Intensity graph save as tiff with z value

[dk91]

Hello,

I have an intensity graph that I would like to save as tiff with its z value (contrast). When I save as tiff, it saves as raw intensity graph (contrast from 0-255) without contrast that I'm seeing from the graph. Is there a way to save the intensity graph with current contrast?

Thanks in advance.

[zou]

You forgot to wire the "Color Palette" when you save to tiff.

[dk91]

Hi George,

Thanks for the reply. I wired color palette as below but doesn't seem to change. Is this the right way to get color from the intensity graph?

Thanks.

[zou]

Did you take a look the image before save to file?

[dk91]

Hello George,

Sorry about the late response - I was on other project for awhile. Now I'm back to this project. Can you elaborate little bit further about what you meant by to look at image before save? I changed contrast of intensity graph (max/min) but saved image doesn't show updated contrast. Thank you for the help.

 

[wiebe@CARYA]

The Z-scale property of the intensity graph only specifies the colors. The min value of the Z-scale will get the lowest specified color, the max value will get the highest specified color (the table should be 256 colors IIRC). The Z-scale might be set to autoscale, so you need to read them from the property node as well. It could even be set to Logarithmic...

So to use those in a tiff, you need to scale the colors or the data to a format the tiff uses (could be 0-1 or 0-255), not sure, don't have vision installed right now.

[dk91]

Hello,

Thanks for the reply. The tiff color palette scale is 0 - 255. So, what you mean is I need to rescale color table (basically it gives me an array of 0 - 255 of RGB [{0,0,0}, {1,1,1}, {2,2,2},....,{255,255,255}]) using Z-scale min and max values? Is there an example? It doesn't seem to make any difference when I tried.

Thank you.

[wiebe@CARYA]

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@dk91 wrote:

Thanks for the reply. The tiff color palette scale is 0 - 255. So, what you mean is I need to rescale color table (basically it gives me an array of 0 - 255 of RGB [{0,0,0}, {1,1,1}, {2,2,2},....,{255,255,255}]) using Z-scale min and max values? Is there an example? It doesn't seem to make any difference when I tried.

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Be very careful. The R, G and B values have a range. But to what floating value does the maximum value map? That's another range. So there are two ranges.

The intensity graph has a color scale. These are defined as R, G and B values of 0-255. But the floating value that gets the first color, and the floating value that gets the maximum color are not defined by those colors. You need the z-scale minimum and maximum for that as well.

So in short: both the intensity graph as the tiff have a minimum and maximum z-scale, and 256 colors defined as R, G and B with a scale (could very well be 0-1 for tiff, not sure).

I think the tiff will regard floating number 0 as the lowest color, and 1 as highest color. So you need to:

1) scale all data to so the intensity graph's color scale minimum is 0 (subtract minimum from data), and the maximum color scale of the intensity graph is 1 (divide data by max-min). So:

Tiff_Data = (Data - Int_Graph_Min) / (Int_Graph_Max - Int_Graph_Min)

2) Make sure the color scale uses the correct format. Maybe you need to divide those colors by 255, so R, G and B are 0-1. Not sure.

If one of them is off, it won't work.

[dk91]

So do you mean scale the actual intensity data? Say if my z-scale min and max are 20 and 40 (ZScale.Marker Values property node returns current min/max scale). I should do ([2D intensity data] - 20) / 20. And Intensity graph's ColorTbl (RGB) property should be scaled to either 0-1 or 0-255. When I tried this, returned image is all black...I must be missing something...

[dk91]

I think I see it now. From the intensity data, I get min and max values and re-scaled them. But the result is the same. Any suggestion on what I'm doing wrong?