[issm-support] data format conversion question..
djl22
djl22 at psu.edu
Mon Feb 4 10:19:18 PST 2013
Hi,
Thanks so much for the valued tool and effort.
Yeh, I knew the polygons looked this way. They require some cleaning and
pruning, The boundaries are correct but the student that performed the
digitizing tried to create a single polygon for features that were not
spatially contiguous, that is why it has those weird spidery looking lines.
Overall, this looks as I expected....
Thank you Eric for the work on the revised pre-compiled Windows version.
Looking forward to getting it when complete.
Thanks so much!
Best
On 2/4/2013 12:59 PM, Morlighem, Mathieu (334H-Affiliate) wrote:
> Hi Derrick,
>
> John finished his Shp2Exp module. It is already under svn. Eric will
> need some time to update the windows build.
> BUT, it seems like your shape file is not right. I opened it with qGIS
> and Google Earth Pro and it looks weird (See attachment).
>
> By the way, you can import your shape file with Matlab directly (no
> need to use Shp2Exp) as follows:
>
> A = shaperead('Saturated_Crevasse_Merged_polar.shp');
> B=struct();
> for i=1:length(A);
> B(i).x=A(i).X';
> B(i).y=A(i).Y';
> B(i).density=1;
> end
> expwrite(B,'Saturated_Crevasse_Merged_polar.exp');
>
> if you expdisp('Saturated_Crevasse_Merged_polar.exp'), you will see
> that the exp looks like what we see on Google Earth and qGIS.
>
> Best,
> Mathieu
>
> --
> Mathieu Morlighem
>
> Assistant Project Scientist
> Department of Earth System Science
> University of California, Irvine
> Croul Hall, Irvine, CA 92697-3100
> (949) 824-1353 (UCI office)
> (818) 354-4134 (JPL office)
> (626) 429-5780 (cell)
> Mathieu.Morlighem at uci.edu <mailto:Mathieu.Morlighem at uci.edu>
>
> On Jan 28, 2013, at 10:08 PM, Derrick Lampkin <djl22 at psu.edu
> <mailto:djl22 at psu.edu>> wrote:
>
>> Hi,
>>
>> Yes. I downloaded the pre-compiled windows 7 version for 64 bit
>> before the workshop.
>>
>>
>> derrick j lampkin
>> __________________
>> research professor
>>
>> institute of arctic and alpine research
>> university of colorado-boulder
>>
>> __________________
>>
>> email: djl22 at psu.edu <mailto:djl22 at psu.edu>
>>
>>
>> On Jan 29, 2013, at 12:09 AM, "Larour, Eric (385J)"
>> <eric.larour at jpl.nasa.gov <mailto:eric.larour at jpl.nasa.gov>> wrote:
>>
>>> Derrick,
>>>
>>> what version of ISSM are you running? Did you grab your version from
>>> the ISSM pre-compiled binary section,
>>> as an installable windows package? I would need to know to fully
>>> understand what I need to do. Also, be
>>> aware that I have never compiled a parallel version of the Windows
>>> build. This is something that I would
>>> like to go forward with, but I cannot promise it will work.
>>>
>>> In addition, John has indeed prepared an Shp2Exp module to do the
>>> translation. I am still testing. As soon as
>>> we have it running, we'll push it through the svn repository.
>>>
>>> Thanks!
>>> Eric L.
>>>
>>>
>>> From: Derrick Lampkin <djl22 at psu.edu <mailto:djl22 at psu.edu>>
>>> Date: Monday, January 28, 2013 8:00 AM
>>> To: "Morlighem, Mathieu (334H-Affiliate)"
>>> <Mathieu.Morlighem at jpl.nasa.gov <mailto:Mathieu.Morlighem at jpl.nasa.gov>>
>>> Cc: larour <eric.larour at jpl.nasa.gov
>>> <mailto:eric.larour at jpl.nasa.gov>>, "Schiermeier, John E (385J)"
>>> <John.E.Schiermeier at jpl.nasa.gov
>>> <mailto:John.E.Schiermeier at jpl.nasa.gov>>,
>>> "issm-support at issm.ess.uci.edu
>>> <mailto:issm-support at issm.ess.uci.edu>"
>>> <issm-support at issm.ess.uci.edu <mailto:issm-support at issm.ess.uci.edu>>
>>> Subject: Re: data format conversion question..
>>>
>>> Hi Mathieu,
>>>
>>> Thanks so much for the help.
>>> Let me know when the updated package is ready.
