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Scijava/scijava javadoc parser/javadoc to yaml (#79)
* Parse docs with our own annotation processor * Name javadoc'd Op params after name in method * Fix YAML issues * Make minor fixes * Restore IterableInterval copier Without it, it's really difficult to match the request in the tests. Since it isn't hurting anything to have it, we might as well keep it. * Convert command line arg to boolean-like Since we're storing far less information now, I think it's a lot easier to just have an opt-in toggle, and I don't see anyone wanting to only parse some packages. * Rename to SciJava Ops Indexer @ctrueden and @hinerm and I decided that we should specialize this module on Ops, because we don't yet have a use case beyond Ops. * "Op-ify" the yaml This makes the logic more complex - let's clean it up in the following commits * Rename annotation processor option * Move inner class HACK out of SciJava Common * Rename and add documentation to OpImplData * Cleanup JavadocAnnotationProcessor * Clean up OpImplData A lot (i.e. all) of the fields are shared, so let's move them upstream * Enable YAML Ops to infer their type * Require correct no. params for implNote ops * Validate Ops declared in javadoc * Add Op version to the parser * Fix indentation * Rename Annotation Processor * Add comment explaining the false return * Combine OpImplNoteParser and YamlJavadocBuilder * Remove commented out log message * Update Services * Add LICENSE for adapted Therapi code * Remove InvalidOpJavadocException Wasn't being used * Various small clean-up changes * Format module-info.java * Clean up OpDependencyMemberParsers * Remove TODO in YAML version parsing * Throw IAE when Op yaml has no name * Partition name parser into its own method * Remove hints from method * Remove SciJava Parse2 dependency It wasn't used * OpFieldImplData: Document parseAdditionalTags * OpImplData: Javadoc for parsing additional tags * OpImplNoteParser: Convert Field to Method No real reason to keep it as a field * OpMethodImplData: simplify * ProcessingUtils: Add documentation * Write README for the Ops Indexer * Improve ImplNote parser regex
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‎.github/build.sh‎

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@@ -1,4 +1,4 @@
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#!/bin/sh
22
curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/master/ci-build.sh
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mvn -Djavadoc.skip -pl scijava/scijava-taglets clean install
3+
mvn -Djavadoc.skip -pl scijava/scijava-taglets,scijava/scijava-ops-indexer -am clean install
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sh ci-build.sh

‎imagej/imagej-ops2/src/main/java/module-info.java‎

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@@ -26,120 +26,9 @@
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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module net.imagej.ops2 {
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open module net.imagej.ops2 {
3030
exports net.imagej.ops2;
3131

