A python (python3) script to digitize plot (Under developement)
- Remove all the text from the image. Only axis and plot should be left.
This is from MacFadden and Koshland, PNAS 1990.
It should be trimmed. Ideally you should also remove the top border. You can use gimp
or imagemagick
or any other tool for cropping.
- Then we run the script like this.
./plotdigitizer.py -i ./figures/trimmed.png -p 0,0 -p 10,0 -p 0,1
Option -i
accepts the input file.
We need at least 3 of them to map the coordinate systems onto the pixel-system
in the image. These points are passed by repeated -p
options. In the example
above, we have given three data-points 0,0
(where x-axis and y-axis intesect)
, 20,0
(a point on x-axis) and 0,1
(a point on y-axis).
We are going to click on the image to locate these coordinates later. Make sure to click in the same order.
- The data-points will be dumped to a csv file. If
--plot
option is given from command line, it will also plot the computed data-points. This requiresmatplotlib
.
Notice the errors near the boxes; since we have not trimmed them.
IMP: Bottom left corner of the image is (0,0)
in most plots. However, for
opencv which we are using in this project, top-left is mapped to (0,0)
. This
may cause subtle effects if you are not careful when passing values of location
manually. See issue #1 for discussion. I got these values from program gimp
.
./plotdigitizer.py -i ./figures/trimmed.png -p 0,0 -p 20,0 -p 0,1 \
-l 22,295 -l 142,295 -l 22,215 --plot
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.
You might be interested in more versatile WebPlotDigitizer by Ankit Rohatagi.
If you enhance the script, feel free to send a PR.