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src/main/java/de/embl/cba/n5/ome/zarr/writers/imgplus/WriteImgPlusToN5BdvOmeZarr.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,136 @@ | ||
| package de.embl.cba.n5.ome.zarr.writers.imgplus; | ||
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| import bdv.export.ExportMipmapInfo; | ||
| import bdv.export.ProgressWriter; | ||
| import bdv.export.ProposeMipmaps; | ||
| import bdv.export.SubTaskProgressWriter; | ||
| import bdv.spimdata.SequenceDescriptionMinimal; | ||
| import bdv.spimdata.SpimDataMinimal; | ||
| import bdv.spimdata.XmlIoSpimDataMinimal; | ||
| import de.embl.cba.n5.ome.zarr.loaders.N5OMEZarrImageLoader; | ||
| import de.embl.cba.n5.util.DownsampleBlock; | ||
| import de.embl.cba.n5.util.ExportScalePyramid; | ||
| import de.embl.cba.n5.util.writers.WriteImgPlusToN5; | ||
| import de.embl.cba.n5.ome.zarr.readers.N5OmeZarrReader; | ||
| import ij.IJ; | ||
| import ij.ImagePlus; | ||
| import mpicbg.spim.data.SpimDataException; | ||
| import mpicbg.spim.data.generic.sequence.BasicViewSetup; | ||
| import mpicbg.spim.data.registration.ViewRegistration; | ||
| import mpicbg.spim.data.registration.ViewRegistrations; | ||
| import mpicbg.spim.data.sequence.FinalVoxelDimensions; | ||
| import net.imglib2.FinalDimensions; | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| import org.janelia.saalfeldlab.n5.Compression; | ||
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.Map; | ||
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| import static de.embl.cba.n5.util.writers.WriteImgPlusToN5Helper.*; | ||
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| public class WriteImgPlusToN5BdvOmeZarr extends WriteImgPlusToN5 { | ||
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| @Override | ||
| public void export(ImagePlus imp, int[][] resolutions, int[][] subdivisions, String xmlPath, | ||
| AffineTransform3D sourceTransform, DownsampleBlock.DownsamplingMethod downsamplingMethod, | ||
| Compression compression, String[] viewSetupNames) { | ||
| if (resolutions.length == 0) { | ||
| IJ.showMessage("Invalid resolutions - length 0"); | ||
| return; | ||
| } | ||
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| if (subdivisions.length == 0) { | ||
| IJ.showMessage(" Invalid subdivisions - length 0"); | ||
| return; | ||
| } | ||
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| if (resolutions.length != subdivisions.length) { | ||
| IJ.showMessage("Subsampling factors and chunk sizes must have the same number of elements"); | ||
| return; | ||
| } | ||
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| String seqFilename = xmlPath; | ||
| if (!seqFilename.endsWith(".xml")) | ||
| seqFilename += ".xml"; | ||
| final File seqFile = getSeqFileFromPath(seqFilename); | ||
| if (seqFile == null) { | ||
| return; | ||
| } | ||
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| final File zarrFile = getOmeZarrFileFromXmlPath(seqFilename); | ||
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| // TODO - check transform and downsampling mode | ||
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| Parameters exportParameters = new Parameters(resolutions, subdivisions, seqFile, zarrFile, sourceTransform, | ||
| downsamplingMethod, compression, viewSetupNames); | ||
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| export(imp, exportParameters); | ||
| } | ||
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| // TODO - split some of this into common functions | ||
| @Override | ||
| protected Parameters generateDefaultParameters(ImagePlus imp, String xmlPath, AffineTransform3D sourceTransform, | ||
| DownsampleBlock.DownsamplingMethod downsamplingMethod, Compression compression, | ||
| String[] viewSetupNames) { | ||
| FinalVoxelDimensions voxelSize = getVoxelSize(imp); | ||
| FinalDimensions size = getSize(imp); | ||
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| // propose reasonable mipmap settings | ||
| final int maxNumElements = 64 * 64 * 64; | ||
| final ExportMipmapInfo autoMipmapSettings = ProposeMipmaps.proposeMipmaps( | ||
| new BasicViewSetup(0, "", size, voxelSize), | ||
| maxNumElements); | ||
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| int[][] resolutions = autoMipmapSettings.getExportResolutions(); | ||
| int[][] subdivisions = autoMipmapSettings.getSubdivisions(); | ||
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| if (resolutions.length == 0 || subdivisions.length == 0 || resolutions.length != subdivisions.length) { | ||
| IJ.showMessage("Error with calculating default subdivisions and resolutions"); | ||
| return null; | ||
| } | ||
|
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| String seqFilename = xmlPath; | ||
| if (!seqFilename.endsWith(".xml")) | ||
| seqFilename += ".xml"; | ||
| final File seqFile = getSeqFileFromPath(seqFilename); | ||
| if (seqFile == null) { | ||
| return null; | ||
| } | ||
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| final File zarrFile = getOmeZarrFileFromXmlPath(seqFilename); | ||
