Hi Dan,
I have executed all the commands as mentioned they work fine for both the
las1.2 and 1.4 data.
las2las also successfully created new las files for both the versions.
A separate .lax file is also created and I’m unable to read it though…below are
the outputs.
Hope this info helps for further troubleshooting.
Thanks,
Nash
(spdlib) [nxg650@vdi-n3 las]$ lasinfo -i 687000-6092000.las
lasinfo (160606) report for 687000-6092000.las
reporting all LAS header entries:
file signature: 'LASF'
file source ID: 0
global_encoding: 1
project ID GUID data 1-4: 00000000-0000-0000-0000-000000000000
version major.minor: 1.2
system identifier: 'LAStools (c) by Martin Isenburg'
generating software: 'lasclip (131105) commercial'
file creation day/year: 22/2014
header size: 227
offset to point data: 229
number var. length records: 0
point data format: 1
point data record length: 28
number of point records: 12347548
number of points by return: 11952454 373899 21147 48 0
scale factor x y z: 0.01 0.01 0.01
offset x y z: -0 -0 -0
min x y z: 687000.00 6092000.00 562.53
max x y z: 687999.99 6092999.99 942.59
the header is followed by 2 user-defined bytes
reporting minimum and maximum for all LAS point record entries ...
X 68700000 68799999
Y 609200000 609299999
Z 56253 94259
intensity 0 235
return_number 1 4
number_of_returns 1 4
edge_of_flight_line 0 1
scan_direction_flag 0 1
classification 1 7
scan_angle_rank -15 12
user_data 87 87
point_source_ID 112 134
gps_time 70360612.990889 70367015.415621
number of first returns: 11952454
number of intermediate returns: 21196
number of last returns: 11952424
number of single returns: 11578526
overview over number of returns of given pulse: 11578526 705530 63300 192 0 0 0
histogram of classification of points:
18300 unclassified (1)
10614832 ground (2)
521324 low vegetation (3)
211803 medium vegetation (4)
980967 high vegetation (5)
322 noise (7)
(spdlib) [nxg650@vdi-n3 las]$ lasindex -i 687000-6092000.las
before complete 100000 -20
after minimum_points 100000
largest interval gap increased to 1385
after maximum_intervals 7520
For LAS1.4 data:
(spdlib) [nxg650@vdi-n3 Orthometric]$ lasinfo -i
ACT2015-C3-ORT_6826096_55_0002_0002.LAS
lasinfo (160606) report for ACT2015-C3-ORT_6826096_55_0002_0002.LAS
reporting all LAS header entries:
file signature: 'LASF'
file source ID: 0
global_encoding: 16
project ID GUID data 1-4: 00000000-0000-0000-0000-000000000000
version major.minor: 1.4
system identifier: ''
generating software: 'TerraScan'
file creation day/year: 53/2016
header size: 375
offset to point data: 1083
number var. length records: 1
point data format: 6
point data record length: 30
number of point records: 58907333
number of points by return: 56144061 2069495 587611 97501 8288
scale factor x y z: 0.01 0.01 0.01
offset x y z: -0 -0 -0
min x y z: 682000.00 6096000.00 472.10
max x y z: 683999.99 6097999.99 706.30
start of waveform data packet record: 0
start of first extended variable length record: 0
number of extended_variable length records: 0
extended number of point records: 58907333
extended number of points by return: 56144061 2069495 587611 97501 8288 370 7
0 0 0 0 0 0 0 0
variable length header record 1 of 1:
reserved 0
user ID 'LASF_Projection'
record ID 2112
length after header 654
description 'OGC WKT'
WKT OGC COORDINATE SYSTEM:
PROJCS["GDA94 / MGA zone
55",GEOGCS["GDA94",DATUM["Geocentric_Datum_of_Australia_1994",SPHEROID["GRS
1980",6378137,298.257222101,AUTHORITY["EPSG","7019"]],TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6283"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.01745329251994328,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4283"]],UNIT["metre",1,AUTHORITY["EPSG","9001"]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",147],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",10000000],AUTHORITY["EPSG","28355"],AXIS["Easting",EAST],AXIS["Northing",NORTH]]
reporting minimum and maximum for all LAS point record entries ...
