http://imagej.273.s1.nabble.com/Disjoint-ROI-selection-using-macro-language-tp3692854p3692858.html
> the ROI Manager items have labels 0001-... to 0064-...,
schemes. It is very taxing on my walnut-sized-brain. It wasn't so bad
results table (1-based)... argh!
> 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
command. With the fictional click-command it works as long as the
additions to the ROI Manager. Then I thought I could step through the
would select only those that qualify. Since the click-command is
>
> I don't know how to do this in a macro; at least I am not aware of a
> setKeyDown("command") or setKeyDown("ctrl")
>
> With "shift", one would select a contiguous range of lines.
>
>
> Best wishes,
>
> Michael
> ________________________________________________________________
>
> On 16 Apr 2009, at 21:03, Ben Tupper wrote:
>
>> 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