From Peter.Webb at getech.com Tue Jun 5 22:00:26 2018 From: Peter.Webb at getech.com (Peter Webb) Date: Tue, 5 Jun 2018 12:00:26 +0000 Subject: [GPlates-discuss] pygplates - motion paths Message-ID: Dear users, I am relatively new to both python and pygplates. I have managed to create a script which: 1. reads a text file of points, using csv.reader 2. creates a gpml file of the points, using pygplates.PointOnSphere and pygplates.Feature 3. assigns plate id to the points, using pygplates.partition_into_plates 4. converts the points to motion paths, using pygplates.Feature.create_motion_path I now want to export the motion path for each point as a polyline feature for use in ArcMap and/or export the paleolatitude/longitude values for each path as a text file. Currently, my attempt to write the motion path features to a shapefile only writes the present day locations of the points Is it possible to extract and export the polyline geometry of the motion path using pygplates? I would appreciate any advice, many thanks. Thank you for your help, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From john.cannon at sydney.edu.au Tue Jun 5 23:13:01 2018 From: john.cannon at sydney.edu.au (John Cannon) Date: Tue, 5 Jun 2018 13:13:01 +0000 Subject: [GPlates-discuss] pygplates - motion paths In-Reply-To: References: Message-ID: Hi Peter, To export the reconstructed motion paths (polylines) to Shapefile directly you can use this sample code: https://protect-au.mimecast.com/s/FFGGCBNZwLiJMYzLFz4YY3?domain=gplates.org ...where, in your case, you have already created the motion path features. Here each seed point results in an exported polyline (the reconstructed motion path from that seed point). For exporting to a text file you could base it off the following sample code: https://protect-au.mimecast.com/s/sUP6CD1jy9trn4D8S5N--s?domain=gplates.org ...except, in the inner for loop (that iterates over points in a reconstructed motion path), you can output each lat/lon to text file instead of printing. And if exporting the motion paths as they look at present day you could set the reconstruction time to zero (in pygplates.reconstruct() in the above sample codes). Regards, John From: GPlates-discuss On Behalf Of Peter Webb Sent: Tuesday, 5 June 2018 10:00 PM To: gplates-discuss at mailman.sydney.edu.au Subject: [GPlates-discuss] pygplates - motion paths Dear users, I am relatively new to both python and pygplates. I have managed to create a script which: 1. reads a text file of points, using csv.reader 2. creates a gpml file of the points, using pygplates.PointOnSphere and pygplates.Feature 3. assigns plate id to the points, using pygplates.partition_into_plates 4. converts the points to motion paths, using pygplates.Feature.create_motion_path I now want to export the motion path for each point as a polyline feature for use in ArcMap and/or export the paleolatitude/longitude values for each path as a text file. Currently, my attempt to write the motion path features to a shapefile only writes the present day locations of the points Is it possible to extract and export the polyline geometry of the motion path using pygplates? I would appreciate any advice, many thanks. Thank you for your help, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From Peter.Webb at getech.com Wed Jun 6 17:34:47 2018 From: Peter.Webb at getech.com (Peter Webb) Date: Wed, 6 Jun 2018 07:34:47 +0000 Subject: [GPlates-discuss] pygplates - motion paths In-Reply-To: References: Message-ID: Thank you John, that has worked for me. Peter From: GPlates-discuss On Behalf Of John Cannon Sent: 05 June 2018 14:13 To: GPlates general discussion mailing list Subject: Re: [GPlates-discuss] pygplates - motion paths Hi Peter, To export the reconstructed motion paths (polylines) to Shapefile directly you can use this sample code: https://protect-au.mimecast.com/s/-Ox6CMwvLQTVD2YVfw1n7P?domain=gplates.org ...where, in your case, you have already created the motion path features. Here each seed point results in an