Priority: Low
re: issue https://github.com/Unidata/netcdf-c/issues/1329
HDF5 has the ability to programmatically define new filters,
as opposed to using HDF5_PLUGIN_PATH env variable.
This PR adds support for that feature.
Not clear how useful this is, though.
See docs/filters.md for details.
A user suggested that the nccopy -F option
syntax should be extended to support specification
of multiple (or all) variables in a single -F option.
The new syntax allows:
1. '*' as the name of the variable; this means apply the
filter to all variables in the data set.
2. *var1|var2|...* as the variable name to indicate that the filter
should be applied to the multiple specified variables.
re: issue https://github.com/Unidata/netcdf-c/issues/1278
re: issue https://github.com/Unidata/netcdf-c/issues/876
re: issue https://github.com/Unidata/netcdf-c/issues/806
* Major change to the handling of 8-byte parameters for nc_def_var_filter.
The old code was not well thought out.
* The new algorithm is documented in docs/filters.md.
* Added new utility file plugins/H5Zutil.c to support
* Modified plugins/H5Zmisc.c to use new algorithm
the new algorithm.
* Renamed include/ncfilter.h to include/netcdf_filter.h
and made it an installed header so clients can access the
new algorithm utility.
* Fixed nc_test4/tst_filterparser.c and nc_test4/test_filter_misc.c
to use the new algorithm
* libdap4/ fixes:
* d4swap.c has an error in the endian pre-processing such
that record counts were not being swapped correctly.
* d4data.c had an error in that checksums were being computed
after endian swapping rather than before.
* ocinitialize() was never being called, so xxdr bigendian handling
was never set correctly.
* Required adding debug statements to occompile
* Found and fixed memory leak in ncdump.c
Not tested:
* HDF4
* Pnetcdf
* parallel HDF5
re: issue https://github.com/Unidata/netcdf-c/issues/1156
Starting with HDF5 version 1.10.x, the plugin code MUST be
careful when using the standard *malloc()*, *realloc()*, and
*free()* function.
In the event that the code is allocating, reallocating, or
free'ing memory that either came from -- or will be exported to --
the calling HDF5 library, then one MUST use the corresponding
HDF5 functions *H5allocate_memory()*, *H5resize_memory()*,
*H5free_memory()* [5] to avoid memory failures.
Additionally, if your filter code leaks memory, then the HDF5 library
generates a failure something like this.
````
H5MM.c:232: H5MM_final_sanity_check: Assertion `0 == H5MM_curr_alloc_bytes_s' failed.
````
This PR modifies the code in the plugins directory to
conform to these new requirements.
This raises a question about the libhdf5 code where this
same problem may occur. We need to scan especially nc4hdf.c
to look for this problem.
re: https://github.com/Unidata/netcdf-c/issues/972
The current szip plugin code in the HDF5 library has some
unexpected behaviors that require some changes to how
nc_inq_var_szip is implemented and to the corresponding tests:
nc_test4/{test_szip,tst_vars3}.
Specifically, the following can happen:
1. The number of parameters provided by the user will be two,
but the number of parameters returned by nc_inq_var_filter
will be four because the HDF5 code (H5Zszip) will add two
extra parameters for internal use. It turns out that the two
parameters provided when calling nc_def_var_filter correspond
to the first two parameters of the four parameters returned
by nc_inq_var_filter.
2. The nc_inq_var_szip values corresponding to the ones provided
by the caller may be different than those provided by
nc_def_var_filter. The value of the options_mask argument is
known to add additional flag bits, and the pixels_per_block
parameter may be modified.
and https://github.com/Unidata/netcdf-c/issues/708
Expand the NC_INMEMORY capabilities to support writing and accessing
the final modified memory.
Three new functions have been added:
nc_open_memio, nc_create_mem, and nc_close_memio.
The following new capabilities were added.
1. nc_open_memio() allows the NC_WRITE mode flag
so a chunk of memory can be passed in and be modified
2. nc_create_mem() allows the NC_INMEMORY flag to be set
to cause the created file to be kept in memory.
3. nc_close_mem() allows the final in-memory contents to be
retrieved at the time the file is closed.
4. A special flag, NC_MEMIO_LOCK, is provided to ensure that
the provided memory will not be freed or reallocated.
Note the following.
1. If nc_open_memio() is called with NC_WRITE, and NC_MEMIO_LOCK is not set,
then the netcdf-c library will take control of the incoming memory.
This means that the original memory block should not be freed
but the block returned by nc_close_mem() must be freed.
2. If nc_open_memio() is called with NC_WRITE, and NC_MEMIO_LOCK is set,
then modifications to the original memory may fail if the space available
is insufficient.
Documentation is provided in the file docs/inmemory.md.
A test case is provided: nc_test/tst_inmemory.c driven by
nc_test/run_inmemory.sh
WARNING: changes were made to the dispatch table for
the close entry. From int (*close)(int) to int (*close)(int,void*).
2. Fixed plugin building (nc_test4/hdf5plugins)
to be done properly by cmake and automake.
4. Duplicated part of the nc_test4 filter test code
in examples/C
An incomplete and untested set of hooks exist
for OS-X in nc_test4/findplugins.in. They need testing.
2. Factored out the parameter string parsing for ncgen and nccopy
int libdispatch/dfilter.c + include/ncfilter.h
3. Allow a parameter string to use constant types other than
unsigned int. See docs/filters.md for details.
4. Moved the old content of include/netcdf_filter.h into include/netcdf.h
and removed include/netcdf_filter.h as no longer needed.
5. Force the test filter (bzip2) in nc_test4/filter_test to
be built using BUILT_SOURCES.
to docs/filter.md
2. Moved location of filter.md in documentation
3. Add a template file as the basis for building new filters.
4. Did some test case cleanup
1. Allow nccopy to apply filters, especially on the output file.
This provides a third way to do this other than using ncgen or
programatically
2. Make sure that even if the filter code is not available, it is
possible to see the filter id and parameters for variables using
e.g ncdump -hs.
3. Fix bug in nccopy so that the input file does
not necessarily have to be netcdf-4.
4. At last minute decided to change to using a
single "_Filter" attribute for ncgen
5. Added a test to tst_filter.sh to generate C code using ncgen.
This relies on the HDF5 capability to
dynamically load compression filters.
Note that a compression filter is just
a subcase of filters.
The primary user-visible changes are as follows:
1. Add a standard header "netcdf_filter.h" that defines
the necessary API extensions
2. Modify ncgen to support two new special attributes
"_Filter_ID" and "_Filter_Parameters" so that compression
can be turned on when creating a file using ncgen.
4. Add a detailed description of filtering support
to the user's guide; see the file filters.md
5. Add a test case directory for this: nc_test4/filter_test.
It is fragile and a ./configure flags (-enable-filter-test)
is defined (default disabled) to shut this off this test
to avoid spurious 'make check' failures.
Note that the HDF5 documentation is not up-to-date, so
much of what is encoded here comes from examining the
actual code in the file H5PL.c in the HDF5 source code.
