Unable to specify output directory in image writer node

KNIME Extensions
1

Hi this is Miguel,

I am quite new to KNIME but I am enjoying a lot learning and developing workflows.

I have created an image processing workflow to be run from the command line. I specify some node variables through the worflow variable administration such that I can run the workflow from a python script like this:

call(["/Applications/KNIME3.3.1.app/Contents/MacOS/knime","-nosplash","-nosave","-application",

"org.knime.product.KNIME_BATCH_APPLICATION","-workflowFile=/path_to_workflow/nucleus_detect.zip",

"-workflow.variable=output_path,""/path/_to_output/"",String",

"-workflow.variable=extension,""tif"",String"])

The workflow variable named "output_path" replaces the selection of output directory in the "image writer" node. 

This may be a trivial question, but the path I indicate through the command line is ignored and replaced by the default path in the workflow variable administration.

Do I need to add anything else ass workflow variable or am I just indicating the wrong path? 

2

Hi Miguel,

I happy you are enjoying KNIME so far. I just tried to set the output directory of the Image Writer node, using the following bash script and that worked well, maybe something is wrong with the python script?

#!/bin/sh
/home/gabriel/bin/knime-full_3.2.1/knime -nosplash -nosave -application \
org.knime.product.KNIME_BATCH_APPLICATION \
-workflowFile="path/to/workflow.knwf" \
-workflow.variable=output_path,"/output/folder/path",String

 

 

best,

Gabriel

3

Hi Gabriel, sorry for the delayed answer back, multitasking...

My main concern is that I do not know how should I introduce the workflow variable information into the node. Right now I am creating a workflow variable called output_path. Then I go to the Image Writer node configuration and in the flow variables menu I indicate that the directory key should use the workflow variable output_path (as shown in image of link). 

http://imgur.com/a/uQAmY

I am introducing other paths and variables through this method in other nodes so I think that the flow variable slot I am using is not the correct or either I should specify the name in other manner.

Thank for the previous response :D

Miguel

 

5

I also want to save images to a directory, by flow variable. Is this possible?

6

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