exported polyline (the reconstructed motion path from that seed point). For exporting to a text file you could base it off the following sample code: https://protect-au.mimecast.com/s/3Tj0CNLwM9i5JZp5c4hV52?domain=gplates.org ...except, in the inner for loop (that iterates over points in a reconstructed motion path), you can output each lat/lon to text file instead of printing. And if exporting the motion paths as they look at present day you could set the reconstruction time to zero (in pygplates.reconstruct() in the above sample codes). Regards, John From: GPlates-discuss > On Behalf Of Peter Webb Sent: Tuesday, 5 June 2018 10:00 PM To: gplates-discuss at mailman.sydney.edu.au Subject: [GPlates-discuss] pygplates - motion paths Dear users, I am relatively new to both python and pygplates. I have managed to create a script which: 1. reads a text file of points, using csv.reader 2. creates a gpml file of the points, using pygplates.PointOnSphere and pygplates.Feature 3. assigns plate id to the points, using pygplates.partition_into_plates 4. converts the points to motion paths, using pygplates.Feature.create_motion_path I now want to export the motion path for each point as a polyline feature for use in ArcMap and/or export the paleolatitude/longitude values for each path as a text file. Currently, my attempt to write the motion path features to a shapefile only writes the present day locations of the points Is it possible to extract and export the polyline geometry of the motion path using pygplates? I would appreciate any advice, many thanks. Thank you for your help, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.kuhn at informatik.uni-hamburg.de Thu Jun 14 00:20:41 2018 From: michael.kuhn at informatik.uni-hamburg.de (Michael Kuhn) Date: Wed, 13 Jun 2018 16:20:41 +0200 Subject: [GPlates-discuss] GPlates package in Spack Message-ID: Dear all, I just wanted to let you know that a package for GPlates has just been merged into Spack, a package manager for supercomputers. Installing should be as easy as cloning the Spack repository and doing: $ ./bin/spack install -v gplates If you do not have a fitting compiler (GCC 4.9.4 seems to be the last supported version), you need to do something like this first: $ ./bin/spack install -v gcc at 4.9.4 $ ./bin/spack compiler find $(./bin/spack location -i gcc at 4.9.4) This should be a nice way for people using unsupported Linux distributions or those that want to compile GPlates themselves. One small request: As part of creating the package, I figured out the upper version bounds of some dependencies. It would be great if someone could update the GPlates website and repository with those versions. You can find them here (look for the depends_on statements): https://protect-au.mimecast.com/s/QVftCBNZwLiJWlO4IzAiG3?domain=github.com Moreover, a few more problems are documented in the package file (such as GPlates not building in parallel, problems with FindPythonLibs and the gplates binary only being installed for the Release target). If you want to reply, please keep me CC'd as I am not subscribed to the mailing list. If you have any suggestions for improvements, please let me know. Thanks! Best regards, Michael -- Dr. Michael Kuhn Universit?t Hamburg Faculty of Mathematics, Informatics and Natural Sciences Department of Informatics Research Group Scientific Computing Bundesstra?e 45a D-20146 Hamburg +49 40 460094-108 (telephone) michael.kuhn at informatik.uni-hamburg.de https://protect-au.mimecast.com/s/IIvECD1jy9trYOkVh5k0w-?domain=uni-hamburg.de https://protect-au.mimecast.com/s/fGxRCE8kz9to46NDUpzM5z?domain=wr.informatik.uni-hamburg.de From franziska.franeck at nhm.uio.no Thu Jun 14 22:51:01 2018 From: franziska.franeck at nhm.uio.no (Franziska Franeck) Date: Thu, 14 Jun 2018 12:51:01 +0000 Subject: [GPlates-discuss] reference question Earthbyte plate IDs Message-ID: <659c6a05445c42bd8dd77568e799340b@mail-ex04.exprod.uio.no> Hei, I am using the earthbyte plate IDs in one of my project for identifying