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Merged
ctrueden merged 4 commits into from
Jan 22, 2025
Merged

Remove geom3D Ops in favor of imglib2-mesh usage #267

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ee80dba
Update to ImgLib2 v7 + geom3D Ops to imglib2-mesh
hinerm Jun 4, 2024
a708ff0
Update docs
gselzer Aug 19, 2024
603226c
MeshFeatureTests.assertTriangleEquality: javadoc
gselzer Jan 16, 2025
06074da
Bump scijava-ops-image version
gselzer Jan 16, 2025
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4 changes: 2 additions & 2 deletions docs/ops/doc/examples/mesh_viz.rst
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Expand Up @@ -61,13 +61,13 @@ The following script accepts the binary dataset as its sole input, and creates t
mesh = ops.op("geom.marchingCubes").input(mask).apply()
println("mesh = ${mesh} [${mesh.triangles().size()} triangles, ${mesh.vertices().size()} vertices]")

meshVolume = ops.op("geom.size").input(mesh).apply().getRealDouble()
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@gselzer gselzer Jan 15, 2025

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@elevans @ctrueden let's debate whether this causes a breakage in backwards compatibility. On one hand, this line of code will no longer work unless we write a wrapper in this repo around it (and the whole point of this PR is to get rid of those), which would lead to it being a breaking change. This is pretty convincing for me, but playing devil's advocate, the apply() will return you an Object, and so you are violating the return type contract i.e. on paper we didn't do anything wrong.

I still lead towards this being a breaking change that requires a major version bump, though.

meshVolume = ops.op("geom.size").input(mesh).apply()
println("mesh volume = " + meshVolume)

hull = ops.op("geom.convexHull").input(mesh).apply()
println("hull = ${hull} [${hull.triangles().size()} triangles, ${hull.vertices().size()} vertices]")

hullVolume = ops.op("geom.size").input(hull).apply().getRealDouble()
hullVolume = ops.op("geom.size").input(hull).apply()
println("hull volume = $hullVolume")

// Convert ImgLib2 meshes to 3D Viewer meshes.
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2 changes: 1 addition & 1 deletion docs/ops/doc/examples/scyjava.rst
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Expand Up @@ -121,7 +121,7 @@ Activate the ``scijava-ops`` conda/mamba environment and run the following Pytho
"""
mesh = ops.op("geom.marchingCubes").input(rai).apply()
# Mesh volume returned in voxels
volume = ops.op("geom.size").input(mesh).apply().getRealDouble()
volume = ops.op("geom.size").input(mesh).apply()

# Convert voxels to um^3
for c in cal:
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4 changes: 2 additions & 2 deletions docs/ops/doc/examples/volume_labeling.rst
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Expand Up @@ -273,7 +273,7 @@ In addition to the result tables, the label imdage (also known as an *index imag
ab_table.appendRow()
# measure mesh/sample geometry and stats
ab_table.set("{} size (pixels)".format(ch_a_name), i, ops.op("stats.size").input(sample).apply())
ab_table.set("{} volume (um^3)".format(ch_a_name), i, ops.op("geom.size").input(mesh).apply().getRealFloat() * (x_cal * y_cal * z_cal))
ab_table.set("{} volume (um^3)".format(ch_a_name), i, ops.op("geom.size").input(mesh).apply() * (x_cal * y_cal * z_cal))
ab_table.set("{} sphericity".format(ch_a_name), i, ops.op("geom.sphericity").input(mesh).apply())
i += 1
# create a table for the "B" mask and make measurements
Expand All @@ -296,7 +296,7 @@ In addition to the result tables, the label imdage (also known as an *index imag
b_table.appendRow()
# measure mesh/sample geometry and stats
b_table.set("{} size (pixels)".format(ch_b_name), j, ops.op("stats.size").input(sample).apply())
b_table.set("{} volume (um^3)".format(ch_b_name), j, ops.op("geom.size").input(mesh).apply().getRealFloat() * (x_cal * y_cal * z_cal))
b_table.set("{} volume (um^3)".format(ch_b_name), j, ops.op("geom.size").input(mesh).apply() * (x_cal * y_cal * z_cal))
b_table.set("{} sphericity".format(ch_b_name), j, ops.op("geom.sphericity").input(mesh).apply())
j += 1

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8 changes: 6 additions & 2 deletions scijava-discovery-test/pom.xml
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Expand Up @@ -103,14 +103,18 @@
-->
<scijava.jvm.build.version>[11.0.17,)</scijava.jvm.build.version>
<scijava.jvm.version>11</scijava.jvm.version>

<!-- TEMP: Can be removed once present in pom-scijava -->
<scijava-discovery.version>1.0.1-SNAPSHOT</scijava-discovery.version>
<scijava-ops-spi.version>1.0.1-SNAPSHOT</scijava-ops-spi.version>
</properties>

<dependencies>
<!-- SciJava dependencies -->
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-ops-spi</artifactId>
<version>${project.version}</version>
<version>${scijava-ops-spi.version}</version>
</dependency>

