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Memory allocation problemHello,
I'm trying to create a huge topographic map of europe using srtm3 data. Dowload and conversion seemed to work flawlessly; now i'm trying to paste 41 rows of 1°lat and 98°long together in one single grd grid, which will be used to create the map. Unfortunatly each row is 540 mb big, and after having pasted the 5 first rows, grdpaste dies badly, with the following error message: GMT fatal error: grdpaste could not allocate memory [3.2 Gb] I have an old amd athlon xp 1,6 ghz with 1gb RAM, and 2Gb SWAP. Do I need the full 41x540Mb (which will be the size of the final grid) amount of swap ? Is there no way to tell grdpaste to directly write the new row a the end of the final grid file, on the hdd, without mapping the whole thing into memory ? Thank you for your help, Felix To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Memory allocation problemfelix.schalck wrote:
> Hello, > > I'm trying to create a huge topographic map of europe using srtm3 > data. Dowload and conversion seemed to work flawlessly; now i'm trying > to paste 41 rows of 1°lat and 98°long together in one single grd grid, > which will be used to create the map. Unfortunatly each row is 540 mb > big, and after having pasted the 5 first rows, grdpaste dies badly, > with the following error message: > > GMT fatal error: grdpaste could not allocate memory [3.2 Gb] > > I have an old amd athlon xp 1,6 ghz with 1gb RAM, and 2Gb SWAP. Do I > need the full 41x540Mb (which will be the size of the final grid) > amount of swap ? Is there no way to tell grdpaste to directly write > the new row a the end of the final grid file, on the hdd, without > mapping the whole thing into memory ? > Why are you trying to do that (which obviously you won't succeed)? There is no way that on papers the size we are used to deal with you would ever tell the difference between a 48x91º map produced with SRTM3 and , for example, SRTM+ plus or ETOPO2. Even if you find a way to paste together 41x540 = 21.6 Gb your next question would be "How can I make grdimage swallow a 21 Gb grid?" J. Luis To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Memory allocation problemDear Felix,
I think the "grd" tools are an inefficient way to deal with this much data. A better way is to work in the native binary integer format of your machine. Once the entire area is assembled you can make an entry for the native binary file in your "grdraster.info" and use GMT's "grdraster" to extract subsets of the data as "grd" files. If you are trying to handle the entire area at once, think about whether you really need to do this. There are (20 * 60)^2 data points in each 1x1 degree cell, and you have a 41 * 98 degree area. If I've done my math right, that is almost 6 x 10^9 data points. If for example you wanted to use GMT's "grdimage" to image the entire area at once, you would need an absurd amount of memory. The operating system can give you virtual memory (it shouldn't have to be RAM, unless the kernel has a limit on how much you can allocate to one process), but you would need 64-bit addressing and it would take forever to run. Also, do you have a display device that can handle that many pixels? If you want high-resolution images, work in smaller areas. If you want a map of an area 41 by 98, consider reducing the data sampling. "grdraster" can do this if you simply want to sub-sample every N'th point. If you are worried about aliasing, then build some averaging in when you assemble the tiles. It sounds like you have used "grdpaste" to assemble the tiles in east- west rows. Good, because that isn't easy to do with any other tool. Once you have done that, you can use "grd2xyz -ZTLh ..." on each completed row's "grd" file, to dump it to native binary. The native binaries can then be assembled using "cat" to append each row to the end of the row to the north, building from north to south. Caution: I know the SRTMv2 30 arc second tiles are "pixel registered", so this will work directly. But if I remember correctly maybe the 3 arc second tiles are "grid registered" which means that the edge values are repeated. If you simply "cat" in the above recipe you will get a row of data repeated twice at each 1 degree edge. You don't want that. The solution is to skip writing the last row on every row except the last one, where you need to skip writing the first one. To skip some bytes in a binary stream, use "dd". So grd2xyz -ZTLh ... | dd ... followed by "cat" should build something you