Performance of the medical image noise filters

Image processing is a such an interesting vast area that has been the focus of many researchers for decades now.

Developing an image processing application is the product of several skills such as programming, mathematics, computer science and of course a creative intuition. 

One of the most significant implementation of image processing is in medical imaging, which ranges from image enhancement, segmentation, pattern recognition, automatic and semi-automatic computer-aided diagnosis (CAD) and detection and so forth. 

Among all, one of the most popular and often necessary tasks is noise filtering. Additive Gaussian white noise, multiplicative speckle noise and salt and pepper noise are some of the common noises that most medical images suffer from. Speckle noise is probably the worst type of noise that is incident on medical images such as Ultrasound and Optical Coherence Tomography. Speckle is a random granular shaped noise that is generated due to the coherence nature of the signal and unlike Gaussian noise is multiplied to the original signal.

Over the years a couple of dozen filters have been developed for annealing the images. I try to mention them here as much as I can remember for reference so that anyone with interest would be able to look them up. Mean & Median filters, Adaptive median filter, Gaussian, Lee, Enhanced Lee, Kuan, Mode, Frost, Homomorphic, Gamma maximum a posteriori (Gamma MAP), Rotating Kernel Transform (RKT) filter, Wiener, Gabor, Hybrid Median Filter (HMF), Kuwahara, Symmetric Nearest Neighbour (SNN), Wavelet filters, Curvelet filters, Peronna-Malik Diffusion filters: isotropic & anisotropic diffusion filter, Speckle Reducing Anisotropic Diffusion (SRAD), Nonlinear Complex Diffusion Filter (NCDF), et cetera. I have a pretty complete collection of most of these filters, so you can let me know if you needed any, of course the MATLAB codes.

I also would like to say that selecting the best filter for your application depends on several factors such as what type of noise you want to filter? How fast you need your filter to respond? How clean and noise free you need your output image? And so on... But according to my experience for very basic, I repeat very basic filtering, Adaptive Median does a superb job considering its simplicity. And for rather heavier filtering diffusion filtering is just fantastic: fast, reliable and bold. Wavelet filtering is also very popular but personally I would rather the diffusion filtering. In case you need directinality in your filtering, you need to go for Curvelet Filtering.

I said all these because today I wanted to say something about measuring the performance of noise filters. In other words, what quality metrics are there to compare the efficiency of the filters. Well, there are a few parameters defined, which more or less express the ability of a filter, for example, Signal to Noise Ratio (SNR), Peak SNR (PSNR), Mean Square Error (MSE), Structural Similarity (SSIM), Equivalent Number of Looks (ENL) and so on and so forth. I was to mention the formulas for all these factors but then I thought they are quite easy to find. I also must add that some of these like SNR have different definitions in different texts. Some like to use an ROI (Region of Interest) based definition and some say it is too subjective but they are not my intention to talk here. Actually, besides the fact that there are no standard formula for these factors, they often require an original noise-free image for reference and then they measure the performance of the filter accordingly. But in most real-life actual cases such as medical images, we usually do not have access to the original noiseless image. So what do we got to do then? We either need to come up with another type of parameter or manipulate the formulation so that it works without the need for the noiseless image. 

Well, I said all of the above as an introduction to mention the following two items.

1) There is a parameter called the Edge-Preservation Factor (EPF) or the cross-correlation factor that is often denoted by the Greek Beta, that shows how much the edges are preserved in a noise annealing procedure. Beta is real number between 0 and 1. The bigger it is (closer to 1), the more edges have remained intact during filtering. Personally, I believe it is one of the greatest parameters for the job. Especially for speckle filtering and for medical images that most of the information are in the edges, Beta can be a very reliable. It has a rather lengthy formula that I am sure you can easily find in scholastic papers. I also have created its MATLAB code, so drop me a line if you ever needed to use it. 

2) As mentioned above, without the original noise-free image, it is very difficult to compare the performance of noise filters. well, one can always go for synthetic images. Create an image containing the features of your typical medical image, add randomly your noise of choice, then try to filter the noisy image. Now having the original image, you can compare multiple filters easier. But this method also has its own issues. 

I want to suggest a very simple yet valid and valuable method. Take the mean and the standard deviation of all the pixels in your images. The best filtered image is the one that has the least standard deviation and at the same time its mean is closest to the original noisy image. Quite simple aye! And it works like a charm too. 

