wipp/wipp-egt-plugin repository overview

We need to properly mount host directories and then we need to provide egt arguments. Additional environment variables can be set to enable logging.

⁠Example usage

docker run -v $INPUT_DIR_HOST:$CONTAINER_DIR_INPUTS  -v $OUTPUT_DIR_HOST:$CONTAINER_DIR_OUTPUTS \
-e GLOG_v=3 -e GLOG_logtostderr=1 $CONTAINER_IMAGE \
  -i $CONTAINER_DIR_INPUTS/$IMAGE_RELATIVE_PATH -o $CONTAINER_DIR_OUTPUTS \
 -d "16U"  --level "0" --minhole "1000" --maxhole "inf" --minobject "3000" -x "0"   --op "and" --minintensity "0" --maxintensity "100" -e "loader=2;tile=10;intensity=0;"

⁠Mounting directories

Input and Output directories on the host should be mounted as volumes in the container, for example in /tmp/ :

INPUT_DIR_HOST=/path/on/host/to/inputDirectory
OUTPUT_DIR_HOST=path/on/host/to/outputDirectory
CONTAINER_DIR_INPUTS=/path/in/container/to/inputs
CONTAINER_DIR_OUTPUTS=/path/in/container/to/outputs

Now we provide the path to the image(s) within the container

IMAGE_RELATIVE_PATH=tiled_stitched_c01t020p1_pyramid_1024.ome.tif

CONTAINER_IMAGE=wipp/wipp-egt-plugin:1.1.1

⁠Container command arguments

• -i $IMAGES_PATH : path to the images in the container
• -o $OUTPUT_DIR_HOST : path to the ouput directory in the container
• -d depth : depth and encoding of the ouput images : 8U, 16U or 32F (8bits or 16bits unsigned intergers or float)
• -l level : level at which running the algorithm
• -m minHole : minimum size of a hole
• -s minObjectSize : mnimum size of an object
• -g greedy : the greedy parameter (int in range -50 < greedy < 50)
• -c compression : compression scheme (see : https://www.awaresystems.be/imaging/tiff/tifftags/compression.html⁠)
• -e expertmode : currently undocumented

⁠Environment variables

Environment variables can be set to generate logs.

• GLOG_logtostderr=1 : print tostderr instead of log file
• GLOG_v=[0..4] : set log level between 0 and 4 for more detailed logs

Log Levels :

1. no logs.
2. basic info and execution time.
3. algorithmic steps.
4. detailed logs.
5. very detailed logs.