Bug in FindMaxima output (ImageJ 1.43o) ?

[Jean-Christophe AME-2]

Hi All,

I think I found a problem with Process>Binary>Find Maxima

When the result is equal to 0 (zero), the result doesn't go to the  
ouput window "results". Meaning that the counting value for that  
specific ROI is also not recorded.  This is important as I am setting  
an automatic counting system of particles (foci) within nuclei using  
this function.

Thanks for any help,


Jean-Christophe


It's on a Mac using 10.5.8. and the last java update.
here is the macro I wrote but it is the same when it is used manually.

*******************
i = 0;
do {
roiManager("Select", (i));run("Unsharp Mask...", "radius=1 mask=0.50");
run("Find Maxima...", "noise=18 output=Count");
i = i + 1;
  } while (i<= roiManager("count"));
***************************

________________________
Jean-Christophe Amé, PhD
Équipe "Poly(ADP-ribosyl)ation et intégrité du génome"
Institut de Recherche de l'École de Biotechnologie de Strasbourg
FRE3211 du CNRS - UdS
Université de Strasbourg
École Supérieure de Biotechnologie de Strasbourg
Pôle API
Parc d'innovation, Boulevard Sébastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: [phone]
Fax.: [phone]

http://parplink.u-strasbg.fr
http://idg.u-strasbg.fr/

« Science sans conscience n'est que ruine de l'âme ...» (François  
Rabelais, 1483-1553)

[Gabriel Landini]

On Thursday 04 Feb 2010  15:41:54 you wrote:
> When the result is equal to 0 (zero), the result doesn't go to the
> ouput window "results". Meaning that the counting value for that
> specific ROI is also not recorded.  This is important as I am setting
> an automatic counting system of particles (foci) within nuclei using
> this function.

Yes, I can confirm this too. With a black image, (maxima not found) there is
no result of counts (which should be "0") sent to the Results Table.

Cheers,
G.

[Jean-Christophe AME-2]

Hi Wayne,
It works... I will try it tomorrow on real data.

Thanks you all so much for your reactivity.

Sincerely,

Jean-Christophe


Le 4 févr. 10 à 18:39, Rasband, Wayne (NIH/NIMH) [E] a écrit :

> Hi Michael,
>
> I applied your proposed bugfix to the 1.43p7 daily build, and it  
> appears to work. You can see the changes at the ImageJ Git repository
>
>
> Best regards,
>
> -wayne
>
> On Feb 4, 2010, at 11:11 AM, Michael Schmid wrote:
>
>> Hi Wayne,
>>
>> here is a proposal for a bugfix (I have not tried, but I think that
>> it should be ok):
>>
>> in MaximumFinder.analyzeAndMarkMaxima at the top:
>>
>> //unchanged line:
>>        boolean displayOrCount = imp!=null &&
>> (outputType==POINT_SELECTION||outputType==LIST||outputType==COUNT);
>> //new lines:
>>        if (displayOrCount) {
>>            xyVector=new Vector();
>>            roi = imp.getRoi();
>>        }
>>
>> further down, we can eliminate the creation of a new xyVector:
>>
>>            if (maxPossible) {
>>                int offset = pList[nearestI];
>>                types[offset] |= MAX_POINT;
>>                if (displayOrCount && !(this.excludeOnEdges &&
>> isEdgeMaximum)) {
>> //no reason to check for xyVector=null, just continue like this:
>>                    int x = offset % width;
>>
>> then before creating a roi we should check whether the vector is not
>> empty:
>>
>> //changed line:
>>            if (outputType == POINT_SELECTION && npoints>0) {
>> //rest unchanged:
>>                int[] xpoints = new int[npoints];
>>
>>
>> Best wishes,
>>
>> Michael
>> ________________________________________________________________
>> Michael Schmid                    email: [hidden email]
>> Institut für Angewandte Physik, Technische Universität Wien
>> Wiedner Hauptstr. 8-10/134, A 1040 Wien, Austria
>> Tel. [phone] or -13453, Fax [phone]
>> ________________________________________________________________
>>
>> Begin forwarded message:
>>
>>> From: Gabriel Landini <[hidden email]>
>>> Date: 4 February 2010 16:44:57 GMT+01:00
>>> To: [hidden email]
>>> Subject: Re: Bug in FindMaxima output (ImageJ 1.43o) ?
>>> Reply-To: ImageJ Interest Group <[hidden email]>
>>>
>>> On Thursday 04 Feb 2010  15:41:54 you wrote:
>>>> When the result is equal to 0 (zero), the result doesn't go to the
>>>> ouput window "results". Meaning that the counting value for that
>>>> specific ROI is also not recorded.  This is important as I am  
>>>> setting
>>>> an automatic counting system of particles (foci) within nuclei  
>>>> using
>>>> this function.
>>>
>>> Yes, I can confirm this too. With a black image, (maxima not found)
>>> there is
>>> no result of counts (which should be "0") sent to the Results Table.
>>>
>>> Cheers,
>>> G.
>>
>

________________________
Jean-Christophe Amé, PhD
Équipe "Poly(ADP-ribosyl)ation et intégrité du génome"
Institut de Recherche de l'École de Biotechnologie de Strasbourg
FRE3211 du CNRS - UdS
Université de Strasbourg
École Supérieure de Biotechnologie de Strasbourg
Pôle API
Parc d'innovation, Boulevard Sébastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: [phone]
Fax.: [phone]

http://parplink.u-strasbg.fr
http://idg.u-strasbg.fr/

« Science sans conscience n'est que ruine de l'âme ...» (François  
Rabelais, 1483-1553)