Starting to work at GII

That's it. I've finished my  2 years Post-Doc adventure at TAU.
I'm now starting to work on the Israel national Earthquake Early Warning System (EEWS).
As of tomorrow, I'm going to work at the Seismology Division of the Geophysical Institute of Israel (GII).

EQMet TSA-SMA setup for SeisComp3

The following post will describe how to install EQMet INTERNET-READY STRONG MOTION ACCELEROGRAPH (TSA-SMA) and set it up for SeisComp3.


Following the instruction in the manual:
The initial steps are to connect the TSA-SMA to electricity, GPS and a computer via the USB device connection.
Then, connect to the device via serial connection.
On windows: read the manual and follow the orders using putty. Don’t forget to download the driver for the device from EQMet site (http://www.eqmet.com/eng/Linux-cdc-acm.zip)

On Linux:
install cu:
# sudo yum install uucp
get the tty of the connection:
# dmesg | grep 'tty'
on my system it was: ttyACM0 but it can be ttyS[1234] or serial.
next I connect to the device:
# cu -l /dev/ttyACM0 -s 115200
it takes a while to prompt for user and password (root,kmi) press enter if does not prompt.
I need to assign an IP based on the mac address so I check the mac:
# ifconfig
after I got the IP, it is easy to connect via http sftp and ssh.

for static IP, edit /etc/network/interfaces:
replace:
iface eth0 inet dhcp
with:
iface eth0 inet static
address <IP>
netmask <MASK>
gateway <GATEWAY>
dns-nameservers <DNS-SERVER>

connect to the device via http.

Next go to Parameters:hardware menu option.

update to your preferable network-station-location-channel ID in:

- Network ID

- Unit ID and Site ID

- dig1 ChX ID

- dig1 ChX Location code

where X in channel 1, 2 or 3.

press OK.

Next, following the response mail I got for EQmet support regarding seedlink connection:

Sir,

The limited version of Rockhound in the TSA-SMA does not support continuous recording. However, you can approximate continuous recording by adding the SEEDLink mirror module and configuring it to accept data from the RockToSlink module at address 127.0.0.1, port 18000 (or as configured). You should add this module after installing and adding in the RockToSlink module.

This module writes the received MiniSEED packets out to storage and breaks the files at approximately the specified duration (depending on MiniSEED packet contents). If you add this module, you should also consider adding an auto file delete module to avoid filling the storage. A file sender module may also be useful (SSH, FTP, or email).

The RockToSlink module for Rockhound is provided by ISTI, New York. The module and documentation is available from ISTI at http://www.isti2.com/RockToSLink/

Technical support for RockToSLink is available from ISTI at isti-info@isti.com. SEEDlink is a public domain program and protocols. Support for these programs including detailed protocol descriptions or installation and setup of the programs is not provided by Kinemetrics.

Regards,

EQMet, Technical Support
support@eqmet.com

installe the RockToSlink module and add it to the workflow:

1. Download the rocktoslik module from http://www.isti2.com/RockToSLink/dist_pub/:
> wget -v http://www.isti2.com/RockToSLink/dist_pub/RockToSLink_v1.0_dist.zip
2. Unzip it:
> unzip RockToSLink_v1.0_dist.zip
following the instractions in http://www.isti2.com/RockToSLink/current_dist/docs/RockToSLink_ovr.html:
3. sftp to the device:
> sftp root@<IP>
4. Change directory to module location:
> cd  /usr/rock/SMARTSDist/injar
5 Upload the module-update jar file:
> put RockToSLink_update.jar
6. connect via ssh:
> ssh root@<IP>
7. Change directory to module location:
> cd  /usr/rock/SMARTSDist/injar
8. Rename "RockToSLink_update.jar" to "update.jar"
> mv RockToSLink_update.jar update.jar
9. Reboot the instrument:
> reboot
Now add the RockToLink module to device layout:
10. In the device http menue Parameters: Advanced features, add options for Add/Remove Modules, Replace Modules and Advanced Modules.
11. In Module Add, add the RockToLink module.
12. Press apply changes now.

Now go to system operation and make sure all settings are correct.

enjoy.

