Plotting big and small data in the same graph

(Jan 31, 2008)

Today, I helped Justin to help his friend (Jen Han?) to plot an Excel diagram with big and small data. If we use default settings, small data will just lie on the x-axis. To solve this, we need to add a secondary axis. We can do it as follows.

From a chart with default settings, try selecting a small data series. If we cannot select it, just select any thing in the chart and keep pressing arrow keys up or down to circulate highlight until we reach the small data series. Then, right click and choose 'Format Data Series...'. Next, look for an axis option and plot the small series on a secondary axis.

We will get a result like what I show below

Figure 1. An Excel plot with two y-axes (the right one is referred to as a secondary axis in Excel)

Credit: thank you ProjectWoman whom I got the information from

We should try to reduce initialization task ourselves

(Jan 30, 2008)

I tried implement an efficient way to build an isotropic image. For a long time, I thought a compiler optimization will handle initialization overhead automatically, but for Visual C++ 2005, it does not.

Consider the following code:

for( int z = 0; z < y =" 0;" x =" 0;"> arVoxels[8];
NVImage_t arValues[8]; // keep H.U. values of relevant voxels


In fact, we can move all declarations outside the most outer loop (z) as follows:

float fX, fY, fZ; // for true position
float fa, fb, fc; // relative voxel distance as in 2.1.
NVVoxel arVoxels[8];
NVImage_t arValues[8]; // keep H.U. values of relevant voxels

for( int z = 0; z < y =" 0;" x =" 0;" z =" 0;" y =" 0;" x =" 0;"> arVoxels[8];
NVImage_t arValues[8]; // keep H.U. values of relevant voxels

We can see that for each z, there will be two threads. Hence, if we move declarations to the most outer loop, two threads will use the same variable storage, and that is not correct. What we should do is moving these declarations just one step outer as shown below:

#pragma omp parallel
for( int z = 0; z < y =" 0;"> arVoxels[8];
NVImage_t arValues[8]; // keep H.U. values of relevant voxels

for( int x = 0; x < nNewSizeX-2; x++ ) {

From my experiment, this makes things much faster since array initialization is expensive. Note: we can even reduce initialization further if we divide the loop ourselves and create 'multiple sections'. For each section, declare its own variables. I, however, will not do this since the code will be clutter, and we have to know the number of sections before hand, which is normally equal to the number of physical cores in a system. Thus, changing CPU may cause some performance issue. Using OpenMP in this way, nonetheless, is very flexible regarding to system configurations.

Associativity in Modern CPU Cache

(Jan 30, 2008)

Recently, I have used OpenMP to perform multi-processing a lot. However, OpenMP may cause 'false share' often if we are not careful. False share is a situation that two threads write in a different memory locations, but unfortunately, the two memory locations are assigned the same cache slot. If this situation happens, performance will be degraded significantly.

Cache associativity will play an important role on this issue, especially if we have 8 cores or more.
So, let's look at cache associativity for some modern CPUs.

AMD Athlon 64 X2 has 2-way associative L1 cache and 16-way for L2 cache (ref).
AMD Phenom has 2-way associative L1 cache, 16-way for L2 and 32-way for L3 cache s (ref-page 4)

Intel Core 2 E4000 and E6000 series: 8-way associative L1 cache (ref-page 9) and from what I got from CPU-Z, it has 16-way associative L2 cache.

Intel Core 2 E8000 series: 8-way associative L1 cache and 24-way associative L2 cache (from CPU-Z).

So, I think CPUs from both manufactures should do well in scaling, but from what I got from Tom's hardware, Phenom scales very well and better than Core 2 Quad. I, however, cannot confirm this until both platform are more matured and more serious evaluation are available.

New line positioning problem in Visual Studio 2005

(Jan 29, 2008)

I encountered a curious problem about new line positioning in Visual Studio 2005, specifically Visual C++, from time to time. The issue is when I press enter to insert a new line. The cursor will not move down to a new line, but stick to the same line.

Today, I noticed that code folding may cause some issue about this. If the last function in a file is folded, this problem may occur.

(see Processor3.cpp)

Display ampersand in MFC controls

(Jan 25, 2008)

I tried to display an ampersand (&) in MFC controls (Visual C++ 2005), specifically tab controls. The problem is a literal "A & B" was displayed "A B" in MFC controls.

To fix this, we have to replace & with &&. Namely, use "A && B", instead of "A & B".

source: http://forums.microsoft.com/MSDN/ShowPost.aspx?PostID=1597754&SiteID=1

How to fix "Insufficient system resources to complete the API"

(Jan 23, 2008)

There is a blog complaining about this. It shows some reasons that this issue is a major problem for a laptop. I agree with him, although mine is a desktop.

As of Jan 23, 2008, Microsoft does not have a patch for this issue, but hotfix is available from here

Mysterious MFC Compile Error

(Jan 23, 2008)

I got a mysterious compile error today. It said one of a resource ID, IDD_SUP_VENA_CAVA is not defined / declared in this line:

// Dialog Data
enum { IDD = IDD_SUP_VENA_CAVA };

Dr. Yu suggested me include resource.h. I did and it worked fine, but I really don't understand why I don't need such includes in other places. That's why I think it's mysterious.

MFC: Practice using tab control

(Jan 19, 2008)

After try using MFC's tab control (CTabCtrl) from http://www.forteach.net/Programming/c/26492.html
and
http://www.ucancode.net/faq/CTabCtrl-VC-SetWindowPos.htm

The first one seems to give more concise and be easier to follow.

There are also some important points I'd like to note:
1. Do not forget to change 'style' of a tab sheet from 'popup' to 'child'. If you do not make such change, the position of a tab sheet may be at the top left corner of the screen.

2. Tab sheet should be set to have no border (Border = none).

3. CTabCtrl must be derived. It seems there is no simpler way for this, although initialization code for our derived class may be very common as used in http://www.forteach.net/Programming/c/26492.html

4. Tab control must have this message map,

ON_NOTIFY_REFLECT(TCN_SELCHANGE, OnSelchange).

Otherwise, changing tab is impossible.

5. As usual before a dialog which has a derived tab control in it can be shown, we need to 'Create' it. Declaration does not mean 'Create' at all.

m_myDialog.Create( IDD_MAIN_DLG );
m_myDialog.ShowWindow( SW_SHOW );

6. Properties for a common tab sheet are shown in the following images:



Private copy: http://docs.google.com/Doc?id=dggq8h5d_38hbbr8bcb

Blood system in the mediastinum

(Jan 14, 2008)

I found an image of major blood vessels in mediastinum. It tells me about the names of blood vessels I want to know, especially, azygos vein, right and left innominate veins.

By the way, I'd like visualization in this page
(http://seram2006.pulso.com/modules.php?name=posters&idcongresssection=&d_op=viewposter&sec=&idpaper=880&part=2&full=&papertype=2&haveportada=1&viewposter=1)

Folder Listing in Apache

Default configuration value for folder listing in recent Apache servers seems to change. Now, by default, we cannot list folder contents without an index file. To allow folder listing without an index file, we need to set an option properly. If we start from a fresh installation of Apache 2.2, the default option is

Options FollowSymLinks

We can change it to

Options Indexes FollowSymLinks


And, directory listing will work just fine. Note: 'Deny from all' directive may still prevent us from viewing a page. We can delete or comment out the directive to view contents.

To make folder listing looks better, we should also employ fancy style by uncomment the second following line:
# Fancy directory listings
#Include conf/extra/httpd-autoindex.conf

Please consult http://httpd.apache.org/docs/1.3/mod/core.html#options for details.

Web folder ของ Thai Club

If we want to access a web folder of an organization in Penn State, we need to know its path on a server. To find what it is, we can go to www.work.psu.edu, log in and choose 'Add More Space (Quota Manager)'. Then, we will see a folder path in a drop-down menu. We can use the path to access our web folder.

