NetCDF C Interface Guide ************************ This document describes the C interface to the netCDF library. This document applies to netCDF version 3.6.1. This document was last updated on 16 January 2006. For a complete description of the netCDF format and utilities see *Note Top: (netcdf)Top. 1 Use of the NetCDF Library *************************** You can use the netCDF library without knowing about all of the netCDF interface. If you are creating a netCDF dataset, only a handful of routines are required to define the necessary dimensions, variables, and attributes, and to write the data to the netCDF dataset. (Even less are needed if you use the ncgen utility to create the dataset before running a program using netCDF library calls to write data.) Similarly, if you are writing software to access data stored in a particular netCDF object, only a small subset of the netCDF library is required to open the netCDF dataset and access the data. Authors of generic applications that access arbitrary netCDF datasets need to be familiar with more of the netCDF library. In this chapter we provide templates of common sequences of netCDF calls needed for common uses. For clarity we present only the names of routines; omit declarations and error checking; omit the type-specific suffixes of routine names for variables and attributes; indent statements that are typically invoked multiple times; and use ... to represent arbitrary sequences of other statements. Full parameter lists are described in later chapters. 1.1 Creating a NetCDF Dataset ============================= Here is a typical sequence of netCDF calls used to create a new netCDF dataset: nc_create /* create netCDF dataset: enter define mode */ ... nc_def_dim /* define dimensions: from name and length */ ... nc_def_var /* define variables: from name, type, ... */ ... nc_put_att /* put attribute: assign attribute values */ ... nc_enddef /* end definitions: leave define mode */ ... nc_put_var /* provide values for variables */ ... nc_close /* close: save new netCDF dataset */ Only one call is needed to create a netCDF dataset, at which point you will be in the first of two netCDF modes. When accessing an open netCDF dataset, it is either in define mode or data mode. In define mode, you can create dimensions, variables, and new attributes, but you cannot read or write variable data. In data mode, you can access data and change existing attributes, but you are not permitted to create new dimensions, variables, or attributes. One call to nc_def_dim is needed for each dimension created. Similarly, one call to nc_def_var is needed for each variable creation, and one call to a member of the nc_put_att family is needed for each attribute defined and assigned a value. To leave define mode and enter data mode, call nc_enddef. Once in data mode, you can add new data to variables, change old values, and change values of existing attributes (so long as the attribute changes do not require more storage space). Single values may be written to a netCDF variable with one of the members of the nc_put_var1 family, depending on what type of data you have to write. All the values of a variable may be written at once with one of the members of the nc_put_var family. Arrays or array cross-sections of a variable may be written using members of the nc_put_vara family. Subsampled array sections may be written using members of the nc_put_vars family. Mapped array sections may be written using members of the nc_put_varm family. (Subsampled and mapped access are general forms of data access that are explained later.) Finally, you should explicitly close all netCDF datasets that have been opened for writing by calling nc_close. By default, access to the file system is buffered by the netCDF library. If a program terminates abnormally with netCDF datasets open for writing, your most recent modifications may be lost. This default buffering of data is disabled by setting the NC_SHARE flag when opening the dataset. But even if this flag is set, changes to attribute values or changes made in define mode are not written out until nc_sync or nc_close is called. 1.2 Reading a NetCDF Dataset with Known Names ============================================= Here we consider the case where you know the names of not only the netCDF datasets, but also the names of their dimensions, variables, and attributes. (Otherwise you would have to do "inquire" calls.) The order of typical C calls to read data from those variables in a netCDF dataset is: nc_open /* open existing netCDF dataset */ ... nc_inq_dimid /* get dimension IDs */ ... nc_inq_varid /* get variable IDs */ ... nc_get_att /* get attribute values */ ... nc_get_var /* get values of variables */ ... nc_close /* close netCDF dataset */ First, a single call opens the netCDF dataset, given the dataset name, and returns a netCDF ID that is used to refer to the open netCDF dataset in all subsequent calls. Next, a call to nc_inq_dimid for each dimension of interest gets the dimension ID from the dimension name. Similarly, each required variable ID is determined from its name by a call to nc_inq_varid Once variable IDs are known, variable attribute values can be retrieved using the netCDF ID, the variable ID, and the desired attribute name as input to a member of the nc_get_att family (typically nc_get_att_text or nc_get_att_double) for each desired attribute. Variable data values can be directly accessed from the netCDF dataset with calls to members of the nc_get_var1 family for single values, the nc_get_var family for entire variables, or various other members of the nc_get_vara, nc_get_vars, or nc_get_varm families for array, subsampled or mapped access. Finally, the netCDF dataset is closed with nc_close. There is no need to close a dataset open only for reading. 1.3 Reading a netCDF Dataset with Unknown Names =============================================== It is possible to write programs (e.g., generic software) which do such things as processing every variable, without needing to know in advance the names of these variables. Similarly, the names of dimensions and attributes may be unknown. Names and other information about netCDF objects may be obtained from netCDF datasets by calling inquire functions. These return information about a whole netCDF dataset, a dimension, a variable, or an attribute. The following template illustrates how they are used: nc_open /* open existing netCDF dataset */ ... nc_inq /* find out what is in it */ ... nc_inq_dim /* get dimension names, lengths */ ... nc_inq_var /* get variable names, types, shapes */ ... nc_inq_attname /* get attribute names */ ... nc_inq_att /* get attribute types and lengths */ ... nc_get_att /* get attribute values */ ... nc_get_var /* get values of variables */ ... nc_close /* close netCDF dataset */ As in the previous example, a single call opens the existing netCDF dataset, returning a netCDF ID. This netCDF ID is given to the nc_inq routine, which returns the number of dimensions, the number of variables, the number of global attributes, and the ID of the unlimited dimension, if there is one. All the inquire functions are inexpensive to use and require no I/O, since the information they provide is stored in memory when a netCDF dataset is first opened. Dimension IDs use consecutive integers, beginning at 0. Also dimensions, once created, cannot be deleted. Therefore, knowing the number of dimension IDs in a netCDF dataset means knowing all the dimension IDs: they are the integers 0, 1, 2, ...up to the number of dimensions. For each dimension ID, a call to the inquire function nc_inq_dim returns the dimension name and length. Variable IDs are also assigned from consecutive integers 0, 1, 2, ... up to the number of variables. These can be used in nc_inq_var calls to find out the names, types, shapes, and the number of attributes assigned to each variable. Once the number of attributes for a variable is known, successive calls to nc_inq_attname return the name for each attribute given the netCDF ID, variable ID, and attribute number. Armed with the attribute name, a call to nc_inq_att returns its type and length. Given the type and length, you can allocate enough space to hold the attribute values. Then a call to a member of the nc_get_att family returns the attribute values. Once the IDs and shapes of netCDF variables are known, data values can be accessed by calling a member of the nc_get_var1 family for single values, or members of the nc_get_var, nc_get_vara, nc_get_vars, or nc_get_varm for various kinds of array access. 1.4 Adding New Dimensions, Variables, Attributes ================================================ An existing netCDF dataset can be extensively altered. New dimensions, variables, and attributes can be added or existing ones renamed, and existing attributes can be deleted. Existing dimensions, variables, and attributes can be renamed. The following code template lists a typical sequence of calls to add new netCDF components to an existing dataset: nc_open /* open existing netCDF dataset */ ... nc_redef /* put it into define mode */ ... nc_def_dim /* define additional dimensions (if any) */ ... nc_def_var /* define additional variables (if any) */ ... nc_put_att /* define additional attributes (if any) */ ... nc_enddef /* check definitions, leave define mode */ ... nc_put_var /* provide values for new variables */ ... nc_close /* close netCDF dataset */ A netCDF dataset is first opened by the nc_open call. This call puts the open dataset in data mode, which means existing data values can be accessed and changed, existing attributes can be changed (so long as they do not grow), but nothing can be added. To add new netCDF dimensions, variables, or attributes you must enter define mode, by calling nc_redef. In define mode, call nc_def_dim to define new dimensions, nc_def_var to define new variables, and a member of the nc_put_attfamily to assign new attributes to variables or enlarge old attributes. You can leave define mode and reenter data mode, checking all the new definitions for consistency and committing the changes to disk, by calling nc_enddef. If you do not wish to reenter data mode, just call nc_close, which will have the effect of first calling nc_enddef. Until the nc_enddef call, you may back out of all the redefinitions made in define mode and restore the previous state of the netCDF dataset by calling nc_abort. You may also use the nc_abort call to restore the netCDF dataset to a consistent state if the call to nc_enddef fails. If you have called nc_close from definition mode and the implied call to nc_enddef fails, nc_abort will automatically be called to close the netCDF dataset and leave it in its previous consistent state (before you entered define mode). At most one process should have a netCDF dataset open for writing at one time. The library is designed to provide limited support for multiple concurrent readers with one writer, via disciplined use of the nc_sync function and the NC_SHARE flag. If a writer makes changes in define mode, such as the addition of new variables, dimensions, or attributes, some means external to the library is necessary to prevent readers from making concurrent accesses and to inform readers to call nc_sync before the next access. 1.5 Error Handling ================== The netCDF library provides the facilities needed to handle errors in a flexible way. Each netCDF function returns an integer status value. If the returned status value indicates an error, you may handle it in any way desired, from printing an associated error message and exiting to ignoring the error indication and proceeding (not recommended!). For simplicity, the examples in this guide check the error status and call a separate function to handle any errors. The nc_strerror function is available to convert a returned integer error status into an error message string. Occasionally, low-level I/O errors may occur in a layer below the netCDF library. For example, if a write operation causes you to exceed disk quotas or to attempt to write to a device that is no longer available, you may get an error from a layer below the netCDF library, but the resulting write error will still be reflected in the returned status value. 