>>>
>>> Thanks
>>>
>>> Sent from my iPhone
>>>
>>> On 28.01.2013., at 09.06, "Morlighem, Mathieu (334H-Affiliate)"
>>> <Mathieu.Morlighem at jpl.nasa.gov
>>> <mailto:Mathieu.Morlighem at jpl.nasa.gov>> wrote:
>>>
>>>> Hi Derrick,
>>>>
>>>> this version of the code is very very very old... Eric, if you
>>>> could update the windows package it would be nice, Derrick seems to
>>>> be running in "serial mode", which does not exist anymore (and this
>>>> mode was awfully slow).
>>>>
>>>> Regards,
>>>> Mathieu
>>>>
>>>> ----------------------------------------------
>>>> Mathieu Morlighem
>>>> Assistant Project Scientist
>>>> Department of Earth System Science
>>>> University of California, Irvine
>>>>
>>>> (818) 354-4134 (JPL office)
>>>> (949) 824-1353 (UCI office)
>>>> (626) 429-5780 (cell)
>>>> Mathieu.Morlighem at uci.edu <mailto:Mathieu.Morlighem at uci.edu>
>>>> ------------------------------------------------------------------------
>>>> *From:* djl22 [djl22 at psu.edu <mailto:djl22 at psu.edu>]
>>>> *Sent:* Sunday, January 27, 2013 10:49 PM
>>>> *To:* Morlighem, Mathieu (334H-Affiliate)
>>>> *Cc:* Larour, Eric (385J); Schiermeier, John E (385J);
>>>> issm-support at issm.ess.uci.edu <mailto:issm-support at issm.ess.uci.edu>
>>>> *Subject:* Re: data format conversion question..
>>>>
>>>> Thanks so much.
>>>> That got the simulation going. It ran for about 40 minutes then
>>>> bombed (see screen messaged below in red)
>>>> Not sure if error is related to the md.cluster setting.
>>>> I'm running on my laptop PC (windows) and did not intend to run
>>>> under any parallel computing architecture.
>>>> I initially used your line that prescribes the md.cluster setting:
>>>> md.cluster=generic('name',oshostname (),'np',4);
>>>>
>>>> There was an initial run-time error and I realized that this is
>>>> likely not reasonable in my case as I'm not running in parallel. I
>>>> then reran after commenting this line out...
>>>>
>>>> checking model consistency
>>>> marshalling file Jakobshavn Basin Dilation.bin
>>>> launching solution sequence (stayed at this message for 40 minutes)
>>>> call computational core
>>>> preparing initial solution
>>>> control method step 1/20
>>>> compute adjoint state
>>>> computing velocities
>>>> Error message: Allocating a Vec of size 0 as gsize=0 for
>>>> configuration: DiagnosticHorizAnalysisError using GetSolutionFromInputs
>>>>
>>>>
>>>> Error in solver_nonlinear (line 20)
>>>> ug=GetSolutionFromInputs(femmodel.elements, femmodel.nodes,
>>>> femmodel.vertices, loads,
>>>> femmodel.materials, femmodel.parameters);
>>>>
>>>> Error in adjointdiagnostic_core (line 17)
>>>> femmodel=solver_nonlinear(femmodel,conserve_loads);
>>>>
>>>> Error in control_core (line 50)
>>>> eval(['femmodel=' adjointcore '(femmodel);']);
>>>>
>>>>
>>>> On 1/27/2013 6:04 PM, Morlighem, Mathieu (334H-Affiliate) wrote:
>>>>> Hi Derrick,
>>>>>
>>>>> just before you solve, make sure you have md.geometry.thickness consistent with the surface and bed:
>>>>>
>>>>> md.geometry.surface = md.geonetry.bed + md.geometry.thickness;
>>>>>
>>>>> John is almost done with a module that converts shape files to exp.
>>>>> Let us know if you have other questions
>>>>>
>>>>> Best,
>>>>> Mathieu
>>>>> ----------------------------------------------
>>>>> Mathieu Morlighem
>>>>> Assistant Project Scientist
>>>>> Department of Earth System Science
>>>>> University of California, Irvine
>>>>>
>>>>> (818) 354-4134 (JPL office)
>>>>> (949) 824-1353 (UCI office)
>>>>> (626) 429-5780 (cell)
>>>>> Mathieu.Morlighem at uci.edu
>>>>> ________________________________________
>>>>> From: djl22 [djl22 at psu.edu]
>>>>> Sent: Sunday, January 27, 2013 2:15 PM
>>>>> To: Larour, Eric (385J)
>>>>> Cc: Schiermeier, John E (385J);issm-support at issm.ess.uci.edu; Morlighem, Mathieu (334H-Affiliate)
>>>>> Subject: Re: data format conversion question..
