http://imagej.273.s1.nabble.com/Disjoint-ROI-selection-using-macro-language-tp3692854p3692857.html
the ROI Manager items have labels 0001-... to 0064-..., corresponding
I did succeed in selecting three items manually (lines 0, 3, 7, i.e.
0001-..., 0004.. and 0008-...) together with command-click and then
use More>Combine. It is a bit nasty since the context menus
interferes with it. Measure on the combined ROI gave me an area of
> Hi Michael,
>
> Thanks for responding so quickly.
>
> The first issue is a result of my own boneheadedness. Note that
> the left most particle looks like it is labeled "0". It is
> actually "10" but the label was cutoff and I fooled myself.
>
> I can confirm that the ij.jar is the size you specify and that
> ImageJ thinks it is v1.42l. Restarting ImageJ seems to make no
> difference.
>
> Can you explain how you made those selections manually? I can't
> make that happen manually or in the macro.
>
> Thanks again,
> Ben
>
>
>
>
>
> On Apr 16, 2009, at 2:23 PM, Michael Schmid wrote:
>
>> Hi Ben,
>>
>> using a very similar system (but MacOS 10.4.11, not 10.5), I have
>> neither problems with 1.42l nor with the nightly build of a few
>> days ago.
>>
>> Selecting the ROIs manually works as expected.
>>
>> After running the macro, the log says:
>> area[ 0 ]= 433
>> area[ 3 ]= 434
>> area[ 7 ]= 278
>> Expected total area for 3 items= 1145
>> after measure, nResults= 129 area=1145
>>
>> ImageJ Properties:
>>
>> Java properties applets can read:
>> java.version: 1.5.0_16
>> java.vendor: Apple Computer, Inc.
>> mrj.version: 1040.1.5.0_16-275
>> os.name: Mac OS X
>> os.version: 10.4.11
>> os.arch: i386
>> file.separator: /
>> path.separator: :
>> line.separator: <lf>
>>
>> Java properties only applications can read:
>> (...)
>> user.country: US
>> file.encoding: MacRoman
>> java.home: /System/Library/Frameworks/JavaVM.framework/Versions/
>> 1.5.0/Home
>> java.class.path: (...) /ij.jar:/System/Library/Java/Extensions/
>> QTJava.zip:/System/Library/Frameworks/JavaVM.framework/Versions/
>> 1.5.0/Classes/.compatibility/14compatibility.jar
>> java.ext.dirs: /Library/Java/Extensions:/System/Library/Java/
>> Extensions:/System/Library/Frameworks/JavaVM.framework/Versions/
>> 1.5.0/Home/lib/ext
>> java.io.tmpdir: /tmp
>>
>> Other properties:
>> (... same as yours)
>> Prefs.weightedColor: true
>> Prefs.blackCanvas: false
>> Prefs.pointAutoMeasure: false
>> Prefs.pointAutoNextSlice: false
>> Prefs.requireControlKey: false
>> Prefs.useInvertingLut: false
>> Prefs.antialiasedTools: true
>> Prefs.useInvertingLut: false
>> Prefs.intelByteOrder: false
>> Prefs.doubleBuffer: false
>> Prefs.noPointLabels: true
>> Prefs.disableUndo: false
>> (...)
>> Sample images dir:
http://rsb.info.nih.gov/ij/images/>> Screen size: 1680x1050
>> Memory in use: 3738K of 800MB (<1%)
>>
>> Is it really 1.42l or a nightly build previous to 1.42l that you
>> are using?
>> The released 1.42l ij.jar has 1.373.997 bytes.
>>
>> Maybe something got stuck - does the problem go away if you
>> restart ImageJ?
>>
>>
>> Michael
>> ________________________________________________________________
>>
>> On 16 Apr 2009, at 19:44, Ben Tupper wrote:
>>
>>> Hi All,
>>>
>>> I think I have managed to completely confuse myself and would
>>> love some help getting straightened out...
>>>
>>> (1) As I manually select an item in the ROI Manager list it is
>>> not the item highlighted in the mask. For example, highlighting
>>> the first item in the ROI Manager list will outline the second
>>> particle in the mask. (I often confuse the indices between
>>> roiManager("select", x); and getResults("Something", x); where x
>>> is either zero-based or one-based. This is going to really drive
>>> me bonkers.)
>>>
>>> (2) I expected the total area of the new combined ROI to equal
>>> the sum of the areas in the selection (they do not equal - in
>>> fact, it looks like only the first particle is added.) A year
>>> ago I thought I had this all figured out, but now I can't get it
>>> to behave as I would like. I have written a macro (below) is to
>>> select some arbitrary number of ROIs and combine them into one.
