Skip to content

Use Therapi Discovery in ImageJ Ops2 #49

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ctrueden merged 3 commits into from
Jun 30, 2022
Merged

Use Therapi Discovery in ImageJ Ops2 #49

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
fc18204
Convert ImageJ Ops2 to Therapi
gselzer Nov 12, 2021
3593d4d
Convert OpCollections to Therapi Discovery
gselzer Nov 12, 2021
8a62ad7
Clean up imports
gselzer Nov 15, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
1 change: 1 addition & 0 deletions imagej/imagej-ops2/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -219,6 +219,7 @@

<!-- NB: Deploy releases to the ImageJ Maven repository. -->
<releaseProfiles>deploy-to-imagej</releaseProfiles>
<therapi.packages></therapi.packages>
</properties>

<build>
Expand Down
227 changes: 114 additions & 113 deletions imagej/imagej-ops2/src/main/java/module-info.java
View file
Open in desktop

Large diffs are not rendered by default.

8 changes: 4 additions & 4 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,7 @@

import org.scijava.function.Computers;
import org.scijava.function.Functions;
import org.scijava.ops.spi.Op;
import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;

/**
* This algorithm calculates Li et al.'s ICQ (intensity correlation quotient).
Expand All @@ -49,8 +47,8 @@
* Type of the first image
* @param <U>
* Type of the second image
*@implNote op names='coloc.icq'
*/
@Plugin(type = Op.class, name = "coloc.icq")
public class LiICQ<T extends RealType<T>, U extends RealType<U>, V extends RealType<V>>
implements Functions.Arity4<Iterable<T>, Iterable<U>, DoubleType, DoubleType, Double> {

Expand Down Expand Up @@ -121,7 +119,9 @@ private double computeMeanUOf(final Iterable<U> in) {

}

@Plugin(type = Op.class, name = "coloc.icq")
/**
*@implNote op names='coloc.icq'
*/
class LiICQSimple<T extends RealType<T>, U extends RealType<U>, V extends RealType<V>>
implements BiFunction<Iterable<T>, Iterable<U>, Double> {

Expand Down
5 changes: 1 addition & 4 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,6 @@
import net.imglib2.util.IterablePair;
import net.imglib2.util.Pair;

import org.scijava.ops.spi.Op;
import org.scijava.plugin.Plugin;

/**
* This algorithm calculates Kendall's Tau-b rank correlation coefficient
* <p>
Expand Down Expand Up @@ -72,8 +69,8 @@
* @author Johannes Schindelin
* @author Ellen T Arena
* @param <T>
*@implNote op names='coloc.kendallTau'
*/
@Plugin(type = Op.class, name = "coloc.kendallTau")
public class KendallTauBRank<T extends RealType<T>, U extends RealType<U>>
/* extends Algorithm<T> */ implements BiFunction<Iterable<T>, Iterable<U>, Double> {

Expand Down
8 changes: 4 additions & 4 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,9 +49,7 @@

import org.scijava.function.Computers;
import org.scijava.function.Functions;
import org.scijava.ops.spi.Op;
import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
import org.scijava.util.IntArray;

/**
Expand All @@ -64,8 +62,8 @@
* @author Ellen T Arena
* @author Shulei Wang
* @author Curtis Rueden
*@implNote op names='coloc.maxTKendallTau'
*/
@Plugin(type = Op.class, name = "coloc.maxTKendallTau")
public class MTKT<T extends RealType<T>, U extends RealType<U>>
implements Functions.Arity3<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Long, Double>
{
Expand Down Expand Up @@ -249,7 +247,9 @@ static double calculateKendallTau(final double[][] rank,

}

@Plugin(type = Op.class, name = "coloc.maxTKendallTau")
/**
*@implNote op names='coloc.maxTKendallTau'
*/
class MTKTSimple<T extends RealType<T>, U extends RealType<U>>
implements BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>
{
Expand Down
12 changes: 7 additions & 5 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,18 +48,16 @@
import net.imglib2.view.Views;

import org.scijava.function.Computers;
import org.scijava.ops.spi.Op;
import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;

/**
* This algorithm repeatedly executes a colocalization algorithm, computing a
* p-value. It is based on a new statistical framework published by Wang et al
* (2017) IEEE Signal Processing "Automated and Robust Quantification of
* Colocalization in Dual-Color Fluorescence Microscopy: A Nonparametric
* Statistical Approach".
*@implNote op names='coloc.pValue'
*/
@Plugin(type = Op.class, name = "coloc.pValue")
public class DefaultPValue<T extends RealType<T>, U extends RealType<U>> implements
Computers.Arity7<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, Dimensions, Long, ExecutorService, PValueResult> {

Expand Down Expand Up @@ -192,7 +190,9 @@ private static <V> RandomAccessibleInterval<V> trim(final RandomAccessibleInterv
}
}

@Plugin(type = Op.class, name = "coloc.pValue")
/**
*@implNote op names='coloc.pValue'
*/
class PValueSimpleWithRandomizations<T extends RealType<T>, U extends RealType<U>> implements
Computers.Arity5<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, ExecutorService, PValueResult> {

Expand All @@ -219,7 +219,9 @@ public void compute(RandomAccessibleInterval<T> in1, RandomAccessibleInterval<U>

}

@Plugin(type = Op.class, name = "coloc.pValue")
/**
*@implNote op names='coloc.pValue'
*/
class PValueSimple<T extends RealType<T>, U extends RealType<U>> implements
Computers.Arity4<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, ExecutorService, PValueResult> {

Expand Down
5 changes: 1 addition & 4 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,16 +35,13 @@
import net.imglib2.util.IterablePair;
import net.imglib2.util.Pair;

import org.scijava.ops.spi.Op;
import org.scijava.plugin.Plugin;

/**
* A class that represents the mean calculation of the two source images in the
* data container. It implements the FAST calculation for Pearson's Correlation.
*
* @author Ellen T Arena
*@implNote op names='coloc.pearsons'
*/
@Plugin(type = Op.class, name = "coloc.pearsons")
public class DefaultPearsons<T extends RealType<T>, U extends RealType<U>> implements
BiFunction<Iterable<T>, Iterable<U>, Double>
{
Expand Down
Loading