Digitize plots and extract trajectories.
Project description
PlotDigitizer
A python (python3) script to digitize plot (Under developement)
Usage
- Remove all the text from the image. Only axis and plot should be left.
For example, following image is from MacFadden and Koshland, PNAS 1990.
It should be trimmed. Remove the top border. You can use gimp
or imagemagick
or gthumb
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 three -p
(points) to map the coordinates onto the pixels of the
image. In the example above, we have given three coordinates: 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 thse points on the pixels, 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 output.png
is passed, it will also plot the computed data-points tooutput.png
. This requiresmatplotlib
.
Notice the errors near the boxes; since we have not trimmed them.
Passing the location of coordinates manually
IMP/FIXME: 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 output.png
Dependencies
Install Python bindings of opencv
manually. On ubuntu box, it is available in
official repositories ie., $ sudo apt install python3-opencv
. You can also
use the Python wheel available here https://pypi.org/project/opencv-python/
e.g. $ pip install opencv-python --user
.
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.
You might be interested in more versatile WebPlotDigitizer by Ankit Rohatagi.
Development
If you enhance the script, feel free to send a PR.
Project details
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