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I am having troubling to get rid of these black regions in my ListContourPlot

enter image description here

Here is the sample data from the one of region form the figure! (Thank you @Corey979 for helping me to find place to share the data)

http://pastebin.com/y6XG4hib

The sample data plot looks like this

enter image description here

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  • $\begingroup$ Or to irregular distribution, like missing points. You can check if this effect is present with a subset of your sample (first 1000 points, or every 1000th point, or so), and then upload this smaller sample on, e.g., pastebin.com $\endgroup$ – corey979 Jan 19 '17 at 18:06
  • $\begingroup$ @corey979 Thank you! I was able to get some part of the image $\endgroup$ – Saesun Kim Jan 19 '17 at 19:02
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Your data has issues, and you need to do some kind of smoothing before you can use ListContourPlot.

data = << "http://pastebin.com/raw/y6XG4hib";
ListPointPlot3D[data]

Mathematica graphics

From there you can see the issue, but it's clearer if you isolate one of those lines,

GatherBy[data, First] // ReplaceAll[{x_, y_, z_} :> {y, z}] // 
  First // ListPlot

Mathematica graphics

Mathematica wants to use some kind of interpolation when making a contour plot, but there's no way to make a decent interpolating function for this. Without fixing your data (preferably at the source), the best you can do is to turn off interpolation altogether

ListContourPlot[data, InterpolationOrder -> 0, 
 ColorFunction -> "BlueGreenYellow", PlotLegends -> Automatic]

Mathematica graphics

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