Ubuntu 10.04 LTS on my IBM Thinkpad R50e

I decided to upgrade from 9.04 to 10.04 LTS the other day. I was hoping the installation will be smooth. However, the installation suddenly stopped after a few minutes with the display going blank and disk activity stopping. After some googling, I found out that is a bug that occurs in systems with Intel graphics adapters. I found a workaround here. Specifically, I switched to VESA as the graphics driver to use during the installation by passing some options to the kernel.

I used the following partitioning scheme:
/ - 10GB
/home - 5GB
/opt - 3GB
swap - 500MB

The next step then is to customize the installation and add additional software. Before that, I need configure the dual screen setup. Since VESA does not support dual screen, I need to change the driver in /etc/X11/xorg.conf to "intel".  However, this causes the system to hang. The workaround I followed is to use a kernel from Karmic(2.6.31-20-generic). Installing a new kernel is new to me since 10.04 uses GRUB2 and there is no longer /boot/grub/menu.lst.

The following are the initial packages I installed to get a functioning system ready for work:
*Acrobat Reader (for reading journal articles)
*Thunderbird (for email)
*Flash Plug-in (for watching great table tennis matches)
*MPlayer and gecko-mediaplayer (for listening to RJ100)
*VLC (for watching Big Bang Theory and How I Met Your Mother)
*GYachE (for allowing me to see "invisible" people in YM)
*build-essential,qemu,nasm (for OS programming stuff)
*Subversion (for checking out source code of projects)
*vpnc (for allowing me to connect to ICS VPN)
*GVim (may favorite text editor)
*XAMPP (I use this for PHP and MySQL programming instead of the packages from Ubuntu itself)

So far, my 10.04 experience is great!

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Congratulations to my first batch of advisees

• Richard Christiensen E. Aluning
• Adora Alexis B. Cabuyadao
• Mark Joseph G. Caliston
• Axel S. Trajano 

Do your best out there!

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Visual C# 2008 and MySQL using ODBC

1. Download MySQL 5.1 Server here
2. Download ODBC MySQL Connector here
3. MySQL Server Installation








4. ODBC Connector


5. ODBC Configuration






6. Here is a Sample Code.

For more information click here

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Using the Geospatial Data Abstraction Library (GDAL) in Ubuntu

For a project, I need to process SRTM elevation data. GDAL is a software library that makes it easy to read and write raster geospatial data formats. I decided to give it a try since SRTM data uses the ESRI grid format supported by the library.

1. Install the the GDAL libraries and utilities

$ apt-get install libgdal1-1.5.0 gdal-bin

2. Sample code. The SRTM data file path is in the variable pszFilename. The code is based on the tutorial.

#include <stdio.h>
#include <gdal.h>>
int main()
{
    GDALDatasetH  hDataset;
    char *pszFilename = "/media/DATA/srtm_61_10.asc";
    GDALDriverH   hDriver;
    double        adfGeoTransform[6];
    GDALRasterBandH hBand;
    int             nBlockXSize, nBlockYSize;
    int             bGotMin, bGotMax;
    double          adfMinMax[2];
    float *pafScanline;
    int   nXSize;
    int i;

    GDALAllRegister();
    hDataset = GDALOpen( pszFilename, GA_ReadOnly );
    if( hDataset == NULL )
    {
        printf("Cannot open file.");
    }
    hDriver = GDALGetDatasetDriver( hDataset );
    printf( "Driver: %s/%s\n",
            GDALGetDriverShortName( hDriver ),
            GDALGetDriverLongName( hDriver ) );
    printf( "Size is %dx%dx%d\n",
            GDALGetRasterXSize( hDataset ), 
            GDALGetRasterYSize( hDataset ),
            GDALGetRasterCount( hDataset ) );
    if( GDALGetProjectionRef( hDataset ) != NULL )
        printf( "Projection is `%s'\n", GDALGetProjectionRef( hDataset ) );
    if( GDALGetGeoTransform( hDataset, adfGeoTransform ) == CE_None )
    {
        printf( "Origin = (%.6f,%.6f)\n",
                adfGeoTransform[0], adfGeoTransform[3] );
        printf( "Pixel Size = (%.6f,%.6f)\n",
                adfGeoTransform[1], adfGeoTransform[5] );
    }
    hBand = GDALGetRasterBand( hDataset, 1 );
    GDALGetBlockSize( hBand, &nBlockXSize, &nBlockYSize );
    printf( "Block=%dx%d Type=%s, ColorInterp=%s\n",
            nBlockXSize, nBlockYSize,
            GDALGetDataTypeName(GDALGetRasterDataType(hBand)),
            GDALGetColorInterpretationName(
            GDALGetRasterColorInterpretation(hBand)) 
    );
    adfMinMax[0] = GDALGetRasterMinimum( hBand, &bGotMin );
    adfMinMax[1] = GDALGetRasterMaximum( hBand, &bGotMax );
    if( ! (bGotMin && bGotMax) )
      GDALComputeRasterMinMax( hBand, TRUE, adfMinMax );
    printf( "Min=%.3fd, Max=%.3f\n", adfMinMax[0], adfMinMax[1] );
    if( GDALGetOverviewCount(hBand) > 0 )
      printf( "Band has %d overviews.\n", GDALGetOverviewCount(hBand));
    if( GDALGetRasterColorTable( hBand ) != NULL )
      printf( "Band has a color table with %d entries.\n", 
                 GDALGetColorEntryCount(
                 GDALGetRasterColorTable( hBand ) ) 
      );
    nXSize = GDALGetRasterBandXSize( hBand );
    pafScanline = (float *) CPLMalloc(sizeof(float)*nXSize);
    GDALRasterIO( hBand, GF_Read, 0, 0, nXSize, 1, 
                    pafScanline, nXSize, 1, GDT_Float32, 
                     0, 0 );
    for (i=0;i<20;i++){
      printf("%f\n", pafScanline[i]);
    }
}

