diff --git a/pom.xml b/pom.xml index 19d6933..4018202 100644 --- a/pom.xml +++ b/pom.xml @@ -98,6 +98,8 @@ gpl_v3 BigDataViewer developers. + 10.4.14 + sign,deploy-to-scijava diff --git a/src/main/java/bdv/ij/CreateXmlForImarisPlugIn.java b/src/main/java/bdv/ij/CreateXmlForImarisPlugIn.java new file mode 100644 index 0000000..aea4626 --- /dev/null +++ b/src/main/java/bdv/ij/CreateXmlForImarisPlugIn.java @@ -0,0 +1,171 @@ +/*- + * #%L + * Fiji plugins for starting BigDataViewer and exporting data. + * %% + * Copyright (C) 2014 - 2023 BigDataViewer developers. + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ +package bdv.ij; + +import java.awt.FileDialog; +import java.awt.Frame; +import java.io.File; +import java.io.FilenameFilter; +import java.io.IOException; +import java.util.concurrent.atomic.AtomicBoolean; + +import javax.swing.JFileChooser; +import javax.swing.filechooser.FileFilter; + +import org.scijava.command.Command; +import org.scijava.plugin.Plugin; + +import bdv.BigDataViewer; +import bdv.ij.util.ProgressWriterIJ; +import bdv.img.imaris.Imaris; +import bdv.spimdata.SpimDataMinimal; +import bdv.spimdata.XmlIoSpimDataMinimal; +import bdv.viewer.ViewerOptions; +import ij.IJ; +import ij.ImageJ; +import ij.Prefs; +import mpicbg.spim.data.SpimDataException; + +@Plugin(type = Command.class, + menuPath = "Plugins>BigDataViewer>Create XML for Imaris file") +public class CreateXmlForImarisPlugIn implements Command +{ + static String lastDatasetPath = ""; + + public static void main( final String[] args ) + { + ImageJ.main( args ); + new CreateXmlForImarisPlugIn().run(); + } + @Override + public void run() + { + if ( Prefs.setIJMenuBar ) + System.setProperty( "apple.laf.useScreenMenuBar", "true" ); + + File file = null; + + if ( Prefs.useJFileChooser ) + { + final JFileChooser fileChooser = new JFileChooser(); + fileChooser.setSelectedFile( new File( lastDatasetPath ) ); + fileChooser.setFileFilter( new FileFilter() + { + @Override + public String getDescription() + { + return "ims files"; + } + + @Override + public boolean accept( final File f ) + { + if ( f.isDirectory() ) + return true; + if ( f.isFile() ) + { + final String s = f.getName(); + final int i = s.lastIndexOf('.'); + if (i > 0 && i < s.length() - 1) { + final String ext = s.substring(i+1).toLowerCase(); + return ext.equals( "ims" ); + } + } + return false; + } + } ); + + final int returnVal = fileChooser.showOpenDialog( null ); + if ( returnVal == JFileChooser.APPROVE_OPTION ) + file = fileChooser.getSelectedFile(); + } + else // use FileDialog + { + final FileDialog fd = new FileDialog( ( Frame ) null, "Open", FileDialog.LOAD ); + fd.setDirectory( new File( lastDatasetPath ).getParent() ); + fd.setFile( new File( lastDatasetPath ).getName() ); + final AtomicBoolean workedWithFilenameFilter = new AtomicBoolean( false ); + fd.setFilenameFilter( new FilenameFilter() + { + private boolean firstTime = true; + + @Override + public boolean accept( final File dir, final String name ) + { + if ( firstTime ) + { + workedWithFilenameFilter.set( true ); + firstTime = false; + } + + final int i = name.lastIndexOf( '.' ); + if ( i > 0 && i < name.length() - 1 ) + { + final String ext = name.substring( i + 1 ).toLowerCase(); + return ext.equals( "ims" ); + } + return false; + } + } ); + fd.setVisible( true ); + if ( !workedWithFilenameFilter.get() ) + { + fd.setFilenameFilter( null ); + fd.setVisible( true ); + } + final String filename = fd.getFile(); + if ( filename != null ) + { + file = new File( fd.getDirectory() + filename ); + } + } + + if ( file != null ) + { + try + { + final String imsFilename = file.getAbsolutePath(); + lastDatasetPath = imsFilename; + final SpimDataMinimal spimData = Imaris.openIms( imsFilename ); + final String xmlFilename = xmlFilename( imsFilename ); + new XmlIoSpimDataMinimal().save( spimData, xmlFilename ); + IJ.showMessage( "created " + xmlFilename ); + } + catch ( final IOException | SpimDataException e ) + { + throw new RuntimeException( e ); + } + } + } + + private static String xmlFilename( String s ) + { + String f = s.endsWith( ".ims" ) ? s.substring( 0, s.length() - 4 ) : s; + if ( !new File( f + ".xml" ).exists() ) + return f + ".xml"; + + int i = 2; + while ( new File( f + i + ".xml" ).exists() ) + ++i; + return f + i + ".xml"; + } +} diff --git a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java index 69c56fc..a100e5d 100644 --- a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java +++ b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java @@ -55,6 +55,9 @@ import bdv.spimdata.SequenceDescriptionMinimal; import bdv.spimdata.SpimDataMinimal; import bdv.spimdata.XmlIoSpimDataMinimal; +import bdv.img.imagestack.ImageStackImageLoader; +import bdv.img.n5.N5ImageLoader; +import bdv.img.virtualstack.VirtualStackImageLoader; import fiji.util.gui.GenericDialogPlus; import ij.IJ; import ij.ImageJ; @@ -63,6 +66,7 @@ import ij.gui.DialogListener; import ij.gui.GenericDialog; import mpicbg.spim.data.generic.sequence.BasicViewSetup; +import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader; import mpicbg.spim.data.registration.ViewRegistration; import mpicbg.spim.data.registration.ViewRegistrations; import mpicbg.spim.data.sequence.Channel; @@ -139,19 +143,44 @@ public void run() progressWriter.out().println( "starting export..." ); // create ImgLoader wrapping the image - final ImagePlusImgLoader< ? > imgLoader; - switch ( imp.getType() ) + final TypedBasicImgLoader< ? > imgLoader; + final Runnable clearCache; + final boolean isVirtual = imp.getStack() != null && imp.getStack().isVirtual(); + if ( isVirtual ) { - case ImagePlus.GRAY8: - imgLoader = ImagePlusImgLoader.createGray8( imp, params.minMaxOption, params.rangeMin, params.rangeMax ); - break; - case ImagePlus.GRAY16: - imgLoader = ImagePlusImgLoader.createGray16( imp, params.minMaxOption, params.rangeMin, params.rangeMax ); - break; - case ImagePlus.GRAY32: - default: - imgLoader = ImagePlusImgLoader.createGray32( imp, params.minMaxOption, params.rangeMin, params.rangeMax ); - break; + final VirtualStackImageLoader< ?, ?, ? > il; + switch ( imp.getType() ) + { + case ImagePlus.GRAY8: + il = VirtualStackImageLoader.createUnsignedByteInstance( imp ); + break; + case ImagePlus.GRAY16: + il = VirtualStackImageLoader.createUnsignedShortInstance( imp ); + break; + case ImagePlus.GRAY32: + default: + il = VirtualStackImageLoader.createFloatInstance( imp ); + break; + } + imgLoader = il; + clearCache = il.getCacheControl()::clearCache; + } + else + { + switch ( imp.getType() ) + { + case ImagePlus.GRAY8: + imgLoader = ImageStackImageLoader.createUnsignedByteInstance( imp ); + break; + case ImagePlus.GRAY16: + imgLoader = ImageStackImageLoader.createUnsignedShortInstance( imp ); + break; + case ImagePlus.GRAY32: + default: + imgLoader = ImageStackImageLoader.createFloatInstance( imp ); + break; + } + clearCache = () -> {}; } final int numTimepoints = imp.getNFrames(); @@ -174,8 +203,7 @@ public void run() timepoints.add( new TimePoint( t ) ); final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, imgLoader, null ); - Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo; - perSetupExportMipmapInfo = new HashMap<>(); + final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = new HashMap<>(); final ExportMipmapInfo mipmapInfo = params.setMipmapManual ? new ExportMipmapInfo( params.resolutions, params.subdivisions ) : autoMipmapSettings; @@ -189,7 +217,6 @@ public void run() // required for all original planes contributing to a "plane of // blocks" at the current level. If this is more than 1/4 of // available memory, use the loopback image. - final boolean isVirtual = imp.getStack().isVirtual(); final long planeSizeInBytes = imp.getWidth() * imp.getHeight() * imp.getBytesPerPixel(); final long ijMaxMemory = IJ.maxMemory(); final int numCellCreatorThreads = Math.max( 1, PluginHelper.numThreads() - 