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Removed deprecated -k n examples for nccopy and ncgen, fixed ncks examples
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Russ Rew
parent
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119
docs/FAQ.md
119
docs/FAQ.md
@ -92,7 +92,7 @@ Another freely available tool,
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developed as a netCDF add-in for MS Excel that can facilitate the
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conversion of netCDF data to and from text form.
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Note that ncdump and similar tools can print metadata and data values
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Note that **ncdump** and similar tools can print metadata and data values
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from netCDF files, but in general they don't understand coordinate
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systems specified in the metadata, only variable arrays and their
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indices. To interpret georeferencing metadata so you can print the data
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@ -109,13 +109,13 @@ How do I convert ASCII or text data to netCDF? {#How-do-I-convert-ASCII-or-text-
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One way to convert data in text form to netCDF is to use the **ncgen**
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tool that is part of the netCDF software distribution. Using ncgen for
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tool that is part of the netCDF software distribution. Using **ncgen** for
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this purpose is a two-step process:
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1. Convert text data to a file in [CDL
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form](/software/netcdf/docs/netcdf.html#CDL-Syntax) using a text
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editor or text manipulation tools
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2. Convert the CDL representation to netCDF using the ncgen tool with
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2. Convert the CDL representation to netCDF using the **ncgen** tool with
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the "-o" or "-b" option
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For more information, see the [ncgen
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@ -348,8 +348,8 @@ build netCDF from source on various platforms. Often, it's as easy as
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running
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~~~~ {.boldcode}
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./configure
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make check install
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./configure
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make check install
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~~~~
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* * * * *
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@ -545,9 +545,9 @@ If you have an unusual combination of compilers or platform, you may
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have to set a few environment variables before invoking
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~~~~ {.boldcode}
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./configure
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make test
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make install
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./configure
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make test
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make install
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~~~~
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For details, see the [NetCDF Installation and Porting
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@ -581,7 +581,7 @@ If you invoke
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~~~~
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the last line of the resulting output will identify the version
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associated with the ncdump utility. You can also call one of the
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associated with the **ncdump** utility. You can also call one of the
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functions `nc_inq_libvers()`, `nf_inq_libvers()`, or
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`nf90_inq_libvers()` from C, Fortran-77, or Fortran-90 programs to get a
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version string.
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@ -681,10 +681,13 @@ user-block of 512, 1024, 2048, ... bytes before what is actually an
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With netCDF version 4.0 or later, there is an easy way that will
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distinguish between netCDF-4 and netCDF-4 classic model files, using the
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"-k" option to ncdump to determine the kind of file, for example:
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"-k" option to **ncdump** to determine the kind of file, for example:
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~~~~~ {.boldcode}
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ncdump -k foo.nc
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classic
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~~~~~
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ncdump -k foo.nc
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classic
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In a program, you can call the function
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[nc\_inq\_format](http://www.unidata.ucar.edu/netcdf/docs/netcdf-c.html#nc_005finq-Family)
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@ -878,7 +881,7 @@ To write compressed data, what changes do I need to make to my netCDF-3 program?
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-----------------
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The nccopy utility in versions 4.1.2 and later supports a "-d *level*"
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The **nccopy** utility in versions 4.1.2 and later supports a "-d *level*"
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deflate option that copies a netCDF file, compressing all variables
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using the specified level of deflation and default chunking parameters,
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or you can specify chunking with the "-c" option.