can manage with "grdraster". Good luck. walter Walter H F Smith Chairman, GEBCO SCDB Geophysicist, Laboratory for Satellite Altimetry NOAA NESDIS code E/RA-31 1335 East West Hwy, room 5408 Silver Spring MD 20910-3226 tel 301-713-2857, extension 126 fax 301-713-3136 Walter.HF.Smith@... On Sep 24, 2008, at 9:15 AM, felix.schalck wrote: > Hello, > > I'm trying to create a huge topographic map of europe using srtm3 > data. Dowload and conversion seemed to work flawlessly; now i'm > trying to paste 41 rows of 1°lat and 98°long together in one single > grd grid, which will be used to create the map. Unfortunatly each > row is 540 mb big, and after having pasted the 5 first rows, > grdpaste dies badly, with the following error message: > > GMT fatal error: grdpaste could not allocate memory [3.2 Gb] > > I have an old amd athlon xp 1,6 ghz with 1gb RAM, and 2Gb SWAP. Do > I need the full 41x540Mb (which will be the size of the final grid) > amount of swap ? Is there no way to tell grdpaste to directly write > the new row a the end of the final grid file, on the hdd, without > mapping the whole thing into memory ? > > Thank you for your help, > > Felix > > To unsubscribe, send the message "signoff gmt-help" to > listserv@... To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Memory allocation problemHello,Interesting task, Felix. It sounds Herculean in nature! I couldn't gather what the specifics were for your topo map, but if you are merely making a colorized map with grdimage, you probably could "layer" a series of grdimage calls (to each srtm3 row) to a single, output postscript file (it too might get large, but it only resides on the hdd). In other words, instead of trying to build a single huge .grd file, take each row's .grd file as a "slice," apply a single color table across all slices, and "build" the map directly. If you were hoping to plot contour lines, that might be more problematic as the contours may not line-up across slices. I've never tried it myself, so I'm not sure what the edge effects might look like. Also, if you were thinking of using grdimage and hoping to apply a grdgradient, you'll have to work out the specifics for that and apply them uniformly for each row. Its an ugly problem, but there are alternatives. Furthermore, others may have tricks I'm not aware of. But, as you've discovered, trying to create a single .grd file using grdpaste just isn't going to work. As Joaquim wrote, what is the final size of the graphic? If you're putting it on a A4-sized sheet, then you can reduce the resolution a huge amount with grdsample, then do your grdpastes. If you're wall-papering the hallway of your office, then split the rows into regions and work that way. Again, a little creative thinking will work, either way. I just saw Walter's reply and that sounds like yet another possible solution. Good luck. John Robbins --
To unsubscribe, send the message "signoff gmt-help" to listserv@...
Cryospheric
Branch, Code 614.1 NASA
Goddard Space Flight Center Greenbelt,
Maryland 20771 Web:
ICESat Home Page Email:
John.Robbins@... |
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Re: Memory allocation problemMany thanks for all three replies; i did not expect so fast and so
precise replies. Basically, the main problem i read out of your emails is the lack of details, so here are some more: The project is mainly designed for personal use (even though people around me show some interest); it could be described as sort of a therapy - and is thus quite important for me. The main objectives of the map is precision; time is no problem, since the whole work can take weeks if necessary. The final map is not intended to be printed, but rather to be directly read on my 22" screen, by scrolling and zooming to the desired area. I was planning a resolution of about 5000x4200 px, which gives a scala of 1:4000000, but this resolution is not fixed yet, and depends on the SRTM3 based grdimage results. I made a first map with GLOBE data, but the details level is just not enough, and at my resolution, it gives soapy results; and that's why I turned to SRTM3 data. In terms of gmt, the first map was an Albers projection of aera R-8/32/75/61r, with settings Jb15/30/40/60/1:4000000. The new map is expected to have the same settings, and thus be drawn in three steps: 1 - barymetry, with grdimage 2 - topography, with grdimage 3 - Coastlines, Rivers and polit. borders, with ps coast I think I'm going to make 2 or three separate files, one with topography/barymetry, and one with coastlines, the