Posted by
Wayne Rasband on
Aug 28, 2009; 8:24pm
URL: http://imagej.273.s1.nabble.com/Line-length-and-tracing-exception-window-tp3691355p3691357.html
On Aug 28, 2009, at 3:14 PM, Michael Schmid wrote:
> Hi David,
>
> yes, I could reproduce the exception with the lastest daily build.
> (Windows XP, Java 1.5.0_09)
> It can occur when typing 'M' before the line segment has more than one
> point (i.e., while it has only one anchor at the starting point, and
> the
> end point is still under cursor control), but it can also occur with
> longer selections.
> After the exception, everything becomes weird; the image is not updated
> any more, the keyboard shortcuts don't work (seems that the
> ImageCanvas is
> damaged). It starts to work again if I use the rectangular selection
> and
> move the cursor into the ImageCanvas (sometimes I have to click into
> it).
>
> Even more strange: It seems that the problem needs a calibration with
> less
> than 1 unit per pixel.
This bug is fixed in the 1.43g daily build.
> One related issue: I do not understand why "Measure" on a polygon roi
> with
> line thickness>1 always creates a spline fit.
ImageJ uses the straighten function (Edit>Selection>Straighten) to
measure area, mean, etc. of segmented lines selections with a width
greater than 1 pixel, and the straighten function does a spline fit.
-wayne
>
> Michael
> ________________________________________________________________
>
> On Tue, August 25, 2009 23:36, David Chatelet wrote:
>> Hi,
>> I am trying to measure the vein length of leaves but ImageJ stops and
>> a
>> exception window open. Here is what I do:
>> First I open a tiff or jpeg image of a scale bar. I trace a certain
>> distance, go to the set scale window, enter the known length and unit,
>> check "global" and click OK. Then I open a tiff image showing a leaf
>> venation (same resolution and dimension than the scale bar image),
>> select
>> the polygon selection tool, increase the line width to 10 and change
>> its
>> color so I can see it. First I trace a box on my image, measure its
>> surface area (M key) and embed it on my image (D key). Then I reset
>> the
>> result window, select the segmented line tool and start tracing lines
>> following the vein pattern. Everytime I stop, I press the M key to
>> measure
>> the length of the line I just traced, followed by the D key to embed
>> the
>> line on my image. Problems: (1) the lines (traced with the segmented
>> line
>> tool) don’t appear on the image when I press D and (2) after about 10
>> measurements, ImageJ stop and an exception window appear with the
>> following message:
>> java.lang.ArrayIndexOutOfBoundsException: 0
>> at ij.gui.PolygonRoi.fitSplineForStraightening(PolygonRoi.java:617)
>> at ij.plugin.Straightener.straightenLine(Straightener.java:98)
>> at ij.plugin.filter.Analyzer.measureLength(Analyzer.java:327)
>> at ij.plugin.filter.Analyzer.measure(Analyzer.java:203)
>> at ij.plugin.filter.Analyzer.run(Analyzer.java:86)
>> at ij.plugin.filter.PlugInFilterRunner.processOneImage
>> (PlugInFilterRunner.java:245)
>> at
>> ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:
>> 102)
>> at ij.IJ.runPlugIn(IJ.java:150)
>> at ij.Executer.runCommand(Executer.java:121)
>> at ij.Executer.run(Executer.java:58)
>> at java.lang.Thread.run(Thread.java:619)
>>
>> What is going on? I have Vista home premium 32bit and this method was
>> working fine with ImageJ 1.38. But I upgraded ImageJ recently and it
>> is no
>> good anymore. Any help would be greatly appreciated. Thanks.
>>
>> David
>>
>