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problem with incomplete contrast adjustment

Finn Peters
8 posts
Hi,

in the following macro I do contrast and brightness adjustments on two
images (one in red the other in green) and subsequently a selection of
the red image is laid over the green image. Now I am quite puzzled
because the same macro seemingly by chance yields different results (see
attached jpgs) In the first case it worked out but in the second example
only the upper part of the green image has been adjusted in contrast.
The bottom part still has the same linear contrast as in the orignial image.

I really have no idea what could be the reason for this.

cheers,

Finn


macro code:


inputFolder = getDirectory("Input folder");
files = getFileList(inputFolder);
count = 0;
id = 0;
for (i = 0; i < files.length; i++) {
         open(inputFolder + files[i]);
         id2 = id;
         id = getImageID();
         count++;
         if ((count % 2) == 0) {
             selectImage(id);
             run("8-bit");
             run("Red");
             setAutoThreshold("Default");
             //run("Threshold...");
             setThreshold(3, 7);
             run("Create Selection");
             run("RGB Color");
             run("Copy");

             selectImage(id2);
             run("Brightness/Contrast..."); setMinAndMax(16, 44);
             run("Paste");
             run("Select None");

             name = getTitle();
             saveAs("Tiff", "C:/Users/Admins/Desktop/test/target/"+name+
"_merged.tif");
             close();
             close();
             count = 0;
         }}

merged version 1.jpg (3K) Download Attachment
merged version 2.jpg (2K) Download Attachment
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Re: problem with incomplete contrast adjustment

Krs5
454 posts
Dear Finn,

It seems that the macro sometimes get ahead of itself. If you include

wait(100); after setMinAndMax(16, 44); it might solve the problem, at least it did on my test dataset.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
College of Medicine, Biological Sciences and Psychology

http://www.le.ac.uk/biochem/microscopy/home.html


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Finn Peters
Sent: 23 August 2011 13:17
To: [hidden email]
Subject: problem with incomplete contrast adjustment

Hi,

in the following macro I do contrast and brightness adjustments on two images (one in red the other in green) and subsequently a selection of the red image is laid over the green image. Now I am quite puzzled because the same macro seemingly by chance yields different results (see attached jpgs) In the first case it worked out but in the second example only the upper part of the green image has been adjusted in contrast.
The bottom part still has the same linear contrast as in the orignial image.

I really have no idea what could be the reason for this.

cheers,

Finn


macro code:


inputFolder = getDirectory("Input folder"); files = getFileList(inputFolder); count = 0; id = 0; for (i = 0; i < files.length; i++) {
         open(inputFolder + files[i]);
         id2 = id;
         id = getImageID();
         count++;
         if ((count % 2) == 0) {
             selectImage(id);
             run("8-bit");
             run("Red");
             setAutoThreshold("Default");
             //run("Threshold...");
             setThreshold(3, 7);
             run("Create Selection");
             run("RGB Color");
             run("Copy");

             selectImage(id2);
             run("Brightness/Contrast..."); setMinAndMax(16, 44);
             run("Paste");
             run("Select None");

             name = getTitle();
             saveAs("Tiff", "C:/Users/Admins/Desktop/test/target/"+name+
"_merged.tif");
             close();
             close();
             count = 0;
         }}
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Re: problem with incomplete contrast adjustment

Finn Peters
8 posts
Dear Kees,

thank you for the reply. I tried it with a pause up to wait(10000) after
setMINAndMax(16,44); and at additional other positions. It still does
not work. It doesn't even work if I only run a macro of the following
two lines on a single image:
run("Brightness/Contrast..."); setMinAndMax(16, 44);
I guess there must be a problem with my computer somewhere. I will try
to make the macro in Photoshop.

