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macro loop Analyze Particles

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lechristophe

macro loop Analyze Particles

Dear ImageJers,

I'm totally confused about a piece of macro code I'm trying to debug
with no success. I want to analyze particles for each slice of a
stack, but I want to have an automatic threshold detection for each
slice separately (as the intensity levels of the objects can be very
different from one slice to another), so I cannot just launch the
Analyze Particle command for the whole stack. I've tested that if you
trigger an AutoThreshold for each slice and then do an Analyze
Particle with the "slice" argument, it will do what I want.

So I just want to loop that for each slice, and I've written this piece of code:

//code starts

macro "multi_detector" {
run("Set Scale...", "distance=0 known=1 pixel=1 unit=pixel");
run("Set Measurements...", "area mean circularity feret's
integrated slice redirect=None decimal=3");
StackID=getImageID();
print("\\Clear");
print("start");
print("source ID "+StackID);
print(nSlices+" slices");

for (k=0; k<nSlices; k++) {
print("begin loop slice "+(k+1));
selectImage(StackID);
setSlice(k+1);
setAutoThreshold();
run("Analyze Particles...", "size=50-Infinity
circularity=0.00-1.00 show=Masks display record slice");
print("AP slice "+(k+1)+" done");
MASK1ID=getImageID();
print("mask ID for slice"+(k+1)+":"+MASK1ID);
}
print("finished");
}

// code ends

But the "for" loop doesn't work ! It does the first slice and then
finishes. What is the problem here ? I'm sure it is something evident
but I can't find what... I've added a lot of prints for debugging but
the macro is just a couple of instructions, and I can't manage to find
what's wrong. By the way, this is IJ 1.41a with Java 1.6 dp under OSX
10.4.

On a related note, having an option in the Analyze Particles command
to batch the Analyze Particle on a stack with a different automatic
threshold for each slice would be great, so my macro would shrink to
one line, and I would'nt have to reconstruct the mask stack
afterwars...

Thank you for your help,

Christophe

Michael Schmid

Re: macro loop Analyze Particles

Hi Christophe,

after the loop runs once, it seems that the foreground image is
the mask, and the mask has only one slice.
You have to add
selectImage(StackID);
before the end of the loop.

Michael
________________________________________________________________

On 7 May 2008, at 10:38, Christophe Leterrier wrote:

> Dear ImageJers,
>
> I'm totally confused about a piece of macro code I'm trying to debug
> with no success. I want to analyze particles for each slice of a
> stack, but I want to have an automatic threshold detection for each
> slice separately (as the intensity levels of the objects can be very
> different from one slice to another), so I cannot just launch the
> Analyze Particle command for the whole stack. I've tested that if you
> trigger an AutoThreshold for each slice and then do an Analyze
> Particle with the "slice" argument, it will do what I want.
>
> So I just want to loop that for each slice, and I've written this
> piece of code:
>
>
> //code starts
>
> macro "multi_detector" {
> run("Set Scale...", "distance=0 known=1 pixel=1 unit=pixel");
> run("Set Measurements...", "area mean circularity feret's
> integrated slice redirect=None decimal=3");
> StackID=getImageID();
> print("\\Clear");
> print("start");
> print("source ID "+StackID);
> print(nSlices+" slices");
>
> for (k=0; k<nSlices; k++) {
> print("begin loop slice "+(k+1));
> selectImage(StackID);
> setSlice(k+1);
> setAutoThreshold();
> run("Analyze Particles...", "size=50-Infinity
> circularity=0.00-1.00 show=Masks display record slice");
> print("AP slice "+(k+1)+" done");
> MASK1ID=getImageID();
> print("mask ID for slice"+(k+1)+":"+MASK1ID);
> }
> print("finished");
> }
>
>
> // code ends
>
> But the "for" loop doesn't work ! It does the first slice and then
> finishes. What is the problem here ? I'm sure it is something evident
> but I can't find what... I've added a lot of prints for debugging but
> the macro is just a couple of instructions, and I can't manage to find
> what's wrong. By the way, this is IJ 1.41a with Java 1.6 dp under OSX
> 10.4.
>
> On a related note, having an option in the Analyze Particles command
> to batch the Analyze Particle on a stack with a different automatic
> threshold for each slice would be great, so my macro would shrink to
> one line, and I would'nt have to reconstruct the mask stack
> afterwars...
>
> Thank you for your help,
>
> Christophe

lechristophe

Re: macro loop Analyze Particles

But the first instruction of the loop is
selectImage(StackID);
before the setSlice command...so how come it doesn't select the stack
? would it be possible that it reevaluates the "nSlices" variable in
the for arguments with the current active image ? So the best would be
to store the number of slices of the source stack as a fixed variable
and loop on that...