1 ); @@ -228,7 +255,7 @@ public void afterEachPlane( final boolean usedLoopBack ) final long actuallyFree = max - total + free; if ( actuallyFree < max / 2 ) - imgLoader.clearCache(); + clearCache.run(); } } @@ -291,12 +318,6 @@ protected static class Parameters final File hdf5File; - final MinMaxOption minMaxOption; - - final double rangeMin; - - final double rangeMax; - final boolean deflate; final boolean split; @@ -308,7 +329,7 @@ protected static class Parameters public Parameters( final boolean setMipmapManual, final int[][] resolutions, final int[][] subdivisions, final File seqFile, final File hdf5File, - final MinMaxOption minMaxOption, final double rangeMin, final double rangeMax, final boolean deflate, + final boolean deflate, final boolean split, final int timepointsPerPartition, final int setupsPerPartition ) { this.setMipmapManual = setMipmapManual; @@ -316,9 +337,6 @@ public Parameters( this.subdivisions = subdivisions; this.seqFile = seqFile; this.hdf5File = hdf5File; - this.minMaxOption = minMaxOption; - this.rangeMin = rangeMin; - this.rangeMax = rangeMax; this.deflate = deflate; this.split = split; this.timepointsPerPartition = timepointsPerPartition; @@ -332,12 +350,6 @@ public Parameters( static String lastChunkSizes = "{32,32,4}, {16,16,8}, {8,8,8}"; - static int lastMinMaxChoice = 2; - - static double lastMin = 0; - - static double lastMax = 65535; - static boolean lastSplit = false; static int lastTimepointsPerPartition = 0; @@ -350,12 +362,6 @@ public Parameters( protected Parameters getParameters( final double impMin, final double impMax, final ExportMipmapInfo autoMipmapSettings ) { - if ( lastMinMaxChoice == 0 ) // use ImageJs... - { - lastMin = impMin; - lastMax = impMax; - } - while ( true ) { final GenericDialogPlus gd = new GenericDialogPlus( "Export for BigDataViewer" ); @@ -367,15 +373,6 @@ protected Parameters getParameters( final double impMin, final double impMax, fi gd.addStringField( "Hdf5_chunk_sizes", lastChunkSizes, 25 ); final TextField tfChunkSizes = ( TextField ) gd.getStringFields().lastElement(); - gd.addMessage( "" ); - final String[] minMaxChoices = new String[] { "Use ImageJ's current min/max setting", "Compute min/max of the (hyper-)stack", "Use values specified below" }; - gd.addChoice( "Value_range", minMaxChoices, minMaxChoices[ lastMinMaxChoice ] ); - final Choice cMinMaxChoices = (Choice) gd.getChoices().lastElement(); - gd.addNumericField( "Min", lastMin, 0 ); - final TextField tfMin = (TextField) gd.getNumericFields().lastElement(); - gd.addNumericField( "Max", lastMax, 0 ); - final TextField tfMax = (TextField) gd.getNumericFields().lastElement(); - gd.addMessage( "" ); gd.addCheckbox( "split_hdf5", lastSplit ); final Checkbox cSplit = ( Checkbox ) gd.getCheckboxes().lastElement(); @@ -390,59 +387,37 @@ protected Parameters getParameters( final double impMin, final double impMax, fi gd.addMessage( "" ); PluginHelper.addSaveAsFileField( gd, "Export_path", lastExportPath, 25 ); -// gd.addMessage( "" ); -// gd.addMessage( "This Plugin is developed by Tobias Pietzsch (pietzsch@mpi-cbg.de)\n" ); -// Bead_Registration.addHyperLinkListener( ( MultiLineLabel ) gd.getMessage(), "mailto:pietzsch@mpi-cbg.de" ); - final String autoSubsampling = ProposeMipmaps.getArrayString( autoMipmapSettings.getExportResolutions() ); final String autoChunkSizes = ProposeMipmaps.getArrayString( autoMipmapSettings.getSubdivisions() ); - gd.addDialogListener( new DialogListener() - { - @Override - public boolean dialogItemChanged( final GenericDialog dialog, final AWTEvent e ) + gd.addDialogListener( ( dialog, e ) -> { + gd.getNextBoolean(); + gd.getNextString(); + gd.getNextString(); + gd.getNextBoolean(); + gd.getNextNumber(); + gd.getNextNumber(); + gd.getNextBoolean(); + gd.getNextString(); + if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cManualMipmap ) { - gd.getNextBoolean(); - gd.getNextString(); - gd.getNextString(); - gd.getNextChoiceIndex(); - gd.getNextNumber(); - gd.getNextNumber(); - gd.getNextBoolean(); - gd.getNextNumber(); - gd.getNextNumber(); - gd.getNextBoolean(); - gd.getNextString(); - if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cMinMaxChoices ) + final boolean useManual = cManualMipmap.getState(); + tfSubsampling.setEnabled( useManual ); + tfChunkSizes.setEnabled( useManual ); + if ( !useManual ) { - final boolean enable = cMinMaxChoices.getSelectedIndex() == 2; - tfMin.setEnabled( enable ); - tfMax.setEnabled( enable ); + tfSubsampling.setText( autoSubsampling ); + tfChunkSizes.setText( autoChunkSizes ); } - else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cManualMipmap ) - { - final boolean useManual = cManualMipmap.getState(); - tfSubsampling.setEnabled( useManual ); - tfChunkSizes.setEnabled( useManual ); - if ( !useManual ) - { - tfSubsampling.setText( autoSubsampling ); - tfChunkSizes.setText( autoChunkSizes ); - } - } - else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cSplit ) - { - final boolean split = cSplit.getState(); - tfSplitTimepoints.setEnabled( split ); - tfSplitSetups.setEnabled( split ); - } - return true; } + else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cSplit ) + { + final boolean split = cSplit.getState(); + tfSplitTimepoints.setEnabled( split ); + tfSplitSetups.setEnabled( split ); + } + return true; } ); - final boolean enable = lastMinMaxChoice == 2; - tfMin.setEnabled( enable ); - tfMax.setEnabled( enable ); - tfSubsampling.setEnabled( lastSetMipmapManual ); tfChunkSizes.setEnabled( lastSetMipmapManual ); if ( !lastSetMipmapManual ) @@ -461,9 +436,6 @@ else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && lastSetMipmapManual = gd.getNextBoolean(); lastSubsampling = gd.getNextString(); lastChunkSizes = gd.getNextString(); - lastMinMaxChoice = gd.getNextChoiceIndex(); - lastMin = gd.getNextNumber(); - lastMax = gd.getNextNumber(); lastSplit = gd.getNextBoolean(); lastTimepointsPerPartition = ( int ) gd.getNextNumber(); lastSetupsPerPartition = ( int ) gd.getNextNumber(); @@ -489,14 +461,6 @@ else if ( resolutions.length != subdivisions.length ) continue; } - final MinMaxOption minMaxOption; - if ( lastMinMaxChoice == 0 ) - minMaxOption = MinMaxOption.TAKE_FROM_IMAGEPROCESSOR; - else if ( lastMinMaxChoice == 1 ) - minMaxOption = MinMaxOption.COMPUTE; - else - minMaxOption = MinMaxOption.SET; - String seqFilename = lastExportPath; if ( !seqFilename.endsWith( ".xml" ) ) seqFilename += ".xml"; @@ -510,6 +474,7 @@ else if ( lastMinMaxChoice == 1 ) final String hdf5Filename = seqFilename.substring( 0, seqFilename.length() - 4 ) + ".h5"; final File hdf5File = new File( hdf5Filename ); - return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, hdf5File, minMaxOption, lastMin, lastMax, lastDeflate, lastSplit, lastTimepointsPerPartition, lastSetupsPerPartition ); } + return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, hdf5File, lastDeflate, lastSplit, lastTimepointsPerPartition, lastSetupsPerPartition ); + } } } diff --git a/src/main/java/bdv/ij/OpenImarisPlugIn.java b/src/main/java/bdv/ij/OpenImarisPlugIn.java index 32cbfeb..ebaf600 100644 --- a/src/main/java/bdv/ij/OpenImarisPlugIn.java +++ b/src/main/java/bdv/ij/OpenImarisPlugIn.java @@ -43,7 +43,7 @@ import ij.Prefs; @Plugin(type = Command.class, - menuPath = "Plugins>BigDataViewer>Open Imaris (experimental)") + menuPath = "Plugins>BigDataViewer>Open Imaris") public class OpenImarisPlugIn implements Command { static String lastDatasetPath = ""; diff --git a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java index 667555d..32dcd5a 100644 --- a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java +++ b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java @@ -57,6 +57,7 @@ * * @author Tobias Pietzsch <tobias.pietzsch@gmail.com> */ +@Deprecated public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgLoader< T > { public static enum MinMaxOption