Sometime people clamp down the background of the image artificially to zero (black) or anything uniform; in this case, I guess, it is wiser to take into account only the signal area and discard the background as it induces a false shift in the mean and variance. 

Hope it was not too long, was it? 

Good Luck...              

I believe in the "Holocaust" but ...

As a young educated man I think I am mature enough to logically reason about an incident without any biasing from my religion, past right/wrong understandings, personal opinions and so forth; and only lay down the facts and draw a logical conclusion.
First of all, before entering in any judgment against me, I must strongly express that I believe Holocaust happened and that it is, without a single doubt, the most distressing genocide of all times along with the darkest, most shameful relic of the history of human being. I say that because all the bloodshed during the long history of man, after Adam and Eve were expelled from heaven, took place in ages were wisdom and rationality were in the minority and people were unfamiliar with the truth, sophistication, common sense and so on and so forth; the civilization trusted sorcery, witchcraft or the their brightest hours religion that was supported by miracles instead of rationale and intelligence.
But Holocaust took place in times when Germany were the home to two thirds of Nobel prize winners. Education was a must rather than a luxury and Europe had already experienced the suffocation before the Renaissance and the pain and agony of multiple wars. At such times, a genocide in dimensions of the "Holocaust" was so far from a sound mind.
But.... I must protest to some specific aspects of the scenario:
First and foremost, most importantly, it makes me utterly uncomfortable to realize that no lawful or unlawful, private or public, official or otherwise, biased or unbiased party has the permission to question the "Holocaust" or as it is referred to by Jews: the "Shoah". No media has the authority to publish or publicize anything even remotely siding with anti-Seminism or revisionism. The fact that the Jewish community unjustly underwent so much terror, trauma, pain and agony and is not fair to them to have them defend their honor or repeatedly prove what had happened to them. But, personally I think, people are smart enough to opt for the truth.

6 million, 5 million, 3 million or 1.5 million... There is not a reliable source to conclude the actual number of victims. But all of them are over a million people. It is a population of a large city today. Can you imagine one whole city to be eliminated within a few months time??? The method of choice, according to eye witnesses and perpetrators, was suffocation by gas in deliberately constructed, disguised as wash & shower facilities, establishments called gas chambers. Each consisted of several spaces the size of a large bedroom. Some say the gas was carbon-monoxide (CO) generated from a diesel exhaust. But, my very basic chemistry & physics knowledge suggests that diesel exhaust is not able to generate that much CO besides the soot and is highly impractical for the purpose. Germans had many Nobel prize winners and best engineers in the world who could certainly come up with something more sensible for such purpose.
Another fishy fact is that the number of witnesses and their credibility is highly under question. After Hitler killed himself and his right hand also committed suicide (or was murdered) in prison, Hess I think was his name or something like this, there is absolutely no high rank SS official, who was directly involved, not just a low level petty officer, on the record who was properly tried in a neutral court who kept records or at least elaborately interviewed. For a phenomenon at this scale, one escaped victim, a barber, a passerby who observed an empty train from cross the street and one singular petty officer certainly are not considered as concluding evidence.
Also, well I am not supposed to say think but what the heck... I think Hitler had extraordinary leadership skills such as Khomeini. These guys have that Charismatic effect on their people and by the knowledge I think I have from such leaders, I can say that the one thing that they all have in common is that: "they certainly believe in whatever they say and also they believe it to be the truth". And mass murder is the byproduct of leaders who lack ideology and know that they don't have much to offer so they prefer people to be scared of them just like Saddam Hussein. Hitler committed suicide that I think was very bold of him. whereas Saddam, MohammadReza Shah of Iran etc, cowardly either fled to a hole or surrendered. In any event, in my eye, mass murder, genocide and betrayal to the man kind is their shield to their fear. They know the place they occupy is not rightfully theirs. They know what they truly deserve so they kill to prove their power, because they know no better way. It is the only way they can feed their pain and anguish they are in.
But true charismatic leaders, they do not kill unless it is the only means to their ultimate goal or they truly have to. Take Iran-Iraq war for example, Saddam easily used chemical weapons and left thousands Iranians dead or as good as. Khomeini could have just as easily done the same but he chose not to. Mohammadreza Shah of Pahlavi just as easily opened fire to his own people protesting in the streets on many occasions. Something after thirty plus years you see again in the same streets just because the leader up there also lacks charisma and fears from his own shadow. I mean it is the exact same psychology, same symptoms, only the names have changed. It is interesting how history repeats itself in only three decades. And surprisingly people have not yet learned nothing.
Oh, I got distracted too far from the subject...Anyway, I think the "Holocaust" in these claimed dimensions, cannot be Hitler's, neither physically nor psychologically. Ergo, there are a few possibilities: it did not happen in these dimensions and shape and form; or it did not happen under Hitler's direct commands or he was not aware of its exact nature; or it did not happen at all. The second possibility is almost unlikely, as eliminating millions of people by tricking your boss sounds not just funny but impossible. The third possibility is also out of the question because there are just too many facts for it to be a hoax. Then it is only the first option left. And it also fits why they would not let anyone to even speak against it!! So... bang.... it is solved... Holocaust was mischievously altered perhaps to fit some other purpose.
All and all, it is just a theory. I may be wrong and it happened exactly it was projected....... Nah.... it is just too far from it.....
Anyhow, I can not wait to see what everyone's ideas are, but of course without egotistic exhortation.
Good luck.....         