>>>
>>> //START MACRO
>>> run("Blobs (25K)");
>>> setAutoThreshold();
>>> //run("Threshold...");
>>> setThreshold(125, 255);
>>> run("Convert to Mask");
>>> run("Set Measurements...", "area mean standard modal min centroid
>>> center perimeter bounding fit shape feret's integrated median
>>> skewness kurtosis redirect=None decimal=3");
>>> run("Analyze Particles...", "size=0-Infinity
>>> circularity=0.00-1.00 show=Nothing display clear record add");
>>>
>>> //combine items 0, 3 and 7 into one ROI
>>> index = newArray(0,3,7);
>>> area = 0;
>>> for (i=0; i<index.length; i++){
>>> a = getResult("Area", index[i]);
>>> area = area + a;
>>> print("area[", index[i], "]=", a);
>>> }
>>> print("Expected total area for 3 items=", area);
>>>
>>> setKeyDown("shift")
>>> roiManager("select", 0);
>>> setKeyDown("shift")
>>> roiManager("select", 3);
>>> setKeyDown("shift")
>>> roiManager("select", 7);
>>>
>>> roiManager("Add");
>>> roiManager("Measure");
>>> print("after measure, nResults=", nResults ," area=" + getResult
>>> ("Area", nResults-1));
>>>
>>> //END MACRO
>>>
>>> I note there is a bug-fix in ROI manager regarding combining ROIs
>>> for v1.42f, but I am running v1.42l.
>>>
>>>
>>> Ben Tupper
>>>
>>>
>>>
>>> Java properties applets can read:
>>> java.version: 1.5.0_16
>>> java.vendor: Apple Inc.
>>> mrj.version: 1050.1.5.0_16-284
>>> os.name: Mac OS X
>>> os.version: 10.5.6
>>> os.arch: i386
>>> file.separator: /
>>> path.separator: :
>>> line.separator: <lf>
>>>
>>> Java properties only applications can read:
>>> user.name: ben
>>> user.home: /Users/ben
>>> user.dir: /Applications/ImageJ
>>> user.country: US
>>> file.encoding: MacRoman
>>> java.home: /System/Library/Frameworks/JavaVM.framework/Versions/
>>> 1.5.0/Home
>>> java.class.path: /Applications/ImageJ/ImageJ.app/../ij.jar:/
>>> System/Library/Java/Extensions/QTJava.zip
>>> java.ext.dirs: /Library/Java/Extensions:/System/Library/Java/
>>> Extensions:/System/Library/Frameworks/JavaVM.framework/Versions/
>>> 1.5.0/Home/lib/ext
>>> java.io.tmpdir: /tmp
>>>
>>> Other properties:
>>> IJ.getVersion: 1.42l
>>> IJ.isJava2: true
>>> IJ.isJava15: true
>>> IJ.isJava16: false
>>> IJ.isLinux: false
>>> IJ.isMacintosh: true
>>> IJ.isMacOSX: true
>>> IJ.isWindows: false
>>> IJ.isVista: false
>>> IJ.is64Bit: false
>>> Menus.getPlugInsPath: /Applications/ImageJ/plugins/
>>> Menus.getMacrosPath: /Applications/ImageJ/macros/
>>> Prefs.getHomeDir: /Applications/ImageJ
>>> Prefs.getThreads: 2 (2 cores)
>>> Prefs.open100Percent: false
>>> Prefs.blackBackground: false
>>> Prefs.useJFileChooser: false
>>> Prefs.weightedColor: false
>>> Prefs.blackCanvas: false
>>> Prefs.pointAutoMeasure: false
>>> Prefs.pointAutoNextSlice: false
>>> Prefs.requireControlKey: false
>>> Prefs.useInvertingLut: false
>>> Prefs.antialiasedTools: true
>>> Prefs.useInvertingLut: false
>>> Prefs.intelByteOrder: false
>>> Prefs.doubleBuffer: false
>>> Prefs.noPointLabels: false
>>> Prefs.disableUndo: false
>>> Prefs dir: /Users/ben/Library/Preferences
>>> Current dir: /Users/Shared/data/441.2009-04-23.400A4X_03 2/
>>> Sample images dir:
http://rsb.info.nih.gov/ij/images/>>> Screen size: 1440x900
>>> Memory in use: 11MB of 400MB (2%)
>
> Ben Tupper