32-
// -- Open plugins to scijava-ops, therapi
33-
opens net.imagej.ops2.adapt to therapi.runtime.javadoc, org.scijava.ops.engine;
34-
opens net.imagej.ops2.adapt.complexLift to therapi.runtime.javadoc, org.scijava.ops.engine;
35-
opens net.imagej.ops2.coloc to therapi.runtime.javadoc, org.scijava.ops.engine;
36-
opens net.imagej.ops2.coloc.icq to therapi.runtime.javadoc, org.scijava.ops.engine;
37-
opens net.imagej.ops2.coloc.kendallTau to therapi.runtime.javadoc, org.scijava.ops.engine;
38-
opens net.imagej.ops2.coloc.maxTKendallTau to therapi.runtime.javadoc, org.scijava.ops.engine;
39-
opens net.imagej.ops2.coloc.pearsons to therapi.runtime.javadoc, org.scijava.ops.engine;
40-
opens net.imagej.ops2.coloc.pValue to therapi.runtime.javadoc, org.scijava.ops.engine;
41-
opens net.imagej.ops2.convert to therapi.runtime.javadoc, org.scijava.ops.engine;
42-
opens net.imagej.ops2.convert.clip to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.convert.copy to therapi.runtime.javadoc, org.scijava.ops.engine;
44-
opens net.imagej.ops2.copy to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.create to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.deconvolve to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.deconvolve.accelerate to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.eval to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.features.haralick to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.features.haralick.helper to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.features.hog to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.features.lbp2d to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.features.tamura2d to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.features.zernike to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.addNoise to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.bilateral to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.convolve to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.correlate to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.derivative to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.derivativeGauss to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.dog to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.fft to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.fftSize to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.gauss to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.hessian to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.ifft to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.pad to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.sigma to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.sobel to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.tubeness to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.filter.vesselness to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.geom to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.geom.geom2d to org.scijava, therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.geom.geom3d to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.identity to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.ascii to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.cooccurrenceMatrix to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.distancetransform to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.fill to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.histogram to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.integral to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.invert to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.normalize to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.image.watershed to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.imagemoments to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.imagemoments.centralmoments to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.imagemoments.hu to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.imagemoments.moments to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.imagemoments.normalizedcentralmoments to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.labeling to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.labeling.cca to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.linalg.rotate to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.logic to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.map.neighborhood to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.math to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.math.multiply to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.morphology to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.morphology.thin to therapi.runtime.javadoc, org.scijava.ops.engine;
100-
opens net.imagej.ops2.project to therapi.runtime.javadoc, org.scijava.ops.engine;
101-
opens net.imagej.ops2.segment.detectJunctions to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.segment.detectRidges to therapi.runtime.javadoc, org.scijava.ops.engine;
103-
opens net.imagej.ops2.slice to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.stats to therapi.runtime.javadoc, org.scijava.ops.engine;
105-
opens net.imagej.ops2.stats.regression.leastSquares to therapi.runtime.javadoc, org.scijava.ops.engine;
106-
opens net.imagej.ops2.thread.chunker to therapi.runtime.javadoc, org.scijava.ops.engine;
107-
opens net.imagej.ops2.threshold to therapi.runtime.javadoc, org.scijava.ops.engine;
108-
opens net.imagej.ops2.threshold.apply to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.threshold.huang to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.threshold.ij1 to therapi.runtime.javadoc, org.scijava.ops.engine;
111-
opens net.imagej.ops2.threshold.intermodes to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.threshold.isoData to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.threshold.li to therapi.runtime.javadoc, org.scijava.ops.engine;
114-
opens net.imagej.ops2.threshold.localBernsen to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.threshold.localContrast to therapi.runtime.javadoc, org.scijava.ops.engine;
116-
opens net.imagej.ops2.threshold.localMean to therapi.runtime.javadoc, org.scijava.ops.engine;
117-
opens net.imagej.ops2.threshold.localMedian to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.threshold.localMidGrey to therapi.runtime.javadoc, org.scijava.ops.engine;
119-
opens net.imagej.ops2.threshold.localNiblack to therapi.runtime.javadoc, org.scijava.ops.engine;
120-
opens net.imagej.ops2.threshold.localPhansalkar to therapi.runtime.javadoc, org.scijava.ops.engine;
121-
opens net.imagej.ops2.threshold.localSauvola to therapi.runtime.javadoc, org.scijava.ops.engine;
122-
opens net.imagej.ops2.threshold.maxEntropy to therapi.runtime.javadoc, org.scijava.ops.engine;
123-
opens net.imagej.ops2.threshold.maxLikelihood to therapi.runtime.javadoc, org.scijava.ops.engine;
124-
opens net.imagej.ops2.threshold.mean to therapi.runtime.javadoc, org.scijava.ops.engine;
125-
opens net.imagej.ops2.threshold.minError to therapi.runtime.javadoc, org.scijava.ops.engine;
126-
opens net.imagej.ops2.threshold.minimum to therapi.runtime.javadoc, org.scijava.ops.engine;
127-
opens net.imagej.ops2.threshold.moments to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.threshold.otsu to therapi.runtime.javadoc, org.scijava.ops.engine;
129-
opens net.imagej.ops2.threshold.percentile to therapi.runtime.javadoc, org.scijava.ops.engine;
130-
opens net.imagej.ops2.threshold.renyiEntropy to therapi.runtime.javadoc, org.scijava.ops.engine;
131-
opens net.imagej.ops2.threshold.rosin to therapi.runtime.javadoc, org.scijava.ops.engine;
132-
opens net.imagej.ops2.threshold.shanbhag to therapi.runtime.javadoc, org.scijava.ops.engine;
133-
opens net.imagej.ops2.threshold.triangle to therapi.runtime.javadoc, org.scijava.ops.engine;
134-
opens net.imagej.ops2.threshold.yen to therapi.runtime.javadoc, org.scijava.ops.engine;
135-
opens net.imagej.ops2.topology to therapi.runtime.javadoc, org.scijava.ops.engine;
136-
opens net.imagej.ops2.topology.eulerCharacteristic to therapi.runtime.javadoc, org.scijava.ops.engine;
137-
opens net.imagej.ops2.transform to therapi.runtime.javadoc, org.scijava.ops.engine;
138-
opens net.imagej.ops2.types to therapi.runtime.javadoc, org.scijava.ops.engine, org.scijava.types;
139-
opens net.imagej.ops2.types.adapt to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.types.maxValue to therapi.runtime.javadoc, org.scijava.ops.engine;
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opens net.imagej.ops2.types.minValue to therapi.runtime.javadoc, org.scijava.ops.engine;
142-
14332
requires java.scripting;
14433
requires net.imagej.mesh2;
14534
requires net.imglib2;

‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/ConvertTypes.java‎

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Original file line numberDiff line numberDiff line change
@@ -62,161 +62,161 @@ public final class ConvertTypes<C extends ComplexType<C>, T extends IntegerType<
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/**
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* @input input
65-
* @output output
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* @container output
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* @implNote op names='convert.bit'
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*/
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public final Computers.Arity1<C, BitType> complexToBit = (input, output) -> output.set(input.getRealDouble() != 0);
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/**
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* @input input
72-
* @output output
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* @container output
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* @implNote op names='convert.bit'
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*/
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public final Computers.Arity1<T, BitType> integerToBit = (input, output) -> output.set(input.getIntegerLong() != 0);
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint2'
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*/
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public final Computers.Arity1<C, Unsigned2BitType> complexToUint2 = (input, output) -> output.set((long) input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint2'
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*/
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public final Computers.Arity1<T, Unsigned2BitType> integerToUint2 = (input, output) -> output.set(input.getIntegerLong());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint4'
9595
*/
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public final Computers.Arity1<C, Unsigned4BitType> complexToUint4 = (input, output) -> output.set((long) input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint4'
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*/
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public final Computers.Arity1<T, Unsigned4BitType> integerToUint4 = (input, output) -> output.set(input.getIntegerLong());
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/**
106106
* @input input
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* @output output
107+
* @container output
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* @implNote op names='convert.byte'
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*/
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public final Computers.Arity1<C, ByteType> complexToInt8 = (input, output) -> output.set((byte) input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.byte'
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*/
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public final Computers.Arity1<T, ByteType> integerToInt8 = (input, output) -> output.set((byte) input.getIntegerLong());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint8'
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*/
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public final Computers.Arity1<C, UnsignedByteType> complexToUint8 = (input, output) -> output.set((int) input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint8'
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*/
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public final Computers.Arity1<T, UnsignedByteType> integerToUint8 = (input, output) -> output.set(input.getInteger());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint12'
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*/
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public final Computers.Arity1<C, Unsigned12BitType> complexToUint12 = (input, output) -> output.set((long) input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint12'
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*/
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public final Computers.Arity1<T, Unsigned12BitType> integerToUint12 = (input, output) -> output.set(input.getIntegerLong());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.int16'
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*/
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public final Computers.Arity1<C, ShortType> complexToInt16 = (input, output) -> output.set((short) input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.int16'
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*/
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public final Computers.Arity1<T, ShortType> integerToInt16 = (input, output) -> output.set((short) input.getIntegerLong());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint16'
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*/
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public final Computers.Arity1<C, UnsignedShortType> complexToUint16 = (input, output) -> output.set((int) input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint16'
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*/
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public final Computers.Arity1<T, UnsignedShortType> integerToUint16 = (input, output) -> output.set(input.getInteger());
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/**
176176
* @input input
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* @output output
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* @container output
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* @implNote op names='convert.int32'
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*/
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public final Computers.Arity1<C, IntType> complexToInt32 = (input, output) -> output.set((int) input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
185185
* @implNote op names='convert.int32'
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*/
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public final Computers.Arity1<T, IntType> integerToInt32 = (input, output) -> output.set(input.getInteger());
188188

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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.uint32'
193193
*/
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public final Computers.Arity1<C, UnsignedIntType> complexToUint32 = (input, output) -> output.set((long) input.getRealDouble());
195195

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/**
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* @input input
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* @output output
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* @container output
199199
* @implNote op names='convert.uint32'
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*/
201201
public final Computers.Arity1<T, UnsignedIntType> integerToUint32 = (input, output) -> output.set(input.getIntegerLong());
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203203
/**
204204
* @input input
205-
* @output output
205+
* @container output
206206
* @implNote op names='convert.int64'
207207
*/
208208
public final Computers.Arity1<C, LongType> complexToInt64 = (input, output) -> output.set((long) input.getRealDouble());
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210210
/**
211211
* @input input
212-
* @output output
212+
* @container output
213213
* @implNote op names='convert.int64'
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*/
215215
public final Computers.Arity1<T, LongType> integerToInt64 = (input, output) -> output.set(input.getIntegerLong());
216216

217217
/**
218218
* @input input
219-
* @output output
219+
* @container output
220220
* @implNote op names='convert.uint64'
221221
*/
222222
public final Computers.Arity1<C, UnsignedLongType> complexToUint64 = (input, output) -> {
@@ -231,7 +231,7 @@ public final class ConvertTypes<C extends ComplexType<C>, T extends IntegerType<
231231

232232
/**
233233
* @input input
234-
* @output output
234+
* @container output
235235
* @implNote op names='convert.uint128'
236236
*/
237237
public final Computers.Arity1<C, Unsigned128BitType> complexToUint128 = (input, output) -> {
@@ -246,36 +246,36 @@ public final class ConvertTypes<C extends ComplexType<C>, T extends IntegerType<
246246

247247
/**
248248
* @input input
249-
* @output output
249+
* @container output
250250
* @implNote op names='convert.uint128'
251251
*/
252252
public final Computers.Arity1<T, Unsigned128BitType> integerToUint128 = (input, output) -> output.set(input.getBigInteger());
253253

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/**
255255
* @input input
256-
* @output output
256+
* @container output
257257
* @implNote op names='convert.float32'
258258
*/
259259
public final Computers.Arity1<C, FloatType> complexToFloat32 = (input, output) -> output.set(input.getRealFloat());
260260

261261
/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.cfloat32'
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*/
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public final Computers.Arity1<C, ComplexFloatType> complexToCfloat32 = (input, output) -> output.set(input.getRealFloat(),
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input.getImaginaryFloat());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.float64'
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*/
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public final Computers.Arity1<C, DoubleType> complexToFloat64 = (input, output) -> output.set(input.getRealDouble());
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/**
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* @input input
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* @output output
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* @container output
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* @implNote op names='convert.cfloat64'
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*/
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public final Computers.Arity1<C, ComplexDoubleType> complexToCfloat64 = (input, output) -> output.set(input.getRealDouble(),

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