Getting Started: imagefilterΒΆ

I. OVERVIEW

The ‘RP_imagefilter’ analysis conducts a simple filtering process of an image for later processing. This is primarily used to ‘clean up’ the output image from the ‘RP_mask’ analysis, and as such should be used in parallel.

Two main filters are applied: the first is an area-based filter, where all mask-labeled objects with a connected pixel count smaller than ‘bwareaval’ will be removed. The second filter is a simple median filter.

II. HOW TO USE

First, open the ‘user_config’ text file in your ‘Root_Processing’ directory. The parameters used in ‘RP_imagefilter’ are in the 5th section, and there will be four parameters. In order, they are:

  1. image_filename: this is the full image filename (including directory) where the image is to be found.
  2. output_filename: this is the full image filename (including directory) where the image is to be saved. If the directory is not present, the analysis will automatically make the directory.
  3. bwareaval: this is the scalar value of the minimum pixel count (i.e. pixel area) to be removed.
  4. medfilterval: this is the window size to be used for the median filter.

III. RUNNING THE CODE

This analysis can be conducted using the [‘RP_imagefilter’] string in the ‘RP_run’ module.