http://imagej.273.s1.nabble.com/Disjoint-ROI-selection-using-macro-language-tp3692854p3692856.html
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"
thinks it is v1.42l. Restarting ImageJ seems to make no difference.
> 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%)