LSM303 accelerometer on RaspberryPi

After getting my new LSM303 accelerometer, I got my great electronics tec. Daviv Shtibelman to wire it up for RPI.
Connecting LSM303 pins 1 (SCL), 2 (SDA), 6 (GND) and 8 (V3V) to pins 5 (SCL), 3 (SDA), 6 (GND) and 1 (V3V) on the Pi board.
On my ArchlinuxARM OS I had to install i2c-tools:
> pacman -S i2c-tools
And add i2c modules:
> echo i2c-dev > /etc/modules-load.d/ i2c.conf
> echo i2c-bcm2708 >> /etc/modules-load.d/ i2c.conf
> reboot

now to check it works:
> i2cdetect -y 1
got a message like this:
     0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f
00:          -- -- -- -- -- -- -- -- -- -- -- -- --
10: -- -- -- -- -- -- -- -- -- 19 -- -- -- -- 1e --
20: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
30: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
40: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
50: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
60: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
70: -- -- -- -- -- -- -- --

Now, following this, I test it and it works. Now I'm up for creating my own code.

Made some changes to the code:

main.cpp

#include"LSM303DLHC.h"
#include<stdio.h>
#include <unistd.h>


/*
   getHeading() calculates a tilt-compensated heading.
   A float between 0 and 360 degrees is returned. You need
   to pass this function both a magneto and acceleration array.
 
   Headings are calculated as specified in AN3192:
   http://www.sparkfun.com/datasheets/Sensors/Magneto/Tilt%20Compensated%20Compass.pdf
 
*/

float getHeading(LSM303& lsm303dlhc);

#define PI 3.141592654


int main(void)
{
    uint8_t bajt;
    const char *fileN = "/dev/i2c-1";
    LSM303 lsm303dlhc(fileN);

    lsm303dlhc.enalbe();

    while(1)
    {
        lsm303dlhc.readAccelerationRaw();
        lsm303dlhc.readMagnetometerRaw();
        printf("acc [m/s^2]: \e[27;1;31m %f \e[m \e[27;1;32m %f \e[m \e[27;1;34m %f \e[m mag:  \e[27;1;31m %d \e[m  \e[27;1;32m %d \e[m \e[27;1;34m %d\e[m %fdeg\n",
               (int16_t)lsm303dlhc.acc_x_raw*0.00957,(int16_t)lsm303dlhc.acc_y_raw*0.00957,-(int16_t)lsm303dlhc.acc_z_raw*0.00957,
               (int16_t)lsm303dlhc.mag_x_raw, (int16_t)lsm303dlhc.mag_y_raw, (int16_t)lsm303dlhc.mag_z_raw,getHeading(lsm303dlhc));
        usleep(10);
       }

    }


float getHeading(LSM303& lsm303dlhc)
{
  float heading,pitch,roll,xh,yh,zh;
  // see section 1.2 in app note AN3192
  int magValue[3];
  float accelValue[3];
  magValue[0] = (int16_t)lsm303dlhc.mag_x_raw;
  magValue[1] = (int16_t)lsm303dlhc.mag_y_raw;
  magValue[2] = (int16_t)lsm303dlhc.mag_z_raw;
  accelValue[0] = (int16_t)lsm303dlhc.acc_x_raw*0.000976531;
  accelValue[1] = (int16_t)lsm303dlhc.acc_y_raw*0.000976531;
  accelValue[2] = -(int16_t)lsm303dlhc.acc_z_raw*0.000976531;

    // see appendix A in app note AN3192
  pitch = asin(-accelValue[0]);
  roll = asin(accelValue[1]/cos(pitch));

  xh = magValue[0] * cos(pitch) + magValue[2] * sin(pitch);
  yh = magValue[0] * sin(roll) * sin(pitch) + magValue[1] * cos(roll) - magValue[2] * sin(roll) * cos(pitch);
  zh = -magValue[0] * cos(roll) * sin(pitch) + magValue[1] * sin(roll) + magValue[2] * cos(roll) * cos(pitch);

  heading = 180*atan2(yh,xh)/PI;

  if (heading <0)
    heading += 360;

  return heading;
}

LSM303DLHC.cpp:

#include"LSM303DLHC.h"
#include<math.h>
#include<stdio.h>

/*Conection to Raspberry PI:
 LSM303     Raspberry PI
 VDD    ->  3V3(PIN 1)
 SDA    ->  SDA(PIN 3)
 SCL    ->  SCL(PIN 5)
 GND    ->  GND(PIN 6)
*/