palaeocontinents (PBDB output). Unfortunately I am struggling to find the correct reference. Can anyone tell me which reference is the correct one for the plate IDs? I see Wright et al. (2013) refer to the IDs since the actual ID list is from 2007 I doubt that this is the correct reference. I'd really apprechiate your help! Thanks a lot in advance, Franziska From Christian.Heine at shell.com Fri Jun 15 00:10:55 2018 From: Christian.Heine at shell.com (Christian.Heine at shell.com) Date: Thu, 14 Jun 2018 14:10:55 +0000 Subject: [GPlates-discuss] reference question Earthbyte plate IDs In-Reply-To: <659c6a05445c42bd8dd77568e799340b@mail-ex04.exprod.uio.no> References: <659c6a05445c42bd8dd77568e799340b@mail-ex04.exprod.uio.no> Message-ID: Hi Franziska, > I am using the earthbyte plate IDs in one of my project for identifying > palaeocontinents (PBDB output). Unfortunately I am struggling to find > the correct reference. > Can anyone tell me which reference is the correct one for the plate IDs? This depends a bit on which PlateID data you are using... > I see Wright et al. (2013) refer to the IDs since the actual ID list is > from 2007 I doubt that this is the correct reference. There are quite some incarnations of PlateIDs around which have changed with time and the various releases of GPlates. So it would be good to know which version you are using - "the earthbyte plate IDs" is a bit vague. I **think** that the first 'official' citation for PlateID assignments was Maria Seton et al.'s 2012 Earth Sci Rev paper which was at the time incorporated in the GPlates Sample Data as base model. That paper is also referenced in the Wright et al. 2013 paper. Previous PlateID versions were never published as such if I recall correctly, but they were released as GPlates Sample Data - in that case you should probably use Boyden et al., 2011 [1]. If you're looking to find out which plate polygon assignment PBDB uses, you might have to ask them. I cannot find any info on the plate polygon versions on the PBDB website. Might well be that this is the Seton et al., ESR 2012 model. Hope I haven't misunderstood your question, Christian [1] Boyden, James A. and M?ller, R. Dietmar and Gurnis, Michael and Torsvik, Trond H. and Clark, James A. and Turner, Mark and Ivey-Law, Hamish and Watson, Robin J. and Cannon, John S. (2011) Next-generation plate-tectonic reconstructions using GPlates. In: Geoinformatics: Cyberinfrastructure for the Solid Earth Sciences. Cambridge University Press , Cambridge, pp. 95-113. ISBN 9780521897150. https://protect-au.mimecast.com/s/nY-mCxnMRvtqn4XRH82iKU?domain=authors.library.caltech.edu From franziska.franeck at nhm.uio.no Fri Jun 15 17:40:27 2018 From: franziska.franeck at nhm.uio.no (Franziska Franeck) Date: Fri, 15 Jun 2018 07:40:27 +0000 Subject: [GPlates-discuss] reference question Earthbyte plate IDs In-Reply-To: References: <659c6a05445c42bd8dd77568e799340b@mail-ex04.exprod.uio.no> Message-ID: <60b547bafade4c5dbdc8bce742c48ca3@mail-ex04.exprod.uio.no> Hei Christian, Thanks a lot for your fast reply. I am sorry for being not more specific. https://protect-au.mimecast.com/s/wfaLCr8DLRt3J2Lyf72deg?domain=earthbyte.org I am using the plateID assignment from this page (and just saw that the licence was a separate link.. sorry for overlooking that.). So I guess I have to cite M?ller et al. (2008), Age, spreading rates and spreading asymmetry of the world's ocean crust. Where can I find overviews of later/updated versions or does anyone know which of the versions is used in Wright et al. 2013, since I believe that this is the version used in PBDB? Best regards, Franziska >-----Original Message----- >From: GPlates-discuss [mailto:gplates-discuss-bounces at mailman.sydney.edu.au] >On Behalf Of Christian.Heine at shell.com >Sent: Thursday, June 14, 2018 4:11 PM >To: gplates-discuss at mailman.sydney.edu.au >Subject: Re: [GPlates-discuss] reference question Earthbyte plate IDs > >Hi Franziska, > >> I am using the earthbyte plate IDs in one of my project for >> identifying palaeocontinents (PBDB output). Unfortunately I am >> struggling to find the correct reference. >> Can anyone tell me which reference is the correct one for the plate IDs? > >This depends a bit on which PlateID data you are using... > >> I see Wright et al. (2013) refer to the IDs since the actual ID list >> is from 2007 I doubt that this is the correct reference. > >There are quite some incarnations of PlateIDs around which have changed with >time and the various releases of GPlates. So it would be good to know which >version you are using - "the earthbyte plate IDs" is a bit vague. > >I **think** that the first 'official' citation for PlateID assignments was Maria >Seton et al.'s 2012 Earth Sci Rev paper which was at the time incorporated in the >GPlates Sample Data as base model. That paper is also referenced in the Wright >et al. 2013 paper. Previous PlateID versions were never published as such if I >recall correctly, but they were released as GPlates Sample Data - in that case you >should probably use Boyden et al., 2011 [1]. > >If you're looking to find out which plate polygon assignment PBDB uses, you >might have to ask them. I cannot find any info on the plate polygon versions on >the PBDB website. Might well be that this is the Seton et al., ESR 2012 model. > >Hope I haven't misunderstood your question, Christian > > >[1] Boyden, James A. and M?ller, R. Dietmar and Gurnis, Michael and Torsvik, >Trond H. and Clark, James A. and Turner, Mark and Ivey-Law, Hamish and Watson, >Robin J. and Cannon, John S. (2011) Next-generation plate-tectonic >reconstructions using GPlates. In: Geoinformatics: Cyberinfrastructure for the >Solid Earth Sciences. Cambridge University Press , Cambridge, pp. 95-113. ISBN >9780521897150. https://protect-au.mimecast.com/s/RLvqCvl0PoC0VAMJfXBpKk?domain=authors.library.caltech.edu > >_______________________________________________ >GPlates-discuss mailing list >GPlates-discuss at mailman.sydney.edu.au >https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss From mark.brandon at yale.edu Sat Jun 16 02:52:24 2018 From: mark.brandon at yale.edu (Mark Brandon) Date: Fri, 15 Jun 2018 12:52:24 -0400 Subject: [GPlates-discuss] reference question Earthbyte plate IDs In-Reply-To: <60b547bafade4c5dbdc8bce742c48ca3@mail-ex04.exprod.uio.no> References: <659c6a05445c42bd8dd77568e799340b@mail-ex04.exprod.uio.no> <60b547bafade4c5dbdc8bce742c48ca3@mail-ex04.exprod.uio.no> Message-ID: <6C0CD431-9A05-415D-BC82-34F2DB3C6C86@yale.edu> You can find documentation on this issue by searching the web with the terms: plate id and gplates. Also, you can use the feature select option in gplates to select and identify plate ids from the gplates map. Best, Mark > On Jun 15, 2018, at 3:40 AM, Franziska Franeck wrote: > > Hei Christian, > Thanks a lot for your fast reply. I am sorry for being not more specific. > https://protect-au.mimecast.com/s/EQfKCjZrzqH1NQz9HWbj3d?domain=earthbyte.org > I am using the plateID assignment from this page (and just saw that the licence was a separate link.. sorry for overlooking that.). So I guess I have to cite M?ller et al. (2008), Age, spreading rates and spreading asymmetry of the world's ocean crust. > Where can I find overviews of later/updated versions or does anyone know which of the versions is used in Wright et al. 2013, since I believe that this is the version used in PBDB? > Best regards, > Franziska > >> -----Original Message----- >> From: GPlates-discuss [mailto:gplates-discuss-bounces at mailman.sydney.edu.au] >> On Behalf Of Christian.Heine at shell.com >> Sent: Thursday, June 14, 2018 4:11 PM >> To: gplates-discuss at mailman.sydney.edu.au >> Subject: Re: [GPlates-discuss] reference question Earthbyte plate IDs >> >> Hi Franziska, >> >>> I am using the earthbyte plate IDs in one of my project for >>> identifying palaeocontinents (PBDB output). Unfortunately I am >>> struggling to find the correct reference. >>> Can anyone tell me which reference is the correct one for the plate IDs? >> >> This