Image fusion with "Save as (compressed) TIFF stacks" stopped working

[pawlowska]

I am attempting to fuse images with following parameters (screenshot). I used it tens of times, but a few weeks ago (maybe after a Fiji update?) this stopped working.

Messages appear in the log up to:

Thu Sep 26 15:16:13 CEST 2019: Saving file D:\temp\tifs\.\fused_tp_0_ch_0.tif

then, a file is created, but it ends up being an empty single slice file and following output appears in the Console: `tpId=0 setupId=0 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=1 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=2 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=3 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=4 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=5 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=6 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=7 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=8 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=9 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=10 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm

tpId=0 setupId=11 Calibration (transformed): (1.4501160092807426, 1.4501160092807426, 1.4501160092807426) µm (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 (1.0, 1.0, 1.0) testing scale: 3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (1.0, 1.0, 1.0) valid: true bestScaling: 1.0 testing scale: 3d-affine: (2.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0) (2.0, 2.0, 1.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (4.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 2.0, 0.0) (4.0, 4.0, 2.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (8.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0, 0.0, 0.0, 0.0, 4.0, 0.0) (8.0, 8.0, 4.0) valid: false bestScaling: 1.0 testing scale: 3d-affine: (16.0, 0.0, 0.0, 0.0, 0.0, 16.0, 0.0, 0.0, 0.0, 0.0, 8.0, 0.0) (16.0, 16.0, 8.0) valid: false bestScaling: 1.0 Choosing resolution level: 1.0 x 1.0 x 1.0 Exception in thread "Thread-17" java.util.concurrent.RejectedExecutionException: Task java.util.concurrent.FutureTask@2d05586b rejected from java.util.concurrent.ThreadPoolExecutor@633c01c5[Terminated, pool size = 0, active threads = 0, queued tasks = 0, completed tasks = 12] at java.util.concurrent.ThreadPoolExecutor$AbortPolicy.rejectedExecution(ThreadPoolExecutor.java:2063) at java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:830) at java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1379) at java.util.concurrent.AbstractExecutorService.invokeAll(AbstractExecutorService.java:238) at net.imglib2.display.projector.MultithreadedIterableIntervalProjector2D.map(MultithreadedIterableIntervalProjector2D.java:178) at net.imglib2.img.display.imagej.ImageJVirtualStack.getSlice(ImageJVirtualStack.java:148) at net.imglib2.img.display.imagej.ImageJVirtualStack.getPixelsZeroBasedIndex(ImageJVirtualStack.java:155) at net.imglib2.img.display.imagej.AbstractVirtualStack.getPixels(AbstractVirtualStack.java:89) at net.imglib2.img.display.imagej.AbstractVirtualStack.getProcessor(AbstractVirtualStack.java:111) at ij.io.ImageWriter.write16BitVirtualStack(ImageWriter.java:101) at ij.io.ImageWriter.write(ImageWriter.java:277) at ij.io.TiffEncoder.write(TiffEncoder.java:129) at ij.io.TiffEncoder.write(TiffEncoder.java:150) at net.preibisch.mvrecon.process.export.Save3dTIFF.saveTiffStack(Save3dTIFF.java:164) at net.preibisch.mvrecon.process.export.Save3dTIFF.exportImage(Save3dTIFF.java:138) at net.preibisch.mvrecon.fiji.plugin.Image_Fusion.cacheAndExport(Image_Fusion.java:346) at net.preibisch.mvrecon.fiji.plugin.Image_Fusion.fuse(Image_Fusion.java:265) at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.FusionPopup$MyActionListener$1.run(FusionPopup.java:82) at java.lang.Thread.run(Thread.java:748) `