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setfileoption

Sets a number of file-format-specific options.

Prototype

	procedure setfileoption (
		format_or_file [1] : string or file,  
		option         [1] : string,          
		value                                 
	)

Arguments

format_or_file

Either a string specifying a file format, or a reference to a file opened with addfile or addfiles. If set as a string the value must be equal to one of the suffixes accepted by NCL as the indicator of a supported format (e.g. "nc", "grb", or "GRIB"), or else "bin" to specify an option supported for binary files.

option

A case-insensitive string containing the name of an NCL-supported file option.

value

A scalar value or one-dimensional array containing the desired value(s) to be assigned to the option. The type of this argument is dependent on the requirements of the option being set.

Description

This procedure allows the user to set a number of options that are dependent on the format of the file accessed. The options have varying restrictions concerning when they may be set and the values that are acceptable. If the first argument is a string specifying a format, then the option setting applies to any file of the specified format when it is first opened using addfile or addfiles. If the first argument is the string "bin", then the option setting applies to subsequent calls to the built-in binary data reading functions or binary data writing procedures. Files referenced by existing file variables will not be affected. On the other hand, options set using a file variable as the first argument affect only the specified file, and may alter NCL's treatment of it dynamically.

NetCDF file format options

DefineMode
Default value: True

This option may be set only for files opened for writing. (Prior to version 4.3.1, it defaulted to False.) When set True, rather than performing each operation atomically, NCL keeps the NetCDF library in define mode without closing the file while dimensions, attributes, and variables are defined using the functions filedimdef, fileattdef, filevardef, and filevarattdef. The file remains open in define mode until variable data is read or written, the option is set False again, or the file variable is deleted. Setting this option True while dimensions, variables and attributes are first defined can improve performance dramatically for files with large dimensions or many variables and attributes. Care should be taken to define all dimensions, attributes, and variables before writing actual data to the file.

CompressionLevel
Default value: -1

Specify the level of data compression as an integer in the range 0 through 9. Increasing values indicate greater compression. Compression is lossless. There are tradeoffs between the time spent compressing the file, versus the amount of compression achieved. Informal tests show that compression level 9 results in a file only a few percent smaller than a compression level 5 file, but it requires 4 or 5 times the amount of time to create it. (This option is ignored unless the Format option is set to "NetCDF4Classic" or "NetCDF4".)

Format
Default value: "Classic"

You may set this option only prior to opening a new NetCDF file in "create" mode. The first argument must be a string specifying the NetCDF format, such as "nc". This string-valued option currently has four valid values, two of which are synonyms.

A value of "Classic" indicates that a standard NetCDF file should be created. Standard NetCDF files are more limited with respect to size. Assuming the underlying file system has support for large files, the total size can exceed 2 GB, but there are severe restrictions regarding the number of large variables and the order in which they are written. In general, the standard format should be used if and only if it is known that the total file size will be less than 2 GB.

The two synonymous values, "LargeFile" and "64BitOffset", indicate that a NetCDF file with support for larger variables and a theoretically much larger total size (about 9.22e+18 bytes) should be created. Each fixed-size variable, or each 'record' (first dimension) of a variable with an unlimited dimension of a 64-bit offset file can have a size of up to 4 GB.

Again, assuming the underlying file system has support for large files, recent versions of NCL can transparently read NetCDF files in either the classic or the 64-bit offset format. For more detailed information about large file support in NetCDF see http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/Large-File-Support.html.

In version 4.3.1 or later, you can specify "NetCDF4Classic" to create a file using the NetCDF 4 classic model format. The classic model constrains the interface to the constructs provided by NetCDF 3 and earlier. However, the underlying file format, like that of all NetCDF 4 files, is HDF 5. Files written in this format can take advantage of the built-in file compression available in HDF 5. Use the CompressionLevel option (see above) to enable compression. Also the HDF 5 format removes virtually all restrictions on file and individual variable size.