latter in vectorized format, and then merge the files via GIMP. Note: Since it's a conical projection, the top portion of the aera needs to be much larger than the average one; that's why I got data from -25 to 67. Unfortunately, i did not find out how to build a trapezoid grid with grd tools, and thus end with some 3-5 Gigs of empty space (ocean) below Iceland, and west of France. So, up to your reactions: As Mr Smith pointed it, perhaps processing the whole data in one command might not be a good idea, even though I have access every night to a 64bit cpu, and the native binary solution seems to be very promising. That's why I would like more details about Mr Robbin's grdimage "slices" solution, which could not only relieve the memory problem, but also further graphical processing via GIMP, and on top of that address the "ocean-waste-problem". How is that doable ? Do I only need to keep the same projection settings for every slice, change the aera, and run the grdimage command 40 times ? And than paste everything together with gimp. Would they fit to each other ? What about the gradient ? Map title, coastlines and other details could be created in another file, and become a "background" layer to paste the topographic slices. I'm rather new to the GMT tools, and any comments, advices of more experienced users are really welcome, to help me create this map. Thanks in advance, Felix John Robbins wrote: > felix.schalck wrote: >> Hello, >> >> I'm trying to create a huge topographic map of europe using srtm3 >> data. Dowload and conversion seemed to work flawlessly; now i'm >> trying to paste 41 rows of 1°lat and 98°long together in one single >> grd grid, which will be used to create the map. Unfortunatly each row >> is 540 mb big, and after having pasted the 5 first rows, grdpaste >> dies badly, with the following error message: >> >> GMT fatal error: grdpaste could not allocate memory [3.2 Gb] >> >> I have an old amd athlon xp 1,6 ghz with 1gb RAM, and 2Gb SWAP. Do I >> need the full 41x540Mb (which will be the size of the final grid) >> amount of swap ? Is there no way to tell grdpaste to directly write >> the new row a the end of the final grid file, on the hdd, without >> mapping the whole thing into memory ? >> >> Thank you for your help, >> >> Felix >> >> > Interesting task, Felix. It sounds Herculean in nature! > > I couldn't gather what the specifics were for your topo map, but if > you are merely making a colorized map with grdimage, you probably > could "layer" a series of grdimage calls (to each srtm3 row) to a > single, output postscript file (it too might get large, but it only > resides on the hdd). In other words, instead of trying to build a > single huge .grd file, take each row's .grd file as a "slice," apply a > single color table across all slices, and "build" the map directly. > > If you were hoping to plot contour lines, that might be more > problematic as the contours may not line-up across slices. I've never > tried it myself, so I'm not sure what the edge effects might look like. > > Also, if you were thinking of using grdimage and hoping to apply a > grdgradient, you'll have to work out the specifics for that and apply > them uniformly for each row. > > Its an ugly problem, but there are alternatives. Furthermore, others > may have tricks I'm not aware of. But, as you've discovered, trying to > create a single .grd file using grdpaste just isn't going to work. > > As Joaquim wrote, what is the final size of the graphic? If you're > putting it on a A4-sized sheet, then you can reduce the resolution a > huge amount with grdsample, then do your grdpastes. If you're > wall-papering the hallway of your office, then split the rows into > regions and work that way. Again, a little creative thinking will > work, either way. > > I just saw Walter's reply and that sounds like yet another possible > solution. Good luck. > > John Robbins > > -- > > Cryospheric Branch, Code 614.1 > > NASA Goddard Space Flight Center > > Greenbelt, Maryland 20771 > > Web: ICESat Home Page <http://icesat.gsfc.nasa.gov/> > > Email: John.Robbins@... <mailto:John.Robbins@...> > > To unsubscribe, send the message "signoff gmt-help" to > listserv@... To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Memory allocation problemDear Felix,
