Hi Kelsey, So is the error still with finding the .lax file even after one has been generated using lasindex?
The .lax file isn’t used in SPDLib, I’m not sure why LASlib is giving an error for that file. Most the files I’ve tested with don’t have a corresponding .lax file and they work fine. Obvious question but have you tested with a different LAS file? You can test with this one: http://browse.ceda.ac.uk/browse/neodc/arsf/2014/RG13_06/RG13_06-2014_303_Maliau_Basin/LiDAR/flightlines/discrete_laser/las1.2/LDR-RG13_06-2014-303-35.LAS <http://browse.ceda.ac.uk/browse/neodc/arsf/2014/RG13_06/RG13_06-2014_303_Maliau_Basin/LiDAR/flightlines/discrete_laser/las1.2/LDR-RG13_06-2014-303-35.LAS> And the following command: spdtranslate --if LAS --of UPD -i LDR-RG13_06-2014-303-35.LAS -o LDR-RG13_06-2014-303-35.spd -x FIRST_RETURN I know this file works on my system. Thanks, Dan > On 22 Aug 2016, at 08:01, Kelsey A. Druken <kelsey.dru...@anu.edu.au> wrote: > > Hi Daniel, > > Thanks so much for the help there, much appreciated. That explained a lot, > thank you. Unfortunately, the v3.3 is still crashing with a seg fault (but > those lastool commands seem to execute fine). > > However, thanks to the info you shared in the last email, I was able to work > backwards and get the v3.2 working on our system. In the interest of time, I > might leave the intricacies of why v3.3 is still falling over until Adam here > returns from overseas travels, as he is more familiar with running these > workflows. > > > Nash, I'll followup separately in a moment to work out a time to go over how > to get v3.2 working on the VDI for you. That should at least give you > something working now on our systems :) > > > Thanks so much again Daniel for the help. > > > Cheers, > Kelsey > > > > > > --- > Kelsey A. Druken > Earth Systems Data Service Specialist > National Computational Infrastructure (NCI) > Leonard Huxley Building, Mills Road > The Australian National University > Canberra ACT 0200 Australia > > > E: kelsey.dru...@anu.edu.au <mailto:kelsey.dru...@anu.edu.au> > T: +61 2 6125 2479 > W: nci.org.au <http://nci.org.au/> > > > On Mon, Aug 22, 2016 at 4:43 PM, Adam Steer <adam.st...@anu.edu.au > <mailto:adam.st...@anu.edu.au>> wrote: > Great sleuthing Kelsey :) now we are growing another lidar person! > > I had not even thought to check about .lax files. I am also pretty sure you > can also use lastools in batch mode to generate lax files for all Nash's data > at once. > > Dan - is there an 'ignore lasindex' switch in spdtranslate? > > Cheers > Adam > From: Daniel Clewley <daniel.clew...@gmail.com > <mailto:daniel.clew...@gmail.com>> > Sent: Monday, 22 August 2016 3:39:43 PM > To: Kelsey Druken > Cc: spdlib-develop; Narsimha Garlapati > Subject: Re: [spdlib-develop] seg fault to wkt file errors > > Hi Kelsey, > > Thanks for the info. A ‘.lax’ file is a separate file containing a spatial > index for a LAS file. This sounds like LASlib (which the latest version of > SPDLib uses to read a LAS file) is looking for the file and not finding it. > > Nash, was there a .lax file associated with the original LAS file which has > been separated at some point? > > If you run the LAStools version of lasinfo (this will be installed with the > latest version of SPDLib or can be downloaded separately) what output does > this give: > > lasinfo -i 687000-6092000.las > > You could also try exporting to a new LAS file: > > las2las -i 687000-6092000.las -o 687000-6092000_test.las > > It these work OK try to generate a .lax file using: > > lasindex -i 687000-6092000.las > > If they don’t work then LASlib can’t read the LAS file so SPD won’t be able > to. > > This might explain why it worked with the previous version (which used libLAS > and is unaware of .lax files) but not the newest version of SPDLib (which > uses LASlib). > > Thanks, > > Dan > >> On 22 Aug 2016, at 05:38, Kelsey A. Druken <kelsey.dru...@anu.edu.au >> <mailto:kelsey.dru...