X 68200000 68399999
Y 609600000 609799999
Z 45289 68704
intensity 1 23471
return_number 1 7
number_of_returns 1 7
edge_of_flight_line 0 1
scan_direction_flag 1 1
classification 1 18
scan_angle_rank -30 30
user_data 0 0
point_source_ID 21 658
gps_time 98121.834417 366792.864636
extended_return_number 1 7
extended_number_of_returns 1 7
extended_classification 1 18
extended_scan_angle -4999 5000
extended_scanner_channel 0 0
WARNING: 5 points outside of header bounding box
number of first returns: 56144061
number of intermediate returns: 693826
number of last returns: 56143320
number of single returns: 54073874
WARNING: point type is 6 but (legacy) number of point records in header is
58907333 instead zero.
WARNING: point type is 6 but (legacy) number of points by return [1] in header
is 56144061 instead zero.
WARNING: point type is 6 but (legacy) number of points by return [2] in header
is 2069495 instead zero.
WARNING: point type is 6 but (legacy) number of points by return [3] in header
is 587611 instead zero.
WARNING: point type is 6 but (legacy) number of points by return [4] in header
is 97501 instead zero.
WARNING: point type is 6 but (legacy) number of points by return [5] in header
is 8288 instead zero.
overview over extended number of returns of given pulse: 54073874 2964234
1470652 356733 39608 2183 49 0 0 0 0 0 0 0 0
histogram of classification of points:
4343 unclassified (1)
24819353 ground (2)
30312995 low vegetation (3)
735082 medium vegetation (4)
3006491 high vegetation (5)
6674 noise (7)
11229 water (9)
11166 Reserved for ASPRS Definition (18)
+-> flagged as extended overlap: 20263354
real min z smaller than header min z by 19.210000
(spdlib) [nxg650@vdi-n3 Orthometric]$ las2las -i
ACT2015-C3-ORT_6826096_55_0002_0002.LAS -o test.LAS
(spdlib) [nxg650@vdi-n3 Orthometric]$ lasindex -i
ACT2015-C3-ORT_6826096_55_0002_0002.LAS
before complete 100000 -20
after minimum_points 100000
largest interval gap increased to 1941
after maximum_intervals 8000
From: Daniel Clewley <[email protected]<mailto:[email protected]>>
Date: Monday, 22 August 2016 at 3:39 PM
To: Kelsey Druken <[email protected]<mailto:[email protected]>>
Cc: Narsimha Garlapati
<[email protected]<mailto:[email protected]>>,
spdlib-develop
<[email protected]<mailto:[email protected]>>
Subject: Re: 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
<[email protected]<mailto:[email protected]>> 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: [email protected]<mailto:[email protected]>
T: +61 2 6125 2479
W: nci.org.au<http://nci.org.au/>
On Mon, Aug 22, 2016 at 2:11 PM, Narsimha Garlapati
<[email protected]<mailto:[email protected]>> 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"
<[email protected]<mailto:[email protected]>>
Date: Monday, 22 August 2016 at 11:55 AM
To: Daniel Clewley <[email protected]<mailto:[email protected]>>
Cc: Narsimha Garlapati
<[email protected]<mailto:[email protected]>>,
spdlib-develop
<[email protected]<mailto:[email protected]>>
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: [email protected]<mailto:[email protected]>
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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>>
Date: Wednesday, 17 August 2016 at 10:34 PM
To: Narsimha Garlapati
<[email protected]<mailto:[email protected]>>
Cc: spdlib-develop
<[email protected]<mailto:[email protected]>>
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
<[email protected]<mailto:[email protected]>> 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
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 <[email protected]<mailto:[email protected]>>
Date: Wednesday, 17 August 2016 at 4:27 PM
To: Narsimha Garlapati
<[email protected]<mailto:[email protected]>>
Cc: spdlib-develop
<[email protected]<mailto:[email protected]>>
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/
Thanks,
Dan
On 17 Aug 2016, at 05:26, Narsimha Garlapati
<[email protected]<mailto:[email protected]>> 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
[email protected]<mailto:[email protected]>
Segmentation fault
Regards,
Narsimha
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