How to turn off the Amazon search in the dash

The latest distribution of Ubuntu (12.10, Quantal Quetzal) has an improved search function, which by default includes searching Amazon. This can be very handy if you like Amazon, but it also raises concerns for privacy. The issue is hot topic in the Ubuntu community, with some saying, that it's a good source of revenue for the Canonical, the Ubuntu developers, but other's being concerned about the commercialisation of a open source operating system.
I think having Amazon included is a interesting option, but I do think, that it should not be default, but rather optional, maybe it could be included in the installation menu, when you set keyboard option, time zone, etc.
Also, Ubuntu is a international project, people from all over the world use this distribution, but Amazon is available only in selected countries.
To turn off the Amazon search, click on the Dash Home and search for privacy. Then turn the switch "Include online search results" to off.

This will turn off all online searches in the Dash.

Installing Japanese input on Ubuntu 12.10

In my last post I wrote about the terminal command that will enable Japanese input in Qt-4 applications, for example Anki, a flash card program for studying languages or basically anything else.
On localizing Japan, a step by step introduction on how to install the IBUS system is laid out, but when I followed it, I had the problem, that the IBUS icon did not show up in the toolbar, so I found a terminal command to fix that:

ibus-daemon -drx

Also, on Ubuntu 12.10, Ibus-qt4 should already be installed by default if you use the software centre to install Japanese input, but it did not work. I uninstalled it using

sudo apt-get remove --purge ibus-qt4

And reinstalled it using:

sudo apt-get install ibus-qt4

Now, Japanese input is working, but we'll see how it goes...

Anthy Japanese Input in Anki

Anthy is an IBUS method to input Japanese characters, write in hiragana and click F7 for conversion to Katakana. This works fine in the standard applications, like LibreOffice, or Firefox, but does not work in Qt applications, as is Anki.

Qt is a cross-platform application framework that is widely used for developing application software with a graphical user interface (GUI). (from wikipedia)

To fix this I stumbled upon this solution:

$ sudo apt-get install ibus-qt4

Restart Anki, and it works.

Image processing using Fiji ImageJ and Adobe Photoshop / Illustrator

This is my workflow for processing SEM or TEM images to make them publication ready. Images from SEM are usually saved as tif files and come in two versions. One contains the scale bar and other information, the other one does not. I want to get the scale bar from one image and put it into the empty one: In Fij, I open both images and use set scale to extract the scale from the first image. I then set the same scale in the second image, and input a scale bar using Analyze -> Tools -> Scale bar.
Then I open the image in photoshop and crop it to size (8.25cm width, 600dpi) and turn it into grayscale.
Then I open the image in Illustrator and insert a scale bar (2mm high), with writing at 10pt, bold and Myriad Pro.

Installing additional LaTeX fonts using the command line

After installing LaTeX, I tried to compile a paper written using the achemso class. This is a class written and maintained by Joseph Wright for the journals of the American Chemical Society. Unfortunately, I did get some error, that related to a missing font. In the original achemso.dtx file it said that we need a few packages, one of them is mathpazo. This was not installed on my system so I downloaded an additional font package: sudo apt-get install texlive-fonts-recommended texlive-fonts-extra

Installing Driver for Ethernet Atheros Commuications AR8162

After I installed ubuntu I noticed a few major problems. The first is that I do not have any internet connection, neither ethernet nor wifi. So I needed to find out how to fix that.
First, I found out what controllers are installed using the lspci command.
The output (last two lines) gave me the following:
Network controller: Intel Corporation Centrino Wireless-N 2230 (rev c4)
Ethernet controller: Atheros Communications Inc. AR8162 Fast Ethernet (rev 10)

After googling around, I found out that the driver for the ethernet is not installed on my system, so I need to do that manually. As I did not have an internet connection, I downloaded the driver from this website. According to the forum post above, I need to use the following file:
compat-wireless-2012-02-28-p.tar.bz2

I saved it onto a flash drive and copied it onto the Desktop. Then I ran the following commands:

cd ~/Desktop
tar -xvf compat-wireless-2012-02-28-p.tar.bz2
cd compat-wireless-2012-02-28-p
scripts/driver-select alx
make
sudo make install

I got a lot of output, some referencing to the grub bootloader and Windows 7, so I rebooted into Windows 7 to check everything was still ok, which it was. I then booted back into ubuntu, and voila, the ethernet connection was working.