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@ -952,26 +955,37 @@ Every netCDF-3 file can be read or written by a netCDF version 4
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library, so in that respect netCDF-3 files are already netCDF-4 files
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and need no conversion. But if you want to convert a classic or 64-bit
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offset format file into a netCDF-4 format or netCDF-4 classic model
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format file, the easiest way is to use the nccopy utility from netCDF
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versions 4.1 and later. For example to convert a classic format file
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foo3.nc to a netCDF-4 classic format file foo4.nc, use:
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format file, the easiest way is to use the **nccopy** utility. For example
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to convert a classic format file foo3.nc to a netCDF-4 format file
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foo4.nc, use:
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nccopy -k 4 foo3.nc foo4c.nc
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~~~~~~~~~~~~~~~~~~~~~~~~~ {.boldcode}
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nccopy -k netCDF-4 foo3.nc foo4.nc
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~~~~~~~~~~~~~~~~~~~~~~~~~
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To convert a classic format file foo3.nc to a netCDF-4 classic
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model format file foo4c.nc, you could use:
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~~~~~~~~~~~~~~~~~~~~~~~~~~ {.boldcode}
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nccopy -k netCDF-4-classic foo3.nc foo4c.nc
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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If you have installed [NCO](/netcdf/docs/software.html#NCO), the NCO
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utility "ncks" can be used to accomplish the same task, as follows:
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ncks -4 foo3.nc foo4c.nc
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~~~~~~~~~~~~~~~~~~~~~~~~ {.boldcode}
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ncks -7 foo3.nc foo4c.nc
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~~~~~~~~~~~~~~~~~~~~~~~~
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Another method is available for relatively small files, using the ncdump
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and ncgen utilities (built with a netCDF-4 library). Assuming
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Another method is available for relatively small files, using the **ncdump**
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and **ncgen** utilities (built with a netCDF-4 library). Assuming
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"small3.nc" is a small classic format or 64-bit offset format netCDF
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file, you can create an equivalent netCDF-4 classic file named
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"small4c.nc" as follows:
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file, you can create an equivalent netCDF-4 file named
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"small4.nc" as follows:
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~~~~ {.boldcode}
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ncdump small3.nc > small.cdl
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ncgen -o small4c.nc -k 4 small.cdl
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ncgen -o small4.nc -k netCDF-4-classic small.cdl
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~~~~
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Why might someone want to convert netCDF-4 files into netCDF-3 files? {#Why-might-someone-want-to-convert-netCDF-4-files-into-netCDF-3-files}
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@ -998,19 +1012,23 @@ library, or because no features of the enhanced model were used in
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writing the file, then there are several ways to convert it to a
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netCDF-3 file.
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You can use the nccopy utility from netCDF versions 4.1 and later. For
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You can use the **nccopy** utility. For
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example to convert a netCDF-4 classic-model format file foo4c.nc to a
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classic format file foo3.nc, use:
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nccopy -k classic foo4c.nc foo3.nc
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~~~~~~~~~~~~~~~~~~~~~~~~~ {.boldcode}
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nccopy -k classic foo4c.nc foo3.nc
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~~~~~~~~~~~~~~~~~~~~~~~~~
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If you have installed [NCO](/netcdf/docs/software.html#NCO), the NCO
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utility "ncks" can be used to accomplish the same task, as follows:
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ncks -3 foo4c.nc foo3.nc
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~~~~~~~~~~~~~~~~~~~~~~~~~ {.boldcode}
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ncks -3 foo4c.nc foo3.nc
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~~~~~~~~~~~~~~~~~~~~~~~~~
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For a relatively small netCDF-4 classic model file, "small4c.nc" for
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example, you can also use the ncdump and ncgen utilities to create an
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example, you can also use the **ncdump** and **ncgen** utilities to create an
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equivalent netCDF-3 classic format file named "small3.nc" as follows:
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~~~~ {.boldcode}
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@ -1086,9 +1104,9 @@ netCDF libraries don't use the file extension. A user can currently
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create a netCDF file with any extension, even one not consistent with
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the format of the file.
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The ncgen utility uses ".nc" as a default extension for output, but this
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The **ncgen** utility uses ".nc" as a default extension for output, but this
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can be overridden using the "-o" option to specify the name for the
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output file. Recent versions of ncgen also have a "-k" option to specify
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output file. Recent versions of **ncgen** also have a "-k" option to specify
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what kind of output file is desired, selecting any of the 4 format
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variants, using either a numeric code or a text string. Most other
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netCDF client software pays no attention to the file extension, so using
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@ -1160,18 +1178,18 @@ user-defined types.
