Writing images with Image Writer or with Table Writer

KNIME Extensions
1

Hello,

I have problems saving/exporting tables with images or images themselves.

Is it possible to save tables with IMG+ columns using Table Writer node? I get this error message:

ERROR     Buffer     CODING PROBLEM    Writing cells to temporary buffer must not throw RuntimeException
ERROR     Table Writer     Execute failed: Error while writing to buffer, failed to write to file "knime_container_20121017_5651594336083644268.bin.gz": Failed copying file stores to local handler

Then I wanted to save images separately from tables/data. Depending of what I try I get these errors:

OME-TIFF(uncompressed): Image Writer     Execute failed: ("NullPointerException"): null OME-XML(uncompressed) or .tif: ERROR     ImgWriterNodeModel     Error while writing images: Pixel type not supported by this format.

JPG: ERROR     ImgWriterNodeModel     Error while writing images: uint16 not supported by the selected image format. Supported are uint8 .

PNG same thing.

I have single images 16-bit, normalized and rescaled to 1/4 of original dimensions. How can I save these images?

Cheers,

Martin

2

Hi Martin,

thanks a lot for reporting your problems.

The first issue with the Table Writer-node: you are right but it'll take a bit to fix it. As a first workaround just save your workflow (Ctrl + s) before executing the Table Writer or set the memory policies (configure dialog) of the node connected to the Table Writer to "Write tables to disc"). I'll keep you updated, when the problem is solved.

Second, the Image Writer: honestly the error messages are not super-understandable and need some improvements. The problem here is, that not every image format you want to write supports all pixel-types (i.e. byte, unsigned byte, short ...). OME-XML and tiff at least support UnsignedShortType, ByteType and UnsignedByteType, JPG only supports UnsignedByteType. Hence, you have to use the "Image Converter" first to provide the right pixel-type (hint: choose "Scale" as Conversion method in the configure dialog of the Image Converter). In general, the Image Writer definitely needs a revision and we'll do it as soon as possible.

Hope, you are able to proceed with these workarounds ...

Best, Martin

 

3

hello, I am really struggling in writing an series of images using image writer. my node sequence is

1. image to labeling

2. Extract Outline Labeling

3. Labeling to image

4. Inverter

5. Image Converter

6. Image writer.

I cannot configure 5. and 6. to save the image I want. seems like the start image format (Byte TYpe) cannot be saved properly even after conversion  with node 6...

Any help would be gratefully received!

thanks.

Paolo

 

 

4

Hi Paolo,

to what format do you convert and with which config? What's the Image Writer log output?

Thanks!

Christian

5

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