Hi All,
I chatted with Curtis Rueden a bit today about trying this developmental
feature extraction stuff out. He said I should note any successes or challenges
as it might help your progress. He suggested potentially to post on the pull
request but it seemed a bit long for there.
First of all, fantastic stuff. You are bringing so much quantitative power to
the fingertips of a lot of individuals like myself. Thank you! Secondly, sorry
if I'm using anything inappropriately in the rundown below but this is my best
shot at trying to give you some feedback on my attempt to use your code. Also,
I totally realize things are still in flux so I didn't necessarily have
expectations that all this stuff would work immediately for me.
As of what was synced to the imagej-ops : outputop-service branch tonight, I
was able to successfully get measures from a `FirstOrderStatFeatureSet` for a
set of `LabelRegion`s that I got from a `Img<UnsignedByteType>` using
`ConnectedComponents` (from latest ImgLib2-algorithm SNAPSHOT but just
temporarily copied to its own class local for this test) and apply them to an
`Img<UnsignedShortType>` using `Regions.sample(myLabelRegion, myImg)`. I think
I did most of these tests using connected components detected using a
4-connected structuring element (if that matters at all).
I ran into an issue with the `GeometricFeatureSet` where I got a
`````
java.lang.ArrayIndexOutOfBoundsException: -1
java.util.ArrayList.elementData(ArrayList.java:400)
java.util.ArrayList.remove(ArrayList.java:477)
net.imagej.ops.geometric.polygon.DefaultConvexHullOp.run(DefaultConvexHullOp.java:127)
`````
All my regions are quite sizeable (all between 1000 and 6000 pixels, see end of
email) so I'm not sure why this would happen. I'm basically doing the following
for this test using the same regions as I used with the
`FirstOrderStatFeatureSet`
`````
GeometricFeatureSet opGeometric = ij.op().op(GeometricFeatureSet.class,
LabelRegion.class);
List<Pair<String, DoubleType>> results =
opGeometric.getFeatureList(Regions.iterable(myLabelRegion));
`````
I'm also having a problem with `Haralick2DFeatureSet` using those same
`LabelRegion`s.
`````
java.lang.ArrayIndexOutOfBoundsException: -1
net.imglib2.roi.labeling.LabelRegion.dimension(LabelRegion.java:459)
net.imglib2.AbstractWrappedInterval.dimension(AbstractWrappedInterval.java:59)
net.imagej.ops.features.haralick.helper.CooccurrenceMatrix2D.run(CooccurrenceMatrix2D.java:119)
`````
I'm testing the `Haralick2DFeatureSet` as follows...
````
Haralick2DFeatureSet<UnsignedShortType> opHaralick2DHor =
ij.op(Haralick2DFeatureSet.class, (IterableInterval<UnsignedShortType>) image,
8d, 1d, "HORIZONTAL");
List<Pair<String, DoubleType>> results =
opHaralick2DHor.getFeatureList(Regions.sample(myLabelRegion, image));
`````
The `HistogramFeatureSet` appears to work. I think I don't have my image
adjusted right to see appropriate values in the histogram output though as I
seem to get all 0's. I assumed the "number of bins" parameter would autoscale
the data according to the image type (e.g., UnsignedShortType image scaled to
fit in 256 levels/bins) but I can see why that was likely a bad assumption.
The `ImageMomentsFeatureSet` seems to work fine.
I got the following error trying to use the `Zernike` feature set...
`````
java.lang.NumberFormatException
java.math.BigDecimal.<init>(BigDecimal.java:470)
java.math.BigDecimal.<init>(BigDecimal.java:739)
java.math.BigDecimal.valueOf(BigDecimal.java:1069)
net.imagej.types.BigComplex.setReal(BigComplex.java:225)
net.imagej.ops.features.zernike.ZernikeComputer.normalize(ZernikeComputer.java:193)
net.imagej.ops.features.zernike.ZernikeComputer.fastZernikeComputation(ZernikeComputer.java:151)
`````
I'm using it as follows on the 8-bit mask image
`````
ZernikeFeatureSet<UnsignedByteType> opZernike =
ij.op().op(ZernikeFeatureSet.class, (IterableInterval<UnsignedByteType>) mask,
true, true, 1, 3);
List<Pair<String, DoubleType>> results =
opZernike.getFeatureList(Regions.sample(myLabelRegion, mask));
`````
I figured, in case I'm doing a bunch of things wrong, it would be easier for
you to just have the data I'm using to see if you get the same issues using
your own code. The images that I'm using are here...
https://drive.google.com/folderview?id=0BzopfqjGpdu8flBNTHdjXzN2eUJhR1NCNmNTbHJ5T3RNVDJRbmdwVnJiYnI0Nk43ZXp3QzA&usp=sharing
<https://drive.google.com/folderview?id=0BzopfqjGpdu8flBNTHdjXzN2eUJhR1NCNmNTbHJ5T3RNVDJRbmdwVnJiYnI0Nk43ZXp3QzA&usp=sharing>
The folder includes a small txt output of only the label regions that I'm
analyzing (their pixel areas and centers of mass), given I am not using all
labeled objects that come from the connected components analysis. Lastly, my
label indices start at 0 if you are looking to match up output from
ConnectedComponents with this.
If you have any feedback on where I might be doing things wrong, please let me
know.
Thanks!
Jay
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