In version 6.1.0 or later, you can specify "NetCDF4" to create a file using the NetCDF 4 model format. The underlying file format, like that of all NetCDF 4 files, is HDF 5. Files written in this format can take advantage of the NetCDF-4 features, such as compression, chunking, etc, and new data types such as string, vlen, compound, enum, opaque.

HeaderReserveSpace
Default value: 0

This option may be set only for files opened for writing. This integer-valued option may be used to reserve extra space at the beginning of a NetCDF file in order to define new dimensions, variables, or attributes after variable data has been written. It specifies the number of bytes to reserve in the header portion of the file in addition to the bytes used for the currently defined dimensions, variables, and attributes. Note that the space is reserved only when variable data is actually written to the file.

MissingToFillValue
Default value: True

This logical-valued option has an effect only when set prior to opening an existing NetCDF file in read or write mode. If set to True, it causes a "virtual" _FillValue attribute to be created for any variable that has the attribute missing_value but not _FillValue. The purpose is to more gracefully handle files that use the COARDS-compliant missing_value instead of _FillValue to indicate missing data. Note that if a variable in a file has both a missing_value and a _FillValue, or if it has neither, the option does nothing. The virtual _FillValue attribute is not actually part of the NetCDF file, but only appears to be from within the NCL environment. However, it is propagated upon assignment of the variable just like any other attribute. If the file is opened for writing and you assign to the attribute, it becomes an actual attribute. Therefore to make it a permanent part of a file you could simply execute a statement such as:

f->v@_FillValue = f->v@_FillValue
Unfortunately, there is no simple way within NCL to tell whether a particular instance of a _FillValue attribute (where there is also a missing_value attribute with the same value) is virtual or actual. However note that executing the statement above is a harmless no-op if the variable's _FillValue attribute actually exists in the file.

PreFill
Default value: True

This logical-valued option may be set only for files opened for writing. If set False, NCL alters the standard behavior of the NetCDF library such that variable element locations in the file are not "pre-filled" with the missing (fill) value associated with the variable. This can noticeably improve performance when writing large datasets. However, if you set this option False, you are responsible for ensuring that all the elements of the variables you have defined are assigned a valid value.

SuppressClose
Default value: True

This logical-valued option may be set for any NetCDF file. (Before version 4.3.1, it defaulted to False.) When set to False NCL opens a file each time an operation involving reading or writing data occurs and closes it again when the operation is complete. This helps ensure the file's integrity but may result in loss of performance. When this option is set to True, NCL will only only close the file when the user invokes 'delete' on the file object variable, the option is set False again, or when NCL exits. Note that when set to True, if NCL quits unexpectedly there is a small possibility that a file open for writing may corrupted. The DefineMode option also keeps the file open, but only until the first operation that requires leaving define mode is completed. SuppressClose and DefineMode may be used together in files open for writing.

Users who invoke the addfiles function to open many files in an aggregated list should be aware that there are limits on the number of files that can be simultaneously open. Many is, of course, a relative term. OPeNDAP-enabled NCL is restricted by the OPeNDAP NetCDF client library to 64 open files when accessing NetCDF files either locally or over the network. Otherwise, typical Unix/Linux systems usually allow 1024 open files, although this value can vary for older or less-common sytems, and it can also be tweaked when building the OS kernel. The actual number of open files possible may be somewhat less than the limit because of file descriptors used internally. In cases where these values might be exceeded, setting this option to False removes the limitation on the number of files in an aggregated list.

Shuffle
Default value: 1

This option has two valid (integer) values: 1, and 0, where 1 means turning HDF5 (compression) shuffle filter on, and 0 means off. Turning the shuffle filter on can improve the compression ratio for integer data.

This option has an effect only when writing full model NetCDF4 compressed files. When writing NetCDF4 classic model file using the Standard file structure (see the FileStructure option) the shuffle filter is always on, regardless of the setting of this option. This option can only be set after the file has been created.

GRIB file format options

DefaultNCEPPTable
Default value: "Operational"

This option applies only to GRIB1-formatted files.