1.6 Compiling and Linking with the NetCDF Library ================================================= Details of how to compile and link a program that uses the netCDF C or FORTRAN interfaces differ, depending on the operating system, the available compilers, and where the netCDF library and include files are installed. Nevertheless, we provide here examples of how to compile and link a program that uses the netCDF library on a Unix platform, so that you can adjust these examples to fit your installation. Every C file that references netCDF functions or constants must contain an appropriate #include statement before the first such reference: #include Unless the netcdf.h file is installed in a standard directory where the C compiler always looks, you must use the -I option when invoking the compiler, to specify a directory where netcdf.h is installed, for example: cc -c -I/usr/local/netcdf/include myprogram.c Alternatively, you could specify an absolute path name in the #include statement, but then your program would not compile on another platform where netCDF is installed in a different location. Unless the netCDF library is installed in a standard directory where the linker always looks, you must use the -L and -l options to link an object file that uses the netCDF library. For example: cc -o myprogram myprogram.o -L/usr/local/netcdf/lib -lnetcdf Alternatively, you could specify an absolute path name for the library: cc -o myprogram myprogram.o -l/usr/local/netcdf/lib/libnetcdf.a 2 Datasets ********** This chapter presents the interfaces of the netCDF functions that deal with a netCDF dataset or the whole netCDF library. A netCDF dataset that has not yet been opened can only be referred to by its dataset name. Once a netCDF dataset is opened, it is referred to by a netCDF ID, which is a small nonnegative integer returned when you create or open the dataset. A netCDF ID is much like a file descriptor in C or a logical unit number in FORTRAN. In any single program, the netCDF IDs of distinct open netCDF datasets are distinct. A single netCDF dataset may be opened multiple times and will then have multiple distinct netCDF IDs; however at most one of the open instances of a single netCDF dataset should permit writing. When an open netCDF dataset is closed, the ID is no longer associated with a netCDF dataset. Functions that deal with the netCDF library include: * Get version of library. * Get error message corresponding to a returned error code. The operations supported on a netCDF dataset as a single object are: * Create, given dataset name and whether to overwrite or not. * Open for access, given dataset name and read or write intent. * Put into define mode, to add dimensions, variables, or attributes. * Take out of define mode, checking consistency of additions. * Close, writing to disk if required. * Inquire about the number of dimensions, number of variables, number of global attributes, and ID of the unlimited dimension, if any. * Synchronize to disk to make sure it is current. * Set and unset nofill mode for optimized sequential writes. * After a summary of conventions used in describing the netCDF interfaces, the rest of this chapter presents a detailed description of the interfaces for these operations. 2.1 NetCDF Library Interface Descriptions ========================================= Each interface description for a particular netCDF function in this and later chapters contains: * a description of the purpose of the function; * a C function prototype that presents the type and order of the formal parameters to the function; * a description of each formal parameter in the C interface; * a list of possible error conditions; and * an example of a C program fragment calling the netCDF function (and perhaps other netCDF functions). The examples follow a simple convention for error handling, always checking the error status returned from each netCDF function call and calling a handle_error function in case an error was detected. For an example of such a function, *Note nc_strerror::. 2.2 Get error message corresponding to error status: nc_strerror ================================================================ The function nc_strerror returns a static reference to an error message string corresponding to an integer netCDF error status or to a system error number, presumably returned by a previous call to some other netCDF function. The list of netCDF error status codes is available in the appropriate include file for each language binding. Usage ===== const char * nc_strerror(int ncerr); `ncerr' An error status that might have been returned from a previous call to some netCDF function. Errors ====== If you provide an invalid integer error status that does not correspond to any netCDF error message or or to any system error message (as understood by the system strerror function), nc_strerror returns a string indicating that there is no such error status. Example ======= Here is an example of a simple error handling function that uses nc_strerror to print the error message corresponding to the netCDF error status returned from any netCDF function call and then exit: #include ... void handle_error(int status) { if (status != NC_NOERR) { fprintf(stderr, "%s\n", nc_strerror(status)); exit(-1); } } 2.3 Get netCDF library version: nc_inq_libvers ============================================== The function nc_inq_libvers returns a string identifying the version of the netCDF library, and when it was built. Usage ===== const char * nc_inq_libvers(void); Errors ====== This function takes no arguments, and thus no errors are possible in its invocation. Example ======= Here is an example using nc_inq_libvers to print the version of the netCDF library with which the program is linked: #include ... printf("%s\n", nc_inq_libvers()); 2.4 Create a NetCDF Dataset: nc_create ====================================== This function creates a new netCDF dataset, returning a netCDF ID that can subsequently be used to refer to the netCDF dataset in other netCDF function calls. The new netCDF dataset opened for write access and placed in define mode, ready for you to add dimensions, variables, and attributes. A creation mode flag specifies: * whether to overwrite any existing dataset with the same name, * whether access to the dataset is shared, * whether this file should be in netCDF classic format (the default), or the new 64-bit offset format. Usage ===== int nc_create (const char* path, int cmode, int *ncidp); `path' The file name of the new netCDF dataset. `cmode' The creation mode flag. The following flags are available: NC_NOCLOBBER, NC_SHARE, and NC_64BIT_OFFSET. Setting NC_NOCLOBBER means you do not want to clobber (overwrite) an existing dataset; an error (NC_EEXIST) is returned if the specified dataset already exists. The NC_SHARE flag is appropriate when one process may be writing the dataset and one or more other processes reading the dataset concurrently; it means that dataset accesses are not buffered and caching is limited. Since the buffering scheme is optimized for sequential access, programs that do not access data sequentially may see some performance improvement by setting the NC_SHARE flag. Setting NC_64BIT_OFFSET causes netCDF to create a 64-bit offset format file, instead of a netCDF classic format file. The 64-bit offset format imposes far fewer restrictions on very large (i.e. over 2 GB) data files. *Note Large File Support: (netcdf)Large File Support. A zero value (defined for convenience as NC_CLOBBER) specifies the default behavior: overwrite any existing dataset with the same file name and buffer and cache accesses for efficiency. The dataset will be in netCDF classic format. *Note NetCDF Classic Format Limitations: (netcdf)NetCDF Classic Format Limitations. `ncidp' Pointer to location where returned netCDF ID is to be stored. Errors ====== nc_create returns the value NC_NOERR if no errors occurred. Possible causes of errors include: * Passing a dataset name that includes a directory that does not exist. * Specifying a dataset name of a file that exists and also specifying NC_NOCLOBBER. * Specifying a meaningless value for the creation mode. * Attempting to create a netCDF dataset in a directory where you don't have permission to create files. Examples ======== In this example we create a netCDF dataset named foo.nc; we want the dataset to be created in the current directory only if a dataset with that name does not already exist: #include ... int status; int ncid; ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); In this example we create a netCDF dataset named foo_large.nc. It will be in the 64-bit offset format. #include ... int status; int ncid; ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); A variant of nc_create, nc__create (note the double underscore) allows users to specify two tuning parameters for the file that it is creating. These tuning parameters are not written to the data file, they are only used for so long as the file remains open after an nc__create. Usage ===== int nc__create(const char *path, int cmode, size_t initialsz, size_t *chunksizehintp, int *ncidp); `path' The file name of the new netCDF dataset. `cmode' The creation mode flag. The following flags are available: NC_NOCLOBBER, NC_SHARE, and NC_64BIT_OFFSET. Setting NC_NOCLOBBER means you do not want to clobber (overwrite) an existing dataset; an error (NC_EEXIST) is returned if the specified dataset already exists. The NC_SHARE flag is appropriate when one process may be writing the dataset and one or more other processes reading the dataset concurrently; it means that dataset accesses are not buffered and caching is limited. Since the buffering scheme is optimized for sequential access, programs that do not access data sequentially may see some performance improvement by setting the NC_SHARE flag. Setting NC_64BIT_OFFSET causes netCDF to create a 64-bit offset format file, instead of a netCDF classic format file. The 64-bit offset format imposes far fewer restrictions on very large (i.e. over 2 GB) data files. *Note Large File Support: (netcdf)Large File Support. A zero value (defined for convenience as NC_CLOBBER) specifies the default behavior: overwrite any existing dataset with the same file name and buffer and cache accesses for efficiency. The dataset will be in netCDF classic format. *Note NetCDF Classic Format Limitations: (netcdf)NetCDF Classic Format Limitations. `initialsz' On some systems, and with custom I/O layers, it may be advantageous to set the size of the output file at creation time. This parameter sets the initial size of the file at creation time. `chunksizehintp' The argument referenced by chunksizehintp controls a space versus time tradeoff, memory allocated in the netcdf library versus number of system calls. Because of internal requirements, the value may not be set to exactly the value requested. The actual value chosen is returned by reference. Using the value NC_SIZEHINT_DEFAULT causes the library to choose a default. How the system chooses the default depends on the system. On many systems, the "preferred I/O block size" is available from the stat() system call, struct stat member st_blksize. If this is available it is used. Lacking that, twice the system pagesize is used. Lacking a call to discover the system pagesize, we just set default chunksize to 8192. The chunksize is a property of a given open netcdf descriptor ncid, it is not a persistent property of the netcdf dataset. `ncidp' Pointer to location where returned netCDF ID is to be stored. Errors ====== nc__create returns the value NC_NOERR if no errors occurred. Possible causes of errors include: * Passing a dataset name that includes a directory that does not exist. * Specifying a dataset name of a file that exists and also specifying NC_NOCLOBBER. * Specifying a meaningless value for the creation mode. * Attempting to create a netCDF dataset in a directory where you don't have permission to create files. Examples ======== In this example we create a netCDF dataset named foo.nc; we want the dataset to be created in the current directory only if a dataset with that name does not already exist: #include ... int status; int ncid; ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); In this example we create a netCDF dataset named foo_large.nc. It will be in the 64-bit offset format. #include ... int status; int ncid; ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); 2.5 Create a NetCDF Dataset With Performance Options: nc__create ================================================================ This function is a variant of nc_create, nc__create (note the double underscore) allows users to specify two tuning parameters for the file that it is creating. These tuning parameters are not written to the data file, they are only used for so long as the file remains open after an nc__create. This function creates a new netCDF dataset, returning a netCDF ID that can subsequently be used to refer to the netCDF dataset in other netCDF function calls. The new netCDF dataset opened for write access and placed in define mode, ready for you to add dimensions, variables, and attributes. A creation mode flag specifies whether to overwrite any existing dataset with the same name and whether access to the dataset is shared, and whether this file should be in netCDF classic format (the default), or the new 64-bit offset format. Usage ===== int nc__create(const char *path, int cmode, size_t initialsz, size_t *chunksizehintp, int *ncidp); `path' The file name of the new netCDF dataset. `cmode' The creation mode flag. The following flags are available: NC_NOCLOBBER, NC_SHARE, and NC_64BIT_OFFSET. Setting NC_NOCLOBBER means you do not want to clobber (overwrite) an existing dataset; an error (NC_EEXIST) is returned if the specified dataset already exists. The NC_SHARE flag is appropriate when one process may be writing the dataset and one or more other processes reading the dataset concurrently; it means that dataset accesses are not buffered and caching is limited. Since the buffering scheme is optimized for sequential access, programs that do not access data sequentially may see some performance improvement by setting the NC_SHARE flag. Setting NC_64BIT_OFFSET causes netCDF to create a 64-bit offset format file, instead of a netCDF classic format file. The 64-bit offset format imposes far fewer restrictions on very large (i.e. over 2 GB) data files. *Note Large File Support: (netcdf)Large File Support. A zero value (defined for convenience as NC_CLOBBER) specifies the default behavior: overwrite any existing dataset with the same file name and buffer and cache accesses for efficiency. The dataset will be in netCDF classic format. *Note NetCDF Classic Format Limitations: (netcdf)NetCDF Classic Format Limitations. `initialsz' This parameter sets the initial size of the file at creation time. `chunksizehintp' The argument referenced by chunksizehintp controls a space versus time tradeoff, memory allocated in the netcdf library versus number of system calls. Because of internal requirements, the value may not be set to exactly the value requested. The actual value chosen is returned by reference. Using the value