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Commit 560cc858 authored by Stephan Preibisch's avatar Stephan Preibisch
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Removed resave plugin. It lives now in 

https://github.com/fiji/spimreconstruction/blob/revised-spimdata/src/main/java/spim/fiji/plugin/resave/Generic_Resave_HDF5.java
parent 5122cea2
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fiji/src/main/java/bdv/ij/ResavePlugin.java deleted 100644 → 0
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package bdv.ij;
import fiji.util.gui.GenericDialogPlus;
import ij.IJ;
import ij.gui.DialogListener;
import ij.gui.GenericDialog;
import ij.plugin.PlugIn;
import java.awt.AWTEvent;
import java.awt.Checkbox;
import java.awt.TextField;
import java.awt.event.ItemEvent;
import java.io.File;
import java.util.Map;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileFilter;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.ImgLoader;
import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
import bdv.export.SubTaskProgressWriter;
import bdv.export.WriteSequenceToHdf5;
import bdv.ij.util.PluginHelper;
import bdv.ij.util.ProgressWriterIJ;
import bdv.img.hdf5.Hdf5ImageLoader;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
public class ResavePlugin implements PlugIn
{
public static void main( final String[] args )
{
new ResavePlugin().run( null );
}
public static class Parameters
{
boolean setMipmapManual;
int[][] resolutions;
int[][] subdivisions;
File seqFile;
File hdf5File;
public Parameters( final boolean setMipmapManual, final int[][] resolutions, final int[][] subdivisions, final File seqFile, final File hdf5File )
{
this.setMipmapManual = setMipmapManual;
this.resolutions = resolutions;
this.subdivisions = subdivisions;
this.seqFile = seqFile;
this.hdf5File = hdf5File;
}
public void setSeqFile( final File seqFile ) { this.seqFile = seqFile; }
public void setHDF5File( final File hdf5File ) { this.hdf5File = hdf5File; }
public void setResolutions( final int[][] resolutions ) { this.resolutions = resolutions; }
public void setSubdivisions( final int[][] subdivisions ) { this.subdivisions = subdivisions; }
public void setMipmapManual( final boolean setMipmapManual ) { this.setMipmapManual = setMipmapManual; }
public File getSeqFile() { return seqFile; }
public File getHDF5File() { return hdf5File; }
public int[][] getResolutions() { return resolutions; }
public int[][] getSubdivisions() { return subdivisions; }
public boolean getMipmapManual() { return setMipmapManual; }
}
@Override
public void run( final String arg )
{
final File file = getInputXML();
if ( file == null )
return;
final XmlIoSpimDataMinimal io = new XmlIoSpimDataMinimal();
SpimDataMinimal spimData;
try
{
spimData = io.load( file.getAbsolutePath() );
}
catch ( final SpimDataException e )
{
throw new RuntimeException( e );
}
final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = ProposeMipmaps.proposeMipmaps( spimData.getSequenceDescription() );
final Parameters params = getParameters( perSetupExportMipmapInfo.get( 0 ), true );
if ( params == null )
return;
final ProgressWriter progressWriter = new ProgressWriterIJ();
progressWriter.out().println( "starting export..." );
// write hdf5
writeHDF5( spimData.getSequenceDescription(), params, perSetupExportMipmapInfo, progressWriter );
// write xml sequence description
writeXML( spimData, io, params.seqFile, params.hdf5File, progressWriter );
}
public static void writeHDF5( final AbstractSequenceDescription< ?, ?, ? > seq, final Parameters params, final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo, final ProgressWriter progressWriter )
{
final boolean setMipmapManual = params.setMipmapManual;
final int[][] manualResolutions = params.resolutions;
final int[][] manualSubdivisions = params.subdivisions;
if ( setMipmapManual )
WriteSequenceToHdf5.writeHdf5File( seq, manualResolutions, manualSubdivisions, params.hdf5File, new SubTaskProgressWriter( progressWriter, 0, 0.95 ) );
else
