genericmappingtools / gmt-for-geodesy Goto Github PK

The readme file suggests that by Running the test_1.sh script:

A window should pop up with a colored relief map of northern Africa.

but instead i get the following message:

./test_1.sh: line 3: gmt: command not found
./test_1.sh: line 4: gmt: command not found
./test_1.sh: line 5: gmt: command not found
./test_1.sh: line 6: gmt: command not found

@maxrjones, we should changes the links to https://github.com/meghanrjones in the readme files, right?

Hello all- I am having trouble making grdimage work for me. I attempted to execute the following one-liner:

$ gmt grdimage @earth_day_30m -Rg -JW-65/15c -B -png map -Vd

and received the following debug message:

gmt.exe [DEBUG]: GMT_Create_Session: Terminal width = 116
gmt.exe [DEBUG]: Obtained the ppid from parent: 21892
gmt.exe [DEBUG]: Enter: gmtinit_new_GMT_ctrl
gmt.exe [DEBUG]: GMT->session.SHAREDIR = c:/programs/gmt6/share
gmt.exe [DEBUG]: GMT->session.HOMEDIR = C:/Users/13173
gmt.exe [DEBUG]: GMT->session.USERDIR = C:/Users/13173/.gmt [created]
gmt.exe [DEBUG]: GMT->session.CACHEDIR = C:/Users/13173/.gmt/cache [created]
gmt.exe [DEBUG]: GMT: 0. Will try to find subdir=postscriptlight stem = PSL_custom_fonts suffix=.txt
gmt.exe [DEBUG]: GMT: 1. gmt_getsharepath trying current dir
gmt.exe [DEBUG]: GMT: 2. gmt_getsharepath trying USERDIR C:/Users/13173/.gmt
gmt.exe [DEBUG]: GMT: 3. gmt_getsharepath trying USERDIR subdir C:/Users/13173/.gmt/postscriptlight
gmt.exe [DEBUG]: GMT: 4. gmt_getsharepath trying SHAREDIR subdir c:/programs/gmt6/share/postscriptlight
gmt.exe [DEBUG]: GMT: 5. gmt_getsharepath trying SHAREDIR c:/programs/gmt6/share
gmt.exe [DEBUG]: GMT: 6. gmt_getsharepath failed
gmt.exe [DEBUG]: Map distance calculation will be Cartesian
gmt.exe [DEBUG]: Exit: gmtinit_new_GMT_ctrl
gmt.exe [DEBUG]: Enter: New_PSL_Ctrl
gmt.exe [DEBUG]: Exit: New_PSL_Ctrl
gmt.exe [DEBUG]: Enter: gmt_manage_workflow
gmt.exe [DEBUG]: Exit : gmt_manage_workflow
gmt.exe [DEBUG]: Enter: PSL_beginsession
gmt.exe [DEBUG]: Exit : PSL_beginsession
gmt.exe [DEBUG]: Enter: PSL_setdefaults
gmt.exe [DEBUG]: Exit : PSL_setdefaults
gmt.exe [DEBUG]: Enter: gmtlib_io_init
gmt.exe [DEBUG]: Exit : gmtlib_io_init
gmt.exe [DEBUG]: Enter: gmt_hash_init
gmt.exe [DEBUG]: Exit: gmt_hash_init
gmt.exe [DEBUG]: Enter: gmt_hash_init
gmt.exe [DEBUG]: Exit: gmt_hash_init
gmt.exe [DEBUG]: Enter: gmt_reload_settings
gmt.exe [DEBUG]: The PROJ_GEODESIC set to Vincenty
gmt.exe [DEBUG]: Look for file C:/Users/13173/gmt.conf
gmt.exe [DEBUG]: Look for file C:/Users/13173/.gmt/gmt.conf
gmt.exe [DEBUG]: Look for file C:/Users/13173/.gmt/server/gmt.conf
gmt.exe [DEBUG]: Look for file C:/Users/13173/.gmt/cache/gmt.conf
gmt.exe [DEBUG]: Could not find file gmt.conf
gmt.exe [DEBUG]: Exit: gmt_reload_settings
gmt.exe [DEBUG]: Enter: gmtlib_plot_C_format
gmt.exe [DEBUG]: Exit: gmtlib_plot_C_format
gmt.exe [DEBUG]: Enter: gmtinit_get_history
gmt.exe [DEBUG]: Enter: gmt_hash_init
gmt.exe [DEBUG]: Exit: gmt_hash_init
gmt.exe [DEBUG]: Failed to release lock (Error <158>: The segment is already unlocked.
)
gmt.exe [DEBUG]: Exit: gmtinit_get_history
gmt.exe [DEBUG]: GMT_Create_Session initialized GMT structure
gmt.exe [DEBUG]: Loading core GMT shared library: gmt_w32.dll
gmt.exe [DEBUG]: Shared Library # 0 (core). Path = gmt_w32.dll
gmt.exe [DEBUG]: Loading GMT plugins from: C:/programs/gmt6/bin/gmt_plugins
gmt.exe [DEBUG]: Shared Library # 1 (supplements). Path = C:/programs/gmt6/bin/gmt_plugins/supplements_w32.dll
gmt.exe [DEBUG]: Local file C:/Users/13173/.gmt/server/gmt_data_server.txt found
gmt.exe [DEBUG]: File C:/Users/13173/.gmt/server/gmt_data_server.txt less than 24 hours old, refresh is premature.
gmt.exe [DEBUG]: Load contents from C:/Users/13173/.gmt/server/gmt_data_server.txt
gmt.exe [DEBUG]: Local file C:/Users/13173/.gmt/server/gmt_hash_server.txt found
gmt.exe [DEBUG]: File C:/Users/13173/.gmt/server/gmt_hash_server.txt less than 24 hours old, refresh is premature.
gmt.exe [DEBUG]: Input remote grid modified to have registration: @earth_day_30m_p
gmt.exe [DEBUG]: Revised options: map png
