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netcdf-c/ncdump/ncdump.1
Dennis Heimbigner 3ffe7be446 Enhance/Fix filter support 
re: Discussion https://github.com/Unidata/netcdf-c/discussions/2214

The primary change is to support so-called "standard filters".
A standard filter is one that is defined by the following
netcdf-c API:
````
int nc_def_var_XXX(int ncid, int varid, size_t nparams, unsigned* params);
int nc_inq_var_XXXX(int ncid, int varid, int* usefilterp, unsigned* params);
````
So for example, zstandard would be a standard filter by defining
the functions *nc_def_var_zstandard* and *nc_inq_var_zstandard*.

In order to define these functions, we need a new dispatch function:
````
int nc_inq_filter_avail(int ncid, unsigned filterid);
````
This function, combined with the existing filter API can be used
to implement arbitrary standard filters using a simple code pattern.
Note that I would have preferred that this function return a list
of all available filters, but HDF5 does not support that functionality.

So this PR implements the dispatch function and implements
the following standard functions:
    + bzip2
    + zstandard
    + blosc
Specific test cases are also provided for HDF5 and NCZarr.
Over time, other specific standard filters will be defined.

## Primary Changes
* Add nc_inq_filter_avail() to netcdf-c API.
* Add standard filter implementations to test use of *nc_inq_filter_avail*.
* Bump the dispatch table version number and add to all the relevant
   dispatch tables (libsrc, libsrcp, etc).
* Create a program to invoke nc_inq_filter_avail so that it is accessible
  to shell scripts.
* Cleanup szip support to properly support szip
  when HDF5 is disabled. This involves detecting
  libsz separately from testing if HDF5 supports szip.
* Integrate shuffle and fletcher32 into the existing
  filter API. This means that, for example, nc_def_var_fletcher32
  is now a wrapper around nc_def_var_filter.
* Extend the Codec defaulting to allow multiple default shared libraries.

## Misc. Changes
* Modify configure.ac/CMakeLists.txt to look for the relevant
  libraries implementing standard filters.
* Modify libnetcdf.settings to list available standard filters
  (including deflate and szip).
* Add CMake test modules to locate libbz2 and libzstd.
* Cleanup the HDF5 memory manager function use in the plugins.
* remove unused file include//ncfilter.h
* remove tests for the HDF5 memory operations e.g. H5allocate_memory.
* Add flag to ncdump to force use of _Filter instead of _Deflate
  or _Shuffle or _Fletcher32. Used for testing.
2022-03-14 12:39:37 -06:00

