External Software

These are some external packages which you might need to use.

Digitizing Data

During the course of your research, you will inevitably need to compare with previously published calculations or experiment. Therefore, you will need to digitize data. Two open source programs which are very effective at digitizing data are g3data and WebPlotDigitizer. The former is very simple to use, but only good for manually extracting data point by point. The latter is very powerful, capable of automatically extracting data and allowing the user to tweak the result as needed.

g3data

You can install g3data on Ubuntu using apt. The basic recipe for using g3data is:

  1. Screen grab a plot from some digital resource and save as a raster image you like (png, jpeg, etc).

  2. Open the image using g3data.

  3. Calibrate g3data by specifying two vertical and two horizontal reference points.

  4. Now you can click on the image and it will store this point. Do this for all data points.

  5. All stored points can then be output to a file or to standard out.

WebPlotDigitizer

A WebPlotDigitizer executable can be downloaded for Ubuntu. The procedure for manual point extraction is basically the same as g3data. Automatic extraction has a bunch of features to aid extraction, like color matching and region selection.

Viewing hdf5 files

hdf5 has become a popular format for storing data on disk. Unfortunately, it can be annoying to inspect the data from the command line. There are a few tools out there to address this task. I tested vitables, which is a GUI that seems to do the job. It can be installed with apt. Basically, you can point and click on simple data types, but not everything. In any case, it will give you some idea of what the file contains.

Dealing with docx

For reasons unknown, people still use MS Word and its clones. If you need to generate content for a docx file, you can still use latex and convert it to a docx file using pandoc. While this is not perfect, it is pretty impressive what pandoc can do. To convert a typical latex document with a bibliography, do

pandoc -o main.docx -t docx --bibliography=main.bib main.tex