@anu.edu.au>> wrote: >> >> Hi Nash, >> >> Of course- please feel free. (I will note, I did try a few different >> versions and combinations of libraries in my troubleshooting but I think it >> is still good for you to have a try.) >> >> >> >> Dan- apologies to bother you but could I just ask one quick question >> regarding the software? If I do a strace when trying to execute this sample >> command: >> >> $ spdtranslate --if LAS --of SPD -b 10 -x LAST_RETURN -i >> ./687000-6092000.las -o lidartest.spd --temppath ./tempspd >> >> >> the segmentation fault continually happens after this statement where it >> can't find a file of the same name with the extension '.lax': >> >> open("./687000-6092000.lax", O_RDONLY) = -1 ENOENT (No such file or >> directory) >> >> --- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=0x6} --- >> >> +++ killed by SIGSEGV +++ >> >> >> I am not familiar with lidar processing tools myself, so my apologies in >> advance if this is a silly question. My colleague (Adam, more familiar with >> lidar- gave me this command/file as a representative test). Thanks in >> advance if you had any tips based on this output. >> >> >> >> Cheers, >> Kelsey >> >> >> >> --- >> Kelsey A. Druken >> Earth Systems Data Service Specialist >> National Computational Infrastructure (NCI) >> Leonard Huxley Building, Mills Road >> The Australian National University >> Canberra ACT 0200 Australia >> >> >> E: kelsey.dru...@anu.edu.au <mailto:kelsey.dru...@anu.edu.au> >> T: +61 2 6125 2479 <tel:%2B61%202%206125%202479> >> W: nci.org.au <http://nci.org.au/> >> >> >> On Mon, Aug 22, 2016 at 2:11 PM, Narsimha Garlapati >> <narsimha.garlap...@anu.edu.au <mailto:narsimha.garlap...@anu.edu.au>> wrote: >> Hi Kelsey, >> >> Thanks for troubleshooting these technical issues, hope they can be fixed >> soon. >> >> Meanwhile is it okay if I follow Adams instructions and revert to spd3-2 >> version? >> >> >> >> Cheers, >> >> Nash >> >> >> >> From: "Kelsey A. Druken" <kelsey.dru...@anu.edu.au >> <mailto:kelsey.dru...@anu.edu.au>> >> Date: Monday, 22 August 2016 at 11:55 AM >> To: Daniel Clewley <daniel.clew...@gmail.com >> <mailto:daniel.clew...@gmail.com>> >> Cc: Narsimha Garlapati <narsimha.garlap...@anu.edu.au >> <mailto:narsimha.garlap...@anu.edu.au>>, spdlib-develop >> <spdlib-develop@lists.sourceforge.net >> <mailto:spdlib-develop@lists.sourceforge.net>> >> >> >> Subject: Re: seg fault to wkt file errors >> >> >> >> Hi Nash (and Dan), >> >> >> >> I started from scratch and reinstalled everything per Dan's instructions, we >> still get the seg fault unfortunately. I am pretty certain though this is >> something on our end and not the software, I just need to test the manual >> build, like Dan suggests, and if that still returns the same error- we'll >> have to pass this onto the more advanced systems guys here at NCI. >> >> >> >> One tiny bit of good news however- I didn't know that part about order >> mattering with the conda channels. (Thank you Dan- very useful.) This solved >> one of our hdf4 library conflicts that we had to previously modify. >> >> >> >> Sorry again Nash that this has been such a painful process. Like I said, >> I'll do the manual build and then if that still fails- I'll pass it up to >> others here at NCI. >> >> >> >> >> >> Cheers, >> >> Kelsey >> >> >> >> >> >> >> >> >> >> >> >> --- >> >> Kelsey A. Druken >> >> Earth Systems Data Service Specialist >> >> National Computational Infrastructure (NCI) >> >> Leonard Huxley Building, Mills Road >> >> The Australian National University >> >> Canberra ACT 0200 Australia >> >> >> >> >> >> E: kelsey.dru...@anu.edu.au <mailto:kelsey.dru...@anu.edu.au> >> T: +61 2 6125 2479 <tel:%2B61%202%206125%202479> >> W: nci.org.au <http://nci.org.au/> >> >> >> >> >> On Fri, Aug 19, 2016 at 9:44 PM, Daniel Clewley <daniel.clew...@gmail.com >> <mailto:daniel.clew...