begin [INFORMATION]: Creating a workflow directory C:/Users/13173/.gmt/sessions/gmt_session.21892
begin [DEBUG]: The PROJ_GEODESIC set to Vincenty
begin [DEBUG]: Look for file C:/Users/13173/gmt.conf
begin [DEBUG]: Look for file C:/Users/13173/.gmt/gmt.conf
begin [DEBUG]: Look for file C:/Users/13173/.gmt/server/gmt.conf
begin [DEBUG]: Look for file C:/Users/13173/.gmt/cache/gmt.conf
begin [DEBUG]: Could not find file gmt.conf
begin [DEBUG]: Set session name to be map png
begin [DEBUG]: Begin Workflow. Session ID = 21892. Directory C:/Users/13173/.gmt/sessions/gmt_session.21892 created.
begin [DEBUG]: GMT now running in modern mode [Session ID = 21892]
gmt.exe [DEBUG]: Map distance calculation will be using great circle approximation with authalic auxiliary latitudes
and authalic (R_2) radius = 6371007.1809 m, in meter.
gmt.exe [DEBUG]: Use PS filename C:/Users/13173/.gmt/sessions/gmt_session.21892/gmt_0.ps-
gmt.exe [DEBUG]: gmtinit_get_current_panel: No current panel selected so not in subplot mode
gmt.exe [DEBUG]: Revised options: @earth_day_30m_p -Rg -JW-65/15c -B -Vd
grdimage [DEBUG]: History: Process -Rg
grdimage [DEBUG]: History: Process -JW-65/15c
grdimage [DEBUG]: Map distance calculation will be using great circle approximation with authalic auxiliary latitudes and authalic (R_2) radius = 6371007.1809 m, in meter.
grdimage [DEBUG]: Map distance calculation will be using great circle approximation with authalic auxiliary latitudes and authalic (R_2) radius = 6371007.1809 m, in meter.
grdimage [DEBUG]: Remote file (null) exists locally as C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage [DEBUG]: Replace file @earth_day_30m_p.tif with C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage [DEBUG]: Projected grid is non-orthogonal, nonlinear, or dpi was changed
grdimage [DEBUG]: Found readable file C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage [DEBUG]: C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif considered a valid image instead of
grid. Open via GDAL
grdimage [DEBUG]: Reset MAP_ANNOT_OBLIQUE to anywhere
grdimage [INFORMATION]: Central meridian set with -J (295) implies -R115/475/-90/90
grdimage [DEBUG]: Projected values in meters: -1.80199e+07 1.80199e+07 -9.00996e+06 9.00996e+06
grdimage [DEBUG]: Computed automatic parameters using dimension scaling: 0.908088
grdimage [DEBUG]: Auto-frame interval for axis 0 item 0: d = 60 f = 15
grdimage [INFORMATION]: Auto-frame interval for x-axis (item 0): a60f15
grdimage [DEBUG]: Auto-frame interval for axis 1 item 0: d = 60 f = 15
grdimage [INFORMATION]: Auto-frame interval for y-axis (item 0): a60f15
grdimage [INFORMATION]: Map scale is 2402.66 km per cm or 1:2.40266e+08.
grdimage [INFORMATION]: gmt_map_setup perimeter search region: 0/360/-90/90.
grdimage [INFORMATION]: Allocate memory and read image file C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage [DEBUG]: Given full path to file C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage [DEBUG]: Given full path to file C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage [DEBUG]: Found readable file C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage [DEBUG]: Object ID 0 : Registered Image File C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
as an Input resource with geometry Surface [n_objects = 1]
grdimage [DEBUG]: gmtapi_begin_io: Input resource access is now enabled [container]
grdimage [DEBUG]: gmtapi_import_image: Passed ID = 0 and mode = 135168
grdimage [DEBUG]: Found readable file C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage (gmt_gdalread.c:914(gmt_gdalread)): FYI: gmt_M_free given a NULL pointer - ignored
grdimage [DEBUG]: Map distance calculation will be using great circle approximation with authalic auxiliary latitudes and authalic (R_2) radius = 6371007.1809 m, in meter.
grdimage [DEBUG]: Geographic input grid, longitudes span exactly 360
grdimage [INFORMATION]: Reading image from file C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif
grdimage [DEBUG]: Found readable file C:/Users/13173/.gmt/server/earth/earth_day/earth_day_30m_p.tif

