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Tuesday, November 29th, 2005

HWP54G FC4 Linux Install Success!

How I got my Hawking HWP54G Wireless-G PCI card working with Fedora Core 4 Linux, and links to drivers, instructions, a chipset forum and a Fedora forum, so that you can do it too. The drivers and chipset forum should help even if you are using a different version of Linux.

Ok, so I just recently announced that I would be using the above blurb as an intro to any post covering this topic, but I might not be needing it much longer, because I got it working! I’m going to try and cover in this post the important points that I learned along the way.

First off, my Hawking HWP54G Wireless-G PCI network interface card uses the Ralink RT2500 chipset. (All the links in my opening blurb are for the RT2500.) The chipset, not the manufacturer or model of your card, is the important factor in finding and installing the right drivers for your NIC with Linux. I’ve seen reports that this model card may use the Prism54 or TI acx111 chipsets. If you don’t know your card’s chipset, try the following:

If it turns out you have the Prism54 chipset, go to the Prism54 Project for Linux drivers. For the acx111, I found an excellent howto at House of Craig, and drivers are at the ACX100 SourceForge Project.

On to my experience with the RT2500. Right away I should say that the rt2x00 drivers are NOT compatible with the smp kernel. Now, I’m a Linux noob, so I found the Unofficial Fedora FAQ a great place to get help on the basics. I also made a significant mistake when I installed Fedora Core 4 – I didn’t include the Kernel Sources and the Development Tools packages. I couldn’t even make the driver. There’s a forum string that covers this topic at the rt2x00 project, but take my word for it – it’s easier to reinstall Fedora than to try loading the missing rpm’s and building the symbolic links required. I found a good guide to FC4 installation and package selection by Mauriat Miranda that I’m going to use to start over myself (more later.)

All right. We’ve made sure we have all the packages installed with Fedora that we need, and we’ve downloaded and uncompressed the rt2500 driver. Go to the /Module directory and open up Readme with a text editor. If you’re working in command line, then “gedit readme“. Ignore everything and go down to the end where it says “INFORMATION FOR FEDORA CORE 3 USERS (USE AT YOUR OWN RISK !!!)”. It says FC3, but it works with FC4 as well. With Fedora, we’re not going to build the configuration utility (so you don’t need qt or qmake) and we’re most definitely not going to put in the configuration file RT2500STA.dat – doing so can mess everything up. There. I just saved you a bunch of time and headaches, so feel free to buy me a beer. As for other distros, you’re going to have to follow the readme. If you need qt, let me save you some time hunting around the Trolltech site and give you the link to the qt open source edition download, because they do their best to hide it.

To summarize my linked sources, in a terminal window:

I left out all the fancy $ and # prompt stuff that confused me before. If you get an error during the make or make install-fedora, well I’m sorry, but it’s off to the forums with you. I’ve already given instructions on how to avoid all the stuff that tripped me up, and avoiding is way better than troubleshooting.

Now we use the system-config-network utility, which you find by going to Desktop > System Settings > Network, or typing “system-config-network” as root. If your make and make install-fedora worked, you should see an entry for wlan0 that includes “Ralink rt2500” in the description on the Hardware tab. Double-click on the wlan0 line to open up the properties for that device.

Fedora system-config-network utility

Here is where you enter in all the details for connecting to your wireless network. You need to know your ESSID, the channel you use, whether you use DHCP or your ip address and your access point and dns server ip’s if you don’t; your WEP key if you use it (I do) and your WPA info (which I don’t know anything about because not all of my NICs are WPA capable yet- but I’m working on it.) If you don’t know this basic information about your wireless network, you need to learn all about it, because chances are you’re not taking the steps you need to secure your wireless network from interlopers and eavesdroppers. If you know what I’m talking about, just don’t have the details, then use Windows or your router configuration to get the information. And be sure – here’s what tripped me up until this morning – to put “0x” in front of your WEP key to identify the string as hexadecimal.

That last one had me really stumped. I was not only using the Fedora system-config-network tool, I went to the commandline and used iwconfig to manually enter the parameters and ifconfig to try to get the device “up” (both of which require you to be logged on as root to use.) I did notice than whenever I tried to activate the device using the GUI tool, iwconfig reported that the WEP key had been changed, and that the changed key was always the same, and it didn’t have any letters in it, but I didn’t put two and two together. I also noticed that iwconfig reported my access point’s MAC address correctly and a signal strength, so I figured I was talking to my WAP (I keep a cheat sheet next to my computer of all my network MACs, ip addresses and other goodies.) After I got it all straight, I activated the wlan0 device, opened Firefox, typed in the ip of my access point, and presto! I was in the configuration menu, and I was online!

