ADDBAR is a python script which automatically crops the image portion of the pdf file(s) of atomic force microscopy (AFM) images produced by NanoScope Software (Veeco Instruments Inc.). In addition, a scale bar whose length is one-fifth of the width of the image is superimposed in the bottom-right corner.
All parsing, cropping, and manipulation of the input pdf file is done using the pyPDF library. No other dependencies are required.
All dependencies can be installed using pip. pip does not come pre-installed with the python virtual machine, so you need to install it manually.
- Install pip (if you do not have it installed)
# yum install python-pip
or
$ sudo apt-get install python-pip
for linux machines.
- Upgrade
pip.
$ sudo pip install pip --upgrade
- Install all required dependencies by typing
$ pip install -r requirements.txt
At the command line, type
$ python addbar.py
> Enter name of file (excluding '.pdf')
Enter the name of the pdf file (without typing '.pdf'). The file may be multiple pages. For example if you have a file named example.pdf, type example.
> How many output channels (usually 1 or 2)?
1
This question asks how many output channels there are in the pdf file. For
instance, if each page has only the height data, the number of output channels
is 1. If there are 2 output data channels, such as the height and amplitude
data in the pdf file, then the number of output channels is 2.
> Output filename without '.pdf' (default: 'example-addbar.pdf')?
Type the name of the output file you want. The default (just pressing Enter)
is the name of the input file with the -addbar suffix appended, in which
case, a file named example-addbar.pdf, with all the cropped images and scale
bars added, will be produced.