array with all Vector header records, if any) */
        char command[GMT_GRID_COMMAND_LEN320]; /* name of generating command */
        char remark[GMT_GRID_REMARK_LEN160];   /* comments re this data set */
        const char          *ProjRefPROJ4;  /* To store a referencing system string in PROJ.4 format */
        const char          *ProjRefWKT;    /* To store a referencing system string in WKT format */
        int                  ProjRefEPSG;   /* To store a referencing system EPSG code */
        void                *hidden;        /* ---- Variables "hidden" from the API ---- */
    };

The full definition of the `GMT_UNIVECTOR` union that holds a pointer to any array or matrix type:

    union GMT_UNIVECTOR {
        uint8_t  *uc1;       /* Pointer for unsigned 1-byte array */
        int8_t   *sc1;       /* Pointer for signed 1-byte array */
        uint16_t *ui2;       /* Pointer for unsigned 2-byte array */
        int16_t  *si2;       /* Pointer for signed 2-byte array */
        uint32_t *ui4;       /* Pointer for unsigned 4-byte array */
        int32_t  *si4;       /* Pointer for signed 4-byte array */
        uint64_t *ui8;       /* Pointer for unsigned 8-byte array */
        int64_t  *si8;       /* Pointer for signed 8-byte array */
        float    *f4;        /* Pointer for float array */
        double   *f8;        /* Pointer for double array */
    };

### Appendix B: GMT constants

To increase readability we have encoded many simple integer constants as named enum. These are listed in the tables below and used as flags to various API functions.

> constant | description
> --- | ---
> GMT_CHAR | int8_t, 1-byte signed integer type
> GMT_UCHAR | int8_t, 1-byte unsigned integer type
> GMT_SHORT | int16_t, 2-byte signed integer type
> GMT_USHORT | uint16_t, 2-byte unsigned integer type
> GMT_INT | int32_t, 4-byte signed integer type
> GMT_UINT | uint32_t, 4-byte unsigned integer type
> GMT_LONG | int64_t, 8-byte signed integer type
> GMT_ULONG | uint64_t, 8-byte unsigned integer type
> GMT_FLOAT | 4-byte data float type
> GMT_DOUBLE | 8-byte data float type

> The known data types in the GMT API.

When GMT_Open_VirtualFile is used with a NULL pointer to create a virtual file for returning results from a GMT module and you are using a GMT_MATRIX or GMT_VECTOR as your container, you may prescribe the data type used for the underlying arrays. The constants below can be added to the `direction` argument in order to change the default data types [float for matrix and double for vector].

> constant | description
> --- | ---
> GMT_VIA_CHAR | Select GMT_CHAR as array type
> GMT_VIA_UCHAR | Select GMT_UCHAR as array type
> GMT_VIA_SHORT | Select GMT_SHORT as array type
> GMT_VIA_USHORT | Select GMT_USHORT as array type
> GMT_VIA_INT | Select GMT_INT as array type
> GMT_VIA_UINT | Select GMT_UINT as array type
> GMT_VIA_LONG | Select GMT_LONG as array type
> GMT_VIA_ULONG | Select GMT_ULONG as array type
> GMT_VIA_FLOAT | Select GMT_FLOAT as array type
> GMT_VIA_DOUBLE | Select GMT_DOUBLE as array type

> Flags to select the type of arrays used in output GMT_MATRIX or GMT_VECTOR.

### Footnotes

[ 1 ]

or via a very confusing and ever-changing myriad of low-level library functions for bold programmers.

[ 2 ]

Currently, C/C++, FORTRAN, MATLAB and Julia are being tested.

[ 3 ]

This may change in later releases.

[ 4 ]

However, there is no thread-support yet, so you will need to manage your own threads.