ImageJ - Re: Specific color channel to retrieve from an image in a plugin

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Re: Specific color channel to retrieve from an image in a plugin

Posted by Philippe GENDRE on
URL: http://imagej.273.s1.nabble.com/Specific-color-channel-to-retrieve-from-an-image-in-a-plugin-tp5004950p5005079.html

Thanks to Herbie and Rob.

Herbie : yes you are right, it is not slow it takes time but what Rob
proposes is considerably faster and it is just what I try to do.

Rob : I use the following lines :
int[] colPixels = (int[]) ip.getPixels();
int PixelCount = ip.getPixelCount();
int[] redVal=new int[PixelCount];
int[] greenVal=new int[PixelCount];
int[] blueVal=new int[PixelCount];

for (int x = 0; x < PixelCount; x++) {

int pixVal = colPixels [x];
//get red , green and blue values from pixVal
redVal[x] = (pixVal & 0xff0000) >> 16;
greenVal[x] = (pixVal & 0x00ff00) >> 8;
blueVal[x] = (pixVal & 0x0000ff);

if (blueVal[x] <redVal[x] &&blueVal[x]
<greenVal[x] )
blueVal[x] =0;
}

ImageProcessor ipB = new
ColorProcessor(frame_width,frame_height,blueVal);

In my case, this code is 3 times faster than the previous one.
Another request is how to cast blueVal values into a ByteProcessor without
consuming time. Adding the line ipB=ipB.convertToByte(false) is time
consuming.

Best regards,

Philippe

2013/10/7 Rob van 't Hof <[hidden email]>

> Sorry, just noticed that there is a line that is not needed: the // get
> brightness etc comment. The perils of copy and paste.
> Also you can further speed up things using multithreading if you use a
> more modern processor with multiple cores. this only gives substantial
> benefits if you are using really largish images (mine can be up to 100
> Mpixels).
> Rob
>
>
> On 07/10/2013 13:15, Rob van 't Hof wrote:
>
>> Hi,
>> getPixelValue is not particularly fast. The fastest way of going through
>> an image pixel by pixel is using the 1-dimensional array access methods.
>>
>> Here is a code snippet:
>>
>> int[] colPixels = (int[]) ip.getPixels();
>> PixelCount = ip.getPixelCount();
>>
>> for (int x = 0; x < PixelCount; x++) {
>> //get brightness from shading image
>> int pixVal = colPixels [x];
>> //get red , green and blue values from pixVal
>> int redVal = (pixVal & 0xff0000) >> 16;
>> int greenVal = (pixVal & 0x00ff00) >> 8;
>> int blueVal = (pixVal & 0x0000ff);
>>
>> if (blueVal <redVal &&blueVal <greenVal )
>> blueVal =0;
>> }
>> }
>>
>> Hope this helps,
>>
>> Rob
>>
>>
>>
>> On 07/10/2013 11:26, Herbie wrote:
>>
>>> Philippe,
>>>
>>> you say you need to inspect every pixel of your image and that this is
>>> slow.
>>>
>>> Sorry, but I don't think it is slow but it simply takes time, especially
>>> if your images are big. Don't you agree?
>>>
>>> If you do the loop over all pixels in Java, I see little chance to speed
>>> up the desired process.
>>>
>>> Best
>>>
>>> Herbie
>>> ______________________________**___________
>>> On 07.10.13 10:16, Philippe GENDRE wrote:
>>>
>>>> Dear List,
>>>>
>>>> Recently, I posted a question to this list to retrieve a specific color
>>>> channel (the red one for example) from a RGB image. The answer
>>>> (ImageProcessor red = ((ColorProcessor)ip).**getChannel(1, null);) is
>>>> perfect
>>>> but I have realized that it is not what I need. In fact I need to
>>>> retrieve
>>>> a specific color of pixel for example the blue ones and not the
>>>> intensity
>>>> of the channel. According to that I wrote the following code:
>>>> ImageProcessor ipR=((ColorProcessor)ip).**getChannel(1,null);
>>>> ImageProcessor ipG=((ColorProcessor)ip).**getChannel(2,null);
>>>> ImageProcessor ipB=((ColorProcessor)ip).**getChannel(3,null);
>>>>
>>>> for (int x=0; x<frame_width; x++){
>>>> for (int y=0; y<frame_height; y++){
>>>> if
>>>> (ipB.getPixelValue(x,y)<ipR.**getPixelValue(x,y)&&ipB.**
>>>> getPixelValue(x,y)<ipG.**getPixelValue(x,y))
>>>> ipB.set(x,y,0);
>>>> }
>>>> }
>>>> That sounds good but slow. How to speed up this ?
>>>>
>>>> Best regards,
>>>>
>>>> Philippe
>>>>
>>>>
>>>> 2013/9/26 Philippe GENDRE <[hidden email]>
>>>>
>>>> ImageProcessor red = ((ColorProcessor)ip).**getChannel(1, null) is
>>>>> exactly
>>>>> what I needed.
>>>>>
>>>>> This list is a marvel. Thanks a lot.
>>>>>
>>>>> Philippe
>>>>>
>>>>>
>>>>> 2013/9/26 Rasband, Wayne (NIH/NIMH) [E] <[hidden email]>
>>>>>
>>>>> On Sep 26, 2013, at 1:02 PM, Philippe GENDRE wrote:
>>>>>
>>>>>>
>>>>>> Dear List,
>>>>>>>
>>>>>>> I need to retrieve the red channel of an RGB image plus object as an
>>>>>>>
>>>>>> image
>>>>>>
>>>>>>> processor in a plugin.
>>>>>>>
>>>>>>> What is the best solution ?
>>>>>>>
>>>>>>
>>>>>> Use the ImageProcessor.getChannel() method. Here is a JavaScript
>>>>>> example:
>>>>>>
>>>>>> imp = IJ.openImage("http://imagej.**nih.gov/ij/images/clown.jpg<http://imagej.nih.gov/ij/images/clown.jpg>
>>>>>> ");
>>>>>> ip = imp.getProcessor();
>>>>>> red = ip.getChannel(1, null);
>>>>>> new ImagePlus("Red Channel", red).show();
>>>>>>
>>>>>> In a plugin, it would look like this:
>>>>>>
>>>>>> ImagePlus imp = IJ.openImage("
>>>>>> http://imagej.nih.gov/ij/**images/clown.jpg<http://imagej.nih.gov/ij/images/clown.jpg>
>>>>>> ");
>>>>>> ImageProcessor ip = imp.getProcessor();
>>>>>> ImageProcessor red = ((ColorProcessor)ip).**getChannel(1, null);
>>>>>> new ImagePlus("Red Channel", red).show();
>>>>>>
>>>>>> -wayne
>>>>>>
>>>>>> --
>>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>>
>>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>
>>>
>>
> --
> _____________________________
> Dr. Rob van 't Hof
> Reader
>
> Centre for Molecular Medicine
> MRC IGMM
> University of Edinburgh
> Western General Hospital
> Crewe Road, Edinburgh EH4 2XU
> United Kingdom
>
> Phone: (+44)-131-6511031
> email: [hidden email]
> _____________________________
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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