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Fatiando a Terra

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5 May 2021
@_slack_fatiando_U020T6U7BTQ:matrix.orgDarrenM changed their display name from _slack_fatiando_U020T6U7BTQ to DarrenM.17:17:11
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@_slack_fatiando_U020TJC33HC:matrix.orgLoughlin Tuck joined the room.18:47:13
@_slack_fatiando_U020TJC33HC:matrix.orgLoughlin Tuck changed their display name from _slack_fatiando_U020TJC33HC to Loughlin Tuck.18:47:14
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@_slack_fatiando_U020TJC33HC:matrix.orgLoughlin Tuck changed their profile picture.19:17:59
@_slack_fatiando_U020TJC33HC:matrix.orgLoughlin Tuck Hi,  I think this is a question most suitable for #fatiando-verde:matrix.org but also possibly #fatiando-harmonica:matrix.org I have been trying to find a method that will spatially filter grids (specifically magnetic anomaly data). For example, if I wanted to bandpass filter a mag grid (example) between 1,000m - 10,000m, is there a function that would do that? (I would assume this is done in the frequency domain with potentially a Butterworth filter?). I expected a function like this in Fatiando... but could not find it?  It is something I think I remember in the Spatial Analyst package of ESRI's ArcMap. But I have cannot find any decent python code that I can conform to my needs; particularly that might retain the spatial referencing. Any pointers? Thanks in advance,  Loughlin 19:17:59
@_slack_fatiando_UMGLPTLAW:matrix.orgCraig Miller GMT would probably do that with a combination of grdfft and grdfilter or using a filter directly within grdfft https://docs.generic-mapping-tools.org/6.1/grdfft.html 22:22:15
@_slack_fatiando_UMGLPTLAW:matrix.orgCraig Miller (edited) ... do that => ... do that with a combination of `grdfft` and `grdfilter` or using a filter directly within grdfft <https://docs.generic-mapping-tools.org/6.1/grdfft.html> 22:25:56
@_slack_fatiando_U020TJC33HC:matrix.orgLoughlin Tuck
In reply toundefined
Thank you! I will try it tomorrow but it looks like exactly what I was looking for.   On quick inspection of the installation instructions, I see that there is no pip install for GMT. Might you, or anyone, know how to install this in colab? I tried: !pip install git+https://github.com/GenericMappingTools/gmt.git  but I get an error: Collecting git+https://github.com/GenericMappingTools/gmt.git Cloning https://github.com/GenericMappingTools/gmt.git to /tmp/pip-req-build-cscim40v Running command git clone -q https://github.com/GenericMappingTools/gmt.git /tmp/pip-req-build-cscim40v ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Which might not be unexpected as the instructions suggest this needs to be built from source. Might anyone know how to install GMT into google colabs?
23:59:45
6 May 2021
@_slack_fatiando_U020TJC33HC:matrix.orgLoughlin Tuck
In reply toundefined
(edited) ... looking for. => ... looking for.   On quick inspection of the installation <http://gmt.soest.hawaii.edu/projects/gmt/wiki/Installing#Installing-instructions|instructions>, I see that there is no pip install for GMT. Might you, or anyone, know how to install this in colab? I tried: !pip install git+<https://github.com/GenericMappingTools/gmt.git>  but I get an error: Collecting git+<https://github.com/GenericMappingTools/gmt.git> Cloning <https://github.com/GenericMappingTools/gmt.git> to /tmp/pip-req-build-cscim40v Running command git clone -q <https://github.com/GenericMappingTools/gmt.git> /tmp/pip-req-build-cscim40v ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Which might not be unexpected as the instructions suggest this needs to be built from source. Might anyone know how to install GMT into google colabs?