Recently I proposed to add a number as a prefix to the folder names (so the folders are order when they are sorted alphabetically. Should I make a PR (and fix some links, I guess)?

I am thinking of using index 0 and 1 digit:
0_bash
1_basics
2_line_symbols
3_grids
...

Based on the questions of the students I think that in the next edition we should show:

1. an example with a shp files. Maybe one from GADM (its licence says "The data are freely available for academic use.").
2. how to work with the user-dir?
3. the DCW-collections.
4. how to add a north and scale (basemap -Td and -L).
5. add transparency (-t)

Other suggestions to discuss:

1. Add legends?
2. how to work with makecpt ?
3. how to add text on the map (gmt text)?

I'm trying to run the test1 in Ubuntu 20.04

kamogelo@kamogelo:/usr/bin/gmt-for-geodesy/0_hw1$ ./test_1.sh
GPL Ghostscript 9.55.0: **** Could not open the file test1.pdf .
**** Unable to open the initial device, quitting.
psconvert [ERROR]: System call [gs -q -dNOPAUSE -dBATCH -dNOSAFER -dPDFSETTINGS=/prepress -dDownsampleColorImages=false -dDownsampleGrayImages=false -dDownsampleMonoImages=false -dUseFlateCompression=true -dEmbedAllFonts=true -dSubsetFonts=true -dMonoImageFilter=/FlateEncode -dAutoFilterGrayImages=false -dGrayImageFilter=/FlateEncode -dAutoFilterColorImages=false -dColorImageFilter=/FlateEncode -dSCANCONVERTERTYPE=2 -dALLOWPSTRANSPARENCY -dMaxBitmap=2147483647 -dUseFastColor=true -sDEVICE=pdfwrite -g4895x5211 -r720 -sOutputFile='test1.pdf' '/home/kamogelo/.gmt/sessions/gmt_session.65478/psconvert_65482d.eps'] returned error 256.
end [ERROR]: Failed to call psconvert
end [ERROR]: gmtinit_process_figures returned error 79

