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Re: batch measurements to single data file

Posted by Justin Walker-2 on Nov 19, 2007; 5:59pm
URL: http://imagej.273.s1.nabble.com/batch-measurements-to-single-data-file-tp3697980p3697982.html

Super!  I knew it would be something simple like that.

Thanks a ton

- Justin


Wayne Rasband wrote:

> Remove 'clear' from
>
>   run("Analyze Particles...", "size=0.15-Infinity
> circularity=0.00-1.00 show=Nothing display exclude clear");
>
> It is equivalent to checking "Clear Results" in the Analyze Particles
> dialog box.
>
> -wayne
>
>
> On Nov 19, 2007, at 12:27 PM, Justin Walker wrote:
>
>> I have put together a simple macro to (batch) perform various
>> manipulations and then measure particle diameters for a series of
>> several hundred images of liquid droplets.  Everything works fine,
>> except for each image that runs, the results window discards the data
>> from the previous image.
>>
>> I'm sure there is a simple way to change that, but I've been
>> searching the documentation and mailing list archives all morning and
>> haven't been able to find anything useful.  Is there a simple way to
>> have the data from previous measurements preserved when a new image
>> is opened and processed?  Alternatively, is there a way I can have
>> the results dumped to a data file (but a single data file for all the
>> data with each measurement on a new line?).  I tried having a save as
>> command as part of my macro, but it kept trying to over-write the
>> data file on each iteration.
>>
>> I have attached my macro.
>>
>> Thanks;
>>
>> - Justin Walker, Ph. D. Student
>> University of Maryland
>> College Park, MD, USA
>> [hidden email]
>> 301-405-1920
>> macro "Batch Particle Size" {
>>     dir = getDirectory("Choose a Directory ");
>>     list = getFileList(dir);
>>     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("Deinterlace ");
>>         run("8-bit");
>>         setAutoThreshold();
>>         //run("Threshold...");
>>         setAutoThreshold();
>>         setThreshold(0, 164);
>>         run("Convert to Mask");
>>         run("Fill Holes");
>>         run("Watershed");
>>         run("Analyze Particles...", "size=0.15-Infinity
>> circularity=0.00-1.00 show=Nothing display exclude clear");
>>             close();
>>         }
>>     }
>> }