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First working version of the CZ CryoET Data Portal demo #548
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2b3cd59
First working version of the CZ CryoET Data Portal demo
kephale 71dc201
Remove some residual code
kephale 09c5531
Create a CellImg instead of ArrayImg
kephale cb9cce2
WIP: OpenOrganelle demo
kephale edb128c
Merge remote-tracking branch 'origin/main' into cryoet-zarr
kephale 12ef7ac
Merge branch 'main' into cryoet-zarr
kephale dbf1a6f
Merge remote-tracking branch 'origin/main' into cryoet-zarr
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156 changes: 156 additions & 0 deletions
156
src/main/kotlin/sc/iview/commands/demo/advanced/LoadCryoETDataPortal.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,156 @@ | ||
| /*- | ||
| * #%L | ||
| * Scenery-backed 3D visualization package for ImageJ. | ||
| * %% | ||
| * Copyright (C) 2016 - 2024 sciview developers. | ||
| * %% | ||
| * 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 HOLDERS 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. | ||
| * #L% | ||
| */ | ||
| package sc.iview.commands.demo.advanced | ||
|
|
||
| import graphics.scenery.Origin | ||
| import graphics.scenery.volumes.Colormap | ||
| import net.imagej.lut.LUTService | ||
| import net.imagej.ops.OpService | ||
| import net.imglib2.FinalInterval | ||
| import net.imglib2.RandomAccessibleInterval | ||
| import net.imglib2.img.Img | ||
| import net.imglib2.img.array.ArrayImgs | ||
| import net.imglib2.img.cell.CellImgFactory | ||
| import net.imglib2.loops.LoopBuilder | ||
| import net.imglib2.type.numeric.ARGBType | ||
| import net.imglib2.type.numeric.integer.UnsignedByteType | ||
| import net.imglib2.type.numeric.real.FloatType | ||
| import net.imglib2.view.Views | ||
| import org.embl.mobie.io.ome.zarr.openers.OMEZarrS3Opener | ||
| import org.joml.Vector3f | ||
| import org.joml.Vector4f | ||
| import org.scijava.command.Command | ||
| import org.scijava.command.CommandService | ||
| import org.scijava.log.LogService | ||
| import org.scijava.plugin.Menu | ||
| import org.scijava.plugin.Parameter | ||
| import org.scijava.plugin.Plugin | ||
| import org.scijava.ui.UIService | ||
| import sc.iview.SciView | ||
| import sc.iview.commands.MenuWeights | ||
|
|
||
| @Plugin(type = Command::class, | ||
| label = "Load CryoET Data Portal demo", | ||
| menuRoot = "SciView", | ||
| menu = [Menu(label = "Demo", weight = MenuWeights.DEMO), | ||
| Menu(label = "Advanced", weight = MenuWeights.DEMO_ADVANCED), | ||
| Menu(label = "Load CryoET Data Portal demo", weight = MenuWeights.DEMO_ADVANCED_CREMI)]) | ||
| class LoadCryoETDataPortal : Command { | ||
| @Parameter | ||
| private lateinit var log: LogService | ||
|
|
||
| @Parameter | ||
| private lateinit var sciview: SciView | ||
|
|
||
| @Parameter | ||
| private lateinit var lut: LUTService | ||
|
|
||
| private var zarrPath = "https://files.cryoetdataportal.cziscience.com/10000/TS_043/Tomograms/VoxelSpacing13.480/CanonicalTomogram/TS_043.zarr" | ||
|
|
||
| /** | ||
| * When an object implementing interface `Runnable` is used | ||
| * to create a thread, starting the thread causes the object's | ||
| * `run` method to be called in that separately executing | ||
| * thread. | ||
| * | ||
| * | ||
| * The general contract of the method `run` is that it may | ||
| * take any action whatsoever. | ||
| * | ||
| * @see Thread.run | ||
| */ | ||
|
|
||
| override fun run() { | ||
