Problem with ROI Manager in BatchMode

Posted by Winfried Wurm on
URL: http://imagej.273.s1.nabble.com/Problem-with-ROI-Manager-in-BatchMode-tp3682680.html

Dear ImageJ community,

I´ve encountered some Problems by using the Batchmode together with the ROI Manager in my Macro. I wrote a Macro which counts Foci in a Binary Image, selects the Outline of the Focus in every Slice and adds it to the ROI Manager. The ROIs are than measured in a second Channel.
The Macro works fine if setBatchMode(false). But when I turn it true, the Measurements are completely nonsense.
I think that I´ve tracked the error down to the creation of the Selection in the second Channel. When I let the Macro fill the ROIs in the second Channel the ROI in every Slice has the shape of the ROI of the last added ROI, but are good when I manually select them in the ROI Manager afterwards or when BatchMode is turned off.

Since the Macro is very long I will only add the part of the Code which I think makes the trouble, the measuring in the second Channel.
At this point, the ROI Manager has a least two ROIs added.


                focus++;
                hc=false;
                selectWindow("cell.tif");
                run("Select None");
                m=(roiManager("count")-1);
                for(r=0;r<=m;r++)
                {
                   roiManager("deselect");
                   roiManager("select",r);
                   arg="enlarge="+px;
                   run("Enlarge...", arg);
                   run("Measure")
                   if(getResult("Max")==255)
                    hc=true;
                  run("Fill", "slice");
                }
                selectWindow("foci.tif");
                roiManager("Reset");
                if(hc==true)
                        HC++;
                else
                        EC++;



Can anyone help me fix this Problem?
Thx for Helping in advance
Winfried Wurm