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tpietzschtpietzsch
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Don't convert to UnisignedShortType when exporting to HDF5
1 parent 8924674 commit f58a988

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+69
-104
lines changed

1 file changed

+69
-104
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‎src/main/java/bdv/ij/ExportImagePlusPlugIn.java‎

Lines changed: 69 additions & 104 deletions
Original file line numberDiff line numberDiff line change
@@ -55,6 +55,9 @@
5555
import bdv.spimdata.SequenceDescriptionMinimal;
5656
import bdv.spimdata.SpimDataMinimal;
5757
import bdv.spimdata.XmlIoSpimDataMinimal;
58+
import bdv.img.imagestack.ImageStackImageLoader;
59+
import bdv.img.n5.N5ImageLoader;
60+
import bdv.img.virtualstack.VirtualStackImageLoader;
5861
import fiji.util.gui.GenericDialogPlus;
5962
import ij.IJ;
6063
import ij.ImageJ;
@@ -63,6 +66,7 @@
6366
import ij.gui.DialogListener;
6467
import ij.gui.GenericDialog;
6568
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
69+
import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
6670
import mpicbg.spim.data.registration.ViewRegistration;
6771
import mpicbg.spim.data.registration.ViewRegistrations;
6872
import mpicbg.spim.data.sequence.Channel;
@@ -139,19 +143,44 @@ public void run()
139143
progressWriter.out().println( "starting export..." );
140144

141145
// create ImgLoader wrapping the image
142-
final ImagePlusImgLoader< ? > imgLoader;
143-
switch ( imp.getType() )
146+
final TypedBasicImgLoader< ? > imgLoader;
147+
final Runnable clearCache;
148+
final boolean isVirtual = imp.getStack() != null && imp.getStack().isVirtual();
149+
if ( isVirtual )
144150
{
145-
case ImagePlus.GRAY8:
146-
imgLoader = ImagePlusImgLoader.createGray8( imp, params.minMaxOption, params.rangeMin, params.rangeMax );
147-
break;
148-
case ImagePlus.GRAY16:
149-
imgLoader = ImagePlusImgLoader.createGray16( imp, params.minMaxOption, params.rangeMin, params.rangeMax );
150-
break;
151-
case ImagePlus.GRAY32:
152-
default:
153-
imgLoader = ImagePlusImgLoader.createGray32( imp, params.minMaxOption, params.rangeMin, params.rangeMax );
154-
break;
151+
final VirtualStackImageLoader< ?, ?, ? > il;
152+
switch ( imp.getType() )
153+
{
154+
case ImagePlus.GRAY8:
155+
il = VirtualStackImageLoader.createUnsignedByteInstance( imp );
156+
break;
157+
case ImagePlus.GRAY16:
158+
il = VirtualStackImageLoader.createUnsignedShortInstance( imp );
159+
break;
160+
case ImagePlus.GRAY32:
161+
default:
162+
il = VirtualStackImageLoader.createFloatInstance( imp );
163+
break;
164+
}
165+
imgLoader = il;
166+
clearCache = il.getCacheControl()::clearCache;
167+
}
168+
else
169+
{
170+
switch ( imp.getType() )
171+
{
172+
case ImagePlus.GRAY8:
173+
imgLoader = ImageStackImageLoader.createUnsignedByteInstance( imp );
174+
break;
175+
case ImagePlus.GRAY16:
176+
imgLoader = ImageStackImageLoader.createUnsignedShortInstance( imp );
177+
break;
178+
case ImagePlus.GRAY32:
179+
default:
180+
imgLoader = ImageStackImageLoader.createFloatInstance( imp );
181+
break;
182+
}
183+
clearCache = () -> {};
155184
}
156185

157186
final int numTimepoints = imp.getNFrames();
@@ -174,8 +203,7 @@ public void run()
174203
timepoints.add( new TimePoint( t ) );
175204
final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, imgLoader, null );
176205

177-
Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo;
178-
perSetupExportMipmapInfo = new HashMap<>();
206+
final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = new HashMap<>();
179207
final ExportMipmapInfo mipmapInfo = params.setMipmapManual
180208
? new ExportMipmapInfo( params.resolutions, params.subdivisions )
181209
: autoMipmapSettings;
@@ -189,7 +217,6 @@ public void run()
189217
// required for all original planes contributing to a "plane of
190218
// blocks" at the current level. If this is more than 1/4 of
191219
// available memory, use the loopback image.
192-
final boolean isVirtual = imp.getStack().isVirtual();
193220
final long planeSizeInBytes = imp.getWidth() * imp.getHeight() * imp.getBytesPerPixel();
194221
final long ijMaxMemory = IJ.maxMemory();
195222
final int numCellCreatorThreads = Math.max( 1, PluginHelper.numThreads() - 1 );
@@ -228,7 +255,7 @@ public void afterEachPlane( final boolean usedLoopBack )
228255
final long actuallyFree = max - total + free;
229256