At this point, I have to give a shout out to Mark Wallace (serialmonkey) and Ivo van Doorn (IvD) of the rt2x00 SourceForge project and to bitrain at fedoraforum.org for their most useful information, especially Mark, with whom I corresponded, and who gave me encouragement.

If you found this information useful, please add a comment to this post; and if you know something else – information or a good link that I can add, contact me. I’ll make up a more complete howto later.

P.S. I think I made such a mess of my FC4 installation that I’m going to reinstall it and start over. The thing that is pushing me to this is that I tried updating over the internet and it froze during the rpm install. At least it will give me an oppurtunity to follow my own advice, and possibly spot any errors!

Posted by Greg as Hardware & Drivers, Networking, OS at 05:47 PST

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Monday, November 28th, 2005

Just Can’t Win

Wouldn’t you know it? On Friday I go back to my June 27 post that I keep talking about (you’ll soon see why I’m making vague references) and write a whole new intro. I was hoping the much better opening sentence would replace the blurb that appears when searching for “(that wireless NIC model)” and “(that non-Windows, non-Mac family of OS)” on (that famous search engine). The new intro also directs people to a much better location for the help they need, so I figured I was doing everyone a favor. Unfortunately, the (famous search engine) ‘bot came around just the day before, and it’s only been hitting that post about once every two weeks, so I expected that it might take a while for the blurb to get updated.

But this morning I narcissistically checked (the famous search engine) using (the same terms), and find out that I’m now the number one search result, but it now points to my last post, which doesn’t really discuss how to get the (wireless NIC model) working, but how my earlier posts rank on (the famous search engine)!! WTF! So I guess I have go hack this more recent post to try and accomplish the same thing. I should probably preface every post I write about (the same subject) with the same intro. I’m actually starting to feel a little guilty, because the search engines should actually be pointing people straight to the rt2x00 Open Source Project homepage, which is where I got the help I needed (and still need!) and other people can get it, too.

As a matter of fact, I’m heading over there myself. I did some more work ever the Thanksgiving break and have new problems, which I’ll write about separately.

Posted by Greg as My Website at 11:35 PST

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Tuesday, November 22nd, 2005

Giving Help with Linux

How I got my Hawking HWP54G PCI wireless card working with Linux, and links to drivers, instructions and forums so that you can do it too.

If you came here through a search engine link, you should try my updated post for more details and tons of links.

(This, I guess, is going to be my standard intro whenever I discuss this topic.)

On the lighter side, yesterday I was contacted directly by someone who was trying to get his Hawking HWP54G PCI wireless card working with Linux, in this case Slackware 10.1. It’s the first time anyone other than a friend has asked me for advice about Linux, and I feel like I’ve now been inducted into the Linux community at large. It’s especially interesting that this user contacted me from Italia. With David’s permission, I have posted the entire email exchange.

I’m assuming David found me through a search engine. Like I’ve said before, search engine hits involving some permutation of “linux” “hawking” “hwp54g” and distro names are the biggest source of traffic to my website. (Well, except for a couple of weeks earlier this month, when my post on mpip.org made my Cancer Survivor post the number one entry point outside of feeds and bot crawls.) I checked my logs and in the last two days I got two redirects from google.it using the terms “driver fedora ralink” and eleven from google.com that included “hwp54g”. So I ran the google.it search myself and saw that I was ranked number 9 out of 9,260 hits, and on google.com I’m 16th out of 11,900 for “hwp54g” and 6 out of 554 for “hwp54g linux”. Pretty cool! It’s amazing how much higher I appear in the Google search results since my site went from a RageRank of 2 to a 3, something I didn’t discover until a friend looked for my blog and told me that I was the number one result for “greg perry san diego”, out of 1,790,000! That was November 1st, and I hadn’t bothered to check my PageRank for three months. I’ve been meaning to crow about this since then, which shows how busy I’ve been.

