How to read current density calibration from an image in a macro

[Stein Rørvik]

Hello,

I have some 16 bit CT images (similar to the CT image available in the open samples menu) for which I need to read the current density calibration from within a macro. I cannot figure out how to do that in a reliable way. The density values are calibrated from minus a few thousands to plus a few thousands across the 0-65535 range.

There is already a "calibrate(pixelValue)" macro available; what I need is a function like "uncalibrate(densityValue)" or "getRawPixelValue(densityValue)" to get the corresponding pixel value.

I wrote these lines as a workaround, but this approach does not work if the image is not straight line calibrated.

calibOffset = calibrate(0);
calibSlope = calibrate(1)-calibrate(0);
rawValue = (calibValue-calibOffset)/calibSlope;

Suggestions?

Stein

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[Rasband, Wayne (NIH/NIMH) [E]]

> On Oct 20, 2015, at 6:55 AM, Stein Rørvik <[hidden email]> wrote:
>
> Hello,
>
> I have some 16 bit CT images (similar to the CT image available in the open samples menu) for which I need to read the current density calibration from within a macro. I cannot figure out how to do that in a reliable way. The density values are calibrated from minus a few thousands to plus a few thousands across the 0-65535 range.
>
> There is already a "calibrate(pixelValue)" macro available; what I need is a function like "uncalibrate(densityValue)" or "getRawPixelValue(densityValue)" to get the corresponding pixel value.
>
> I wrote these lines as a workaround, but this approach does not work if the image is not straight line calibrated.
>
> calibOffset = calibrate(0);
> calibSlope = calibrate(1)-calibrate(0);
> rawValue = (calibValue-calibOffset)/calibSlope;

16-bit CT images normally use straight line calibration so the above approach should work. For images that are not straight line calibrated, call the Calibration.getRawValue() method in a script, for example:

  value = -440;
  img = IJ.getImage();
  cal = img.getCalibration()
  rawValue = cal.getRawValue(value);
  print(rawValue);

You can use the eval() function to run this code in a macro, for example:

  value = -440;
  code = "IJ.getImage().getCalibration().getRawValue("+value+")";
  rawValue = eval("js", code);
  print(rawValue);

-wayne

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