#define LSM303DLHC_MAG_ADDRESS            (0x3C >> 1)
#define LSM303DLHC_ACC_ADDRESS            (0x32 >> 1)

LSM303::LSM303(const char * i2cDeviceName) : i2c_lsm303(i2cDeviceName)
{

}

uint8_t LSM303::readAccRegister(uint8_t regAddr)
{
    i2c_lsm303.addrSet(LSM303DLHC_ACC_ADDRESS);
    return i2c_lsm303.readByte(regAddr);
}

uint8_t LSM303::readMagRegister(uint8_t regAddr)
{
    i2c_lsm303.addrSet(LSM303DLHC_MAG_ADDRESS);
    return i2c_lsm303.readByte(regAddr);
}

void LSM303::writeAccRegister(uint8_t regAddr,uint8_t byte)
{
    i2c_lsm303.addrSet(LSM303DLHC_ACC_ADDRESS);
    i2c_lsm303.writeByte(regAddr, byte);

}

void LSM303::writeMagRegister(uint8_t regAddr, uint8_t byte)
{
    i2c_lsm303.addrSet(LSM303DLHC_MAG_ADDRESS);
    i2c_lsm303.writeByte(regAddr, byte);

}

void LSM303::enalbe(void)
{
   writeAccRegister(LSM303_CTRL_REG1, 0b10010111);
   writeAccRegister(LSM303_CTRL_REG4, 0b00001000);

   writeMagRegister(LSM303_MR_REG, 0x00);
}

void LSM303::readAccelerationRaw(void)
{
    uint8_t block[6];

    i2c_lsm303.addrSet(LSM303DLHC_ACC_ADDRESS);

    i2c_lsm303.readBlock(0x80 | LSM303_OUT_X_L_A, sizeof(block), block);
    acc_x_raw = (int16_t)(block[0] | (block[1] << 8)) >> 4;
    acc_y_raw = (int16_t)(block[2] | block[3] << 8) >> 4;
    acc_z_raw = (int16_t)(block[4] | block[5] << 8) >> 4;

}

void LSM303::readMagnetometerRaw(void)
{
    uint8_t block[6];

    i2c_lsm303.addrSet(LSM303DLHC_MAG_ADDRESS);
    i2c_lsm303.readBlock(0x80 | LSM303_OUT_X_H_M, sizeof(block), block);

    mag_x_raw = (int16_t)(block[1] | block[0] << 8);
    mag_y_raw = (int16_t)(block[5] | block[4] << 8);
    mag_z_raw = (int16_t)(block[3] | block[2] << 8);

}

void LSM303::readAcceleration(void)
{
    readAccelerationRaw();
}

Done with the PhD., Moving forward

Finally, I finished my PhD. and now it time to move forward.
Taking my Professors advice, I'm making the first steps in the world of seismology and I'm going to spend the next few years in Tel-Aviv University, working with Dr. Alon Ziv and Dr. Hillel Wust-Bloch.
The main work is building and maintain a local mini seismic-array network. I am going to actually place the seismometers, connect the dataloggers and build the server to collect the data. We are going to use different devices - Lennartz LE-3Dlite1DV MkII seismometers, Trillium broadband seismometers, TSA-SMA accelerometers and Summit M Hydra dataloggers. On the server side, We are going to use Seiscomp3 as our main framework, but we probably research for new algorithms and Seiscomp3 modules to better suit it to our needs.

Me getting the PhD. diploma from Prof. Rivka Carmi, presedent of BGU

JoyWarrior24F14 Udev rules

The JW24F14 device is accessible as a HID only as root. In order to access it as a user, I had to write a UDEV rule with the help of this post. more info about udev rules can be found here.
issue the command:
> sudo vi /etc/udev/rules.d/10-JoyWarrior24F14.rules
and when in editing mode (i) add:

# Rules for accessing JoyWarrior24F14 HID as user:
SUBSYSTEM=="usb", ATTRS{idVendor}=="07C0", ATTRS{idProduct}=="0140", MODE:="666", GROUP="users"
SUBSYSTEM=="usb", ATTRS{idVendor}=="07c0", ATTRS{idProduct}=="1116", MODE:="666", GROUP="users"