This string-valued option has two valid values: "Operational" or "Reanalysis". It specifies whether to default to the use of the NCEP operational parameter table (http://www.ncl.ucar.edu/Document/Manuals/Ref_Manual/ncep_opn.htm) or the NCEP reanalysis parameter table (http://www.ncl.ucar.edu/Document/Manuals/Ref_Manual/ncep_reanal.htm). The option only applies in cases where NCL, on its own, cannot definitively determine which of these tables to use because of historical ambiguities in NCEP usage.

InitialTimeCoordinateType
Default value: "Numeric"

This option applies to GRIB1- and GRIB2-formatted files.

This string-valued option has two valid values: "Numeric" or "String". A value of "Numeric" makes the initial time coordinates conform to a COARDS-compliant numeric time in hours since 1800-01-01 (00.00).

Prior to version 4.2.0.a034, this option defaulted to "String". NCL used an array of strings to represent the coordinate values of an initial time dimension. This representation proved to be problematic, both because it did not conform to standard CF and COARDS conventions, and because it was difficult to use in a context where numerical properties such as monotonicity were usually expected. The "String" default was originally retained for backwards compatibility, but because of the problems described above, it was decided to make the default "Numeric".

By setting this option to "String", you can maintain backwards compatibility with versions before 4.3.0. If this option is set after adding a GRIB file, any initial time dimensions in the file will immediately be updated to reflect the new option value.

Note: in NCL's representation of GRIB1 and GRIB2 files, the initial time dimension is distinguished from the forecast time dimension, whose coordinate values are numerical offsets from a particular initial time.

SingleElementDimensions
Default value: "None"

This option applies to GRIB1- and GRIB2-formatted files.

This string-valued option allows the user to specify that variables with only a single initial time, forecast time, level, ensemble or probability value, usually handled as attributes, be treated as containing single element dimensions. A value of "None" means that no single-element dimensions will appear in NCL's representation of the GRIB file. Conversely, if the option is given the value "All", then all possible dimensions will be created for each variable. Otherwise, the desired single element dimensions may be specified individually. The valid choices are "Initial_time", "Forecast_time", "Level", "Ensemble", and "Probability". Since this option can take an array of values, you can specify more than one of these dimension types as the option value. However, the options "None" and "All" override the individual dimension specifications.

Note that dimensions are not created if the variable does not have an actual value associated with the dimension type, regardless of the value given to this option. For example, variables that are not part of an ensemble forecast will never have an ensemble dimension, and variables whose level type (e.g. Tropopause) does not have a numerical value will never have a level dimension. In the case of level types, it may depend on who wrote the record: files written by some centers may give no value for certain level types where others may use the numerical value 0. The intent of this option is to make it easier to concatenate conforming variables from multiple files together.

TimePeriodSuffix
Default value: True

This option applies to GRIB1- and GRIB2-formatted files. A value of True indicates that statistically-processed variables such as averages and accumulations have a time period and time unit added after the suffix indicating the statistical variable type. For example, the suffix "_avg3h" represents a 3 hour average. These suffixes are required to uniquely characterize otherwise identically-named variables that have different periods and/or units within the same file. However, when concatenating variables from different files using the addfiles function differences in these suffixes can prevent individual variables from being concatenated into a single composite variable when it is actually desireable. Setting this option to False removes the time period and units from the variable name leaving only the statistical processing type (e.g. "_avg" for an average or "_acc" for an accumulation).

ThinnedGridInterpolation
Default value: "Cubic" ("Linear" if using bitmask arrays)

This option applies to GRIB1- and GRIB2-formatted files.

This string-valued option has two valid values: "Cubic" or "Linear". This option may be set for any GRIB file, but only has an effect when the GRIB file contains data on a thinned grid. Note: up to version 4.2.0.a034 of NCL, the default was "Linear". However, the "Cubic" value has been shown to produce better results, hence, as of version 4.3.0, it is the default setting. The exception is when bitmask arrays are encountered. In this case, "Linear" will be the default because "Cubic" interpolation cannot be applied in the presence of bitmask arrays.