00:19:59
@_slack_fatiando_UMGLPTLAW:matrix.orgCraig Miller
In reply to@_slack_fatiando_U020TJC33HC:matrix.org
Thank you! I will try it tomorrow but it looks like exactly what I was looking for.   On quick inspection of the installation instructions, I see that there is no pip install for GMT. Might you, or anyone, know how to install this in colab? I tried: !pip install git+https://github.com/GenericMappingTools/gmt.git  but I get an error: Collecting git+https://github.com/GenericMappingTools/gmt.git Cloning https://github.com/GenericMappingTools/gmt.git to /tmp/pip-req-build-cscim40v Running command git clone -q https://github.com/GenericMappingTools/gmt.git /tmp/pip-req-build-cscim40v ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Which might not be unexpected as the instructions suggest this needs to be built from source. Might anyone know how to install GMT into google colabs?
you could try install pygmt https://www.pygmt.org/latest/install.html which I believe also takes care of installing GMT. GMT itself isn't python, but pygmt allows you to access GMT from a python api.
06:13:42
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply toundefined
I've been trying to install pygmt on Colab for the Harmonica tutorial in Transform21 without any success. To do so I tried installing Miniconda first, failing in every attempt 😞 But, if you just need to run gmt you could try installing it directly from the apt package manager. Try this:
! sudo apt install gmt
I think it will not install the latest gmt, but maybe the version it acutally gets is enough for running grdfft and grdfilter
12:14:36
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply to@_slack_fatiando_UMFSBQVMG:matrix.org
I've been trying to install pygmt on Colab for the Harmonica tutorial in Transform21 without any success. To do so I tried installing Miniconda first, failing in every attempt 😞 But, if you just need to run gmt you could try installing it directly from the apt package manager. Try this:
sudo apt install gmt
I think it will not install the latest gmt, but maybe the version it acutally gets is enough for running grdfft and grdfilter
For the record, if you try installing pygmt you need to be careful about the version of gmt . As rule of thumb, always go for the latest release of gmt
12:15:09
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply toundefined
(edited) ... this: ```sudo apt ... => ... this: ```! sudo apt ...
12:15:35
@_slack_fatiando_U020TJC33HC:matrix.orgLoughlin Tuck
In reply to@_slack_fatiando_UMFSBQVMG:matrix.org
I've been trying to install pygmt on Colab for the Harmonica tutorial in Transform21 without any success. To do so I tried installing Miniconda first, failing in every attempt 😞 But, if you just need to run gmt you could try installing it directly from the apt package manager. Try this:
! sudo apt install gmt
I think it will not install the latest gmt, but maybe the version it acutally gets is enough for running grdfft and grdfilter
Hi,  Thank you both for you help. Craig Miller. I was able to get gmt running through pygmt and pygmt.grdfilter to work in a conda environment. I could not find pygmt.grdfft, but I don't immediately need it. I guess not all gmt functions are accessible through pygmt? Regardless, this is a great help, thank you. santisoler. pygmt and its requirements seems to install without error in colabs. When I try and import it, I get: "GMTCLibNotFoundError: Error loading GMT shared library at 'libgmt.so'. libgmt.so: cannot open shared object file: No such file or directory". I see no reference to gmt in the pip install list. For my conda instance, I am using gmt v6.1.1. I had tried to install this using the miniconda work around as well in colabs. After endless messages it errored with "ModuleNotFoundError: No module named 'conda'". If you do find a solution for colabs, perhaps you can post it. I could not figure out how to run gmt directly in colab. Regardless, I appreciate the help. Cheers,
14:24:44
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply to@_slack_fatiando_U020TJC33HC:matrix.org
Hi,  Thank you both for you help. Craig Miller. I was able to get gmt running through pygmt and pygmt.grdfilter to work in a conda environment. I could not find pygmt.grdfft, but I don't immediately need it. I guess not all gmt functions are accessible through pygmt? Regardless, this is a great help, thank you. santisoler. pygmt and its requirements seems to install without error in colabs. When I try and import it, I get: "GMTCLibNotFoundError: Error loading GMT shared library at 'libgmt.so'. libgmt.so: cannot open shared object file: No such file or directory". I see no reference to gmt in the pip install list. For my conda instance, I am using gmt v6.1.1. I had tried to install this using the miniconda work around as well in colabs. After endless messages it errored with "ModuleNotFoundError: No module named 'conda'". If you do find a solution for colabs, perhaps you can post it. I could not figure out how to run gmt directly in colab. Regardless, I appreciate the help. Cheers,
We experienced the same error with pygmt on MacOS. We solve it by using Python 3.9 instead of Python 3.8
14:45:11
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply toundefined
You can run any command on the shell in Jupyter Notebooks by using the ! symbol, for exmaple:
! gmt --version
14:47:22
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply toundefined
(edited) ... for exmaple: => ... for exmaple: ```! gmt --version```
14:47:58
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply to@_slack_fatiando_UMFSBQVMG:matrix.org
You can run any command on the shell in Jupyter Notebooks by using the ! symbol, for exmaple:
! gmt --version
> pygmt and its requirements seems to install without error in colabs. How did you manage to install it? Through conda ?