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| return new Parameters(resolutions, subdivisions, seqFile, zarrFile, sourceTransform, | ||
| downsamplingMethod, compression, viewSetupNames); | ||
| } | ||
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| @Override | ||
| protected void writeFiles(SequenceDescriptionMinimal seq, Map<Integer, ExportMipmapInfo> perSetupExportMipmapInfo, | ||
| Parameters params, ExportScalePyramid.LoopbackHeuristic loopbackHeuristic, | ||
| ExportScalePyramid.AfterEachPlane afterEachPlane, int numCellCreatorThreads, | ||
| ProgressWriter progressWriter, int numTimepoints, int numSetups) throws IOException, SpimDataException { | ||
| WriteSequenceToN5OmeZarr.writeOmeZarrFile(seq, perSetupExportMipmapInfo, | ||
| params.downsamplingMethod, | ||
| params.compression, params.n5File, | ||
| loopbackHeuristic, afterEachPlane, numCellCreatorThreads, | ||
| new SubTaskProgressWriter(progressWriter, 0, 0.95)); | ||
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| // write xml sequence description | ||
| final N5OMEZarrImageLoader zarrLoader = new N5OMEZarrImageLoader( | ||
| new N5OmeZarrReader(params.n5File.getAbsolutePath()), seq); | ||
| final SequenceDescriptionMinimal seqh5 = new SequenceDescriptionMinimal(seq, zarrLoader); | ||
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| final ArrayList<ViewRegistration> registrations = new ArrayList<>(); | ||
| for (int t = 0; t < numTimepoints; ++t) | ||
| for (int s = 0; s < numSetups; ++s) | ||
| registrations.add(new ViewRegistration(t, s, params.sourceTransform)); | ||
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| final File basePath = params.seqFile.getParentFile(); | ||
| final SpimDataMinimal spimData = new SpimDataMinimal(basePath, seqh5, new ViewRegistrations(registrations)); | ||
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| new XmlIoSpimDataMinimal().save(spimData, params.seqFile.getAbsolutePath()); | ||
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| progressWriter.setProgress(1.0); | ||
| } | ||
| } |
130 changes: 130 additions & 0 deletions
130
src/main/java/de/embl/cba/n5/ome/zarr/writers/imgplus/WriteImgPlusToN5OmeZarr.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| package de.embl.cba.n5.ome.zarr.writers.imgplus; | ||
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| import bdv.export.ExportMipmapInfo; | ||
| import bdv.export.ProgressWriter; | ||
| import bdv.export.ProposeMipmaps; | ||
| import bdv.export.SubTaskProgressWriter; | ||
| import bdv.spimdata.SequenceDescriptionMinimal; | ||
| import de.embl.cba.n5.util.DownsampleBlock; | ||
| import de.embl.cba.n5.util.ExportScalePyramid; | ||
| import de.embl.cba.n5.util.writers.WriteImgPlusToN5; | ||
| import ij.IJ; | ||
| import ij.ImagePlus; | ||
| import mpicbg.spim.data.SpimDataException; | ||
| import mpicbg.spim.data.generic.sequence.BasicViewSetup; | ||
| import mpicbg.spim.data.sequence.FinalVoxelDimensions; | ||
| import net.imglib2.FinalDimensions; | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| import org.janelia.saalfeldlab.n5.Compression; | ||
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.Map; | ||
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| import static de.embl.cba.n5.util.writers.WriteImgPlusToN5Helper.getSize; | ||
| import static de.embl.cba.n5.util.writers.WriteImgPlusToN5Helper.getVoxelSize; | ||
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| public class WriteImgPlusToN5OmeZarr extends WriteImgPlusToN5 { | ||
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| // TODO - deal with transforms properly - is there somewhere in ome-zarr this can be written? | ||
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| // export, generating default source transform, and default resolutions / subdivisions | ||
| @Override | ||
| public void export( ImagePlus imp, String zarrPath, DownsampleBlock.DownsamplingMethod downsamplingMethod, | ||
| Compression compression ) { | ||
| super.export( imp, zarrPath, downsamplingMethod, compression ); | ||
| } | ||
|
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| // export, generating default resolutions / subdivisions | ||
| @Override | ||
| public void export(ImagePlus imp, String zarPath, AffineTransform3D sourceTransform, | ||
| DownsampleBlock.DownsamplingMethod downsamplingMethod, Compression compression ) { | ||
| super.export( imp, zarPath, sourceTransform, downsamplingMethod, compression ); | ||
| } | ||
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|
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| // export, generating default resolutions / subdivisions | ||
| @Override | ||
| public void export(ImagePlus imp, String zarrPath, AffineTransform3D sourceTransform, | ||
| DownsampleBlock.DownsamplingMethod downsamplingMethod, Compression compression, | ||
| String[] viewSetupNames ) { | ||
| super.export( imp, zarrPath, sourceTransform, downsamplingMethod, compression, viewSetupNames ); | ||
| } | ||
