A Python3 command line utility to digitize plots in batch mode.

This utility is useful when you have a lot of similar plots such as EEG, ECG recordings. See examples below.

For one-off use cases, you will find web-based digitizer WebPlotDigitizer by Ankit Rohatagi much more easier to use.

Installation

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

Preparing image

Crop the image and leave only axis and trajectories. I used the gthumb utility on Linux. You can also use imagemagick or gimp.

The following image is from MacFadden and Koshland, PNAS 1990 after trimming. One should also remove top and right axes. I didn't because I want to highlight the limitation of this tool!

Run

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

We need at least three points (-p option) to map x- and y-axis onto the image.

In the example above, these are 0,0 (where x-axis and y-axis intersect) , 10,0 (a point on the x-axis), and 0,1 (a point on the y-axis). To map these points on the image, you will be asked to click on these points. 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.

If you don't have 0,0 in your image, you must provide 4 points: 2 on the x-axis and 2 on the y-axis.

The data points will be dumped to a CSV file specified by --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. Very useful when debugging/testing.

Notice the error near the right y-axis.

Using in batch mode

You can pass the coordinates of points in the image at the command prompt. This allows it to run in 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

How to find coordinates of axes points

In the example above, point 0,0 is mapped to coordinate 22,295 i.e., the data point 0,0 is on the 22nd row and 295th column of the image (assuming that the bottom left of the image is the first row, first column (0,0)). I have included a utility plotdigitizer-locate (script plotdigitizer/locate.py), which you can use to find the coordinates of points.

$ plotdigitizer-locate figures/trimmed.png

or, by directly using the script:

$ python3 plotdigitizer/locate.py figures/trimmed.png

This command opens the image in a simple window. You can click on a point, and its coordinates will be written on the image. Note them down.

Examples

Base 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

Light grids

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

With grids

plotdigitizer  figures/graph_with_grid.png \
		-p 200,0 -p 1000,0 -p 0,50 \
        -l 269,69 -l 1789,69 -l 82,542 \
		--plot figures/graph_with_grid.result.png

Image credit: Yang yi, Wang

Note that legend was not removed in the original figure and it has screwed up the detection below it.

Limitations

This application has the following limitations:

• Only b/w images are supported for now. Color images will be converted to grayscale upon reading.
• Each plot should have only one trajectory.

Need help

Open an issue and please attach the sample plot.

Related Projects

1. WebPlotDigitizer by Ankit Rohatagi is very versatile.