230257
if ( actuallyFree < max / 2 )
231-
imgLoader.clearCache();
258+
clearCache.run();
232259
}
233260
}
234261

@@ -291,12 +318,6 @@ protected static class Parameters
291318

292319
final File hdf5File;
293320

294-
final MinMaxOption minMaxOption;
295-
296-
final double rangeMin;
297-
298-
final double rangeMax;
299-
300321
final boolean deflate;
301322

302323
final boolean split;
@@ -308,17 +329,14 @@ protected static class Parameters
308329
public Parameters(
309330
final boolean setMipmapManual, final int[][] resolutions, final int[][] subdivisions,
310331
final File seqFile, final File hdf5File,
311-
final MinMaxOption minMaxOption, final double rangeMin, final double rangeMax, final boolean deflate,
332+
final boolean deflate,
312333
final boolean split, final int timepointsPerPartition, final int setupsPerPartition )
313334
{
314335
this.setMipmapManual = setMipmapManual;
315336
this.resolutions = resolutions;
316337
this.subdivisions = subdivisions;
317338
this.seqFile = seqFile;
318339
this.hdf5File = hdf5File;
319-
this.minMaxOption = minMaxOption;
320-
this.rangeMin = rangeMin;
321-
this.rangeMax = rangeMax;
322340
this.deflate = deflate;
323341
this.split = split;
324342
this.timepointsPerPartition = timepointsPerPartition;
@@ -332,12 +350,6 @@ public Parameters(
332350

333351
static String lastChunkSizes = "{32,32,4}, {16,16,8}, {8,8,8}";
334352

335-
static int lastMinMaxChoice = 2;
336-
337-
static double lastMin = 0;
338-
339-
static double lastMax = 65535;
340-
341353
static boolean lastSplit = false;
342354

343355
static int lastTimepointsPerPartition = 0;
@@ -350,12 +362,6 @@ public Parameters(
350362

351363
protected Parameters getParameters( final double impMin, final double impMax, final ExportMipmapInfo autoMipmapSettings )
352364
{
353-
if ( lastMinMaxChoice == 0 ) // use ImageJs...
354-
{
355-
lastMin = impMin;
356-
lastMax = impMax;
357-
}
358-
359365
while ( true )
360366
{
361367
final GenericDialogPlus gd = new GenericDialogPlus( "Export for BigDataViewer" );
@@ -367,15 +373,6 @@ protected Parameters getParameters( final double impMin, final double impMax, fi
367373
gd.addStringField( "Hdf5_chunk_sizes", lastChunkSizes, 25 );
368374
final TextField tfChunkSizes = ( TextField ) gd.getStringFields().lastElement();
369375

370-
gd.addMessage( "" );
371-
final String[] minMaxChoices = new String[] { "Use ImageJ's current min/max setting", "Compute min/max of the (hyper-)stack", "Use values specified below" };
372-
gd.addChoice( "Value_range", minMaxChoices, minMaxChoices[ lastMinMaxChoice ] );
373-
final Choice cMinMaxChoices = (Choice) gd.getChoices().lastElement();
374-
gd.addNumericField( "Min", lastMin, 0 );
375-
final TextField tfMin = (TextField) gd.getNumericFields().lastElement();
376-
gd.addNumericField( "Max", lastMax, 0 );
377-
final TextField tfMax = (TextField) gd.getNumericFields().lastElement();
378-
379376
gd.addMessage( "" );
380377
gd.addCheckbox( "split_hdf5", lastSplit );
381378
final Checkbox cSplit = ( Checkbox ) gd.getCheckboxes().lastElement();
@@ -390,59 +387,37 @@ protected Parameters getParameters( final double impMin, final double impMax, fi
390387
gd.addMessage( "" );
391388
PluginHelper.addSaveAsFileField( gd, "Export_path", lastExportPath, 25 );
392389