@gmail.com>> wrote: >> >> Hi Narsimha, >> >> I think the problem is some packages from the osgeo channel are being pulled >> in but it should be using ones from conda-forge. Try: >> >> conda clean --tar --packages --yes >> conda create -n spdlib_condaforge -c conda-forge -c rios -c osgeo spdlib=3.3 >> >> Note the conda-forge channel is passed in first (this is important with the >> latest version of conda, which I only found out recently). >> >> The only package pulled in from osgeo should be spdlib. >> >> If you still have problems try removing and reinstalling miniconda then >> running the commands above again. >> >> >> >> This is as stable a build as we have available. Note if you want a more >> stable build you may wish to build all the packages from source rather than >> relying on the conda packages. >> >> >> >> Thanks, >> >> Dan >> >> >> >> >> >> On 19 August 2016 at 12:19, Narsimha Garlapati >> <narsimha.garlap...@anu.edu.au <mailto:narsimha.garlap...@anu.edu.au>> wrote: >> >> Hi Dan, >> >> >> >> I have several versions of LAS data (1.2,1.3 and 1.4) and would like to >> process them. >> >> >> >> I’m using a virtual desktop with Gnome terminal and I think it’s a Centos OS. >> >> >> >> Below is the conda list from my new installations. Another colleague from >> Adam’s team is also experiencing the similar “seg errors”. >> >> >> >> So far we are unable to troubleshoot this problem, when you get a chance can >> you please provide us some suggestions so that we can create a stable >> version. >> >> >> >> >> >> (spdlib) [nxg650@vdi-n16 ~]$ conda list >> >> # packages in environment at >> /g/data1/xc0/user/Garlapati/miniconda3/envs/spdlib: >> >> # >> >> cairo 1.12.18 6 >> >> boost 1.61.0 py35_1 conda-forge >> >> cgal 4.8.1 py35_0 conda-forge >> >> curl 7.49.1 0 conda-forge >> >> expat 2.1.0 1 conda-forge >> >> freexl 1.0.2 1 conda-forge >> >> gdal 2.1.1 np111py35_1 conda-forge >> >> giflib 5.1.2 1 conda-forge >> >> hdf5 1.8.17 2 conda-forge >> >> icu 56.1 4 conda-forge >> >> jpeg 9b 0 conda-forge >> >> json-c 0.12 0 conda-forge >> >> kealib 1.4.6 3 conda-forge >> >> libdap4 3.18.0 2 conda-forge >> >> libiconv 1.14 3 conda-forge >> >> libnetcdf 4.4.0 2 conda-forge >> >> libpng 1.6.23 0 conda-forge >> >> libspatialite 4.3.0a 9 conda-forge >> >> libtiff 4.0.6 6 conda-forge >> >> libuuid 1.0.3 1 conda-forge >> >> libxml2 2.9.4 0 conda-forge >> >> postgresql 9.5.3 2 conda-forge >> >> proj.4 4.9.2 0 conda-forge >> >> fontconfig 2.11.1 6 >> >> freetype 2.5.5 1 >> >> glib 2.43.0 1 >> >> harfbuzz 0.9.39 1 >> >> libffi 3.2.1 0 >> >> mkl 11.3.3 0 >> >> numpy 1.11.1 py35_0 >> >> openssl 1.0.2h 1 >> >> geos 3.4.2 0 osgeo >> >> gmp 5.1.2 0 osgeo >> >> gsl 2.1 2 osgeo >> >> hdf4 4.2.11 3 osgeo >> >> mpfr 3.1.2 0 osgeo >> >> openjpeg 2.1.0 0 osgeo >> >> spdlib 3.3.0 0 osgeo >> >> tuiview 1.1.8 py35_1 osgeo >> >> xerces-c 3.1.1 0 osgeo >> >> pango 1.39.0 1 >> >> pip 8.1.2 py35_0 >> >> pixman 0.32.6 0 >> >> pyqt 4.11.4 py35_4 >> >> python 3.5.2 0 >> >> qt 4.8.7 4 >> >> readline 6.2 2 >> >> lastools 20160606 0 rios >> >> setuptools 25.1.6 py35_0 >> >> sip 4.18 py35_0 >> >> sqlite 3.13.0 0 >> >> tk 8.5.18 0 >> >> wheel 0.29.0 py35_0 >> >> xz 5.2.2 0 >> >> zlib 1.2.8 3 >> >> >> >> Regards, >> >> Nash >> >> From: Daniel Clewley <daniel.clew...@gmail.com >> <mailto:daniel.clew...@gmail.com>> >> Date: Wednesday, 17 August 2016 at 10:34 PM >> To: Narsimha Garlapati <narsimha.garlap...@anu.edu.au >> <mailto:narsimha.garlap...@anu.edu.au>> >> Cc: spdlib-develop <spdlib-develop@lists.sourceforge.net >> <mailto:spdlib-develop@lists.sourceforge.net>> >> Subject: Re: seg fault to wkt file errors >> >> >> >> Hi Narsimha, >> >> >> >> This is a problem with how you are calling the command. You have ‘-i’ >> followed by ‘--input_proj’, rather than the input. This is interpreted as >> having the input as ‘--input_proj’, then you are using ‘GDA94MGAZn55.wkt’ as >> an argument without a flag. >> >> >> >> Also it needs to be a file not a web address. >> >> >> >> As for reverting to a previous version from an earlier email I was under the >> impression you needed LAS 1.3 support which is only available in the latest >> version (hence why you needed the