NC_SIZEHINT_DEFAULT causes the library to choose a default. How the system chooses the default depends on the system. On many systems, the "preferred I/O block size" is available from the stat() system call, struct stat member st_blksize. If this is available it is used. Lacking that, twice the system pagesize is used. Lacking a call to discover the system pagesize, we just set default chunksize to 8192. The chunksize is a property of a given open netcdf descriptor ncid, it is not a persistent property of the netcdf dataset. `ncidp' Pointer to location where returned netCDF ID is to be stored. Errors ====== nc_create returns the value NC_NOERR if no errors occurred. Possible causes of errors include: * Passing a dataset name that includes a directory that does not exist. * Specifying a dataset name of a file that exists and also specifying NC_NOCLOBBER. * Specifying a meaningless value for the creation mode. * Attempting to create a netCDF dataset in a directory where you don't have permission to create files. Examples ======== In this example we create a netCDF dataset named foo.nc; we want the dataset to be created in the current directory only if a dataset with that name does not already exist. We also specify that chunksize and initial size for the file. #include ... int status; int ncid; int intialsz = 2048; int *chunksize; ... *chunksize = 1024; status = nc__create("foo.nc", NC_NOCLOBBER, initialsz, chunksize, &ncid); if (status != NC_NOERR) handle_error(status); 2.6 Open a NetCDF Dataset for Access: nc_open ============================================= The function nc_open opens an existing netCDF dataset for access. Usage ===== int nc_open (const char *path, int omode, int *ncidp); `path' File name for netCDF dataset to be opened. `omode' A zero value (or NC_NOWRITE) specifies the default behavior: open the dataset with read-only access, buffering and caching accesses for efficiency Otherwise, the creation mode is NC_WRITE, NC_SHARE, or NC_WRITE|NC_SHARE. Setting the NC_WRITE flag opens the dataset with read-write access. ("Writing" means any kind of change to the dataset, including appending or changing data, adding or renaming dimensions, variables, and attributes, or deleting attributes.) The NC_SHARE flag is appropriate when one process may be writing the dataset and one or more other processes reading the dataset concurrently; it means that dataset accesses are not buffered and caching is limited. Since the buffering scheme is optimized for sequential access, programs that do not access data sequentially may see some performance improvement by setting the NC_SHARE flag. `ncidp' Pointer to location where returned netCDF ID is to be stored. Errors ====== nc_open returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The specified netCDF dataset does not exist. * A meaningless mode was specified. Example ======= Here is an example using nc_open to open an existing netCDF dataset named foo.nc for read-only, non-shared access: #include ... int status; int ncid; ... status = nc_open("foo.nc", 0, &ncid); if (status != NC_NOERR) handle_error(status); 2.7 Open a NetCDF Dataset for Access with Performance Tuning: nc__open ====================================================================== A function opens a netCDF dataset for access with an additional performance tuning parameter. Usage ===== int nc__open(const char *path, int mode, size_t *chunksizehintp, int *ncidp); `path' File name for netCDF dataset to be opened. `omode' A zero value (or NC_NOWRITE) specifies the default behavior: open the dataset with read-only access, buffering and caching accesses for efficiency Otherwise, the creation mode is NC_WRITE, NC_SHARE, or NC_WRITE|NC_SHARE. Setting the NC_WRITE flag opens the dataset with read-write access. ("Writing" means any kind of change to the dataset, including appending or changing data, adding or renaming dimensions, variables, and attributes, or deleting attributes.) The NC_SHARE flag is appropriate when one process may be writing the dataset and one or more other processes reading the dataset concurrently; it means that dataset accesses are not buffered and caching is limited. Since the buffering scheme is optimized for sequential access, programs that do not access data sequentially may see some performance improvement by setting the NC_SHARE flag. `chunksizehintp' The argument referenced by chunksizehintp controls a space versus time tradeoff, memory allocated in the netcdf library versus number of system calls. Because of internal requirements, the value may not be set to exactly the value requested. The actual value chosen is returned by reference. Using the value NC_SIZEHINT_DEFAULT causes the library to choose a default. How the system chooses the default depends on the system. On many systems, the "preferred I/O block size" is available from the stat() system call, struct stat member st_blksize. If this is available it is used. Lacking that, twice the system pagesize is used. Lacking a call to discover the system pagesize, we just set default chunksize to 8192. The chunksize is a property of a given open netcdf descriptor ncid, it is not a persistent property of the netcdf dataset. `ncidp' Pointer to location where returned netCDF ID is to be stored. Errors ====== nc__open returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The specified netCDF dataset does not exist. * A meaningless mode was specified. Example ======= Here is an example using nc__open to open an existing netCDF dataset named foo.nc for read-only, non-shared access: #include ... int status; int ncid; int *chunksize; ... *chunksize = 1024; status = nc_open("foo.nc", 0, chunksize, &ncid); if (status != NC_NOERR) handle_error(status); 2.8 Put Open NetCDF Dataset into Define Mode: nc_redef ====================================================== The function nc_redef puts an open netCDF dataset into define mode, so dimensions, variables, and attributes can be added or renamed and attributes can be deleted. Usage ===== int nc_redef(int ncid); `ncid' netCDF ID, from a previous call to nc_open or nc_create. Errors ====== nc_redef returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The specified netCDF dataset is already in define mode. * The specified netCDF dataset was opened for read-only. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_redef to open an existing netCDF dataset named foo.nc and put it into define mode: #include ... int status; int ncid; ... status = nc_open("foo.nc", NC_WRITE, &ncid); /* open dataset */ if (status != NC_NOERR) handle_error(status); ... status = nc_redef(ncid); /* put in define mode */ if (status != NC_NOERR) handle_error(status); 2.9 Leave Define Mode: nc_enddef ================================ The function nc_enddef takes an open netCDF dataset out of define mode. The changes made to the netCDF dataset while it was in define mode are checked and committed to disk if no problems occurred. Non-record variables may be initialized to a "fill value" as well. *Note nc_set_fill::. The netCDF dataset is then placed in data mode, so variable data can be read or written. This call may involve copying data under some circumstances. For a more extensive discussion *Note File Structure and Performance: (netcdf)File Structure and Performance. Usage ===== int nc_enddef(int ncid); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. Errors ====== nc_enddef returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The specified netCDF dataset is not in define mode. * The specified netCDF ID does not refer to an open netCDF dataset. * The size of one or more variables exceed the size constraints for whichever variant of the file format is in use). *Note Large File Support: (netcdf)Large File Support. Example ======= Here is an example using nc_enddef to finish the definitions of a new netCDF dataset named foo.nc and put it into data mode: #include ... int status; int ncid; ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); ... /* create dimensions, variables, attributes */ status = nc_enddef(ncid); /*leave define mode*/ if (status != NC_NOERR) handle_error(status); 2.10 Leave Define Mode with Performance Tuning: nc__enddef ========================================================== The function nc__enddef takes an open netCDF dataset out of define mode. The changes made to the netCDF dataset while it was in define mode are checked and committed to disk if no problems occurred. Non-record variables may be initialized to a "fill value" as well. *Note nc_set_fill::. The netCDF dataset is then placed in data mode, so variable data can be read or written. This call may involve copying data under some circumstances. For a more extensive discussion *Note File Structure and Performance: (netcdf)File Structure and Performance. Caution: this function exposes internals of the netcdf version 1 file format. Users should use nc_enddef in most circumstances. This function may not be available on future netcdf implementations. The current netcdf file format has three sections, the "header" section, the data section for fixed size variables, and the data section for variables which have an unlimited dimension (record variables). The header begins at the beginning of the file. The index (offset) of the beginning of the other two sections is contained in the header. Typically, there is no space between the sections. This causes copying overhead to accrue if one wishes to change the size of the sections, as may happen when changing names of things, text attribute values, adding attributes or adding variables. Also, for buffered i/o, there may be advantages to aligning sections in certain ways. The minfree parameters allow one to control costs of future calls to nc_redef, nc_enddef by requesting that minfree bytes be available at the end of the section. The align parameters allow one to set the alignment of the beginning of the corresponding sections. The beginning of the section is rounded up to an index which is a multiple of the align parameter. The flag value ALIGN_CHUNK tells the library to use the chunksize (see above) as the align parameter. The file format requires mod 4 alignment, so the align parameters are silently rounded up to multiples of 4. The usual call, nc_enddef(ncid); is equivalent to nc_enddef(ncid, 0, 4, 0, 4); The file format does not contain a "record size" value, this is calculated from the sizes of the record variables. This unfortunate fact prevents us from providing minfree and alignment control of the "records" in a netcdf file. If you add a variable which has an unlimited dimension, the third section will always be copied with the new variable added. Usage ===== int nc__enddef(int ncid, size_t h_minfree, size_t v_align, size_t v_minfree, size_t r_align); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `h_minfree' Sets the pad at the end of the "header" section. `v_align' Controls the alignment of the beginning of the data section for fixed size variables. `v_minfree' Sets the pad at the end of the data section for fixed size variables. `r_align' Controls the alignment of the beginning of the data section for variables which have an unlimited dimension (record variables). Errors ====== nc__enddef returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The specified netCDF dataset is not in define mode. * The specified netCDF ID does not refer to an open netCDF dataset. * The size of one or more variables exceed the size constraints for whichever variant of the file format is in use). *Note Large File Support: (netcdf)Large File Support. Example ======= Here is an example using nc_enddef to finish the definitions of a new netCDF dataset named foo.nc and put it into data mode: #include ... int status; int ncid; ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); ... /* create dimensions, variables, attributes */ status = nc_enddef(ncid); /*leave define mode*/ if (status != NC_NOERR) handle_error(status); 2.11 Close an Open NetCDF Dataset: nc_close =========================================== The function nc_close closes an open netCDF dataset. If the dataset is in define mode, nc_enddef will be called before closing. (In this case, if nc_enddef returns an error, nc_abort will automatically be called to restore the dataset to the consistent state before define mode was last entered.) After an open netCDF dataset is closed, its netCDF ID may be reassigned to the next netCDF dataset that is opened or created. Usage ===== int nc_close(int ncid); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. Errors ====== nc_close returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * Define mode was entered and the automatic call made to nc_enddef failed. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_close to finish the definitions of a new netCDF dataset named foo.nc and release its netCDF ID: #include ... int status; int ncid; ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); ... /* create dimensions, variables, attributes */ status = nc_close(ncid); /* close netCDF dataset */ if (status != NC_NOERR) handle_error(status); 2.12 Inquire about an Open NetCDF Dataset: nc_inq Family ======================================================== Members of the nc_inq family of functions return information about an open netCDF dataset, given its netCDF ID. Dataset inquire functions may be called from either define mode or data mode. The first function, nc_inq, returns values for the number of dimensions, the number of variables, the number of global attributes, and the dimension ID of the dimension defined with unlimited length, if any. The other functions in the family each return just one of these items of information. For C, these functions include nc_inq, nc_inq_ndims, nc_inq_nvars, nc_inq_natts, and nc_inq_unlimdim. An additional function, nc_inq_format, returns the (rarely needed) format version. No I/O is performed when these functions are called, since the required information is available in memory for each open netCDF dataset. Usage ===== int nc_inq (int ncid, int *ndimsp, int *nvarsp, int *ngattsp, int *unlimdimidp); int nc_inq_ndims (int ncid, int *ndimsp); int nc_inq_nvars (int ncid, int *nvarsp); int nc_inq_natts (int ncid, int *ngattsp); int nc_inq_unlimdim (int ncid, int *unlimdimidp); int nc_inq_format (int ncid, int *formatp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `ndimsp' Pointer to location for returned number of dimensions defined for this netCDF dataset. `nvarsp' Pointer to location for returned number of variables defined for this netCDF dataset. `ngattsp' Pointer to location for returned number of global attributes defined for this netCDF dataset. `unlimdimidp' Pointer to location for returned ID of the unlimited dimension, if there is one for this netCDF dataset. If no unlimited length dimension has been defined, -1 is returned. `formatp' Pointer to location for returned format version, one of NC_FORMAT_CLASSIC, NC_FORMAT_64BIT, NC_FORMAT_NETCDF4, NC_FORMAT_NETCDF4_CLASSIC. Errors ====== All members of the nc_inq family return the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_inq to find out about a netCDF dataset named foo.nc: #include ... int status, ncid, ndims, nvars, ngatts, unlimdimid; ... status = nc_open("foo.nc", NC_NOWRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid); if (status != NC_NOERR) handle_error(status); 2.13 Synchronize an Open NetCDF Dataset to Disk: nc_sync ======================================================== The function nc_sync offers a way to synchronize the disk copy of a netCDF dataset with in-memory buffers. There are two reasons you might want to synchronize after writes: * To minimize data loss in case of abnormal termination, or * To make data available to other processes for reading immediately after it is written. But note that a process that already had the dataset open for reading would not see the number of records increase when the writing process calls nc_sync; to accomplish this, the reading process must call nc_sync. This function is backward-compatible with previous versions of the netCDF library. The intent was to allow sharing of a netCDF dataset among multiple readers and one writer, by having the writer call nc_sync after writing and the readers call nc_sync before each read. For a writer, this flushes buffers to disk. For a reader, it makes sure that the next read will be from disk rather than from previously cached buffers, so that the reader will see changes made by the writing process (e.g., the number of records written) without having to close and reopen the dataset. If you are only accessing a small amount of data, it can be expensive in computer resources to always synchronize to disk after every write, since you are giving up the benefits of buffering. An easier way to accomplish sharing (and what is now recommended) is to have the writer and readers open the dataset with the NC_SHARE flag, and then it will not be necessary to call nc_sync at all. However, the nc_sync function still provides finer granularity than the NC_SHARE flag, if only a few netCDF accesses need to be synchronized among processes. It is important to note that changes to the ancillary data, such as attribute values, are not propagated automatically by use of the NC_SHARE flag. Use of the nc_sync function is still required for this purpose. Sharing datasets when the writer enters define mode to change the data schema requires extra care. In previous releases, after the writer left define mode, the readers were left looking at an old copy of the dataset, since the changes were made to a new copy. The only way readers could see the changes was by closing and reopening the dataset. Now the changes are made in place, but readers have no knowledge that their internal tables are now inconsistent with the new dataset schema. If netCDF datasets are shared across redefinition, some mechanism external to the netCDF library must be provided that prevents access by readers during redefinition and causes the readers to call nc_sync before any subsequent access. When calling nc_sync, the netCDF dataset must be in data mode. A netCDF dataset in define mode is synchronized to disk only when nc_enddef is called. A process that is reading a netCDF dataset that another process is writing may call nc_sync to get updated with the changes made to the data by the writing process (e.g., the number of records written), without having to close and reopen the dataset. Data is automatically synchronized to disk when a netCDF dataset is closed, or whenever you leave define mode. Usage ===== int nc_sync(int ncid); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. Errors ====== nc_sync returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The netCDF dataset is in define mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_sync to synchronize the disk writes of a netCDF dataset named foo.nc: #include ... int status; int ncid; ... status = nc_open("foo.nc", NC_WRITE, &ncid); /* open for writing */ if (status != NC_NOERR) handle_error(status); ... /* write data or change attributes */ status = nc_sync(ncid); /* synchronize to disk */ if (status != NC_NOERR) handle_error(status); 2.14 Back Out of Recent Definitions: nc_abort ============================================= You no longer need to call this function, since it is called automatically by nc_close in case the dataset is in define mode and something goes wrong with committing the changes. The function nc_abort just closes the netCDF dataset, if not in define mode. If the dataset is being created and is still in define mode, the dataset is deleted. If define mode was entered by a call to nc_redef, the netCDF dataset is restored to its state before definition mode was entered and the dataset is closed. Usage ===== int nc_abort(int ncid); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. Errors ====== nc_abort returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * When called from define mode while creating a netCDF dataset, deletion of the dataset failed. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_abort to back out of redefinitions of a dataset named foo.nc: #include ... int ncid, status, latid; ... status = nc_open("foo.nc", NC_WRITE, &ncid);/* open for writing */ if (status != NC_NOERR) handle_error(status); ... status = nc_redef(ncid); /* enter define mode */ if (status != NC_NOERR) handle_error(status); ... status = nc_def_dim(ncid, "lat", 18L, &latid); if (status != NC_NOERR) { handle_error(status); status = nc_abort(ncid); /* define failed, abort */ if (status != NC_NOERR) handle_error(status); } 2.15 Set Fill Mode for Writes: nc_set_fill ========================================== This function is intended for advanced usage, to optimize writes under some circumstances described below. The function nc_set_fill sets the fill mode for a netCDF dataset open for writing and returns the current fill mode in a return parameter. The fill mode can be specified as either NC_FILL or NC_NOFILL. The default behavior corresponding to NC_FILL is that data is pre-filled with fill values, that is fill values are written when you create non-record variables or when you write a value beyond data that has not yet been written. This makes it possible to detect attempts to read data before it was written. For more information on the use of fill values *Note Fill Values::. For information about how to define your own fill values *Note Attribute Conventions: (netcdf)Attribute Conventions. The behavior corresponding to NC_NOFILL overrides the default behavior of prefilling data with fill values. This can be used to enhance performance, because it avoids the duplicate writes that occur when the netCDF library writes fill values that are later overwritten with data. A value indicating which mode the netCDF dataset was already in is returned. You can use this value to temporarily change the fill mode of an open netCDF dataset and then restore it to the previous mode. After you turn on NC_NOFILL mode for an open netCDF dataset, you must be certain to write valid data in all the positions that will later be read. Note that nofill mode is only a transient property of a netCDF dataset open for writing: if you close and reopen the dataset, it will revert to the default behavior. You can also revert to the default behavior by calling nc_set_fill again to explicitly set the fill mode to NC_FILL. There are three situations where it is advantageous to set nofill mode: 1. Creating and initializing a netCDF dataset. In this case, you should set nofill mode before calling nc_enddef and then write completely all non-record variables and the initial records of all the record variables you want to initialize. 2. Extending an existing record-oriented netCDF dataset. Set nofill mode after opening the dataset for writing, then append the additional records to the dataset completely, leaving no intervening unwritten records. 3. Adding new variables that you are going to initialize to an existing netCDF dataset. Set nofill mode before calling nc_enddef then write all the new variables completely. If the netCDF dataset has an unlimited dimension and the last record was written while in nofill mode, then the dataset may be shorter than if nofill mode was not set, but this will be completely transparent if you access the data only through the netCDF interfaces. The use of this feature may not be available (or even needed) in future releases. Programmers are cautioned against heavy reliance upon this feature. Usage ===== int nc_set_fill (int ncid, int fillmode, int *old_modep); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `fillmode' Desired fill mode for the dataset, either NC_NOFILL or NC_FILL. `old_modep' Pointer to location for returned current fill mode of the dataset before this call, either NC_NOFILL or NC_FILL. Errors ====== nc_set_fill returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The specified netCDF ID does not refer to an open netCDF dataset. * The specified netCDF ID refers to a dataset open for read-only access. * The fill mode argument is neither NC_NOFILL nor NC_FILL.. Example ======= Here is an example using nc_set_fill to set nofill mode for subsequent writes of a netCDF dataset named foo.nc: #include ... int ncid, status, old_fill_mode; ... status = nc_open("foo.nc", NC_WRITE, &ncid); /* open for writing */ if (status != NC_NOERR) handle_error(status); ... /* write data with default prefilling behavior */ status = nc_set_fill(ncid, NC_NOFILL, &old_fill_mode); /* set nofill */ if (status != NC_NOERR) handle_error(status); ... /* write data with no prefilling */ 2.16 Set Default Creation Format: nc_set_default_format ======================================================= This function is intended for advanced users. Starting in version 3.6, netCDF introduced a new data format, the first change in the underlying binary data format since the netCDF interface was released. The new format, 64-bit offset format, was introduced to greatly relax the limitations on creating very large files. Users are warned that creating files in the 64-bit offset format makes them unreadable by the netCDF library prior to version 3.6.0. For reasons of compatibility, users should continue to create files in netCDF classic format. Users who do want to use 64-bit offset format files can create them directory from nc_create, using the proper cmode flag. (*note nc_create::). The function nc_set_default_format allows the user to change the format of the netCDF file to be created by future calls to nc_create (or nc__create) without changing the cmode flag. This allows the user to convert a program to use 64-bit offset formation without changing all calls the nc_create. *Note Large File Support: (netcdf)Large File Support. Once the default format is set, all future created files will be in the desired format. Two constants are provided in the netcdf.h file to be used with this function, NC_FORMAT_64BIT and NC_FORMAT_CLASSIC. If a non-NULL pointer is provided, it is assumed to point to an int, where the existing default format will be written. Using nc_create with a cmode including NC_64BIT_OFFSET overrides the default format, and creates a 64-bit offset file. Usage ===== int nc_set_default_format(int format, int *old_formatp); `format' Either NC_FORMAT_CLASSIC (the default setting) or NC_FORMAT_64BIT. `old_formatp' Either NULL (in which case it will be ignored), or a pointer to an int where the existing default format (i.e. before being changed to the new format) will be written. This allows you to get the existing default format while setting a new default format. Errors ====== nc_set_default_format returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * Invalid format. The only valid formats are NC_FORMAT_CLASSIC and NC_FORMAT_64BIT. Trying to set the default format to something else will result in an invalid argument error. (NC_EINVAL) Example ======= Here is an example using nc_set_default_format to create the same file in both formats with the same nc_create call: #include ... int ncid, status, old_fill_mode; ... status = nc_open("foo.nc", NC_WRITE, &ncid); /* open for writing */ if (status != NC_NOERR) handle_error(status); ... /* write data with default prefilling behavior */ status = nc_set_fill(ncid, NC_NOFILL, &old_fill_mode); /* set nofill */ if (status != NC_NOERR) handle_error(status); ... /* write data with no prefilling */ 3 Dimensions ************ 3.1 Dimensions Introduction =========================== Dimensions for a netCDF dataset are defined when it is created, while the netCDF dataset is in define mode. Additional dimensions may be added later by reentering define mode. A netCDF dimension has a name and a length. At most one dimension in a netCDF dataset can have the unlimited length, which means variables using this dimension can grow along this dimension. There is a suggested limit (1024) to the number of dimensions that can be defined in a single netCDF dataset. The limit is the value of the predefined macro NC_MAX_DIMS. The purpose of the limit is to make writing generic applications simpler. They need only provide an array of NC_MAX_DIMS dimensions to handle any netCDF dataset. The implementation of the netCDF library does not enforce this advisory maximum, so it is possible to use more dimensions, if necessary, but netCDF utilities that assume the advisory maximums may not be able to handle the resulting netCDF datasets. Ordinarily, the name and length of a dimension are fixed when the dimension is first defined. The name may be changed later, but the length of a dimension (other than the unlimited dimension) cannot be changed without copying all the data to a new netCDF dataset with a redefined dimension length. Dimension lengths in the C interface are type size_t rather than type int to make it possible to access all the data in a netCDF dataset on a platform that only supports a 16-bit int data type, for example MSDOS. If dimension lengths were type int instead, it would not be possible to access data from variables with a dimension length greater than a 16-bit int can accommodate. A netCDF dimension in an open netCDF dataset is referred to by a small integer called a dimension ID. In the C interface, dimension IDs are 0, 1, 2, ..., in the order in which the dimensions were defined. Operations supported on dimensions are: * Create a dimension, given its name and length. * Get a dimension ID from its name. * Get a dimension's name and length from its ID. * Rename a dimension. 