cheers,

Finn

> Dear Finn,
>
> It seems that the macro sometimes get ahead of itself. If you include
>
> wait(100); after setMinAndMax(16, 44); it might solve the problem, at least it did on my test dataset.
>
> Best wishes
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Centre for Core Biotechnology Services
> College of Medicine, Biological Sciences and Psychology
>
> http://www.le.ac.uk/biochem/microscopy/home.html
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Finn Peters
> Sent: 23 August 2011 13:17
> To:[hidden email]
> Subject: problem with incomplete contrast adjustment
>
> Hi,
>
> in the following macro I do contrast and brightness adjustments on two images (one in red the other in green) and subsequently a selection of the red image is laid over the green image. Now I am quite puzzled because the same macro seemingly by chance yields different results (see attached jpgs) In the first case it worked out but in the second example only the upper part of the green image has been adjusted in contrast.
> The bottom part still has the same linear contrast as in the orignial image.
>
> I really have no idea what could be the reason for this.
>
> cheers,
>
> Finn
>
>
> macro code:
>
>
> inputFolder = getDirectory("Input folder"); files = getFileList(inputFolder); count = 0; id = 0; for (i = 0; i<  files.length; i++) {
>           open(inputFolder + files[i]);
>           id2 = id;
>           id = getImageID();
>           count++;
>           if ((count % 2) == 0) {
>               selectImage(id);
>               run("8-bit");
>               run("Red");
>               setAutoThreshold("Default");
>               //run("Threshold...");
>               setThreshold(3, 7);
>               run("Create Selection");
>               run("RGB Color");
>               run("Copy");
>
>               selectImage(id2);
>               run("Brightness/Contrast..."); setMinAndMax(16, 44);
>               run("Paste");
>               run("Select None");
>
>               name = getTitle();
>               saveAs("Tiff", "C:/Users/Admins/Desktop/test/target/"+name+
> "_merged.tif");
>               close();
>               close();
>               count = 0;
>           }}
>
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Re: problem with incomplete contrast adjustment

Michael Schmid
2136 posts
Hi Finn,

Did you try to remove the
   run("Brightness/Contrast...");
statement and just leave the setMinAndMax?

I think that you don't need to show the B&C panel. I have not  
analyzed it carefully, but the following might happen:

If the B&C panel needs some time to get displayed, its  
windowActivated gets called asynchronously and runs the 'setup'  
procedure, which takes a new snapshot in case of an RGB image.
This may cause a lot of trouble.

Michael
________________________________________________________________

On 24 Aug 2011, at 16:57, Finn Peters wrote:

> Dear Kees,
>
> thank you for the reply. I tried it with a pause up to wait(10000)  
> after setMINAndMax(16,44); and at additional other positions. It  
> still does not work. It doesn't even work if I only run a macro of  
> the following two lines on a single image:
> run("Brightness/Contrast..."); setMinAndMax(16, 44);
> I guess there must be a problem with my computer somewhere. I will  
> try to make the macro in Photoshop.
>
> cheers,
>
> Finn
>
>> Dear Finn,
>>
>> It seems that the macro sometimes get ahead of itself. If you include
>>
>> wait(100); after setMinAndMax(16, 44); it might solve the problem,  
>> at least it did on my test dataset.
>>
>> Best wishes
>>
>> Kees
>>
>>
>> Dr Ir K.R. Straatman
>> Senior Experimental Officer
>> Centre for Core Biotechnology Services
>> College of Medicine, Biological Sciences and Psychology
>>
>> http://www.le.ac.uk/biochem/microscopy/home.html
>>
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf  
>> Of Finn Peters
>> Sent: 23 August 2011 13:17
>> To:[hidden email]
>> Subject: problem with incomplete contrast adjustment
>>
>> Hi,
>>
>> in the following macro I do contrast and brightness adjustments on  
>> two images (one in red the other in green) and subsequently a  
>> selection of the red image is laid over the green image. Now I am  
>> quite puzzled because the same macro seemingly by chance yields  
>> different results (see attached jpgs) In the first case it worked  
>> out but in the second example only the upper part of the green  
>> image has been adjusted in contrast.
>> The bottom part still has the same linear contrast as in the  
>> orignial image.
>>
>> I really have no idea what could be the reason for this.
>>
>> cheers,
>>
>> Finn
>>
>>
>> macro code:
>>
>>
>> inputFolder = getDirectory("Input folder"); files = getFileList
>> (inputFolder); count = 0; id = 0; for (i = 0; i<  files.length; i+
>> +) {
>>           open(inputFolder + files[i]);
>>           id2 = id;
>>           id = getImageID();
>>           count++;
>>           if ((count % 2) == 0) {
>>               selectImage(id);
>>               run("8-bit");
>>               run("Red");
>>               setAutoThreshold("Default");
>>               //run("Threshold...");
>>               setThreshold(3, 7);
>>               run("Create Selection");
>>               run("RGB Color");
>>               run("Copy");
>>
>>               selectImage(id2);
>>               run("Brightness/Contrast..."); setMinAndMax(16, 44);
>>               run("Paste");
>>               run("Select None");
>>
>>               name = getTitle();
>>               saveAs("Tiff", "C:/Users/Admins/Desktop/test/
>> target/"+name+
>> "_merged.tif");
>>               close();
>>               close();
>>               count = 0;
>>           }}
>>
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Re: problem with incomplete contrast adjustment