393-
// gd.addMessage( "" );
394-
// gd.addMessage( "This Plugin is developed by Tobias Pietzsch ([email protected])\n" );
395-
// Bead_Registration.addHyperLinkListener( ( MultiLineLabel ) gd.getMessage(), "mailto:[email protected]" );
396-
397390
final String autoSubsampling = ProposeMipmaps.getArrayString( autoMipmapSettings.getExportResolutions() );
398391
final String autoChunkSizes = ProposeMipmaps.getArrayString( autoMipmapSettings.getSubdivisions() );
399-
gd.addDialogListener( new DialogListener()
400-
{
401-
@Override
402-
public boolean dialogItemChanged( final GenericDialog dialog, final AWTEvent e )
392+
gd.addDialogListener( ( dialog, e ) -> {
393+
gd.getNextBoolean();
394+
gd.getNextString();
395+
gd.getNextString();
396+
gd.getNextBoolean();
397+
gd.getNextNumber();
398+
gd.getNextNumber();
399+
gd.getNextBoolean();
400+
gd.getNextString();
401+
if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cManualMipmap )
403402
{
404-
gd.getNextBoolean();
405-
gd.getNextString();
406-
gd.getNextString();
407-
gd.getNextChoiceIndex();
408-
gd.getNextNumber();
409-
gd.getNextNumber();
410-
gd.getNextBoolean();
411-
gd.getNextNumber();
412-
gd.getNextNumber();
413-
gd.getNextBoolean();
414-
gd.getNextString();
415-
if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cMinMaxChoices )
403+
final boolean useManual = cManualMipmap.getState();
404+
tfSubsampling.setEnabled( useManual );
405+
tfChunkSizes.setEnabled( useManual );
406+
if ( !useManual )
416407
{
417-
final boolean enable = cMinMaxChoices.getSelectedIndex() == 2;
418-
tfMin.setEnabled( enable );
419-
tfMax.setEnabled( enable );
408+
tfSubsampling.setText( autoSubsampling );
409+
tfChunkSizes.setText( autoChunkSizes );
420410
}
421-
else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cManualMipmap )
422-
{
423-
final boolean useManual = cManualMipmap.getState();
424-
tfSubsampling.setEnabled( useManual );
425-
tfChunkSizes.setEnabled( useManual );
426-
if ( !useManual )
427-
{
428-
tfSubsampling.setText( autoSubsampling );
429-
tfChunkSizes.setText( autoChunkSizes );
430-
}
431-
}
432-
else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cSplit )
433-
{
434-
final boolean split = cSplit.getState();
435-
tfSplitTimepoints.setEnabled( split );
436-
tfSplitSetups.setEnabled( split );
437-
}
438-
return true;
439411
}
412+
else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cSplit )
413+
{
414+
final boolean split = cSplit.getState();
415+
tfSplitTimepoints.setEnabled( split );
416+
tfSplitSetups.setEnabled( split );
417+
}
418+
return true;
440419
} );
441420

442-
final boolean enable = lastMinMaxChoice == 2;
443-
tfMin.setEnabled( enable );
444-
tfMax.setEnabled( enable );
445-
446421
tfSubsampling.setEnabled( lastSetMipmapManual );
447422
tfChunkSizes.setEnabled( lastSetMipmapManual );
448423
if ( !lastSetMipmapManual )
@@ -461,9 +436,6 @@ else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED &&
461436
lastSetMipmapManual = gd.getNextBoolean();
462437
lastSubsampling = gd.getNextString();
463438
lastChunkSizes = gd.getNextString();
464-
lastMinMaxChoice = gd.getNextChoiceIndex();
465-
lastMin = gd.getNextNumber();
466-
lastMax = gd.getNextNumber();
467439
lastSplit = gd.getNextBoolean();
468440
lastTimepointsPerPartition = ( int ) gd.getNextNumber();
469441
lastSetupsPerPartition = ( int ) gd.getNextNumber();
@@ -489,14 +461,6 @@ else if ( resolutions.length != subdivisions.length )
489461
continue;
490462
}
491463

492-
final MinMaxOption minMaxOption;
493-
if ( lastMinMaxChoice == 0 )
494-
minMaxOption = MinMaxOption.TAKE_FROM_IMAGEPROCESSOR;
495-
else if ( lastMinMaxChoice == 1 )
496-
minMaxOption = MinMaxOption.COMPUTE;
497-
else
498-
minMaxOption = MinMaxOption.SET;
499-
500464
String seqFilename = lastExportPath;
501465
if ( !seqFilename.endsWith( ".xml" ) )
502466
seqFilename += ".xml";
@@ -510,6 +474,7 @@ else if ( lastMinMaxChoice == 1 )
510474
final String hdf5Filename = seqFilename.substring( 0, seqFilename.length() - 4 ) + ".h5";
511475
final File hdf5File = new File( hdf5Filename );
512476

513-
return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, hdf5File, minMaxOption, lastMin, lastMax, lastDeflate, lastSplit, lastTimepointsPerPartition, lastSetupsPerPartition ); }
477+
return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, hdf5File, lastDeflate, lastSplit, lastTimepointsPerPartition, lastSetupsPerPartition );
478+
}
514479
}
515480
}

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