WriteSequenceToHdf5.writeHdf5File( seq, perSetupExportMipmapInfo, params.hdf5File, new SubTaskProgressWriter( progressWriter, 0, 0.95 ) );
}
public static < T extends AbstractSpimData< A >, A extends AbstractSequenceDescription< ?, ?, ? super ImgLoader< ? > > > void writeXML(
final T spimData,
final XmlIoAbstractSpimData< A, T > io,
final File seqFile,
final File hdf5File,
final ProgressWriter progressWriter )
{
final A seq = spimData.getSequenceDescription();
final Hdf5ImageLoader hdf5Loader = new Hdf5ImageLoader( hdf5File, null, null, false );
seq.setImgLoader( hdf5Loader );
spimData.setBasePath( seqFile.getParentFile() );
try
{
io.save( spimData, seqFile.getAbsolutePath() );
}
catch ( final SpimDataException e )
{
throw new RuntimeException( e );
}
progressWriter.setProgress( 1.0 );
progressWriter.out().println( "done" );
}
static boolean lastSetMipmapManual = false;
static String lastSubsampling = "{1,1,1}, {2,2,1}, {4,4,2}";
static String lastChunkSizes = "{16,16,16}, {16,16,16}, {16,16,16}";
public static String lastExportPath = "/Users/pietzsch/Desktop/spimrec2.xml";
public static File getInputXML()
{
final JFileChooser fileChooser = new JFileChooser();
fileChooser.setFileFilter( new FileFilter()
{
@Override
public String getDescription()
{
return "xml 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( "xml" );
}
}
return false;
}
} );
if ( fileChooser.showOpenDialog( null ) == JFileChooser.APPROVE_OPTION )
return fileChooser.getSelectedFile();
else
return null;
}
public static Parameters getParameters( final ExportMipmapInfo autoMipmapSettings, final boolean askForXMLPath )
{
while ( true )
{
final GenericDialogPlus gd = new GenericDialogPlus( "Export for BigDataViewer" );
gd.addCheckbox( "manual mipmap setup", lastSetMipmapManual );
final Checkbox cManualMipmap = ( Checkbox ) gd.getCheckboxes().lastElement();
gd.addStringField( "Subsampling factors", lastSubsampling, 25 );
final TextField tfSubsampling = ( TextField ) gd.getStringFields().lastElement();
gd.addStringField( "Hdf5 chunk sizes", lastChunkSizes, 25 );
final TextField tfChunkSizes = ( TextField ) gd.getStringFields().lastElement();
if ( askForXMLPath )
PluginHelper.addSaveAsFileField( gd, "Export path", lastExportPath, 25 );
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 )
{
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 );
}
}
return true;
}
} );
tfSubsampling.setEnabled( lastSetMipmapManual );
tfChunkSizes.setEnabled( lastSetMipmapManual );
if ( !lastSetMipmapManual )
{
tfSubsampling.setText( autoSubsampling );
tfChunkSizes.setText( autoChunkSizes );
}
gd.showDialog();
if ( gd.wasCanceled() )
return null;
lastSetMipmapManual = gd.getNextBoolean();
lastSubsampling = gd.getNextString();
lastChunkSizes = gd.getNextString();
lastExportPath = gd.getNextString();
// parse mipmap resolutions and cell sizes
final int[][] resolutions = PluginHelper.parseResolutionsString( lastSubsampling );
final int[][] subdivisions = PluginHelper.parseResolutionsString( lastChunkSizes );
if ( resolutions.length == 0 )
{
IJ.showMessage( "Cannot parse subsampling factors " + lastSubsampling );
continue;
}
if ( subdivisions.length == 0 )
{
IJ.showMessage( "Cannot parse hdf5 chunk sizes " + lastChunkSizes );
continue;
}
else if ( resolutions.length != subdivisions.length )
{
IJ.showMessage( "subsampling factors and hdf5 chunk sizes must have the same number of elements" );
continue;
}
final File seqFile, hdf5File;
if ( askForXMLPath )
{
String seqFilename = lastExportPath;
if ( !seqFilename.endsWith( ".xml" ) )
seqFilename += ".xml";
seqFile = new File( seqFilename );
final File parent = seqFile.getParentFile();
if ( parent == null || !parent.exists() || !parent.isDirectory() )
{
IJ.showMessage( "Invalid export filename " + seqFilename );
continue;
}
final String hdf5Filename = seqFilename.substring( 0, seqFilename.length() - 4 ) + ".h5";
hdf5File = new File( hdf5Filename );
}
else
{
seqFile = hdf5File = null;
}
return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, hdf5File );
}
}
}
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