I do not disagree with the other suggestions sent in reply to your first posting. Since you also want to do the Albers Conic projection there is additional overhead in projecting the coordinates, and this makes it even harder to work in the full resolution of SRTM3. But I do not think you have to. Here is why: You say you want a final resolution of about 5000 by 4200 pixels. Your previous email said you were trying to assemble an area 98 by 41 degrees, with, as I pointed out, 1200x1200 pixels per degree, or a total of 5.8 x 10^9 input data points. But your total number of output pixels is 2.1 x 10^7. In other words, the input data quantity is more than 100 times the needed output quantity. (The above calculation is rough, as it ignores what happens when the data are projected. One could use mapproject to compute the dimensions of your map and do a smarter calculation. I'm just trying to get an order of magnitude estimate here.) So it seems that you could decimate (literally, reduce by a factor of 10) the input data quantity in each dimension and things should be satisfactory. If this is true, then it should be possible to build your map from an input of 30-arc-second, not 3-arc-second, data. Thus I am surprised that you were unsatisfied with the results from the GLOBE data. Try the SRTM (version 2) 30 arc second data, and see what you think. Or, to include the ocean area, use SRTM30PLUS (there's a new version in the last few days) at http://topex.ucsd.edu If working with 30-arc-second data as input proves to be unsatisfactory, then the following approach may work: Use GMT tools as you did to assemble the 1x1 degree tiles of SRTM 3 data. Use "grd2xyz" to dump each one as lon,lat,height and pipe this through "mapproject" with your desired projection, using the -R and - J for the entire area, not just the tile. Concatenate the results for all tiles, or at least for many tiles in a "chunk" (a subset area, to avoid having total size too big) and pipe the result through "blockmean" with the -R and -I [and -F] set not in lon,lat coordinates but now in x,y map projected coordinates, so you average the data into the final pixels you intend to use. If this has to be done in several chunks then later cat all chunks together and run through blockmean with the same parameters again; this will clean up the overlap zones of the chunks. Finally, the output of blockmean can be input to xyz2grd (again, -R and -I are now in projected xy) to make your grid file from which you can image, contour, etc. this will work. it just takes patience. w Walter H F Smith Chairman, GEBCO SCDB Geophysicist, Laboratory for Satellite Altimetry NOAA NESDIS code E/RA-31 1335 East West Hwy, room 5408 Silver Spring MD 20910-3226 tel 301-713-2857, extension 126 fax 301-713-3136 Walter.HF.Smith@... On Sep 24, 2008, at 11:41 AM, felix.schalck wrote: > Many thanks for all three replies; i did not expect so fast and so > precise replies. Basically, the main problem i read out of your > emails is the lack of details, so here are some more: > > The project is mainly designed for personal use (even though people > around me show some interest); it could be described as sort of a > therapy - and is thus quite important for me. The main objectives > of the map is precision; time is no problem, since the whole work > can take weeks if necessary. The final map is not intended to be > printed, but rather to be directly read on my 22" screen, by > scrolling and zooming to the desired area. I was planning a > resolution of about 5000x4200 px, which gives a scala of 1:4000000, > but this resolution is not fixed yet, and depends on the SRTM3 > based grdimage results. I made a first map with GLOBE data, but the > details level is just not enough, and at my resolution, it gives > soapy results; and that's why I turned to SRTM3 data. > > In terms of gmt, the first map was an Albers projection of aera > R-8/32/75/61r, with settings Jb15/30/40/60/1:4000000. The new map > is expected to have the same settings, and thus be drawn in three > steps: > > 1 - barymetry, with grdimage > 2 - topography, with grdimage > 3 - Coastlines, Rivers and polit. borders, with ps coast > > I think I'm going to make 2 or three separate files, one with > topography/barymetry, and one with coastlines, the latter in > vectorized format, and then merge the files via GIMP. > > Note: Since it's a conical projection, the top portion of the aera > needs to be much larger than the average one; that's why I got data > from -25 to 67. Unfortunately, i did not find out how to build a > trapezoid grid with grd tools, and thus end with some 3-5 Gigs of > empty space (ocean) below Iceland, and west of France. > > So, up to your reactions: As Mr Smith pointed it, perhaps > processing the whole data in one command