grdimage shows strange lines

[htyeim]

Below is an example of the problem.

The code that can reproduce the figure can be found below (in macOS 10.15.4 and GMT was installed using brew)

using Libdl
push!(Libdl.DL_LOAD_PATH, "/usr/local/Cellar/gmt/6.0.0_5/lib")
using GMT
function peaks_test(; N = 49, grid = true) # modified from GMT.peaks
	x, y = GMT.meshgrid(range(-3, stop = 3, length = N))

	z =  3 * (1 .- x).^2 .* exp.(-(x.^2) - (y .+ 1).^2) - 10 * (x ./ 5 - x.^3 - y.^5) .* exp.(-x.^2 - y.^2)
	   - 1 / 3 * exp.(-(x .+ 1).^2 - y.^2)

	if (grid)
		x = collect(range(-30, stop = 30, length = N)) 
        y = deepcopy(x) 
        x .+= 100
        y .+= 25
	z = Float32.(z)
	G = GMT.GMTgrid("", "", 0, [x[1], x[end], y[1], y[end], minimum(z), maximum(z)], [x[2] - x[1], y[2] - y[1]],
					0, NaN, "", "", "", "", x, y, z, "x", "y", "z", "")
		return G
	else
		return x, y, z
	end
end
G = peaks_test(N = 200)

# no problem
grdimage(G, region =  (70, 130, -5, 55),nan_alpha = true, figsize = 15,
        proj = :Mercator ,color = :jet,fmt = :png, show = true)

# has problem
grdimage(G, region =  (65, 130, 15, 47), figsize = 15,
        proj = :Mercator ,color = :jet,fmt = :png, show = true)

# has problem
grdimage(G, region =  (70, 130, 5, 47),nan_alpha = true, figsize = 15,
        proj = :Mercator ,color = :jet,fmt = :png, show = true)

The only difference is the region of basemap and that of grid data. Is it a bug or did I misuse the function?

[joa-quim]

Right, I can reproduce this but I think it's a bug in GMT itself because I can reproduce it in the equivalent Matlab wrapper too.

One other thing, since you installed GMT with homebrew and it stores the libs on standard places, you should not need to do the step

using Libdl
push!(Libdl.DL_LOAD_PATH, "/usr/local/Cellar/gmt/6.0.0_5/lib")

could you please confirm that?

[joa-quim]

Opened an issue in GMT
And, BTW, thanks for the report.

[htyeim]

Thanks!

---

One other thing, since you installed GMT with homebrew and it stores the libs on standard places, you should not need to do the step

using Libdl
push!(Libdl.DL_LOAD_PATH, "/usr/local/Cellar/gmt/6.0.0_5/lib")

could you please confirm that?

Before I upgraded GMT/julia using brew upgrade/brew cu --all, I didn't need to add these two lines. However, at some point (I don't know what happened exactly...), if I don't add these two lines I will get some errors. Below is a example (code from gallery):

               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.4.1 (2020-04-14)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using GMT