I'll try, thanks !

On Wed, May 7, 2008 at 10:57 AM, Michael Schmid <[hidden email]> wrote:

> Hi Christophe,
>
> after the loop runs once, it seems that the foreground image is
> the mask, and the mask has only one slice.
> You have to add
> selectImage(StackID);
> before the end of the loop.
>
> Michael
> ________________________________________________________________
>
>
>
> On 7 May 2008, at 10:38, Christophe Leterrier wrote:
>
>
> > Dear ImageJers,
> >
> > I'm totally confused about a piece of macro code I'm trying to debug
> > with no success. I want to analyze particles for each slice of a
> > stack, but I want to have an automatic threshold detection for each
> > slice separately (as the intensity levels of the objects can be very
> > different from one slice to another), so I cannot just launch the
> > Analyze Particle command for the whole stack. I've tested that if you
> > trigger an AutoThreshold for each slice and then do an Analyze
> > Particle with the "slice" argument, it will do what I want.
> >
> > So I just want to loop that for each slice, and I've written this piece of
> code:
> >
> >
> > //code starts
> >
> > macro "multi_detector" {
> > run("Set Scale...", "distance=0 known=1 pixel=1 unit=pixel");
> > run("Set Measurements...", "area mean circularity feret's
> > integrated slice redirect=None decimal=3");
> > StackID=getImageID();
> > print("\\Clear");
> > print("start");
> > print("source ID "+StackID);
> > print(nSlices+" slices");
> >
> > for (k=0; k<nSlices; k++) {
> > print("begin loop slice "+(k+1));
> > selectImage(StackID);
> > setSlice(k+1);
> > setAutoThreshold();
> > run("Analyze Particles...", "size=50-Infinity
> > circularity=0.00-1.00 show=Masks display record slice");
> > print("AP slice "+(k+1)+" done");
> > MASK1ID=getImageID();
> > print("mask ID for slice"+(k+1)+":"+MASK1ID);
> > }
> > print("finished");
> > }
> >
> >
> > // code ends
> >
> > But the "for" loop doesn't work ! It does the first slice and then
> > finishes. What is the problem here ? I'm sure it is something evident
> > but I can't find what... I've added a lot of prints for debugging but
> > the macro is just a couple of instructions, and I can't manage to find
> > what's wrong. By the way, this is IJ 1.41a with Java 1.6 dp under OSX
> > 10.4.
> >
> > On a related note, having an option in the Analyze Particles command
> > to batch the Analyze Particle on a stack with a different automatic
> > threshold for each slice would be great, so my macro would shrink to
> > one line, and I would'nt have to reconstruct the mask stack
> > afterwars...
> >
> > Thank you for your help,
> >
> > Christophe
> >
>

AdamC

Re: macro loop Analyze Particles

In reply to this post by lechristophe

I think it doesn't like the fact you don't define nSlices.

I added the line
Slice=nSlices
and changed k<nSlices to k<Slices

I think this fixes it:

adam

//code starts

macro "multi_detector" {
run("Set Scale...", "distance=0 known=1 pixel=1 unit=pixel");
run("Set Measurements...", "area mean circularity feret's
integrated slice redirect=None decimal=3");
StackID=getImageID();
Slices=nSlices; //Line changed by Adam
print("\\Clear");
print("start");
print("source ID "+StackID);
print(nSlices+" slices");

for (k=0; k<Slices; k++) { //Changed by Adam
print("begin loop slice "+(k+1));
selectImage(StackID);
setSlice(k+1);
setAutoThreshold();
run("Analyze Particles...", "size=50-Infinity
circularity=0.00-1.00 show=Masks display record slice");
print("AP slice "+(k+1)+" done");
MASK1ID=getImageID();
print("mask ID for slice"+(k+1)+":"+MASK1ID);
}
print("finished");
}

// code ends
On 7 May 2008, at 16:38, Christophe Leterrier wrote:

Winnok H. De Vos

Re: macro loop Analyze Particles

Dear
If you only set a threshold and don't apply it, I believe you should also
add "limit" to the measurement settings.
Kind regards,
winnok

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Adam
Cliffe
Sent: woensdag 7 mei 2008 11:14
To: [hidden email]
Subject: Re: macro loop Analyze Particles

I think it doesn't like the fact you don't define nSlices.

