How to read HDF4 file?

[daxinnan]

I see an example for HDF5 as follows:

using GMT
file = "A2016152023000.L2_LAC_SST.nc=gd?HDF5:\"A2016152023000.L2_LAC_SST.nc\"";
sst  = gmt("read -Tg " * file * ":https://geophysical_data/sst");

Now I have a HDF4 file, and I run `gdalinfo "filename.hdf".

PS C:\Users\usrname\Desktop> gdalinfo ".\2014068005444_41824_CS_2B-GEOPROF-LIDAR_GRANULE_P2_R05_E06_F00.hdf"
Driver: HDF4/Hierarchical Data Format Release 4
Files: .\2014068005444_41824_CS_2B-GEOPROF-LIDAR_GRANULE_P2_R05_E06_F00.hdf
Size is 512, 512
Metadata:
  HDFEOSVersion=HDFEOS_V2.5
Subdatasets:
  SUBDATASET_1_NAME=HDF4_EOS:EOS_SWATH:".\2014068005444_41824_CS_2B-GEOPROF-LIDAR_GRANULE_P2_R05_E06_F00.hdf":2B-GEOPROF-LIDAR:CloudFraction
  SUBDATASET_1_DESC=[37082x125] CloudFraction 2B-GEOPROF-LIDAR (8-bit integer)
...
Corner Coordinates:
Upper Left  (    0.0,    0.0)
Lower Left  (    0.0,  512.0)
Upper Right (  512.0,    0.0)
Lower Right (  512.0,  512.0)
Center      (  256.0,  256.0)

I'm a new one to use gmt. I don't know how to use the information to read HDF4 in julia.
Any one can help me? Thank you, guys.

[joa-quim]

Try this. The logic to be followed is that explained in GDAL docs to access to subdatasets.

file = "2014068005444_41824_CS_2B-GEOPROF-LIDAR_GRANULE_P2_R05_E06_F00.hdf=gd?HDF4_EOS:EOS_SWATH:\"2014068005444_41824_CS_2B-GEOPROF-LIDAR_GRANULE_P2_R05_E06_F00.hdf\":2B-GEOPROF-LIDAR:CloudFraction";

out = gmt("read -Tg " * file);

[daxinnan]

Maybe there is an error about my gmt,

julia> out = gmt("read -Tg " * file);
ERROR: could not load library "libgmt"
libgmt.so: 无法打开共享对象文件: 没有那个文件或目录 # I guess it means Can't open share object file, No such file or directory.
Stacktrace:
 [1] GMT_Create_Session at /home/usrname/.julia/packages/GMT/VY9y7/src/libgmt.jl:6 [inlined] (repeats 2 times)
 [2] gmt(::String) at /home/usrname/.julia/packages/GMT/VY9y7/src/gmt_main.jl:125
 [3] top-level scope at none:0

julia> versioninfo()
Julia Version 1.4.1
Commit 381693d3df* (2020-04-14 17:20 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-8.0.1 (ORCJIT, haswell)
Environment:
  JULIA_NUM_THREADS = 4

$ gmt --version
6.0.0

My system is Ubuntu 20.04, I use xarray by using PyCall temporarily.

[daxinnan]

When I run ]test GMT, some errors occur. I'll push the relative information later.

[joa-quim]

Ah, you are on Linux and probably did not install GMT on a standard place so the OS does not know where the GMT shared libs are. Try this from the README.md

On OSX, with a manual GMT build and dependencies obtained with Homebrew (that are installed at /user/local/lib), I had to help Julia finding MY libgmt.dylib, with (this line should than be added to the ~/.julia/config/startup.jl file)

using Libdl
push!(Libdl.DL_LOAD_PATH, "/Users/j/programs/gmt6/lib")

[daxinnan]

Sorry for replying late, I run the code at terminal:

ldconfig -p | grep libgmt
	libgmt.so.6 (libc6,x86-64) => /lib/x86_64-linux-gnu/libgmt.so.6

and install gmt like ythis:

sudo aptitude install gmt gmt-dcw gmt-gshhg

What does the meaning of "/Users/j/programs/gmt6/lib"?

Error in detail:

julia> file = "2014068005444_41824_CS_2B-GEOPROF_GRANULE_P1_R05_E06_F00.hdf=gd?HDF4_EOS:EOS_SWATH:\"2014068005444_41824_CS_2B-GEOPROF_GRANULE_P1_R05_E06_F00.hdf\""
"2014068005444_41824_CS_2B-GEOPROF_GRANULE_P1_R05_E06_F00.hdf=gd?HDF4_EOS:EOS_SWATH:\"2014068005444_41824_CS_2B-GEOPROF_GRANULE_P1_R05_E06_F00.hdf\""

julia> out = gmt("read -Tg " * file * ":2B-GEOPROF:CPR_Cloud_mask");
ERROR: could not load library "libgmt"
libgmt.so: 无法打开共享对象文件: 没有那个文件或目录
Stacktrace:
 [1] GMT_Create_Session at /home/usrname/.julia/packages/GMT/VY9y7/src/libgmt.jl:6 [inlined] (repeats 2 times)
 [2] gmt(::String) at /home/usrname/.julia/packages/GMT/VY9y7/src/gmt_main.jl:125
 [3] top-level scope at REPL[16]:1
caused by [exception 1]
UndefVarError: API not defined
Stacktrace:
 [1] gmt(::String) at /home/usrname/.julia/packages/GMT/VY9y7/src/gmt_main.jl:122
 [2] top-level scope at REPL[16]:1

[joa-quim]

What does the meaning of "/Users/j/programs/gmt6/lib"?

It means the path to the directory where you have libgmt.so. The one above, is an example of my own case. Several people have reported this trouble and solved it the DL_LOAD_PATH setting.

Now, I have no idea why some people need to do that. The Travis CI tests run on a Linux machine and they run fine.

[joa-quim]

Can I close this issue?