Iranians- "Les Miserables" of the century!!

Victor Hugo, created one of the masterpieces of the 19th century, Les Miserables. The magnum opus, which was translated in nearly every viable language, many times, as "The miserable ones", "The victims", "The poor" and "The wretched", not only depicts a sad and sorrowful period of French or in general the European history but also can be considered as a factual illustration of moral philosophy, justice, anti-monarchism and even Paris architecture.
What triggered me to think of this superb piece, is this little page I found online regarding the resignation of "Mirhossein Mossavi" from the PM post at the final year of the 8-year war, right before the Geneva convention, which put an end to the war on 1988 or 1367. 
I strongly urge to selectively read this small but critical piece of Iran's history facts, here. At least, skim through the letters passed between the three or four monumental figures of Iran's history after revolution, who are Khomeini, Khamanei, Rafsanjani, as the Supremem Leader, President and the Head of Parliament & Head Chief of War. 
Frankly, I am neither in the mood nor have the least desire to elaborate, from my eye, what had happened. But the least I can do is just to lay a few facts, I think is critical for the choices that we have to make today, as devoted Persians. 
The year was 1988 (1367), when Iranian parents nearly lost ONE MILLION loved ones to the totally unnecessary, and maybe preventable ( just maybe, I can't say I am an expert on war) doomed war.
Most of them, lacked enough education to read the papers or write a simple letter to someone. 
I am stunned, how this man Mousavi, has the nerves today to send our second and third generation youth to the streets again only this time to open their chest to the bullets that left Iranian guns instead of Iraqi guns.
The stupid legions of that time struggled for years to find a minister to introduce to the parliament, let alone a Prime minister, now in this situation, he resigns and vanishes for days only to spoil himself for the supreme leader, Khomeini. "Bizarre" is all I can say. The president and Parliament started looking around for him to insist on changing his mind... now that if you truly want him back, how come instead of working with him and supporting him, drove the man mad enough to resignation? Or perhaps he was just seeking attention, I dare say?
Khomeini send him a letter to say exactly what the president Khamenei had already said before in his letter! only this time Mousavi listened and returned back to cabinet?! How weird is that? So it was not about the contents of the letter, but about the writer of it.
What do you think ? He just wanted to spoil himself for the supreme leader? Or he actually needed attention? Or he genuinely required more support from them? But if so, how did he shamefully vanished for a few days when the country is at war? given the awful circumstances of that time... 
Did Imam really have that Charisma that everyone just mindlessly listened to him, obeyed without objection? His words were the ultimate rule... 
Once Natiq Noori, head of the parliament at one stage, after parliament voted for a singular minister, writes a letter to Imam, as he believed Imam is not quite happy with Parliament's decision. So Natiq tries to enforce Imam's ruling to overrule Parliament's voting. In this incident Imam's reply is interesting actually:
"In the Islamic Republic, except under very unique, hostile circumstances that Islam or the integrity of the regime are at risk and only such decision must be rendered by knowledgeable experts, nobody is allowed to enforce or impose their vote to someone else; and may God forbid that day... I will do my utmost that only be referring a judgement or decision to me, no one's right is ignored, a position is wrecked or a career damaged."
It is , I must say, such a nobel ideology and so big of the master of the Islamic Republic. I also believe that he also believed in whatever he said. And in many cases he was right but the only problem is that the coat he made for our dear Persia, did not fit her. Truly Iran had and still has certain theological and Islamic ethical aspects but what he totally neglected or at best misinterpreted was our deep deep nationalistic aspects. You can, by no means, just all of a sudden diminish 2500 plus years of heritage. They tried and O God, how they tried to diminish our Persian heritage by all means. How they belittled the ceremonies of the last Wednesday of the year, the 4shanbe soori" that our destitute people turned to making bombs and hand grenades instead of happily grooving & jumping over fire made of the year's perished households. So sad ...     
Does Khamanei think he either definitely has the same "charisma" or he must somehow find the same "charisma" but nobody actually listens to him? Khomeini was selected by a revolution! where Khamenei was selected by a few ayatollahs whom hardly had any credibility... 
Well, people, there are just a million question marks in my head, whirling around that I want to shout them out. But please, for the sake of Iran's future, for the sake of all of us and our children... I beg of you, Do NOT under no desperate circumstances, never ever again trust anyone who had anything to do the so called Islamic Republic. If you think Iran need an Islamic Republic, well at least yell out "We don't want THIS Islamic Republic"... What we have in Iran and have had for the past three decades, was hardly Islamic and never a Republic. Please, do not trust Mousavi. Do not trust anyone whose living was ever supplied by this regime. We need a fresh breath... Not the kind who resigns to call attention. It is such a pitiful waste that you take a bullet while shouting "Mirhossein" in the streets. 
God, I start to sound more dramatic everyday. But the fact of the matter is that it certainly is dramatic.               

How Fatty Ali Shah tickles me!

I just cannot get his grace, the Fat-ih-Ali shah of Kajar, out of my head. I simply cannot believe how easy and trouble free he was, not just during his monarchy but even before when he was a young prince in his uncle's palace. His uncle, Agha Mohammad Khan of Kajars who was castrated at a very early age and thus  had grown severe psychological complexities due to his nueteration, would always encouraged him to sexual reproduction in order to, in his eye, spread the royal Kajar blood and name. Ergo, he would have praised his nephew quite generously every time he bred or picked another permanent or temporary wife. 
Aside from his extensive sexual procreative misdemeanors, which lasted even up to the end of his nearly 28 years of sovereignty, his grace had a rather efficient and practical international policies. Every single time he felt he was having trouble in the battles, he tried to solve the issue via dialogue and signing agreements and contracts, which basically consisted of giving land so that the enemy would stop invading. 
See, quite simple and practical with the least bloodshed possible, don't you think?! 
He, as mentioned previously, had assembled a strong relationship with British generals and colonels and at one lengthy stage, following one of those contracts, delivered the whole Persian army to some British general for training. 
Oh God, how we had to sob and pray and tried much more harder for ourselves not to challenge similar torment ever again! And how the mother land, Iran, is bearing equivalent trauma at the moment, only with a contemporary image and ensemble. 
What do you think my friends? What seems to be our problem that we have to go through the same agony dynasty after dynasty, Kajar, Pahlavi, Khomeini... This last one has no remorse and no shame whatsoever... They truly believe what they do it Godly and categorically right by nature. 
I think, we lack leaders. We have very good people scattered around the world, from best American and European universities, businesses, governmental jobs and to NASA and so on and so forth. But we definitely lack charismatic leader, like Amir Kabir, Nader shah, Shah Abbas and Mossadeq. Hey look, in every case, we destroyed them with our own bloody hands. Amir Kabir, stabbed in back by his own, Mossadeq, oh the great Mossadeq, the only Iranian politician in Iran's history who spectacularly defended Iran in an International court in a foreign language for over three hours, betrayed by his own nation he fought for so hard. Nader shah Afshar, the son of sword, who actually survived Iran from being broken into pieces and uniting the country once again, was stabbed in his asleep by the captain of his guards in his own palace. God, shame on us people, shame on us... seriously. 
We, with our own bloody hands, blow up, shatter, burn and spread the ashes of every single chance that God throws at us most mercifully. If I was God ( اءوذ بالله) I would have never ever again given us another chance. Thanks God for his never-ending compassionate and mercifulness.
And yes, I believe, we have very few eligible people with abundant education and knowledge and proper character who at the same time posses that "it factor", the charisma. 
Please, be extremely vigilant that this time if we were lucky enough to find such person, we must ALL, and I mean ALL, support him/her. For once, let us halt, listen and allow him/her to do the job. Instead of being judgmental and offensive, let us be obedience and sympathetic. 
What do you say, huh?                
Oh, one of the last or maybe the last survivor of the Kajars is Ms. Sara Shahi. She is a successful Hollywood actress. Extremely beautiful. May God of Iran bless her. 
I pray for us to have enough power and wisdom to protect our motherland, Persia.   

The Dynasty of the Kajars

The truth... O the truth! Don't you just hate it to your bones when you see someone tries to alter history only to fit or maintain his current miserable affairs. 

Us, electronic engineers, would know that no circuit works without  proper biasing. But, however, I can not believe how much this singular word bothers me once used in any context other than electronics! 

Golestan & Torkamanchay agreements, as were taught to us, somewhat appropriately, were quite shameful turning points in our land's history. If not for them, Azerbaijan and so many other countries at the margin of the Caspian sea, as well as the Bahrain's might have been within the Islamic Republic of Iran by now (I guess they have been pretty lucky in that sense, aye). Anyways, our job is just to read, comprehend and learn in order to implement later, don't you think?!

Well, enough jabbering around. My sole aim was to introduce to you "The Dynasty of the Kajars". It is a translation and added notes of "Sir Harford Bridges" of the Eastern India Company, of parts of the Persian reign, made available to him by "Fatty Ali Shah" (as printed by Bridges himself) of Kajars. I am not sure if you would enjoy as much as I did, reading this book, but it certainly gives you a rather exquisite and divergent perspective. 

Oh, I almost forgot to mention the most important part; this book, the original version was only printed a couple of hundred copies. It was the absolutely amazing and awesome "Google" (Google books) that converted it to digital, which version is available to us online now. I, unfortunately, could not find any translated version to Farsi yet, but I am sure someone must have tried to convert it back to Farsi. If you know who please kindly let me know, otherwise I would be delighted to embark on it myself, LOL. 

I am not even sure, if any of the hardcopies are available in any library or museum in Iran, but I am sure there are plenty that you may be able to locate in British libraries.

I would be glad to hear your ideas about the book, about Sir Bridges and of course the Kajars and especially Fatty Ali Shah (Fat-ih-ali shah).

        

Iran-Iraq war, Khoramshahr, Jahanara, Banisadr, Patriotism

The war between Iran and Iraq, known as the “imposed war” or the “holy war”, between Saddam & Khomeini, which took the lives of nearly 1 million, started in 1359 in the Persian calendar or on September 1980 and lasted till, if I am not mistaken, till August 1988.

The turning point of the war, for Iranians, was the recapturing of Khoramshahr in the province of Khuzestan, which was seized and captured by Iraqi forces at very early stages of the war and left Iranian military and the whole country and people in turmoil. The commander in chief of the “Operation Beit-ol-Moqadas” which led to the liberation of the city on the 24th of May and capturing nearly 15000 Iraqi POWs, was Colonel Mohammad Ali Jahanara, a faithful and patriot soldier from the city of blood, Khoramshahr. He is most definitely, confessed by so many, one of, if not “the one” bravest soldiers, the nation was blessed to have for a very long time. It is believed that Colonel Jahanara and his friends under his orders, almost single-handedly with the least resources, successfully seized the city and apprehended the Iraqis. Too sad that almost five months after the liberation of his city, him and many of his brave friends who were in the Beit-ol-Moqadas passed due to a flight malfunction on their way to Tehran from the front. His memory is and will always be with us. It is souls like Jahanara’s that give meaning to our land, Iran. May God bless his soul.

So many would want to disturb his patriotic character and essence of his spirit by distracting it and mixing up with his religious beliefs. There is absolutely no single doubt that he is a Martyr of Iran and had very strong and faithful religious and Islamic beliefs. There is absolutely no doubt that as a soldier he was under the command of Khomeini as the leader of his country and the war at that stage. But it is important to know that his bravery has nothing to do with these and everything to do with his nationalistic and patriotic principles.