I added the line
Slice=nSlices
and changed k<nSlices to k<Slices

I think this fixes it:

adam

//code starts

macro "multi_detector" {
run("Set Scale...", "distance=0 known=1 pixel=1 unit=pixel");
run("Set Measurements...", "area mean circularity feret's
integrated slice redirect=None decimal=3");
StackID=getImageID();
Slices=nSlices; //Line changed by Adam
print("\\Clear");
print("start");
print("source ID "+StackID);
print(nSlices+" slices");

for (k=0; k<Slices; k++) { //Changed by Adam
print("begin loop slice "+(k+1));
selectImage(StackID);
setSlice(k+1);
setAutoThreshold();
run("Analyze Particles...", "size=50-Infinity
circularity=0.00-1.00 show=Masks display record slice");
print("AP slice "+(k+1)+" done");
MASK1ID=getImageID();
print("mask ID for slice"+(k+1)+":"+MASK1ID);
}
print("finished");
}

// code ends
On 7 May 2008, at 16:38, Christophe Leterrier wrote:

Dr Adam Cliffe
Research Fellow
Rørth Lab
Cell Migration Group
Temasek Lifescience Laboratory
1 Research Link
National University of Singapore
Singapore 117604

tel: (65) 6872 8406
fax: (65) 6872 7007

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8:07

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Michael Schmid

Re: macro loop Analyze Particles

In reply to this post by lechristophe

Hi Christophe,

nSlices is a function, not a variable, and it relates to the
current foreground image. You may use parentheses,
nSlices()
but you need not.
http://rsb.info.nih.gov/ij/developer/macro/functions.html#N

Michael
________________________________________________________________

On 7 May 2008, at 11:07, Christophe Leterrier wrote:

> But the first instruction of the loop is
> selectImage(StackID);
> before the setSlice command...so how come it doesn't select the stack
> ? would it be possible that it reevaluates the "nSlices" variable in
> the for arguments with the current active image ? So the best would be
> to store the number of slices of the source stack as a fixed variable
> and loop on that...
>
> I'll try, thanks !
>
>
>
> On Wed, May 7, 2008 at 10:57 AM, Michael Schmid
> <[hidden email]> wrote:
>> Hi Christophe,
>>
>> after the loop runs once, it seems that the foreground image is
>> the mask, and the mask has only one slice.
>> You have to add
>> selectImage(StackID);
>> before the end of the loop.
>>
>> Michael
>> ________________________________________________________________
>>
>>
>>
>> On 7 May 2008, at 10:38, Christophe Leterrier wrote:
>>
>>
>>> Dear ImageJers,
>>>
>>> I'm totally confused about a piece of macro code I'm trying to debug
>>> with no success. I want to analyze particles for each slice of a
>>> stack, but I want to have an automatic threshold detection for each
>>> slice separately (as the intensity levels of the objects can be very
>>> different from one slice to another), so I cannot just launch the
>>> Analyze Particle command for the whole stack. I've tested that if
>>> you
>>> trigger an AutoThreshold for each slice and then do an Analyze
>>> Particle with the "slice" argument, it will do what I want.
>>>
>>> So I just want to loop that for each slice, and I've written this
>>> piece of
>> code:
>>>
>>>
>>> //code starts
>>>
>>> macro "multi_detector" {
>>> run("Set Scale...", "distance=0 known=1 pixel=1 unit=pixel");
>>> run("Set Measurements...", "area mean circularity feret's
>>> integrated slice redirect=None decimal=3");
>>> StackID=getImageID();
>>> print("\\Clear");
>>> print("start");
>>> print("source ID "+StackID);
>>> print(nSlices+" slices");
>>>
>>> for (k=0; k<nSlices; k++) {
>>> print("begin loop slice "+(k+1));
>>> selectImage(StackID);
>>> setSlice(k+1);
>>> setAutoThreshold();
>>> run("Analyze Particles...", "size=50-Infinity
>>> circularity=0.00-1.00 show=Masks display record slice");
>>> print("AP slice "+(k+1)+" done");
>>> MASK1ID=getImageID();
>>> print("mask ID for slice"+(k+1)+":"+MASK1ID);
>>> }
>>> print("finished");
>>> }
>>>
>>>
>>> // code ends
>>>
>>> But the "for" loop doesn't work ! It does the first slice and then
>>> finishes. What is the problem here ? I'm sure it is something
>>> evident
>>> but I can't find what... I've added a lot of prints for debugging
>>> but
>>> the macro is just a couple of instructions, and I can't manage to
>>> find
>>> what's wrong. By the way, this is IJ 1.41a with Java 1.6 dp under
>>> OSX
>>> 10.4.
>>>
>>> On a related note, having an option in the Analyze Particles command
>>> to batch the Analyze Particle on a stack with a different automatic
>>> threshold for each slice would be great, so my macro would shrink to
>>> one line, and I would'nt have to reconstruct the mask stack
>>> afterwars...
>>>
>>> Thank you for your help,
>>>
>>> Christophe
>>>
>>