Compiling points2grid on Fedora with g++

Gridding large [x,y,z] point cloud datasets. Matlab and python have both failed me with their inefficient use of memory. So I'm having to turn to other tools.

Points2Grid is a tool, written in C++, which promises to do the job in a simple intuitive way. It accepts ascii and las (lidar) formats and outputs gridded data, plus gridded data densities.

First install LIBLAS which is Lidar data translation libraries. The recommended version is 1.2.1. I installed liblas 1.6.1 because it was the oldest version on the site that had a working link. I installed this by issuing:

Make a note of where the libraries are installed. On my system: /usr/local/include/liblas/

Download points2grid from here. 

In Interpolation.h, adjust MEM_LIMIT variable in the  file to reflect the memory limitations of your system. From the README guide, 

"As a rule of thumb, set the MEM_LIMIT to be (available memory in bytes)/55. For jobs that generate

grids cells greater than the MEM_LIMIT, points2grid goes "out-of-core", resulting in significantly worse performance."

Find this value using:

I then had to point the code to where the liblas directories had been installed. In Interpolation.cpp, replace:

It should then install with a simple 'make' command. Happy gridding!

Create Custom Launchers in Fedora

I just finished installed SmartGit on my new OS, like I did the last one

SmartGit is a simple bash script that I had to run from the command line. This time I decided I wanted a program launcher from my applications menu and my 'favourites bar' (or whatever that thing on the left hand side of the desktop is called!) 

So first I moved the smartgit folder from ~/Downloads/ to /usr/local/ and made the .sh script executable



Then to create a launcher I made a new .desktop file:



and added the following:

Of course the 'Icon' can be anything you like - I chose the one which comes with the program out of sheer non-inventiveness! In Applications it will appear under All and Accessories. Right click and 'Add to Favourites' and it will appear on your side bar.

Installing Mb-System on Fedora 17

MB-System is the only fully open-source software I am aware of for swath sonar data including multibeam and sidescan backscatter. As such, I'm really hoping using it works out for me!

Compiling it on a fresh install of Fedora 17 wasn't that straight-forward (took me about 5 hours to figure all this out), so I thought I'd put together a little how-to for the benefit of myself, and hopefully you.

I've broken it down into a few stages so some sort of semblance of order can be imposed on this random collection of installation notes.

Step 1: download the software from ftp server here

In the terminal:

For me this created a folder called 'mbsystem-5.3.1982'

Step 2: install pre-requisites

A) Generic Mapping Tools (GMT). You need to go to the Downloads tab, then click on the INSTALL FORM link. This will take you to a page where you can download the installation script, and fill in an online form of your parameter settings which you can submit and save the resulting page as a textfile which becomes the input to the bash script. Sounds confusing, but it's not - the instructions on the page are adequate. I opted to allow GMT to install netCDF for me. Then in the terminal I did this:

B) Perl parallel forkmanager:

C) X11

D) openmotif

E) fftw

F) ghostview - I had to install this indirectly using kde3:

(Note to Fedora - why oh why oh why are B, C, and F above not installed by default!?)

G)  OTPSnc tidal prediction software: download from here

untar, and cd to the directory

first double check that ncdump and ncgen are installed (which ncdump ncgen)

then edit the makefile so it reads:

then in the terminal issue:

Hopefully this compiles without errors, then I moved them to a executable directory:

H) openGL libraries (again I had to do this indirectly, this time through mesa):

Step 3: prepare mbsystem makefiles

cd mbsystem-5.3.1982/

You have to go in and point install_makefiles to where all your libraries are. This is time-consuming and involves a lot of ls, which, and whereis!

Here's a copy of the lines I edited in my install_makefiles parameters:

Then in the terminal

Step 3: install mbsystem

first I had to do this (but you may not need to)

I then updated my ~/.bashrc so the computer can find all these lovely new files:

Test the install by issuing



you should see the manual pages come up. Right, now down to the business of multibeam analysis!

em1 to ethX on Fedora 17 (how to install matlab if you don't have eth)

I have just moved from Ubuntu 12.04 to Fedora 17. No reason other than necessity for my new job. I'm still happy with Ubuntu and even don't mind Unity!

First thing I wanted to do, of course, was install matlab. It turns out I had a bit of work to do to get it installed on my Dell Precision machine! So here's a post to help out anyone who has the same problem.

If you don't have some eth listed when you ifconfig (I had the NIC listed as em1), matlab will install but you can't activate it. The problem is described on their website  

Basically, Fedora udev names NICs (network cards) embedded on the motherboard as em1, em2 (etc) rather then eth0, eth1 (etc). More details here

The two solutions listed on the Mathworks for changing the names back to eth do not work in my Fedora install. The reason why the first one doesn't work is because there is no /etc/iftab file. the reason why the second one works is because udev rules are not listed in etc (they are in lib instead and have different names and structures)

Thankfully, Fedora has built in a mechanism to modify the names of NICs post install. You do it by editing the following file

/lib/udev/rules.d/71-biosdevname.rules

so the line which reads

GOTO="netdevicename_end"

commented by default, is uncommented

Then you need to edit
/etc/default/grub

by adding the following line to the bottom:

biosdevname=0

Then I backed up my ifcfg em1 network script by issuing

cp /etc/sysconfig/network-scripts/ifcfg-em1 /etc/sysconfig/network-scripts/ifcfg-em1.old

then I renamed it eth0 (the number can be anything, I believe, between 0 and 9, and matlab will figure it out when it activates):

mv /etc/sysconfig/network-scripts/ifcfg-em1 /etc/sysconfig/network-scripts/ifcfg-eth0

and edited ifcfg-eth0 so the line which read

DEVICE="em1"

to read:

DEVICE="eth0"

This is all the information the machine needs, when it boots up, to change the naming convention from em1 back over to eth0.

Upon reboot, ifconfig shows eth0 where em1 was before (dmesg | grep eth would also show the change), and matlab installs perfectly.

A satisfyingly geeky end to a Tuesday!