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.\" $Header: /upc/share/CVS/netcdf-3/ncdump/ncdump.1,v 1.10 2009/07/28 14:48:36 russ Exp $
.TH NCDUMP 1 "2012-03-08" "Release 4.2" "UNIDATA UTILITIES"
.SH NAME
ncdump \- Convert netCDF file to text form (CDL)
.SH SYNOPSIS
.ft B
.HP
ncdump
.nh
\%[\-chistxwF]
\%[\-v \fIvar1,...\fP]
\%[\-b \fIlang\fP]
\%[\-f \fIlang\fP]
\%[\-l \fIlen\fP]
\%[\-n \fIname\fP]
\%[\-p \fIf_digits[,d_digits]\fP]
\%[\-g \fIgrp1,...\fP]
\%\fIfile\fP
.br
.ft B
.HP
ncdump
.nh
\%-k
\%\fIfile\fP
.hy
.ft
.SH DESCRIPTION
.LP
The \fBncdump\fP utility generates a text representation of a
specified netCDF file on standard output, optionally excluding some or
all of the variable data in the output. The text representation is in
a form called CDL (network Common Data form Language) that can be
viewed, edited, or serve as input to \fBncgen\fP, a companion program
that can generate a binary netCDF file from a CDL file. Hence
\fBncgen\fP and \fBncdump\fP can be used as inverses to transform the
data representation between binary and text representations. See
\fBncgen\fP documentation for a description of CDL and netCDF
representations.
.LP
\fBncdump\fP may also be used to determine what kind of netCDF file is used
(which variant of the netCDF file format) with the \-k option.
.LP
If DAP support was enabled when \fBncdump\fP was built, the file name
may specify a DAP URL. This allows \fBncdump\fP to access data sources
from DAP servers, including data in other formats than netCDF. When
used with DAP URLs, \fBncdump\fP shows the translation from the DAP
data model to the netCDF data model.
.LP
\fBncdump\fP may also be used as a simple browser for netCDF data
files, to display the dimension names and lengths; variable names, types,
and shapes; attribute names and values; and optionally, the values of
data for all variables or selected variables in a netCDF file. For
netCDF-4 files, groups and user-defined types are also included in
ncdump output.
.LP
\fBncdump\fP uses `_' to represent data values that are equal to the
`_FillValue' attribute for a variable, intended to represent data that
has not yet been written. If a variable has no `_FillValue'
attribute, the default fill value for the variable type is used unless
the variable is of byte type.
.LP
\fBncdump\fP defines a default display format used for each type of
netCDF data, but this can be changed if a `C_format' attribute is
defined for a netCDF variable. In this case, \fBncdump\fP will use
the `C_format' attribute to format each value. For example, if
floating-point data for the netCDF variable `Z' is known to be
accurate to only three significant digits, it would be appropriate to
use the variable attribute
.RS
.HP
Z:C_format = "%.3g"
.RE
.SH OPTIONS
.IP "\fB-c\fP"
Show the values of \fIcoordinate\fP variables (1D variables with the
same names as dimensions) as well as the declarations of all
dimensions, variables, attribute values, groups, and user-defined
types. Data values of non-coordinate variables are not included in
the output. This is usually the most suitable option to use for a brief look
at the structure and contents of a netCDF file.
.IP "\fB-h\fP"
Show only the \fIheader\fP information in the output, that is, output only
the declarations for the dimensions, variables, attributes,
groups, and user-defined types of the input file, but no data values for
any variables. The output is identical to using the \fB-c\fP option except
that the values of coordinate variables are not included. (At most one of
\fB-c\fP or \fB-h\fP options may be present.)
.IP "\fB-v\fP \fIvar1,...\fP"
The output will include data values for the specified variables, in
addition to the declarations of all dimensions, variables, and
attributes. One or more variables must be specified by name in the
comma-delimited list following this option. The list must be a single
argument to the command, hence cannot contain unescaped blanks or
other white space characters. The named variables must be valid
netCDF variables in the input-file. A variable within a group in a
netCDF-4 file may be specified with an absolute path name, such as
`/GroupA/GroupA2/var'. Use of a relative path name such as `var' or
`grp/var' specifies all matching variable names in the file. The
default, without this option and in the absence of the \fB-c\fP or
\fB-h\fP options, is to include data values for \fIall\fP variables in
the output.
.IP "\fB-b\fP \fI[c|f]\fP"
A brief annotation in the form of a CDL comment (text beginning with the
characters ``//'') will be included in the data section of the output for
each `row' of data, to help identify data values for multidimensional
variables. If \fIlang\fP begins with `C' or `c', then C language
conventions will be used (zero-based indices, last dimension varying
fastest). If \fIlang\fP begins with `F' or `f', then Fortran language
conventions will be used (one-based indices, first dimension varying
fastest). In either case, the data will be presented in the same order;
only the annotations will differ. This option may be useful for browsing
through large volumes of multidimensional data.
.IP "\fB-f\fP \fI[c|f]\fP"
Full annotations in the form of trailing CDL comments (text beginning
with the characters ``//'') for every data value (except individual
characters in character arrays) will be included in the data section.
If \fIlang\fP begins with `C' or `c', then C language conventions will
be used. If \fIlang\fP begins with `F' or `f', then Fortran language
conventions will be used. In either case, the data will be presented
in the same order; only the annotations will differ. This option may
be useful for piping data into other filters, since each data value
appears on a separate line, fully identified. (At most one of '\-b' or '\-f' options may be present.)
.IP "\fB-l\fP \fIlength\fP"
Changes the default maximum line length (80) used in formatting lists of
non-character data values.
.IP "\fB-n\fP \fIname\fP"
CDL requires a name for a netCDF file, for use by \fBncgen \-b\fP in
generating a default netCDF file name. By default, \fIncdump\fP constructs
this name from the last component of the file name of the input netCDF file
by stripping off any extension it has. Use the \fB-n\fP option to specify a
different name. Although the output file name used by \fBncgen \-b\fP can be
specified, it may be wise to have \fIncdump\fP change the default name to
avoid inadvertently overwriting a valuable netCDF file when using
\fBncdump\fP, editing the resulting CDL file, and using \fBncgen \-b\fP to
generate a new netCDF file from the edited CDL file.