<!-- Test scope dependencies -->
Expand All @@ -122,7 +126,7 @@
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-discovery</artifactId>
<version>${project.version}</version>
<version>${scijava-discovery.version}</version>
</dependency>
</dependencies>

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61 changes: 17 additions & 44 deletions scijava-legacy/pom.xml
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Expand Up @@ -98,34 +98,44 @@
-->
<scijava.jvm.build.version>[11.0.17,)</scijava.jvm.build.version>
<scijava.jvm.version>11</scijava.jvm.version>

<!-- TEMP: Can be removed once present in pom-scijava -->
<scijava-common3.version>1.0.1-SNAPSHOT</scijava-common3.version>
<scijava-discovery.version>1.0.1-SNAPSHOT</scijava-discovery.version>
<scijava-ops-api.version>1.0.1-SNAPSHOT</scijava-ops-api.version>
<scijava-ops-engine.version>1.0.1-SNAPSHOT</scijava-ops-engine.version>
<scijava-ops-spi.version>1.0.1-SNAPSHOT</scijava-ops-spi.version>
<scijava-priority.version>1.0.1-SNAPSHOT</scijava-priority.version>
<scijava-progress.version>1.0.1-SNAPSHOT</scijava-progress.version>
<scijava-types.version>1.0.1-SNAPSHOT</scijava-types.version>
</properties>

<dependencies>
<!-- SciJava dependencies -->
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-discovery</artifactId>
<version>${project.version}</version>
<version>${scijava-discovery.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-ops-api</artifactId>
<version>${project.version}</version>
<version>${scijava-ops-api.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-priority</artifactId>
<version>${project.version}</version>
<version>${scijava-priority.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-progress</artifactId>
<version>${project.version}</version>
<version>${scijava-progress.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-types</artifactId>
<version>${project.version}</version>
<version>${scijava-types.version}</version>
</dependency>

<!-- ImgLib2 dependencies -->
Expand Down Expand Up @@ -153,7 +163,7 @@
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-common3</artifactId>
<version>${project.version}</version>
<version>${scijava-common3.version}</version>
<!--
NB: Scope is compile because it is a transitive compile-time dependency,
and overriding it to test scope here would cause the main build to fail
Expand All @@ -163,7 +173,7 @@
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-ops-engine</artifactId>
<version>${project.version}</version>
<version>${scijava-ops-engine.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
Expand All @@ -181,49 +191,12 @@
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<annotationProcessorPaths>
<path>
<groupId>org.scijava</groupId>
<artifactId>scijava-ops-indexer</artifactId>
<version>${project.version}</version>
</path>
<path>
<groupId>org.scijava</groupId>
<artifactId>scijava-common</artifactId>
<version>${scijava-common.version}</version>
</path>
</annotationProcessorPaths>
<fork>true</fork>
<compilerArgs>
<arg>-Ascijava.ops.parse="${scijava.ops.parse}"</arg>
<arg>-Ascijava.ops.opVersion="${project.version}"</arg>
</compilerArgs>
</configuration>
</plugin>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<configuration>
<links>
<link>https://javadoc.scijava.org/Java11/</link>
<link>https://javadoc.scijava.org/ImageJ2/</link>
<link>https://javadoc.scijava.org/ImgLib2/</link>
<link>https://javadoc.scijava.org/SciJava/</link>
<link>https://javadoc.scijava.org/Guava/</link>
<link>https://javadoc.scijava.org/JAMA/</link>
</links>
<tagletArtifacts>
<tagletArtifact>
<groupId>org.scijava</groupId>
<artifactId>scijava-taglets</artifactId>
<version>${project.version}</version>
</tagletArtifact>
</tagletArtifacts>
<tags>
<tag>
<name>implNote</name>
<placement>a</placement>
<head>Implementation Note:</head>
</tag>
</tags>
</configuration>
</plugin>
<plugin>
Expand Down
21 changes: 15 additions & 6 deletions scijava-ops-api/pom.xml
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Expand Up @@ -108,39 +108,48 @@
-->
<scijava.jvm.build.version>[11.0.17,)</scijava.jvm.build.version>
<scijava.jvm.version>11</scijava.jvm.version>

<!-- TEMP: Can be removed once present in pom-scijava -->
<scijava-common3.version>1.0.1-SNAPSHOT</scijava-common3.version>
<scijava-discovery.version>1.0.1-SNAPSHOT</scijava-discovery.version>
<scijava-function.version>1.0.1-SNAPSHOT</scijava-function.version>
<scijava-priority.version>1.0.1-SNAPSHOT</scijava-priority.version>
<scijava-struct.version>1.0.1-SNAPSHOT</scijava-struct.version>
<scijava-types.version>1.0.1-SNAPSHOT</scijava-types.version>