might not be a good idea, > even though I have access every night to a 64bit cpu, and the > native binary solution seems to be very promising. That's why I > would like more details about Mr Robbin's grdimage "slices" > solution, which could not only relieve the memory problem, but also > further graphical processing via GIMP, and on top of that address > the "ocean-waste-problem". How is that doable ? Do I only need to > keep the same projection settings for every slice, change the aera, > and run the grdimage command 40 times ? And than paste everything > together with gimp. Would they fit to each other ? What about the > gradient ? > Map title, coastlines and other details could be created in another > file, and become a "background" layer to paste the topographic slices. > > I'm rather new to the GMT tools, and any comments, advices of more > experienced users are really welcome, to help me create this map. > > Thanks in advance, > > Felix > > > John Robbins wrote: >> felix.schalck wrote: >>> Hello, >>> >>> I'm trying to create a huge topographic map of europe using srtm3 >>> data. Dowload and conversion seemed to work flawlessly; now i'm >>> trying to paste 41 rows of 1°lat and 98°long together in one >>> single grd grid, which will be used to create the map. >>> Unfortunatly each row is 540 mb big, and after having pasted the >>> 5 first rows, grdpaste dies badly, with the following error message: >>> >>> GMT fatal error: grdpaste could not allocate memory [3.2 Gb] >>> >>> I have an old amd athlon xp 1,6 ghz with 1gb RAM, and 2Gb SWAP. >>> Do I need the full 41x540Mb (which will be the size of the final >>> grid) amount of swap ? Is there no way to tell grdpaste to >>> directly write the new row a the end of the final grid file, on >>> the hdd, without mapping the whole thing into memory ? >>> >>> Thank you for your help, >>> >>> Felix >>> >>> >> Interesting task, Felix. It sounds Herculean in nature! >> >> I couldn't gather what the specifics were for your topo map, but >> if you are merely making a colorized map with grdimage, you >> probably could "layer" a series of grdimage calls (to each srtm3 >> row) to a single, output postscript file (it too might get large, >> but it only resides on the hdd). In other words, instead of trying >> to build a single huge .grd file, take each row's .grd file as a >> "slice," apply a single color table across all slices, and "build" >> the map directly. >> >> If you were hoping to plot contour lines, that might be more >> problematic as the contours may not line-up across slices. I've >> never tried it myself, so I'm not sure what the edge effects might >> look like. >> >> Also, if you were thinking of using grdimage and hoping to apply a >> grdgradient, you'll have to work out the specifics for that and >> apply them uniformly for each row. >> >> Its an ugly problem, but there are alternatives. Furthermore, >> others may have tricks I'm not aware of. But, as you've >> discovered, trying to create a single .grd file using grdpaste >> just isn't going to work. >> >> As Joaquim wrote, what is the final size of the graphic? If you're >> putting it on a A4-sized sheet, then you can reduce the resolution >> a huge amount with grdsample, then do your grdpastes. If you're >> wall-papering the hallway of your office, then split the rows into >> regions and work that way. Again, a little creative thinking will >> work, either way. >> >> I just saw Walter's reply and that sounds like yet another >> possible solution. Good luck. >> >> John Robbins >> >> -- >> >> Cryospheric Branch, Code 614.1 >> >> NASA Goddard Space Flight Center >> >> Greenbelt, Maryland 20771 >> >> Web: ICESat Home Page <http://icesat.gsfc.nasa.gov/> >> >> Email: John.Robbins@... <mailto:John.Robbins@...> >> >> To unsubscribe, send the message "signoff gmt-help" to >> listserv@... > > To unsubscribe, send the message "signoff gmt-help" to > listserv@... To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Large PS files conversion ?Hi,
How can you convert a huge GMT-made ps file to any other format, and especially PNG or PDF, while keeping the entire content ? I tried every conversion app I have, including ps2raster, and always end with a a4-size cut picture. Only GIMP import-option keeps original size; but the antialiasing sucks. Perhaps this is a problem of media-size ? Can't you make custom sized pdfs ? Thanks for your help, Felix To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Large PS files conversion ?Hi
I think you can try with Gsview or Acrobat Distiller.
