Posted by
Stephan Bender on
URL: http://imagej.273.s1.nabble.com/Getting-the-number-of-pixels-which-values-are-below-a-certain-threshold-tp3688975p3688979.html
Hi Michael,
wow, thank you!
There's only one problem now:
I tried it with a DICOM image of which I know that appr. 100000 pixels
are in the range of -2048 --> -500.
However, the macro returns 262144 pixels, which is 100% of the pixels
(the image is 512x512). Maybe it is related to the bit depth you use to
differ cases? Sorry, I am really a newbie with ImageJ...
All of my images are 16bit...
This is the macro how I run it:
name = getArgument;
if (name=="") exit ("No argument!");
setBatchMode(true);
open(name);
threshold=-500;
getStatistics(area, mean, min, max, std, histogram);
result=0;
for (i=0; i<lengthOf(histogram); i++) {
if (bitDepth()==32)
value=min+(max-min)*i/(lengthOf(histogram)-1);
else
value=calibrate(i);
if (value<threshold) result+=histogram[i];
}
perc=result*100/(getWidth*getHeight);
print(getTitle+": "+getWidth+"x"+getHeight+" "+result+" "+perc+" %");
As I run it from the shell, I can process the result using pipes.
However, thank you also for the tip with the file output.
Best regards,
Stephan
Am 02.03.2010 18:28, schrieb Michael Schmid:
> Hi Stephan,
>
> loops in the macro language are like in C or Java, except that you
> need no type declaration.
>
> Also there was one problem with my idea: Using 'min, max' is correct
> for 32-bit images only (>90% of my images are 32 bit, so I did not
> think about this), and there was a 'minus 1' was missing).
>
> So, without trying it for all image types...
>
> //find number of pixels below a threshold
> threshold=-500;
> getStatistics(area, mean, min, max, std, histogram);
> result=0;
> for (i=0; i<lengthOf(histogram); i++) {
> if (bitDepth()==32)
> value=min+(max-min)*i/(lengthOf(histogram)-1);
> else
> value=calibrate(i);
> if (value<threshold) result+=histogram[i];
> }
> path=getDirectory("temp")+"ij_result.txt";
> f = File.open(path);
> print(f, result);
>
>
> Note that your macro would print to the 'Log' window, you won't be
> able to access this from the shell or a Batch file. The macro above
> prints to a file in the temp directory (depending on the operating
> system, on Unix-like systems: /tmp/). Use
> print(getDirectory("temp"));
> to see where it goes. You can also use getDirectory("home") or any
> other directory you like.
>
> By the way, instead of calling ImageJ from the shell (or Batch file
> under Windows) for each file, it might be faster to create a file with
> all the filenames and have ImageJ open the file and process the
> complete list in a loop.
>
>
> Michael
> ________________________________________________________________
>
> On 2 Mar 2010, at 13:34, Stephan Bender wrote:
>
>> Hi Michael,
>>
>> thanks for the advice. However, I still do not get it because of the
>> loop you describe.
>>
>> This is how I would start with the macro:
>>
>> name = getArgument;
>> if (name=="") exit ("No argument!");
>> setBatchMode(true);
>> open(name);
>> // here goes the loop
>> print(getTitle+": "+result);
>>
>> Can you please help me with the loop?
>>
>> Thank you!
>>
>> Best regards,
>>
>> Stephan
>>
>> Am 02.03.2010 11:05, schrieb Michael Schmid:
>>> Hi Stephan,
>>>
>>> this should be easy:
>>> getStatistics(area, mean, min, max, std, histogram);
>>> In a 'for' loop, sum up all values in the histogram array from index
>>> 0 to
>>> floor(lengthOf(histogram)*(threshold-min)/(max-min))
>>> where threshold is -500 in your case.
>>> Write the result to a file:
>>> f = File.open(path);
>>> print(f, result);
>>> in your shell script or batch file, you can read the value from the
>>> file.
>>>
>>>
>>> Michael
>>> ________________________________________________________________
>>>
>>> On 1 Mar 2010, at 18:18, Stephan Bender wrote:
>>>
>>>> Hello,
>>>>
>>>> I'm quite new to ImageJ, I hope someone can help me with this task:
>>>>
>>>> I need get the number of pixels which values are below a certain
>>>> threshold. The image format is DICOM (16 bit), and I need the result
>>>> on a Unix command line, so I guess I'll have to use a macro function.
>>>> A common image has appr. 60% of the pixel values from -2048 to -500,
>>>> I need to know the exact number of pixels below -500.
>>>>
>>>> Thank you very much for your help!
>>>>
>>>> Best regards,
>>>>
>>>> Stephan