plotdigitizer 0.1.2

Extract raw data from plots images

A Python3 utility to digitize plots.

Installation

$ python3 -m pip install plotdigitizer 
$ plotdigitizer --help

Usage

First, remove all text from the image, leave only axis and the plot. I use gthumb utility. You can also use imagemagick or gimp.

Following image is from MacFadden and Koshland, PNAS 1990 after trimming. One can also remove top and right axis.

Run the utility

plotdigitizer ./figures/trimmed.png -p 0,0 -p 10,0 -p 0,1

We need three points (-p option) to map axes onto the images. In the example above, these are 0,0 (where x-axis and y-axis intesect) , 20,0 (a point on x-axis) and 0,1 (a point on y-axis). To map these points on the image, you will be asked to click on these points on the image. Make sure to click in the same order and click on the points as precisely as you could. Any error in this step will propagate.

The data-points will be dumped to a csv file e.g., --output /path/to/file.csv.

If --plot output.png is passed, a plot of the extracted data-points will be saved to output.png. This requires matplotlib.

Notice the errors near the boxes; since we have not trimmed them.

Using in batch mode

You can also pass the location of points in the image at the command prompt. This allows it to run in the batch mode without any need for the user to click on the image.

plotdigitizer ./figures/trimmed.png -p 0,0 -p 20,0 -p 0,1 -l 22,295 -l 142,295 -l 22,215 --plot output.png

Examples

plotdigitizer figures/graphs_1.png \
		-p 1,0 -p 6,0 -p 0,3 \
		-l 165,160 -l 599,160 -l 85,60 \
		--plot figures/graphs_1.result.png \
		--preprocess

plotdigitizer  figures/ECGImage.png \
		-p 1,0 -p 5,0 -p 0,1 -l 290,337 \
		-l 1306,338 -l 106,83 \
		--plot figures/ECGImage.result.png

Limitations

Currently this script has following limitations:

• Background must not be transparent. It might work with transparent background but I've not tested it.
• Only b/w images are supported for now. Color images will be converted to grayscale upon reading.
• One image should have only one trajectory.

Related projects by others

1. WebPlotDigitizer by Ankit Rohatagi is very versatile.