julia> bar(rand(15),              # Generate the dataset
           color=:rainbow,        # The color scale
           figsize=(14,8),        # The fig size (14 x 8 cm)
           title="Colored bars",  # The fig title
           fmt=:png,              # The image format
           show=true)
ERROR: could not load library "libgmt"
dlopen(libgmt.dylib, 1): image not found
Stacktrace:
 [1] GMT_Create_Session at /Users/t/.julia/packages/GMT/VY9y7/src/libgmt.jl:6 [inlined] (repeats 2 times)
 [2] gmt(::String, ::Array{Float64,2}) at /Users/t/.julia/packages/GMT/VY9y7/src/gmt_main.jl:125
 [3] read_data(::Dict{Symbol,Any}, ::String, ::String, ::Array{Float64,2}, ::String, ::Bool, ::Bool) at /Users/t/.julia/packages/GMT/VY9y7/src/common_options.jl:2154
 [4] read_data at /Users/t/.julia/packages/GMT/VY9y7/src/common_options.jl:2121 [inlined]
 [5] common_plot_xyz(::String, ::Array{Float64,2}, ::String, ::Bool, ::Bool, ::Pair{Symbol,Any}, ::Vararg{Pair{Symbol,Any},N} where N) at /Users/t/.julia/packages/GMT/VY9y7/src/psxy.jl:50
 [6] #bar#174 at /Users/t/.julia/packages/GMT/VY9y7/src/plot.jl:351 [inlined]
 [7] top-level scope at REPL[2]:1
caused by [exception 1]
UndefVarError: API not defined
Stacktrace:
 [1] gmt(::String, ::Array{Float64,2}) at /Users/user/.julia/packages/GMT/VY9y7/src/gmt_main.jl:122
 [2] read_data(::Dict{Symbol,Any}, ::String, ::String, ::Array{Float64,2}, ::String, ::Bool, ::Bool) at /Users/user/.julia/packages/GMT/VY9y7/src/common_options.jl:2154
 [3] read_data at /Users/user/.julia/packages/GMT/VY9y7/src/common_options.jl:2121 [inlined]
 [4] common_plot_xyz(::String, ::Array{Float64,2}, ::String, ::Bool, ::Bool, ::Pair{Symbol,Any}, ::Vararg{Pair{Symbol,Any},N} where N) at /Users/user/.julia/packages/GMT/VY9y7/src/psxy.jl:50
 [5] #bar#174 at /Users/user/.julia/packages/GMT/VY9y7/src/plot.jl:351 [inlined]
 [6] top-level scope at REPL[2]:1

julia>

I think the problem might be the path /gmt/6.0.0_5/ isn't in lib [?]. At first, I though the problem might be the updated path, and If I remember correctly, I removed, reinstalled, rebuilt GMT.jl several times, but I still get the errors. Then I googled it and found this solution. I didn't report it since it can be solved by adding two lines of code.

[joa-quim]

Yes, that's a general problem in unix when the shared libs are not stored in standard places. But homebrew makes symbolic links to /usr/local/lib and that is a standard place so the shared libs there should be findable without further help. Don't you have a (symbolic link) libgmt.dylib in /usr/local/lib?

Ah, and BTW, you don't need to repeat those 2 lies all the time, just add them to the startup.jl file

[htyeim]

I will add the lines in startup.jl, thanks!

libgmt.dylib is in /usr/local/lib

 /usr/local/lib  ls |grep gmt
gmt
libgmt.6.0.0.dylib
libgmt.6.dylib
libgmt.dylib

 /usr/local/lib  ls -l libgmt.dylib
lrwxr-xr-x  1 t  staff  38 Apr  8 09:08 libgmt.dylib -> ../Cellar/gmt/6.0.0_5/lib/libgmt.dylib

 /usr/local/lib  ls -l ../Cellar/gmt/6.0.0_5/lib/libgmt.dylib
lrwxr-xr-x  1 t  staff  14 Oct 31 11:25 ../Cellar/gmt/6.0.0_5/lib/libgmt.dylib -> libgmt.6.dylib

 /usr/local/lib  ls -l ../Cellar/gmt/6.0.0_5/lib/libgmt.6.dylib
lrwxr-xr-x  1 t  staff  18 Oct 31 11:25 ../Cellar/gmt/6.0.0_5/lib/libgmt.6.dylib -> libgmt.6.0.0.dylib

  /usr/local/lib  ls -l ../Cellar/gmt/6.0.0_5/lib/libgmt.6.0.0.dylib
-r--r--r--  1 t  staff  3677296 Apr  8 09:08 ../Cellar/gmt/6.0.0_5/lib/libgmt.6.0.0.dylib

Then I have no idea what happens when julia says ERROR: could not load library "libgmt".

[joa-quim]

Don't know either. Unix is very complicated and Macs even more.

[htyeim]

Yes, they are complicated (I would like to add GMT and julia as well...). I tested some julia code that used GMT.jl about one month ago and it ran perfectly. Then I ran the same code without any modification three days ago, I got tons of errors. Anyway, it's OK since it's very easy to solve.

[joa-quim]

BTW, this issue was fixed upstream so I'm closing it