Do you think if he was a secular of Buddhist Khoramshahri boy under no organised military service, he would not defend his home to his last breath? Do you think it was his faith in Islam that defined him or his love to his land? I hate to ask rhetorical questions but I am positive that his Islamic beliefs only shaped and strengthened his love for his land and Iran. I am myself a traditional boy and consider myself a Muslim. I would never disregard or belittle my faith but I also refuse to let my spiritual beliefs to upset my judgement for the TRUTH.

Khomeini was a great a man, there is no doubt about it that how capable and charismatic he was, otherwise he would never be able to do what he did in a zillion years but personally I do think he was categorically misguided in some aspects. He says: Nationalism (patriotism) is against Islam. I mean how wrong is that. If a man has no love for his mother or his mother land how do you believe he is going to be able to love his God?

A wise man once told me that there are only three true loves: Love for the creator, Love for your mother and love for your land... It is not that you love whatever created you! It means you will love whatever gives meaning to you, if it is your wife, well then so be it. If it is your car or a pair of denim pants..... I believe this is where the sense of care and solicitude, which comes from within relates to whomever or whatever defines you.

Well, I am terribly sorry I fell a bit far from the point. I wanted to talk about President Banisadr. At the very stages of the war, President Banisadr, who was the commander in chief of all Iran’s armed forces at the time, was discharged, expelled and banished from Iran to France, due to his conducts and disagreements with Ruhollah Khomeini, which led to his impeachment by the Iranian Parliament instructed by Khomeini. Before even Khomeini sign the impeachment papers, the revolutionary guards went after Banisadr but luckily he was smart enough to arrange for his own deportation.

Anyhow, the information we have about Banisadr as well as our judgement (by “we” I mean the second generation Iranian Juniors who grew up in Iran after the revolution) is very much tangled to the doped instructions and knowledge that were fed to most of us by the media or during our high school or tertiary education. As president Banisadr, himself, lucky for us, is present, I suggest we have to dig deeper to catch more legitimate and valid information to have a clear judgement of President Banisadr.

During my military service and especially during the first two months of the training, they were very keen to project a disloyal and betraying image of Banisadr. Even one instructor, poorly tried to tell a story to us of how Jahanara bravely slapped banisadr heavily in the face in a meeting and left the room. Well, as I was not present there myself and have not spoken to anyone with concrete knowledge about the meeting, if there ever was such meeting, I will not even try to judge regarding this matter. I am not saying Banisadr was not ever disloyal or a traitor or else he was a faithful president who was falsely accused!

What I am very much interested in, is this statement that is being associated with the name of Banisadr almost every time he is referred to in the Islamic Republic of Iran:

“We need to give land to buy time ... Khoramshahr and Abadan are neither politically nor logistically essential to us at this stage (early stages of the war)”

I have emailed President Banisadr, asking him regarding this statement, but unfortunately have not yet received any response. In case there is any, I will quickly post it for everyone to know.

I am very much concerned and curious about this single statement of Banisadr for obvious reasons.

I think I have written too long and am going to have to leave the rest to you guys to decide.

I only would like to raise this question: why after the liberation of Khoramshahr, the war still continued?Aand why it became awfully lengthy?

If you feel like you have an answer to these please let me know via comments or emailing me.

I certainly value a good debate here.

Good luck and good bye for the moment...

I must acknowledge "Ashoura" for the lovely poster.

FARVAHAR

Farvahar is believed to be one of the prime emblems of the Zoroastrianism, which is the state religion of ancient Iran. Thus, Farvahar is widely illustrated in many aspects of Persian heritage as a crest. Farvahar is thought to represent the “Fravashi” or the guardian angel. Ergo the monarch used it is a its divine royal glory, the Fravashi of the king, protecting his authority and in turn the emperor and its people. 

Zoroastrianism, allegedly, manifest a clearer ideology behind the Farvahar emblem. According to Zoroastrians It is the Essence of Wisdom and is seen to be the guardian spirit of man.

The face represents the consciousness of man.

The torso represents the body of man.

The right hand pointing upwards represents the right path which is the path of truth.

The left hand holding a ring represents sovereignty and power.

The two tassels on both sides of the tail represent the need for moderation in life.