Posted by Greg as Hardware & Drivers, My Website, Networking, OS at 21:15 PST

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In Memoriam

John Forest Waters, 1964 John Waters, 1964 yearbook photo

My friend and coworker, John Forest Waters, died last night at 17:15 PST. In the last seven years when I knew him, he was cantankerous, stubborn, often opinionated, intelligent, direct, and getting a rise out of him was very entertaining. I loved him dearly.

Working and traveling with John was always a great pleasure. His command of corrosion control was deep and insightful, even if he preferred to have others do the calculations for him that always just ended up showing he had made the right choices initially. He was also a cold war warrior. One night on the road, after a couple of drinks, I found out that his fluency in Russian and German had been acquired back in the sixties, when he had been seconded by the Army to the not-then-acknowledged NSA as an intercept operator, and that he had found himself a little too forward of the lines one August night, 1968, in Czechoslovakia. One of my strongest and favorite memories of him will always be his reaction when I showed him the NSA for Kids website.

John, like me, was a second generation corrosion engineer. His father, F. Otto Waters, was one of the pioneers of the corrosion control industry. It’s interesting that he, like his brother Don and me, seemed to have sought escape from his destiny by joining the Army, but we all ended up back in the field that we started in during summers in high school. Otto’s company, Waters Consultants, (and John) was passed on to PSG Corrosion Engineering, which eventually became part of Corrpro Companies, Inc.

In the near future I’ll be thinking a lot about his wife, Barby, and and his sister Holly. But right now I’m grieving for my own loss.

Posted by Greg as Family & Friends at 07:23 PST

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Monday, November 21st, 2005

Death is Visiting My Office

I came into the office this morning after getting back from my trip to Seymour Johnson AFB and found out one of my coworkers went into the hospital last week and he’s pretty bad off. Later this morning I heard that his liver and kidneys had failed and his family expects him to lose his fight for life today.

It’s come as a complete shock. I was just on the road with John last month at Scott AFB, and there was nothing to indicate that he was having a problem. I was also close to his brother, Don, who died suddenly last year. I really feel for their family.

Posted by Greg as Family & Friends at 11:42 PST

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Working with DICOM Files

I was having problems working with digital files that came with my PET scan. A little research revealed the existence of the DICOM standard for medical image files, and I found many free DICOM image viewers, but although I downloaded at least four different viewers, I couldn’t open any of the files on the cd I got. Most of the files did not have extensions, so I was guessing at which ones were the images, but some of the files that contained useful information when opened with a hex editor showed DICOM standard headers. (My favorite hex editor used to be Hackman, which is really a complete disassembler/reverse engineering suite, but I found a much simpler and faster hex editor function in my PSPad text editor, which I use to write generic code.) I also noticed that several files had JFIF header info after the DICOM headers, and in accordance with the “Quick and Dirty Tricks” section at David Clunie’s site, I stripped off the DICOM header info and should have had a JPEG image file, but none of my viewers, including the regular image programs IrfanView and Gimp, could open these files.

[UPDATE: Found one! Try Medirec – I’m having trouble opening the raw files (don’t know if that’s a problem with the DR Systems files, or the viewer, or me), but by stripping out the header info and saving the result as a *.jpg file, I have a 12-bit greyscale lossy jpeg that I can open in this viewer – in Windows.]

I started reading up on the DICOM standard and the DR Systems compliance document, but that bogged me down pretty quickly. So I sent off an email to David Clunie. With his permission, here’s his answer:

Hi Greg

I took a look at the files that you sent, and there is nothing seriously
wrong with them with respect to anything that might confuse a viewer.

The problem you are having is simply that the images are encoded
using the 12 bit lossy JPEG transfer syntax, and many viewers just
don’t support that. Further, if you extract the JPEG bitstream,
most consumer image viewers won’t support the 12 bit JPEG form
as opposed to the usual 8 bit JPEG form either.

The bottom line is that you either need to use a viewer that
handles the JPEG DICOM transfer syntaxes, or find a way to
have the DR Systems CD creation tool encoded them uncompressed
(even if they were stored in the PACS compressed, which is
likely with that system).

I would also point out that lossy compression of PET images is
probably not cool from the perspective of quantitative PET
measurements (like SUV), though the likely error, if any, would
be very small.

