Hi! Very nice and useful initiative. I'm implementing laser altimetry simulations in python and happen to need the GMT grdtrack function to extract elevation data from a topography basemap. Is this function already implemented in pygmt or do you plan to implement it at some point? Thanks!
Hi @steo85it, I'm using grdtrack myself and would be happy to implement it. Already have some code and will submit an issue and pull request which you're more than welcome to contribute to :)
At the moment the pygmt.grdtrack implementation requires you to load the table data into a pandas.DataFrame and the grid into an xarray.DataArray. Would it be better to have grdtrack work directly on files as well, or would this be the way to go? Thoughts?
Hi Pedro, as Eric said, it is possible to do that. We're working on a conda package for the 6.0.0rc3 so that you could install in a separate environment without having to manipulate your PATH. We're having of trouble getting that to work still but I'll post here when we have it.
Hii,good afternoon I am titu from India. I need some suggestions.Actually I know gmt for plotting maps but it is based on the shell scripting which is quite tidious in nature.So i need a python based gmt tool for making the script easier for map plottings.So is this pygmt can help me ???
@ChiaraMarieni_twitter are you using Windows? Make sure you have GMT installed as well. See https://www.pygmt.org/dev/install.html#finding-the-gmt-shared-library. PyGMT doesn't yet work well on Windows. We're having some issues and progress is slow since most developers are on Mac and Linux.
I just have a small comment/request about the option
projection="W8i". For people who are only interested in running pygmt in a notebook, the size of the image isn't too important: just as you don't specify an image size when using things like imshow, it would probably be best to set this to some default value. Perhaps a better way to specify the options would be to use something like projection="W", size="8i".
Hello, I have installed GMT6 on window10, and I can start it by cmd, then I installed pygmt through pycharm. I'm sure I have installed the dependency packages. When I run "import pygmt" "pygmt.test()", some error information appear：“est.py: error: unrecognized arguments: --mpl；inifile: None； assert status == 0, "Some tests have failed."； AssertionError: Some tests have failed. ”. Can anybody help me? Thank you.
@seisman @weiji14 thanks for picking up PyGMT development in my absence. I owe you both a beer/coffee (to be claimed at AGU?). I'm just coming back and going through my notifications to see what was done in the mean time. One thing we should discuss is the underlying
pygmt.clib module. I'm not very happy with it and I think you both probably have noticed that it has some design flaws. A priority for me for the following months is to see what could be done about it. Since that's the core of our package, it would be great to have that be pretty stable for our 0.1 release after GMT 6 is finally out. What do you think?
Is there any discussion group for "how to" questions ? I am having problems using pygmt.Figure.grdimage with xarray.DataArray returned by xarray.open_rasterio. I am reading a geotiff file using xarray.open_rasterio, and when putting the result (named "da") into pygmt.Figure.grdimage, it gives me the following error :"GMTInvalidInput: Invalid number of grid dimensions '3'. Must be 2." I tried using "da[0]" but nothing happens expect eventually the crash of the kernel. I think it is more because I am not sure of what should we put into pygmt.Figure.grdimage than a problem with the function... did anyone ever plot a geotiff with pygmt ? thanks
it could be that you need to squeeze an empty third dimension with
da.squeeze()
@liamtoney here is what I get for
`<xarray.DataArray (band: 1, y: 2450, x: 2872)>
[7036400 values with dtype=float32]
Coordinates:
da:`<xarray.DataArray (band: 1, y: 2450, x: 2872)>
[7036400 values with dtype=float32]
Coordinates:
- band (band) int64 1
- y (y) float64 -20.84 -20.84 -20.84 -20.85 ... -21.42 -21.42 -21.42
- x (x) float64 55.19 55.19 55.19 55.19 ... 55.86 55.86 55.86 55.86
Attributes:
transform: (0.00023395274717030208, 0.0, 55.19145732801233, 0.0, -0....
crs: +init=epsg:4326
res: (0.00023395274717030208, 0.00023395274717030208)
is_tiled: 0
nodatavals: (-9999.0,)
scales: (1.0,)
offsets: (0.0,)
AREA_OR_POINT: Area`
@egayer I see. As-is, your
da has three dimensions: band, x, and y. You should be able to use da.squeeze() to remove the length-1 dimension band. Then your grdimage command should work since you'll have a legitimately 2D array. xarray docs are not great on this, so here's the docs for the equivalent numpy command documentation. Let me know if that helps!
Hi @khaynie-usgs, thanks for your interest! Legends/colorbars are in the works currently and I believe are set for the 0.1 release (core devs please correct me if I'm wrong). I'm not sure about xyz2grd, maybe @leouieda or @weiji14 can comment on that. The Python package
xarray may be able to handle some of the cases you use xyz2grd for, I'd recommend checking it out.
Oops, just catching up on the activity here. Thanks for the offer @leouieda :laughing:, GMT6 is pretty much out now (see release) so we can start doing some major work. Personally I'd like to not refactor the clib too much in the short-term because of the PyGMT workshop I'm hosting on Nov 12, but I agree that long-term there could be some improvements on that front.
@khaynie-usgs, the
legend module has just been implemented today (thanks @liamtoney!) and colorbar is just awaiting review (see GenericMappingTools/pygmt#332) before it gets merged in so hopefully soon. As for xyz2grd, if you'd like to open an feature request on Github here we can start working on it (though I must warn you it might take a while...). Depending on your use case though, @liamtoney is right that xarray might have a way to do it.
By the way everyone, there's a new GMT community forum at https://forum.generic-mapping-tools.org/ you can sign up for with your Github account or by email. It's still a bit new but I recommend checking it out.
@EqualMa, it's certainly been raised before at GenericMappingTools/pygmt#288 and I think @seisman has tried to implement it in GenericMappingTools/pygmt#293.
Hi Alex, any projection available in GMT is also available in PyGMT: https://docs.generic-mapping-tools.org/latest/gmt.html#j-full
For info, pyshtools now has implemented geopgraphic projections with both pygmt and cartopy. Here is a notebook showing how everything works: https://htmlpreview.github.io/?https://github.com/MarkWieczorek/SHTOOLS/blob/cartopy/docs/pages/mydoc/notebooks/Introduction-4.html
If you have any comments, let me know.
If you have any comments, let me know.
FYI, we just put out a new release of pyshtools, which is our first to include experimental support for map projections using pygmt! If you would like to check out how this was implemented, please see this notebook: https://shtools.oca.eu/shtools/public/pages/mydoc/notebooks/Introduction-4.html
mark-wieczorek You can also check out the numerous examples on https://www.generic-mapping-tools.org/ if you are ok with using the command line.
@geophysics91 please start with this tutorial, I think it will help you achieve your goal.