| val task = sciview.taskManager.newTask("CryoETDataPortal", "Loading dataset") | ||
|
|
||
| task.status = "Reading dataset" | ||
| val spimData = OMEZarrS3Opener.readURL(zarrPath) | ||
| val setupId = 0 | ||
| val timepointId = 0 | ||
| val rawRaiVolume = ( | ||
| spimData.getSequenceDescription() | ||
| .getImgLoader() | ||
| .getSetupImgLoader(setupId) | ||
| .getImage(timepointId) | ||
| ) as RandomAccessibleInterval<FloatType> | ||
|
|
||
| // Calculate half of the z-dimension | ||
| val halfZ = rawRaiVolume.dimension(2) / 2 | ||
|
|
||
| // Define the interval for half of the z-axis | ||
| val minInterval = longArrayOf(0, 0, 0) | ||
| val maxInterval = longArrayOf(rawRaiVolume.dimension(0) - 1, rawRaiVolume.dimension(1) - 1, halfZ) | ||
| val halfZInterval = FinalInterval(minInterval, maxInterval) | ||
|
|
||
| // Create a view over half of the z-axis | ||
| val halfZView = Views.interval(rawRaiVolume, halfZInterval) | ||
|
|
||
| // Create a CellImgFactory for UnsignedByteType with a specified cell size | ||
| val cellSize = 64 | ||
| val factory = CellImgFactory<UnsignedByteType>(UnsignedByteType(), cellSize, cellSize, cellSize) | ||
|
|
||
| // Create an empty RandomAccessibleInterval of UnsignedByteType with half z-dimension using the factory | ||
| val halfDimensions = longArrayOf(rawRaiVolume.dimension(0), rawRaiVolume.dimension(1), halfZ + 1) | ||
| val halfRaiVolume: Img<UnsignedByteType> = factory.create(*halfDimensions) | ||
|
|
||
|
|
||
| // Copy and convert the data from the view into the new RAI | ||
| LoopBuilder.setImages(halfZView as RandomAccessibleInterval<FloatType>, halfRaiVolume).forEachPixel { input, output -> | ||
| output.setInteger(((input.get() + 26f) / 60 * 255.0).toInt().coerceIn(0, 255)) | ||
| } | ||
|
|
||
|
|
||
| val colormapVolume = lut.loadLUT(lut.findLUTs().get("Grays.lut")) | ||
|
|
||
| val v = sciview.addVolume(halfRaiVolume, "CryoET Data Portal") { | ||
| origin = Origin.FrontBottomLeft | ||
| this.spatialOrNull()?.scale = Vector3f(1f, 1f, 1f) | ||
| // transferFunction = TransferFunction.ramp(0.3f, 0.1f, 0.1f) | ||
| // min 20, max 180, color map fire | ||
|
|
||
| // transferFunction.addControlPoint(0.3f, 0.5f) | ||
| // transferFunction.addControlPoint(0.8f, 0.01f) | ||
| converterSetups.get(0).setDisplayRange(0.0, 255.0) | ||
| colormap = Colormap.fromColorTable(colormapVolume) | ||
| } | ||
|
|
||
| task.completion = 100.0f | ||
| } | ||
|
|
||
| companion object { | ||
| @Throws(Exception::class) | ||
| @JvmStatic | ||
| fun main(args: Array<String>) { | ||
| val sv = SciView.create() | ||
| val command = sv.scijavaContext!!.getService(CommandService::class.java) | ||
| val argmap = HashMap<String, Any>() | ||
| command.run(LoadCryoETDataPortal::class.java, true, argmap) | ||
| } | ||
| } | ||
| } |
123 changes: 123 additions & 0 deletions
123
src/main/kotlin/sc/iview/commands/demo/advanced/LoadOpenOrganelle.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| /*- | ||
| * #%L | ||
| * Scenery-backed 3D visualization package for ImageJ. | ||
| * %% | ||
| * Copyright (C) 2016 - 2024 sciview developers. | ||
| * %% | ||
| * 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 HOLDERS 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. | ||
| * #L% | ||
| */ | ||
| package sc.iview.commands.demo.advanced | ||
|
|
||
| import bdv.util.volatiles.VolatileViews | ||
| import graphics.scenery.Origin | ||
| import graphics.scenery.volumes.Colormap | ||
| import graphics.scenery.volumes.Volume | ||
| import net.imagej.lut.LUTService | ||
