Image Writer issue with Multi-channel images

KNIME Extensions
1

Hi,

I'm have trouble writing/saving cropped segments of multi-channel input (4 channels). The input is unsignedShort. Here is error in "DEBUG mode": I've tried the following formats: TIFF/OME-TIFF/ICS/APNG

 

Thanks,

 

Reddy

-------------------------------------------------LOG-----------------------------------------------------------------------------------

DEBUG Image Writer         0:854      File: C:\Users\xxx\Documents\temp\temp\nuc_00.tif 
 Type:UnsignedShortTypeformat: Tagged Image File Format
WARN  Image Writer         0:854      Image has more than 3 channels. These channels might be ignored my some formats.
DEBUG Image Writer         0:854      BitsPerSample length (1) does not match SamplesPerPixel (4)
DEBUG Image Writer         0:854      publish(
    context = org.scijava.Context@8edd41c
    consumed = false
    progress = -1
    maximum = -1
    status = Initializing Nuclei_7
    warning = false,null,null), called from non-EDT Thread:null
DEBUG Image Writer         0:854      BitsPerSample length (1) does not match SamplesPerPixel (4)
WARN  Image Writer         0:854      Expected positive value for PhysicalSizeX; got 0.0
WARN  Image Writer         0:854      Expected positive value for PhysicalSizeY; got 0.0
DEBUG Image Writer         0:854      getHandle(id = C:\Users\xxx\Documents\temp\temp\nuc_00.tif, writable = true)
DEBUG Image Writer         0:854      no handle was mapped for this ID
DEBUG Image Writer         0:854      NIO: allocate: mapped=false, start=0, size=0
DEBUG Image Writer         0:854      Location.getHandle: C:\Users\gudlap\Documents\temp\temp\nuc_00.tif -> io.scif.io.NIOFileHandle@6f2b092f
DEBUG Image Writer         0:854      publish(
    context = org.scijava.Context@8edd41c
    consumed = false
    progress = 0
    maximum = 1
    status = Saving plane 1/1
    warning = false,null,null), called from non-EDT Thread:null
DEBUG Image Writer         0:854      reset
ERROR Image Writer         0:854      Execute failed: ("ArrayIndexOutOfBoundsException"): null
DEBUG Image Writer         0:854      Execute failed: ("ArrayIndexOutOfBoundsException"): null
java.lang.ArrayIndexOutOfBoundsException
DEBUG Image Writer         0:854      Image Writer 0:854 doBeforePostExecution
DEBUG Image Writer         0:854      Image Writer 0:854 has new state: POSTEXECUTE
DEBUG Image Writer         0:854      Image Writer 0:854 doAfterExecute - failure
DEBUG Image Writer         0:854      reset
DEBUG Image Writer         0:854      clean output ports.
DEBUG Image Writer         0:854      Removing handler 6ff7e1ac-67ba-4b19-8949-a5022e51f083 (Image Writer 0:854: <no directory>) - 31 remaining
DEBUG Image Writer         0:854      Image Writer 0:854 has new state: IDLE
DEBUG Image Writer         0:854      Configure succeeded. (Image Writer)
DEBUG Image Writer         0:854      Image Writer 0:854 has new state: CONFIGURED
DEBUG Image Writer         0:854      Segmentation_Classification 0 has new state: CONFIGURED
DEBUG NodeContainer                   ROOT  has new state: IDLE

----------------------------------------------------------------------------------------------------------------------------------------------------

2

Hi Reddy,

thanks for reporting. It's X,Y,Channel, with Channel=4? I will try to reproduce and fix.
 

Thanks,

Christian

 

3

Christian --

My apologies for multiple posting of the same issue. For some reason my forum messages/posts were showing up as "archived" or "pending authorization".

Back to the issue at hand. Yes, it is X, Y, Channel (Ch =4). Let me know if want test images/workflow.

Looking forward to the fix.

 

Best,

 

-Reddy

4

Hi Reddy,

can you provide me some test images + workflow? Unfortunately, I wasn't able to reproduce the problem locally.

Thanks!

Christian

5

Christian -

Try this image. 

 

Reddy

6

Hi Reddy,

the problem should be fixed with the latest nightly build.

7

Christian -

 

Thanks for taking care of this issue. I can confirm that it works for writing multi-channel (4-colors) image(s) as ome.tifs. But when using .tiff/.tif (for 4 color channels), the first channel is written for all four channels.

I'm fine with OME.TIF output format.

 

Best,

Reddy

8

Hi Reddy,

thanks for reporting. I forwarded the issue to the SCIFIO guys.

Best,

Christian

9

This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.