Finn Peters
8 posts
Hi Michael and Wayne,

thank's very much for your advice! After removing
run("Brightness/Contrast..."); the macro works perfectly and faster too.

cheers,

Finn


> Hi Finn,
>
> Did you try to remove the
>   run("Brightness/Contrast...");
> statement and just leave the setMinAndMax?
>
> I think that you don't need to show the B&C panel. I have not analyzed
> it carefully, but the following might happen:
>
> If the B&C panel needs some time to get displayed, its windowActivated
> gets called asynchronously and runs the 'setup' procedure, which takes
> a new snapshot in case of an RGB image.
> This may cause a lot of trouble.
>
> Michael
> ________________________________________________________________
>
> On 24 Aug 2011, at 16:57, Finn Peters wrote:
>
>> Dear Kees,
>>
>> thank you for the reply. I tried it with a pause up to wait(10000)
>> after setMINAndMax(16,44); and at additional other positions. It
>> still does not work. It doesn't even work if I only run a macro of
>> the following two lines on a single image:
>> run("Brightness/Contrast..."); setMinAndMax(16, 44);
>> I guess there must be a problem with my computer somewhere. I will
>> try to make the macro in Photoshop.
>>
>> cheers,
>>
>> Finn
>>
>>> Dear Finn,
>>>
>>> It seems that the macro sometimes get ahead of itself. If you include
>>>
>>> wait(100); after setMinAndMax(16, 44); it might solve the problem,
>>> at least it did on my test dataset.
>>>
>>> Best wishes
>>>
>>> Kees
>>>
>>>
>>> Dr Ir K.R. Straatman
>>> Senior Experimental Officer
>>> Centre for Core Biotechnology Services
>>> College of Medicine, Biological Sciences and Psychology
>>>
>>> http://www.le.ac.uk/biochem/microscopy/home.html
>>>
>>>
>>> -----Original Message-----
>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf
>>> Of Finn Peters
>>> Sent: 23 August 2011 13:17
>>> To:[hidden email]
>>> Subject: problem with incomplete contrast adjustment
>>>
>>> Hi,
>>>
>>> in the following macro I do contrast and brightness adjustments on
>>> two images (one in red the other in green) and subsequently a
>>> selection of the red image is laid over the green image. Now I am
>>> quite puzzled because the same macro seemingly by chance yields
>>> different results (see attached jpgs) In the first case it worked
>>> out but in the second example only the upper part of the green image
>>> has been adjusted in contrast.
>>> The bottom part still has the same linear contrast as in the
>>> orignial image.
>>>
>>> I really have no idea what could be the reason for this.
>>>
>>> cheers,
>>>
>>> Finn
>>>
>>>
>>> macro code:
>>>
>>>
>>> inputFolder = getDirectory("Input folder"); files =
>>> getFileList(inputFolder); count = 0; id = 0; for (i = 0; i<  
>>> files.length; i++) {
>>>           open(inputFolder + files[i]);
>>>           id2 = id;
>>>           id = getImageID();
>>>           count++;
>>>           if ((count % 2) == 0) {
>>>               selectImage(id);
>>>               run("8-bit");
>>>               run("Red");
>>>               setAutoThreshold("Default");
>>>               //run("Threshold...");
>>>               setThreshold(3, 7);
>>>               run("Create Selection");
>>>               run("RGB Color");
>>>               run("Copy");
>>>
>>>               selectImage(id2);
>>>               run("Brightness/Contrast..."); setMinAndMax(16, 44);
>>>               run("Paste");
>>>               run("Select None");
>>>
>>>               name = getTitle();
>>>               saveAs("Tiff",
>>> "C:/Users/Admins/Desktop/test/target/"+name+
>>> "_merged.tif");
>>>               close();
>>>               close();
>>>               count = 0;
>>>           }}
>>>
>