I then ran an update of Ubuntu using

sudo apt-get update

Terminal Commands

There are a few commands I use in the Terminal that are worth writing down.

To get information about ethernet and w-lan:
ifconfig -a

To save the output of a command to a file, use the > sign. The file gets saved straight into the home directory:

ifconfig -a > saveoutput.txt  

To get information about controllers:

lspci

Update the whole system using:

sudo apt-get update

Installing Ubuntu along side Windows 7 (Dual Boot)

I wanted to install Ubuntu next to Windows 7, without reinstalling Windows from scratch.
Apparently, Windows doesn't really like any other operating systems on the same computer (go figure), so it's important, that Windows is installed first. If not, and you update it at any point, it might screw everything up. So that's good to know.

Ubuntu can be downloaded for free from http://www.ubuntu.com/ and you can either burn it onto a CD or create a bootable flash drive.

To start from the CD, press F12 as soon as the Dell Logo appears on startup. This will get you into the startup menu, where you can choose the CD. Ubuntu will load and you can choose if you want to try it or install it. I tried it first to check what works. I found that the FN keys on the keyboard work fine, but I was not able to establish a internet connection using Wireless nor Ethernet.
On my super old Toshiba Satellite (2005) I could get an Ethernet connection straight away, so I guess, this is a problem with new drivers. How to download missing drivers for Dell Inspiron is described on the blog Agnipulse.

Clicking on the Install Ubuntu icon brings back up the install wizard. After skipping the wifi connection, I resized partition manually, under 'Something else'.

Under Linux, the partitions are labelled differently, but it's easy to recognise which one is which.

1. /dev/sda1 fat 16 is OEM
2. /dev/sda2 ntfs  is the Recovery
3. /dev/sda3 ntfs is the main HD
4. /dev/sda4 is the (not used) hibernation

I completely deleted sda4, which frees up 8 GB of space. Then I changed sda3 to be 100'000 MB (100 GB).
I then created 4 partitions using this online manual.
Ubuntu installed within 5 mins and then the laptop rebooted into Windows 7. I used EasyBCD, the software recommended on that website, to tell Windows, that it was sharing the drive with a linux OS.

Partitions of Windows 7 on Dell inspiron

I have recently purchase a Dell inspiron Ultrabook with Windows 7 Home edition. It came pre-installed with Windows and a lot of Dell software, so although my solid state hard drive (SSD) is 256 GB large, I have 181 GB free out of 216 GB. So how does this work?

Opening Disk Management shows that the main (and only) drive has 4 partitions:

1. 39 MB: OEM
2. 13.81 GB: Recovery
3. 216.62 GB: OS(C:) NTFS
4. 8.01 GB

Four partitions are the maximum a hard drive can handle. But I would like to install Ubuntu on this laptop as a dual boot next to Windows. That means, I need to get rid of one partition and free up some space.

The first partition is for the Windows Bootloader, the second is the Windows Recovery, number three is the 'regular' partition on which Windows is installed and can be accessed with the explorer. The fourth partition is for hibernation.

It's a good idea to get the Recovery onto some external media. Just follow the steps in the Dell Data Safe Local Backup. (Article ID : 266282). In my case, this were 3 DVDs.

Hibernation under Windows 7 is a deep sleep modus, where everything that was in the RAM gets written on the hard drive and then the power consumption is reduced. That's why the hibernation partition is 8 GB large, the same as the RAM in the laptop. Basically, it's a good idea to have it when you are not using the laptop and are on battery. But, SSDs don't like to have stuff written in one special part of the hard drive as it reduces the life of the SSD; and so it is not recommended to have hibernation with SSDs.

On the Sevenforums is a good manual on how to turn off (and on) hibernation. Turning it off will free an extra 8 GB of space on the hard drive.

Hibernation can be turned off using the windows command line in administrator mode. This is called an elevated command prompt. In the start menu, right click on command prompt and run as administrator. This will change the command prompt to C:\Windows\System32. Now, disable hibernation by typing powercfg -h off. To enable hibernation type powercfg -h on.

Hello World!

The aims of this blog are to publish solutions for problems I have encountered using various operating systems and programs.