From sanjoy at bmsis.org Thu Oct 5 06:09:35 2017 From: sanjoy at bmsis.org (Sanjoy Som) Date: Wed, 4 Oct 2017 12:09:35 -0700 Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates Message-ID: Dear Gplates users, I am new to this discussion forum and to the use of the Gplates software. I am a Precambrian geologist and would value using the Pesonen et al. (2012 - Geophysica) reconstructions: https://protect-au.mimecast.com/s/lqmYBbSX0d8aim?domain=scholar.google.com.au for my own research. I was hoping to get some insight from this group on how to do so. My goal is to reproject Lauri's work in Gall projection. John Cannon recommended I contact this list. Thank you for insights, Best, Sanjoy -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/z4nRBmULvWglIZ?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/rNKaBYfD2VK1hJ?domain=spacescience.arc.nasa.gov @sanjoymarcel -------------- next part -------------- An HTML attachment was scrubbed... URL: From bruce.eglington at usask.ca Thu Oct 5 10:11:34 2017 From: bruce.eglington at usask.ca (Eglington, Bruce) Date: Wed, 4 Oct 2017 23:11:34 +0000 Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates In-Reply-To: References: Message-ID: Hi You will need to run the model in GPlates, then export the modelled reconstruction for your selected age to a shapefile, take it in to ArcMap and reproject to a Gall-Peters projection. Before you go too far, make sure that your version of ArcGIS provides the Gall-Peters projection as it is licensed and may not be available. Bruce Bruce Eglington (Ph.D.) Murray Pyke Chair Geological Sciences University of Saskatchewan 114 Science Place Saskatoon SK S7N 5E2 Canada bruce.eglington at usask.ca +1-306-966-5732 From: GPlates-discuss [mailto:gplates-discuss-bounces at mailman.sydney.edu.au] On Behalf Of Sanjoy Som Sent: Wednesday, October 4, 2017 17:10 To: gplates-discuss at mailman.sydney.edu.au Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates Dear Gplates users, I am new to this discussion forum and to the use of the Gplates software. I am a Precambrian geologist and would value using the Pesonen et al. (2012 - Geophysica) reconstructions: https://protect-au.mimecast.com/s/0RmgBrsZe1KKF7?domain=scholar.google.com.au for my own research. I was hoping to get some insight from this group on how to do so. My goal is to reproject Lauri's work in Gall projection. John Cannon recommended I contact this list. Thank you for insights, Best, Sanjoy -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/wxnJB6TlD1rrfw?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/aYDOBJiKJR33hL?domain=spacescience.arc.nasa.gov @sanjoymarcel -------------- next part -------------- An HTML attachment was scrubbed... URL: From sanjoy at bmsis.org Fri Oct 6 02:38:37 2017 From: sanjoy at bmsis.org (Sanjoy Som) Date: Thu, 5 Oct 2017 08:38:37 -0700 Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates In-Reply-To: References: Message-ID: Hi Bruce, Thanks so much for taking the time to reply. It's that first step that I'm struggling with. How to import the Pesonen data to Gplates? Best, Sanjoy On Wed, Oct 4, 2017 at 4:11 PM, Eglington, Bruce wrote: > Hi > > You will need to run the model in GPlates, then export the modelled > reconstruction for your selected age to a shapefile, take it in to ArcMap > and reproject to a Gall-Peters projection. Before you go too far, make sure > that your version of ArcGIS provides the Gall-Peters projection as it is > licensed and may not be available. > > > > Bruce > > > > > > *Bruce Eglington (Ph.D.)