3.2 Create a Dimension: nc_def_dim ================================== The function nc_def_dim adds a new dimension to an open netCDF dataset in define mode. It returns (as an argument) a dimension ID, given the netCDF ID, the dimension name, and the dimension length. At most one unlimited length dimension, called the record dimension, may be defined for each netCDF dataset. Usage ===== int nc_def_dim (int ncid, const char *name, size_t len, int *dimidp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `name' Dimension name. Must begin with an alphabetic character, followed by zero or more alphanumeric characters including the underscore ('_'). Case is significant. `len' Length of dimension; that is, number of values for this dimension as an index to variables that use it. This should be either a positive integer (of type size_t) or the predefined constant NC_UNLIMITED. `dimidp' Pointer to location for returned dimension ID. Errors ====== nc_def_dim returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The netCDF dataset is not in definition mode. * The specified dimension name is the name of another existing dimension. * The specified length is not greater than zero. * The specified length is unlimited, but there is already an unlimited length dimension defined for this netCDF dataset. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_def_dim to create a dimension named lat of length 18 and a unlimited dimension named rec in a new netCDF dataset named foo.nc: #include ... int status, ncid, latid, recid; ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_def_dim(ncid, "lat", 18L, &latid); if (status != NC_NOERR) handle_error(status); status = nc_def_dim(ncid, "rec", NC_UNLIMITED, &recid); if (status != NC_NOERR) handle_error(status); 3.3 Get a Dimension ID from Its Name: nc_inq_dimid ================================================== The function nc_inq_dimid returns (as an argument) the ID of a netCDF dimension, given the name of the dimension. If ndims is the number of dimensions defined for a netCDF dataset, each dimension has an ID between 0 and ndims-1. Usage ===== int nc_inq_dimid (int ncid, const char *name, int *dimidp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `name' Dimension name, a character string beginning with a letter and followed by any sequence of letters, digits, or underscore ('_') characters. Case is significant in dimension names. `dimidp' Pointer to location for the returned dimension ID. Errors ====== nc_inq_dimid returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: The name that was specified is not the name of a dimension in the netCDF dataset. The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_inq_dimid to determine the dimension ID of a dimension named lat, assumed to have been defined previously in an existing netCDF dataset named foo.nc: #include ... int status, ncid, latid; ... status = nc_open("foo.nc", NC_NOWRITE, &ncid); /* open for reading */ if (status != NC_NOERR) handle_error(status); ... status = nc_inq_dimid(ncid, "lat", &latid); if (status != NC_NOERR) handle_error(status); 3.4 Inquire about a Dimension: nc_inq_dim Family ================================================ This family of functions returns information about a netCDF dimension. Information about a dimension includes its name and its length. The length for the unlimited dimension, if any, is the number of records written so far. The functions in this family include nc_inq_dim, nc_inq_dimname, and nc_inq_dimlen. The function nc_inq_dim returns all the information about a dimension; the other functions each return just one item of information. Usage ===== int nc_inq_dim (int ncid, int dimid, char* name, size_t* lengthp); int nc_inq_dimname (int ncid, int dimid, char *name); int nc_inq_dimlen (int ncid, int dimid, size_t *lengthp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `dimid' Dimension ID, from a previous call to nc_inq_dimid or nc_def_dim. `name' Returned dimension name. The caller must allocate space for the returned name. The maximum possible length, in characters, of a dimension name is given by the predefined constant NC_MAX_NAME. (This doesn't include the null terminator, so declare your array to be size NC_MAX_NAME+1). The returned character array will be null-terminated. `lengthp' Pointer to location for returned length of dimension. For the unlimited dimension, this is the number of records written so far. Errors ====== These functions return the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The dimension ID is invalid for the specified netCDF dataset. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_inq_dim to determine the length of a dimension named lat, and the name and current maximum length of the unlimited dimension for an existing netCDF dataset named foo.nc: #include ... int status, ncid, latid, recid; size_t latlength, recs; char recname[NC_MAX_NAME+1]; ... status = nc_open("foo.nc", NC_NOWRITE, &ncid); /* open for reading */ if (status != NC_NOERR) handle_error(status); status = nc_inq_unlimdim(ncid, &recid); /* get ID of unlimited dimension */ if (status != NC_NOERR) handle_error(status); ... status = nc_inq_dimid(ncid, "lat", &latid); /* get ID for lat dimension */ if (status != NC_NOERR) handle_error(status); status = nc_inq_dimlen(ncid, latid, &latlength); /* get lat length */ if (status != NC_NOERR) handle_error(status); /* get unlimited dimension name and current length */ status = nc_inq_dim(ncid, recid, recname, &recs); if (status != NC_NOERR) handle_error(status); 3.5 Rename a Dimension: nc_rename_dim ===================================== The function nc_rename_dim renames an existing dimension in a netCDF dataset open for writing. If the new name is longer than the old name, the netCDF dataset must be in define mode. You cannot rename a dimension to have the same name as another dimension. Usage ===== int nc_rename_dim(int ncid, int dimid, const char* name); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `dimid' Dimension ID, from a previous call to nc_inq_dimid or nc_def_dim. `name' New dimension name. Errors ====== nc_rename_dim returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The new name is the name of another dimension. * The dimension ID is invalid for the specified netCDF dataset. * The specified netCDF ID does not refer to an open netCDF dataset. * The new name is longer than the old name and the netCDF dataset is not in define mode. Example ======= Here is an example using nc_rename_dim to rename the dimension lat to latitude in an existing netCDF dataset named foo.nc: #include ... int status, ncid, latid; ... status = nc_open("foo.nc", NC_WRITE, &ncid); /* open for writing */ if (status != NC_NOERR) handle_error(status); ... status = nc_redef(ncid); /* put in define mode to rename dimension */ if (status != NC_NOERR) handle_error(status); status = nc_inq_dimid(ncid, "lat", &latid); if (status != NC_NOERR) handle_error(status); status = nc_rename_dim(ncid, latid, "latitude"); if (status != NC_NOERR) handle_error(status); status = nc_enddef(ncid); /* leave define mode */ if (status != NC_NOERR) handle_error(status); 4 Variables *********** 4.1 Introduction ================ Variables for a netCDF dataset are defined when the dataset is created, while the netCDF dataset is in define mode. Other variables may be added later by reentering define mode. A netCDF variable has a name, a type, and a shape, which are specified when it is defined. A variable may also have values, which are established later in data mode. Ordinarily, the name, type, and shape are fixed when the variable is first defined. The name may be changed, but the type and shape of a variable cannot be changed. However, a variable defined in terms of the unlimited dimension can grow without bound in that dimension. A netCDF variable in an open netCDF dataset is referred to by a small integer called a variable ID. Variable IDs reflect the order in which variables were defined within a netCDF dataset. Variable IDs are 0, 1, 2,..., in the order in which the variables were defined. A function is available for getting the variable ID from the variable name and vice-versa. Attributes (*note Attributes::) may be associated with a variable to specify such properties as units. Operations supported on variables are: * Create a variable, given its name, data type, and shape. * Get a variable ID from its name. * Get a variable's name, data type, shape, and number of attributes from its ID. * Put a data value into a variable, given variable ID, indices, and value. * Put an array of values into a variable, given variable ID, corner indices, edge lengths, and a block of values. * Put a subsampled or mapped array-section of values into a variable, given variable ID, corner indices, edge lengths, stride vector, index mapping vector, and a block of values. * Get a data value from a variable, given variable ID and indices. * Get an array of values from a variable, given variable ID, corner indices, and edge lengths. * Get a subsampled or mapped array-section of values from a variable, given variable ID, corner indices, edge lengths, stride vector, and index mapping vector. * Rename a variable. 4.2 Language Types Corresponding to netCDF external data types ============================================================== The following table gives the netCDF external data types and the corresponding type constants for defining variables in the C interface: Type C #define Bits byte NC_BYTE 8 char NC_CHAR 8 short NC_SHORT 16 int NC_INT 32 float NC_FLOAT 32 double NC_DOUBLE 64 The first column gives the netCDF external data type, which is the same as the CDL data type. The next column gives the corresponding C preprocessor macro for use in netCDF functions (the preprocessor macros are defined in the netCDF C header-file netcdf.h). The last column gives the number of bits used in the external representation of values of the corresponding type. Note that there are no netCDF types corresponding to 64-bit integers or to characters wider than 8 bits in the current version of the netCDF library. 4.3 Create a Variable: `nc_def_var' =================================== The function nc_def_var adds a new variable to an open netCDF dataset in define mode. It returns (as an argument) a variable ID, given the netCDF ID, the variable name, the variable type, the number of dimensions, and a list of the dimension IDs. Usage ===== int nc_def_var (int ncid, const char *name, nc_type xtype, int ndims, const int dimids[], int *varidp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `name' Variable name. Must begin with an alphabetic character, followed by zero or more alphanumeric characters including the underscore ('_'). Case is significant. `xtype' One of the set of predefined netCDF external data types. The type of this parameter, nc_type, is defined in the netCDF header file. The valid netCDF external data types are NC_BYTE, NC_CHAR, NC_SHORT, NC_INT, NC_FLOAT, and NC_DOUBLE. `ndims' Number of dimensions for the variable. For example, 2 specifies a matrix, 1 specifies a vector, and 0 means the variable is a scalar with no dimensions. Must not be negative or greater than the predefined constant NC_MAX_VAR_DIMS. `dimids' Vector of ndims dimension IDs corresponding to the variable dimensions. If the ID of the unlimited dimension is included, it must be first. This argument is ignored if ndims is 0. `varidp' Pointer to location for the returned variable ID. Errors ====== nc_def_var returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The netCDF dataset is not in define mode. * The specified variable name is the name of another existing variable. * The specified type is not a valid netCDF type. * The specified number of dimensions is negative or more than the constant NC_MAX_VAR_DIMS, the maximum number of dimensions permitted for a netCDF variable. * One or more of the dimension IDs in the list of dimensions is not a valid dimension ID for the netCDF dataset. * The number of variables would exceed the constant NC_MAX_VARS, the maximum number of variables permitted in a netCDF dataset. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_def_var to create a variable named rh of type double with three dimensions, time, lat, and lon in a new netCDF dataset named foo.nc: #include ... int status; /* error status */ int ncid; /* netCDF ID */ int lat_dim, lon_dim, time_dim; /* dimension IDs */ int rh_id; /* variable ID */ int rh_dimids[3]; /* variable shape */ ... status = nc_create("foo.nc", NC_NOCLOBBER, &ncid); if (status != NC_NOERR) handle_error(status); ... /* define dimensions */ status = nc_def_dim(ncid, "lat", 5L, &lat_dim); if (status != NC_NOERR) handle_error(status); status = nc_def_dim(ncid, "lon", 10L, &lon_dim); if (status != NC_NOERR) handle_error(status); status = nc_def_dim(ncid, "time", NC_UNLIMITED, &time_dim); if (status != NC_NOERR) handle_error(status); ... /* define variable */ rh_dimids[0] = time_dim; rh_dimids[1] = lat_dim; rh_dimids[2] = lon_dim; status = nc_def_var (ncid, "rh", NC_DOUBLE, 3, rh_dimids, &rh_id); if (status != NC_NOERR) handle_error(status); 4.4 Get a Variable ID from Its Name: nc_inq_varid ================================================= The function nc_inq_varid returns the ID of a netCDF variable, given its name. Usage ===== int nc_inq_varid (int ncid, const char *name, int *varidp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `name' Variable name for which ID is desired. `varidp' Pointer to location for returned variable ID. Errors ====== nc_inq_varid returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The specified variable name is not a valid name for a variable in the specified netCDF dataset. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_inq_varid to find out the ID of a variable named rh in an existing netCDF dataset named foo.nc: #include ... int status, ncid, rh_id; ... status = nc_open("foo.nc", NC_NOWRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid (ncid, "rh", &rh_id); if (status != NC_NOERR) handle_error(status); 4.5 Get Information about a Variable from Its ID: nc_inq_var ============================================================ family A family of functions that returns information about a netCDF variable, given its ID. Information about a variable includes its name, type, number of dimensions, a list of dimension IDs describing the shape of the variable, and the number of variable attributes that have been assigned to the variable. The function nc_inq_var returns all the information about a netCDF variable, given its ID. The other functions each return just one item of information about a variable. These other functions include nc_inq_varname, nc_inq_vartype, nc_inq_varndims, nc_inq_vardimid, and nc_inq_varnatts. Usage ===== int nc_inq_var (int ncid, int varid, char *name, nc_type *xtypep, int *ndimsp, int dimids[], int *nattsp); int nc_inq_varname (int ncid, int varid, char *name); int nc_inq_vartype (int ncid, int varid, nc_type *xtypep); int nc_inq_varndims (int ncid, int varid, int *ndimsp); int nc_inq_vardimid (int ncid, int varid, int dimids[]); int nc_inq_varnatts (int ncid, int varid, int *nattsp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `name' Returned variable name. The caller must allocate space for the returned name. The maximum possible length, in characters, of a variable name is given by the predefined constant NC_MAX_NAME. (This doesn't include the null terminator, so declare your array to be size NC_MAX_NAME+1). The returned character array will be null-terminated. `xtypep' Pointer to location for returned variable type, one of the set of predefined netCDF external data types. The type of this parameter, nc_type, is defined in the netCDF header file. The valid netCDF external data types are NC_BYTE, NC_CHAR, NC_SHORT, NC_INT, NC_FLOAT, and NC_DOUBLE. `ndimsp' Pointer to location for returned number of dimensions the variable was defined as using. For example, 2 indicates a matrix, 1 indicates a vector, and 0 means the variable is a scalar with no dimensions. `dimids' Returned vector of *ndimsp dimension IDs corresponding to the variable dimensions. The caller must allocate enough space for a vector of at least *ndimsp integers to be returned. The maximum possible number of dimensions for a variable is given by the predefined constant NC_MAX_VAR_DIMS. `nattsp' Pointer to location for returned number of variable attributes assigned to this variable. These functions return the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: The variable ID is invalid for the specified netCDF dataset. The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_inq_var to find out about a variable named rh in an existing netCDF dataset named foo.nc: #include ... int status /* error status */ int ncid; /* netCDF ID */ int rh_id; /* variable ID */ nc_type rh_type; /* variable type */ int rh_ndims; /* number of dims */ int rh_dims[NC_MAX_VAR_DIMS]; /* variable shape */ int rh_natts /* number of attributes */ ... status = nc_open ("foo.nc", NC_NOWRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid (ncid, "rh", &rh_id); if (status != NC_NOERR) handle_error(status); /* we don't need name, since we already know it */ status = nc_inq_var (ncid, rh_id, 0, &rh_type, &rh_ndims, rh_dims, &rh_natts); if (status != NC_NOERR) handle_error(status); 4.6 Write a Single Data Value: nc_put_var1_ TYPE ================================================ The functions nc_put_var1_ TYPE put a single data value of the specified type into a variable of an open netCDF dataset that is in data mode. Inputs are the netCDF ID, the variable ID, an index that specifies which value to add or alter, and the data value. The value is converted to the external data type of the variable, if necessary. Usage ===== int nc_put_var1_text (int ncid, int varid, const size_t index[], const char *tp); int nc_put_var1_uchar (int ncid, int varid, const size_t index[], const unsigned char *up); int nc_put_var1_schar (int ncid, int varid, const size_t index[], const signed char *cp); int nc_put_var1_short (int ncid, int varid, const size_t index[], const short *sp); int nc_put_var1_int (int ncid, int varid, const size_t index[], const int *ip); int nc_put_var1_long (int ncid, int varid, const size_t index[], const long *lp); int nc_put_var1_float (int ncid, int varid, const size_t index[], const float *fp); int nc_put_var1_double(int ncid, int varid, const size_t index[], const double *dp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `index[]' The index of the data value to be written. The indices are relative to 0, so for example, the first data value of a two-dimensional variable would have index (0,0). The elements of index must correspond to the variable's dimensions. Hence, if the variable uses the unlimited dimension, the first index would correspond to the unlimited dimension. `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to the data value to be written. If the type of data values differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== nc_put_var1_ TYPE returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * The specified indices were out of range for the rank of the specified variable. For example, a negative index or an index that is larger than the corresponding dimension length will cause an error. * The specified value is out of the range of values representable by the external data type of the variable. * The specified netCDF is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_put_var1_double to set the (1,2,3) element of the variable named rh to 0.5 in an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with time, lat, and lon, so we want to set the value of rh that corresponds to the second time value, the third lat value, and the fourth lon value: #include ... int status; /* error status */ int ncid; /* netCDF ID */ int rh_id; /* variable ID */ static size_t rh_index[] = {1, 2, 3}; /* where to put value */ static double rh_val = 0.5; /* value to put */ ... status = nc_open("foo.nc", NC_WRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid (ncid, "rh", &rh_id); if (status != NC_NOERR) handle_error(status); ... status = nc_put_var1_double(ncid, rh_id, rh_index, &rh_val); if (status != NC_NOERR) handle_error(status); 4.7 Write an Entire Variable: nc_put_var_ TYPE ============================================== The nc_put_var_ TYPE family of functions write all the values of a variable into a netCDF variable of an open netCDF dataset. This is the simplest interface to use for writing a value in a scalar variable or whenever all the values of a multidimensional variable can all be written at once. The values to be written are associated with the netCDF variable by assuming that the last dimension of the netCDF variable varies fastest in the C interface. The values are converted to the external data type of the variable, if necessary. Take care when using the simplest forms of this interface with record variables when you don't specify how many records are to be written. If you try to write all the values of a record variable into a netCDF file that has no record data yet (hence has 0 records), nothing will be written. Similarly, if you try to write all of a record variable but there are more records in the file than you assume, more data may be written to the file than you supply, which may result in a segmentation violation. Usage ===== int nc_put_var_text (int ncid, int varid, const char *tp); int nc_put_var_uchar (int ncid, int varid, const unsigned char *up); int nc_put_var_schar (int ncid, int varid, const signed char *cp); int nc_put_var_short (int ncid, int varid, const short *sp); int nc_put_var_int (int ncid, int varid, const int *ip); int nc_put_var_long (int ncid, int varid, const long *lp); int nc_put_var_float (int ncid, int varid, const float *fp); int nc_put_var_double(int ncid, int varid, const double *dp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to a block of data values to be written. The order in which the data will be written to the netCDF variable is with the last dimension of the specified variable varying fastest. If the type of data values differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== Members of the nc_put_var_ TYPE family return the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * One or more of the specified values are out of the range of values representable by the external data type of the variable. * One or more of the specified values are out of the range of values representable by the external data type of the variable. * The specified netCDF dataset is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_put_var_double to add or change all the values of the variable named rh to 0.5 in an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with time, lat, and lon, and that there are three time values, five lat values, and ten lon values. #include ... #define TIMES 3 #define LATS 5 #define LONS 10 int status; /* error status */ int ncid; /* netCDF ID */ int rh_id; /* variable ID */ double rh_vals[TIMES*LATS*LONS]; /* array to hold values */ int i; ... status = nc_open("foo.nc", NC_WRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid (ncid, "rh", &rh_id); if (status != NC_NOERR) handle_error(status); ... for (i = 0; i < TIMES*LATS*LONS; i++) rh_vals[i] = 0.5; /* write values into netCDF variable */ status = nc_put_var_double(ncid, rh_id, rh_vals); if (status != NC_NOERR) handle_error(status); 4.8 Write an Array of Values: nc_put_vara_ TYPE =============================================== The function nc_put_vara_ TYPE writes values into a netCDF variable of an open netCDF dataset. The part of the netCDF variable to write is specified by giving a corner and a vector of edge lengths that refer to an array section of the netCDF variable. The values to be written are associated with the netCDF variable by assuming that the last dimension of the netCDF variable varies fastest in the C interface. The netCDF dataset must be in data mode. Usage ===== int nc_put_vara_ type (int ncid, int varid, const size_t start[], const size_t count[], const type *valuesp); int nc_put_vara_text (int ncid, int varid, const size_t start[], const size_t count[], const char *tp); int nc_put_vara_uchar (int ncid, int varid, const size_t start[], const size_t count[], const unsigned char *up); int nc_put_vara_schar (int ncid, int varid, const size_t start[], const size_t count[], const signed char *cp); int nc_put_vara_short (int ncid, int varid, const size_t start[], const size_t count[], const short *sp); int nc_put_vara_int (int ncid, int varid, const size_t start[], const size_t count[], const int *ip); int nc_put_vara_long (int ncid, int varid, const size_t start[], const size_t count[], const long *lp); int nc_put_vara_float (int ncid, int varid, const size_t start[], const size_t count[], const float *fp); int nc_put_vara_double(int ncid, int varid, const size_t start[], const size_t count[], const double *dp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `start' A vector of size_t integers specifying the index in the variable where the first of the data values will be written. The indices are relative to 0, so for example, the first data value of a variable would have index (0, 0, ... , 0). The size of start must be the same as the number of dimensions of the specified variable. The elements of start must correspond to the variable's dimensions in order. Hence, if the variable is a record variable, the first index would correspond to the starting record number for writing the data values. `count' A vector of size_t integers specifying the edge lengths along each dimension of the block of data values to be written. To write a single value, for example, specify count as (1, 1, ... , 1). The length of count is the number of dimensions of the specified variable. The elements of count correspond to the variable's dimensions. Hence, if the variable is a record variable, the first element of count corresponds to a count of the number of records to write. `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to a block of data values to be written. The order in which the data will be written to the netCDF variable is with the last dimension of the specified variable varying fastest. If the type of data values differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== nc_put_vara_ TYPE returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * The specified corner indices were out of range for the rank of the specified variable. For example, a negative index, or an index that is larger than the corresponding dimension length will cause an error. * The specified edge lengths added to the specified corner would have referenced data out of range for the rank of the specified variable. For example, an edge length that is larger than the corresponding dimension length minus the corner index will cause an error. * One or more of the specified values are out of the range of values representable by the external data type of the variable. * The specified netCDF dataset is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_put_vara_double to add or change all the values of the variable named rh to 0.5 in an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with time, lat, and lon, and that there are three time values, five lat values, and ten lon values. #include ... #define TIMES 3 #define LATS 5 #define LONS 10 int status; /* error status */ int ncid; /* netCDF ID */ int rh_id; /* variable ID */ static size_t start[] = {0, 0, 0}; /* start at first value */ static size_t count[] = {TIMES, LATS, LONS}; double rh_vals[TIMES*LATS*LONS]; /* array to hold values */ int i; ... status = nc_open("foo.nc", NC_WRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid (ncid, "rh", &rh_id); if (status != NC_NOERR) handle_error(status); ... for (i = 0; i < TIMES*LATS*LONS; i++) rh_vals[i] = 0.5; /* write values into netCDF variable */ status = nc_put_vara_double(ncid, rh_id, start, count, rh_vals); if (status != NC_NOERR) handle_error(status); 4.9 Write a Subsampled Array of Values: nc_put_vars_ TYPE ========================================================= Each member of the family of functions nc_put_vars_ TYPE writes a subsampled (strided) array section of values into a netCDF variable of an open netCDF dataset. The subsampled array section is specified by giving a corner, a vector of counts, and a stride vector. The netCDF dataset must be in data mode. Usage ===== int nc_put_vars_text (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const char *tp); int nc_put_vars_uchar (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const unsigned char *up); int nc_put_vars_schar (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const signed char *cp); int nc_put_vars_short (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const short *sp); int nc_put_vars_int (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const int *ip); int nc_put_vars_long (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const long *lp); int nc_put_vars_float (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const float *fp); int nc_put_vars_double(int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const double *dp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `start' A vector of size_t integers specifying the index in the variable where the first of the data values will be written. The indices are relative to 0, so for example, the first data value of a variable would have index (0, 0, ... , 0). The elements of start correspond, in order, to the variable's dimensions. Hence, if the variable is a record variable, the first index corresponds to the starting record number for writing the data values. `count' A vector of size_t integers specifying the number of indices selected along each dimension. To write a single value, for example, specify count as (1, 1, ... , 1). The elements of count correspond, in order, to the variable's dimensions. Hence, if the variable is a record variable, the first element of count corresponds to a count of the number of records to write. `stride' A vector of ptrdiff_t integers that specifies the sampling interval along each dimension of the netCDF variable. The elements of the stride vector correspond, in order, to the netCDF variable's dimensions (stride[0] gives the sampling interval along the most slowly varying dimension of the netCDF variable). Sampling intervals are specified in type-independent units of elements (a value of 1 selects consecutive elements of the netCDF variable along the corresponding dimension, a value of 2 selects every other element, etc.). A NULL stride argument is treated as (1, 1, ... , 1). `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to a block of data values to be written. The order in which the data will be written to the netCDF variable is with the last dimension of the specified variable varying fastest. If the type of data values differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== nc_put_vars_ TYPE returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * The specified start, count and stride generate an index which is out of range. * One or more of the specified values are out of the range of values representable by the external data type of the variable. * The specified netCDF is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example of using nc_put_vars_float to write - from an internal array - every other point of a netCDF variable named rh which is described by the C declaration float rh[4][6] (note the size of the dimensions): #include ... #define NDIM 2 /* rank of netCDF variable */ int ncid; /* netCDF ID */ int status; /* error status */ int rhid; /* variable ID */ static size_t start[NDIM] /* netCDF variable start point: */ = {0, 0}; /* first element */ static size_t count[NDIM] /* size of internal array: entire */ = {2, 3}; /* (subsampled) netCDF variable */ static ptrdiff_t stride[NDIM] /* variable subsampling intervals: */ = {2, 2}; /* access every other netCDF element */ float rh[2][3]; /* note subsampled sizes for */ /* netCDF variable dimensions */ ... status = nc_open("foo.nc", NC_WRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid(ncid, "rh", &rhid); if (status != NC_NOERR) handle_error(status); ... status = nc_put_vars_float(ncid, rhid, start, count, stride, rh); if (status != NC_NOERR) handle_error(status); 4.10 Write a Mapped Array of Values: nc_put_varm_ TYPE ====================================================== The nc_put_varm_ TYPE family of functions writes a mapped array section of values into a netCDF variable of an open netCDF dataset. The mapped array section is specified by giving a corner, a vector of counts, a stride vector, and an index mapping vector. The index mapping vector is a vector of integers that specifies the mapping between the dimensions of a netCDF variable and the in-memory structure of the internal data array. No assumptions are made about the ordering or length of the dimensions of the data array. The netCDF dataset must be in data mode. Usage ===== int nc_put_varm_text (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const ptrdiff_t imap[], const char *tp); int nc_put_varm_uchar (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const ptrdiff_t imap[], const unsigned char *up); int nc_put_varm_schar (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const ptrdiff_t imap[], const signed char *cp); int nc_put_varm_short (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const ptrdiff_t imap[], const short *sp); int nc_put_varm_int (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const ptrdiff_t imap[], const int *ip); int nc_put_varm_long (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const ptrdiff_t imap[], const long *lp); int nc_put_varm_float (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const ptrdiff_t imap[], const float *fp); int nc_put_varm_double(int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], const ptrdiff_t imap[], const double *dp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `start' A vector of size_t integers specifying the index in the variable where the first of the data values will be written. The indices are relative to 0, so for example, the first data value of a variable would have index (0, 0, ... , 0). The elements of start correspond, in order, to the variable's dimensions. Hence, if the variable is a record variable, the first index corresponds to the starting record number for writing the data values. `count' A vector of size_t integers specifying the number of indices selected along each dimension. To write a single value, for example, specify count as (1, 1, ... , 1). The elements of count correspond, in order, to the variable's dimensions. Hence, if the variable is a record variable, the first element of count corresponds to a count of the number of records to write. `stride' A vector of ptrdiff_t integers that specifies the sampling interval along each dimension of the netCDF variable. The elements of the stride vector correspond, in order, to the netCDF variable's dimensions (stride[0] gives the sampling interval along the most slowly varying dimension of the netCDF variable). Sampling intervals are specified in type-independent units of elements (a value of 1 selects consecutive elements of the netCDF variable along the corresponding dimension, a value of 2 selects every other element, etc.). A NULL stride argument is treated as (1, 1, ... , 1). `imap' A vector of ptrdiff_t integers that specifies the mapping between the dimensions of a netCDF variable and the in-memory structure of the internal data array. The elements of the index mapping vector correspond, in order, to the netCDF variable's dimensions (imap[0] gives the distance between elements of the internal array corresponding to the most slowly varying dimension of the netCDF variable). Distances between elements are specified in type-independent units of elements (the distance between internal elements that occupy adjacent memory locations is 1 and not the element's byte-length as in netCDF 2). A NULL argument means the memory-resident values have the same structure as the associated netCDF variable. `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to the location used for computing where the data values will be found; the data should be of the type appropriate for the function called. If the type of data values differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== nc_put_varm_ TYPE returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * The specified start, count, and stride generate an index which is out of range. Note that no error checking is possible on the imap vector. * One or more of the specified values are out of the range of values representable by the external data type of the variable. * The specified netCDF is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= The following imap vector maps in the trivial way a 4x3x2 netCDF variable and an internal array of the same shape: float a[4][3][2]; /* same shape as netCDF variable */ int imap[3] = {6, 2, 1}; /* netCDF dimension inter-element distance */ /* ---------------- ---------------------- */ /* most rapidly varying 1 */ /* intermediate 2 (=imap[2]*2) */ /* most slowly varying 6 (=imap[1]*3) */ Using the imap vector above with nc_put_varm_float obtains the same result as simply using nc_put_var_float. Here is an example of using nc_put_varm_float to write - from a transposed, internal array - a netCDF variable named rh which is described by the C declaration float rh[6][4] (note the size and order of the dimensions): #include ... #define NDIM 2 /* rank of netCDF variable */ int ncid; /* netCDF ID */ int status; /* error status */ int rhid; /* variable ID */ static size_t start[NDIM] /* netCDF variable start point: */ = {0, 0}; /* first element */ static size_t count[NDIM] /* size of internal array: entire netCDF */ = {6, 4}; /* variable; order corresponds to netCDF */ /* variable -- not internal array */ static ptrdiff_t stride[NDIM]/* variable subsampling intervals: */ = {1, 1}; /* sample every netCDF element */ static ptrdiff_t imap[NDIM] /* internal array inter-element distances; */ = {1, 6}; /* would be {4, 1} if not transposing */ float rh[4][6]; /* note transposition of netCDF variable */ /* dimensions */ ... status = nc_open("foo.nc", NC_WRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid(ncid, "rh", &rhid); if (status != NC_NOERR) handle_error(status); ... status = nc_put_varm_float(ncid, rhid, start, count, stride, imap, rh); if (status != NC_NOERR) handle_error(status); Here is another example of using nc_put_varm_float to write - from a transposed, internal array - a subsample of the same netCDF variable, by writing every other point of the netCDF variable: #include ... #define NDIM 2 /* rank of netCDF variable */ int ncid; /* netCDF ID */ int status; /* error status */ int rhid; /* variable ID */ static size_t start[NDIM] /* netCDF variable start point: */ = {0, 0}; /* first element */ static size_t count[NDIM] /* size of internal array: entire */ = {3, 2}; /* (subsampled) netCDF variable; order of */ /* dimensions corresponds to netCDF */ /* variable -- not internal