And of Thai Club, the path is /:/services/www/clubs/wwwroot/up/thai

เพลงสู้ต่อไป

เคยได้ยินเพลงนี้มาประมาณสิบปีแ้ล้วตั้งแต่อยู่ที่ไทย พยายามค้นอยู่นานว่ามันคือเพลงอะไร แต่ก็ไม่เจอเพราะเคยถามเพื่อนแล้วเพื่อนเข้าใจผิดว่าเป็นเพลงเปลวไฟในไอหมอก แต่ท่จริงแล้วมันชื่อว่าเพลง 'สู้ต่อไป' ของศิลปินที่เรียกตัวเองว่าชาร์ค http://www.oknation.net/blog/print.php?id=90571

(keywords ที่ใช้ค้นแล้วเจอคือ มองไม่เห็นทาง โลกสลัว
แต่ก่อนเราค้นด้วยคำว่า 'แม้จะมองไม่เห็นทาง' และ/หรือ 'โลกสลัวไร้แสงสว่าง' แต่ก็ค้นไม่เจอ

วันปีใหม่นี้ลองค้นอีกทีด้วยตัดคำโน้นคำนี้ออก สุดท้ายก็ค้นเจอ งงเหมือนกันว่ากูเกิลทำดัชนีการค้นหายังไงกันแน่)

ขอคัดลอกเนื้อร้องไว้สักหน่อย กลับไทยไปแล้วคิดว่าจะหามาซื้อเก็บไว้เหมือนกัน นาน ๆ ถึงจะมีเพลงที่เราคิดถึงอยู่บ่อย ๆ

สู้ต่อไป
ร้อง : ชาร์ค (Shark)
เนื้อเร้อง : ชาร์ค
ทำนอง : ชาร์ค & กันต์
โปรดิวเซอร์ : พลรักษ์ โอชกะ
สังกัด : ไนน์ตี้ไนน์ โปรโมชั่น

********************

เดินก้าวไปบนทาง ที่แสนลำบาก
ใจและกายเหนื่อยจน หมดแรงอ่อนล้า
จำต้องทนฝืนทุกข์ตรม ไม่หมดลมหายใจต้องสู้
สู้ต่อไป..สู้ต่อ..ฮ้าฮา

เดินต่อไปเถอะเดิน แม้ไม่เห็นทาง
อะไรกีดขวางบอกใจ ต้องข้ามให้ไหว
แม้อาจล้มลุกคลุกคลาน ไม่ว่านานแสนนานจะสู้
ก็รู้ทั้งรู้ไม่สู้ ไม่เหลืออะไร

แม้จะมองไม่เห็นทาง โลกสลัวไร้แสงสว่าง
ไร้คนช่วยนำทาง..ฮ้าฮา
แต่ใจบอกตัวไม่ต้องกลัว เกิดเป็นคนชีวิตต้องสู้
สู้จนยิบตา ดูให้ดี

จะมองแต่โลกในแง่ดี ชีวิตนี้แสนมีคุณค่า
ที่ผ่านมายิ่งทำให้เรา แกร่งแข็ง
สักวันชะตาต้องหมุนเวียน เปลี่ยนแปรผันทุกข์ตรมคลี่คลาย
และฝันที่เราฝันใฝ่ จะกลายเป็นจริง

Server-Side Include in Apache

(Nov 26, 2007)

I tried using server-side include (SSI) feature in Apache 2.2.6. I followed all steps in its documents. These are:
1. use Options +Include in
2. use AddType text/html .shtml
AddOutputFilter INCLUDES .shtml
within mime_module (just uncomment these two lines in httpd.conf)
3. use an include element, such as

However, it turned out that my stuff did not work. I spent about two hours to figure this out. Finally, I knew that .shtml did not mean a file to be included., but .shtml meant a file that included other files. Namely, I just renamed a 'master' file, menu.html, to menu.shtml, and every thing worked fine.

Moreover, a file to be included can be .html, no need to make it .shtml.

Note: although it is possible that we can allow .html to be a master file in the same way by adding AddOutputFilter INCLUDES .html, I will not do this since 3rd party server may not allow us to do this (I think it might slow down the web server).

หัดใช้ SSE

(Nov 23, 2007) (Thanksgiving Night)

Today, I tried using vector instructions (SSE2 to be specific) in Visual C++ 2003. There are something worth noting:
1. we might always want to use _mm_malloc( data_size, 16 ) in place of new operator to make sure that our dynamically array will be aligned at 16 bytes (this is a restriction for many operations in SSE2; otherwise we will get memory exception). More details can be found at http://www.x86.org/articles/sse_pt3/simd3.htm and http://www.tacc.utexas.edu/resources/user_guides/intel/c_ug/linux117.htm

Remember that, to free the allocated memory, use _mm_free.

