Limiting histogram to ROI

[Michael Doube]

Dear all,

A small code question.  I want to generate an autothreshold using a
histogram generated from all slices in a stack, and limited to an ROI if
one is present.  I thought that simply calling

ImageProcessor sliceIP = stack.getProcessor(z);
int[] sliceHistogram = sliceIP.getHistogram();

would give me a histogram of the slice, or the pixels in the ROI if an
ROI was drawn, because of this method description:

"int[] ij.process.ImageProcessor.getHistogram()

Returns the histogram of the image or ROI. Returns a luminosity
histogram for RGB images and null for float images."

However, it seems like the ROI is being ignored.
Is this because I call ImageStack.getProcessor() rather than
ImagePlus.getProcessor()?

I use this approach in getStackHistogram, line 338 here:
http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/ThresholdMinConn.java

Michael

[Michael Doube]

Please ignore this, I fixed it (and it was indeed because
ImagePlus.getImageStack.getProcessor(int i) returns an ImageProcessor
without an ROI, so you have to reset the ROI each time...)

On 15/07/10 10:59, Michael Doube wrote:

> Dear all,
>
> A small code question.  I want to generate an autothreshold using a
> histogram generated from all slices in a stack, and limited to an ROI if
> one is present.  I thought that simply calling
>
> ImageProcessor sliceIP = stack.getProcessor(z);
> int[] sliceHistogram = sliceIP.getHistogram();
>
> would give me a histogram of the slice, or the pixels in the ROI if an
> ROI was drawn, because of this method description:
>
> "int[] ij.process.ImageProcessor.getHistogram()
>
> Returns the histogram of the image or ROI. Returns a luminosity
> histogram for RGB images and null for float images."
>
> However, it seems like the ROI is being ignored.
> Is this because I call ImageStack.getProcessor() rather than
> ImagePlus.getProcessor()?
>
> I use this approach in getStackHistogram, line 338 here:
> http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/ThresholdMinConn.java
>
> Michael

... [show rest of quote]

--
Dr Michael Doube  BPhil BVSc PhD MRCVS
Research Associate
Department of Bioengineering
Imperial College London
South Kensington Campus
London  SW7 2AZ
United Kingdom

[Jacqueline Ross]

Dear All,

Can anyone tell me how I might create multiple ROIs in a single image,
crop them all out as individual images and then run the "Draw Random
Dots" inside each individual ROI?

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/