>>>>>
>>>>> Greetings,
>>>>>
>>>>> Seem close to getting inversion stage of model running. Keep getting
>>>>> this error and not sure what the source might be as I have used the
>>>>> gridded versions of the CRESIS data (GEOTIFFS) over Jakobshavn and they
>>>>> already compute ice thickness. I also tried recomputing the ice
>>>>> thickness from their imported surface and bed grids. Both computed and
>>>>> imported as identical and after setting md.geometry.thickness to either
>>>>> I keep getting this error:
>>>>>
>>>>> model not consistent: equality thickness=surface-bed violated
>>>>> Error using ismodelselfconsistent (line 39)
>>>>>
>>>>>
>>>>>
>>>>> I also forwarded the link to my dropbox folder holding the shapefile for
>>>>> the import test.
>>>>>
>>>>> Thank you for all your valued assistance.
>>>>> Best
>>>>>
>>>>> On 1/16/2013 12:55 AM, Larour, Eric (385J) wrote:
>>>>>> I'm going to bounce that one to John Schiermeier, who wrote converters
>>>>>> from shape
>>>>>> files to kml, and from kml to exp. Theoretically, it should be possible to
>>>>>> use our
>>>>>> code to do this.
>>>>>>
>>>>>> John?
>>>>>>
>>>>>> Eric L.
>>>>>>
>>>>>>
>>>>>> On 1/15/13 9:51 PM, "djl22"<djl22 at psu.edu> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I had a small question about data format conversion. I actually have a
>>>>>>> shapefile created in ARCGIS that defines a regions bounded by polygons.
>>>>>>> I know I can get them imported into matlab, but I want to use them in a
>>>>>>> similar way as you did in your Jakobshavn example where you create an
>>>>>>> Argus file to define regions for shear margin softening.
>>>>>>> The issue is converting my shapefile into the Argus format without
>>>>>>> retracing the shapefile using exptool (which is possible, the primary
>>>>>>> reservation is that some of my polygon geometry is a bit complex in
>>>>>>> spots), or without having to buy ARGUS ONE personally.
>>>>>>>
>>>>>>> Any ideas?
>>>>>>>
>>>>>>> Thank you very much.
>>>>>>> Best
>>>>>>>
>>>>>>> On 12/31/2012 5:18 PM, Larour, Eric (385J) wrote:
>>>>>>>> Derrick,
>>>>>>>>
>>>>>>>> I ran your example and everything went fine. So the only thing right now
>>>>>>>> I can think
>>>>>>>> of is that your model is not in sync with svelint (i.e. svelint is not a
>>>>>>>> vertex based vector of
>>>>>>>> size (md.mesh.numberofvertices,1)). To check on that, could you send me
>>>>>>>> the results of the following?
>>>>>>>>
>>>>>>>>
>>>>>>>>>> md.mesh
>>>>>>>>>> whos x y svelocity svelint
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>> Eric L.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 12/31/12 1:53 PM, "Larour, Eric (385J)"<eric.larour at jpl.nasa.gov>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Derrick,
>>>>>>>>>
>>>>>>>>> I'm also puzzled as to why bang is giving you an error. I am right now
>>>>>>>>> working
>>>>>>>>> on reproducing the bug from your procedure document. Will keep you
>>>>>>>>> posted
>>>>>>>>> as soon
>>>>>>>>> as I find the bug. Should not be long.
>>>>>>>>>
>>>>>>>>> For further reference, please includeissm-support at issm.ess.uci.edu in
>>>>>>>>> your reply
>>>>>>>>> all, so other ISSM folks can also help you :)
>>>>>>>>>
>>>>>>>>> Eric L.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 12/31/12 12:17 AM, "djl22"<djl22 at psu.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I think I found a way through it. I tried working with the original
>>>>>>>>>> data, which provides surface velocity over the entire Greenland ice
>>>>>>>>>> sheet projected in polar stereographic. I used geotiffread to import
>>>>>>>>>> the
>>>>>>>>>> GEOTIFF image. I used exptool to draw my domain as a sub-region
>>>>>>>>>> (Jakobshavn area) from the imported image and set the initial
>>>>>>>>>> resolution
>>>>>>>>>> of my mesh at 2km (2000m). The output mesh looks about right. I then
>>>>>>>>>> extract the pixel center coordinates using the pixcenters command:
>>>>>>>>>>>> info=geotiffinfo(filename);From
>>>>>>>>>>>> [x,y] = pixcenters(info);
>>>>>>>>>> This gets my coordinates for pixel centers. I then have to flip my (y)
>>>>>>>>>> coordinates because the InterpFromGridToMesh command complains that
>>>>>>>>>> the
>>>>>>>>>> values should be decreasing. After doing so I run the
>>>>>>>>>> InterpFromGridToMesh command and here things get odd. I notice that in
>>>>>>>>>> your examples the velx and vely variables in your Searise and
>>>>>>>>>> jakobshavn
>>>>>>>>>> examples are entered in the InterpFromGridToMesh command as the
>>>>>>>>>> transpose of these variables, is this correct? (i.e.
