Frangi Vesselness Filter #525

gselzer · 2017-10-05T20:39:40Z

This PR adds an implementation for Frangi's Multiscale Vessel Enhancement Filter, a filter that is given a grayscale, white-on-black image of vessel structures and returns an image that highlights the vessel structures and removes noise.

This PR closes issue #490.

stelfrich

I really like the implementation. Thanks for your work @gselzer! I'd suggest to reuse the imglib2 implementation Intervals.numElements() instead of an own implementation of DefaultFrangi.numberOfPoints(). Otherwise it's just minor stuff...

stelfrich · 2017-10-20T07:32:33Z

src/main/java/net/imagej/ops/commands/filter/FrangiVesselness.java

+ * allowing users to specify:
+ * 		1) The scales desired for the filter application
+ * 		2) The physical spacing between image data points
+ * 		3) Whether or not the pre-Gaussian filter should be performed.


I find the term "pre-Gaussian" a bit misleading. To me, this implies that a Gaussian is applied to an image before the computation. In practice, however, it is applied for each scale, isn't it?

You're right. I fixed it.

stelfrich · 2017-10-20T07:33:19Z

src/main/java/net/imagej/ops/commands/filter/FrangiVesselness.java

+	@Parameter
+	private Img<T> input;
+
+	@Parameter(label = "Gauss before:")


Maybe something like "Apply Gaussian at each scale:" would be more appropriate?

Yeah, that sounds better.

stelfrich · 2017-10-20T07:35:48Z

src/main/java/net/imagej/ops/commands/filter/FrangiVesselness.java

+	private boolean doGauss;
+
+	@Parameter(label = "Spacing",
+		description = "Physical distance between the observed data points")


Doesn't "Physical distance" imply something like 3 microns? From the implementation, I'd say that is more of a "relative distance": 1,1 implies that we have the same spacing in x and y, whereas 1,1,2 implies that the resolution in z is half of the resolution in x and y.

Yes, that is a better way of expressing that.

stelfrich · 2017-10-20T07:37:08Z

src/main/java/net/imagej/ops/commands/filter/FrangiVesselness.java

+
+	@Override
+	public void run() {
+	//parse the spacing, and scales strings.


Intendation is wrong. Plus, you have used a space in comments before (which is also the preferred way according to the coding style).

stelfrich · 2017-10-20T07:48:56Z

src/main/java/net/imagej/ops/filter/FilterNamespace.java

@@ -47,6 +47,7 @@
 import net.imglib2.algorithm.neighborhood.Shape;
 import net.imglib2.img.Img;
 import net.imglib2.outofbounds.OutOfBoundsFactory;
+import net.imglib2.type.BooleanType;


Where did that come from?

stelfrich · 2017-10-20T07:53:58Z

src/main/java/net/imagej/ops/filter/vesselness/DefaultFrangi.java

+		frangi(input, output, scale);
+	}
+
+	private void frangi(RandomAccessibleInterval<T> in, RandomAccessibleInterval<U> out, int step) {


final parameters?

Sure, I guess we could add that.

stelfrich · 2017-10-20T07:54:29Z

src/main/templates/net/imagej/ops/Ops.list

@@ -104,6 +104,7 @@ namespaces = ```
 		[name: "paddingIntervalOrigin",          iface: "PaddingIntervalOrigin"],
 		[name: "sigma",                          iface: "Sigma",               aliases: ["sigmaFilter", "filterSigma"]],
 		[name: "variance",                       iface: "Variance",            aliases: ["varianceFilter", "filterVariance", "var", "varFilter", "filterVar"]],
+		[name: "vesselness",			 iface: "Vesselness"],


frangiVesselness?

I suppose this makes sense to do.

stelfrich · 2017-10-20T07:55:00Z

src/main/java/net/imagej/ops/filter/vesselness/DefaultFrangi.java

+
+			cursor.fwd();
+
+


Blank line?

stelfrich · 2017-10-20T07:55:49Z

src/main/java/net/imagej/ops/filter/vesselness/DefaultFrangi.java

+		double bd = 2 * beta * beta;
+
+		// OutOfBoundsMirrorStrategy for use when the cursor reaches the edges.
+		OutOfBoundsMirrorFactory<T, RandomAccessibleInterval<T>> osmf = new OutOfBoundsMirrorFactory<T, RandomAccessibleInterval<T>>(


You could make this a @Parameter of the op and set the OutOfBoundsMirrorFactory as default.

What would be the benefit of this?

Sorry for the delay, @gselzer!

We have made the OutOfBoundsFactory a @Parameter in other implementations, so you can feed in another one if you like. I understand that it is an additional parameter to provide, that in practice most user will not overwrite. So I am fine with leaving it as it is, for the sake of usability. However, I wanted to state that this is one of the pitfalls of ImageJ1: making implicit
assumptions about the out-of-bounds strategy without being able to change it...

