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chalkie666/imagejMacros 3

imageJ 1 macros

chalkie666/CUDA_SIMrecon 1

Image reconstruction for structured-illumination microscopy implemented in CUDA

chalkie666/bioformats 0

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

chalkie666/chalkie666.github.io 0

Chalkie.org.uk website

chalkie666/Colocalisation_Analysis 0

Coloc 2 is Fiji's plugin for colocalization analysis. It implements and performs the pixel intensity correlation over space methods of Pearson, Manders, Costes, Li and more, for scatterplots, analysis, automatic thresholding and statistical significance testing.

chalkie666/cudasirecon 0

3D Structured illumination microscopy (3D-SIM) reconstruction software

chalkie666/DeltaVisionScripts 0

a home for miscellaneous scripts for experiment .exp files and other tools used for work arounds or other clever tricks on DeltaVision microscope systems.

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issue closedscijava/scijava-ops

Add Op factory methods

Op methods are intended as a third way between Op fields and regular Op classes. They try to provide the conciseness of @OpFields while still enabling the use of other Ops via OpDependencys. A typical implementation of an Op method may look like this:

@Plugin(type = OpCollection.class)
public class MyOpCollection {

	@OpMethod(names = "test.multiplyNumericStrings")
	@Parameter(key = "numericString1")
	@Parameter(key = "numericString2")
	@Parameter(key = "multipliedNumericStrings", type = ItemIO.OUTPUT)
	@OpDependency(name = "test.parseInteger")
	public BiFunction<String, String, Integer> createMultiplyNumericStringsOp(
		final Function<String, Integer> parseIntegerOp)
	{
		return (i1, i2) -> parseIntegerOp.apply(i1) * parseIntegerOp.apply(i2);
	}
}

Here createMultiplyNumericStringsOp is a factory method ("Op method") that creates and returns the actual "test.multiplyNumericStrings" Op, whenever a new instance of this Op is requested by the user. The @Parameter annotations above the factory method describe the parameters of the returned Op itself, not the factory method. The @OpDependency annotation corresponds to the parameter of the factory method. The Op matching system takes care of resolving this dependency and passes it as an argument which can then be captured by the Op lambda.

The current progress on this issue is captured on branch op-methods, the relevant commits being b4b0d3bbf26cbf19f1cf8b0440cd6ef6fef8d50f through a9e860e6968a8290a80b7d0b157da0fa6661f391. The last of these commits is a (passing) test that further demonstrates the intended behavior.

In the long run, this way of injecting Op dependencies could make "ordinary" Op classes redundant. E.g., the above Op method could be a replacement for the following Op class:

@Plugin(type = Op.class, name = "test.multiplyNumericStrings")
@Parameter(key = "numericString1")
@Parameter(key = "numericString2")
@Parameter(key = "multipliedNumericStrings", type = ItemIO.OUTPUT)
public class MultiplyNumericStrings implements BiFunction<String, String, Integer> {

	@OpDependency(name = "test.parseInteger")
	private Function<String, Integer> parseIntegerOp;

	@Override
	public Integer apply(String i1, String i2) {
		return parseIntegerOp.apply(i1) * parseIntegerOp.apply(i2);
	}
}

The benefit of that is that the factory method could also be used by ciients that don't want to use scijava-op's matching mechanism (given the method is public), simply by calling the method and manually providing a suitable Op as argument. In contrast, using the Op class at the bottom would require the use of reflection as there's no conventional access to the Op dependency field. Also, Op methods could be thought of as an additional layer on top of POJOs to make them searchable and matchable, while keeping the business logic of the Op unaware of scijava-op entirely:

// POJO, no dependencies on scijava-op. Required Op is injected via constructor.
public class MultiplyNumericStrings implements BiFunction<String, String, Integer> {

	private final Function<String, Integer> parseIntegerOp;

	public MultiplyNumericStrings(Function<String, Integer> parseIntegerOp) {
		this.parseIntegerOp = parseIntegerOp;
	}

	@Override
	public Integer apply(String i1, String i2) {
		return parseIntegerOp.apply(i1) * parseIntegerOp.apply(i2);
	}
}
// scijava-ops-specific layer on top
@Plugin(type = OpCollection.class)
public class MyOpCollection {

	@OpMethod(names = "test.multiplyNumericStrings")
	@Parameter(key = "numericString1")
	@Parameter(key = "numericString2")
	@Parameter(key = "multipliedNumericStrings", type = ItemIO.OUTPUT)
	@OpDependency(name = "test.parseInteger")
	public BiFunction<String, String, Integer> createMultiplyNumericStringsOp(
		final Function<String, Integer> parseIntegerOp)
	{
		return new MultiplyNumericStrings(parseIntegerOp);
	}
}

Splitting the declaration and implementation of an Op like this would even allow us to write the declaration in some other language/file format than Java, if this proves beneficial.

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MarcelWiedenmann

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MoltenVK is a Vulkan Portability implementation. It layers a subset of the high-performance, industry-standard Vulkan graphics and compute API over Apple's Metal graphics framework, enabling Vulkan applications to run on iOS and macOS.

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issue closedscijava/pom-scijava-base

Please release 11.3.0 so builds on JDKs >8 become easy

This release must include https://github.com/scijava/pom-scijava-base/commit/5c5e18df2666d9d1818199b45d520ae952cc092d

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axtimwalde

issue commentscijava/pom-scijava-base

Please release 11.3.0 so builds on JDKs >8 become easy

Closed in https://github.com/scijava/pom-scijava-base/releases/tag/pom-scijava-base-12.0.0

axtimwalde

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created tagscijava/pom-scijava-base

tagpom-scijava-base-12.0.0

Low-level base POM for all SciJava-based software

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Mark Hiner

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Bump to next development cycle Signed-off-by: Mark Hiner <hinerm@gmail.com>

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PR closed scijava/pom-scijava-base

Bump Kotlin to 1.4.10

This PR bumps Kotlin from 1.4-M2 to 1.4.10.

+1 -1

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skalarproduktraum

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pull request commentscijava/pom-scijava-base

Bump Kotlin to 1.4.10

Closing in favor of 9b27dd8dc4b5b56cb091129f01d50021eb416ab1

Note that scripting-kotlin is broken until the resolution of https://github.com/scijava/scripting-kotlin/pull/4

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Bump kotlin to 1.4.24

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delete branch scijava/pom-scijava-base

delete branch : openjdk-15

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Stephan Saalfeld

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enable build on OpenJDK-15 by bumping to maven-enforcer-plugin-3.0.0-M3 jacoco-maven-plugin-0.8.6

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Merge pull request #26 from scijava/openjdk-15 enable build on OpenJDK-15

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PR merged scijava/pom-scijava-base

enable build on OpenJDK-15 by bumping to

maven-enforcer-plugin-3.0.0-M3 jacoco-maven-plugin-0.8.6

+14 -3

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axtimwalde

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pull request commentscijava/pom-scijava-base

enable build on OpenJDK-15 by bumping to

@axtimwalde sorry Saalfeld. It took me a while to get comfortable with the melting pot, and it looks like ImageJ 1.53d blew up some API, so we are getting failures all over.

I'm currently melting vs. 1.53c and if that works I'm happy to merge this PR.

axtimwalde

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