| import net.imagej.ops.OpService | ||
| import net.imglib2.FinalInterval | ||
| import net.imglib2.Interval | ||
| import net.imglib2.RandomAccessibleInterval | ||
| import net.imglib2.converter.Converters | ||
| import net.imglib2.img.Img | ||
| import net.imglib2.img.array.ArrayImgs | ||
| import net.imglib2.img.cell.CellImgFactory | ||
| import net.imglib2.loops.LoopBuilder | ||
| import net.imglib2.type.numeric.ARGBType | ||
| import net.imglib2.type.numeric.integer.UnsignedByteType | ||
| import net.imglib2.type.numeric.real.FloatType | ||
| import net.imglib2.type.volatiles.VolatileUnsignedByteType | ||
| import net.imglib2.view.Views | ||
| import org.embl.mobie.io.ome.zarr.openers.OMEZarrS3Opener | ||
| import org.joml.Vector3f | ||
| import org.joml.Vector4f | ||
| import org.scijava.command.Command | ||
| import org.scijava.command.CommandService | ||
| import org.scijava.log.LogService | ||
| import org.scijava.plugin.Menu | ||
| import org.scijava.plugin.Parameter | ||
| import org.scijava.plugin.Plugin | ||
| import org.scijava.ui.UIService | ||
| import sc.iview.SciView | ||
| import sc.iview.commands.MenuWeights | ||
| import net.imglib2.converter.Converter | ||
| import net.imglib2.type.numeric.integer.UnsignedIntType | ||
| import net.imglib2.type.numeric.integer.UnsignedShortType | ||
| import net.imglib2.type.volatiles.VolatileUnsignedIntType | ||
| import net.imglib2.type.volatiles.VolatileUnsignedShortType | ||
| import org.embl.mobie.io.openorganelle.OpenOrganelleS3Opener | ||
|
|
||
| @Plugin(type = Command::class, | ||
| label = "Load Open Organelle demo", | ||
| menuRoot = "SciView", | ||
| menu = [Menu(label = "Demo", weight = MenuWeights.DEMO), | ||
| Menu(label = "Advanced", weight = MenuWeights.DEMO_ADVANCED), | ||
| Menu(label = "Load Open Organelle demo", weight = MenuWeights.DEMO_ADVANCED_CREMI)]) | ||
| class LoadOpenOrganelle : Command { | ||
| @Parameter | ||
| private lateinit var log: LogService | ||
|
|
||
| @Parameter | ||
| private lateinit var sciview: SciView | ||
|
|
||
| @Parameter | ||
| private lateinit var lut: LUTService | ||
|
|
||
| override fun run() { | ||
| val reader = OMEZarrS3Opener( | ||
| "https://janelia-cosem.s3.amazonaws.com", | ||
| "us-west-2", | ||
| "jrc_hela-2") | ||
| OpenOrganelleS3Opener.setLogging(true) | ||
| val image = reader.readKey("jrc_hela-2.n5/em/fibsem-uint16") | ||
|
|
||
| // Assume the data is of UnsignedIntType | ||
| // | ||
| val rai = image.getSequenceDescription().getImgLoader() | ||
|
|
||
| //val colormapVolume = lut.loadLUT(lut.findLUTs().get("Grays.lut")) | ||
|
|
||
| // Wrap the RandomAccessibleInterval with VolatileViews for tiled rendering | ||
| //val volatileRai = VolatileViews.wrapAsVolatile(rai) as RandomAccessibleInterval<VolatileUnsignedShortType> | ||
|
|
||
| // Create and configure the volume | ||
| // val volume = Volume.fromRAI( | ||
| // rai, | ||
| // VolatileUnsignedShortType(), | ||
| // name = "My image", | ||
| // hub = sciview.hub | ||
| // ) | ||
|
|
||
| // sciview.addNode(volume) | ||
| } | ||
|
|
||
| companion object { | ||
| @Throws(Exception::class) | ||
| @JvmStatic | ||
| fun main(args: Array<String>) { | ||
| val sv = SciView.create() | ||
| val command = sv.scijavaContext!!.getService(CommandService::class.java) | ||
| val argmap = HashMap<String, Any>() | ||
| command.run(LoadOpenOrganelle::class.java, true, argmap) | ||
| } | ||
| } | ||
| } |
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@ctrueden, noting the mobio-io dependency