The GRIB documentation refers to these grids as "quasi-regular". The option controls the interpolation performed in converting variable data on the thinned grid to the standard rectangular form that is returned by NCL. If this option is modified after adding a GRIB file, the values of variables defined on one of these thinned grids will be modified.

Binary data file options

ReadByteOrder
Default value: "Native"

This string-valued option has three valid values: "Native", "BigEndian", and "LittleEndian". It allows you to read binary data files written with either big or little endian byte ordering independent of the system on which you are running. It affects the contents of variables read using the binary data reading functions cbinread, fbindirread, fbinrecread, and fbinread, as well as the results of the record counting function fbinnumrec. When this option has a value of "Native", these functions behave as they always have: they expect the data bytes to be ordered according to the conventions of the system on which the code is currently executing. However, if the option is set to "BigEndian" or "LittleEndian" NCL will expect the input data file to be byte-ordered according to the conventions of, respectively, a big-endian or a little-endian system. The functions will then either byte-swap the data or not, as appropriate for the byte ordering of the system executing the code, before assigning the the data to the return variable.

WriteByteOrder
Default value: "Native"

This string-valued option has three valid values: "Native", "BigEndian", and "LittleEndian". It allows you to write binary data files with whatever byte ordering you prefer independent of the system on which you are running. It affects the contents of files written using the binary data writing procedures cbinwrite, fbindirwrite, fbinrecwrite, and fbinwrite. When this option has a value of "Native", these procedures behave as they always have: they write the data bytes ordered according to the conventions of the system on which the code is executing. However, if the option is set to "BigEndian" or "LittleEndian" NCL will write output data files byte-ordered according to the conventions of, respectively, a big-endian or a little-endian system. The procedure will either byte-swap the data or not, as appropriate for the byte ordering of the system executing the code, in order to produce data files with the specified byte ordering.

KeepOpen
Default value: False

Available in version 6.3.0 and later.

This option improves the efficiency of reading Fortran binary records in sequential order, via the fbinrecread function. When set to True, the Fortran file is kept open and the file pointer is left at the beginning of the record following the last one read, allowing the user to read subsequent records faster. When finished reading the file, the user must call fbinrecread once with this option set to False in order to close the file.

RecordMarkerSize
Default value: 4

Available in version 6.1.1 and later.

This option can be set to 4 or 8. It indicates the size in bytes of the record marker at the beginning and end of Fortran sequential files. The following functions recognize this option: fbinrecread, fbinrecwrite, fbinnumrec, fbinread, fbinwrite.

Options that can apply to multiple formats

FileStructure
Default value: "Standard"

Available in version 6.1.1 and later.

This option has two valid string type values: "Advanced", and "Standard", where "Advanced" means NCL will use a newer file structure with the capability of handling groups and more advanced data structures, like compound data types, variable length arrays and enumerated types. You can easily recognize use of the advanced file structure based on the appearance of the output of the print procedure: although the same information is conveyed it appears in a noticeably different form.

The "Standard" file structure is the traditional structure used for all NCL supported file formats prior to NetCDF4. On the other hand, full model NetCDF4 files always use the "Advanced" file structure.

In version 6.1.1, this option only has an effect for classic model NetCDF files (including NetCDF4 classic files). But other than the difference in print output, there should be no difference in the way classic model NetCDF is read or written, regardless of the file structure.

However, beginning with version 6.2.0, this option will work for HDF-EOS5 and shapefiles. Choosing the "Advanced" file structure will allow the user to view these file formats using a representation closer to the structure implied by the native format. Conversely, the "Standard" structure will remain available to let you to view the contents as you alway have; in other words backwards compatibility is maintained. Eventually other supported formats that can make ues of the advanced features, including HDF4 and HDFEOS2, may also be enabled to use the "Advanced" file structure.

Support for HDF5 is also anticipated beginning with version 6.2.0, Like full model NetCDF4, HDF5 will be implemented using the "Advanced" file structure only.