.IP "\fB-p\fP \fIfloat_digits[,double_digits]\fP"
Specifies default precision (number of significant digits) to use in
displaying floating-point or double precision data values for
attributes and variables. If specified, this value overrides the
value of the C_format attribute, if any, for a variable.
Floating-point data will be displayed with \fIfloat_digits\fP
significant digits. If \fIdouble_digits\fP is also specified,
double-precision values will be displayed with that many significant
digits. In the absence of any \fB-p\fP specifications, floating-point
and double-precision data are displayed with 7 and 15 significant
digits respectively. CDL files can be made smaller if less precision
is required. If both floating-point and double precisions are
specified, the two values must appear separated by a comma (no blanks)
as a single argument to the command. (To represent every last bit of
precision in a CDL file for all possible floating-point values
would require \fB-p 9,17\fP.)
.IP "\fB-k\fP"
Show kind of netCDF file the pathname references, one of
`classic', `64-bit offset',`netCDF-4', or `netCDF-4 classic model'. Before version
3.6, there was only one kind of netCDF file, designated as `classic'
(also know as format variant 1). Large file support introduced
another variant of the format, designated as `64-bit offset' (known as
format variant 2). NetCDF-4, uses a third variant of the format,
`netCDF-4' (format variant 3). Another format variant, designated
`netCDF-4 classic model' (format variant 4), is restricted
to features supported by the netCDF-3 data model but represented using
the HDF5 format, so that an unmodified netCDF-3 program can read or
write the file just by relinking with the netCDF-4 library.
The string output by using the `\-k' option may be provided as the
value of the `\-k' option to ncgen(1) to
specify exactly what kind of netCDF file to generate, when you want to
override the default inferred from the CDL.
.IP "\fB-s\fP"
Output special virtual attributes that provide performance-related
information about the file format and variable properties for netCDF-4
data. These special virtual attributes are not actually part of the
data, they are merely a convenient way to display miscellaneous
properties of the data in CDL (and eventually NcML). They include
`_ChunkSizes',
`_DeflateLevel',
`_Endianness',
`_Fletcher32',
`_Format',
`_NoFill',
`_Shuffle', and
`_Storage'.
`_ChunkSizes' is a list of chunk sizes for each dimension of the variable.
`_DeflateLevel' is an
integer between 0 and 9 inclusive if compression has been specified
for the variable.
`_Endianness' is either `little' or `big', depending on
how the variable was stored when first written.
`_Fletcher32' is `true' if the checksum property was set for
the variable.
`_Format' is a global attribute specifying the netCDF format
variant, one of `classic', `64-bit offset', `netCDF-4', or `netCDF-4
classic model'.
`_NoFill' is `true' if the persistent NoFill property was set for the
variable when it was defined.
`_Shuffle' is `true' if use of the shuffle filter was specified for the variable.
`_Storage' is `contiguous' or `compact' or `chunked', depending on how the
variable's data is stored.
.IP "\fB-t\fP"
Controls display of time data, if stored in a variable that uses
a udunits compliant time representation such as `days since
1970-01-01' or `seconds since 2009-03-15 12:01:17', a variable
identified in a "bounds" attribute of such a time variable, or a numeric
attribute of a time variable. If this option is
specified, time data values are displayed as human-readable date-time
strings rather than numerical values, interpreted in terms of a
`calendar' variable attribute, if specified. For numeric attributes
of time variables, the human-readable time value is displayed after the
actual value, in an associated CDL comment. Calendar attribute
values interpreted with this option include the CF Conventions values
`gregorian' or `standard', `proleptic_gregorian', `noleap' or `365_day',
`all_leap' or `366_day', `360_day', and `julian'.
.IP "\fB-i\fP"
Same as the '\-t' option, except output time data as date-time strings
with ISO-8601 standard 'T' separator, instead of a blank.
.IP "\fB-g\fP \fIgrp1,...\fP"
For netCDF-4 files, the output will include data values only for the
specified groups. One or more groups must be specified by name in the
comma-delimited list following this option. The list must be a single
argument to the command. The named groups must be valid netCDF groups
in the input-file. A group in a netCDF-4 file may be specified with
an absolute or relative path name. Use of a relative path name
specifies all matching group names in the file. The default, without
this option and in the absence of the \fB-c\fP or \fB-h\fP options, is
to include data values for \fIall\fP groups in the output.
.IP "\fB-w\fP"
For file names that request remote access using DAP URLs, access data
with client-side caching of entire variables.
.IP "\fB-x\fP"
Output XML (NcML) instead of CDL. The NcML does not include data values.
The NcML output option currently only works for netCDF classic model data.
.IP "\fB-F\fP"
Use _Filter and _Codecs attributes in place of _Fletcher32, _Shuffle, and _Deflate.
.SH EXAMPLES
.LP
Look at the structure of the data in the netCDF file `\fBfoo.nc\fP':
.RS
.HP
ncdump \-c foo.nc
.RE
.LP
Produce an annotated CDL version of the structure and data in the
netCDF file `\fBfoo.nc\fP', using C-style indexing for the annotations:
.RS
.HP
ncdump \-b c foo.nc > foo.cdl
.RE
.LP
Output data for only the variables `uwind' and `vwind' from the netCDF file
`\fBfoo.nc\fP', and show the floating-point data with only three significant
digits of precision:
.RS
.HP
ncdump \-v uwind,vwind \-p 3 foo.nc
.RE
.LP
Produce a fully-annotated (one data value per line) listing of the data for
the variable `omega', using Fortran conventions for indices, and changing the
netCDF dataset name in the resulting CDL file to `omega':
.RS
.HP
ncdump \-v omega \-f fortran \-n omega foo.nc > Z.cdl
.RE
.SH "SEE ALSO"
.LP
.BR ncgen (1),
.BR netcdf (3)
.SH BUGS
.LP
Character arrays that contain a null-byte are treated like C strings, so no
characters after the null byte appear in the output.
.LP
Multidimensional character string arrays are not handled well, since the CDL
syntax for breaking a long character string into several shorter lines is
weak.
.LP
There should be a way to specify that the data should be displayed in
`record' order, that is with the all the values for `record' variables
together that have the same value of the record dimension.
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