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) 2024, SciJava 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 +1,70 @@
+# SciJava Ops FLIM: A fluorescence lifetime analysis library for SciJava Ops.
+
+SciJava Ops FLIM is a collection of FLIM analysis ops based on [FLIMLib](https://github.com/flimlib/flimlib). It extends the single-transient fitting functions in FLIMLib to dataset-level fitting ops. Currently supported fitting ops include: RLD, MLA, Global, Phasor, and single-component Bayesian.
+
+Besides curve fitting, SciJava Ops FLIM also provides a variety of pre-processing options such as pixel binning, intensity thresholding, ROI masking as well as post-processing utility ops for e.g. calculating τ<sub>m</sub> (mean lifetime), A<sub>i</sub>% (fractional contribution) and pseudocoloring the result with LUT.
+
+# Example usage
+Open [test2.sdt](test_files/test2.sdt) in [Fiji](https://fiji.github.io/). Execute in [Script Editor](http://imagej.github.io/Using_the_Script_Editor) as Groovy:
+
+```groovy
+#@ UIService ui
+#@ OpEnvironment op
+#@ ImgPlus img
+
+// set up parameters
+import org.scijava.ops.flim.FitParams
+
+param = new FitParams()
+param.transMap = img; // input 3-dimensional (x, y, t) dataset
+param.xInc= 0.040     // time difference between bins (ns)
+param.ltAxis = 2      // time bins lay along axis #2
+
+// op call
+fittedImg = op.unary("flim.fitLMA").input(param).apply().paramMap
+
+// display each parameter
+zImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 0L).apply()
+AImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 1L).apply()
+tauImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 2L).apply()
+
+ui.show("z", zImg)
+ui.show("A", AImg)
+ui.show("tau", tauImg)
+```
+
+After running this script, the output shown below can be seen by first running the script, and then brightness and contrast (Ctrl + Shift + C, select "Set" and bound the contrast to each image's corresponding range below).
+
+(z in [-1, 1], A in [0, 4], tau in[0, 3]):
+
+![example output](images/example%20z.png)![example output](images/example%20A.png)![example output](images/example%20tau.png)
+
+See more examples in [Demo.ipynb](notebooks/Demo.ipynb) and [groovy.md](groovy.md).
+
+# Using from a Java project
+
+To depend on SciJava Ops FLIM, copy the following to your `pom.xml`:
+
+```xml
+  <properties>
+    <scijava-ops-flim.version>0-SNAPSHOT</scijava-ops-flim.version>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>org.scijava</groupId>
+      <artifactId>scijava-ops-flim</artifactId>
+      <version>${scijava-ops-flim.version}</version>
+    </dependency>
+  </dependencies>
+```
+
+# See also
+
+- [FLIMLib](https://github.com/flimlib/flimlib): Curve fitting library for FLIM
+    - [Debug tutorial](https://github.com/flimlib/flimlib/wiki/Debugging)
+- [FLIMJ Ops](https://github.com/flimlib/flimj-ops): ImageJ Ops for accessing FLIM
+
+# Citation
+
+Comming soon...

scijava-ops-flim/environment.yml

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