Features list for porting Mirone to Julia.

[joa-quim]

This issue is a tentative features list that will be necessary in order to port Mirone to Julia using GLVisualize, but essentially it consists in listing the basic handles graphics capabilities.

Being written in Matlab, Mirone uses the normal Ml scheme of a "figure" that is populated with Menus, buttons (push and toggle buttons), and "axes". The axes is where the images are displayed.

• The axes must be able to plot a frame with the image's coordinates.
• The axes must accept also the plotting of vectors: lines, patches, symbols
• The lines, as well as the the background image, should be able to be assigned uicontextmenu callback functions activated by mouse clicks. For that one must be able to select graphical elements with mouse clicks.
• Windowbuttonmotion callback functions.
• The normal list of buttons: pushbuttons, sliders, popupmenus, checkboxes, radioboxes
• List trees

[joa-quim]

Simon, I recently learned about this

https://github.com/vurtun/nuklear

seams it could be handy to help creating all sort of menus, buttons and relatives.

[SimonDanisch]

that looks like a cool library :)

2016-05-23 23:45 GMT+02:00 Joaquim [email protected]:

Simon, I recently learned about this

https://github.com/vurtun/nuklear

seams it could be handy to help creating all sort of menus, buttons and
relatives.

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[joa-quim]

and there is more. It derives from this lib imgui that is C++ but has a C wrapper.

[SimonDanisch]

Hi, I'm slowly closing in on feature completeness on master ;)
Also, I'd love to port these examples to GLVisualize:
https://www.soest.hawaii.edu/gmt/gmt/gmt_examples.html
I must admit there is a bit of barrier in using GMT for me, so it'd be wonderful if we could tackle this together!

Concerning the features, I'll slowly post examples on vimeo: https://vimeo.com/user8202296
With blog posts and more documentation coming slowly as well ;)
Let me know if, how and when you want to try things out and start prototyping this.

Best,
Simon

[joa-quim]

Hi Simon,

Nice to hear this. Regarding the examples, I have them almost all already 'runable' in Julia in
https://github.com/joa-quim/GMT.jl/blob/master/test/gallery.jl
which are more than the 30 your (old) link links to (most current version is here).

Some updates tough. Between GMT5.2.1 and current SVN version there was a large improvement in the GMT machinery to support external interfaces. The current version of gallery.jl (plus the rest of master) already reflects that but to run it one needs the current GMT SVN. The GMT.jl 0.0.1 should still run but I confess that I don't maintain it anymore. I can prepare you a Windows GMT installer, which will be closer to the next to come (in a couple weeks) GMT5.3

[SimonDanisch]

Oh great :) Would linux be easier?

[joa-quim]

You mean, for you to build GMT? It certainly is because the problem of the dependencies is solved. However, I never tested it in Linux but there is no reason for not to work.

[SimonDanisch]

Okay great! Will try on linux then!

[joa-quim]

Cool, I'll be waiting for the feedback.

[SimonDanisch]

Almost!

[100%] Built target gshhg_version
Scanning dependencies of target gmt
[100%] Building C object src/CMakeFiles/gmt.dir/gmt.c.o
[100%] Linking C executable gmt
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `SSL_get_peer_certificate@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `CRYPTO_num_locks@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `SSL_get_current_compression@OPENSSL_1.0.0'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/libgdal.so: undefined reference to `lzma_stream_decoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `SSL_get_version@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `SSL_use_certificate_file@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `BIO_int_ctrl@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `ENGINE_free@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `CRYPTO_get_id_callback@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `ASN1_STRING_data@OPENSSL_1.0.0'
//usr/lib/libarpack.so.2: undefined reference to `_gfortran_transfer_real_write@GFORTRAN_1.4'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `OPENSSL_config@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `SSL_get_error@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `X509_NAME_get_entry@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `SSL_use_PrivateKey_file@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `X509_STORE_load_locations@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpoppler.so.58: undefined reference to `TIFFDefaultStripSize@LIBTIFF_4.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `ASN1_STRING_length@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `SSL_CIPHER_get_name@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpq.so.5: undefined reference to `sk_num@OPENSSL_1.0.0'
//usr/lib/x86_64-linux-gnu/libpoppler.so.58: undefined reference to `TIFFFdOpen@LIBTIFF_4.0'
...