UseNewHLFS
Default value: False

NOTE: This option is available beginning with version 6.1.0. However, it has been deprecated and may be removed from version 6.2.0 or later.

This option is basically a synonym for the option FileStructure except that it expects a logical value rather than a string. Setting UseNewHLFS to True is equivalent to setting FileStructure to "Advanced". Likewise, setting it False is equivalent to setting FileStructure to "Standard".

See Also

addfile, addfiles, filedimdef, fileattdef, filevardef, filevarattdef, cbinread, fbindirread, fbinrecread, fbinnumrec, fbinread, cbinwrite, fbindirwrite, fbinrecwrite, fbinwrite.

Examples

Example 1

To force addfile to use cubic interpolation whenever data on a thinned (quasi-regular) grid is encountered on a GRIB file, set the ThinnedGridInterpolation option before you open the file:

   setfileoption("grb","ThinnedGridInterpolation","cubic")
   a = addfile("my_file.grb","r")
   . . .
Example 2

When creating a NetCDF file, you can make it write more efficiently and potentially much faster by defining all the dimensions, variables, and attributes on the file before you write any values.

First set the DefineMode option to True after you open the NetCDF file you want to create, which signals to NCL that you plan to define things before writing any values.

You can then set DefineMode back to False once you are done defining everything and are ready to write your data values:

   f = addfile("test.nc","c")
   setfileoption(f,"DefineMode",True)
   filedimdef(f,(/"lat","lon"/), (/100,150/), (/False,False/))
   filevardef(f,"PSfc","float",(/"lat","lon"/))
   atts = 1.0
   atts@_FillValue = -999.0
   atts@long_name = "Surface Pressure"
   filevarattdef(f,"PSfc",atts)
   setfileoption(f,"DefineMode",False) ; (not really necessary)
   ; assign data only to file variable ; would automatically suspend define mode 
   f->Psfc = (/ datavar(0,:,:) /)

For a more detailed example of writing a NetCDF file using this efficient method, see Method 2 on the Output to NetCDF examples page.

Example 3

Set up the binary data reading functions to expect files written with little-endian byte ordering, and the binary data writing procedures to produce big-endian files, regardless of the system on which NCL is running. Produce a big-endian file from a little-endian file containing float data.

   setfileoption("bin","ReadByteOrder","LittleEndian")
   setfileoption("bin","WriteByteOrder","BigEndian")

   v = cbinread("data.littleEndian.bin",-1,"float")
   cbinwrite("data.bigEndian.bin",v)
Example 4

In order to write large variables (>2GB) to a NetCDF file, you must set NetCDF Format option to LargeFile or NetCDF4Classic before you open the file for creation:

   setfileoption("nc","Format","LargeFile")
   f = addfile("my_large_file.nc","c")
or
   setfileoption("nc","Format","NetCDF4Classic")
   f = addfile("my_large_file.nc","c")

It might be asked "Why cannot NCL set this option internally when asked to write a big variable." The answer is that the NetCDF library requires that this decision must be made when the file is first created, before there is any knowledge of the size of variables that will be written. It is possible that eventually the largefile format will be the default NetCDF format, but so far the recommendation from Unidata is to maintain backwards compatibility where possible for applications that can only deal with the original small file format of NetCDF.

Example 5

To create a NetCDF-4 file with NetCDF-4 features, set the NetCDF Format option to NetCDF4 before you open the file for creation:

   setfileoption("nc","Format","NetCDF4")
   f = addfile("my_netcdf4_file.nc","c")

By setting this option, the NetCDF file created will be a NetCDF-4 file, which is actually HDF-5 under the hood. With this option, there is no size limitation to both files and variables, and you can write new data types (string, vlen, compound, enum, opaque), and use new features such as compression and chunking.

Example 6

To force GRIB files that have a single time step to have an explicit 'time' dimension, set the SingleElementDimensions option before you open the file:

   setfileoption("grb","SingleElementDimensions","Initial_time") ; initial_time0_hours
There are numerous options. Please read the description above.