Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/dilawar/plotdigitizer
A Python utility to digitize plots.
https://github.com/dilawar/plotdigitizer
data-extraction digitization image-processing python3
Last synced: 2 days ago
JSON representation
A Python utility to digitize plots.
- Host: GitHub
- URL: https://github.com/dilawar/plotdigitizer
- Owner: dilawar
- License: gpl-3.0
- Created: 2018-07-12T08:20:45.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2024-08-10T15:59:59.000Z (5 months ago)
- Last Synced: 2024-12-24T22:05:48.322Z (9 days ago)
- Topics: data-extraction, digitization, image-processing, python3
- Language: Python
- Homepage:
- Size: 2.15 MB
- Stars: 125
- Watchers: 9
- Forks: 24
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
 [](https://badge.fury.io/py/plotdigitizer) [](https://zenodo.org/badge/latestdoi/140683649)
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](https://apps.automeris.io/wpd4/)
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__
```bash
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.
```bash
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.
```bash
$ plotdigitizer-locate figures/trimmed.png
```
or, by directly using the script:
```bash
$ 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
```bash
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](https://apps.automeris.io/wpd4/) by Ankit
Rohatagi is very versatile.