jfkimberly / addbar

Batch processing of scale bars onto Nanoscope pdf files.

ADDBAR

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.

Dependencies

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

Usage

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.