New journal paper "Validating the semantics of a medical iconic language using ontological reasoning"

I have published a new journal paper:

journalif [j17] Lamy JB, Soualmia LF, Kerdelhué G, Venot A, Duclos C. Validating the semantics of a medical iconic language using ontological reasoning. Journal of Biomedical Informatics 2013;46(1):56-67

Cerealizer 0.8.1

Cerealizer 0.8.1 is out!

This is a new bugfix release. Get it here:

Towards Soya 2.0

Soya 2.0 is coming!

The most striking feature of Soya 2.0 is mini shaders. They allow to write Open GL / GL SL shaders so easily! With GL SL, you have to rewrite the entire rendering pipeline, even if you want to modify only a small part of it...

On the contrary, with Soya's mini shaders, you can write a mini shader that overrides a part of the rendering pipeline (ex customizing the lighting computation), or that adds an extra step in the rendering (ex deforming the model geometry). Then Soya assembles all mini shaders, adds the missing pieces of the rendering pipeline, and generates a GL SL shader.

Additionally, Soya's mini shaders can be written with a Python-like syntax ;)

Soya provides 16 classes mini shaders, each corresponding to a specific part of the rendering pipeline. Here is an example of a "camera-space deform" mini shader, which deforms the model's geometry in camera space:

wavy_mini_shader = soya.MiniShader("wavy", """
uniform float self.time
def void cameraspace_deform_mini_shader():
  current_vertex.x = current_vertex.x + 0.2 * sin(0.2 * self.time + 3 * current_vertex.y)


Mini shaders can be associated to any object: a Model, a Body (an instance of Model), a World (a group of other 3D object) or a Material. When associating a mini shader to a World, it is inherited by all objects inside this World, and automagically combined with objects' own mini shaders. For more details about mini shaders, see the mini-shader-* tutos!

Want to try and start hacking with Soya 2? You're welcome! The development version can be obtained on this mercurial repository:

Other new features include:

  • Support both Python 2.7 and 3.3,

  • Open GL SL shader support,

  • new exporters for Blender 2.6x, with a bugfixed Blender => Cal3D exporter, able to take into account vertex location, normal and texture coords when merging vertices,

  • LOD support for models,

  • pre-rendered background, usefull for slow computer or old-style games,

  • Partial Open GL ES support (not yet finished).

Cerealizer 0.8

Cerealizer 0.8 is out!

This new version supports both Python 2.x and Python 3.x! Get it here:

Songwrite 2 0.4


Songwrite 2 0.4 is out ! This major version adds supports for diatonic accordion tablature and chords. Additionally, repeat symbols have been (greatly) improved, and a new starting screen has been added. And many bugs have been fixed. Enjoy!

Songwrite 2 0.3

Songwrite 2 0.3 is out ! This major version proposes an improved interface, more usable on small screens, and adds many functionalities including appoggiatura, harmonics, F keys on staff, strumming direction, rests,... It also supports Koyabu board, ukulele, and lyre tablatures (my new instrument, although I'll probably be the only one to use them :-)). It requires EditObj 2 0.3.

There are also many bugfixes, and the licence is now GPL v3 (instead of v2).

Here is the full change log:

  • Touchscreen support

  • Lyre, Koyabu board and Ukulele support

  • Support for F key, appoggiatura, harmonics, strumming direction and rests

  • Smarter copy-paste (autochoose between by string / by note pitch more accurately)

  • Name sharp and bemol notes adequately, depending of the tonality

  • Add a window's icon

  • Fontsize options for screen and printing

  • Interval identification: select 2 notes and Songwrite display the corresponding interval in the title bar!

  • Licence changed to GPL v3


  • Lyrics not placed at the bottom were bugged in PS/PDF export/printing

  • Printing tabs with staffs was sometime causing an infinite loop

  • Printing tabs with staffs was not showing # and b rightly on the staff

  • After playing, select the previously selected notes

  • When reducing the length of ALL bars, the newly created bars at the end now use the lew length

  • Take capo into account when playing

  • Can play hammer / pull / legato / slide with no limit of amplitude

  • Fix g8 staff

  • Fix capo

My research area explained graphically

Here is a graphical presentation of my academic research area... Nobody should now says that it is ununderstandable and obscure !