Any idea?

[SimonDanisch]

This looks good though:

s@s-15:~/juliastuff/gmt5-dev/build$ ldd /usr/lib/x86_64-linux-gnu/libpq.so.5
    linux-vdso.so.1 =>  (0x00007ffdbb57b000)
    libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007fc982f92000)
    libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007fc982b37000)
    libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007fc9828ec000)
    libldap_r-2.4.so.2 => /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2 (0x00007fc98269b000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fc98247e000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc9820b4000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fc981eb0000)
    libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007fc981bde000)
    libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007fc9819ae000)
    libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007fc9817aa000)
    libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007fc98159f000)
    liblber-2.4.so.2 => /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2 (0x00007fc98138f000)
    libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007fc981174000)
    libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007fc980f59000)
    libgssapi.so.3 => /usr/lib/x86_64-linux-gnu/libgssapi.so.3 (0x00007fc980d17000)
    libgnutls.so.30 => /usr/lib/x86_64-linux-gnu/libgnutls.so.30 (0x00007fc9809e7000)
    /lib64/ld-linux-x86-64.so.2 (0x0000556e61933000)
    libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007fc9807e3000)
    libheimntlm.so.0 => /usr/lib/x86_64-linux-gnu/libheimntlm.so.0 (0x00007fc9805d9000)
    libkrb5.so.26 => /usr/lib/x86_64-linux-gnu/libkrb5.so.26 (0x00007fc98034f000)
    libasn1.so.8 => /usr/lib/x86_64-linux-gnu/libasn1.so.8 (0x00007fc9800ac000)
    libhcrypto.so.4 => /usr/lib/x86_64-linux-gnu/libhcrypto.so.4 (0x00007fc97fe79000)
    libroken.so.18 => /usr/lib/x86_64-linux-gnu/libroken.so.18 (0x00007fc97fc63000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fc97fa48000)
    libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007fc97f7e4000)
    libidn.so.11 => /usr/lib/x86_64-linux-gnu/libidn.so.11 (0x00007fc97f5b1000)
    libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007fc97f39d000)
    libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6 (0x00007fc97f167000)
    libhogweed.so.4 => /usr/lib/x86_64-linux-gnu/libhogweed.so.4 (0x00007fc97ef34000)
    libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 (0x00007fc97ecb3000)
    libwind.so.0 => /usr/lib/x86_64-linux-gnu/libwind.so.0 (0x00007fc97ea8a000)
    libheimbase.so.1 => /usr/lib/x86_64-linux-gnu/libheimbase.so.1 (0x00007fc97e87b000)
    libhx509.so.5 => /usr/lib/x86_64-linux-gnu/libhx509.so.5 (0x00007fc97e62f000)
    libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007fc97e35a000)
    libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x00007fc97e122000)
    libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 (0x00007fc97df19000)

[joa-quim]

Sorry, no idea why you are getting all those linking errors. I very recently built GMT in WinBuntu using all standard dependencies gotten with apt-get. Except the netcdf lib, all other dependencies come via GDAL so libgdal.so should be the source of the problem.
Witch Linux?

[SimonDanisch]

Ubuntu 16.04

[SimonDanisch]

Some research suggests, that things can get mixed up when anaconda is installed... But I'm not sure if that applies here... The only thing that seems to be linked from anaconda is zlib. I tried changing the zlib include folder in ConfigUser.cmake but this somehow didn't prevent it from linking the anaconda zlib...

[joa-quim]

From what I remember zlib is an optional GMT dependency used for PostScript compression but is also a dependency of HDF5 used by netCDF and GDAL, so that particular ConfigUser.cmake setting would probably not prevent the other libs dendencies.