>>>>>>>>>> vx=InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0);).
>>>>>>>>>> If I enter my velocity grid as such then I get an error. if I enter
>>>>>>>>>> without the transpose the command seems to work, but then I get an odd
>>>>>>>>>> message when I use the output from the Interp command in the following
>>>>>>>>>> bamg command. I get:
>>>>>>>>>>
>>>>>>>>>> Anisotropic mesh adaptation
>>>>>>>>>> Error message: 'field' should have 930 rowsError using BamgMesher
>>>>>>>>>>
>>>>>>>>>> At this point I'm lost as to why its not working. When I attempted to
>>>>>>>>>> run your Searise example as indicated, I ended up with the same exact
>>>>>>>>>> error in running bamg (I ran the lines of code provided directly from
>>>>>>>>>> the example). I also go tthis error when I ran the Searise example:
>>>>>>>>>> Error message: Input parameter of class single not supported yetError
>>>>>>>>>> using InterpFromGridToMesh
>>>>>>>>>>
>>>>>>>>>> when I ran
>>>>>>>>>> vx=InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0);...in this
>>>>>>>>>> case I converted the input variables x1, y1 and velx, vely to double
>>>>>>>>>> (x1=double(x1), etc...) was this necessary to get it to work? The
>>>>>>>>>> command worked after doing this which means ISSM could not recognize
>>>>>>>>>> the
>>>>>>>>>> data type "single" as oppose to "double"
>>>>>>>>>>
>>>>>>>>>> at any rate, i'm now stuck at bamg where I'm attempting to use the
>>>>>>>>>> velocity i assume were interpolated to my initial mesh within my
>>>>>>>>>> custom
>>>>>>>>>> domain to refine my initial mesh which would ideally create finer mesh
>>>>>>>>>> grids near the margins of Jakobshavn than outside of the margins....
>>>>>>>>>>
>>>>>>>>>> Thanks so much for the assistance....
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 12/29/2012 3:04 AM, Larour, Eric (385J) wrote:
>>>>>>>>>>> Dear Derrick,
>>>>>>>>>>>
>>>>>>>>>>> I think the issue is that when you plotted your surface velocities in
>>>>>>>>>>> matlab (before calling exptool
>>>>>>>>>>> on it), you did not specify the x and y coordinates of your image.
>>>>>>>>>>>
>>>>>>>>>>> Typically, in matlab, one does:
>>>>>>>>>>>
>>>>>>>>>>> imagesc(velocity) where velocity is a matrix. This will get you
>>>>>>>>>>> coordinates in scene coordinates.
>>>>>>>>>>>
>>>>>>>>>>> For your example, what you need to do is:
>>>>>>>>>>> imagesc(x,y,velocity),
>>>>>>>>>>> where x=0:(xmax-xmin)/m:xmax and
>>>>>>>>>>> y=0:(ymax-ymin)/n:ymax
>>>>>>>>>>>
>>>>>>>>>>> and m,n is the size of the velocity matrix.
>>>>>>>>>>>
>>>>>>>>>>> If you do this, you will recover from exptools the true vertex
>>>>>>>>>>> coordinates.
>>>>>>>>>>>
>>>>>>>>>>> Tell me how it goes!
>>>>>>>>>>>
>>>>>>>>>>> Thanks!
>>>>>>>>>>> Eric L.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 12/28/12 11:58 PM, "Derrick Lampkin"<djl22 at psu.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Greetings,
>>>>>>>>>>>>
>>>>>>>>>>>> I recently attended the ISSM workshop and found it useful. I'm
>>>>>>>>>>>> attempting
>>>>>>>>>>>> to use the system to model a system in the Jakobshavn outlet basin.