Soya 0.15rc1 is out !

Soya 0.15rc1 is out !

Here is the Changelog :

  • January 2009 : Soya3D 0.15rc1

  • ODE 10 compatibility (required)

  • New collide property for lazer.

  • Quiet mode for soya initialisation and quit

  • New event management system. round event are now stored in main_loop.event and main_loop.raw_event.

  • New round_task attribut for main_loop.

  • Allow screenshot from backbuffer.

  • Allow to use WorldStep instead of WorldQuickStep for ODE iteration.

  • Allow None as angular_velocity, linear_velocity, torque, or force.

  • Allow None as hi_stop, lo_stop

  • Bugfixes

  • Fix delta_x and delta_y in coalesced event

  • Fix AngularMotorJoint API

  • soya initialisation now write in the common stdout and stderr

  • Fix font related segfault when soya wasn't initialised

  • Fix Pudding MainLoop (thanks David Martinez)

  • Work-around for OpenAL bug for absolute sound sources

Using Sunbird calendar on PDA (i.e. wake on RTC alarm on calendar's events)

The attached scripts allow to use Sunbird on PDA, that is to say to wake up automatically the device on Sunbird's alarm. I am successfully using them on the Sharp Netwalker (aka PC-Z1) but it should work on any device that supports wake up on RTC (the Netwalker does only after some hacks) and uses the APM daemon for power-related event management (the Netwalker does ; however for other devices that use ACPI, it should be quite easy to adapt).

To install it, proceed as following:

  1. Install the python-pysqlite2 package.

  2. Copy the attached file (link below) somewhere on your PATH (for example, in /usr/bin) and make this file executable:

    chmod a+x /usr/bin/
  3. Copy the attached file (link below) 50sunbird_rtc_alarm in /etc/apm/suspend.d and make this file executable:

    chmod a+x /etc/apm/suspend.d/50sunbird_rtc_alarm).
  4. Edit . At line 3, indicate the maximum time (in second) your device needs to resume from suspend (the default 10 seconds is right for the Netwalker).

  5. At line 4, indicate the path to the Sunbird's storage file. if you have no idea at all, the following command should give you some hints:

    ls /home/*/.mozilla/sunbird/*/storage.sdb

That's all! Now, every time you suspend the device, is called. It looks Sunbird's calendar for the closest alarm, and, if any, define the device's RTC alarm as needed. Then, the device will wake up a few second before the alarm, and thus Sunbird will be able to beep you.


wake up on RTC alarm for the Netwalker

By default, the Netwalker does not support waking up on RTC alarm, which implies that it cannot be used as a PDA. It has a calendar program (Sunbird), and alarms can be set on events, but the Netwalker will raise the alarm only if the device is on at this time... not good for a PDA !

Actually, the hardware does support waking up on RTC alarm, but this functionality is already used... by the battery drivers ! Any alarm you set will be erased by the drivers of the battery when suspending the Netwalker. It seems that the battery need to be checked every 30 minutes when the device is suspended.

So here is a patch that modifies the battery drivers so as it honors the previously set RTC alarm if it is closer in time. The patch is intended to be applied on the Netwalker's Linux kernel from http :// fsl-imx51/linux-fsl-imx51_2.6.28-15.50fsl1araneo7.tar.gz. See this how to for compiling and flashing the Linux kernel on the Netwalker.

With this patch, the Netwalker can now wake up on RTC alarm. You can verify that by running the commands:

sudo echo 0 > /sys/class/rtc/rtc0/wakealarm
sudo echo `date '+%s' -d '+2minutes'` > /sys/class/rtc/rtc0/wakealarm

And then suspend your Netwalker. It should wake up 2 minutes later.

You can also find below my .config kernel configuration file. I've also disabled the Netwalker's quick keys since they are constantly starting apps even if I don't touch them ; if you want to keep them working, change CONFIG_TOUCHKEY_MXC in .config.

However, wake up on RTC alarm is only the first step for using the Netwalker as a PDA: the next step consists in creating RTC alarm from the calendar program. Stay tuned!



How to update and flash the kernel on the Netwalker (Sharp PC-Z1)

The Netwalker is a very small laptop computer with an ARM CPU, running Ubuntu GNU/Linux. As it uses flash memory instead of a hard drive, you need a special procedure to update the kernel (the Netwalker does not use standard boot loader like Lilo or Grub). This small how to describes how to compile the Linux kernel for the Netwalker, and then how to flash the kernel. I will provide interesting kernel hacks later on this blog.