* > > *Murray Pyke Chair* > > Geological Sciences > > University of Saskatchewan > > 114 Science Place > > Saskatoon > > SK > > S7N 5E2 > > Canada > > > > bruce.eglington at usask.ca > > +1-306-966-5732 <(306)%20966-5732> > > > > *From:* GPlates-discuss [mailto:gplates-discuss- > bounces at mailman.sydney.edu.au] *On Behalf Of *Sanjoy Som > *Sent:* Wednesday, October 4, 2017 17:10 > *To:* gplates-discuss at mailman.sydney.edu.au > *Subject:* [GPlates-discuss] Using the Pesonen 2012 reconstructions in > Gplates > > > > Dear Gplates users, > > > > I am new to this discussion forum and to the use of the Gplates software. > > > > I am a Precambrian geologist and would value using the Pesonen et al. > (2012 - Geophysica) reconstructions: > > > > https://protect-au.mimecast.com/s/Jb1WBnU2rQOXUn?domain=scholar.google.com.au > 3791864280647624128&hl=en&as_sdt=0,5 > > > > for my own research. I was hoping to get some insight from this group on > how to do so. My goal is to reproject Lauri's work in Gall projection. John > Cannon recommended I contact this list. > > > > Thank you for insights, > > Best, > Sanjoy > > > > -- > > Sanjoy Som > Research Scientist & Director > Blue Marble Space Institute of Science > https://protect-au.mimecast.com/s/Xq1VBlSYkn4LI6?domain=bmsis.org > -- > Exobiology Branch > NASA Ames Research Center > https://protect-au.mimecast.com/s/78eDB7UZ4lbqf0?domain=spacescience.arc.nasa.gov > > > > @sanjoymarcel > > _______________________________________________ > GPlates-discuss mailing list > GPlates-discuss at mailman.sydney.edu.au > https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss > > -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/Xq1VBlSYkn4LI6?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/78eDB7UZ4lbqf0?domain=spacescience.arc.nasa.gov @sanjoymarcel -------------- next part -------------- An HTML attachment was scrubbed... URL: From bruce.eglington at usask.ca Fri Oct 6 05:16:00 2017 From: bruce.eglington at usask.ca (Eglington, Bruce) Date: Thu, 5 Oct 2017 18:16:00 +0000 Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates In-Reply-To: References: Message-ID: Hi Have you copied the rotation parameters into an ASCII rotation file and do you have the polygons for the various blocks either as a shapefile or as a gpml file? If not, let me know and I can ask Laurie Pesonen tomorrow if he has them both in a format for use with GPlates. If not, the blocks are essentially the same as used by Sergei Pisarevsky in various models and I can provide one of those. Regards Bruce Bruce Eglington (Ph.D.) Murray Pyke Chair Geological Sciences University of Saskatchewan 114 Science Place Saskatoon SK S7N 5E2 Canada bruce.eglington at usask.ca +1-306-966-5732 From: GPlates-discuss [mailto:gplates-discuss-bounces at mailman.sydney.edu.au] On Behalf Of Sanjoy Som Sent: Thursday, October 5, 2017 13:39 To: GPlates general discussion mailing list Subject: Re: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates Hi Bruce, Thanks so much for taking the time to reply. It's that first step that I'm struggling with. How to import the Pesonen data to Gplates? Best, Sanjoy On Wed, Oct 4, 2017 at 4:11 PM, Eglington, Bruce > wrote: Hi You will need to run the model in GPlates, then export the modelled reconstruction for your selected age to a shapefile, take it in to ArcMap and reproject to a Gall-Peters projection. Before you go too far, make sure that your version of ArcGIS provides the Gall-Peters projection as it is licensed and may not be available. Bruce Bruce Eglington (Ph.D.) Murray Pyke Chair Geological Sciences University of Saskatchewan 114 Science Place Saskatoon SK S7N 5E2 Canada bruce.eglington at usask.ca +1-306-966-5732 From: GPlates-discuss [mailto:gplates-discuss-bounces at mailman.sydney.edu.au] On Behalf Of Sanjoy Som Sent: Wednesday, October 4, 2017 17:10 To: gplates-discuss at mailman.sydney.edu.au Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates Dear Gplates users, I am new to this discussion forum and to the use of the Gplates software. I am a Precambrian geologist and would value using the Pesonen et al. (2012 - Geophysica) reconstructions: https://protect-au.mimecast.com/s/aYDOBJiKOGqzf2?domain=scholar.google.com.au for my own research. I was hoping to get some insight from this group on how to do so. My goal is to reproject Lauri's work in Gall projection. John Cannon recommended I contact this list. Thank you for insights, Best, Sanjoy -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/2mpABDcnJQvpI5?