>>>>>>>>>>>> I
>>>>>>>>>>>> have been using your Jakobshavn example as a template. The exception
>>>>>>>>>>>> is
>>>>>>>>>>>> I'm using a base of surface velocity data derived from NSIDC
>>>>>>>>>>>> (Joughin
>>>>>>>>>>>> data set). I have imported a surface velocity grid as GEOTIFF into
>>>>>>>>>>>> matlab
>>>>>>>>>>>> and I use the exptool to draw the outline of my domain on top of
>>>>>>>>>>>> this
>>>>>>>>>>>> base map. The map is in the polar stereo graphic projection but
>>>>>>>>>>>> when I
>>>>>>>>>>>> create the initial mesh using triangle at the nominal resolution of
>>>>>>>>>>>> the
>>>>>>>>>>>> data (500 m), the grid spacing was not nearly as dense as expected.
>>>>>>>>>>>> I
>>>>>>>>>>>> inspected the domain file I created and the vertices coordinates are
>>>>>>>>>>>> in
>>>>>>>>>>>> scene coordinates (row/column) values and not the projected
>>>>>>>>>>>> coordinates ,
>>>>>>>>>>>> therefore the mesh spacing are not reasonable and do not correspond
>>>>>>>>>>>> to
>>>>>>>>>>>> the specified resolution I indicate in the triangle command. How
>>>>>>>>>>>> might
>>>>>>>>>>>> I
>>>>>>>>>>>> fix this issue?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks
>>>>>>>>>>>>
>>>>>>>>>>>> derrick j lampkin
>>>>>>>>>>>> __________________
>>>>>>>>>>>> research professor
>>>>>>>>>>>>
>>>>>>>>>>>> institute of arctic and alpine research
>>>>>>>>>>>>
>>>>>>>>>>>> university of colorado-boulder
>>>>>>>>>>>>
>>>>>>>>>>>> __________________
>>>>>>>>>>>>
>>>>>>>>>>>> email:djl22 at psu.edu
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> issm-support mailing list
>>>>>>>>>>>> issm-support at issm.ess.uci.eduhttp://issm.ess.uci.edu/cgi-bin/mailman/listinfo/issm-support
>>>>>>>>>> --
>>>>>>>>>> derrick j lampkin
>>>>>>>>>> __________________
>>>>>>>>>> research professor
>>>>>>>>>>
>>>>>>>>>> institute of arctic and alpine research
>>>>>>>>>> university of colorado-boulder
>>>>>>>>>> adjunct
>>>>>>>>>> department of geoscience
>>>>>>>>>> pennsylvania state university
>>>>>>>>>> __________________
>>>>>>>>>>
>>>>>>>>>> email:djl22 at psu.edu
>>>>>>>>>> web:http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
>>>>>>>>> _______________________________________________
>>>>>>>>> issm-support mailing list
>>>>>>>>> issm-support at issm.ess.uci.eduhttp://issm.ess.uci.edu/cgi-bin/mailman/listinfo/issm-support
>>>>>>> --
>>>>>>> derrick j lampkin
>>>>>>> __________________
>>>>>>> research professor
>>>>>>>
>>>>>>> institute of arctic and alpine research
>>>>>>> university of colorado-boulder
>>>>>>> adjunct
>>>>>>> department of geoscience
>>>>>>> pennsylvania state university
>>>>>>> __________________
>>>>>>>
>>>>>>> email:djl22 at psu.edu
>>>>>>> web:http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
>>>>> --
>>>>> derrick j lampkin
>>>>> __________________
>>>>> research professor
>>>>>
>>>>> institute of arctic and alpine research
>>>>> university of colorado-boulder
>>>>> adjunct
>>>>> department of geoscience
>>>>> pennsylvania state university
>>>>> __________________
>>>>>
>>>>> email:djl22 at psu.edu
>>>>> web:http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
>>>>
>>>>
>>>> --
>>>> derrick j lampkin
>>>> __________________
>>>> research professor
>>>>
>>>> institute of arctic and alpine research
>>>> university of colorado-boulder
>>>> adjunct
>>>> department of geoscience
>>>> pennsylvania state university
>>>> __________________
>>>>
>>>> email:djl22 at psu.edu
>>>> web:http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
--
derrick j lampkin
__________________
research professor
institute of arctic and alpine research
university of colorado-boulder
adjunct
department of geoscience
pennsylvania state university
__________________
email: djl22 at psu.edu
web: http://www.geosc.psu.edu/academic-faculty/lampkin-derrick
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