That said, the images are not strictly compliant with the standard,
probably as a result of them being inverted and squeezed into 12
bits rather than 16, but I doubt if that has anything to do with
the problems that you are seeing:

% dciodvfy 196
PETImage
Warning – Optional Type 2C Conditional Element=<patientposition> Module=<generalseries>
Warning – Unrecognized defined term <ring> for attribute <field of View Shape>
Error – Unrecognized enumerated value <monochrome1> for attribute <photometric Interpretation>
Error – Unrecognized enumerated value <0xc> for attribute <bits Stored>
Error – Unrecognized enumerated value <0xb> for attribute <high Bit>

I suspect that the errors are being introduced by the DR Systems
PACS, and not by the Siemens ECAT system.

If you want me to recommend a particular viewer, I would suggest
Osirix, which does open these images just fine (I tried it), though
you need a Mac to use it. It has nice 3D.

If you want to just uncompress the whole lot so that you view
them with an “ordinary” DICOM viewer, then you could try the
dcunjpeg script from my dicom3tools, which depends on the
presence of the Stanford PVRG JPEG codec, both of which are
available on my web site – but these require a unix system
on which to compile them and may be more trouble than it is
worth.

David

First off, I just wanted to give a big public thanks to David, who responded quickly and was very helpful. I started searching for a free image viewer that could handle the 12-bit lossy JPEGs, but haven’t found one yet. There are some commercial medical image reading programs that start around US$4K (!!!), but that’s a little more than I would be willing to spend. I noted that handling 12-bit images are planned for the Gimp 2.4 version, and I’ll be eagerly waiting for that.

Looks like I’m going to have to get back to working on my Fedora Core 4 installation so I can try David’s uncompression scripts, not to mention completing the build my other computer, which is intended to be a Linux-only box. **Sigh**. Why do I get so many interesting projects building up when I have even less time to spend on them?

Posted by Greg as General Science, Software at 05:32 PST

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Friday, November 18th, 2005

North Carolina

I’ve spent this week in Goldsboro, North Carolina, working at Seymour Johnson Air Force Base. It’s been a trying week, as I have suffered from jet lag and a terrible cold the whole time, so I’ve spent most of the time off work either sleeping or trying to sleep. I just now made an attempt to write about it, but I’m still pretty tired, so I’ll try to catch up next week. I fly home to San Diego tomorrow. Hopefully, it won’t be as bad an experience as coming out here was.

Posted by Greg as Posts About Me at 14:15 PST

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Thursday, November 10th, 2005

Full PET Image

I created and posted an animated gif of the upper torso portion of my PET scan, but it’s pretty big – 5.5 MB. I’ve put it on a separate page so it won’t unnecessarily slow down any visitors. If you want to see it, it’s at 2005 PET Scan. I’ve also posted some details about my diagnosis and treatment.

If you found this page because you’ve been diagnosed with malignant melanoma or know someone who has, I’d be more than happy to answer any questions about my experience. I know that when I was first diagnosed, I was starved for information.

Posted by Greg as General Science, Melanoma, Posts About Me at 08:09 PST

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Monday, November 7th, 2005

What Was It Like?

My Mum and Dad both emailed me (Dad was traveling) to congratulate me on the PET scan results, which was a little embarrassing because I posted in my blog before I called to tell them. Dad also called on Saturday.

Although I described the PET scan testing down at the subatomic level and included some calculated physics, I apparently was very skimpy in my description of what it felt like. People who know me would nod and think “typical” about this. Dad and others have asked about it, and I promised to post a picture of the machine. So here it is, boosted from the Siemens site:

Siemens Ecat Accel PET scanner

I lay on the sliding bed part, which is 195 cm long – exactly my height, and there was some concern prior to the exam about whether I would fit. They asked me whether I was more than 17 inches across at my shoulders, and it turned out I was 18 1/2 inches, but upon consultation, the technicians had said I should fit. It turned out to be a little awkward, though – when I was slid through the aperture on a dry run, my elbows hit the sides and were squeezed in. On the actual run, when my arms first entered the hole, I had to clench them up against my body so that they would be in the same position once my elbows entered the ring. It was a little uncomfortable, and it took maybe twenty minutes to half an hour from the time my hands entered to the time my elbows were up against the sides and I could just relax. That’s a long time when you’re trying to lie completely motionless.

The technician explained that I could move the parts of my body that weren’t in the actual hole, but I figured that too much movement could lead to small distortions, so I limited myself to relaxing my arms beforehand and wriggling my feet a little afterwards.