depends a bit on which PlateID data you are using... >> >>> I see Wright et al. (2013) refer to the IDs since the actual ID list >>> is from 2007 I doubt that this is the correct reference. >> >> There are quite some incarnations of PlateIDs around which have changed with >> time and the various releases of GPlates. So it would be good to know which >> version you are using - "the earthbyte plate IDs" is a bit vague. >> >> I **think** that the first 'official' citation for PlateID assignments was Maria >> Seton et al.'s 2012 Earth Sci Rev paper which was at the time incorporated in the >> GPlates Sample Data as base model. That paper is also referenced in the Wright >> et al. 2013 paper. Previous PlateID versions were never published as such if I >> recall correctly, but they were released as GPlates Sample Data - in that case you >> should probably use Boyden et al., 2011 [1]. >> >> If you're looking to find out which plate polygon assignment PBDB uses, you >> might have to ask them. I cannot find any info on the plate polygon versions on >> the PBDB website. Might well be that this is the Seton et al., ESR 2012 model. >> >> Hope I haven't misunderstood your question, Christian >> >> >> [1] Boyden, James A. and M?ller, R. Dietmar and Gurnis, Michael and Torsvik, >> Trond H. and Clark, James A. and Turner, Mark and Ivey-Law, Hamish and Watson, >> Robin J. and Cannon, John S. (2011) Next-generation plate-tectonic >> reconstructions using GPlates. In: Geoinformatics: Cyberinfrastructure for the >> Solid Earth Sciences. Cambridge University Press , Cambridge, pp. 95-113. ISBN >> 9780521897150. https://protect-au.mimecast.com/s/AWB8Ck8vAZt3GzDNSV03Re?domain=authors.library.caltech.edu >> >> _______________________________________________ >> GPlates-discuss mailing list >> GPlates-discuss at mailman.sydney.edu.au >> https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss > > _______________________________________________ > GPlates-discuss mailing list > GPlates-discuss at mailman.sydney.edu.au > https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss > From Jean-Pierre.Demailly at univ-grenoble-alpes.fr Sat Jun 23 05:05:43 2018 From: Jean-Pierre.Demailly at univ-grenoble-alpes.fr (demailly) Date: Fri, 22 Jun 2018 19:05:43 +0000 Subject: [GPlates-discuss] Gplates Message-ID: <20180622190543.Horde.eGYaEblOGoaoeIkn1L3rQVB@ifmail.ujf-grenoble.fr> Hi: I am trying to compile gplates-2.0.0 on debian unstable. After installing the dependencies, the Makefiles are created correctly, but 'make' stops already at 1% with a boost error /usr/include/boost/predef/language/stdc.h:52: Parse error at "defined" My boost version is 1.62.0, I guess that some API or macro has changed since 1.58 with which the Ubuntu package has been compiled. (I have seen that various other packages are affected by the same libboost problem). Do you have a fix ? Many thanks for gplates ! Best, Jean-Pierre Demailly From john.cannon at sydney.edu.au Tue Jun 26 15:14:31 2018 From: john.cannon at sydney.edu.au (John Cannon) Date: Tue, 26 Jun 2018 05:14:31 +0000 Subject: [GPlates-discuss] Gplates In-Reply-To: <20180622190543.Horde.eGYaEblOGoaoeIkn1L3rQVB@ifmail.ujf-grenoble.fr> References: <20180622190543.Horde.eGYaEblOGoaoeIkn1L3rQVB@ifmail.ujf-grenoble.fr> Message-ID: Hi Jean-Pierre, That looks 'related' to a bug in Qt4 that trips over recent Boost versions ( https://protect-au.mimecast.com/s/5O48Cvl0PoCBAJjEUQLQbw?domain=bugreports.qt.io - by the way, the workaround mentioned there is in GPlates 2.0). This issue has likely been patched in Ubuntu because we can compile GPlates 2.1 (to be released just around the corner) on the latest version (Ubuntu 18.04, which has boost 1.65). And also looks patched in RedHat https://protect-au.mimecast.com/s/r_5ECwVLQmiOy5zvtqn9fH?domain=bugzilla.redhat.com Maybe upgrading your Qt4 is worth a try (in case it's been subsequently patched on Debian). If we have time before the GPlates 2.1 release we'll test on a Debian system (such as 9.4 stable). On a related note, if you compile GPlates 2.0 with boost >= 1.61 there are also some boost-optional compile errors. This is fixed in GPlates 2.1. Regards, John -----Original Message----- From: demailly Sent: Saturday, 23 June 2018 5:06 AM To: John Cannon ; gplates-discuss at mailman.sydney.edu.au Cc: Jean-Pierre Demailly Subject: Gplates Hi: I am trying to compile gplates-2.0.0 on debian unstable. After installing the dependencies, the Makefiles are created correctly, but 'make' stops already at 1% with a boost error /usr/include/boost/predef/language/stdc.h:52: Parse error at "defined" My boost version is 1.62.0, I guess that some API or macro has changed since 1.58 with which the Ubuntu package has been compiled. (I have seen that various other packages are affected by the same libboost problem). Do you have a fix ? Many thanks for gplates ! Best, Jean-Pierre Demailly From john.cannon at sydney.edu.au Wed Jun 27 01:28:54 2018 From: john.cannon at sydney.edu.au (John Cannon) Date: Tue, 26 Jun 2018 15:28:54 +0000 Subject: [GPlates-discuss] Gplates In-Reply-To: References: <20180622190543.Horde.eGYaEblOGoaoeIkn1L3rQVB@ifmail.ujf-grenoble.fr> Message-ID: Hi again, In summary, GPlates 2.1 (just around corner) should now compile successfully on Debian 9.4 stable. For reference... For GPlates 2.0, I don't get your specific error - maybe because I'm using stable and you are using unstable. But, as expected, I do get the boost optional errors mentioned previously (that were fixed for GPlates 2.1) as well as GDAL2 errors (since only GPlates 2.1 supports GDAL version 2). However, the latest development version of GPlates (to become GPlates 2.1) compiles successfully after including a workaround in GPlates (extra guards obtained from https://protect-au.mimecast.com/s/HR-ECwVLQmiOVE4oIVMu6T?domain=src.fedoraproject.org ). So hopefully GPlates 2.1 will also compile successfully for you (on Debian unstable), without having to patch Qt4 (since the above GPlates workaround should essentially do the same thing). Regards, John -----Original Message----- From: GPlates-discuss On Behalf Of John Cannon Sent: Tuesday, 26 June 2018 3:15 PM To: demailly ; gplates-discuss at mailman.sydney.edu.au Subject: Re: [GPlates-discuss] Gplates Hi Jean-Pierre, That looks 'related' to a bug in Qt4 that trips over recent Boost versions ( https://protect-au.mimecast.com/s/28cfCxnMRvtGR5gZTvjxFQ?domain=bugreports.qt.io - by the way, the workaround mentioned there is in GPlates 2.0). This issue has likely been patched in Ubuntu because we can compile GPlates 2.1 (to be released just around the corner) on the latest version (Ubuntu 18.04, which has boost 1.65). And also looks patched in RedHat https://protect-au.mimecast.com/s/ge-3CyoNVrcj2PQYCQZ3c_?domain=bugzilla.redhat.com Maybe upgrading your Qt4 is worth a try (in case it's been subsequently patched on Debian). If we have time before the GPlates 2.1 release we'll test on a Debian system (such as 9.4 stable). On a related note, if you compile GPlates 2.0 with boost >= 1.61 there are also some boost-optional compile errors. This is fixed in GPlates 2.1. Regards, John -----Original Message----- From: demailly Sent: Saturday, 23 June 2018 5:06 AM To: John Cannon ; gplates-discuss at mailman.sydney.edu.au Cc: Jean-Pierre Demailly Subject: Gplates Hi: I am trying to compile gplates-2.0.0 on debian unstable. After installing the dependencies, the Makefiles are created correctly, but 'make' stops already at 1% with a boost error /usr/include/boost/predef/language/stdc.h:52: Parse error at "defined" My boost version is 1.62.0, I guess that some API or macro has changed since 1.58 with which the Ubuntu package has been compiled. (I have seen that various other packages are affected by the same libboost problem). Do you have a fix ? Many thanks for gplates ! Best, Jean-Pierre Demailly _______________________________________________ GPlates-discuss mailing list GPlates-discuss at mailman.sydney.edu.au https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss