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[RaiMan <rmhdevelop@xxxxxx>]

I made the following test with your posted image and had no problem,
identifying the hexagons with a minimum similarity of 1.0, as long as
the search patterns do not consist only of pixels of the same color (in
this case some same rectangle is matched with 1.0 for each of these
patterns and even not in a colored area (in my test cols1))

the zipped .sikuli containing my test can be found at:
https://files.me.com/rhocke/az3evg

run on Mac OSX 10.6 using my own build version of the latest X-1.0rc2 in
true 64-Bit using OpenCV 2.2 in 64 Bit.

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https://bugs.launchpad.net/bugs/745606

Title:
  Sikuli X-RC2 cannot identify colours correctly

Status in Sikuli:
  New

Bug description:
  Hi,
  We upgraded from version 0.10.2 to X and our automated test that detect for colour changes have stopped working.

  The GUI application we are testing has some indicators that change colour to warn the user of potential problems. We have some Sikuli tests that test this feature, and since the upgrade the tests are no longer able to detect the colour change.
  These tests worked very well in version 0.10.2.

  Even after knocking the Similarity up to 1.0 it cannot distinguish
  between Yellow and Red.