14:48:39
@_slack_fatiando_UMGLPTLAW:matrix.orgCraig Miller
In reply toundefined
You can actually call any gmt function through the call_module method even if its not part of pygmt, the tutorial video shows how i think
20:16:22
@_slack_fatiando_UMGLPTLAW:matrix.orgCraig Miller
In reply toundefined
(edited) ... of pygmt => ... of pygmt, the tutorial video shows how i think
21:28:59
7 May 2021
@_slack_fatiando_U020TJC33HC:matrix.orgLoughlin Tuck
In reply to@_slack_fatiando_UMGLPTLAW:matrix.org
You can actually call any gmt function through the call_module method even if its not part of pygmt, the tutorial video shows how i think
santisoler. I mean to say that colab doesn't give me any error when I run "!pip install pygmt"... but there must be some issue as it will not import. Also "! gmt --version" will not run either. Colabs runs python version 3.7.10. What method did you use to run v3.8 on colab? A local runtime? Craig Miller. Thanks I may need call_module sooner than I had thought.  Regardless, thank you both for your assistance.
00:16:24
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply to@_slack_fatiando_U020TJC33HC:matrix.org
santisoler. I mean to say that colab doesn't give me any error when I run "!pip install pygmt"... but there must be some issue as it will not import. Also "! gmt --version" will not run either. Colabs runs python version 3.7.10. What method did you use to run v3.8 on colab? A local runtime? Craig Miller. Thanks I may need call_module sooner than I had thought.  Regardless, thank you both for your assistance.
Probably pip installed pygmt but expected gmt to be installed already (I think pip cannot deliver gmt ). I haven't try to install Python 3.9 on Colab. We experienced the libgmt.so error on a MacOS laptop and then solve it locally by upgrading the conda environment to Python 3.9. The easiest way I can think of to install another Python version on Colab is to actually install Miniconda and create your environment (see https://forum.generic-mapping-tools.org/t/installing-pygmt-on-google-colab/898). But as I said before, I couldn't make it work.
11:47:13
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply toundefined
> Also "! gmt --version" will not run either. Have you installed gmt before? You should be able to do so with
! sudo apt install gmt
11:47:54
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler
In reply toundefined
(edited) ... You can do that with ... => ... You should be able to do so with ...
11:48:16
13 May 2021
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisolerRedacted or Malformed Event13:54:10
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler @room 📢  The next Fatiando Community Call is today at 16:00 UTC! The meeting notes and instructions for joining are here https://hackmd.io/@fatiando/community-calls-2021 Feel free to add any topics you'd like to discuss. Hope to see you in a few hours! 13:57:02
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler Today we will be trying the Software Undeground Jitsi instance, we expect higher quality thanks to SWUNG! https://jitsi.softwareunderground.org/fatiando/community-call 13:58:30
@_slack_fatiando_UMFSBQVMG:matrix.orgsantisoler We are live on Youtube: https://www.youtube.com/watch?v=0kElZQwMPSM 16:03:19

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