Compiling the kernel

I used the kernel from Canonical archive. The sources are available here: It is not the same sources used by Sharp, but they work well.

Then, you can grab the Sharp's Netwalker kernel configuration in /sys/config.gz . Uncompress it, rename it ".config", and move it in the kernel source directory. Add in the kernel config the option CONFIG_KS7010_SDIO for the Wifi (strangely it is not present in /sys/config.gz).

Finally, compile the Linux kernel as usual, and install it.

Flashing the kernel

  1. You need a 2 Gb (or more) microSD / microSDHC card. BEWARE : the card will be reformatted and any data on the card will be deleted! You should also make a safe copy of any data on the Netwalker.

  2. Create a microSD recovery card; instruction are in Japanese on Sharp's website, so here is a summary.

  3. Download this script, and uncompress it:

  4. Insert the microSD card in the Netwalker, connect the Netwalker to Internet, and run the script. The script will set up the recovery card. It downloads many data (about 1 Gb) and thus it takes several hours.

  5. The microSD recovery card can be used to reset the Netwalker, reflashing the kernel and erasing all data. This can be done by shutting down the Netwalker, and pressing both mouse button at start- up (you need to press the button quite a long time). However, this is not what we want to do: the objective of this how-to is to flash only the kernel. To do so, follow the next steps.

  6. Mount the microSD card. This can be done with these commands:

mkdir /tmp/test
mount /dev/mmcblk0p1 /tmp/test
  1. Edit file /tmp/test/firmware/spider.srp ,and remove the line "5,ubi.img". This line is responsible for erasing all data on the Netwalker. The next line (4,zImage) is responsible for flashing the kernel, so we keep it.

  2. Replace /tmp/test/firmware/zImage by the new kernel image (typically /boot/vmlinuzXXX).

  3. Edit file /tmp/test/usr/local/bin/ . At line 47 and following, add /tmp/test before /usr/local/bin/... (there is 5 lines to modify).

  4. Connect the Netwalker's power cable.

  5. Run /tmp/test/usr/local/bin/ . Then press "y", wait a few second and press any key to exit.

  6. The kernel has been flashed! Now, reboot the Netwalker and enjoy your new kernel!

Arkanae III 0.1

The first stable release of Arkanae III (0.1) is available! This release includes the two first chapters of the game, which represent about 20% of the game. However, the bad news for you, English reader, is that it is currently available only in French.

Songwrite 2 0.2.1

Songwrite 2 0.2.1 is out ! It fixes many bugs of version 0.2. It is also possible to run it on Qtopia, e.g. on a Zaurus ! This version requires EditObj 2 0.2.1.

Here is the change log :

  • Qt / Qtopia support (tested on Sharp Zaurus)

  • When selecting a note, take the current duration into account in a smarter way

  • Allow to hide the edition panel


  • Fix songref in songbook edition dialog box

  • Fix default filename when exporting

  • Fix filename filter bug in import / export

  • Fix legato in ABC importer

  • Fix dot in ABC importer

  • Fix playlist analysis in ABC importer

  • Fix partial bars in ABC importer

  • Fix hammer/pull update when the second note is modified

  • Fix zoom when editing a new song

  • Fix quarter tripplets

  • Fix Texttab importer and exporter (string tuning was messing around, thanks Adrian Quark)

  • Fix launching from source directory (thanks Slawek)

Songwrite 2 0.2 : Tin whistle release

Songwrite 2 0.2 is out !

It adds support for flute fingering notations (i.e. small schema showing which holes should be covered in the flute, see the screenshot section) for tin whistle and recorder. It also support 6/8 and jig rhythms and can import file in the ABC format, two useful features for Irish music.

Finally, it also provides a new PDF exporter, which is now independent from Lilypond (Consequently, Lilypond is no longer a requirement for Songwrite 2). Lilypond is no longer used for PDF export, because it has poor support for non-staff notations (like tablature or fingering), and because incompatibilities are frequent between two version of Lilypond.

Songwrite 2 0.2 requires the lastest version of EditObj2 (0.2).