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| @Override | ||
| public void export( ImagePlus imp, int[][] resolutions, int[][] subdivisions, String zarrPath, | ||
| AffineTransform3D sourceTransform, DownsampleBlock.DownsamplingMethod downsamplingMethod, | ||
| Compression compression ) { | ||
| export( imp, resolutions, subdivisions, zarrPath, sourceTransform, downsamplingMethod, compression, null ); | ||
| } | ||
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| @Override | ||
| public void export( ImagePlus imp, int[][] resolutions, int[][] subdivisions, String zarrPath, | ||
| AffineTransform3D sourceTransform, DownsampleBlock.DownsamplingMethod downsamplingMethod, | ||
| Compression compression, String[] viewSetupNames ) { | ||
| if ( resolutions.length == 0 ) { | ||
| IJ.showMessage( "Invalid resolutions - length 0" ); | ||
| return; | ||
| } | ||
|
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| if ( subdivisions.length == 0 ) { | ||
| IJ.showMessage( " Invalid subdivisions - length 0" ); | ||
| return; | ||
| } | ||
|
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| if ( resolutions.length != subdivisions.length ) { | ||
| IJ.showMessage( "Subsampling factors and chunk sizes must have the same number of elements" ); | ||
| return; | ||
| } | ||
|
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| final File zarrFile = new File( zarrPath ); | ||
|
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| // TODO - check transform and downsampling mode | ||
|
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| Parameters exportParameters = new Parameters( resolutions, subdivisions, null, zarrFile, sourceTransform, | ||
| downsamplingMethod, compression, viewSetupNames ); | ||
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| export( imp, exportParameters ); | ||
| } | ||
|
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| @Override | ||
| protected Parameters generateDefaultParameters(ImagePlus imp, String zarrPath, AffineTransform3D sourceTransform, | ||
| DownsampleBlock.DownsamplingMethod downsamplingMethod, Compression compression, | ||
| String[] viewSetupNames ) { | ||
| FinalVoxelDimensions voxelSize = getVoxelSize( imp ); | ||
| FinalDimensions size = getSize( imp ); | ||
|
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| // propose reasonable mipmap settings | ||
| final int maxNumElements = 64 * 64 * 64; | ||
| final ExportMipmapInfo autoMipmapSettings = ProposeMipmaps.proposeMipmaps( | ||
| new BasicViewSetup(0, "", size, voxelSize), | ||
| maxNumElements); | ||
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| int[][] resolutions = autoMipmapSettings.getExportResolutions(); | ||
| int[][] subdivisions = autoMipmapSettings.getSubdivisions(); | ||
|
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| if ( resolutions.length == 0 || subdivisions.length == 0 || resolutions.length != subdivisions.length ) { | ||
| IJ.showMessage( "Error with calculating default subdivisions and resolutions"); | ||
| return null; | ||
| } | ||
|
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| final File zarrFile = new File( zarrPath ); | ||
|
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| return new Parameters( resolutions, subdivisions, null, zarrFile, sourceTransform, | ||
| downsamplingMethod, compression, viewSetupNames ); | ||
| } | ||
|
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| @Override | ||
| protected void writeFiles(SequenceDescriptionMinimal seq, Map<Integer, ExportMipmapInfo> perSetupExportMipmapInfo, | ||
| Parameters params, ExportScalePyramid.LoopbackHeuristic loopbackHeuristic, | ||
| ExportScalePyramid.AfterEachPlane afterEachPlane, int numCellCreatorThreads, | ||
| ProgressWriter progressWriter, int numTimepoints, int numSetups ) throws IOException, SpimDataException { | ||
| WriteSequenceToN5OmeZarr.writeOmeZarrFile( seq, perSetupExportMipmapInfo, | ||
| params.downsamplingMethod, | ||
| params.compression, params.n5File, | ||
| loopbackHeuristic, afterEachPlane, numCellCreatorThreads, | ||
| new SubTaskProgressWriter( progressWriter, 0, 0.95 ) ); | ||
|
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| progressWriter.setProgress( 1.0 ); | ||
| } | ||
| } |
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2 changes: 1 addition & 1 deletion
2
.../zarr/projectcreator/DownsampleBlock.java → .../de/embl/cba/n5/util/DownsampleBlock.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| package de.embl.cba.n5.ome.zarr.projectcreator; | ||
| package de.embl.cba.n5.util; | ||
|
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| /*- | ||
| * #%L | ||
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2 changes: 1 addition & 1 deletion
2
...rr/projectcreator/ExportScalePyramid.java → .../embl/cba/n5/util/ExportScalePyramid.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| package de.embl.cba.n5.ome.zarr.projectcreator; | ||
| package de.embl.cba.n5.util; | ||
|
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| /* | ||
| * #%L | ||
|
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