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We recommend proceeding incrementally, supporting features that are
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easier to implement first. For example, handling the six new primitive
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types is relatively straightforward. After that, using recursion (or the
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group iterator interface used in nccopy) to support Groups is not too
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group iterator interface used in **nccopy**) to support Groups is not too
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difficult. Providing support for user-defined types is more of a
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challenge, especially since they can be nested.
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The utility program nccopy, provided in releases 4.1 and later, shows
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The utility program **nccopy**, provided in releases 4.1 and later, shows
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how this can be done using the C interface. It copies an input netCDF
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file in any of the format variants, handling nested groups, strings, and
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any user-defined types, including arbitrarily nested compound types,
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variable-length types, and data of any valid netCDF-4 type. It also
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demonstrates how to handle variables that are too large to fit in memory
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by using an iterator interface. Other generic utility programs can make
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use of parts of nccopy for more complex operations on netCDF data.
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use of parts of **nccopy** for more complex operations on netCDF data.
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* * * * *
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@ -1346,7 +1364,7 @@ variant of the format is used. The version of the format will be
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preserved by the library on writing. If you want to modify a classic
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format file to use the 64-bit offset format so you can make it much
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larger, you will have to create a new file and copy the data to it. The
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nccopy utility available in version 4.1 can copy a classic file to a
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**nccopy** utility available in version 4.1 can copy a classic file to a
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64-bit offset file.
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* * * * *
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@ -1394,29 +1412,31 @@ display the first four bytes of a file, say foo.nc, is to run the
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following command:
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~~~~ {.boldcode}
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od -An -c -N4 foo.nc
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od -An -c -N4 foo.nc
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~~~~
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which will output
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~~~~ {.boldcode}
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C D F 001
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C D F 001
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~~~~
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or
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~~~~ {.boldcode}
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C D F 002
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C D F 002
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~~~~
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depending on whether foo.nc is a classic or 64-bit offset netCDF file,
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respectively.
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With netCDF version 3.6.2 or later, there is an easier way, using the
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"-k" option to ncdump to determine the kind of file, for example:
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"-k" option to **ncdump** to determine the kind of file, for example:
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ncdump -k foo.nc
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classic
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~~~~ {.boldcode}
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ncdump -k foo.nc
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classic
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~~~~
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* * * * *
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@ -1489,13 +1509,10 @@ How do I create a 64-bit offset netCDF file using the ncgen utility? {#How-do-I-
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-----------------
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A new flag, '-k', has been added to ncgen to specify the kind of file
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format variant. By default or if '-k 1' or '-k classic' is specified,
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the generated file will be in netCDF classic format. If '-k 2' or '-k
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64-bit-offset' is specified, the generated file will use the new 64-bit
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offset format. To permit creating very large files quickly, another new
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ncgen flag, '-x', has been added to specify use of nofill mode when
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generating the netCDF file.
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A command-line option, '-k', specifies the kind of file format
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variant. By default or if '-k classic' is specified, the generated
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file will be in netCDF classic format. If '-k 64-bit-offset' is
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specified, the generated file will use the 64-bit offset format.
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* * * * *
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@ -1789,8 +1806,8 @@ interface. As a command-line example, you could convert *fileIn.grib* to
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*fileOut.nc* as follows:
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~~~~ {.boldcode}
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java -Xmx1g -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset \
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-in fileIn.grib -out fileOut.nc [-isLargeFile] [-netcdf4]
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java -Xmx1g -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset \
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-in fileIn.grib -out fileOut.nc [-isLargeFile] [-netcdf4]
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~~~~
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For more details on using netCDF Java, see the CDM man pages for
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@ -1805,10 +1822,10 @@ Can I recover data from a netCDF file that was not closed properly? {#Can-I-reco
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-----------------
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*I have some netcdf files which have data in them and were apparently
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not properly closed. When I examine them using ncdump they report zero
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_I have some netcdf files which have data in them and were apparently
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not properly closed. When I examine them using **ncdump** they report zero
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data points, although the size is a few megabytes. Is there a way of
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recovering them?*
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recovering them?_
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If the files are in classic format or 64-bit offset format (if they were
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created by netCDF version 3.6.3 or earlier, for example), then you can
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