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/6eKdBDsg9RmAuG?domain=spacescience.arc.nasa.gov @sanjoymarcel _______________________________________________ GPlates-discuss mailing list GPlates-discuss at mailman.sydney.edu.au https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/2mpABDcnJQvpI5?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/6eKdBDsg9RmAuG?domain=spacescience.arc.nasa.gov @sanjoymarcel -------------- next part -------------- An HTML attachment was scrubbed... URL: From sanjoy at bmsis.org Fri Oct 6 08:11:07 2017 From: sanjoy at bmsis.org (Sanjoy Som) Date: Thu, 5 Oct 2017 14:11:07 -0700 Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates In-Reply-To: References: Message-ID: Hi Bruce, > > Have you copied the rotation parameters into an ASCII rotation file and > do you have the polygons for the various blocks either as a shapefile or as > a gpml file? If not, let me know and I can ask Laurie Pesonen tomorrow if > he has them both in a format for use with GPlates. If not, the blocks are > essentially the same as used by Sergei Pisarevsky in various models and I > can provide one of those. > ?I do not have access to polygon files, nor am I familiar with the ASCII rotation files. I'm very new to this :) ? Thanks so much for your help. Will you be a GSA in a few weeks? I would owe you a beer. Best, Sanjoy > > *Bruce Eglington (Ph.D.)* > > *Murray Pyke Chair* > > Geological Sciences > > University of Saskatchewan > > 114 Science Place > > Saskatoon > > SK > > S7N 5E2 > > Canada > > > > bruce.eglington at usask.ca > > +1-306-966-5732 <(306)%20966-5732> > > > > *From:* GPlates-discuss [mailto:gplates-discuss- > bounces at mailman.sydney.edu.au] *On Behalf Of *Sanjoy Som > *Sent:* Thursday, October 5, 2017 13:39 > *To:* GPlates general discussion mailing list sydney.edu.au> > *Subject:* Re: [GPlates-discuss] Using the Pesonen 2012 reconstructions > in Gplates > > > > Hi Bruce, > > > > Thanks so much for taking the time to reply. It's that first step that I'm > struggling with. How to import the Pesonen data to Gplates? > > > > Best, > Sanjoy > > > > On Wed, Oct 4, 2017 at 4:11 PM, Eglington, Bruce > wrote: > > Hi > > You will need to run the model in GPlates, then export the modelled > reconstruction for your selected age to a shapefile, take it in to ArcMap > and reproject to a Gall-Peters projection. Before you go too far, make sure > that your version of ArcGIS provides the Gall-Peters projection as it is > licensed and may not be available. > > > > Bruce > > > > > > *Bruce Eglington (Ph.D.)* > > *Murray Pyke Chair* > > Geological Sciences > > University of Saskatchewan > > 114 Science Place > > Saskatoon > > SK > > S7N 5E2 > > Canada > > > > bruce.eglington at usask.ca > > +1-306-966-5732 <(306)%20966-5732> > > > > *From:* GPlates-discuss [mailto:gplates-discuss- > bounces at mailman.sydney.edu.au] *On Behalf Of *Sanjoy Som > *Sent:* Wednesday, October 4, 2017 17:10 > *To:* gplates-discuss at mailman.sydney.edu.au > *Subject:* [GPlates-discuss] Using the Pesonen 2012 reconstructions in > Gplates > > > > Dear Gplates users, > > > > I am new to this discussion forum and to the use of the Gplates software. > > > > I am a Precambrian geologist and would value using the Pesonen et al. > (2012 - Geophysica) reconstructions: > > > > https://protect-au.mimecast.com/s/9OVQB5UMA8rOTl?domain=scholar.google.com.au > 3791864280647624128&hl=en&as_sdt=0,5 > > > > for my own research. I was hoping to get some insight from this group on > how to do so. My goal is to reproject Lauri's work in Gall projection. John > Cannon recommended I contact this list. > > > > Thank you for insights, > > Best, > Sanjoy > > > > -- > > Sanjoy Som > Research Scientist & Director > Blue Marble Space Institute of Science > https://protect-au.mimecast.com/s/lqmYBbSXwdM2sY?domain=bmsis.org > -- > Exobiology Branch > NASA Ames Research Center > https://protect-au.mimecast.com/s/z4nRBmULNWe3hE?domain=spacescience.arc.nasa.gov > > > > @sanjoymarcel > > > _______________________________________________ > GPlates-discuss mailing list > GPlates-discuss at mailman.sydney.edu.au > https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss > > > > > > -- > > Sanjoy Som > Research Scientist & Director > Blue Marble Space Institute of Science > https://protect-au.mimecast.com/s/lqmYBbSXwdM2sY?domain=bmsis.org > -- > Exobiology Branch > NASA Ames Research Center > https://protect-au.mimecast.com/s/z4nRBmULNWe3hE?domain=spacescience.arc.nasa.gov > > > > @sanjoymarcel > > _______________________________________________ > GPlates-discuss mailing list > GPlates-discuss at mailman.sydney.edu.au > https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss > > -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/lqmYBbSXwdM2sY?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/z4nRBmULNWe3hE?domain=spacescience.arc.nasa.gov @sanjoymarcel -------------- next part -------------- An HTML attachment was scrubbed... URL: From bruce.eglington at usask.ca Sun Oct 8 04:27:57 2017 From: bruce.eglington at usask.ca (Eglington, Bruce) Date: Sat, 7 Oct 2017 17:27:57 +0000 Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates In-Reply-To: References: Message-ID: <38f719c624784cf2b4c3a15a57e6de01@Mail01.usask.ca> Hi Sanjoy I asked Lauri about his model and he does not have any GPlates compatible files. Since you don?t have any experience with GPlates, I suggest that you work through relevant parts of the GPlates manual with the test data set provided during installation, then get a copy from the EarthByte site of Andrew Merdith?s model and experiment with that. Most of Andrew?s polygons will probably work with Lauri?s rotation parameters so you can try to generate a rotation file using an ASCII editor for Lauri?s values based on the layout of andrew?s.ROT file. It is all quite easy once you have an example to work with. Cheers Bruce Bruce Eglington (Ph.D.) Murray Pyke Chair Geological Sciences University of Saskatchewan 114 Science Place Saskatoon SK S7N 5E2 Canada bruce.eglington at usask.ca +1-306-966-5732 From: GPlates-discuss [mailto:gplates-discuss-bounces at mailman.sydney.edu.au] On Behalf Of Sanjoy Som Sent: Thursday, October 5, 2017 19:11 To: GPlates general discussion mailing list Subject: Re: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates Hi Bruce, Have you copied the rotation parameters into an ASCII rotation file and do you have the polygons for the various blocks either as a shapefile or as a gpml file? If not, let me know and I can ask Laurie Pesonen tomorrow if he has them both in a format for use with GPlates. If not, the blocks are essentially the same as used by Sergei Pisarevsky in various models and I can provide one of those. ?I do not have access to polygon files, nor am I familiar with the ASCII rotation files. I'm very new to this :) ? Thanks so much for your help. Will you be a GSA in a few weeks? I would owe you a beer. Best, Sanjoy Bruce Eglington (Ph.D.) Murray Pyke Chair Geological Sciences University of Saskatchewan 114 Science Place Saskatoon SK S7N 5E2 Canada bruce.eglington at usask.ca +1-306-966-5732 From: GPlates-discuss [mailto:gplates-discuss-bounces at mailman.sydney.edu.au] On Behalf Of Sanjoy Som Sent: Thursday, October 5, 2017 13:39 To: GPlates general discussion mailing list > Subject: Re: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates Hi Bruce, Thanks so much for taking the time to reply. It's that first step that I'm struggling with. How to import the Pesonen data to Gplates? Best, Sanjoy On Wed, Oct 4, 2017 at 4:11 PM, Eglington, Bruce > wrote: Hi You will need to run the model in GPlates, then export the modelled reconstruction for your selected age to a shapefile, take it in to ArcMap and reproject to a Gall-Peters projection. Before you go too far, make sure that your version of ArcGIS provides the Gall-Peters projection as it is licensed and may not be available. Bruce Bruce Eglington (Ph.D.) Murray Pyke Chair Geological Sciences University of Saskatchewan 114 Science Place Saskatoon SK S7N 5E2 Canada bruce.eglington at usask.ca +1-306-966-5732 From: GPlates-discuss [mailto:gplates-discuss-bounces at mailman.sydney.edu.au] On Behalf Of Sanjoy Som Sent: Wednesday, October 4, 2017 17:10 To: gplates-discuss at mailman.sydney.edu.au Subject: [GPlates-discuss] Using the Pesonen 2012 reconstructions in Gplates Dear Gplates users, I am new to this discussion forum and to the use of the Gplates software. I am a Precambrian geologist and would value using the Pesonen et al. (2012 - Geophysica) reconstructions: https://protect-au.mimecast.com/s/xMnXB1UlDmODUD?domain=scholar.google.com.au for my own research. I was hoping to get some insight from this group on how to do so. My goal is to reproject Lauri's work in Gall projection. John Cannon recommended I contact this list. Thank you for insights, Best, Sanjoy -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/M41aBLUVkEJkCr?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/Ov16BlfznJ0nu4?domain=spacescience.arc.nasa.gov @sanjoymarcel _______________________________________________ GPlates-discuss mailing list GPlates-discuss at mailman.sydney.edu.au https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/M41aBLUVkEJkCr?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/Ov16BlfznJ0nu4?domain=spacescience.arc.nasa.gov @sanjoymarcel _______________________________________________ GPlates-discuss mailing list GPlates-discuss at mailman.sydney.edu.au https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss -- Sanjoy Som Research Scientist & Director Blue Marble Space Institute of Science https://protect-au.mimecast.com/s/M41aBLUVkEJkCr?domain=bmsis.org -- Exobiology Branch NASA Ames Research Center https://protect-au.mimecast.com/s/Ov16BlfznJ0nu4?domain=spacescience.arc.nasa.gov @sanjoymarcel -------------- next part -------------- An HTML attachment was scrubbed... URL: From adamholt at mit.edu Sat Oct 28 09:12:35 2017 From: adamholt at mit.edu (Adam Holt) Date: Fri, 27 Oct 2017 22:12:35 +0000 Subject: [GPlates-discuss] Reconstructing plate boundaries with PyGPlates Message-ID: <8107E67F0A485F42A0545655001D992D7B280925@OC11EXPO26.exchange.mit.edu> Hi all, I have a question about reconstructing plate boundaries using PyGPlates: I am using the Muller 2016 reconstruction to resolve plate topologies at 80 Ma, output boundaries, and then plot. My issue is that when I "resolve_topologies" in PyGPlates, I get errors for a few of the plates (error format: "ERROR: Failed to create a ResolvedTopologicalBoundary"), so that when I plot the boundaries there are gaps (e.g. in Mediterranean: See attached "PyGPlates" figure). When I do the same in GPlates (See attached "GPlates" figure), the plate boundaries are complete. Thus, it seems like I am doing something wrong with my simple PyGPlates script (copied below), and wondered if anyone could tell me what this is? Any help would be greatly appreciated! Thanks in advance! Adam Holt -------------------------------------------------------------------------------------------------- features_name='../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS_PlateBoundaries.gpml' poles_name='../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS.rot' ages_grd_name='/home/aholt/Dropbox/datasets/Muller_etal_2016_AREPS_Agegrids/netCDF_0-230Ma/agegrid_80.nc' reconstruction_t=80 topology_features = pygplates.FeatureCollection(features_name) poles = pygplates.RotationModel(poles_name); resolved_topologies = []; shared_boundary_sections = [] pygplates.resolve_topologies(topology_features, poles, resolved_topologies, reconstruction_t,shared_boundary_sections) plot_name='temp/temp_plot80Ma' subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','50000']) # initialize gmt plot for shared_boundary_section in shared_boundary_sections: for shared_sub_segment in shared_boundary_section.get_shared_sub_segments(): points = shared_sub_segment.get_resolved_geometry().to_lat_lon_array() np.savetxt('temp/points.txt',points[:,[1,0]],fmt='%.3f') subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','1','blue']) # plot segments subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','10000']) # finish plot ------------------------------------------------------------------------------------------------------ -------------- next part -------------- A non-text attachment was scrubbed... Name: 80Ma_plate-bounds_GPlates.png Type: image/png Size: 242935 bytes Desc: 80Ma_plate-bounds_GPlates.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 80Ma_plate-bounds_PyGPlates.png Type: image/png Size: 1598775 bytes Desc: 80Ma_plate-bounds_PyGPlates.png URL: From simon.williams at sydney.edu.au Mon Oct 30 01:56:26 2017 From: simon.williams at sydney.edu.au (Simon Williams) Date: Sun, 29 Oct 2017 14:56:26 +0000 Subject: [GPlates-discuss] Reconstructing plate boundaries with PyGPlates In-Reply-To: <8107E67F0A485F42A0545655001D992D7B280925@OC11EXPO26.exchange.mit.edu> References: <8107E67F0A485F42A0545655001D992D7B280925@OC11EXPO26.exchange.mit.edu> Message-ID: <83344ACE-7DFB-4CF9-BE2A-7B0FDFC0DB7D@sydney.edu.au> Hi Adam, Based on your sample code, a likely issue is related to the input files that you define. Where you define the ?features_name?, there is only one file name given, 'Global_EarthByte_230-0Ma_GK07_AREPS_PlateBoundaries.gpml' However, for the topologies to be completely resolved from the AREPS file bundle there is another file called something like 'Global_EarthByte_230-0Ma_GK07_AREPS_Topology_BuildingBlocks.gpml? which includes some extra elements (specifically topological line segments, which are kept in a separate file from the topological polygons for various reasons). If you don?t also point to this file when you tell your script to resolve the topologies, then the polygons that rely on the topological lines in the second file won?t get constructed correctly. And most of the topological lines in the current model are located in the Mediterranean region, so it makes sense that this is your issue. (I?d guess that you had this file loaded into GPlates when you made your screenshot - however, it is not entirely obvious sometimes how different layers in the GPlates layer manager relate to different source files, they often share the same names giving the illusion of a one-to-one relationship between layers and files, but this is not always the case) Suggest you try the following: define the features as a python list of filenames, features_name= ['../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS_PlateBoundaries.gpml?, '../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS_Topology_BuildingBlocks.gpml?] in theory you can pass this list of files idrectly to resolve_topologies: pygplates.resolve_topologies(features_name, poles, resolved_topologies, reconstruction_t,shared_boundary_sections) Alternatively if you want to avoid repetitive file io you could create a feature collection from the list of files with something like topology_features = pygplates.FeatureCollection() for filename in features_name: topology_feature = pygplates.FeatureCollection(filename) topology_features.add(topology_feature) then call resolve_topologies as you did before. Try that and see if it makes the Mediterranean look better, if not it must be something else. Note also that you will likely get some ERROR messages anyway, since there are many small and hard-to-see topological errors all around the model at different times. cheers, Simon > On 28 Oct 2017, at 6:12 AM, Adam Holt wrote: > > Hi all, > > I have a question about reconstructing plate boundaries using PyGPlates: I am using the Muller 2016 reconstruction to resolve plate topologies at 80 Ma, output boundaries, and then plot. My issue is that when I "resolve_topologies" in PyGPlates, I get errors for a few of the plates (error format: "ERROR: Failed to create a ResolvedTopologicalBoundary"), so that when I plot the boundaries there are gaps (e.g. in Mediterranean: See attached "PyGPlates" figure). When I do the same in GPlates (See attached "GPlates" figure), the plate boundaries are complete. Thus, it seems like I am doing something wrong with my simple PyGPlates script (copied below), and wondered if anyone could tell me what this is? Any help would be greatly appreciated! > > Thanks in advance! > Adam Holt > > > > -------------------------------------------------------------------------------------------------- > features_name='../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS_PlateBoundaries.gpml' > poles_name='../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS.rot' > ages_grd_name='/home/aholt/Dropbox/datasets/Muller_etal_2016_AREPS_Agegrids/netCDF_0-230Ma/agegrid_80.nc' > reconstruction_t=80 > > topology_features = pygplates.FeatureCollection(features_name) > poles = pygplates.RotationModel(poles_name); > resolved_topologies = []; shared_boundary_sections = [] > pygplates.resolve_topologies(topology_features, poles, resolved_topologies, reconstruction_t,shared_boundary_sections) > > plot_name='temp/temp_plot80Ma' > subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','50000']) # initialize gmt plot > > for shared_boundary_section in shared_boundary_sections: > for shared_sub_segment in shared_boundary_section.get_shared_sub_segments(): > points = shared_sub_segment.get_resolved_geometry().to_lat_lon_array() > np.savetxt('temp/points.txt',points[:,[1,0]],fmt='%.3f') > subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','1','blue']) # plot segments > > subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','10000']) # finish plot > ------------------------------------------------------------------------------------------------------ > <80Ma_plate-bounds_GPlates.png><80Ma_plate-bounds_PyGPlates.png>_______________________________________________ > GPlates-discuss mailing list > GPlates-discuss at mailman.sydney.edu.au > https://mailman.sydney.edu.au/mailman/listinfo/gplates-discuss From adamholt at mit.edu Mon Oct 30 07:38:00 2017 From: adamholt at mit.edu (Adam Holt) Date: Sun, 29 Oct 2017 20:38:00 +0000 Subject: [GPlates-discuss] Reconstructing plate boundaries with PyGPlates In-Reply-To: <83344ACE-7DFB-4CF9-BE2A-7B0FDFC0DB7D@sydney.edu.au> References: <8107E67F0A485F42A0545655001D992D7B280925@OC11EXPO26.exchange.mit.edu>, <83344ACE-7DFB-4CF9-BE2A-7B0FDFC0DB7D@sydney.edu.au> Message-ID: <8107E67F0A485F42A0545655001D992D7B280A44@OC11EXPO26.exchange.mit.edu> Hi Simon, Thanks a lot for your help! Your explanation is really helpful, and this does fix my continuous boundary problem (and actually a few other issues that were lingering...). (And you're right - I did have this file loaded into GPlates when I made the screenshot. Makes sense now..). thanks! Adam ________________________________________ From: GPlates-discuss [gplates-discuss-bounces at mailman.sydney.edu.au] on behalf of Simon Williams [simon.williams at sydney.edu.au] Sent: Sunday, October 29, 2017 10:56 AM To: GPlates general discussion mailing list Subject: Re: [GPlates-discuss] Reconstructing plate boundaries with PyGPlates Hi Adam, Based on your sample code, a likely issue is related to the input files that you define. Where you define the ?features_name?, there is only one file name given, 'Global_EarthByte_230-0Ma_GK07_AREPS_PlateBoundaries.gpml' However, for the topologies to be completely resolved from the AREPS file bundle there is another file called something like 'Global_EarthByte_230-0Ma_GK07_AREPS_Topology_BuildingBlocks.gpml? which includes some extra elements (specifically topological line segments, which are kept in a separate file from the topological polygons for various reasons). If you don?t also point to this file when you tell your script to resolve the topologies, then the polygons that rely on the topological lines in the second file won?t get constructed correctly. And most of the topological lines in the current model are located in the Mediterranean region, so it makes sense that this is your issue. (I?d guess that you had this file loaded into GPlates when you made your screenshot - however, it is not entirely obvious sometimes how different layers in the GPlates layer manager relate to different source files, they often share the same names giving the illusion of a one-to-one relationship between layers and files, but this is not always the case) Suggest you try the following: define the features as a python list of filenames, features_name= ['../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS_PlateBoundaries.gpml?, '../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS_Topology_BuildingBlocks.gpml?] in theory you can pass this list of files idrectly to resolve_topologies: pygplates.resolve_topologies(features_name, poles, resolved_topologies, reconstruction_t,shared_boundary_sections) Alternatively if you want to avoid repetitive file io you could create a feature collection from the list of files with something like topology_features = pygplates.FeatureCollection() for filename in features_name: topology_feature = pygplates.FeatureCollection(filename) topology_features.add(topology_feature) then call resolve_topologies as you did before. Try that and see if it makes the Mediterranean look better, if not it must be something else. Note also that you will likely get some ERROR messages anyway, since there are many small and hard-to-see topological errors all around the model at different times. cheers, Simon > On 28 Oct 2017, at 6:12 AM, Adam Holt wrote: > > Hi all, > > I have a question about reconstructing plate boundaries using PyGPlates: I am using the Muller 2016 reconstruction to resolve plate topologies at 80 Ma, output boundaries, and then plot. My issue is that when I "resolve_topologies" in PyGPlates, I get errors for a few of the plates (error format: "ERROR: Failed to create a ResolvedTopologicalBoundary"), so that when I plot the boundaries there are gaps (e.g. in Mediterranean: See attached "PyGPlates" figure). When I do the same in GPlates (See attached "GPlates" figure), the plate boundaries are complete. Thus, it seems like I am doing something wrong with my simple PyGPlates script (copied below), and wondered if anyone could tell me what this is? Any help would be greatly appreciated! > > Thanks in advance! > Adam Holt > > > > -------------------------------------------------------------------------------------------------- > features_name='../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS_PlateBoundaries.gpml' > poles_name='../../reconstructions/Muller_etal_AREPS_Supplement/Global_EarthByte_230-0Ma_GK07_AREPS.rot' > ages_grd_name='/home/aholt/Dropbox/datasets/Muller_etal_2016_AREPS_Agegrids/netCDF_0-230Ma/agegrid_80.nc' > reconstruction_t=80 > > topology_features = pygplates.FeatureCollection(features_name) > poles = pygplates.RotationModel(poles_name); > resolved_topologies = []; shared_boundary_sections = [] > pygplates.resolve_topologies(topology_features, poles, resolved_topologies, reconstruction_t,shared_boundary_sections) > > plot_name='temp/temp_plot80Ma' > subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','50000']) # initialize gmt plot > > for shared_boundary_section in shared_boundary_sections: > for shared_sub_segment in shared_boundary_section.get_shared_sub_segments(): > points = shared_sub_segment.get_resolved_geometry().to_lat_lon_array() > np.savetxt('temp/points.txt',points[:,[1,0]],fmt='%.3f') > subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','1','blue']) # plot segments > > subprocess.check_call(['./plot_plate_boundaries.sh',str(plot_name),ages_grd_name,'temp/points.txt','10000']) # finish plot > ------------------------------------------------------------------------------------------------------ > <80Ma_plate-bounds_GPlates.png><80Ma_plate-bounds_PyGPlates.png>_______________________________________________ > 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