Featuremap Utility

Generate featuremaps. Most of the time you'll be converting prediction files to featuremap files. Or, you may want to generate a featuremap from a spreadsheet containing pyradiomics data.

Need to know

• Who's algorithm is it (who ran it)?
• What is the execution id?
• And sometimes – where are the color files?

You can usually answer the question "who's algorithm" and "execution id" by looking at heatmap_json output.

If there are no color files, run this script in the input folder:

for i in $(ls prediction-*); do
  a=$(echo "$i" | awk -F 'prediction-' '{print $2}')
  awk '{ if ($3>0.0) { print $1" "$2" 100.0 50.0 0.0" } else { print $1" "$2" 1.0 50.0 0.0" } }' "$i" >color-"$a"
done

Build and run

• cd into this directory
• Modify volume mapping in docker-compose.yml (particularly wsi - point it to the appropriate folder under images on the server.
• Then run docker-compose up -d

Put input files in the input directory.
Normal TIL/Cancer input: heatmap_txt
Classified cancer input: heatmap_txt_3classes_separate_class
...
The program will output files to the output directory.

Usage

Prediction files to featuremap

Let's say you have a bunch of prediction files (color-*, prediction-*) and you want to generate featuremaps.
The following command takes two arguments: execution id, and wsi type.
wsi type can be svs, tif, scn, etc.

nohup docker exec quip-maputil pred_to_map exec_id exec_by wsi_type &

Traditionally, the channels are labelled as:

red = TIL
green = Cancer
blue = Tissue

Optional 4th parameter
If it's a cancer-only prediction, add Cancer so that the program knows to put data in the correct channel.

nohup docker exec quip-maputil pred_to_map exec_id exec_by wsi_type Cancer &

Pyradiomics to featuremap

We've generated a bunch of pyradiomics csv files. Here's how to create featuremaps:

docker exec quip-maputil pyrad_to_map exec_id exec_by

Upload to server

Use ImageLoader to load them.

Note: Because ImageLoader does not yet handle execution id, one could add that info to the host via HTTP PATCH calls.