[joa-quim]

You can put any of this in ConfigUser.cmake to reduce the number of dependencies. It may help you track the problem

set (GMT_EXCLUDE_GDAL TRUE)
set (GMT_EXCLUDE_PCRE TRUE)
set (GMT_EXCLUDE_FFTW3 TRUE)
set (GMT_EXCLUDE_LAPACK TRUE)
set (GMT_EXCLUDE_ZLIB TRUE)

[SimonDanisch]

Okay, so this information is more interesting:

s@s-15:~/juliastuff/gmt5-dev/build/src$ ldd libgmt.so.5
./libgmt.so.5: /home/s/anaconda3/lib/liblzma.so.5: no version information available (required by /usr/lib/libgdal.so.1)
./libgmt.so.5: /home/s/anaconda3/lib/libtiff.so.5: no version information available (required by /usr/lib/x86_64-linux-gnu/libpoppler.so.58)
./libgmt.so.5: /home/s/anaconda3/lib/libcrypto.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libpq.so.5)
./libgmt.so.5: /home/s/anaconda3/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libpq.so.5)
./libgmt.so.5: /home/s/anaconda3/lib/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /usr/lib/libarpack.so.2)

[SimonDanisch]

Hmm... After renaming the anaconda folder and removing it from all environment variables, restarting, cmake still inserts all path from anaconda -.- How is it even doing that? :D

[joa-quim]

Did you remove the build dir and start over? It stores things in cache.
On an not useful note, I don't like anaconda that installs me a huge package in .julia to install things that I already have.

[SimonDanisch]

I didn't! Forgot that cmake .. doesn't start new...

[SimonDanisch]

okay, removing anaconda works :) Btw, that wasn't the one installed by Julia, I think...

[ 93%] Building C object src/CMakeFiles/supplib.dir/x2sys/x2sys_merge.c.o
[ 96%] Linking C shared module plugins/supplements.so
[100%] Built target supplib

[SimonDanisch]

Cool:

julia> Pkg.checkout("GMT")
INFO: Checking out GMT master...
INFO: Pulling GMT latest master...
INFO: No packages to install, update or remove

julia> Pkg.test("GMT")
INFO: Testing GMT
INFO: GMT tests passed

Guess I'm all setup now!

[joa-quim]

No wait. The Pkg.test("GMT") does nothing. Please read the header of gallery.jl, you need to set up manually the path of your GMT (SVN) installation so it can find the files needed for running the examples. There is also a gmtest.jl that really run tests by comparing the created ps's to original ones. Those are our true GMT tests but I warn you that many tests FAIL mostly due to font sizes and other figure alignments. These aren't real failures, but some of them are.

[SimonDanisch]

yeah figured that out :) But seems to work now:

[joa-quim]

YES.

[SimonDanisch]

Okay, getting somewhere :)

[joa-quim]

That was quick. The color issues are coming from where?

[SimonDanisch]

What is the color issue? Do you mean the contours? The contour lines are actually just as thick as the iso value at that point, which might look weird?

[joa-quim]

I mean, the deep ocean is black, the variable width white lines (the contours?).
Not that you have also the Hawaiian chain N-S flipped. The brigh spot at ~22.5N is the Big Island, which is the southernmost one.

[SimonDanisch]

Good to know :D Well, that's the default colormap from Plots.jl.

[joa-quim]

I was there a month ago, in a warming up to the second GMT Summit. And that literally because I saw lava from 5 m away when it was entering the sea. I have to create a new GMT example with a picture of it.

[joa-quim]

Hi Simon,

If you update both GMT and GMT.jl you can now do

PS = gmt("pscoast -R-10/-3/37/44 -JM12 -W1p -Ba -P");
img = gmt("psconvert =", PS);

and get an img type whose member img.image holds a RGB band interleaved image created without any intermediate postscript file written to disk.
Now, this works fine on Windows but fails on Mac because it hangs on a popen call. It would be nice to know what is the status of this on Linux.

The other thing I wanted to ask is how can we visualize such data? I know about ImageView, but it works with Tk, that version conflicts with my local Python installation and ends up installing Anaconda in my .julia, which adds up to ~1.5 Gb. And don't want to do that. Any other simpler solution, via Plots.jl perhaps?