2. For those using Visual C++, they have alternatives when they want to aligned data. For example,

__declspec(align(16)) float m_fArray[ARRAY_SIZE];

and 
m_fArray = (float*) _aligned_malloc(ARRAY_SIZE * sizeof(float), 16);

Please see more info at http://www.codeproject.com/cpp/sseintro.asp

3. As can be seen from 2, it is desirable to align our floating-point array as well since this will allow us to cast-and-use the floating-point array.

4. There are interesting classes which are suitable for vector instructions: vector3D and 4x4 Matrix. Please see http://www.x86.org/articles/sse_pt3/simd3.htm (near the page bottom).

More may be available at http://www.codeproject.com/useritems/SSE_optimized_2D_vector.asp (see the source code package).

5. Examples in using add, mul, and sqrt via SSE: http://www.codeproject.com/cpp/sseintro.asp

6. memcpy and _mm_loadu_ps will play an important role to increase speed for convolution since SSE needs to align data at 16 bits, but we want to move convolution window little by little (4 bytes). However, if we interleavedly process data, we need to perform memory move / copy only four times. This should be good for performance improvement.

There is a website about fast factor 2 resampling using SSE at http://mail.gnome.org/archives/beast/2006-March/msg00001.html. I don't know if it does show something related to my convolution problem, but I will one day take a look at it seriously.



7. Very simple example of SSE in GCC: http://www.tuleriit.ee/progs/rexample.php

Deprecated String-Conversion Macro

(Nov 8, 2007)

Today, I spent a lot of time trying to nicely rid of some warning messages:
warning C4995: 'gets': name was marked as #pragma deprecated
warning C4995: 'sprintf': name was marked as #pragma deprecated
warning C4995: 'vsprintf': name was marked as #pragma deprecated
warning C4995: 'strcat': name was marked as #pragma deprecated
warning C4995: 'strcpy': name was marked as #pragma deprecated
warning C4995: 'swprintf': name was marked as #pragma deprecated
warning C4995: 'vswprintf': name was marked as #pragma deprecated
warning C4995: 'wcscat': name was marked as #pragma deprecated
warning C4995: 'wcscpy': name was marked as #pragma deprecated

These seems to happen when I try to employ some ATL stuff along with its string conversion features in Visual C++ 2005. Although, I used ATL 7.0 which should not be deprecated, these warning messages still haunted my compile message.

For some unknown reasons, I found that including iostream would automatically be removed. I don't know why, but it does do a trick.

Update: these warning occurs because those deprecated functions are called internally in conversion macros. If we include iostream, some function calls in these macros may be different. Also note that if we explicitly call those deprecated functions, including iostream will do nothing, and we need to explicitly use secured functions, such as sprintf_s instead.

ITK กับโครงสร้างการพัฒนาซอฟต์แวร์เสรี

(Oct 25, 2007)

ได้ไปเยี่ยมชมเว็บ ITK เพื่อดูความสามารถของชุดเครื่องมืออันนี้ พบว่ามันเป็นเครื่องมือที่น่าสนใจมากทั้งในแง่ของความสามารถ ระบบการพัฒนาแบบเปิด และ ลิขสิทธ์ที่เลือกใช้ แต่จุดที่จะพูดในบล็อกนี้ก็คือเรื่องโครงสร้างการพัฒนาซอฟต์แวร์เสรีที่เค้าใช้ และเครื่องมือในการพัฒนาต่างๆ