SeisComp3 - get events data

After installing  Seiscomp3 and running it for a while, now it is time to play with the data.
As a first step I want to be able to see the events outside the SeisComp3 environment.
This will later serve me when exporting the data to a web page or reports.
The steps described here are: 1) get a list of events, 2) export the data to an xml file and 3) print the data as a bulletin.
1) Get a list of events:
scevtls -d mysql://sysop:sysop@localhost/seiscomp3
Will give a list of event codes like:

Wrong 'begin' format -> setting to None
Setting start to 1970-01-01 00:00:00
Setting end to 2012-10-24 08:17:13
gfz2012uizn
gfz2012atlf
...

where gfz will be the agency prefix and the last 4 letters will be random code.
You can also set begin and end time to get only a time window events. see scevtls documentation.

2) For this example I select one event (in csh environment):
set EVENT = gfz2012uizn
Now we can export the event data to an xml file:
scxmldump -d mysql://sysop:sysop@localhost/seiscomp3 -E $EVENT -P -M -A -o test.xml
see scxmldump for more information

3) Print the data to stdout:
scbulletin -i test.xml
Note that it is possible to skip the xmp part by using:
scbulletin -d mysql://sysop:sysop@localhost/seiscomp3 -E $EVENT
also adding -3 as a flag will output even more details.
see scbulletin for more info.

I'll update later with a python script to export the data to a Google Earth kml file.

Installing SeisComp3 on fedora 17

After installing Fedora 17  I will now describe how to install MySQL server and SeisComp3.

first, install MySQL (following this):
> sudo yum install -y mysql mysql-server

enable and start MySQL service:
> sudo systemctl enable mysqld.service
> sudo systemctl start mysqld.service

Next, secure the server:
> sudo /usr/bin/mysql_secure_installation
(answer yes to all questions and change the MySQL root password)
If you need to change the database location from the default follow this (source):
Stop the service:
> systemctl stop mysqld.service
Copy from default to new location:
> cp -R -p /var/lib/mysql /path/to/new/datadir
Clean unneeded files:
> rm /path/to/new/datadir
(don't worry about error messages - the undeleted files are the databases)
Edit the configuration file:
>  gedit /etc/mysql/my.cnf
(change keyword value of datadir to the new location)
Restart the service:
> systemctl restart mysqld.service

Now to the SeisComp3 install (Zurich version for fedora16 modified for fedora 17):
Add needed packages:
> sudo yum install -y boost-filesystem boost-iostreams boost-program-options boost-serialization boost-signals
boost-thread boost-wave boost-regex boost-devel ncurses python-numeric numpy alsa-utils festival
Link installed libraries (so.1.48) to the needed packages (so.1.47):

> sudo ln -s /usr/lib64/libboost_iostreams.so.1.48.0 /usr/lib64/libboost_iostreams.so.1.47.0

> sudo ln -s /usr/lib64/libboost_filesystem.so.1.48.0 /usr/lib64/libboost_filesystem.so.1.47.0
> sudo ln -s /usr/lib64/libboost_system.so.1.48.0 /usr/lib64/libboost_system.so.1.47.0
> sudo ln -s /usr/lib64/libboost_regex.so.1.48.0 /usr/lib64/libboost_regex.so.1.47.0
> sudo ln -s /usr/lib64/libboost_thread-mt.so.1.48.0 /usr/lib64/libboost_thread-mt.so.1.47.0
> sudo ln -s /usr/lib64/libboost_program_options.so.1.48.0 /usr/lib64/libboost_program_options.so.1.47.0
> sudo ln -s /usr/lib64/libboost_signals.so.1.48.0 /usr/lib64/libboost_signals.so.1.47.0
Put key files in ~/.seiscomp3/key/ directory
Install using the setup and seiscomp config procedures described in the SeisComp3 documentations
add a source to env.sh file in your .bashrc:
source ~/seiscomp3/lib/env.sh

For the seattle release use:
>sudo yum install -y boost boost-devel python-numeric


Don't forget to download and extract to the seiscomp directory, the correct fedora seiscomp package (e.g. seiscomp3-zurich-xxxx.xxx.xx-fedora16-x86_64.tar.gz), the maps (e.g. seiscomp3-maps.tar.gz) and the methadata of GE network (e.g. seiscomp3-metadata-GE-2010.tar.gz).