Maybe @ctrueden has an opinion on that topic as well?

stelfrich · 2017-10-20T07:56:25Z

src/test/java/net/imagej/ops/filter/vesselness/FrangiVesselnessTest.java

+		return new Context(OpService.class, OpMatchingService.class, CacheService.class, ScriptService.class);
+	}
+
+}


Missing newline

This should be fixed in the clean up commit.

ctrueden · 2017-10-27T04:19:08Z

src/main/templates/net/imagej/ops/Ops.list

@@ -104,7 +104,7 @@ namespaces = ```
 		[name: "paddingIntervalOrigin",          iface: "PaddingIntervalOrigin"],
 		[name: "sigma",                          iface: "Sigma",               aliases: ["sigmaFilter", "filterSigma"]],
 		[name: "variance",                       iface: "Variance",            aliases: ["varianceFilter", "filterVariance", "var", "varFilter", "filterVar"]],
-		[name: "vesselness",			 iface: "Vesselness"],
+		[name: "frangiVesselness",			 iface: "FrangiVesselness"],


Be careful with the word refactoring—it means to change the internal structure of code without changing its external behavior. So no API changes! In this case, the API definitely does change because the op interface name changed from Vesselness to FrangiVesselness. So this is not a refactoring. A better commit message would be "Rename vesselness to frangiVesselness."

imagejan · 2017-10-31T13:20:35Z

src/main/templates/net/imagej/ops/Ops.list

@@ -104,6 +104,7 @@ namespaces = ```
 		[name: "paddingIntervalOrigin",          iface: "PaddingIntervalOrigin"],
 		[name: "sigma",                          iface: "Sigma",               aliases: ["sigmaFilter", "filterSigma"]],
 		[name: "variance",                       iface: "Variance",            aliases: ["varianceFilter", "filterVariance", "var", "varFilter", "filterVar"]],
+		[name: "frangiVesselness",			 iface: "FrangiVesselness"],


This should now go to f in the alphabet (and indentation fixed), right?

Oops. You are right. I will change it here and in the namespace.

Original versions of the code used the conditions directly outlined in the paper, however through testing it was discovered that the conditions were not enough to fufill human expectations of the filter. Thus the condidions were altered, and are now explained.

The second part of the conditional for 2D vesselness calculations, which was useful before, is no longer useful. It does not alter the result. As such it has been removed.

ctrueden · 2017-12-05T22:03:53Z

Rebased over latest master. All tests passing, so merging now.

gselzer force-pushed the issue490 branch from 5defc76 to 7017c28 Compare October 5, 2017 20:42

gselzer force-pushed the issue490 branch from e51cb73 to 4c8e711 Compare October 13, 2017 20:49

stelfrich requested changes Oct 20, 2017

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gselzer force-pushed the issue490 branch from 0094680 to c34d010 Compare October 26, 2017 20:04

ctrueden reviewed Oct 27, 2017

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gselzer force-pushed the issue490 branch from 81aaadb to 9dd62c5 Compare October 27, 2017 17:36

hadim mentioned this pull request Oct 29, 2017

Add Frangi filter fiji/FilamentDetector#4

Merged

imagejan reviewed Oct 31, 2017

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stelfrich approved these changes Nov 1, 2017

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ctrueden and others added 18 commits December 5, 2017 15:59

Create Frangi Vesselness Op, add to Ops.list

0ba7e69

Implement Frangi Vesselness Op

63a93a2

Create Frangi Vesselness test

c5eeb62

Implement Frangi Vesselness test

72f88b9

Fix issues in 3D image analysis

f8d91aa

Make 2nd-order-structure param accurate to paper

6520fca

Remove unnecessary condition

c417ea7

The second part of the conditional for 2D vesselness calculations, which was useful before, is no longer useful. It does not alter the result. As such it has been removed.

Add Comand for flexible vesselness filter

d7bbfa2

Fix wording of command params

ec9b09b

Format command

6307e7e

Remove unnecessary import

a314806

Fix parameter naming, general polishing

5d41df1

Format and clean up code

d436e77

Rename vesselness to frangiVesselness

b9d4981

Clean up test

d4b5b67

Remove numberOfPoints(), since it was not used.

c65c7da

Alphabetize frangiVesselness

081d117

ctrueden force-pushed the issue490 branch from 45637ac to 081d117 Compare December 5, 2017 22:03

ctrueden merged commit edd4513 into master Dec 5, 2017

ctrueden deleted the issue490 branch December 5, 2017 22:04

stelfrich mentioned this pull request Dec 14, 2017

Frangi Vesselness filter #490

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Frangi Vesselness Filter #525

Frangi Vesselness Filter #525

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Frangi Vesselness Filter #525

Frangi Vesselness Filter #525

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ctrueden commented Dec 5, 2017