</properties>

<dependencies>
<!-- SciJava dependencies -->
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-common3</artifactId>
<version>${project.version}</version>
<version>${scijava-common3.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-discovery</artifactId>
<version>${project.version}</version>
<version>${scijava-discovery.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-function</artifactId>
<version>${project.version}</version>
<version>${scijava-function.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-priority</artifactId>
<version>${project.version}</version>
<version>${scijava-priority.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-struct</artifactId>
<version>${project.version}</version>
<version>${scijava-struct.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-types</artifactId>
<version>${project.version}</version>
<version>${scijava-types.version}</version>
</dependency>
</dependencies>

Expand Down
44 changes: 30 additions & 14 deletions scijava-ops-engine/pom.xml
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Expand Up @@ -130,6 +130,22 @@
org.scijava.ops.engine" to unnamed module @402e37bc
-->
<scijava.surefire.args>--add-exports org.scijava.ops.engine/org.scijava.ops.engine=ALL-UNNAMED</scijava.surefire.args>

<!-- TEMP: Can be removed once present in pom-scijava -->
<scijava-collections.version>1.0.1-SNAPSHOT</scijava-collections.version>
<scijava-common3.version>1.0.1-SNAPSHOT</scijava-common3.version>
<scijava-discovery.version>1.0.1-SNAPSHOT</scijava-discovery.version>
<scijava-function.version>1.0.1-SNAPSHOT</scijava-function.version>
<scijava-indexer.version>1.0.1-SNAPSHOT</scijava-indexer.version>
<scijava-meta.version>1.0.1-SNAPSHOT</scijava-meta.version>
<scijava-ops-api.version>1.0.1-SNAPSHOT</scijava-ops-api.version>
<scijava-ops-spi.version>1.0.1-SNAPSHOT</scijava-ops-spi.version>
<scijava-priority.version>1.0.1-SNAPSHOT</scijava-priority.version>
<scijava-progress.version>1.0.1-SNAPSHOT</scijava-progress.version>
<scijava-struct.version>1.0.1-SNAPSHOT</scijava-struct.version>
<scijava-taglets.version>1.0.1-SNAPSHOT</scijava-taglets.version>
<scijava-testutil.version>1.0.1-SNAPSHOT</scijava-testutil.version>
<scijava-types.version>1.0.1-SNAPSHOT</scijava-types.version>
</properties>

<dependencies>
Expand All @@ -141,57 +157,57 @@
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-collections</artifactId>
<version>${project.version}</version>
<version>${scijava-collections.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-common3</artifactId>
<version>${project.version}</version>
<version>${scijava-common3.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-meta</artifactId>
<version>${project.version}</version>
<version>${scijava-meta.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-ops-api</artifactId>
<version>${project.version}</version>
<version>${scijava-ops-api.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-ops-spi</artifactId>
<version>${project.version}</version>
<version>${scijava-ops-spi.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-discovery</artifactId>
<version>${project.version}</version>
<version>${scijava-discovery.version}</version>
</dependency>
<dependency>
<groupId> org.scijava</groupId>
<artifactId>scijava-function</artifactId>
<version>${project.version}</version>
<version>${scijava-function.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-priority</artifactId>
<version>${project.version}</version>
<version>${scijava-priority.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-progress</artifactId>
<version>${project.version}</version>
<version>${scijava-progress.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-struct</artifactId>
<version>${project.version}</version>
<version>${scijava-struct.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-types</artifactId>
<version>${project.version}</version>
<version>${scijava-types.version}</version>
</dependency>

<!-- Third-party dependencies -->
Expand Down Expand Up @@ -221,7 +237,7 @@
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-testutil</artifactId>
<version>${project.version}</version>
<version>${scijava-testutil.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
Expand All @@ -235,7 +251,7 @@
<path>
<groupId>org.scijava</groupId>
<artifactId>scijava-ops-indexer</artifactId>
<version>${project.version}</version>
<version>${scijava-indexer.version}</version>
</path>
</annotationProcessorPaths>
<fork>true</fork>
Expand All @@ -259,7 +275,7 @@
<tagletArtifact>
<groupId>org.scijava</groupId>
<artifactId>scijava-taglets</artifactId>
<version>${project.version}</version>
<version>${scijava-taglets.version}</version>
</tagletArtifact>
</tagletArtifacts>
<tags>
Expand Down
7 changes: 3 additions & 4 deletions scijava-ops-engine/src/it/test-ops-api/pom.xml
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Expand Up @@ -31,9 +31,9 @@

<parent>
<groupId>org.scijava</groupId>
<artifactId>scijava-parent</artifactId>
<version>0-SNAPSHOT</version>
<relativePath>../../../..</relativePath>
<artifactId>pom-scijava</artifactId>
<version>39.0.0</version>
<relativePath />
</parent>

<groupId>@project.groupId@</groupId>
Expand Down Expand Up @@ -118,7 +118,6 @@
<enforcer.skip>true</enforcer.skip>
</properties>


<dependencies>
<dependency>
<groupId>org.scijava</groupId>
Expand Down
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