Re: Normalising XY data by Z-direction in stacks

Posted by jamescleverley on
URL: http://imagej.273.s1.nabble.com/Normalising-XY-data-by-Z-direction-in-stacks-tp3685096p3685099.html

Thanks Neil, That was all the pointer I needed to get a modified version of your code snippet to do what I needed.  Next will be to think about effective processing order to maximise speed .... Code below if anyone is interested:

// Make sure image accepts floating point values

run("32-bit");

// get image width x
x = getWidth;
// get image height y
y = getHeight;
// get image depth z
z = nSlices;

for (i=0; i < x; i++){
  for (j=0; j < y; j++){
    // Get max and min value in the x-y coord
    maxValue = 0;
    minValue = 10000;
    for (k=1; k <= z; k++){
     
      setSlice(k);
      currValue = getPixel(i, j);
      if (currValue > maxValue){
        maxValue = currValue;
      }
      if (currValue < minValue){
        minValue = currValue;
      }
    }
    // Set new value normalised to max value
    for (k=1; k <= z; k++){
      setSlice(k);
      currPixelValue = getPixel(i,j);
      newPixelValue = (currPixelValue-(minValue))/(maxValue-minValue);
      putPixel(i, j, (newPixelValue));
    }
  }
}

Much appreciated,

Cheers

James

Dr James Cleverley 
Senior Geochemist
Stream Leader | Mineral Systems & Targeting
Minerals Down Under Research Flagship
CSIRO Earth Science & Resource Engineering
Phone: [phone] | Mobile: [phone]
[hidden email] | www.csiro.au | www.csiro.au/
Address: Australian Resources Research Centre, PO Box 1130, Bentley, WA, 6102

PLEASE NOTE
The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference.
Please consider the environment before printing this email.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Thomson Neil (EAST KENT HOSPITALS UNIVERSITY NHS FOUNDATION TRUST)
Sent: Thursday, 7 April 2011 20:51
To: [hidden email]
Subject: Normalising XY data by Z-direction in stacks

Hi James

I don't know your background, so forgive me if I'm way off the mark...

This should be a pretty trivial problem with some coding. If you haven't looked at the developer<http://rsbweb.nih.gov/ij/developer/index.html> section of he ImageJ website, have a look now. If you've never done any programming then writing a Java plugin might be a bit scary, but the macro language <http://rsbweb.nih.gov/ij/developer/macro/macros.html> should so the trick.

This macro-code snippet might give you an idea on normalisation:

// Make sure image accepts floating point values
run("32-bit");
// get image width x
// get image height y
// get image depth z
for (i=0; i < x; i++){
  for (j=0; i < y; j++){
    // Get max value in the x-y coord
    maxValue = 0;
    for (k=0; i < z; k++){
      setSlice(k);
      currValue = getPixel(x, y);
      if (currValue > maxValue){
        maxValue = currValue;
      }
    }
    // Set new value normalised to max value
    for (k=0; i < z; k++){
      setSlice(k);
      setValue(x, y, getPixel(x, y)/maxValue);
    }
  }
}

Neil

Neil Thomson,
Nuclear Medicine Physics Section,
Medical Physics,
Kent and Canterbury Hospital,
UK. CT1 3NG
[phone]

********************************************************************************************************************

This message may contain confidential information. If you are not the intended recipient please inform the
sender that you have received the message in error before deleting it.
Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents:
to do so is strictly prohibited and may be unlawful.

Thank you for your co-operation.

NHSmail is the secure email and directory service available for all NHS staff in England and Scotland
NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients
NHSmail provides an email address for your career in the NHS and can be accessed anywhere
For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail

********************************************************************************************************************