3. Build the example

$ gcc -lgdal1.5.0 -I/usr/include/gdal -o testgdal.exe testgdal.c

4. Run

$./testgdal.exe
Driver: AAIGrid/Arc/Info ASCII Grid
Size is 6001x6001x1
Projection is `GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9108"]],AXIS["Lat",NORTH],AXIS["Long",EAST],AUTHORITY["EPSG","4326"]]'
Origin = (119.999583,15.000417)
Pixel Size = (0.000833,-0.000833)
Block=6001x1 Type=Int16, ColorInterp=Undefined
Min=-27.000d, Max=2375.000

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On Research Methodologies

Last December 14, 2009 I attended the  Second CAS Student-Faculty Research Conference held at the CAS auditorium. The objective of the conference is to present the research output of the different departments and institutes of the College of Arts and Sciences. There were four plenary presentations in the conference from IMSP, DSS, IC and ICS, and IBS.  The parallel sessions held in the afternoon were divided into four clusters. 

• Social Sciences, Humanities, MST and Education Cluster
• Physics and Chemistry Cluster
• Mathematics, Statistics, and Computer Science Cluster
• Biology and Environment Cluster

I decided to attend at least one presentation from each cluster in order to know what methodologies are used by the researchers in their field and work. Based on my samples, majority of the researchers conducted some form of survey and performed statistical analysis (frequency analysis, regression, test of significance).  Conclusions were drawn from the result of the statistical analysis. Another methodology used is simulation and modeling (Kinetic-Monte-Carlo, Time Series Analysis, Neural Networks, Regression Models). The main justification for using modeling and simulation is that conducting the actual experiment is expensive and time consuming. Model validation, however, was lacking in some of the researches. Product development is another methodology employed. Researchers developed a system (hardware or software), a chemical product, or an experimental setup. The product addresses some problem in the field. A common keyword in the title of the research papers presented  is characterization. Based on my understanding, characterization is providing a quantitative(or qualitative) description of some entity, structure, substance, behaviour, problem, algorithm, etc. Thus, we can probably include characterization as one of the research methodologies. Although, characterization, I think is a broad term. Also, the validity of results of the researches are strengthened if statistical analysis was conducted.

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Making a DOS-bootable USB disk from Ubuntu

It is again the start of a new semester. We need to prepare the laboratory computers for students use. We do this by creating a source disk and doing a disk-copy to the other computers. This approach works because computers in a laboratory have similar specifications.

Last weekend, I run into the problem of making a USB disk DOS-bootable for use in copying hard disks. I needed to create one because the floppy drives in the laboratory computers are not working. The Norton Ghost program needs to run in DOS. The following are the steps I followed to make the disk.

1. Downloaded a FreeDOS disk image from http://www.finnix.org/Balder.
2. Installed Qemu.
$sudo apt-get install qemu
3. Prepared the USB disk by creating a single FAT16 partition. In my Ubuntu box, my USB disk is /dev/sdb.
   $sudo gparted /dev/sdb
   
4. Ran Qemu using the FreeDOS image for the first floppy(A:)  and the USB disk as the second floppy (B:).
$qemu -fda balder10.img -fdb /dev/sdb
5. From within FreeDOS, I formatted drive B: and made it bootable.
   A:\>format /s b:
   
6. Tested if the USB disk is now bootable.
   $qemu -fda /dev/sdb
   
7. Copied the Norton Ghost program to the USB disk.
   

After changing some settings in the BIOS of the PCs in the laboratory, the DOS bootable USB disk from Ubuntu did its job.

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