Why was Japan NOT colonised by any of the European countries when practically all of the Asian countries were being colonised by a European nation? Why did no army even clash against the Japanese army(s)? Please list causes apart from Japan's geographical location.
First of all, this is not true that "practically all Asian nations were colonized by the Europeans". China and Russia were never colonized and this is a very large part of Asia in territory and population. Middle Asia was colonized by Russia, not by West Europe.
European colonizers mostly were successful in those territories close to the ocean. And of these, Japanese example is indeed unique.
Europeans "discovered" Japan in XVI century, and started to penetrate it, setting the trade posts and converting the locals to Christianity. I do not know whether this should be called "colonization" but probably it would lead to colonization, as it lead elsewhere.
However Japanese rulers early recognized the danger, and started effective resistance. They used drastic measures (killed all those converted to Christianity, for example, banned firearms, prohibited overseas travel, etc.) This way they managed to isolate the country almost completely until the middle of 19-th century. One important point was probably the unity of Japan. In other places, Europeans were able to colonize a country by taking sides in local conflicts, or to enlist some people opposing to the rulers (Mexico is an example).
In the 19-th century it was penetrated again. And again the Japanese managed to do the thing nobody else could. They quickly (VERY quickly) modernized their country themselves, in less than 1/2 of a century, I think this feat has no parallel in history, and by the beginning of 20-th century they were a "world power" that nobody would easily colonize.
I repeat that I do not know any similar examples. Hawaii also modernized very quickly, in few years! And for about a century after they remained independent. But they could not prevent Americans from settling there, and as a result a century later they had to become a US territory.
Japan compared to China and India, was small and out of the way. They were also extreme isolationists and had very little interactions with outsiders. It wasn't until the 1850's that the US essentially forced open Japan to the outside world. Essentially for the Europeans, Japan was just out of the way, and of no real importance. The only reason the US forced them open was because they were literally all that was left, and the US wanted its own footholds in Asia.
Another example is that Korea, a natural stopping point before Japan also had relatively little contact with European countries. It seems that the massive goods and trade that Europe was exploiting out of the large countries of India and China stopped their need to go further east in their desire for money.
The treaty of tordesillas between Portugal and Spain essentially split the world between the 2 countries, however, since that split was unclear in the pacific, while other future treaties would put japan into Portuguese domain, Spain argued it was really in their domain, and so neither country could would risk full claim of the country so they did not colonize. Instead they fought through spreading Christianity in about 1550's. Essentially at this time they fought over who the Pope would give exclusive rights to convert japan to Christianity, exclusive conversion rights would also give them exclusive trade rights. In 1575 pope Gregory XIII decided that japan was owned by the Portuguese diocese of Macau. However, the Spanish also got a papal decree in 1600 by pope clement VIII that allowed the Spanish friars to also enter and convert the Japanese. In the next few year the Dutch also started trading with the Japanese, and fighting between the christian groups, as well as internal policy shifts essentially kicked out all of the Spanish/Portuguese Christians, and forced all Japanese to either convert away from Christianity or die. Because of this, the Portuguese and Spanish essentially ceased trade with the Japanese, and only the Dutch had any kind of contact with japan till the 1850's when the US shock and awe'd the Japanese into treating/trading with them.
The English also started trading with japan at about the same time as the Dutch however, they stopped trading after about 10 year due to it being unprofitable for them.
sources - (yes wikipedia, however most of their reference sources checked out)