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Initialize scijava-ops-flim
This new repository contains a port of the flimj-ops library: https://github.com/flimlib/flimj-ops/
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‎pom.xml‎

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<module>scijava-meta</module>
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<module>scijava-ops-api</module>
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<module>scijava-ops-engine</module>
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<module>scijava-ops-flim</module>
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<module>scijava-ops-image</module>
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<module>scijava-ops-legacy</module>
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<module>scijava-ops-indexer</module>

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

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org.scijava.ops.engine.adapt.functional.InplacesToFunctions.Inplace16_14ToFunction16,
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org.scijava.ops.engine.adapt.functional.InplacesToFunctions.Inplace16_15ToFunction16,
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org.scijava.ops.engine.adapt.functional.InplacesToFunctions.Inplace16_16ToFunction16,
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org.scijava.ops.engine.conversionLoss.impl.IdentityLossReporter,
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org.scijava.ops.engine.eval.DefaultEval,
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org.scijava.ops.engine.stats.Mean.MeanFunction;
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‎scijava-ops-engine/src/main/java/org/scijava/ops/engine/matcher/convert/ConvertedOpInfo.java‎

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

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

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org.scijava.ops.engine.adapt.functional.InplacesToFunctions$Inplace16_14ToFunction16
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org.scijava.ops.engine.adapt.functional.InplacesToFunctions$Inplace16_15ToFunction16
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org.scijava.ops.engine.adapt.functional.InplacesToFunctions$Inplace16_16ToFunction16
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org.scijava.ops.engine.conversionLoss.impl.IdentityLossReporter
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org.scijava.ops.engine.eval.DefaultEval
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org.scijava.ops.engine.stats.Mean$MeanFunction

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

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

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

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org.scijava.ops.engine.adapt.functional.InplacesToFunctions.Inplace${arity}_${a}ToFunction${arity},
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#end
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#end
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org.scijava.ops.engine.conversionLoss.impl.IdentityLossReporter,
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org.scijava.ops.engine.eval.DefaultEval,
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org.scijava.ops.engine.stats.Mean.MeanFunction;
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‎scijava-ops-flim/LICENSE.txt‎

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Copyright (c) 2024, SciJava developers.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without modification,
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are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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POSSIBILITY OF SUCH DAMAGE.

‎scijava-ops-flim/README.md‎

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# SciJava Ops FLIM: A fluorescence lifetime analysis library for SciJava Ops.
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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.
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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.
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# Example usage
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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:
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```groovy
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#@ UIService ui
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#@ OpEnvironment op
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#@ ImgPlus img
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// set up parameters
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import org.scijava.ops.flim.FitParams
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param = new FitParams()
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param.transMap = img; // input 3-dimensional (x, y, t) dataset
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param.xInc= 0.040 // time difference between bins (ns)
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param.ltAxis = 2 // time bins lay along axis #2
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// op call
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fittedImg = op.unary("flim.fitLMA").input(param).apply().paramMap
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// display each parameter
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zImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 0L).apply()
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AImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 1L).apply()
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tauImg = op.ternary("transform.hyperSliceView").input(fittedImg, param.ltAxis, 2L).apply()
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ui.show("z", zImg)
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ui.show("A", AImg)
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ui.show("tau", tauImg)
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```
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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).
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(z in [-1, 1], A in [0, 4], tau in[0, 3]):
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![example output](images/example%20z.png)![example output](images/example%20A.png)![example output](images/example%20tau.png)
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See more examples in [Demo.ipynb](notebooks/Demo.ipynb) and [groovy.md](groovy.md).
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# Using from a Java project
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To depend on SciJava Ops FLIM, copy the following to your `pom.xml`:
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```xml
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<properties>
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<scijava-ops-flim.version>0-SNAPSHOT</scijava-ops-flim.version>
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</properties>
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<dependencies>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-ops-flim</artifactId>
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<version>${scijava-ops-flim.version}</version>
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</dependency>
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</dependencies>
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```
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# See also
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- [FLIMLib](https://github.com/flimlib/flimlib): Curve fitting library for FLIM
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- [Debug tutorial](https://github.com/flimlib/flimlib/wiki/Debugging)
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- [FLIMJ Ops](https://github.com/flimlib/flimj-ops): ImageJ Ops for accessing FLIM
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# Citation
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Coming soon...

‎scijava-ops-flim/environment.yml‎

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name: scijava
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channels:
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- conda-forge
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dependencies:
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- beakerx
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- jupyter_contrib_nbextensions
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- numpy
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- openjdk=11

‎scijava-ops-flim/images/example A.png‎

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