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Matt TLAB | 24 Feb 2010 15:21

getFileList Issue

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
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Michael Schmid | 24 Feb 2010 16:20

Re: getFileList Issue

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

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Matt TLAB | 24 Feb 2010 16:59

Re: getFileList Issue

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

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Michael Schmid | 25 Feb 2010 15:00

Re: getFileList Issue

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

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