Running the spinning Earth movie examples now gives this error:

gmt movie 2_earth.sh -C360p -T91 -M55,pdf -N2_earth
coast [ERROR]: Centered (-Xc) and fixed (-Xf) shifts are not available in modern mode

While this makes sense for modern mode in general (infinite paper size...) it makes no sense for movie since here we actually have a specific paper size. So somehow we need to allow that when a movie script is running. Of top of my head here are some options:

1. Let movie set a environmental parameter and we check for that before disallowing -Xc -Xf
2. Let movie (as it converts the main.sh to the actual script that runs in parallel) detect -Xc|f and append an undocumented ! which means "accept this option even in modern mode".
3. Introduce -XC and -XF for this purpose in movie scripts.

I think (2) is pretty simple to implement and does not require users to do anything different (and is backward compatible). Option (3) fails that.

Thoughts?

Dear community,

I met a problem in opening the count.webm and count.mp4. Error messages as follows:

xdg-open: no method available for opening 'count.mp4'

/usr/bin/xdg-open: line 658: 28681 Bus error (core dumped) $browser "$1" > /dev/null 2> /dev/null
xdg-open: no method available for opening 'count.webm'

I am using CentOS Linux release 7.3.1611. I am wondering how to solve the problem.

Best,
Pingping Huang (gmt-for-geodesy learner)

The online workshop I attended one month ago has a great event landing page and a Jupyterbook. The workshop website uses this template (https://github.com/uwhackweek/jupyterbook-template). I know it's too late to build a website this year, but maybe we can do it next year?

• Template: https://github.com/uwhackweek/jupyterbook-template
• Examples:
  • https://icesat-2-2023.hackweek.io/
  • https://snowex-2021.hackweek.io/intro.html
  • https://seisscoped.org/HPS/

When I get the earthquake data from NEIC I run something like this

gmt convert ${URL} -i2,1,3,4+s50,0 -hi1 > 3_quakes.txt

where URL is built by the 3_get_quakes.sh script and is

https://earthquake.usgs.gov/fdsnws/event/1/query.csv?starttime=2018-01-01%0000:00:00&endtime=2018-12-31%0000:00:00&minmagnitude=5&orderby=time-asc

What happens is that we receive a query.csv file which gmt convert reads and converts as indicated. However, query.csv remains in the directory. Anyone who thinks that is bad and that we should find a way for GMT (here gmt convert) to delete it at the end?

Hi instructors, I will be sending out preliminary schedules by this weekend for the UNAVCO/GMT course. However, faulty memory means I am not sure who said they would do what. I am most sure about Eric Xu doing geodesy and @seisman doing Seismology, but not entirely sure of who else have picked something they want to present on. We have the sections on points and lines that @joa-quim have done and Grids and Images that Leo used to do (but he is not available this summer). I am unsure what @meghanrjones and @Esteban82 said in our February community meeting... I am available to do whatever is left over as backup.

Please let me know as soon as possible if you have firmer memories and state what you expect to do. As it seems, we will again do live presentations, with at least the exception of Eric.

The deadline for proposing a short course for the 2023 Technical Short Courses is February 13. I'm opening this issue for discussion about organizing and teaching the short course.

My suggestion is to submit an application with a different proposed format than past years, more similar to the PyGMT short course at EGU, to make timing more flexible for volunteer instructors. In this case, instructors could record presentations ahead of time. We could also host a couple "office hours" where instructors are available to help students with projects. I think it would also be nice to have the wrappers featured a bit more.

@GenericMappingTools/gmt-team and @GenericMappingTools/pygmt-team - can you please share if you'd be interested in contributing to this year's should course and any comments on the proposed new structure?

The application questions have been copied to https://hackmd.io/@pygmt/Hk3DQyxas for drafting.

One user reports that he can't use meca and coupe.

The reason is that he builds GMT source codes and it seems the building is incomplete, so he can use core modules like basemap and coast, but can't use meca, coupe and velo.

I am borrowing a Mac13 and it currently has gmt version 6.3.0. I need version 6.4.0 but am having trouble updating it. I use XQuartz. I have tried typing "brew upgrade gmt" and "sudo brew upgrade gmt" but this is not working. I get these errors. How can I fix this and upgrade?