Linux version not the old Windows version). >> >> >> >> For the seg fault, I’m not sure why this is happening. Are you sure there >> isn’t a problem with the input file? Do you have read access to the input >> file and write access to where you are trying to write to? If it was working >> before on the same file in the same location can you provide me details of >> your system (OS etc.,) also the outputs of: >> >> >> >> conda list >> >> >> >> At the moment you haven’t provided much information to go on. >> >> >> >> Thanks, >> >> >> >> Dan >> >> >> >> On 17 Aug 2016, at 12:40, Narsimha Garlapati <narsimha.garlap...@anu.edu.au >> <mailto:narsimha.garlap...@anu.edu.au>> wrote: >> >> >> >> Hi Dan, >> >> >> >> I have tried to input wkt files in various formats and getting the following >> errors. >> >> >> >> (spdlib) [nxg650@vdi-n4 AHD]$ spdtranslate --if LAS --of SPD -b 10 -x >> LAST_RETURN -i --input_proj GDA94MGAZn55.wkt -i 687000-6092000.las -o >> lidartest.spd >> >> >> >> >> >> PARSE ERROR: Argument: GDA94MGAZn55.wkt >> >> Couldn't find match for argument >> >> >> >> PARSE ERROR: Argument: GDA94MGAZn55.txt >> >> Couldn't find match for argument >> >> >> >> PARSE ERROR: Argument: http://spatialreference.org/ref/epsg/28355/ogcwkt >> <http://spatialreference.org/ref/epsg/28355/ogcwkt> >> Couldn't find match for argument >> >> >> >> Please let me know if I’m going wrong somewhere, by the way do you think is >> it better to revert to a previous stable version? >> >> >> >> Happy to seek your feedback, >> >> >> >> Thanks, >> >> Nash >> >> >> >> From: Daniel Clewley <daniel.clew...@gmail.com >> <mailto:daniel.clew...@gmail.com>> >> Date: Wednesday, 17 August 2016 at 4:27 PM >> To: Narsimha Garlapati <narsimha.garlap...@anu.edu.au >> <mailto:narsimha.garlap...@anu.edu.au>> >> Cc: spdlib-develop <spdlib-develop@lists.sourceforge.net >> <mailto:spdlib-develop@lists.sourceforge.net>> >> Subject: Re: [spdlib-develop] segmentation fault? >> >> >> >> Hi Narsimha, >> >> >> >> From my earlier email: >> >> >> >> You will also need to pass in the projection as a WKT file using >> --input_proj as it is currently segfaulting when trying to read the >> projection from a LAS 1.4 file. >> >> >> >> Is this a LAS 1.4 file? If so you need to pass in a text file containing the >> projection in WKT format using the --input_proj flag. >> >> If you don’t already have a WKT file you can download one from >> http://spatialreference.org/ <http://spatialreference.org/> >> >> >> Thanks, >> >> >> >> Dan >> >> On 17 Aug 2016, at 05:26, Narsimha Garlapati <narsimha.garlap...@anu.edu.au >> <mailto:narsimha.garlap...@anu.edu.au>> wrote: >> >> >> >> Hi Dan, >> >> Finally with the kind support from NCI, I have managed to install the latest >> spdlib. >> >> To test the new installation I have tried to run a spdtranslate and >> experiencing the “segmentation fault” error? >> >> Below is the error message, any suggestions to overcome this? >> >> >> >> (spdlib) [nxg650@vdi-n6 las]$ spdtranslate --if LAS --of SPD -b 10 -x >> LAST_RETURN -i /g/data1/xc0/user/Garlapati/AHD/las/687000-6092000.las -o >> lidartest.spd >> >> spdtranslate SPDLib 3.3.309, Copyright (C) 2016 Sorted Pulse Library (SPD) >> >> This program comes with ABSOLUTELY NO WARRANTY. This is free software, >> >> and you are welcome to redistribute it under certain conditions; See >> >> website (http://www.spdlib.org <http://www.spdlib.org/>). Bugs are to be >> reported on the trac >> >> or directly to spdlib-develop@lists.sourceforge.net >> <mailto:spdlib-develop@lists.sourceforge.net> >> Segmentation fault >> >> >> >> >> >> Regards, >> >> Narsimha >> >> >> >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> spdlib-develop mailing list >> spdlib-develop@lists.sourceforge.net >> <mailto:spdlib-develop@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/spdlib-develop >> <https://lists.sourceforge.net/lists/listinfo/spdlib-develop> >> >> >> >> >> >> >> >> >> > >
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