จากการสังเกตพบว่าทางองค์กรที่จัดตั้งขึ้นมาเพื่อดูแลเรื่องนี้ มีจุดมุ่งหมายที่ผูกไว้กับโครงการที่ค่อนข้างใหญ่คือ The Visible Human Project ทำให้เป้าหมายในการพัฒนาค่อนข้างชัดเจน พร้อมๆกับสามารถเอื้อประโยชน์ให้กับโครงการอื่นที่ต้องการทำอะไรคล้ายๆกันด้วย นอกจากนี้ทางฝ่ายพัฒนาก็ยังได้เลือกใช้เครื่องมือต่างๆ รวมถึงวิธีการเขียนโปรแกรมที่เปิดโอกาสให้มันสามารถใช้งานได้แทบจะในทุกแพล็ตฟอร์ม นับตั้งแต่เรื่องของ multi-threading ที่เลือกใช้ POSIX การพยายามใช้ generic programming ให้มากที่สุดทำให้เป็นไลบรารีที่ยืดหยุ่นมาก การใช้ Doxygen เพื่อสร้างเอกสารของนักพัฒนา การใช้ CMAKE เพื่อให้คนอื่นเอาไปคอมไพล์เองบนแพลตฟอร์มที่ต้องการได้ไม่ยากนัก การใช้ Dart เพื่อทดสอบและรักษาคุณภาพของซอฟต์แวร์ ตลอดจนการใช้ Mantis เป็นตัวตัดตามข้อผิดพลาดและปัญหาต่างๆ ในซอฟต์แวร์ (หลายตัวมีกล่าวถึงไว้ในหน้า Related Software)

เราคิดว่ามันน่าจะเป็นสิ่งที่ดีที่เราจะศึกษาไว้เพื่อที่จะสร้างซอฟต์แวร์เสรีที่ค่อนข้างจะซับซ้อน และต้องอาศัยความร่วมมือจากหลายๆ ฝ่าย วิธีที่ ITK ใช้อยู่น่าจะเป็นหนึ่งในทางเลือกที่ดีที่จะทำให้โครงการอยู่รอดและก้าวหน้าไปสร้างประโยชน์สืบๆ ไปได้ในระยาว

Precompiled header does not exist

Friday Sep 21, 2007

I wasted about 20 minutes to figure out how to solve this compile error: precompiled header does not exist. I performed rebuild the entire solution with the hope that the precompiled header will be recreated.

Finally, I found that we could explicitly tell Visual Studio to create a precompiled header as shown in the figure below. After a successful compilation, Visual Studio will automatically change the 'Create' option to 'Use' option instead.

Visual C++ and LNK2005 Problem

Sep 16, 2007

Today, I badly got strucked with LNK2005 error in Visual C++. According to linking error messages, it was a conflict between nafxcwd.lib and uafxcwd.lib. This issue will arise if one module (library or executable) "Use Unicode Character Set" and another "Use Multi-Byte Character Set".

It is important to note that LNK2005 normally arises because of two or more projects are set differently. There are two spots worth looking:

1. General Setting
2. Code Generation Setting

Notice that there is nothing to do with linking setting, although this issue is linking problem.

More info at:
http://www.velocityreviews.com/forums/t285209-lnk2005error-in-visual-c-v-60.html
http://support.microsoft.com/kb/q148652/

LaTex Equation Editor on the web

Sep 15, 2007

There is an interesting work on the web, and it's free. It is LaTex Equation Editor, http://test.izyba.com/equationeditor/equationeditor.php. This tool creates an image with transparent background, making it easy to embed in other software such as MS PowerPoint.

The drawbacks are:
1. Text in the equation cannot be changed. If we need white text, we will find ourselves in trouble.
2. Text size is a bit too small. I like it bigger in many situations.

Note: if you know a way to handle these problems, please leave a comment in this blog.
Many thanks

Update (Oct 28, 2007): I found a better one. It is Roger's Online Equation Editor at http://rogercortesi.com/eqn/index.php#note. It can generate transparent background. Plus, we can increase resolution of an output to suit our work.

Texmaker: Free cross-platform LaTeX editor

Sep 15, 2007

Texmaker (http://www.xm1math.net/texmaker/) seems to be a very good LaTex editor tool. I used it once a long time ago. It's pretty impressive, and I think it is better than TeXnicCenter (http://www.texniccenter.org/). The tool has no more update for more than a year). However, Texmaker does not have some cool features in WinEdt such as DVI search.

FYI: DVI search is a feature in WinEdt helping a user to find a portion in DVI document corresponding to a target text in the editor. You can try it by ctrl-shift-s in a WinEdt editor. If your DVI file is open, it will jump to the corresponding text.

FYI: there is a forum about LaTex and its editors at forum http://latex-community.org/. This forum has dedicated sections for TeXnicCenter, Texmaker, and WinEdt. Sounds interesting.