Initialize scijava-ops-flim

This new repository contains a port of the flimj-ops library: https://github.com/flimlib/flimj-ops/

pom.xml

@@ -54,6 +54,7 @@
 		<module>scijava-meta</module>
 		<module>scijava-ops-api</module>
 		<module>scijava-ops-engine</module>
+		<module>scijava-ops-flim</module>
 		<module>scijava-ops-image</module>
 		<module>scijava-ops-legacy</module>
 		<module>scijava-ops-indexer</module>

scijava-ops-engine/src/main/java/module-info.java

@@ -532,6 +532,7 @@
 		org.scijava.ops.engine.adapt.functional.InplacesToFunctions.Inplace16_14ToFunction16,
 		org.scijava.ops.engine.adapt.functional.InplacesToFunctions.Inplace16_15ToFunction16,
 		org.scijava.ops.engine.adapt.functional.InplacesToFunctions.Inplace16_16ToFunction16,
+		org.scijava.ops.engine.conversionLoss.impl.IdentityLossReporter,
 		org.scijava.ops.engine.eval.DefaultEval,
 		org.scijava.ops.engine.stats.Mean.MeanFunction;
 

scijava-ops-engine/src/main/java/org/scijava/ops/engine/matcher/convert/ConvertedOpInfo.java

@@ -461,8 +461,9 @@ private double calculatePriority(OpEnvironment env) {
 		List<Type> originalInputs = info.inputTypes();
 		List<Type> inputs = inputTypes();
 		for (int i = 0; i < inputs.size(); i++) {
-			penalty += determineLoss(env, Nil.of(inputs.get(i)), Nil.of(originalInputs
-				.get(i)));
+			var from = inputs.get(i);
+			var to = Types.mapVarToTypes(originalInputs.get(i), typeVarAssigns);
+			penalty += determineLoss(env, Nil.of(from), Nil.of(to));
 		}
 
 		Type opOutput = info.outputType();

scijava-ops-engine/src/main/resources/META-INF/services/org.scijava.ops.spi.Op

@@ -234,5 +234,6 @@ org.scijava.ops.engine.adapt.functional.InplacesToFunctions$Inplace16_13ToFuncti
 org.scijava.ops.engine.adapt.functional.InplacesToFunctions$Inplace16_14ToFunction16
 org.scijava.ops.engine.adapt.functional.InplacesToFunctions$Inplace16_15ToFunction16
 org.scijava.ops.engine.adapt.functional.InplacesToFunctions$Inplace16_16ToFunction16
+org.scijava.ops.engine.conversionLoss.impl.IdentityLossReporter
 org.scijava.ops.engine.eval.DefaultEval
 org.scijava.ops.engine.stats.Mean$MeanFunction

scijava-ops-engine/src/test/java/org/scijava/ops/engine/impl/ServiceLoaderDiscoveryIntegrationTest.java

@@ -47,14 +47,14 @@ public class ServiceLoaderDiscoveryIntegrationTest {
 	public void opDiscoveryRegressionIT() {
 		final Discoverer d = Discoverer.using(ServiceLoader::load);
 		final List<Op> discoveries = d.discover(Op.class);
-		Assertions.assertEquals(236, discoveries.size());
+		Assertions.assertEquals(237, discoveries.size());
 
 		@SuppressWarnings("unused")
 		final OpInfoGenerator g = new OpClassOpInfoGenerator();
 		final List<OpInfo> infos = discoveries.stream() //
 			.flatMap(c -> g.generateInfosFrom(c).stream()) //
 			.collect(Collectors.toList());
-		Assertions.assertEquals(236, infos.size());
+		Assertions.assertEquals(237, infos.size());
 	}
 
 	@Test

scijava-ops-engine/templates/main/java/module-info.vm

@@ -157,6 +157,7 @@ module org.scijava.ops.engine {
 		org.scijava.ops.engine.adapt.functional.InplacesToFunctions.Inplace${arity}_${a}ToFunction${arity},
 #end
 #end
+		org.scijava.ops.engine.conversionLoss.impl.IdentityLossReporter,
 		org.scijava.ops.engine.eval.DefaultEval,
 		org.scijava.ops.engine.stats.Mean.MeanFunction;
 

scijava-ops-flim/LICENSE.txt

@@ -0,0 +1,24 @@
+Copyright (c) 2023, ImageJ2 developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

scijava-ops-flim/README.md

@@ -0,0 +1,12 @@
+# SciJava Ops Flim: A fluorescence lifetime analysis library for SciJava Ops.
+
+This library provides a bridge between SciJava Ops and Flim.
+For Maven projects, this library can be used by adding to your `pom.xml`:
+
+```java
+<dependency>
+	<groupId>org.scijava</groupId>
+	<artifactId>scijava-ops-flim</artifactId>
+	<version>0-SNAPSHOT</version>
+</dependency>
+```

scijava-ops-flim/environment.yml

@@ -0,0 +1,8 @@
+name: scijava
+channels:
+  - conda-forge
+dependencies:
+  - beakerx
+  - jupyter_contrib_nbextensions
+  - numpy
+  - openjdk=11