http://imagej.273.s1.nabble.com/Glitch-with-Batch-Processing-tp5016511p5016516.html
I just want to mention that Marcus also posted this question on the ImageJ
> Hi,
>
> > On May 24, 2016, at 2:24 PM, Dan McDonald <
>
[hidden email]> wrote:
> >
> > Hi Marcus,
> >
> > I ran your code on my machine and everything worked as expected. (I did
> interpret the position of some comment delimiters in a specific manner that
> might be different than actually in your code.)
> >
> > Your example images suggest to me some kind of hiccup occurs after the
> first run("Convert to Mask") triad. Many years ago I started adding wait
> statements after long-processing-time commands to prevent one command from
> starting before another begins. I don't know if that problem of not
> synchronizing properly has been fixed or not in recent time. Your image
> looks like the top 1/3 was processed one way and then the bottom 2/3
> another.
> >
>
> That's a good idea. Another way to help manage which image is active is
> to use getImageID(), selectImage(id) and friends. That way you can
> explicitly manage the images by unique ID rather than by name.
>
>
https://rsb.info.nih.gov/ij/developer/macro/functions.html#getImageID>
> Ben
>
> > Did the macro execute to completion when it gave the output image? It
> does not appear to have been processed with your run('Remove Outliers...")
> command.
> >
> > If it is a synchronization problem adding strategic wait statements or
> putting your macro into setBatchMode(true) mode might help.
> >
> > Best regards,
> >
> > Dan
> >
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Marcus Jones
> > Sent: Tuesday, May 24, 2016 11:47 AM
> > To:
[hidden email]
> > Subject: Glitch with Batch Processing
> >
> > I'm batch processing pictures using a macro to determine percentage of
> green plant tissue from small plot research trials. Every so often a
> picture doesn't appear to process correctly and the coverage estimates are
> greatly underestimated.
> >
> > Examples of the original image and the subsequent image that doesn’t
> process correctly after running through the macro are attached.
> >
> > When I manually set the color threshold levels, convert to binary, and
> run the Analyze Particles function, the vast majority of green tissue is
> properly selected. But for some reason, the plant tissue in the bottom
> 2/3rds of the picture isn’t correctly selected when run through the macro.
> This issue is rather sporadic and doesn’t always occur. I’ve ran entire
> sets of images (50-100) without this occurring.
> >
> > Here is the code for the macro I’m using:
> >
> > run("Set Scale...", "distance=3494.5 known=100 unit=cm"); run("Color
> Threshold..."); // Color Thresholder 1.49m // Autogenerated macro, single
> images only!
> > min=newArray(3);
> > max=newArray(3);
> > filter=newArray(3);
> > a=getTitle();
> > run("HSB Stack");
> > run("Convert Stack to Images");
> > selectWindow("Hue");
> > rename("0");
> > selectWindow("Saturation");
> > rename("1");
> > selectWindow("Brightness");
> > rename("2");
> > min[0]=35;
> > max[0]=125;
> > filter[0]="pass";
> > min[1]=45;
> > max[1]=255;
> > filter[1]="pass";
> > min[2]=0;
> > max[2]=255;
> > filter[2]="pass";
> > for (i=0;i<3;i++){
> > selectWindow(""+i);
> > setThreshold(min[i], max[i]);
> > run("Convert to Mask");
> > if (filter[i]=="stop") run("Invert");
> > }
> > imageCalculator("AND create", "0","1");
> > imageCalculator("AND create", "Result of 0","2"); for (i=0;i<3;i++){
> selectWindow(""+i); close(); } selectWindow("Result of 0"); close();
> selectWindow("Result of Result of 0"); rename(a); // Colour
> Thresholding------------- run("8-bit"); setAutoThreshold("Default");
> //run("Threshold..."); setOption("BlackBackground", false); run("Convert to
> Mask"); run("Remove Outliers...", "radius=2 threshold=50 which=Dark");
> >
> > run("Analyze Particles...", " show=Masks display summarize");
> >
> >
> > I’ve updated to the most recent version of ImageJ to no avail.
> >
> >>> Does anyone know why this is happening and is there anything I can do
> to avoid this?
> >
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
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