I reported earlier that I was disappointed but not surprised that the viewing software that came in the mail was pretty limited, but since then I have played with it a but and found that the tools and buttons give a little more functionality than I first thought. There’s just no help files to tell you how to do this. The image I posted can actually rotate around the vertical axis in a sequence of 32 images, which looks pretty cool, and the moving view makes the whole thing look a lot more detailed than the single image. You can see many bones and internal organs quite clearly. Still, although I found a “Save As” function for each image, the extracted image is horribly crippled as far as resolution goes. I wanted to extract all the images and make an animated gif for posting. I guess I’m back to hacking the images out of the data files. However, this might make a gif too large for posting – maybe I’ll try the extracted version first.

Posted by Greg as Family & Friends, Melanoma, Posts About Me at 16:14 PST

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Wednesday, November 2nd, 2005

Cancer Survivor

While I was gone in Illinois, a cd showed up at home for me. It contained the results of the PET scan I took on October 21st. PET, which stands for Positron Emission Tomography, is this very cool (and very expensive) procedure where you are injected with a sugar, fluorodeoxyglucose, that has a radioactive tag, in this case fluorine 18. You sit in a quiet spot for 45 minutes while the sugar is dispersed through your blood stream, and you don’t want to move at all. The first time I did this, the technician also told me to try not to think?!

The sugar is taken up by cells that need it, and they don’t notice the fluorine atoms releasing positrons as part of their decay. The positrons – yes, antimatter, don’t get to travel very far until they meet an electron and the two particles mutually self destruct, releasing energy in the form of gamma rays and in accordance with E=mc2. Since the mass of the two particles is about 1.82 x 10-30 kg, the energy released by one reaction is about 1.6 x 10-13 kg-m2/sec2 or joules – about one 40-quadrillionth of the energy in a single Tic-Tac. I got to lie on a sliding platform that slowly moved my body through the 3D gamma ray detector, and since there’s a lot of me, it took more than two hours. The gamma rays are paired, so the detector can figure out their point of origin.

Cells take up sugar at varying rates depending on how active they are – the brain, heart and kidneys are hard workers, but nothin’ loves the taste of sugar like a malignant cancer cell! So while tumor cells are noshing, the PET scan is looking for them. And here’s a sample of what it found:

The Metabolic Greg Perry

Of course, my heart damned near stopped when I saw the big dark splotches, but it was easy to figure out heart, bladder, and brain. Finally, conclusive proof of the existence of a brain, despite the speculations of my wife, teenage daughter, parents, several high school teachers and a couple of drill sergeants.

Well, get to it, Greg! Drumroll please…

“No evidence for hypermetabolism to suggest metastatic melanoma, period”

Well, maybe the period was for his voice recognition software, but I don’t care. I have reached the fifth anniversary of my malignant melanoma diagnosis, a significant milestone, and I only had a 60% chance of getting this far. Melanoma is pernicious in that a single cell can apparently hide out or reproduce at a very low rate, and when you thought it was gone, it can decide to pick a nice spot in another organ and start making tumors. I have a lifetime ban on giving blood, and I can’t be an organ donor. But the most dangerous time for reemergence has now passed, and with continuing improvements in detection and treatment, my prospects of dying from something else, and hopefully a lot later, are just getting better.

So I’m feeling really good about this. At least until the nuclear medicine people get the payment from my insurance company and turn around to hit me up for the rest.

I’m also dying to find a 3D reader for the files on the cd. The software that the medical office sent barely meets the HIPAA requirements for providing patients with copies of their records, but the raw data files appear to be stashed away on the disk. They stripped the file extensions off, but a little peeking has already identified the file types, and there seems to be several freeware applications that can open them. The technician noticed me examining the equipment and asked if I was an engineer, but I already know how the thing basically worked – I was looking for manufacturer and model numbers so I could pull spec sheets, hopefully down to the level of file output. I won’t be happy until I get the full 3D information – maybe I can plug it in to some animation software. I hope the bones and joints are discernible – I’ll need that to accurately replicate movement. The resolution of the full scan results (I was able to get the tech to show it to me after my first scan), ought to be just incredible – way more than the image above suggests. The major limiting factor in accuracy should be how still I was able to stay.

Posted by Greg as General Science, Melanoma, Posts About Me at 10:11 PST

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