array */ static ptrdiff_t stride[NDIM] /* variable subsampling intervals: */ = {2, 2}; /* sample every other netCDF element */ static ptrdiff_t imap[NDIM] /* internal array inter-element distances; */ = {1, 3}; /* would be {2, 1} if not transposing */ float rh[2][3]; /* note transposition of (subsampled) */ /* netCDF variable dimensions */ ... status = nc_open("foo.nc", NC_WRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid(ncid, "rh", &rhid); if (status != NC_NOERR) handle_error(status); ... status = nc_put_varm_float(ncid, rhid, start, count, stride, imap, rh); if (status != NC_NOERR) handle_error(status); 4.11 Read a Single Data Value: nc_get_var1_ TYPE ================================================ The functions nc_get_var1_ TYPE get a single data value from a variable of an open netCDF dataset that is in data mode. Inputs are the netCDF ID, the variable ID, a multidimensional index that specifies which value to get, and the address of a location into which the data value will be read. The value is converted from the external data type of the variable, if necessary. Usage ===== int nc_get_var1_text (int ncid, int varid, const size_t index[], char *tp); int nc_get_var1_uchar (int ncid, int varid, const size_t index[], unsigned char *up); int nc_get_var1_schar (int ncid, int varid, const size_t index[], signed char *cp); int nc_get_var1_short (int ncid, int varid, const size_t index[], short *sp); int nc_get_var1_int (int ncid, int varid, const size_t index[], int *ip); int nc_get_var1_long (int ncid, int varid, const size_t index[], long *lp); int nc_get_var1_float (int ncid, int varid, const size_t index[], float *fp); int nc_get_var1_double(int ncid, int varid, const size_t index[], double *dp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `index[]' The index of the data value to be read. The indices are relative to 0, so for example, the first data value of a two-dimensional variable would have index (0,0). The elements of index must correspond to the variable's dimensions. Hence, if the variable is a record variable, the first index is the record number. `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to the location into which the data value is read. If the type of data value differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== nc_get_var1_ TYPE returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * The specified indices were out of range for the rank of the specified variable. For example, a negative index or an index that is larger than the corresponding dimension length will cause an error. * The value is out of the range of values representable by the desired data type. * The specified netCDF is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_get_var1_double to get the (1,2,3) element of the variable named rh in an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with time, lat, and lon, so we want to get the value of rh that corresponds to the second time value, the third lat value, and the fourth lon value: #include ... int status; /* error status */ int ncid; /* netCDF ID */ int rh_id; /* variable ID */ static size_t rh_index[] = {1, 2, 3}; /* where to get value from */ double rh_val; /* where to put it */ ... status = nc_open("foo.nc", NC_NOWRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid (ncid, "rh", &rh_id); if (status != NC_NOERR) handle_error(status); ... status = nc_get_var1_double(ncid, rh_id, rh_index, &rh_val); if (status != NC_NOERR) handle_error(status); 4.12 Read an Entire Variable nc_get_var_ TYPE ============================================= The members of the nc_get_var_ TYPE family of functions read all the values from a netCDF variable of an open netCDF dataset. This is the simplest interface to use for reading the value of a scalar variable or when all the values of a multidimensional variable can be read at once. The values are read into consecutive locations with the last dimension varying fastest. The netCDF dataset must be in data mode. Take care when using the simplest forms of this interface with record variables when you don't specify how many records are to be read. If you try to read all the values of a record variable into an array but there are more records in the file than you assume, more data will be read than you expect, which may cause a segmentation violation. Usage ===== int nc_get_var_text (int ncid, int varid, char *tp); int nc_get_var_uchar (int ncid, int varid, unsigned char *up); int nc_get_var_schar (int ncid, int varid, signed char *cp); int nc_get_var_short (int ncid, int varid, short *sp); int nc_get_var_int (int ncid, int varid, int *ip); int nc_get_var_long (int ncid, int varid, long *lp); int nc_get_var_float (int ncid, int varid, float *fp); int nc_get_var_double(int ncid, int varid, double *dp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to the location into which the data value is read. If the type of data value differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== nc_get_var_ TYPE returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * One or more of the values are out of the range of values representable by the desired type. * The specified netCDF is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_get_var_double to read all the values of the variable named rh from an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with time, lat, and lon, and that there are three time values, five lat values, and ten lon values. #include ... #define TIMES 3 #define LATS 5 #define LONS 10 int status; /* error status */ int ncid; /* netCDF ID */ int rh_id; /* variable ID */ double rh_vals[TIMES*LATS*LONS]; /* array to hold values */ ... status = nc_open("foo.nc", NC_NOWRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid (ncid, "rh", &rh_id); if (status != NC_NOERR) handle_error(status); ... /* read values from netCDF variable */ status = nc_get_var_double(ncid, rh_id, rh_vals); if (status != NC_NOERR) handle_error(status); 4.13 Read an Array of Values: nc_get_vara_ TYPE =============================================== The members of the nc_get_vara_ TYPE family of functions read an array of values from a netCDF variable of an open netCDF dataset. The array is specified by giving a corner and a vector of edge lengths. The values are read into consecutive locations with the last dimension varying fastest. The netCDF dataset must be in data mode. Usage ===== int nc_get_vara_text (int ncid, int varid, const size_t start[], const size_t count[] char *tp); int nc_get_vara_uchar (int ncid, int varid, const size_t start[], const size_t count[] unsigned char *up); int nc_get_vara_schar (int ncid, int varid, const size_t start[], const size_t count[] signed char *cp); int nc_get_vara_short (int ncid, int varid, const size_t start[], const size_t count[] short *sp); int nc_get_vara_int (int ncid, int varid, const size_t start[], const size_t count[] int *ip); int nc_get_vara_long (int ncid, int varid, const size_t start[], const size_t count[] long *lp); int nc_get_vara_float (int ncid, int varid, const size_t start[], const size_t count[] float *fp); int nc_get_vara_double(int ncid, int varid, const size_t start[], const size_t count[] double *dp); `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `start' A vector of size_t integers specifying the index in the variable where the first of the data values will be read. The indices are relative to 0, so for example, the first data value of a variable would have index (0, 0, ... , 0). The length of start must be the same as the number of dimensions of the specified variable. The elements of start correspond, in order, to the variable's dimensions. Hence, if the variable is a record variable, the first index would correspond to the starting record number for reading the data values. `count' A vector of size_t integers specifying the edge lengths along each dimension of the block of data values to be read. To read a single value, for example, specify count as (1, 1, ... , 1). The length of count is the number of dimensions of the specified variable. The elements of count correspond, in order, to the variable's dimensions. Hence, if the variable is a record variable, the first element of count corresponds to a count of the number of records to read. `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to the location into which the data value is read. If the type of data value differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== nc_get_vara_ TYPE returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * The specified corner indices were out of range for the rank of the specified variable. For example, a negative index or an index that is larger than the corresponding dimension length will cause an error. * The specified edge lengths added to the specified corner would have referenced data out of range for the rank of the specified variable. For example, an edge length that is larger than the corresponding dimension length minus the corner index will cause an error. * One or more of the values are out of the range of values representable by the desired type. * The specified netCDF is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example using nc_get_vara_double to read all the values of the variable named rh from an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with time, lat, and lon, and that there are three time values, five lat values, and ten lon values. #include ... #define TIMES 3 #define LATS 5 #define LONS 10 int status; /* error status */ int ncid; /* netCDF ID */ int rh_id; /* variable ID */ static size_t start[] = {0, 0, 0}; /* start at first value */ static size_t count[] = {TIMES, LATS, LONS}; double rh_vals[TIMES*LATS*LONS]; /* array to hold values */ ... status = nc_open("foo.nc", NC_NOWRITE, &ncid); if (status != NC_NOERR) handle_error(status); ... status = nc_inq_varid (ncid, "rh", &rh_id); if (status != NC_NOERR) handle_error(status); ... /* read values from netCDF variable */ status = nc_get_vara_double(ncid, rh_id, start, count, rh_vals); if (status != NC_NOERR) handle_error(status); 4.14 Read a Subsampled Array of Values: nc_get_vars_ TYPE ========================================================= The nc_get_vars_ TYPE family of functions read a subsampled (strided) array section of values from a netCDF variable of an open netCDF dataset. The subsampled array section is specified by giving a corner, a vector of edge lengths, and a stride vector. The values are read with the last dimension of the netCDF variable varying fastest. The netCDF dataset must be in data mode. Usage ===== int nc_get_vars_text (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], char *tp); int nc_get_vars_uchar (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], unsigned char *up); int nc_get_vars_schar (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], signed char *cp); int nc_get_vars_short (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], short *sp); int nc_get_vars_int (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], int *ip); int nc_get_vars_long (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], long *lp); int nc_get_vars_float (int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], float *fp); int nc_get_vars_double(int ncid, int varid, const size_t start[], const size_t count[], const ptrdiff_t stride[], double *dp) `ncid' NetCDF ID, from a previous call to nc_open or nc_create. `varid' Variable ID. `start' A vector of size_t integers specifying the index in the variable where the first of the data values will be read. The indices are relative to 0, so for example, the first data value of a variable would have index (0, 0, ... , 0). The elements of start correspond, in order, to the variable's dimensions. Hence, if the variable is a record variable, the first index corresponds to the starting record number for reading the data values. `count' A vector of size_t integers specifying the number of indices selected along each dimension. To read a single value, for example, specify count as (1, 1, ... , 1). The elements of count correspond, in order, to the variable's dimensions. Hence, if the variable is a record variable, the first element of count corresponds to a count of the number of records to read. `stride' A vector of ptrdiff_t integers specifying, for each dimension, the interval between selected indices. The elements of the stride vector correspond, in order, to the variable's dimensions. A value of 1 accesses adjacent values of the netCDF variable in the corresponding dimension; a value of 2 accesses every other value of the netCDF variable in the corresponding dimension; and so on. A NULL stride argument is treated as (1, 1, ... , 1). `tp' `up' `cp' `sp' `ip' `lp' `fp' `dp' Pointer to the location into which the data value is read. If the type of data value differs from the netCDF variable type, type conversion will occur. *Note Type Conversion: (netcdf)Type Conversion. Errors ====== nc_get_vars_ TYPE returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include: * The variable ID is invalid for the specified netCDF dataset. * The specified start, count and stride generate an index which is out of range. * One or more of the values are out of the range of values representable by the desired type. * The specified netCDF is in define mode rather than data mode. * The specified netCDF ID does not refer to an open netCDF dataset. Example ======= Here is an example that uses nc_get_vars_double to read every other value in each dimension of the variable named rh from an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with time, lat, and lon, and that there are three time values, five lat values, and ten lon values. #include ... #define TIMES 3 #define LATS 5 #define LONS 10 int status;