I have a 2-channel dataset stitched with Bigstitcher and saved as xml/hdf5. I need to extract 1 channel for further processing, so I tried Resave Dataset -> As TIFF... . I get asked if I really want only one 'view' and if I agree to saving current state of XML. No files get created and a java exception happens.
I subsequently tried Resave Dataset -> HDF5 for only 1 channel and this doesn't crash.
Console output:
Exception in thread "Thread-14" java.lang.OutOfMemoryError: Java heap space at net.imglib2.img.basictypeaccess.array.AbstractShortArray.<init>(AbstractShortArray.java:50) at net.imglib2.img.basictypeaccess.array.ShortArray.<init>(ShortArray.java:48) at net.imglib2.img.basictypeaccess.array.ShortArray.createArray(ShortArray.java:59) at net.imglib2.img.basictypeaccess.array.ShortArray.createArray(ShortArray.java:42) at net.imglib2.img.cell.CellImgFactory.create(CellImgFactory.java:146) at net.imglib2.img.cell.CellImgFactory.create(CellImgFactory.java:103) at bdv.img.hdf5.Hdf5ImageLoader$SetupImgLoader.loadImageCompletely(Hdf5ImageLoader.java:423) at bdv.img.hdf5.Hdf5ImageLoader$SetupImgLoader.getImage(Hdf5ImageLoader.java:478) at bdv.AbstractViewerSetupImgLoader.getImage(AbstractViewerSetupImgLoader.java:62) at net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF.writeTIFF(Resave_TIFF.java:241) at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ResavePopup$MyActionListener$1.run(ResavePopup.java:213) at java.lang.Thread.run(Thread.java:748)
Log output:
Using spimdata version: 0.9-revision Using multiview-reconstruction version: 0.11.5 angles selected: 0 channels selected: 0, 1 illuminations selected: 0 tiles selected: 0 Timepoints selected: 0 Only one tile, starting in MultiView mode. Resaving 1 views As TIFF ... Saving 1 of 2 views. Saved XML 'T:/2021_s/s186_stitched_1/s186_P-f0.xml'.
I have a 2-channel dataset stitched with Bigstitcher and saved as xml/hdf5. I need to extract 1 channel for further processing, so I tried Resave Dataset -> As TIFF... . I get asked if I really want only one 'view' and if I agree to saving current state of XML. No files get created and a java exception happens.
I subsequently tried Resave Dataset -> HDF5 for only 1 channel and this doesn't crash.
Console output:
Exception in thread "Thread-14" java.lang.OutOfMemoryError: Java heap space at net.imglib2.img.basictypeaccess.array.AbstractShortArray.<init>(AbstractShortArray.java:50) at net.imglib2.img.basictypeaccess.array.ShortArray.<init>(ShortArray.java:48) at net.imglib2.img.basictypeaccess.array.ShortArray.createArray(ShortArray.java:59) at net.imglib2.img.basictypeaccess.array.ShortArray.createArray(ShortArray.java:42) at net.imglib2.img.cell.CellImgFactory.create(CellImgFactory.java:146) at net.imglib2.img.cell.CellImgFactory.create(CellImgFactory.java:103) at bdv.img.hdf5.Hdf5ImageLoader$SetupImgLoader.loadImageCompletely(Hdf5ImageLoader.java:423) at bdv.img.hdf5.Hdf5ImageLoader$SetupImgLoader.getImage(Hdf5ImageLoader.java:478) at bdv.AbstractViewerSetupImgLoader.getImage(AbstractViewerSetupImgLoader.java:62) at net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF.writeTIFF(Resave_TIFF.java:241) at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ResavePopup$MyActionListener$1.run(ResavePopup.java:213) at java.lang.Thread.run(Thread.java:748)Log output:
Using spimdata version: 0.9-revision Using multiview-reconstruction version: 0.11.5 angles selected: 0 channels selected: 0, 1 illuminations selected: 0 tiles selected: 0 Timepoints selected: 0 Only one tile, starting in MultiView mode. Resaving 1 views As TIFF ... Saving 1 of 2 views. Saved XML 'T:/2021_s/s186_stitched_1/s186_P-f0.xml'.