Hadi
On Tue, Sep 30, 2008 at 1:50 PM, felix.schalck <felix.schalck@...> wrote: Hi, |
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Re: Large PS files conversion ?Thanks for your reply. Unfortunately Gsview cuts to A4 too, and adobe
distiller seems to be a commercial software... Hadi Salimi wrote: > Hi > I think you can try with Gsview or Acrobat Distiller. > Hadi > > On Tue, Sep 30, 2008 at 1:50 PM, felix.schalck > <felix.schalck@... <mailto:felix.schalck@...>> wrote: > > Hi, > > How can you convert a huge GMT-made ps file to any other format, > and especially PNG or PDF, while keeping the entire content ? I > tried every conversion app I have, including ps2raster, and always > end with a a4-size cut picture. Only GIMP import-option keeps > original size; but the antialiasing sucks. > Perhaps this is a problem of media-size ? Can't you make custom > sized pdfs ? > > Thanks for your help, > > Felix > > To unsubscribe, send the message "signoff gmt-help" to > listserv@... <mailto:listserv@...> > > > To unsubscribe, send the message "signoff gmt-help" to > listserv@... To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Large PS files conversion ?Perhaps the command convert of ImageMagick package can you help.
********************************** Milton P. Plasencia Linares Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS Borgo Grotta Gigante 42/C (34010) Sgonico - TRIESTE - ITALIA Tel: +39-040-2140305 Fax: +39-040-2140266 E-mail: mplasencia@... ASAIN (Antarctic Seismographic Argentinean Italian Network) ********************************* Quoting "felix.schalck" <felix.schalck@...>: Thanks for your reply. Unfortunately Gsview cuts to A4 too, and adobe distiller seems to be a commercial software... Hadi Salimi wrote: > Hi > I think you can try with Gsview or Acrobat Distiller. > Hadi > > On Tue, Sep 30, 2008 at 1:50 PM, felix.schalck > <felix.schalck@... <mailto:felix.schalck@...>> wrote: > > Hi, > > How can you convert a huge GMT-made ps file to any other format, > and especially PNG or PDF, while keeping the entire content ? I > tried every conversion app I have, including ps2raster, and always > end with a a4-size cut picture. Only GIMP import-option keeps > original size; but the antialiasing sucks. > Perhaps this is a problem of media-size ? Can't you make custom > sized pdfs ? > > Thanks for your help, > > Felix > > To unsubscribe, send the message "signoff gmt-help" to > listserv@... <mailto:listserv@...> > > > To unsubscribe, send the message "signoff gmt-help" to > listserv@... To unsubscribe, send the message "signoff gmt-help" to listserv@... Email secured by **CeSIT** Check Point gateway ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Large PS files conversion ?if you send your file to me, I am ready convert it with Distiller
Hadi
On Tue, Sep 30, 2008 at 2:48 PM, Milton P. Plasencia Linares <mplasencia@...> wrote: Perhaps the command convert of ImageMagick package can you help. |
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Re: Large PS files conversion ?At 12:20 +0200 30/09/08, felix.schalck wrote:
>How can you convert a huge GMT-made ps file can you put an example on a FTP server to try it? Hervé To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Large PS files conversion ?Most of the suggestions so far have been for utilities
which call gs (ps2raster, convert, gv) but it seems that the underlying problem is gs. Perhaps this could by sidesptepped by producing a png with n times the density at 1/n-th of the size. So if you want an a3 png at 300dpi, instead use ps2raster to make an a4 png at 600dpi or an a5 png at 1200dpi. Just a thought Jim -- J.J. Green, Dept. Applied Mathematics, Hicks Bld., University of Sheffield, UK. +44 (0114) 222 3742 http://sview01.wiredworkplace.net/pub/jjg To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Large PS files conversion ?Is this happening with the -A option on ps2raster?
I have had no trouble converting poster-sized files with "gs", but you have to specify the size of the output image (or have it set correctly in the BoundingBox statement in the PostScript; ps2raster - A is supposed to fix this). If you simply accept the defaults on "gs" then you will get something cut down to your standard page size format. walter On Sep 30, 2008, at 06:20, felix.schalck wrote: > Hi, > > How can you convert a huge GMT-made ps file to any other format, > and especially PNG or PDF, while keeping the entire content ? I > tried every conversion app I have, including ps2raster, and always > end with a a4-size cut picture. Only GIMP import-option keeps > original size; but the antialiasing sucks. > Perhaps this is a problem of media-size ? Can't you make custom > sized pdfs ? > > Thanks for your help, > > Felix > > To unsubscribe, send the message "signoff gmt-help" to > listserv@... To unsubscribe, send the message "signoff gmt-help" to listserv@... |
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Re: Large PS files conversion ? |