Migrate n5 4.0

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "startup-scripts/spark-janelia/flintstone"]
-	path = startup-scripts/spark-janelia/flintstone
-	url = https://github.com/saalfeldlab/flintstone.git
+[submodule "startup-scripts/spark-janelia"]
+	path = startup-scripts/spark-janelia
+	url = https://github.com/JaneliaSciComp/spark-janelia.git

.mvn/wrapper/maven-wrapper.properties

@@ -0,0 +1,3 @@
+wrapperVersion=3.3.4
+distributionType=only-script
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.12/apache-maven-3.9.12-bin.zip

examples/flintstone_janelia_to_paintera_lmt.sh

@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+# Convert a label dataset into a Paintera label-multiset source with a multiscale mipmap pyramid.
+INPUT_CONTAINER="${INPUT_CONTAINER:-sample.n5}"
+INPUT_DATASET="${INPUT_DATASET:-volumes/labels/s0}"
+OUTPUT_CONTAINER="${OUTPUT_CONTAINER:-paintera.n5}"
+OUTPUT_DATASET="${OUTPUT_DATASET:-volumes/labels}"
+
+./startup-scripts/flintstone-paintera-convert.sh 5 -- to-paintera \
+  --container="$INPUT_CONTAINER" \
+  -d "$INPUT_DATASET" \
+  --output-container="$OUTPUT_CONTAINER" \
+  --target-dataset="$OUTPUT_DATASET" \
+    --scale 2 2 2 2 \
+    --block-size=32  \
+    --type=label \
+    --dataset-resolution 18,18,24

examples/nD_to_paintera.sh

@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+# Reduce an nD input to a 3D Paintera source by slicing the non-spatial axes to fixed positions.
+INPUT_CONTAINER="${INPUT_CONTAINER:-sample.zarr}"
+INPUT_DATASET="${INPUT_DATASET:-volumes/raw}"
+OUTPUT_CONTAINER="${OUTPUT_CONTAINER:-paintera.n5}"
+OUTPUT_DATASET="${OUTPUT_DATASET:-volumes/raw}"
+
+paintera-convert to-paintera \
+  --output-container="$OUTPUT_CONTAINER" \
+  --scale 2,2,2 2,2,2 \
+  --block-size=64,64,64 \
+  --container="$INPUT_CONTAINER" \
+    -d "$INPUT_DATASET" \
+      --target-dataset="$OUTPUT_DATASET" \
+      --type=raw \
+      --slice-positions=x,y,z,0,10

examples/to_paintera_lmt.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+# Convert a label dataset into a Paintera label-multiset source with a multiscale mipmap pyramid.
+INPUT_CONTAINER="${INPUT_CONTAINER:-sample.n5}"
+INPUT_DATASET="${INPUT_DATASET:-volumes/labels/s0}"
+OUTPUT_CONTAINER="${OUTPUT_CONTAINER:-paintera.n5}"
+OUTPUT_DATASET="${OUTPUT_DATASET:-volumes/labels}"
+
+paintera-convert to-paintera \
+  --output-container="$OUTPUT_CONTAINER" \
+  --scale 2,2,2 2,2,2 2,2,2 \
+  --block-size=64,64,64 \
+  --container="$INPUT_CONTAINER" \
+    -d "$INPUT_DATASET" \
+      --target-dataset="$OUTPUT_DATASET" \
+      --type=label

examples/to_paintera_winner_takes_all.sh

@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+# Convert a label dataset into a scalar Paintera source using winner-takes-all downsampling.
+INPUT_CONTAINER="${INPUT_CONTAINER:-sample.n5}"
+INPUT_DATASET="${INPUT_DATASET:-volumes/labels/s0}"
+OUTPUT_CONTAINER="${OUTPUT_CONTAINER:-paintera.n5}"
+OUTPUT_DATASET="${OUTPUT_DATASET:-volumes/labels}"
+
+paintera-convert to-paintera \
+  --output-container="$OUTPUT_CONTAINER" \
+  --scale 2,2,2 2,2,2 2,2,2 \
+  --block-size=64,64,64 \
+  --winner-takes-all-downsampling \
+  --container="$INPUT_CONTAINER" \
+    -d "$INPUT_DATASET" \
+      --target-dataset="$OUTPUT_DATASET" \
+      --type=label

examples/to_scalar_multiscale.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+# Extract a Paintera label source into a multiscale uint64 scalar dataset with a downsampling pyramid.
+INPUT_CONTAINER="${INPUT_CONTAINER:-paintera.n5}"
+INPUT_DATASET="${INPUT_DATASET:-volumes/labels}"
+OUTPUT_CONTAINER="${OUTPUT_CONTAINER:-scalar.n5}"
+OUTPUT_DATASET="${OUTPUT_DATASET:-volumes/labels}"
+
+paintera-convert to-scalar \
+  -i "$INPUT_CONTAINER" \
+  -I "$INPUT_DATASET" \
+  -o "$OUTPUT_CONTAINER" \
+  -O "$OUTPUT_DATASET" \
+  --consider-fragment-segment-assignment \
+  --scale 2,2,2 2,2,2 \
+  --block-size=64,64,64 \
+  --resolution=4,4,40 \
+  --xyz-unit=nm

examples/to_scalar_sharded.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+# Extract a Paintera label source into a sharded Zarr3 uint64 scalar dataset with OME-Zarr metadata.
+INPUT_CONTAINER="${INPUT_CONTAINER:-paintera.n5}"
+INPUT_DATASET="${INPUT_DATASET:-volumes/labels}"
+OUTPUT_CONTAINER="${OUTPUT_CONTAINER:-scalar.zarr}"
+OUTPUT_DATASET="${OUTPUT_DATASET:-volumes/labels}"
+
+paintera-convert to-scalar \
+  -i "$INPUT_CONTAINER" \
+  -I "$INPUT_DATASET" \
+  -o "$OUTPUT_CONTAINER" \
+  -O "$OUTPUT_DATASET" \
+  --output-format=ZARR3 \
+  --scale 2,2,2 2,2,2 \
+  --block-size=64,64,64 \
+  --chunks-per-shard=4,4,4 \
+  --resolution=4,4,40 \
+  --xyz-unit=nm