getFileList Issue

[Matt TLAB]

I am attempting to write a macro that will act as a particle counter (I am counting trichomes on plant leaves).  My experience with ImageJ programming is pretty limited.  I want the macro to count particles on all of the images in a folder.  It seems that my macro is not even getting to the point where it is executing the particle analysis.  When I run the macro I get this error message:
')' expected in line 4.
<list> = getFileList(dir);

Here is the code that I have written (up until the commands for the actual particle analysis):
macro "Particle Count" {
dir = getDirectory("C:\Users\Matt\Desktop\Matt\");
list = getFileList(dir);
if (getVersion>="1.40e")
setOption("display labels", true);
setBatchMode(true);
for (i=0; i<list.length; i++) {
path = dir+list[i];
showProgress(i, list.length);
if (!endsWith(path,"/")) open(path);
if (nImages>=1)


Any suggestions?

Thanks,
Matt

[Michael Schmid]

Hi Matt,

the culprit is the String with the directory. In String literals  
(Strings with quotes), the backslash is used for inserting special  
characters. If you want to have a backslash in a String, you have to  
type two backslashes: \\

In "C:\Users\Matt\Desktop\Matt\" the last Backslash is interpreted as
"The following character should be taken as a special character of  
the String: Put a quote character into the String"

So, the closing parenthesis and the semicolon are still part of the  
String, and not interpreted as program text.

You need:
   dir = getDirectory("C:\\Users\\Matt\\Desktop\\Matt\\");


Michael
________________________________________________________________

On 24 Feb 2010, at 15:21, Matt TLAB wrote:

> I am attempting to write a macro that will act as a particle  
> counter (I am
> counting trichomes on plant leaves).  My experience with ImageJ  
> programming
> is pretty limited.  I want the macro to count particles on all of  
> the images
> in a folder.  It seems that my macro is not even getting to the  
> point where
> it is executing the particle analysis.  When I run the macro I get  
> this
> error message:
> ')' expected in line 4.
> <list> = getFileList(dir);
>
> Here is the code that I have written (up until the commands for the  
> actual
> particle analysis):
> macro "Particle Count" {
> dir = getDirectory("C:\Users\Matt\Desktop\Matt\");
> list = getFileList(dir);
> if (getVersion>="1.40e")
> setOption("display labels", true);
> setBatchMode(true);
> for (i=0; i<list.length; i++) {
> path = dir+list[i];
> showProgress(i, list.length);
> if (!endsWith(path,"/")) open(path);
> if (nImages>=1)
>
>
> Any suggestions?
>
> Thanks,
> Matt
> --
> View this message in context: http://n2.nabble.com/getFileList- 
> Issue-tp4626046p4626046.html
> Sent from the ImageJ mailing list archive at Nabble.com.

[Matt TLAB]

Michael,
Thanks!  That fixed that problem.  I am now prompted to select the folder when I run the macro.  The folder I am using right now is a test folder.  It has 5 images in it.  When prompted by the macro, I select the folder and it runs the program on the first image in the folder.  It looks like my code is correct, because the output is exactly what I want it to be (a particle count).  However, after processing the first image in the folder, I get a message that says:
There are no images open.

The program is not moving on to the next image in the folder.  Here is the full text of the macro I wrote.

macro "Particle Count" {
dir = getDirectory("C:\\Users\\Matt\\Desktop\\Matt\\");
list = getFileList(dir);
if (getVersion>="1.40e")
setOption("display labels", true);
setBatchMode(true);
for (i=0; i<list.length; i++) {
path = dir+list[i];
showProgress(i, list.length);
if (!endsWith(path,"/")) open(path);
if (nImages>=1) {run("8-bit");
setAutoThreshold();
//run("Threshold...");
setThreshold(128, 255);
run("Threshold", "thresholded remaining black");
setAutoThreshold();
run("Analyze Particles...", "minimum=1 maximum=999999 bins=20 show=Nothing display summarize record size");
close();
close();}
    }
}


Do I need to add something to get the macro to move through all of the images in the folder?  I thought that the first part of the macro specified this.

Thanks,
Matt

[Michael Schmid]

Hi Matt,

why do you run close() twice? I expect that only one image gets  
opened - 'Analyze Particles' won't create an image with 'show=Nothing'.

I also wonder about the initial two thresholding commands, they don't  
do any harm, but only the second one will be used for Analyze Particles.

Michael
________________________________________________________________

On 24 Feb 2010, at 16:59, Matt TLAB wrote:

> Michael,
> Thanks!  That fixed that problem.  I am now prompted to select the  
> folder
> when I run the macro.  The folder I am using right now is a test  
> folder.  It
> has 5 images in it.  When prompted by the macro, I select the  
> folder and it
> runs the program on the first image in the folder.  It looks like  
> my code is
> correct, because the output is exactly what I want it to be (a  
> particle
> count).  However, after processing the first image in the folder, I  
> get a
> message that says:
> There are no images open.
>
> The program is not moving on to the next image in the folder.  Here  
> is the
> full text of the macro I wrote.
>
> macro "Particle Count" {
> dir = getDirectory("C:\\Users\\Matt\\Desktop\\Matt\\");
> list = getFileList(dir);
> if (getVersion>="1.40e")
> setOption("display labels", true);
> setBatchMode(true);
> for (i=0; i<list.length; i++) {
> path = dir+list[i];
> showProgress(i, list.length);
> if (!endsWith(path,"/")) open(path);
> if (nImages>=1) {run("8-bit");
> setAutoThreshold();
> //run("Threshold...");
> setThreshold(128, 255);
> run("Threshold", "thresholded remaining black");
> setAutoThreshold();
> run("Analyze Particles...", "minimum=1 maximum=999999 bins=20  
> show=Nothing
> display summarize record size");
> close();
> close();}
>     }
> }
>
>
> Do I need to add something to get the macro to move through all of the
> images in the folder?  I thought that the first part of the macro  
> specified
> this.
>
> Thanks,
> Matt
> --
> View this message in context: http://n2.nabble.com/getFileList- 
> Issue-tp4626046p4626658.html
> Sent from the ImageJ mailing list archive at Nabble.com.