Measure intensity from one image based on a set of lines drawn in another.

To run the code, first create the data and output directories:

mkdir {data,output}

Then copy the data to be analysed into the data directory. Then, start the docker container with:

bash runcontainer.sh

This assumes that the data and output directories exist, and that you're running it from the project root directory. You can then run the analysis on a pair of files with, e.g.:

cd /output
python /code/profile_lines.py /data/kymograph_file.png /data/lines_file.png

The script currently writes its output to the working directory. In the container, this will be /output, outside the container it will be the output directory you created earlier (output/ from the root of the project).

It is possible to specify the degree to which the skeletonized line gets dilated using the -d/--dilation option.

Two methods for reducing the y-axis have been implemented: max and mean. The desired option can be specified using the -r/--reduce-method option.

For more help use the -h/--help option.

To plot a single output CSV:

Rscript analysis/individual-line-plot.R output/series_00.csv s0.png

To plot all output:

Rscript analysis/all-series-plot.R output/all_series.csv all.png