Mean value calculation from several files

KNIME Extensions Image Processing
#1

Hello all,

I have a folder with 50 tiff. files. Each tiff file is consisted of several slices (approx. 30-40) and from each slice i am extracting texture features through image features node. Is it possible to separate somehow the tiff files during the analysis and calculate, individually, mean values for each tiff file with out the need to run the workflow 50 times?

Below you can see the workflow i am using.

Screenshot%20(28)
Screenshot%20(28)753×318 11.5 KB

Screenshot%20(29)
Screenshot%20(29)697×964 29.1 KB

Above, is a screenshot from Auto crop node where i have loaded all my tiff files and i ended up with 12800 rows…I am not extracting features from all rows. Row 99 to 129 represents one tiff file and texture features are extracted from each image. One other tiff file is between 1621-1663.

So, is there a way to calculate separately the mean value of texture features for rows 99-129 and 1621-1663 and so on… and end up with 50 different mean values?

Hope this makes sense …

Thank you for your time…

Stephanos

#2

Hi @s.leandrou,

There are two ways to do your processing you can look into using the Chunk Loop Start Loop End nodes, so that you can process each read image separately and end up with a table that only contains the results of each loop iteration.

The more advanced but also much more powerful way is to use the GroupBy node to group the calculated features by their source location and calculate the mean value via an aggregation.

Selection_009
Selection_0091102×430 31.9 KB

Mean Value over several files.knwf (17.4 KB)
best,
Gabriel

2 Likes
#3

Dear Gabriel,

KNIME apart from a vert powerful tool is also supported by a great team!

Thank you for the workflow, this is exactly what i needed

Best,

Stephanos

2 Likes
#4

I am very happy that I could help you :blush: